PSIBLAST 2.11.0+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Stephen F.
Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala,
Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005)
"Protein database searches using compositionally adjusted
substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Alejandro A. Schaffer, L. Aravind, Thomas L. Madden, Sergei
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST
protein database searches with composition-based statistics and
other refinements", Nucleic Acids Res. 29:2994-3005.



Database: uniprot_sprot.fasta
           564,277 sequences; 203,340,877 total letters

Results from round 1


Query= YP_009725298.1 nsp2 [Severe acute respiratory syndrome coronavirus
2]

Length=638
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute resp...  1328    0.0  
sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute re...  1326    0.0  
sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 2...  965     0.0  
sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavirus...  963     0.0  
sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respi...  956     0.0  
sp|P0C6X7|R1AB_SARS Replicase polyprotein 1ab OS=Severe acute res...  954     0.0  
sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus H...  951     0.0  
sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavirus...  949     0.0  
sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus R...  941     0.0  
sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavirus...  939     0.0  
sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavirus...  109     2e-23
sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus H...  109     3e-23
sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavirus...  109     4e-23
sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus H...  108     4e-23
sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavirus...  102     7e-21
sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus 1...  101     9e-21
sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East respi...  92.4    7e-18
sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East res...  92.0    9e-18
sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavirus...  60.8    4e-08
sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus H...  60.5    4e-08
sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmiss...  37.7    0.43 
sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine transmi...  37.7    0.49 
sp|P43349|TCTP_SOLTU Translationally-controlled tumor protein hom...  34.7    1.1  
sp|A0JUY4|RECA_ARTS2 Protein RecA OS=Arthrobacter sp. (strain FB2...  35.4    1.6  
sp|P54334|XKDO_BACSU Phage-like element PBSX protein XkdO OS=Baci...  35.4    2.1  
sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronavir...  35.0    3.3  
sp|Q751L1|RL43_ASHGO 60S ribosomal protein L43 OS=Ashbya gossypii...  32.0    3.6  
sp|Q0W2Y5|RPOP_METAR DNA-directed RNA polymerase subunit P OS=Met...  30.4    4.0  
sp|Q5UQB5|TOP1P_MIMIV DNA topoisomerase 1 type prokaryotic OS=Aca...  34.3    4.6  
sp|Q5J907|TCTP_ELAGV Translationally-controlled tumor protein hom...  32.3    8.0  
sp|P35138|RL15_BACLD 50S ribosomal protein L15 OS=Bacillus lichen...  31.6    9.7  


>sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 PE=1 SV=1
Length=4405

 Score = 1328 bits (3437),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 638/638 (100%), Positives = 638/638 (100%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
Sbjct  181  AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
Sbjct  241  YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
Sbjct  301  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
Sbjct  361  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
Sbjct  421  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
Sbjct  481  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
Sbjct  541  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
Sbjct  601  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
            GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
Sbjct  661  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
Sbjct  721  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
Sbjct  781  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  818


>sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 GN=rep PE=1 
SV=1
Length=7096

 Score = 1326 bits (3431),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 638/638 (100%), Positives = 638/638 (100%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
Sbjct  181  AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
Sbjct  241  YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
Sbjct  301  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
Sbjct  361  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
Sbjct  421  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
Sbjct  481  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
Sbjct  541  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
Sbjct  601  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
            GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
Sbjct  661  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
Sbjct  721  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
Sbjct  781  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  818


>sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 
279/2005 OX=389167 GN=1a PE=3 SV=1
Length=4388

 Score = 965 bits (2494),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 441/638 (69%), Positives = 530/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A+TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W
Sbjct  181  AFTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSEKSYERQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PANAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIG +HTG+ G+  E LN++L+EIL +++VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASANIGASHTGITGDNVETLNEDLMEILNRDRVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SAST AFV+TVKGLDYK FK IVESCGNFKVT+G+AKKGAWNIG++KSIL+PLY F S+A
Sbjct  481  SASTCAFVDTVKGLDYKTFKDIVESCGNFKVTRGRAKKGAWNIGQEKSILTPLYGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+R L+TA +S+  LQ+AAITILDGIS+ SLRLIDAM++TSDL TN+++VMAY
Sbjct  541  AGVIRSIFTRALDTANHSIPDLQRAAITILDGISEQSLRLIDAMVYTSDLLTNSVIVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ  +QWL+N+ GT  +KLKPV  W+E K   G+EFLRD WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQITQWLSNMLGTTVDKLKPVFTWVEAKLSAGIEFLRDAWEILKFLVTGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  +KE V+ F  ++NK L +C D +II GAKL+ LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNLKECVKAFLDVLNKALEMCIDQVIIAGAKLRTLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPL+APKE+ F EG++  T   +EEVVLK G+L+ LE P        ++G
Sbjct  721  IRGKEQLQLLMPLRAPKEVTFFEGDSHDTVFTSEEVVLKNGELEALETPVDSFTNGAVIG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLE+KD E+YCAL+P ++ TNN F+LKGG
Sbjct  781  TPVCVNGLMLLELKDKEQYCALSPGLLATNNVFSLKGG  818


>sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavirus 
279/2005 OX=389167 GN=rep PE=3 SV=1
Length=7079

 Score = 963 bits (2489),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 441/638 (69%), Positives = 530/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A+TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W
Sbjct  181  AFTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSEKSYERQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PANAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIG +HTG+ G+  E LN++L+EIL +++VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASANIGASHTGITGDNVETLNEDLMEILNRDRVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SAST AFV+TVKGLDYK FK IVESCGNFKVT+G+AKKGAWNIG++KSIL+PLY F S+A
Sbjct  481  SASTCAFVDTVKGLDYKTFKDIVESCGNFKVTRGRAKKGAWNIGQEKSILTPLYGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+R L+TA +S+  LQ+AAITILDGIS+ SLRLIDAM++TSDL TN+++VMAY
Sbjct  541  AGVIRSIFTRALDTANHSIPDLQRAAITILDGISEQSLRLIDAMVYTSDLLTNSVIVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ  +QWL+N+ GT  +KLKPV  W+E K   G+EFLRD WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQITQWLSNMLGTTVDKLKPVFTWVEAKLSAGIEFLRDAWEILKFLVTGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  +KE V+ F  ++NK L +C D +II GAKL+ LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNLKECVKAFLDVLNKALEMCIDQVIIAGAKLRTLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPL+APKE+ F EG++  T   +EEVVLK G+L+ LE P        ++G
Sbjct  721  IRGKEQLQLLMPLRAPKEVTFFEGDSHDTVFTSEEVVLKNGELEALETPVDSFTNGAVIG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLE+KD E+YCAL+P ++ TNN F+LKGG
Sbjct  781  TPVCVNGLMLLELKDKEQYCALSPGLLATNNVFSLKGG  818


>sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respiratory 
syndrome coronavirus OX=694009 GN=1a PE=1 SV=1
Length=4382

 Score = 956 bits (2470),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 436/638 (68%), Positives = 529/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPL+CIKD LARAGK+ CTLSEQLD+I++KRGVYCCR+HEHEIAW
Sbjct  181  AVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASP ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+Q+S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+RTL+ A +S+  LQ+AA+TILDGIS+ SLRL+DAM++TSDL TN++++MAY
Sbjct  541  AGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+ GT  EKL+P+ +W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLEIKD E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6X7|R1AB_SARS Replicase polyprotein 1ab OS=Severe acute 
respiratory syndrome coronavirus OX=694009 GN=rep PE=1 SV=1
Length=7073

 Score = 954 bits (2465),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 436/638 (68%), Positives = 529/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPL+CIKD LARAGK+ CTLSEQLD+I++KRGVYCCR+HEHEIAW
Sbjct  181  AVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASP ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+Q+S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+RTL+ A +S+  LQ+AA+TILDGIS+ SLRL+DAM++TSDL TN++++MAY
Sbjct  541  AGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+ GT  EKL+P+ +W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLEIKD E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus 
HKU3 OX=442736 GN=1a PE=3 SV=1
Length=4376

 Score = 951 bits (2458),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 440/636 (69%), Positives = 521/636 (82%), Gaps = 0/636 (0%)

Query  3    TRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYT  62
            TRYVDNNFCGPDGYPLECIKD LARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W+T
Sbjct  183  TRYVDNNFCGPDGYPLECIKDFLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVWFT  242

Query  63   ERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS  122
            ERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRIRS
Sbjct  243  ERSEKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIRS  302

Query  123  VYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQ  182
            VYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYLP 
Sbjct  303  VYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYLPT  362

Query  183  NAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAY  242
            NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVFSYVGC+NK AY
Sbjct  363  NAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFSYVGCYNKRAY  422

Query  243  WVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSA  302
            WVPRASANIG NHTG+ GE  E LN++LLEIL +E+VNINIVGDF+ NEE+AIILASFSA
Sbjct  423  WVPRASANIGANHTGITGENVETLNEDLLEILNRERVNINIVGDFRFNEEVAIILASFSA  482

Query  303  STSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAAR  362
            S SAF+ETVKGLDYK+FK IVESCGN+KVT GK   GAWNIG+Q+SIL+PL  F S+AA 
Sbjct  483  SPSAFIETVKGLDYKSFKVIVESCGNYKVTNGKPVTGAWNIGQQRSILTPLCGFPSQAAG  542

Query  363  VVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYIT  422
            V+RSIFSRTL+ A +S+  LQ+AA+T LDGIS+ SLRL+DAM++TSDL TN++VVMAY+T
Sbjct  543  VIRSIFSRTLDAANHSILDLQRAAVTTLDGISEQSLRLVDAMVYTSDLLTNSVVVMAYVT  602

Query  423  GGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGG  482
            GG+VQ T QWL+N+ GT  +KLKPV  W+E K   GVEFLRD WEI+KF+ T   +++ G
Sbjct  603  GGLVQQTMQWLSNMLGTAVDKLKPVFTWVEAKLSAGVEFLRDAWEILKFLITGVFDVIKG  662

Query  483  QIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVK  542
            QI      IKE V+ F  +VNK L +C D + I G KL+ALNLGE F+  S+GLYR+C++
Sbjct  663  QIQVATDNIKECVKIFLGVVNKALEMCLDQVTIAGTKLRALNLGEVFIAQSRGLYRQCIR  722

Query  543  SREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTP  602
             +E+  LLMPLKAPKE+ FLEG+   T + +EEVVLK+G+L+ LE P        +VGTP
Sbjct  723  GKEQLQLLMPLKAPKEVTFLEGDAHDTVLTSEEVVLKSGELEALETPIDSFTSGAVVGTP  782

Query  603  VCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            VCINGLMLLE+++ E+YCAL+P ++ TNN F LKGG
Sbjct  783  VCINGLMLLELENKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU3 OX=442736 GN=rep PE=3 SV=1
Length=7067

 Score = 949 bits (2452),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 440/636 (69%), Positives = 521/636 (82%), Gaps = 0/636 (0%)

Query  3    TRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYT  62
            TRYVDNNFCGPDGYPLECIKD LARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W+T
Sbjct  183  TRYVDNNFCGPDGYPLECIKDFLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVWFT  242

Query  63   ERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS  122
            ERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRIRS
Sbjct  243  ERSEKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIRS  302

Query  123  VYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQ  182
            VYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYLP 
Sbjct  303  VYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYLPT  362

Query  183  NAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAY  242
            NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVFSYVGC+NK AY
Sbjct  363  NAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFSYVGCYNKRAY  422

Query  243  WVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSA  302
            WVPRASANIG NHTG+ GE  E LN++LLEIL +E+VNINIVGDF+ NEE+AIILASFSA
Sbjct  423  WVPRASANIGANHTGITGENVETLNEDLLEILNRERVNINIVGDFRFNEEVAIILASFSA  482

Query  303  STSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAAR  362
            S SAF+ETVKGLDYK+FK IVESCGN+KVT GK   GAWNIG+Q+SIL+PL  F S+AA 
Sbjct  483  SPSAFIETVKGLDYKSFKVIVESCGNYKVTNGKPVTGAWNIGQQRSILTPLCGFPSQAAG  542

Query  363  VVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYIT  422
            V+RSIFSRTL+ A +S+  LQ+AA+T LDGIS+ SLRL+DAM++TSDL TN++VVMAY+T
Sbjct  543  VIRSIFSRTLDAANHSILDLQRAAVTTLDGISEQSLRLVDAMVYTSDLLTNSVVVMAYVT  602

Query  423  GGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGG  482
            GG+VQ T QWL+N+ GT  +KLKPV  W+E K   GVEFLRD WEI+KF+ T   +++ G
Sbjct  603  GGLVQQTMQWLSNMLGTAVDKLKPVFTWVEAKLSAGVEFLRDAWEILKFLITGVFDVIKG  662

Query  483  QIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVK  542
            QI      IKE V+ F  +VNK L +C D + I G KL+ALNLGE F+  S+GLYR+C++
Sbjct  663  QIQVATDNIKECVKIFLGVVNKALEMCLDQVTIAGTKLRALNLGEVFIAQSRGLYRQCIR  722

Query  543  SREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTP  602
             +E+  LLMPLKAPKE+ FLEG+   T + +EEVVLK+G+L+ LE P        +VGTP
Sbjct  723  GKEQLQLLMPLKAPKEVTFLEGDAHDTVLTSEEVVLKSGELEALETPIDSFTSGAVVGTP  782

Query  603  VCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            VCINGLMLLE+++ E+YCAL+P ++ TNN F LKGG
Sbjct  783  VCINGLMLLELENKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=1a PE=3 SV=1
Length=4380

 Score = 941 bits (2431),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 432/638 (68%), Positives = 523/638 (82%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCR+H HEIAW
Sbjct  181  ALTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCRDHGHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG  TCGYL
Sbjct  301  RSVYPVATPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVSEGPNTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSAADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF+LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFQLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+ +S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPIKGAWNIGQHRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIFSRTL+ A +S+  LQ+AA+TILD IS+ SLRL+DAM++TS+L TN++++MAY
Sbjct  541  AGVIRSIFSRTLDAANHSIPDLQRAAVTILDSISEQSLRLVDAMVYTSNLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+  T  EKL+P+  W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLDTTVEKLRPIFAWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFVDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAVVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIK  E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCINGLMLLEIKANEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=rep PE=3 SV=1
Length=7071

 Score = 939 bits (2426),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 432/638 (68%), Positives = 523/638 (82%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCR+H HEIAW
Sbjct  181  ALTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCRDHGHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG  TCGYL
Sbjct  301  RSVYPVATPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVSEGPNTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSAADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF+LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFQLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+ +S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPIKGAWNIGQHRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIFSRTL+ A +S+  LQ+AA+TILD IS+ SLRL+DAM++TS+L TN++++MAY
Sbjct  541  AGVIRSIFSRTLDAANHSIPDLQRAAVTILDSISEQSLRLVDAMVYTSNLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+  T  EKL+P+  W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLDTTVEKLRPIFAWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFVDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAVVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIK  E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCINGLMLLEIKANEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU4 OX=694007 GN=rep PE=1 SV=1
Length=7119

 Score = 109 bits (273),  Expect = 2e-23, Method: Compositional matrix adjust.
 Identities = 154/670 (23%), Positives = 278/670 (41%), Gaps = 59/670 (9%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSE-QLDF---IDTKRGVYCCREHEHEIAWY  61
            +D   CG +G P+     ++A+ G    TL++ ++D    +D+ R +    +  + + W 
Sbjct  200  IDQYMCGKNGKPIADYAKIVAKEGLT--TLADIEVDVKSRMDSDRFI-VLNKKLYRVVWN  256

Query  62   TERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIR  121
              R    Y  QT F I    + D      P   F + S I  + P ++      F  + R
Sbjct  257  VTRRNVPYPKQTAFTIVSVVQCDD-KDSVPEHTFTIGSQILMVSP-LKATNNKNFNLKQR  314

Query  122  SVYPVASPNECNQ---MCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTC  177
             +Y     +   Q   +  S  + C+ CG  +W TG+ ++     CG      +    + 
Sbjct  315  LLYTFYGKDAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSS  374

Query  178  GYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVG  235
            G +P+NA+    CP  +N      HS A+ +N    K  +  GG+  T+ FGG V++Y+G
Sbjct  375  GLVPRNALFLANCPCANNGAC--SHSAAQVYNILDGKACVEVGGKSFTLTFGGVVYAYMG  432

Query  236  CHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNE  291
            C +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E
Sbjct  433  CCDGTMYFVPRAKSCVS-RIGDAIFTGCTGTWDKVVETANLFLEKAQRSLNFCQQFALTE  491

Query  292  EIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGE----  345
               ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG     
Sbjct  492  ---VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVC  548

Query  346  QKSILSPLYAFA--SEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDA  403
              +I +P  AF    E+ + V +I     +   N    L   +  I+  +  Y +   D 
Sbjct  549  NATINAPFIAFTGLGESFKKVSAI---PWKICSNLKSALDYYSSNIMFRVFPYDIP-CDV  604

Query  404  MMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYE----KLKPVLDWLEEKFKEGV  459
              F   L     + +A  +  V++   +    + GTV       L   L+      +   
Sbjct  605  SNFVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSSACQTALSSFLNACVAASRATA  663

Query  460  EFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAK  519
             F+ D +++ K +            V  A+   + VQ    +++K + L   ++   G K
Sbjct  664  GFINDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTK  723

Query  520  LKALNL-GETFVTHSKGLYRKCVKSREET-----GLLMPLKAPKEIIFL-----EGETLP  568
            L A+   G   +  + G Y  C+ ++ +T      L++P    K+ + +       +T+ 
Sbjct  724  LSAIIYEGREALLFNSGTYF-CLSTKAKTLQGQMNLVLPGDYNKKTLGILDPVPNADTID  782

Query  569  TEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMV  628
                +  V +  G L    +PT+E   + +VG  V ++  + +  +D E Y  L  N  V
Sbjct  783  VNANSTVVDVVHGQL----EPTNEHGPSMIVGNYVLVSDKLFVRTEDEEFY-PLCTNGKV  837

Query  629  TNNTFTLKGG  638
             +  F LKGG
Sbjct  838  VSTLFRLKGG  847


>sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus 
HKU4 OX=694007 GN=1a PE=1 SV=1
Length=4434

 Score = 109 bits (272),  Expect = 3e-23, Method: Compositional matrix adjust.
 Identities = 154/670 (23%), Positives = 278/670 (41%), Gaps = 59/670 (9%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSE-QLDF---IDTKRGVYCCREHEHEIAWY  61
            +D   CG +G P+     ++A+ G    TL++ ++D    +D+ R +    +  + + W 
Sbjct  200  IDQYMCGKNGKPIADYAKIVAKEGLT--TLADIEVDVKSRMDSDRFI-VLNKKLYRVVWN  256

Query  62   TERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIR  121
              R    Y  QT F I    + D      P   F + S I  + P ++      F  + R
Sbjct  257  VTRRNVPYPKQTAFTIVSVVQCDD-KDSVPEHTFTIGSQILMVSP-LKATNNKNFNLKQR  314

Query  122  SVYPVASPNECNQ---MCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTC  177
             +Y     +   Q   +  S  + C+ CG  +W TG+ ++     CG      +    + 
Sbjct  315  LLYTFYGKDAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSS  374

Query  178  GYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVG  235
            G +P+NA+    CP  +N      HS A+ +N    K  +  GG+  T+ FGG V++Y+G
Sbjct  375  GLVPRNALFLANCPCANNGAC--SHSAAQVYNILDGKACVEVGGKSFTLTFGGVVYAYMG  432

Query  236  CHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNE  291
            C +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E
Sbjct  433  CCDGTMYFVPRAKSCVS-RIGDAIFTGCTGTWDKVVETANLFLEKAQRSLNFCQQFALTE  491

Query  292  EIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGE----  345
               ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG     
Sbjct  492  ---VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVC  548

Query  346  QKSILSPLYAFA--SEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDA  403
              +I +P  AF    E+ + V +I     +   N    L   +  I+  +  Y +   D 
Sbjct  549  NATINAPFIAFTGLGESFKKVSAI---PWKICSNLKSALDYYSSNIMFRVFPYDIP-CDV  604

Query  404  MMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYE----KLKPVLDWLEEKFKEGV  459
              F   L     + +A  +  V++   +    + GTV       L   L+      +   
Sbjct  605  SNFVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSSACQTALSSFLNACVAASRATA  663

Query  460  EFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAK  519
             F+ D +++ K +            V  A+   + VQ    +++K + L   ++   G K
Sbjct  664  GFINDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTK  723

Query  520  LKALNL-GETFVTHSKGLYRKCVKSREET-----GLLMPLKAPKEIIFL-----EGETLP  568
            L A+   G   +  + G Y  C+ ++ +T      L++P    K+ + +       +T+ 
Sbjct  724  LSAIIYEGREALLFNSGTYF-CLSTKAKTLQGQMNLVLPGDYNKKTLGILDPVPNADTID  782

Query  569  TEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMV  628
                +  V +  G L    +PT+E   + +VG  V ++  + +  +D E Y  L  N  V
Sbjct  783  VNANSTVVDVVHGQL----EPTNEHGPSMIVGNYVLVSDKLFVRTEDEEFY-PLCTNGKV  837

Query  629  TNNTFTLKGG  638
             +  F LKGG
Sbjct  838  VSTLFRLKGG  847


>sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU5 OX=694008 GN=rep PE=3 SV=1
Length=7182

 Score = 109 bits (272),  Expect = 4e-23, Method: Compositional matrix adjust.
 Identities = 150/674 (22%), Positives = 285/674 (42%), Gaps = 63/674 (9%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG--KASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            +D   CG +G P+     L+A  G  K +   +E     D+ R +   +   + I W  +
Sbjct  200  IDQYMCGKNGKPIAEFAALMASEGITKLADVEAEVKSRTDSDRYI-VFKNKLYRIVWNVQ  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R + +Y  Q+ F +    + DT   + P   F + S I+ I P    +       + R +
Sbjct  259  RKDVAYSKQSAFTMNSIVQLDTME-DVPRHSFTIGSEIQVIAPSTAVQANGHLNLKQRLL  317

Query  124  YPV---ASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      + +E N +  S  + C  CG+ SW TG+ V+     CG      +    + G 
Sbjct  318  YAFYGKQAVSEPNYIYHSAYVDCTSCGKGSWLTGNAVQGFACDCGAHYCANDVDLQSSGL  377

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRT--IAFGGCVFSYVGCH  237
            + +NAV+   CP   + E   +H+L +  +    K  +   G+T  + +GG +++Y+GC 
Sbjct  378  VRKNAVLLTTCPCNKDGEC--KHTLPQLVSMMTDKCDVEVVGKTFILTYGGVIYAYMGCS  435

Query  238  NKCAYWVPRASANIG----CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEI  293
                +++PRA + +        TG  G  S+      L  L++ +  IN V +F L E +
Sbjct  436  GGTMHFIPRAKSCVSKIGDAIFTGCTGTWSKVCETANL-FLERAQHAINFVNEFVLTETV  494

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE----QKSI  349
              +L+  ++S     +  +   ++  +  +   G + VT G   +G  N+G       ++
Sbjct  495  VALLSGTTSSIEELRDLCRNATFEKVRDYLTPRG-WIVTMGSYIEGVINVGAAGVCNAAL  553

Query  350  LSPLY-------AFASEAARVVR--SIFSRTLETAQNSV--RVLQKAAITILDGISQYSL  398
             +P         +F   AA   +  S    TL+   +S+  RV       I   ++ Y+ 
Sbjct  554  NAPFIVLSGLGESFKKVAATPWKLCSSLRETLDHYADSITYRVF---PYDIPCDVTDYTA  610

Query  399  RLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEG  458
             L+D  + T   A     V  Y+   V QLT+     +F +    +   +      +K  
Sbjct  611  LLLDCAVLTGASA---YFVARYVDEKVEQLTNL----VFSSCQSAVAAFVQACMSTYKAT  663

Query  459  VEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGA  518
             +F+ D + ++K +S           V       + ++ F  +++K + L   ++   G+
Sbjct  664  AKFISDMFTLIKVVSERLYVYTSVGFVVVGDYSSQLLKQFMHILSKAMQLLHTTVSWAGS  723

Query  519  KLKAL--NLGETFVTHSKGLYRKCVKS-----REETGLLMPLK-APKEIIFLE----GET  566
            KL ++  N  ++ V  S   Y  CV +     +++  L++P   + K+I  LE      T
Sbjct  724  KLPSVVYNGRDSLVFPSGTYY--CVSTQGRSLQDQFDLVIPGDLSKKQIGILEPTPNSTT  781

Query  567  LPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCI-NGLMLLEIKDTEK-YCALAP  624
            +  ++ T  V +  G L+P ++ + E V    VG  V I N + +  ++D+E  +  L  
Sbjct  782  VDKKINTNVVEVVVGQLEPTKEHSPELV----VGDYVIISNKIFVRSVEDSETVFYPLCT  837

Query  625  NMMVTNNTFTLKGG  638
            +  +    F LKGG
Sbjct  838  DGKIVPTLFRLKGG  851


>sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus 
HKU5 OX=694008 GN=1a PE=3 SV=1
Length=4481

 Score = 108 bits (271),  Expect = 4e-23, Method: Compositional matrix adjust.
 Identities = 150/674 (22%), Positives = 285/674 (42%), Gaps = 63/674 (9%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG--KASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            +D   CG +G P+     L+A  G  K +   +E     D+ R +   +   + I W  +
Sbjct  200  IDQYMCGKNGKPIAEFAALMASEGITKLADVEAEVKSRTDSDRYI-VFKNKLYRIVWNVQ  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R + +Y  Q+ F +    + DT   + P   F + S I+ I P    +       + R +
Sbjct  259  RKDVAYSKQSAFTMNSIVQLDTME-DVPRHSFTIGSEIQVIAPSTAVQANGHLNLKQRLL  317

Query  124  YPV---ASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      + +E N +  S  + C  CG+ SW TG+ V+     CG      +    + G 
Sbjct  318  YAFYGKQAVSEPNYIYHSAYVDCTSCGKGSWLTGNAVQGFACDCGAHYCANDVDLQSSGL  377

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRT--IAFGGCVFSYVGCH  237
            + +NAV+   CP   + E   +H+L +  +    K  +   G+T  + +GG +++Y+GC 
Sbjct  378  VRKNAVLLTTCPCNKDGEC--KHTLPQLVSMMTDKCDVEVVGKTFILTYGGVIYAYMGCS  435

Query  238  NKCAYWVPRASANIG----CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEI  293
                +++PRA + +        TG  G  S+      L  L++ +  IN V +F L E +
Sbjct  436  GGTMHFIPRAKSCVSKIGDAIFTGCTGTWSKVCETANL-FLERAQHAINFVNEFVLTETV  494

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE----QKSI  349
              +L+  ++S     +  +   ++  +  +   G + VT G   +G  N+G       ++
Sbjct  495  VALLSGTTSSIEELRDLCRNATFEKVRDYLTPRG-WIVTMGSYIEGVINVGAAGVCNAAL  553

Query  350  LSPLY-------AFASEAARVVR--SIFSRTLETAQNSV--RVLQKAAITILDGISQYSL  398
             +P         +F   AA   +  S    TL+   +S+  RV       I   ++ Y+ 
Sbjct  554  NAPFIVLSGLGESFKKVAATPWKLCSSLRETLDHYADSITYRVF---PYDIPCDVTDYTA  610

Query  399  RLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEG  458
             L+D  + T   A     V  Y+   V QLT+     +F +    +   +      +K  
Sbjct  611  LLLDCAVLTGASA---YFVARYVDEKVEQLTNL----VFSSCQSAVAAFVQACMSTYKAT  663

Query  459  VEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGA  518
             +F+ D + ++K +S           V       + ++ F  +++K + L   ++   G+
Sbjct  664  AKFISDMFTLIKVVSERLYVYTSVGFVVVGDYSSQLLKQFMHILSKAMQLLHTTVSWAGS  723

Query  519  KLKAL--NLGETFVTHSKGLYRKCVKS-----REETGLLMPLK-APKEIIFLE----GET  566
            KL ++  N  ++ V  S   Y  CV +     +++  L++P   + K+I  LE      T
Sbjct  724  KLPSVVYNGRDSLVFPSGTYY--CVSTQGRSLQDQFDLVIPGDLSKKQIGILEPTPNSTT  781

Query  567  LPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCI-NGLMLLEIKDTEK-YCALAP  624
            +  ++ T  V +  G L+P ++ + E V    VG  V I N + +  ++D+E  +  L  
Sbjct  782  VDKKINTNVVEVVVGQLEPTKEHSPELV----VGDYVIISNKIFVRSVEDSETVFYPLCT  837

Query  625  NMMVTNNTFTLKGG  638
            +  +    F LKGG
Sbjct  838  DGKIVPTLFRLKGG  851


>sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavirus 
133/2005 OX=389230 GN=rep PE=3 SV=1
Length=7126

 Score = 102 bits (253),  Expect = 7e-21, Method: Compositional matrix adjust.
 Identities = 149/668 (22%), Positives = 272/668 (41%), Gaps = 55/668 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSE-QLDF---IDTKRGVYCCREHEHEIAWY  61
            VD   CG +G P+     ++A+ G    TL++ ++D    +D+ R +    +  + + W 
Sbjct  200  VDQYMCGKNGKPIADYAKIVAKEGLT--TLADIEVDVKSRMDSDRFI-VLNKKLYRVVWN  256

Query  62   TERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQP--RVEKKKLDGFMGR  119
              R    Y  QT F +    + D      P   F + S I  + P      K  +     
Sbjct  257  VTRRNVPYSKQTAFTVVSVIQCDD-KESVPEHTFTIGSQILMVSPLKATNNKNFNLKQRL  315

Query  120  IRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCG  178
            + + Y   +  +   +  S  + C+ CG  +W TG+ ++     CG      +    + G
Sbjct  316  LHTFYGKEAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSSG  375

Query  179  YLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVGC  236
             +P+NA+    CP  +N      H+ A+ ++    K  +  GG+  T+ FGG V++Y+GC
Sbjct  376  LVPKNALFLANCPCANNGAC--SHNAAQVYSILDGKACVEVGGKSFTLTFGGVVYAYMGC  433

Query  237  HNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEE  292
             +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E 
Sbjct  434  CDGTMYFVPRAKSCVS-RIGDAIFTGCTGTWDKVVETANLFLEKAQHSLNFCQQFALTE-  491

Query  293  IAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGE----Q  346
              ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG      
Sbjct  492  --VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVCN  549

Query  347  KSILSPLYAFA--SEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAM  404
             +I +P  AF    E+ + V +I     +   N    L      I+  +  Y +   D  
Sbjct  550  ATINAPFIAFTGLGESFKKVAAI---PWKICSNLKSALDYYCSNIMFRVFPYDIP-CDVN  605

Query  405  MFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYE----KLKPVLDWLEEKFKEGVE  460
             F   L     + +A  +  V++   +    + GTV       L   L+      +    
Sbjct  606  DFVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSNACQTALSSFLNACVAASRATAG  664

Query  461  FLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
            F+ D +++ K +            V  A+   + VQ    +++K + L   ++   G KL
Sbjct  665  FISDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTKL  724

Query  521  KALNL-GETFVTHSKGLY----RKCVKSREETGLLMPLKAPKEIIFL-----EGETLPTE  570
             A+   G   +  + G Y     K    +++  L++P    K+ + +       +T+   
Sbjct  725  SAIIYEGREALLFNSGTYFCLSTKAKTLQDQMNLVLPGDYNKKTLGILDPVPNADTIDVT  784

Query  571  VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTN  630
              +  V +  G L    +PT+E   + +VG  V ++  + +   D E Y  L  N  V +
Sbjct  785  ANSTVVDVVHGQL----EPTNEHGPSMIVGNYVLVSDKLFVRTDDEEFY-PLCINGKVVS  839

Query  631  NTFTLKGG  638
              F LKGG
Sbjct  840  TLFRLKGG  847


>sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus 
133/2005 OX=389230 GN=1a PE=3 SV=1
Length=4441

 Score = 101 bits (252),  Expect = 9e-21, Method: Compositional matrix adjust.
 Identities = 149/668 (22%), Positives = 272/668 (41%), Gaps = 55/668 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSE-QLDF---IDTKRGVYCCREHEHEIAWY  61
            VD   CG +G P+     ++A+ G    TL++ ++D    +D+ R +    +  + + W 
Sbjct  200  VDQYMCGKNGKPIADYAKIVAKEGLT--TLADIEVDVKSRMDSDRFI-VLNKKLYRVVWN  256

Query  62   TERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQP--RVEKKKLDGFMGR  119
              R    Y  QT F +    + D      P   F + S I  + P      K  +     
Sbjct  257  VTRRNVPYSKQTAFTVVSVIQCDD-KESVPEHTFTIGSQILMVSPLKATNNKNFNLKQRL  315

Query  120  IRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCG  178
            + + Y   +  +   +  S  + C+ CG  +W TG+ ++     CG      +    + G
Sbjct  316  LHTFYGKEAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSSG  375

Query  179  YLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVGC  236
             +P+NA+    CP  +N      H+ A+ ++    K  +  GG+  T+ FGG V++Y+GC
Sbjct  376  LVPKNALFLANCPCANNGAC--SHNAAQVYSILDGKACVEVGGKSFTLTFGGVVYAYMGC  433

Query  237  HNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEE  292
             +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E 
Sbjct  434  CDGTMYFVPRAKSCVS-RIGDAIFTGCTGTWDKVVETANLFLEKAQHSLNFCQQFALTE-  491

Query  293  IAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGE----Q  346
              ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG      
Sbjct  492  --VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVCN  549

Query  347  KSILSPLYAFA--SEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAM  404
             +I +P  AF    E+ + V +I     +   N    L      I+  +  Y +   D  
Sbjct  550  ATINAPFIAFTGLGESFKKVAAI---PWKICSNLKSALDYYCSNIMFRVFPYDIP-CDVN  605

Query  405  MFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYE----KLKPVLDWLEEKFKEGVE  460
             F   L     + +A  +  V++   +    + GTV       L   L+      +    
Sbjct  606  DFVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSNACQTALSSFLNACVAASRATAG  664

Query  461  FLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
            F+ D +++ K +            V  A+   + VQ    +++K + L   ++   G KL
Sbjct  665  FISDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTKL  724

Query  521  KALNL-GETFVTHSKGLY----RKCVKSREETGLLMPLKAPKEIIFL-----EGETLPTE  570
             A+   G   +  + G Y     K    +++  L++P    K+ + +       +T+   
Sbjct  725  SAIIYEGREALLFNSGTYFCLSTKAKTLQDQMNLVLPGDYNKKTLGILDPVPNADTIDVT  784

Query  571  VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTN  630
              +  V +  G L    +PT+E   + +VG  V ++  + +   D E Y  L  N  V +
Sbjct  785  ANSTVVDVVHGQL----EPTNEHGPSMIVGNYVLVSDKLFVRTDDEEFY-PLCINGKVVS  839

Query  631  NTFTLKGG  638
              F LKGG
Sbjct  840  TLFRLKGG  847


>sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East respiratory 
syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=1a PE=1 SV=1
Length=4391

 Score = 92.4 bits (228),  Expect = 7e-18, Method: Compositional matrix adjust.
 Identities = 119/556 (21%), Positives = 222/556 (40%), Gaps = 61/556 (11%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG-----KASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            VD   CG DG P+     L+A+ G          ++ + D      G    + + + + W
Sbjct  198  VDQYMCGVDGKPISAYAFLMAKDGITKLADVEADVAARAD----DEGFITLKNNLYRLVW  253

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPR----------VEK  110
            + ER +  Y  Q+ F I    + D      P++ F L   I T+ PR          +++
Sbjct  254  HVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQ  312

Query  111  KKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLT  170
            K L  F G+        S      +  S  ++C  CG  SW TG+ ++     CG     
Sbjct  313  KLLYTFYGK-------ESLENPTYIYHSAFIECGSCGNDSWLTGNAIQGFACGCGASYTA  365

Query  171  KE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSLAE---YHNESGLKTILRKGGRTI  224
             +    + G +  NA++   CP           +HS+A+   Y +E     I      T+
Sbjct  366  NDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSER-CNVIADSKSFTL  424

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEI----LQKEKVN  280
             FGG  ++Y GC     Y+VPRA + +      +   G  G  + + +I    L++ + +
Sbjct  425  IFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGDSIF-TGCTGSWNKVTQIANMFLEQTQHS  483

Query  281  INIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGA  340
            +N VG+F +N+ +  IL+  + +     + +KG+     +  +    +  VT G     A
Sbjct  484  LNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNA  542

Query  341  WNIG----EQKSILSPLYAFA--SEAARVVRSIFSRTLETAQNSV-----RVLQKAAITI  389
             N+G    +  +I +P        E+ + V +I  +   + ++++      VL +     
Sbjct  543  INVGGTGLQYAAITAPYVVLTGLGESFKKVATIPYKVCNSVKDTLTYYAHSVLYRVFPYD  602

Query  390  LD-GISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQ-LTSQWLTNIFGTVYEKLKPV  447
            +D G+S +S  L D +    DL+    V   Y    ++Q  T  +++ I  +    +  +
Sbjct  603  MDSGVSSFSELLFDCV----DLS----VASTYFLVRLLQDKTGDFMSTIITSCQTAVSKL  654

Query  448  LDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLA  507
            LD   E  +    FL D   + +     A        V    ++   V+    L+NK + 
Sbjct  655  LDTCFEATEATFNFLLDLAGLFRIFLRNAYVYTSQGFVVVNGKVSTLVKQVLDLLNKGMQ  714

Query  508  LCADSIIIGGAKLKAL  523
            L    +   G+ + A+
Sbjct  715  LLHTKVSWAGSNISAV  730


>sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East 
respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=rep PE=1 SV=1
Length=7078

 Score = 92.0 bits (227),  Expect = 9e-18, Method: Compositional matrix adjust.
 Identities = 122/559 (22%), Positives = 223/559 (40%), Gaps = 67/559 (12%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG-----KASCTLSEQLD---FIDTKRGVYCCREHEHE  57
            VD   CG DG P+     L+A+ G          ++ + D   FI  K  +Y        
Sbjct  198  VDQYMCGVDGKPISAYAFLMAKDGITKLADVEADVAARADDEGFITLKNNLY-------R  250

Query  58   IAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPR----------  107
            + W+ ER +  Y  Q+ F I    + D      P++ F L   I T+ PR          
Sbjct  251  LVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLS  309

Query  108  VEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTE  167
            +++K L  F G+        S      +  S  ++C  CG  SW TG+ ++     CG  
Sbjct  310  LKQKLLYTFYGK-------ESLENPTYIYHSAFIECGSCGNDSWLTGNAIQGFACGCGAS  362

Query  168  NLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSLAE---YHNESGLKTILRKGG  221
                +    + G +  NA++   CP           +HS+A+   Y +E     I     
Sbjct  363  YTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSER-CNVIADSKS  421

Query  222  RTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEI----LQKE  277
             T+ FGG  ++Y GC     Y+VPRA + +      +   G  G  + + +I    L++ 
Sbjct  422  FTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGDSIF-TGCTGSWNKVTQIANMFLEQT  480

Query  278  KVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAK  337
            + ++N VG+F +N+ +  IL+  + +     + +KG+     +  +    +  VT G   
Sbjct  481  QHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFM  539

Query  338  KGAWNIG----EQKSILSPLYAFA--SEAARVVRSIFSRTLETAQNSV-----RVLQKAA  386
              A N+G    +  +I +P        E+ + V +I  +   + ++++      VL +  
Sbjct  540  DNAINVGGTGLQYAAITAPYVVLTGLGESFKKVATIPYKVCNSVKDTLTYYAHSVLYRVF  599

Query  387  ITILD-GISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQ-LTSQWLTNIFGTVYEKL  444
               +D G+S +S  L D +    DL+    V   Y    ++Q  T  +++ I  +    +
Sbjct  600  PYDMDSGVSSFSELLFDCV----DLS----VASTYFLVRLLQDKTGDFMSTIITSCQTAV  651

Query  445  KPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNK  504
              +LD   E  +    FL D   + +     A        V    ++   V+    L+NK
Sbjct  652  SKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVYTSQGFVVVNGKVSTLVKQVLDLLNK  711

Query  505  FLALCADSIIIGGAKLKAL  523
             + L    +   G+ + A+
Sbjct  712  GMQLLHTKVSWAGSNISAV  730


>sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU9 OX=694006 GN=rep PE=1 SV=1
Length=6930

 Score = 60.8 bits (146),  Expect = 4e-08, Method: Compositional matrix adjust.
 Identities = 99/457 (22%), Positives = 174/457 (38%), Gaps = 78/457 (17%)

Query  141  MKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGP  200
            +KC +C    W     +      CG E    +  ++C       V+K   P C       
Sbjct  310  LKCSYCDYYGWTPLKDIGTVNCLCGAE---FQLTSSCVDAESAGVIK---PGC-------  356

Query  201  EHSLAEYHNESGLKTILRKGGRT-IAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVV  259
               +       G++ I   G RT ++FGG ++S +G  N    WVPRA + +   H+G V
Sbjct  357  ---VMLLDKSPGMRLI--PGNRTYVSFGGAIWSPIGKVNGVTVWVPRAYSIVAGEHSGAV  411

Query  260  GEGSE-GLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSA----FVETVKGL  314
            G G    +N  L+E L +    I +  D   N   A  +A+    T A     VE+++GL
Sbjct  412  GSGDTVAINKELVEYLIE---GIRVDADTLDNPTCATFIANLDCDTKAPVVHTVESLQGL  468

Query  315  DYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLET  374
                       C   K+  G          E    +  L A+  + A    ++ SRT E 
Sbjct  469  -----------CLANKIMLGDKPLPT---DEFHPFIVGL-AYHVQRACWYGALASRTFEA  513

Query  375  AQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT  434
             ++ VR  ++         +Q+  ++   +        N  V +AY TG V   ++  + 
Sbjct  514  FRDFVRTEEER-------FAQFFGKVCAPI--------NGCVYLAYTTGRVTLFSAYQVL  558

Query  435  N------------IFGTVYEKLKPVLDWLEEKFKEGVEFLRDGW----EIVKFISTCACE  478
            N            +   V + LKP+L+W+ +K    +   +  W    E +  +      
Sbjct  559  NTAIAKSKDAFGGVAAIVVDMLKPILEWVLKK----MSIAKGAWLPYAEGLLALFKAQFT  614

Query  479  IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYR  538
            +V G+       +     +   L+   ++    S+   G K+ AL  G  +    KG+  
Sbjct  615  VVKGKFQFLRASLNSKCHSLCDLLTTIMSKLLTSVKWAGCKVDALYTGTYYYFSRKGVLT  674

Query  539  KCVKSREETGLLM-PLKAPKEIIFLEGETLPTEVLTE  574
            +     +  GLL+ P +   E+  L+G+      LT+
Sbjct  675  EVQLCAKRLGLLLTPKQQKMEVEVLDGDFDAPVTLTD  711


>sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus 
HKU9 OX=694006 GN=1a PE=3 SV=1
Length=4248

 Score = 60.5 bits (145),  Expect = 4e-08, Method: Compositional matrix adjust.
 Identities = 99/457 (22%), Positives = 174/457 (38%), Gaps = 78/457 (17%)

Query  141  MKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGP  200
            +KC +C    W     +      CG E    +  ++C       V+K   P C       
Sbjct  310  LKCSYCDYYGWTPLKDIGTVNCLCGAE---FQLTSSCVDAESAGVIK---PGC-------  356

Query  201  EHSLAEYHNESGLKTILRKGGRT-IAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVV  259
               +       G++ I   G RT ++FGG ++S +G  N    WVPRA + +   H+G V
Sbjct  357  ---VMLLDKSPGMRLI--PGNRTYVSFGGAIWSPIGKVNGVTVWVPRAYSIVAGEHSGAV  411

Query  260  GEGSE-GLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSA----FVETVKGL  314
            G G    +N  L+E L +    I +  D   N   A  +A+    T A     VE+++GL
Sbjct  412  GSGDTVAINKELVEYLIE---GIRVDADTLDNPTCATFIANLDCDTKAPVVHTVESLQGL  468

Query  315  DYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLET  374
                       C   K+  G          E    +  L A+  + A    ++ SRT E 
Sbjct  469  -----------CLANKIMLGDKPLPT---DEFHPFIVGL-AYHVQRACWYGALASRTFEA  513

Query  375  AQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT  434
             ++ VR  ++         +Q+  ++   +        N  V +AY TG V   ++  + 
Sbjct  514  FRDFVRTEEER-------FAQFFGKVCAPI--------NGCVYLAYTTGRVTLFSAYQVL  558

Query  435  N------------IFGTVYEKLKPVLDWLEEKFKEGVEFLRDGW----EIVKFISTCACE  478
            N            +   V + LKP+L+W+ +K    +   +  W    E +  +      
Sbjct  559  NTAIAKSKDAFGGVAAIVVDMLKPILEWVLKK----MSIAKGAWLPYAEGLLALFKAQFT  614

Query  479  IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYR  538
            +V G+       +     +   L+   ++    S+   G K+ AL  G  +    KG+  
Sbjct  615  VVKGKFQFLRASLNSKCHSLCDLLTTIMSKLLTSVKWAGCKVDALYTGTYYYFSRKGVLT  674

Query  539  KCVKSREETGLLM-PLKAPKEIIFLEGETLPTEVLTE  574
            +     +  GLL+ P +   E+  L+G+      LT+
Sbjct  675  EVQLCAKRLGLLLTPKQQKMEVEVLDGDFDAPVTLTD  711


>sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=1a PE=1 SV=1
Length=4017

 Score = 37.7 bits (86),  Expect = 0.43, Method: Compositional matrix adjust.
 Identities = 94/413 (23%), Positives = 134/413 (32%), Gaps = 95/413 (23%)

Query  5    YVDNNFCGPDGYPL--ECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYT  62
            YVD   CG DG P+     KD                D I+ +   Y C       AW T
Sbjct  113  YVDQYMCGADGKPVIEGDFKDYFGDE-----------DIIEFEGEEYHC-------AWTT  154

Query  63   ERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS  122
             R EK    QT F I+  +    +N + P+   P N   + + P V+K          + 
Sbjct  155  VRDEKPLNQQTLFTIQEIQ----YNLDIPH-KLP-NCATRHVAPPVKKNSKIVLSEDYKK  208

Query  123  VY-----PVASPNECNQMCLSTL------MKCDHCGETSWQTGDFVKATCEFCGTENLTK  171
            +Y     P     +C   C  TL      ++C  CG  S   GD+       CG     K
Sbjct  209  LYDIFGSPFMGNGDCLSKCFDTLHFIAATLRCP-CGSESSGVGDWTGFKTACCGLSGKVK  267

Query  172  EGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVF  231
             G T     P +AVV                            T +  G     F  CV 
Sbjct  268  -GVTLGDIKPGDAVV----------------------------TSMSAGKGVKFFANCVL  298

Query  232  SYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNIN-----IVGD  286
             Y G     + W  +       + T V   G EG  ++ ++   K  V  +     I GD
Sbjct  299  QYAGDVEGVSIW--KVIKTFTVDET-VCTPGFEGELNDFIKPESKSLVACSVKRAFITGD  355

Query  287  FKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQ  346
                    II      ST+ F     GL +K     V+ CG   V        AW + E+
Sbjct  356  IDDAVHDCIITGKLDLSTNLFGNV--GLLFKKTPWFVQKCGALFV-------DAWKVVEE  406

Query  347  ---------KSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITIL  390
                     K I   + +  + A  +V   +  T     N V+ L    + +L
Sbjct  407  LCGSLTLTYKQIYEVVASLCTSAFTIVN--YKPTFVVPDNRVKDLVDKCVKVL  457


>sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=rep PE=1 SV=1
Length=6684

 Score = 37.7 bits (86),  Expect = 0.49, Method: Compositional matrix adjust.
 Identities = 94/413 (23%), Positives = 134/413 (32%), Gaps = 95/413 (23%)

Query  5    YVDNNFCGPDGYPL--ECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYT  62
            YVD   CG DG P+     KD                D I+ +   Y C       AW T
Sbjct  113  YVDQYMCGADGKPVIEGDFKDYFGDE-----------DIIEFEGEEYHC-------AWTT  154

Query  63   ERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS  122
             R EK    QT F I+  +    +N + P+   P N   + + P V+K          + 
Sbjct  155  VRDEKPLNQQTLFTIQEIQ----YNLDIPH-KLP-NCATRHVAPPVKKNSKIVLSEDYKK  208

Query  123  VY-----PVASPNECNQMCLSTL------MKCDHCGETSWQTGDFVKATCEFCGTENLTK  171
            +Y     P     +C   C  TL      ++C  CG  S   GD+       CG     K
Sbjct  209  LYDIFGSPFMGNGDCLSKCFDTLHFIAATLRCP-CGSESSGVGDWTGFKTACCGLSGKVK  267

Query  172  EGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVF  231
             G T     P +AVV                            T +  G     F  CV 
Sbjct  268  -GVTLGDIKPGDAVV----------------------------TSMSAGKGVKFFANCVL  298

Query  232  SYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNIN-----IVGD  286
             Y G     + W  +       + T V   G EG  ++ ++   K  V  +     I GD
Sbjct  299  QYAGDVEGVSIW--KVIKTFTVDET-VCTPGFEGELNDFIKPESKSLVACSVKRAFITGD  355

Query  287  FKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQ  346
                    II      ST+ F     GL +K     V+ CG   V        AW + E+
Sbjct  356  IDDAVHDCIITGKLDLSTNLFGNV--GLLFKKTPWFVQKCGALFV-------DAWKVVEE  406

Query  347  ---------KSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITIL  390
                     K I   + +  + A  +V   +  T     N V+ L    + +L
Sbjct  407  LCGSLTLTYKQIYEVVASLCTSAFTIVN--YKPTFVVPDNRVKDLVDKCVKVL  457


>sp|P43349|TCTP_SOLTU Translationally-controlled tumor protein 
homolog OS=Solanum tuberosum OX=4113 GN=TCTP PE=2 SV=2
Length=168

 Score = 34.7 bits (78),  Expect = 1.1, Method: Composition-based stats.
 Identities = 26/99 (26%), Positives = 48/99 (48%), Gaps = 13/99 (13%)

Query  243  WVPRASA--NIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            WV + +   NIG N +   G   EG++D  +++       ++IV  F+L E+ A     F
Sbjct  35   WVVQGAVDVNIGANPSAEGGGEDEGVDDQAVKV-------VDIVDTFRLQEQPAFDKKQF  87

Query  301  SASTSAFVET----VKGLDYKAFKQIVESCGNFKVTKGK  335
                  +++     ++G   +AFK+ +ES   F ++K K
Sbjct  88   VTYIKRYIKNLTPKLEGEAQEAFKKNIESATKFLLSKLK  126


>sp|A0JUY4|RECA_ARTS2 Protein RecA OS=Arthrobacter sp. (strain 
FB24) OX=290399 GN=recA PE=3 SV=1
Length=351

 Score = 35.4 bits (80),  Expect = 1.6, Method: Compositional matrix adjust.
 Identities = 22/92 (24%), Positives = 39/92 (42%), Gaps = 1/92 (1%)

Query  127  ASPNECNQMCLSTLMKCDHCGETS-WQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAV  185
            A+P+    +  +        G+ S  + GD V+A  E   T ++  + A   G LP+  V
Sbjct  3    AAPDRQKALDAALAQIDKQFGKGSVMRLGDEVRAPIEVIPTGSIALDVALGIGGLPRGRV  62

Query  186  VKIYCPACHNSEVGPEHSLAEYHNESGLKTIL  217
            V+IY P          H++A    + G+   +
Sbjct  63   VEIYGPESSGKTTVALHAVANAQRQGGIAAFI  94


>sp|P54334|XKDO_BACSU Phage-like element PBSX protein XkdO OS=Bacillus 
subtilis (strain 168) OX=224308 GN=xkdO PE=4 SV=2
Length=1332

 Score = 35.4 bits (80),  Expect = 2.1, Method: Compositional matrix adjust.
 Identities = 30/104 (29%), Positives = 49/104 (47%), Gaps = 15/104 (14%)

Query  430  SQWL-TNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCA  488
            S W   N++  + +K++ +   ++EKF +  +F  D W+    I T   E V   +V  +
Sbjct  653  SNWFYDNVWNPIVKKVEDIKTSIKEKFDDARKFFEDAWD---GIETWFNEHVKDPLVKVS  709

Query  489  KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTH  532
            ++I E  Q  F L         DS  +GG   K ++ GE  VTH
Sbjct  710  EKIAEKFQWLFDL--------KDS--VGGFVAKVIHRGEE-VTH  742


>sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronavirus 
(strain FIPV WSU-79/1146) OX=33734 GN=rep PE=1 SV=2
Length=6709

 Score = 35.0 bits (79),  Expect = 3.3, Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 68/192 (35%), Gaps = 33/192 (17%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            YVD   CG DG P+                  E  D+   +  V      E+  AW T R
Sbjct  113  YVDQYMCGADGKPV---------------IEGEFKDYFGDE-DVIIYEGEEYHCAWLTVR  156

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVY  124
             EK    QT   I+  +    +N + P+   P N  I+ + P V+K          R +Y
Sbjct  157  DEKPLWQQTLLTIREIQ----YNLDIPH-KLP-NCAIREVAPPVKKNSKVVLSEEYRKLY  210

Query  125  PV-ASPNECNQMCLSTLMKCDH---------CGETSWQTGDFVKATCEFCGTENLTKEGA  174
             +  SP   N   L+T     H         CG  S   GD+       CG     K G 
Sbjct  211  DIFGSPFMGNGDSLNTCFDSLHFIAATLKCPCGAESSGVGDWTGFKTACCGLHGKVK-GV  269

Query  175  TTCGYLPQNAVV  186
            T     P +A+V
Sbjct  270  TLGAVKPGDAIV  281


>sp|Q751L1|RL43_ASHGO 60S ribosomal protein L43 OS=Ashbya gossypii 
(strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) 
OX=284811 GN=RPL43 PE=3 SV=1
Length=92

 Score = 32.0 bits (71),  Expect = 3.6, Method: Composition-based stats.
 Identities = 19/52 (37%), Positives = 26/52 (50%), Gaps = 3/52 (6%)

Query  326  CGNFKVTKGKAKKGAWNIGE-QKSILSPLYAFASEAARVVRSIFSRTLETAQ  376
            CG   V +G A  G WN    +K++    Y F++ AA  VRS   R  E A+
Sbjct  42   CGKKAVKRGAA--GIWNCSSCKKTVAGGAYTFSTAAAATVRSTIRRLREMAE  91


>sp|Q0W2Y5|RPOP_METAR DNA-directed RNA polymerase subunit P OS=Methanocella 
arvoryzae (strain DSM 22066 / NBRC 105507 / MRE50) 
OX=351160 GN=rpoP PE=3 SV=1
Length=45

 Score = 30.4 bits (67),  Expect = 4.0, Method: Composition-based stats.
 Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 0/40 (0%)

Query  142  KCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLP  181
            KC HC +T     D     C++CG   L KE  T    +P
Sbjct  4    KCAHCKQTVEVDKDMKGVRCQYCGHRILIKERPTAIKRVP  43


>sp|Q5UQB5|TOP1P_MIMIV DNA topoisomerase 1 type prokaryotic OS=Acanthamoeba 
polyphaga mimivirus OX=212035 GN=TOP1P PE=1 SV=1
Length=854

 Score = 34.3 bits (77),  Expect = 4.6, Method: Compositional matrix adjust.
 Identities = 27/105 (26%), Positives = 52/105 (50%), Gaps = 13/105 (12%)

Query  353  LYAFASEAARVVRSIFSRT---LETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSD  409
            +Y+  SE  + +  ++  T   L   +N   V     IT+ D + +Y    +D   FT++
Sbjct  522  IYSIKSENKKHIMEVYEDTDTILLGKENKKIVPTNLGITVNDFLMKYFPEFLD-YKFTAN  580

Query  410  LATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEK  454
            + T+    + Y++ G    T  W+ +I    Y+KLKP++D L ++
Sbjct  581  METD----LDYVSTG----TKNWV-DIVQDFYDKLKPIVDELSKQ  616


>sp|Q5J907|TCTP_ELAGV Translationally-controlled tumor protein 
homolog OS=Elaeis guineensis var. tenera OX=51953 GN=TCTP PE=2 
SV=1
Length=168

 Score = 32.3 bits (72),  Expect = 8.0, Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 51/114 (45%), Gaps = 18/114 (16%)

Query  231  FSYVGCHNKCAY-----WVPRASAN--IGCNHTGVVGEGSEGLNDNLLEILQKEKVNINI  283
            F Y   HN   +     WV + + N  IG N +   GE  EG++D  +++       ++I
Sbjct  18   FPYKEIHNGMLWEVEGKWVIQGAVNVDIGANPSAEGGEEDEGVDDQAVKV-------VDI  70

Query  284  VGDFKLNEEIAIILASFSASTSAFVETVK-GLDYKA---FKQIVESCGNFKVTK  333
            V  F+L E+ A     F      +++ +   LD +    FK+ +E    F ++K
Sbjct  71   VDTFRLQEQPAFDKKQFVTFMKRYIKNLTPKLDAEKQELFKKHIEGATKFLLSK  124


>sp|P35138|RL15_BACLD 50S ribosomal protein L15 OS=Bacillus licheniformis 
(strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 
/ NCIMB 9375 / NRRL NRS-1264 / Gibson 46) OX=279010 GN=rplO 
PE=3 SV=2
Length=146

 Score = 31.6 bits (70),  Expect = 9.7, Method: Composition-based stats.
 Identities = 19/56 (34%), Positives = 30/56 (54%), Gaps = 2/56 (4%)

Query  260  GEGSEGLNDNLLE--ILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKG  313
             EG+E   + LLE  ++ K K  + I+GD KL +++ +    FSAS    +E   G
Sbjct  86   AEGTEVTPELLLETGVISKLKSGVKILGDGKLEKKLTVKANKFSASAKQAIEAAGG  141



Lambda      K        H        a         alpha
   0.319    0.136    0.409    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0410    0.140     1.90     42.6     43.6 

Effective search space used: 68552451906
Results from round 2


Query= YP_009725298.1 nsp2 [Severe acute respiratory syndrome coronavirus
2]

Length=638
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value
Sequences used in model and found again:

sp|P0C6X7|R1AB_SARS Replicase polyprotein 1ab OS=Severe acute res...  931     0.0   
sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavirus...  930     0.0   
sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respi...  928     0.0   
sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 2...  928     0.0   
sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavirus...  925     0.0   
sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus H...  922     0.0   
sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavirus...  913     0.0   
sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus R...  911     0.0   
sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute re...  883     0.0   
sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute resp...  880     0.0   
sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavirus...  710     0.0   
sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus H...  709     0.0   
sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavirus...  709     0.0   
sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus 1...  709     0.0   
sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavirus...  661     0.0   
sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus H...  660     0.0   
sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East res...  604     0.0   
sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East respi...  604     0.0   
sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus H...  387     7e-117
sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavirus...  387     1e-116

Sequences not found previously or not previously below threshold:

sp|P0C6W7|R1AB_CVBEN Replicase polyprotein 1ab OS=Bovine coronavi...  81.0    3e-14
sp|P0C6W8|R1AB_CVBLU Replicase polyprotein 1ab OS=Bovine coronavi...  81.0    3e-14
sp|P0C6T8|R1A_CVBEN Replicase polyprotein 1a OS=Bovine coronaviru...  80.6    3e-14
sp|P0C6T9|R1A_CVBLU Replicase polyprotein 1a OS=Bovine coronaviru...  80.2    4e-14
sp|P0C6W9|R1AB_CVBM Replicase polyprotein 1ab OS=Bovine coronavir...  80.6    4e-14
sp|P0C6U0|R1A_CVBM Replicase polyprotein 1a OS=Bovine coronavirus...  79.8    5e-14
sp|P0C6X6|R1AB_CVHOC Replicase polyprotein 1ab OS=Human coronavir...  77.9    2e-13
sp|P0C6U7|R1A_CVHOC Replicase polyprotein 1a OS=Human coronavirus...  77.5    2e-13
sp|P0C6X0|R1AB_CVBQ Replicase polyprotein 1ab OS=Bovine coronavir...  76.7    4e-13
sp|P0C6U1|R1A_CVBQ Replicase polyprotein 1a OS=Bovine coronavirus...  76.3    6e-13
sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine transmi...  67.9    2e-10
sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmiss...  67.9    3e-10
sp|P0C6X8|R1AB_CVM2 Replicase polyprotein 1ab OS=Murine coronavir...  65.9    1e-09
sp|P0C6Y4|R1AB_PEDV7 Replicase polyprotein 1ab OS=Porcine epidemi...  65.6    1e-09
sp|P0C6V6|R1A_PEDV7 Replicase polyprotein 1a OS=Porcine epidemic ...  65.6    1e-09
sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavirus...  65.2    2e-09
sp|P0C6Y0|R1AB_CVMJH Replicase polyprotein 1ab OS=Murine coronavi...  64.4    3e-09
sp|P0C6V1|R1A_CVMJH Replicase polyprotein 1a OS=Murine coronaviru...  64.0    4e-09
sp|P0C6X2|R1AB_CVHN1 Replicase polyprotein 1ab OS=Human coronavir...  62.5    1e-08
sp|P0C6U3|R1A_CVHN1 Replicase polyprotein 1a OS=Human coronavirus...  62.5    1e-08
sp|P0C6U4|R1A_CVHN2 Replicase polyprotein 1a OS=Human coronavirus...  61.3    3e-08
sp|P0C6X3|R1AB_CVHN2 Replicase polyprotein 1ab OS=Human coronavir...  61.3    3e-08
sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronavir...  60.2    6e-08
sp|P0C6X4|R1AB_CVHN5 Replicase polyprotein 1ab OS=Human coronavir...  59.4    1e-07
sp|P0C6U5|R1A_CVHN5 Replicase polyprotein 1a OS=Human coronavirus...  59.4    1e-07
sp|P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab OS=Human coronavir...  57.9    3e-07
sp|P0C6U6|R1A_CVHNL Replicase polyprotein 1a OS=Human coronavirus...  57.9    3e-07
sp|P0C6X9|R1AB_CVMA5 Replicase polyprotein 1ab OS=Murine coronavi...  56.7    6e-07
sp|P0C6V0|R1A_CVMA5 Replicase polyprotein 1a OS=Murine coronaviru...  56.3    9e-07
sp|P0C6X1|R1AB_CVH22 Replicase polyprotein 1ab OS=Human coronavir...  48.6    2e-04
sp|P0C6U2|R1A_CVH22 Replicase polyprotein 1a OS=Human coronavirus...  48.6    2e-04
sp|P0C6W0|R1AB_BC512 Replicase polyprotein 1ab OS=Bat coronavirus...  42.4    0.014
sp|P0C6F6|R1A_BC512 Replicase polyprotein 1a OS=Bat coronavirus 5...  42.4    0.015
sp|Q3C251|ARGJ_CITLA Arginine biosynthesis bifunctional protein A...  40.9    0.031
sp|Q9KIP9|AGAS_ECOLX D-galactosamine-6-phosphate deaminase AgaS O...  35.1    2.2  
sp|Q6P6T1|C1S_RAT Complement C1s subcomponent OS=Rattus norvegicu...  34.4    4.0  
sp|Q9ZUR7|ARGJ_ARATH Arginine biosynthesis bifunctional protein A...  34.4    4.0  
sp|Q18823|LAM2_CAEEL Laminin-like protein lam-2 OS=Caenorhabditis...  34.4    4.1  
sp|Q9Y7Q9|YCX2_SCHPO Probable metabolite transporter C2H8.02 OS=S...  34.0    5.5  
sp|P42907|AGAS_ECOLI Putative D-galactosamine-6-phosphate deamina...  33.2    7.1  
sp|Q8U221|SYM_PYRFU Methionine--tRNA ligase OS=Pyrococcus furiosu...  33.6    7.8  
sp|Q1LVF0|LAMC1_DANRE Laminin subunit gamma-1 OS=Danio rerio OX=7...  33.2    9.1  


>sp|P0C6X7|R1AB_SARS Replicase polyprotein 1ab OS=Severe acute 
respiratory syndrome coronavirus OX=694009 GN=rep PE=1 SV=1
Length=7073

 Score = 931 bits (2405),  Expect = 0.0, Method: Composition-based stats.
 Identities = 436/638 (68%), Positives = 529/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPL+CIKD LARAGK+ CTLSEQLD+I++KRGVYCCR+HEHEIAW
Sbjct  181  AVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASP ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+Q+S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+RTL+ A +S+  LQ+AA+TILDGIS+ SLRL+DAM++TSDL TN++++MAY
Sbjct  541  AGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+ GT  EKL+P+ +W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLEIKD E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavirus 
279/2005 OX=389167 GN=rep PE=3 SV=1
Length=7079

 Score = 930 bits (2403),  Expect = 0.0, Method: Composition-based stats.
 Identities = 441/638 (69%), Positives = 530/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A+TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W
Sbjct  181  AFTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSEKSYERQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PANAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIG +HTG+ G+  E LN++L+EIL +++VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASANIGASHTGITGDNVETLNEDLMEILNRDRVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SAST AFV+TVKGLDYK FK IVESCGNFKVT+G+AKKGAWNIG++KSIL+PLY F S+A
Sbjct  481  SASTCAFVDTVKGLDYKTFKDIVESCGNFKVTRGRAKKGAWNIGQEKSILTPLYGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+R L+TA +S+  LQ+AAITILDGIS+ SLRLIDAM++TSDL TN+++VMAY
Sbjct  541  AGVIRSIFTRALDTANHSIPDLQRAAITILDGISEQSLRLIDAMVYTSDLLTNSVIVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ  +QWL+N+ GT  +KLKPV  W+E K   G+EFLRD WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQITQWLSNMLGTTVDKLKPVFTWVEAKLSAGIEFLRDAWEILKFLVTGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  +KE V+ F  ++NK L +C D +II GAKL+ LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNLKECVKAFLDVLNKALEMCIDQVIIAGAKLRTLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPL+APKE+ F EG++  T   +EEVVLK G+L+ LE P        ++G
Sbjct  721  IRGKEQLQLLMPLRAPKEVTFFEGDSHDTVFTSEEVVLKNGELEALETPVDSFTNGAVIG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLE+KD E+YCAL+P ++ TNN F+LKGG
Sbjct  781  TPVCVNGLMLLELKDKEQYCALSPGLLATNNVFSLKGG  818


>sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respiratory 
syndrome coronavirus OX=694009 GN=1a PE=1 SV=1
Length=4382

 Score = 928 bits (2399),  Expect = 0.0, Method: Composition-based stats.
 Identities = 436/638 (68%), Positives = 529/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPL+CIKD LARAGK+ CTLSEQLD+I++KRGVYCCR+HEHEIAW
Sbjct  181  AVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQLDYIESKRGVYCCRDHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASP ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEHCGTENLVIEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSVADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+Q+S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+RTL+ A +S+  LQ+AA+TILDGIS+ SLRL+DAM++TSDL TN++++MAY
Sbjct  541  AGVIRSIFARTLDAANHSIPDLQRAAVTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+ GT  EKL+P+ +W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLGTTVEKLRPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFIDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLEIKD E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCVNGLMLLEIKDKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 
279/2005 OX=389167 GN=1a PE=3 SV=1
Length=4388

 Score = 928 bits (2397),  Expect = 0.0, Method: Composition-based stats.
 Identities = 441/638 (69%), Positives = 530/638 (83%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A+TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W
Sbjct  181  AFTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSEKSYERQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYL
Sbjct  301  RSVYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PANAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIG +HTG+ G+  E LN++L+EIL +++VNINIVGDF LNEE+AIILASF
Sbjct  421  AYWVPRASANIGASHTGITGDNVETLNEDLMEILNRDRVNINIVGDFHLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SAST AFV+TVKGLDYK FK IVESCGNFKVT+G+AKKGAWNIG++KSIL+PLY F S+A
Sbjct  481  SASTCAFVDTVKGLDYKTFKDIVESCGNFKVTRGRAKKGAWNIGQEKSILTPLYGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIF+R L+TA +S+  LQ+AAITILDGIS+ SLRLIDAM++TSDL TN+++VMAY
Sbjct  541  AGVIRSIFTRALDTANHSIPDLQRAAITILDGISEQSLRLIDAMVYTSDLLTNSVIVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ  +QWL+N+ GT  +KLKPV  W+E K   G+EFLRD WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQITQWLSNMLGTTVDKLKPVFTWVEAKLSAGIEFLRDAWEILKFLVTGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  +KE V+ F  ++NK L +C D +II GAKL+ LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNLKECVKAFLDVLNKALEMCIDQVIIAGAKLRTLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPL+APKE+ F EG++  T   +EEVVLK G+L+ LE P        ++G
Sbjct  721  IRGKEQLQLLMPLRAPKEVTFFEGDSHDTVFTSEEVVLKNGELEALETPVDSFTNGAVIG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVC+NGLMLLE+KD E+YCAL+P ++ TNN F+LKGG
Sbjct  781  TPVCVNGLMLLELKDKEQYCALSPGLLATNNVFSLKGG  818


>sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU3 OX=442736 GN=rep PE=3 SV=1
Length=7067

 Score = 925 bits (2390),  Expect = 0.0, Method: Composition-based stats.
 Identities = 440/637 (69%), Positives = 521/637 (82%), Gaps = 0/637 (0%)

Query  2    YTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
             TRYVDNNFCGPDGYPLECIKD LARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W+
Sbjct  182  VTRYVDNNFCGPDGYPLECIKDFLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVWF  241

Query  62   TERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIR  121
            TERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRIR
Sbjct  242  TERSEKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIR  301

Query  122  SVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLP  181
            SVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYLP
Sbjct  302  SVYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYLP  361

Query  182  QNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCA  241
             NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVFSYVGC+NK A
Sbjct  362  TNAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFSYVGCYNKRA  421

Query  242  YWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFS  301
            YWVPRASANIG NHTG+ GE  E LN++LLEIL +E+VNINIVGDF+ NEE+AIILASFS
Sbjct  422  YWVPRASANIGANHTGITGENVETLNEDLLEILNRERVNINIVGDFRFNEEVAIILASFS  481

Query  302  ASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAA  361
            AS SAF+ETVKGLDYK+FK IVESCGN+KVT GK   GAWNIG+Q+SIL+PL  F S+AA
Sbjct  482  ASPSAFIETVKGLDYKSFKVIVESCGNYKVTNGKPVTGAWNIGQQRSILTPLCGFPSQAA  541

Query  362  RVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYI  421
             V+RSIFSRTL+ A +S+  LQ+AA+T LDGIS+ SLRL+DAM++TSDL TN++VVMAY+
Sbjct  542  GVIRSIFSRTLDAANHSILDLQRAAVTTLDGISEQSLRLVDAMVYTSDLLTNSVVVMAYV  601

Query  422  TGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVG  481
            TGG+VQ T QWL+N+ GT  +KLKPV  W+E K   GVEFLRD WEI+KF+ T   +++ 
Sbjct  602  TGGLVQQTMQWLSNMLGTAVDKLKPVFTWVEAKLSAGVEFLRDAWEILKFLITGVFDVIK  661

Query  482  GQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCV  541
            GQI      IKE V+ F  +VNK L +C D + I G KL+ALNLGE F+  S+GLYR+C+
Sbjct  662  GQIQVATDNIKECVKIFLGVVNKALEMCLDQVTIAGTKLRALNLGEVFIAQSRGLYRQCI  721

Query  542  KSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGT  601
            + +E+  LLMPLKAPKE+ FLEG+   T + +EEVVLK+G+L+ LE P        +VGT
Sbjct  722  RGKEQLQLLMPLKAPKEVTFLEGDAHDTVLTSEEVVLKSGELEALETPIDSFTSGAVVGT  781

Query  602  PVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            PVCINGLMLLE+++ E+YCAL+P ++ TNN F LKGG
Sbjct  782  PVCINGLMLLELENKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus 
HKU3 OX=442736 GN=1a PE=3 SV=1
Length=4376

 Score = 922 bits (2383),  Expect = 0.0, Method: Composition-based stats.
 Identities = 440/637 (69%), Positives = 521/637 (82%), Gaps = 0/637 (0%)

Query  2    YTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
             TRYVDNNFCGPDGYPLECIKD LARAGK+ CTLSEQLD+I++KRGVYCCREHEHEI W+
Sbjct  182  VTRYVDNNFCGPDGYPLECIKDFLARAGKSMCTLSEQLDYIESKRGVYCCREHEHEIVWF  241

Query  62   TERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIR  121
            TERSEKSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRIR
Sbjct  242  TERSEKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRIR  301

Query  122  SVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLP  181
            SVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG TTCGYLP
Sbjct  302  SVYPVATPQECNDMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVCEGPTTCGYLP  361

Query  182  QNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCA  241
             NAVVK+ CPAC + EVGPEHS+A+YHN S ++T LRKGGRT  FGGCVFSYVGC+NK A
Sbjct  362  TNAVVKMPCPACQDPEVGPEHSVADYHNHSNIETRLRKGGRTKCFGGCVFSYVGCYNKRA  421

Query  242  YWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFS  301
            YWVPRASANIG NHTG+ GE  E LN++LLEIL +E+VNINIVGDF+ NEE+AIILASFS
Sbjct  422  YWVPRASANIGANHTGITGENVETLNEDLLEILNRERVNINIVGDFRFNEEVAIILASFS  481

Query  302  ASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAA  361
            AS SAF+ETVKGLDYK+FK IVESCGN+KVT GK   GAWNIG+Q+SIL+PL  F S+AA
Sbjct  482  ASPSAFIETVKGLDYKSFKVIVESCGNYKVTNGKPVTGAWNIGQQRSILTPLCGFPSQAA  541

Query  362  RVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYI  421
             V+RSIFSRTL+ A +S+  LQ+AA+T LDGIS+ SLRL+DAM++TSDL TN++VVMAY+
Sbjct  542  GVIRSIFSRTLDAANHSILDLQRAAVTTLDGISEQSLRLVDAMVYTSDLLTNSVVVMAYV  601

Query  422  TGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVG  481
            TGG+VQ T QWL+N+ GT  +KLKPV  W+E K   GVEFLRD WEI+KF+ T   +++ 
Sbjct  602  TGGLVQQTMQWLSNMLGTAVDKLKPVFTWVEAKLSAGVEFLRDAWEILKFLITGVFDVIK  661

Query  482  GQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCV  541
            GQI      IKE V+ F  +VNK L +C D + I G KL+ALNLGE F+  S+GLYR+C+
Sbjct  662  GQIQVATDNIKECVKIFLGVVNKALEMCLDQVTIAGTKLRALNLGEVFIAQSRGLYRQCI  721

Query  542  KSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGT  601
            + +E+  LLMPLKAPKE+ FLEG+   T + +EEVVLK+G+L+ LE P        +VGT
Sbjct  722  RGKEQLQLLMPLKAPKEVTFLEGDAHDTVLTSEEVVLKSGELEALETPIDSFTSGAVVGT  781

Query  602  PVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            PVCINGLMLLE+++ E+YCAL+P ++ TNN F LKGG
Sbjct  782  PVCINGLMLLELENKEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=rep PE=3 SV=1
Length=7071

 Score = 913 bits (2359),  Expect = 0.0, Method: Composition-based stats.
 Identities = 432/638 (68%), Positives = 523/638 (82%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCR+H HEIAW
Sbjct  181  ALTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCRDHGHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG  TCGYL
Sbjct  301  RSVYPVATPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVSEGPNTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSAADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF+LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFQLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+ +S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPIKGAWNIGQHRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIFSRTL+ A +S+  LQ+AA+TILD IS+ SLRL+DAM++TS+L TN++++MAY
Sbjct  541  AGVIRSIFSRTLDAANHSIPDLQRAAVTILDSISEQSLRLVDAMVYTSNLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+  T  EKL+P+  W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLDTTVEKLRPIFAWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFVDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAVVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIK  E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCINGLMLLEIKANEQYCALSPGLLATNNVFRLKGG  818


>sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=1a PE=3 SV=1
Length=4380

 Score = 911 bits (2354),  Expect = 0.0, Method: Composition-based stats.
 Identities = 432/638 (68%), Positives = 523/638 (82%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            A TRYVDNNFCGPDGYPLECIKDLLARAGK+ CTLSEQLD+I++KRGVYCCR+H HEIAW
Sbjct  181  ALTRYVDNNFCGPDGYPLECIKDLLARAGKSMCTLSEQLDYIESKRGVYCCRDHGHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            +TERS+KSYE QTPFEIK AKKFDTF GECP FVFPLNS +K IQPRVEKKK +GFMGRI
Sbjct  241  FTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFPLNSKVKVIQPRVEKKKTEGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVA+P ECN M LSTLMKC+HC E SWQT DF+KATCE CGTENL  EG  TCGYL
Sbjct  301  RSVYPVATPQECNNMHLSTLMKCNHCDEVSWQTCDFLKATCEQCGTENLVSEGPNTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            P NAVVK+ CPAC + E+GPEHS A+YHN S ++T LRKGGRT  FGGCVF+YVGC+NK 
Sbjct  361  PTNAVVKMPCPACQDPEIGPEHSAADYHNHSNIETRLRKGGRTRCFGGCVFAYVGCYNKR  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASA+IG  HTG+ G+  E LN++LLEIL +E+VNINIVGDF+LNEE+AIILASF
Sbjct  421  AYWVPRASADIGSGHTGITGDNVETLNEDLLEILSRERVNINIVGDFQLNEEVAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAF++T+K LDYK+FK IVESCGN+KVTKGK  KGAWNIG+ +S+L+PL  F S+A
Sbjct  481  SASTSAFIDTIKSLDYKSFKTIVESCGNYKVTKGKPIKGAWNIGQHRSVLTPLCGFPSQA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            A V+RSIFSRTL+ A +S+  LQ+AA+TILD IS+ SLRL+DAM++TS+L TN++++MAY
Sbjct  541  AGVIRSIFSRTLDAANHSIPDLQRAAVTILDSISEQSLRLVDAMVYTSNLLTNSVIIMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            +TGG+VQ TSQWL+N+  T  EKL+P+  W+E K   GVEFL+D WEI+KF+ T   +IV
Sbjct  601  VTGGLVQQTSQWLSNLLDTTVEKLRPIFAWIEAKLSAGVEFLKDAWEILKFLITGVFDIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
             GQI   +  IK+ V+ F  +VNK L +C D + I GAKL++LNLGE F+  SKGLYR+C
Sbjct  661  KGQIQVASDNIKDCVKCFVDVVNKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            ++ +E+  LLMPLKAPKE+ FLEG++  T + +EEVVLK G+L+ LE P        +VG
Sbjct  721  IRGKEQLQLLMPLKAPKEVTFLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAVVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIK  E+YCAL+P ++ TNN F LKGG
Sbjct  781  TPVCINGLMLLEIKANEQYCALSPGLLATNNVFRLKGG  818


>sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 GN=rep PE=1 
SV=1
Length=7096

 Score = 883 bits (2281),  Expect = 0.0, Method: Composition-based stats.
 Identities = 638/638 (100%), Positives = 638/638 (100%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
Sbjct  181  AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
Sbjct  241  YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
Sbjct  301  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
Sbjct  361  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
Sbjct  421  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
Sbjct  481  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
Sbjct  541  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
Sbjct  601  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
            GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
Sbjct  661  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
Sbjct  721  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
Sbjct  781  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  818


>sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 PE=1 SV=1
Length=4405

 Score = 880 bits (2273),  Expect = 0.0, Method: Composition-based stats.
 Identities = 638/638 (100%), Positives = 638/638 (100%), Gaps = 0/638 (0%)

Query  1    AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  60
            AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
Sbjct  181  AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW  240

Query  61   YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  120
            YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
Sbjct  241  YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI  300

Query  121  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  180
            RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
Sbjct  301  RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL  360

Query  181  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  240
            PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
Sbjct  361  PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC  420

Query  241  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
            AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
Sbjct  421  AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  480

Query  301  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  360
            SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
Sbjct  481  SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA  540

Query  361  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  420
            ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
Sbjct  541  ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY  600

Query  421  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  480
            ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
Sbjct  601  ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV  660

Query  481  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  540
            GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
Sbjct  661  GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC  720

Query  541  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  600
            VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
Sbjct  721  VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG  780

Query  601  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
            TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
Sbjct  781  TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  818


>sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU4 OX=694007 GN=rep PE=1 SV=1
Length=7119

 Score = 710 bits (1832),  Expect = 0.0, Method: Composition-based stats.
 Identities = 148/667 (22%), Positives = 269/667 (40%), Gaps = 53/667 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKA--SCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            +D   CG +G P+     ++A+ G    +    +    +D+ R +    +  + + W   
Sbjct  200  IDQYMCGKNGKPIADYAKIVAKEGLTTLADIEVDVKSRMDSDRFI-VLNKKLYRVVWNVT  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R    Y  QT F I    + D      P   F + S I  + P ++      F  + R +
Sbjct  259  RRNVPYPKQTAFTIVSVVQCDD-KDSVPEHTFTIGSQILMVSP-LKATNNKNFNLKQRLL  316

Query  124  YPVA---SPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      +  +   +  S  + C+ CG  +W TG+ ++     CG      +    + G 
Sbjct  317  YTFYGKDAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSSGL  376

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVGCH  237
            +P+NA+    CP  +N      HS A+ +N    K  +  GG+  T+ FGG V++Y+GC 
Sbjct  377  VPRNALFLANCPCANNGAC--SHSAAQVYNILDGKACVEVGGKSFTLTFGGVVYAYMGCC  434

Query  238  NKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEEI  293
            +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E  
Sbjct  435  DGTMYFVPRAKSCVSRI-GDAIFTGCTGTWDKVVETANLFLEKAQRSLNFCQQFALTE--  491

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGEQ----K  347
             ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG       
Sbjct  492  -VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVCNA  550

Query  348  SILSPLYAFAS--EAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMM  405
            +I +P  AF    E+ + V +I     +   N    L   +  I+  +  Y +   D   
Sbjct  551  TINAPFIAFTGLGESFKKVSAI---PWKICSNLKSALDYYSSNIMFRVFPYDIP-CDVSN  606

Query  406  FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGT----VYEKLKPVLDWLEEKFKEGVEF  461
            F   L     + +A  +  V++   +    + GT        L   L+      +    F
Sbjct  607  FVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSSACQTALSSFLNACVAASRATAGF  665

Query  462  LRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLK  521
            + D +++ K +            V  A+   + VQ    +++K + L   ++   G KL 
Sbjct  666  INDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTKLS  725

Query  522  ALNL-GETFVTHSKGLY----RKCVKSREETGLLMPLKAPKEIIFL-----EGETLPTEV  571
            A+   G   +  + G Y     K    + +  L++P    K+ + +       +T+    
Sbjct  726  AIIYEGREALLFNSGTYFCLSTKAKTLQGQMNLVLPGDYNKKTLGILDPVPNADTIDVNA  785

Query  572  LTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNN  631
             +  V +  G L+    PT+E   + +VG  V ++  + +  +D E Y  L  N  V + 
Sbjct  786  NSTVVDVVHGQLE----PTNEHGPSMIVGNYVLVSDKLFVRTEDEEFY-PLCTNGKVVST  840

Query  632  TFTLKGG  638
             F LKGG
Sbjct  841  LFRLKGG  847


>sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus 
HKU4 OX=694007 GN=1a PE=1 SV=1
Length=4434

 Score = 709 bits (1831),  Expect = 0.0, Method: Composition-based stats.
 Identities = 148/667 (22%), Positives = 269/667 (40%), Gaps = 53/667 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKA--SCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            +D   CG +G P+     ++A+ G    +    +    +D+ R +    +  + + W   
Sbjct  200  IDQYMCGKNGKPIADYAKIVAKEGLTTLADIEVDVKSRMDSDRFI-VLNKKLYRVVWNVT  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R    Y  QT F I    + D      P   F + S I  + P ++      F  + R +
Sbjct  259  RRNVPYPKQTAFTIVSVVQCDD-KDSVPEHTFTIGSQILMVSP-LKATNNKNFNLKQRLL  316

Query  124  YPVA---SPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      +  +   +  S  + C+ CG  +W TG+ ++     CG      +    + G 
Sbjct  317  YTFYGKDAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSSGL  376

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVGCH  237
            +P+NA+    CP  +N      HS A+ +N    K  +  GG+  T+ FGG V++Y+GC 
Sbjct  377  VPRNALFLANCPCANNGAC--SHSAAQVYNILDGKACVEVGGKSFTLTFGGVVYAYMGCC  434

Query  238  NKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEEI  293
            +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E  
Sbjct  435  DGTMYFVPRAKSCVSRI-GDAIFTGCTGTWDKVVETANLFLEKAQRSLNFCQQFALTE--  491

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGEQ----K  347
             ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG       
Sbjct  492  -VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVCNA  550

Query  348  SILSPLYAFAS--EAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMM  405
            +I +P  AF    E+ + V +I     +   N    L   +  I+  +  Y +   D   
Sbjct  551  TINAPFIAFTGLGESFKKVSAI---PWKICSNLKSALDYYSSNIMFRVFPYDIP-CDVSN  606

Query  406  FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGT----VYEKLKPVLDWLEEKFKEGVEF  461
            F   L     + +A  +  V++   +    + GT        L   L+      +    F
Sbjct  607  FVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSSACQTALSSFLNACVAASRATAGF  665

Query  462  LRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLK  521
            + D +++ K +            V  A+   + VQ    +++K + L   ++   G KL 
Sbjct  666  INDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTKLS  725

Query  522  ALNL-GETFVTHSKGLY----RKCVKSREETGLLMPLKAPKEIIFL-----EGETLPTEV  571
            A+   G   +  + G Y     K    + +  L++P    K+ + +       +T+    
Sbjct  726  AIIYEGREALLFNSGTYFCLSTKAKTLQGQMNLVLPGDYNKKTLGILDPVPNADTIDVNA  785

Query  572  LTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNN  631
             +  V +  G L+    PT+E   + +VG  V ++  + +  +D E Y  L  N  V + 
Sbjct  786  NSTVVDVVHGQLE----PTNEHGPSMIVGNYVLVSDKLFVRTEDEEFY-PLCTNGKVVST  840

Query  632  TFTLKGG  638
             F LKGG
Sbjct  841  LFRLKGG  847


>sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavirus 
133/2005 OX=389230 GN=rep PE=3 SV=1
Length=7126

 Score = 709 bits (1831),  Expect = 0.0, Method: Composition-based stats.
 Identities = 146/667 (22%), Positives = 268/667 (40%), Gaps = 53/667 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKA--SCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            VD   CG +G P+     ++A+ G    +    +    +D+ R +    +  + + W   
Sbjct  200  VDQYMCGKNGKPIADYAKIVAKEGLTTLADIEVDVKSRMDSDRFI-VLNKKLYRVVWNVT  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R    Y  QT F +    + D      P   F + S I  + P ++      F  + R +
Sbjct  259  RRNVPYSKQTAFTVVSVIQCDD-KESVPEHTFTIGSQILMVSP-LKATNNKNFNLKQRLL  316

Query  124  ---YPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
               Y   +  +   +  S  + C+ CG  +W TG+ ++     CG      +    + G 
Sbjct  317  HTFYGKEAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSSGL  376

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVGCH  237
            +P+NA+    CP  +N      H+ A+ ++    K  +  GG+  T+ FGG V++Y+GC 
Sbjct  377  VPKNALFLANCPCANNGAC--SHNAAQVYSILDGKACVEVGGKSFTLTFGGVVYAYMGCC  434

Query  238  NKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEEI  293
            +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E  
Sbjct  435  DGTMYFVPRAKSCVSRI-GDAIFTGCTGTWDKVVETANLFLEKAQHSLNFCQQFALTE--  491

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGEQ----K  347
             ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG       
Sbjct  492  -VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVCNA  550

Query  348  SILSPLYAFAS--EAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMM  405
            +I +P  AF    E+ + V +I     +   N    L      I+  +  Y +   D   
Sbjct  551  TINAPFIAFTGLGESFKKVAAI---PWKICSNLKSALDYYCSNIMFRVFPYDIP-CDVND  606

Query  406  FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGT----VYEKLKPVLDWLEEKFKEGVEF  461
            F   L     + +A  +  V++   +    + GT        L   L+      +    F
Sbjct  607  FVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSNACQTALSSFLNACVAASRATAGF  665

Query  462  LRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLK  521
            + D +++ K +            V  A+   + VQ    +++K + L   ++   G KL 
Sbjct  666  ISDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTKLS  725

Query  522  ALNL-GETFVTHSKGLY----RKCVKSREETGLLMPLKAPKEIIFL-----EGETLPTEV  571
            A+   G   +  + G Y     K    +++  L++P    K+ + +       +T+    
Sbjct  726  AIIYEGREALLFNSGTYFCLSTKAKTLQDQMNLVLPGDYNKKTLGILDPVPNADTIDVTA  785

Query  572  LTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNN  631
             +  V +  G L+    PT+E   + +VG  V ++  + +   D E Y  L  N  V + 
Sbjct  786  NSTVVDVVHGQLE----PTNEHGPSMIVGNYVLVSDKLFVRTDDEEFY-PLCINGKVVST  840

Query  632  TFTLKGG  638
             F LKGG
Sbjct  841  LFRLKGG  847


>sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus 
133/2005 OX=389230 GN=1a PE=3 SV=1
Length=4441

 Score = 709 bits (1829),  Expect = 0.0, Method: Composition-based stats.
 Identities = 146/667 (22%), Positives = 268/667 (40%), Gaps = 53/667 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKA--SCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            VD   CG +G P+     ++A+ G    +    +    +D+ R +    +  + + W   
Sbjct  200  VDQYMCGKNGKPIADYAKIVAKEGLTTLADIEVDVKSRMDSDRFI-VLNKKLYRVVWNVT  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R    Y  QT F +    + D      P   F + S I  + P ++      F  + R +
Sbjct  259  RRNVPYSKQTAFTVVSVIQCDD-KESVPEHTFTIGSQILMVSP-LKATNNKNFNLKQRLL  316

Query  124  ---YPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
               Y   +  +   +  S  + C+ CG  +W TG+ ++     CG      +    + G 
Sbjct  317  HTFYGKEAVQQPGYIYHSAYVDCNACGRGTWCTGNAIQGFACDCGANYSANDVDLQSSGL  376

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGR--TIAFGGCVFSYVGCH  237
            +P+NA+    CP  +N      H+ A+ ++    K  +  GG+  T+ FGG V++Y+GC 
Sbjct  377  VPKNALFLANCPCANNGAC--SHNAAQVYSILDGKACVEVGGKSFTLTFGGVVYAYMGCC  434

Query  238  NKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEEI  293
            +   Y+VPRA + +       +  G  G  D ++E     L+K + ++N    F L E  
Sbjct  435  DGTMYFVPRAKSCVSRI-GDAIFTGCTGTWDKVVETANLFLEKAQHSLNFCQQFALTE--  491

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGN--FKVTKGKAKKGAWNIGEQ----K  347
             ++LA  S +TS F E        +++++ +   N  F VT G   + A NIG       
Sbjct  492  -VVLAILSGTTSTFEELRDLCHNASYEKVRDHLVNHGFVVTIGDYIRDAINIGANGVCNA  550

Query  348  SILSPLYAFAS--EAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMM  405
            +I +P  AF    E+ + V +I     +   N    L      I+  +  Y +   D   
Sbjct  551  TINAPFIAFTGLGESFKKVAAI---PWKICSNLKSALDYYCSNIMFRVFPYDIP-CDVND  606

Query  406  FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGT----VYEKLKPVLDWLEEKFKEGVEF  461
            F   L     + +A  +  V++   +    + GT        L   L+      +    F
Sbjct  607  FVELLLDCGKLTVA-TSYFVLRYLDEKFDTVLGTVSNACQTALSSFLNACVAASRATAGF  665

Query  462  LRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLK  521
            + D +++ K +            V  A+   + VQ    +++K + L   ++   G KL 
Sbjct  666  ISDMFKLFKVLMHKLYVYTSCGYVAVAEHSSKIVQQVLDIMSKAMKLLHTNVSWAGTKLS  725

Query  522  ALNL-GETFVTHSKGLY----RKCVKSREETGLLMPLKAPKEIIFL-----EGETLPTEV  571
            A+   G   +  + G Y     K    +++  L++P    K+ + +       +T+    
Sbjct  726  AIIYEGREALLFNSGTYFCLSTKAKTLQDQMNLVLPGDYNKKTLGILDPVPNADTIDVTA  785

Query  572  LTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNN  631
             +  V +  G L+    PT+E   + +VG  V ++  + +   D E Y  L  N  V + 
Sbjct  786  NSTVVDVVHGQLE----PTNEHGPSMIVGNYVLVSDKLFVRTDDEEFY-PLCINGKVVST  840

Query  632  TFTLKGG  638
             F LKGG
Sbjct  841  LFRLKGG  847


>sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU5 OX=694008 GN=rep PE=3 SV=1
Length=7182

 Score = 661 bits (1704),  Expect = 0.0, Method: Composition-based stats.
 Identities = 143/670 (21%), Positives = 281/670 (42%), Gaps = 55/670 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG--KASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            +D   CG +G P+     L+A  G  K +   +E     D+ R +   +   + I W  +
Sbjct  200  IDQYMCGKNGKPIAEFAALMASEGITKLADVEAEVKSRTDSDRYI-VFKNKLYRIVWNVQ  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R + +Y  Q+ F +    + DT   + P   F + S I+ I P    +       + R +
Sbjct  259  RKDVAYSKQSAFTMNSIVQLDTME-DVPRHSFTIGSEIQVIAPSTAVQANGHLNLKQRLL  317

Query  124  YPV---ASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      + +E N +  S  + C  CG+ SW TG+ V+     CG      +    + G 
Sbjct  318  YAFYGKQAVSEPNYIYHSAYVDCTSCGKGSWLTGNAVQGFACDCGAHYCANDVDLQSSGL  377

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRT--IAFGGCVFSYVGCH  237
            + +NAV+   CP   + E   +H+L +  +    K  +   G+T  + +GG +++Y+GC 
Sbjct  378  VRKNAVLLTTCPCNKDGEC--KHTLPQLVSMMTDKCDVEVVGKTFILTYGGVIYAYMGCS  435

Query  238  NKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEEI  293
                +++PRA + +       +  G  G    + E     L++ +  IN V +F L E +
Sbjct  436  GGTMHFIPRAKSCVSKI-GDAIFTGCTGTWSKVCETANLFLERAQHAINFVNEFVLTETV  494

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE----QKSI  349
              +L+  ++S     +  +   ++  +  +   G + VT G   +G  N+G       ++
Sbjct  495  VALLSGTTSSIEELRDLCRNATFEKVRDYLTPRG-WIVTMGSYIEGVINVGAAGVCNAAL  553

Query  350  LSPLY-------AFASEAARVVR--SIFSRTLETAQNSVRVLQKAAITILDGISQYSLRL  400
             +P         +F   AA   +  S    TL+   +S+   +     I   ++ Y+  L
Sbjct  554  NAPFIVLSGLGESFKKVAATPWKLCSSLRETLDHYADSI-TYRVFPYDIPCDVTDYTALL  612

Query  401  IDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVE  460
            +D  + T   A     V  Y+   V QLT+     +F +    +   +      +K   +
Sbjct  613  LDCAVLTGASA---YFVARYVDEKVEQLTNL----VFSSCQSAVAAFVQACMSTYKATAK  665

Query  461  FLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
            F+ D + ++K +S           V       + ++ F  +++K + L   ++   G+KL
Sbjct  666  FISDMFTLIKVVSERLYVYTSVGFVVVGDYSSQLLKQFMHILSKAMQLLHTTVSWAGSKL  725

Query  521  KAL--NLGETFVTHSKGLY---RKCVKSREETGLLMPLK-APKEIIFLE----GETLPTE  570
             ++  N  ++ V  S   Y    +    +++  L++P   + K+I  LE      T+  +
Sbjct  726  PSVVYNGRDSLVFPSGTYYCVSTQGRSLQDQFDLVIPGDLSKKQIGILEPTPNSTTVDKK  785

Query  571  VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCI-NGLMLLEIKDTEK-YCALAPNMMV  628
            + T  V +  G L+P ++ + E     +VG  V I N + +  ++D+E  +  L  +  +
Sbjct  786  INTNVVEVVVGQLEPTKEHSPEL----VVGDYVIISNKIFVRSVEDSETVFYPLCTDGKI  841

Query  629  TNNTFTLKGG  638
                F LKGG
Sbjct  842  VPTLFRLKGG  851


>sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus 
HKU5 OX=694008 GN=1a PE=3 SV=1
Length=4481

 Score = 660 bits (1703),  Expect = 0.0, Method: Composition-based stats.
 Identities = 143/670 (21%), Positives = 281/670 (42%), Gaps = 55/670 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG--KASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            +D   CG +G P+     L+A  G  K +   +E     D+ R +   +   + I W  +
Sbjct  200  IDQYMCGKNGKPIAEFAALMASEGITKLADVEAEVKSRTDSDRYI-VFKNKLYRIVWNVQ  258

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R + +Y  Q+ F +    + DT   + P   F + S I+ I P    +       + R +
Sbjct  259  RKDVAYSKQSAFTMNSIVQLDTME-DVPRHSFTIGSEIQVIAPSTAVQANGHLNLKQRLL  317

Query  124  YPV---ASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      + +E N +  S  + C  CG+ SW TG+ V+     CG      +    + G 
Sbjct  318  YAFYGKQAVSEPNYIYHSAYVDCTSCGKGSWLTGNAVQGFACDCGAHYCANDVDLQSSGL  377

Query  180  LPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRT--IAFGGCVFSYVGCH  237
            + +NAV+   CP   + E   +H+L +  +    K  +   G+T  + +GG +++Y+GC 
Sbjct  378  VRKNAVLLTTCPCNKDGEC--KHTLPQLVSMMTDKCDVEVVGKTFILTYGGVIYAYMGCS  435

Query  238  NKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNEEI  293
                +++PRA + +       +  G  G    + E     L++ +  IN V +F L E +
Sbjct  436  GGTMHFIPRAKSCVSKI-GDAIFTGCTGTWSKVCETANLFLERAQHAINFVNEFVLTETV  494

Query  294  AIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE----QKSI  349
              +L+  ++S     +  +   ++  +  +   G + VT G   +G  N+G       ++
Sbjct  495  VALLSGTTSSIEELRDLCRNATFEKVRDYLTPRG-WIVTMGSYIEGVINVGAAGVCNAAL  553

Query  350  LSPLY-------AFASEAARVVR--SIFSRTLETAQNSVRVLQKAAITILDGISQYSLRL  400
             +P         +F   AA   +  S    TL+   +S+   +     I   ++ Y+  L
Sbjct  554  NAPFIVLSGLGESFKKVAATPWKLCSSLRETLDHYADSI-TYRVFPYDIPCDVTDYTALL  612

Query  401  IDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVE  460
            +D  + T   A     V  Y+   V QLT+     +F +    +   +      +K   +
Sbjct  613  LDCAVLTGASA---YFVARYVDEKVEQLTNL----VFSSCQSAVAAFVQACMSTYKATAK  665

Query  461  FLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
            F+ D + ++K +S           V       + ++ F  +++K + L   ++   G+KL
Sbjct  666  FISDMFTLIKVVSERLYVYTSVGFVVVGDYSSQLLKQFMHILSKAMQLLHTTVSWAGSKL  725

Query  521  KAL--NLGETFVTHSKGLY---RKCVKSREETGLLMPLK-APKEIIFLE----GETLPTE  570
             ++  N  ++ V  S   Y    +    +++  L++P   + K+I  LE      T+  +
Sbjct  726  PSVVYNGRDSLVFPSGTYYCVSTQGRSLQDQFDLVIPGDLSKKQIGILEPTPNSTTVDKK  785

Query  571  VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCI-NGLMLLEIKDTEK-YCALAPNMMV  628
            + T  V +  G L+P ++ + E     +VG  V I N + +  ++D+E  +  L  +  +
Sbjct  786  INTNVVEVVVGQLEPTKEHSPEL----VVGDYVIISNKIFVRSVEDSETVFYPLCTDGKI  841

Query  629  TNNTFTLKGG  638
                F LKGG
Sbjct  842  VPTLFRLKGG  851


>sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East 
respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=rep PE=1 SV=1
Length=7078

 Score = 604 bits (1558),  Expect = 0.0, Method: Composition-based stats.
 Identities = 136/672 (20%), Positives = 261/672 (39%), Gaps = 55/672 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG--KASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            VD   CG DG P+     L+A+ G  K +   ++     D   G    + + + + W+ E
Sbjct  198  VDQYMCGVDGKPISAYAFLMAKDGITKLADVEADVAARAD-DEGFITLKNNLYRLVWHVE  256

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R +  Y  Q+ F I    + D      P++ F L   I T+ PR +   +     + + +
Sbjct  257  RKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLL  315

Query  124  YPV---ASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      S      +  S  ++C  CG  SW TG+ ++     CG      +    + G 
Sbjct  316  YTFYGKESLENPTYIYHSAFIECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGM  375

Query  180  LPQNAVVKIYCPACHNSEVGP--EHSLAEYHNESG--LKTILRKGGRTIAFGGCVFSYVG  235
            +  NA++   CP           +HS+A+  +        I      T+ FGG  ++Y G
Sbjct  376  IKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERCNVIADSKSFTLIFGGVAYAYFG  435

Query  236  CHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNE  291
            C     Y+VPRA + +      +   G  G  + + +     L++ + ++N VG+F +N+
Sbjct  436  CEEGTMYFVPRAKSVVSRIGDSI-FTGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVND  494

Query  292  EIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQK  347
             +  IL+  + +     + +KG+     +  +    +  VT G     A N+G    +  
Sbjct  495  VVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYA  553

Query  348  SILSPLYAFAS--EAARVVRSIFSRTLETAQNSV-----RVLQKAAITILD-GISQYSLR  399
            +I +P        E+ + V +I  +   + ++++      VL +     +D G+S +S  
Sbjct  554  AITAPYVVLTGLGESFKKVATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSEL  613

Query  400  LIDAMMFTSDLATNNLVVMAYITGGVVQ-LTSQWLTNIFGTVYEKLKPVLDWLEEKFKEG  458
            L D +  +        V   Y    ++Q  T  +++ I  +    +  +LD   E  +  
Sbjct  614  LFDCVDLS--------VASTYFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEAT  665

Query  459  VEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGA  518
              FL D   + +     A        V    ++   V+    L+NK + L    +   G+
Sbjct  666  FNFLLDLAGLFRIFLRNAYVYTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGS  725

Query  519  KLKALNL--GETFVTHSKGLY---RKCVKSREETGLLMPLKAPKEIIFLEGETLP-----  568
             + A+     E+ +  S   Y    K    +++  +++P +  K+ + L   T       
Sbjct  726  NISAVIYSGRESLIFPSGTYYCVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVS  785

Query  569  TEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTE--KYCALAPNM  626
              V +  V    G L+     T+      +VG  V I+  + +  K+ +   +     N 
Sbjct  786  VTVSSNMVETVVGQLEQ----TNMHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNG  841

Query  627  MVTNNTFTLKGG  638
                  F LKGG
Sbjct  842  HAVPTLFRLKGG  853


>sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East respiratory 
syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=1a PE=1 SV=1
Length=4391

 Score = 604 bits (1557),  Expect = 0.0, Method: Composition-based stats.
 Identities = 136/672 (20%), Positives = 261/672 (39%), Gaps = 55/672 (8%)

Query  6    VDNNFCGPDGYPLECIKDLLARAG--KASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTE  63
            VD   CG DG P+     L+A+ G  K +   ++     D   G    + + + + W+ E
Sbjct  198  VDQYMCGVDGKPISAYAFLMAKDGITKLADVEADVAARAD-DEGFITLKNNLYRLVWHVE  256

Query  64   RSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSV  123
            R +  Y  Q+ F I    + D      P++ F L   I T+ PR +   +     + + +
Sbjct  257  RKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLL  315

Query  124  YPV---ASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGY  179
            Y      S      +  S  ++C  CG  SW TG+ ++     CG      +    + G 
Sbjct  316  YTFYGKESLENPTYIYHSAFIECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGM  375

Query  180  LPQNAVVKIYCPACHNSEVGP--EHSLAEYHNESG--LKTILRKGGRTIAFGGCVFSYVG  235
            +  NA++   CP           +HS+A+  +        I      T+ FGG  ++Y G
Sbjct  376  IKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERCNVIADSKSFTLIFGGVAYAYFG  435

Query  236  CHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE----ILQKEKVNINIVGDFKLNE  291
            C     Y+VPRA + +      +   G  G  + + +     L++ + ++N VG+F +N+
Sbjct  436  CEEGTMYFVPRAKSVVSRIGDSI-FTGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVND  494

Query  292  EIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQK  347
             +  IL+  + +     + +KG+     +  +    +  VT G     A N+G    +  
Sbjct  495  VVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYA  553

Query  348  SILSPLYAFAS--EAARVVRSIFSRTLETAQNSV-----RVLQKAAITILD-GISQYSLR  399
            +I +P        E+ + V +I  +   + ++++      VL +     +D G+S +S  
Sbjct  554  AITAPYVVLTGLGESFKKVATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSEL  613

Query  400  LIDAMMFTSDLATNNLVVMAYITGGVVQ-LTSQWLTNIFGTVYEKLKPVLDWLEEKFKEG  458
            L D +  +        V   Y    ++Q  T  +++ I  +    +  +LD   E  +  
Sbjct  614  LFDCVDLS--------VASTYFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEAT  665

Query  459  VEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGA  518
              FL D   + +     A        V    ++   V+    L+NK + L    +   G+
Sbjct  666  FNFLLDLAGLFRIFLRNAYVYTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGS  725

Query  519  KLKALNL--GETFVTHSKGLY---RKCVKSREETGLLMPLKAPKEIIFLEGETLP-----  568
             + A+     E+ +  S   Y    K    +++  +++P +  K+ + L   T       
Sbjct  726  NISAVIYSGRESLIFPSGTYYCVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVS  785

Query  569  TEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTE--KYCALAPNM  626
              V +  V    G L+     T+      +VG  V I+  + +  K+ +   +     N 
Sbjct  786  VTVSSNMVETVVGQLEQ----TNMHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNG  841

Query  627  MVTNNTFTLKGG  638
                  F LKGG
Sbjct  842  HAVPTLFRLKGG  853


>sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus 
HKU9 OX=694006 GN=1a PE=3 SV=1
Length=4248

 Score = 387 bits (995),  Expect = 7e-117, Method: Composition-based stats.
 Identities = 134/660 (20%), Positives = 242/660 (37%), Gaps = 96/660 (15%)

Query  7    DNNFCGPDGYPLECIKDLLA--RAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            D      +G  +E +  LL   ++      L   L    T+ G Y   +   ++A    R
Sbjct  181  DQYGFDNNGILVEPVMKLLGVIKSDFTLEQLLAALGKYRTEDG-YDLPDGYVKVAIKVGR  239

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLN--SIIKTIQPRVEKKKLDGFMGRIRS  122
                   Q+ F +             P + +P +  S+++  +P             + S
Sbjct  240  KAVPVLKQSIFTVVGVT-----EQLVPGYYYPFSTSSVVEHTKPTRGGPVGKTVEAVMLS  294

Query  123  VYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQ  182
            +Y   + N    +     +KC +C    W     +      CG E    +  ++C     
Sbjct  295  LYGTNNYNPATPV---ARLKCSYCDYYGWTPLKDIGTVNCLCGAE---FQLTSSCVDAES  348

Query  183  NAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRT-IAFGGCVFSYVGCHNKCA  241
              V+K   P C          +       G++ I   G RT ++FGG ++S +G  N   
Sbjct  349  AGVIK---PGC----------VMLLDKSPGMRLI--PGNRTYVSFGGAIWSPIGKVNGVT  393

Query  242  YWVPRASANIGCNHTGVVGEGSE-GLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
             WVPRA + +   H+G VG G    +N  L+E L +    I +  D   N   A  +A+ 
Sbjct  394  VWVPRAYSIVAGEHSGAVGSGDTVAINKELVEYLIE---GIRVDADTLDNPTCATFIANL  450

Query  301  SASTSA----FVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAF  356
               T A     VE+++GL           C   K+  G          E    +  L A+
Sbjct  451  DCDTKAPVVHTVESLQGL-----------CLANKIMLGDKPLPT---DEFHPFIVGL-AY  495

Query  357  ASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLV  416
              + A    ++ SRT E  ++ VR  ++         +Q+  ++   +        N  V
Sbjct  496  HVQRACWYGALASRTFEAFRDFVRTEEER-------FAQFFGKVCAPI--------NGCV  540

Query  417  VMAYITGGVVQLTSQWLTN------------IFGTVYEKLKPVLDWLEEKFKEGVEFLRD  464
             +AY TG V   ++  + N            +   V + LKP+L+W+ +K    +   + 
Sbjct  541  YLAYTTGRVTLFSAYQVLNTAIAKSKDAFGGVAAIVVDMLKPILEWVLKK----MSIAKG  596

Query  465  GW----EIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
             W    E +  +      +V G+       +     +   L+   ++    S+   G K+
Sbjct  597  AWLPYAEGLLALFKAQFTVVKGKFQFLRASLNSKCHSLCDLLTTIMSKLLTSVKWAGCKV  656

Query  521  KALNLGETFVTHSKGLYRKCVKSREETGLLM-PLKAPKEIIFLEGETLPTEVLTE-EVVL  578
             AL  G  +    KG+  +     +  GLL+ P +   E+  L+G+      LT+ E+  
Sbjct  657  DALYTGTYYYFSRKGVLTEVQLCAKRLGLLLTPKQQKMEVEVLDGDFDAPVTLTDLELEE  716

Query  579  KTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
             TG L+ +   +       + GT V +   + +  +D   Y  +     V    F L+GG
Sbjct  717  CTGVLEEVFGASD---VKLVKGTLVSLASKLFVRTEDGFLYRYVKSGG-VLGKAFRLRGG  772


>sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU9 OX=694006 GN=rep PE=1 SV=1
Length=6930

 Score = 387 bits (994),  Expect = 1e-116, Method: Composition-based stats.
 Identities = 134/660 (20%), Positives = 242/660 (37%), Gaps = 96/660 (15%)

Query  7    DNNFCGPDGYPLECIKDLLA--RAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            D      +G  +E +  LL   ++      L   L    T+ G Y   +   ++A    R
Sbjct  181  DQYGFDNNGILVEPVMKLLGVIKSDFTLEQLLAALGKYRTEDG-YDLPDGYVKVAIKVGR  239

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLN--SIIKTIQPRVEKKKLDGFMGRIRS  122
                   Q+ F +             P + +P +  S+++  +P             + S
Sbjct  240  KAVPVLKQSIFTVVGVT-----EQLVPGYYYPFSTSSVVEHTKPTRGGPVGKTVEAVMLS  294

Query  123  VYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQ  182
            +Y   + N    +     +KC +C    W     +      CG E    +  ++C     
Sbjct  295  LYGTNNYNPATPV---ARLKCSYCDYYGWTPLKDIGTVNCLCGAE---FQLTSSCVDAES  348

Query  183  NAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRT-IAFGGCVFSYVGCHNKCA  241
              V+K   P C          +       G++ I   G RT ++FGG ++S +G  N   
Sbjct  349  AGVIK---PGC----------VMLLDKSPGMRLI--PGNRTYVSFGGAIWSPIGKVNGVT  393

Query  242  YWVPRASANIGCNHTGVVGEGSE-GLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF  300
             WVPRA + +   H+G VG G    +N  L+E L +    I +  D   N   A  +A+ 
Sbjct  394  VWVPRAYSIVAGEHSGAVGSGDTVAINKELVEYLIE---GIRVDADTLDNPTCATFIANL  450

Query  301  SASTSA----FVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAF  356
               T A     VE+++GL           C   K+  G          E    +  L A+
Sbjct  451  DCDTKAPVVHTVESLQGL-----------CLANKIMLGDKPLPT---DEFHPFIVGL-AY  495

Query  357  ASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLV  416
              + A    ++ SRT E  ++ VR  ++         +Q+  ++   +        N  V
Sbjct  496  HVQRACWYGALASRTFEAFRDFVRTEEER-------FAQFFGKVCAPI--------NGCV  540

Query  417  VMAYITGGVVQLTSQWLTN------------IFGTVYEKLKPVLDWLEEKFKEGVEFLRD  464
             +AY TG V   ++  + N            +   V + LKP+L+W+ +K    +   + 
Sbjct  541  YLAYTTGRVTLFSAYQVLNTAIAKSKDAFGGVAAIVVDMLKPILEWVLKK----MSIAKG  596

Query  465  GW----EIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
             W    E +  +      +V G+       +     +   L+   ++    S+   G K+
Sbjct  597  AWLPYAEGLLALFKAQFTVVKGKFQFLRASLNSKCHSLCDLLTTIMSKLLTSVKWAGCKV  656

Query  521  KALNLGETFVTHSKGLYRKCVKSREETGLLM-PLKAPKEIIFLEGETLPTEVLTE-EVVL  578
             AL  G  +    KG+  +     +  GLL+ P +   E+  L+G+      LT+ E+  
Sbjct  657  DALYTGTYYYFSRKGVLTEVQLCAKRLGLLLTPKQQKMEVEVLDGDFDAPVTLTDLELEE  716

Query  579  KTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG  638
             TG L+ +   +       + GT V +   + +  +D   Y  +     V    F L+GG
Sbjct  717  CTGVLEEVFGASD---VKLVKGTLVSLASKLFVRTEDGFLYRYVKSGG-VLGKAFRLRGG  772


>sp|P0C6W7|R1AB_CVBEN Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain 98TXSF-110-ENT) OX=233262 GN=rep PE=3 SV=1
Length=7094

 Score = 81.0 bits (198),  Expect = 3e-14, Method: Composition-based stats.
 Identities = 113/663 (17%), Positives = 196/663 (30%), Gaps = 114/663 (17%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE--------ILQK  276
             FGGCV+           W+P   +++  ++ G+V  G  G    + E         L  
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGCKAIVKETNLICKALYLDY  519

Query  277  EKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKA  336
             +     +   +L     +       +   +   ++ +DY   ++   S   F V     
Sbjct  520  VQHKCGNLHQRELLGVSDVWHKQLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGF  579

Query  337  KKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY  396
                 +    ++      A + +A                         A  I   +   
Sbjct  580  MPFLLDDLVPRAY---YLAVSGQAFC---------------------DYADKICHAVVSK  615

Query  397  SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFK  456
            S  L+D          +    + Y+   +V L +Q  ++   +   K+         K  
Sbjct  616  SKELLDV------SLDSLSAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHFF-----KTF  663

Query  457  EGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFFKLVNKFLALCADSI  513
                 L   W +   +   A  +V   I              Q F  +    L     + 
Sbjct  664  TTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFRSVAKVVLDSLRVTF  722

Query  514  IIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---APKEIIFLEGE  565
            I G +     + +    G       +GL        +   L MP +   A ++ I+L+G 
Sbjct  723  IDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKAKQKPIYLKGS  782

Query  566  TLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPN  625
                 +    V + T  L P         E P V   +CI   + +  K  +KY  +  +
Sbjct  783  GSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAGDKYYPVVVD  836

Query  626  MMV  628
              V
Sbjct  837  GHV  839


>sp|P0C6W8|R1AB_CVBLU Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain 98TXSF-110-LUN) OX=233264 GN=rep PE=3 SV=1
Length=7094

 Score = 81.0 bits (198),  Expect = 3e-14, Method: Composition-based stats.
 Identities = 113/663 (17%), Positives = 196/663 (30%), Gaps = 114/663 (17%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE--------ILQK  276
             FGGCV+           W+P   +++  ++ G+V  G  G    + E         L  
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGCKAIVKETNLICKALYLDY  519

Query  277  EKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKA  336
             +     +   +L     +       +   +   ++ +DY   ++   S   F V     
Sbjct  520  VQHKCGNLHQRELLGVSDVWHKQLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGF  579

Query  337  KKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY  396
                 +    ++      A + +A                         A  I   +   
Sbjct  580  MPFLLDDLVPRAY---YLAVSGQAFC---------------------DYADKICHAVVSK  615

Query  397  SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFK  456
            S  L+D          +    + Y+   +V L +Q  ++   +   K+         K  
Sbjct  616  SKELLDV------SLDSLSAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHFF-----KTF  663

Query  457  EGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFFKLVNKFLALCADSI  513
                 L   W +   +   A  +V   I              Q F  +    L     + 
Sbjct  664  TTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFRSVAKVVLDSLRVTF  722

Query  514  IIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---APKEIIFLEGE  565
            I G +     + +    G       +GL        +   L MP +   A ++ I+L+G 
Sbjct  723  IDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKAKQKPIYLKGS  782

Query  566  TLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPN  625
                 +    V + T  L P         E P V   +CI   + +  K  +KY  +  +
Sbjct  783  GSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAGDKYYPVVVD  836

Query  626  MMV  628
              V
Sbjct  837  GHV  839


>sp|P0C6T8|R1A_CVBEN Replicase polyprotein 1a OS=Bovine coronavirus 
(strain 98TXSF-110-ENT) OX=233262 GN=1a PE=3 SV=1
Length=4383

 Score = 80.6 bits (197),  Expect = 3e-14, Method: Composition-based stats.
 Identities = 113/663 (17%), Positives = 196/663 (30%), Gaps = 114/663 (17%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE--------ILQK  276
             FGGCV+           W+P   +++  ++ G+V  G  G    + E         L  
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGCKAIVKETNLICKALYLDY  519

Query  277  EKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKA  336
             +     +   +L     +       +   +   ++ +DY   ++   S   F V     
Sbjct  520  VQHKCGNLHQRELLGVSDVWHKQLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGF  579

Query  337  KKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY  396
                 +    ++      A + +A                         A  I   +   
Sbjct  580  MPFLLDDLVPRAY---YLAVSGQAFC---------------------DYADKICHAVVSK  615

Query  397  SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFK  456
            S  L+D          +    + Y+   +V L +Q  ++   +   K+         K  
Sbjct  616  SKELLDV------SLDSLSAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHFF-----KTF  663

Query  457  EGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFFKLVNKFLALCADSI  513
                 L   W +   +   A  +V   I              Q F  +    L     + 
Sbjct  664  TTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFRSVAKVVLDSLRVTF  722

Query  514  IIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---APKEIIFLEGE  565
            I G +     + +    G       +GL        +   L MP +   A ++ I+L+G 
Sbjct  723  IDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKAKQKPIYLKGS  782

Query  566  TLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPN  625
                 +    V + T  L P         E P V   +CI   + +  K  +KY  +  +
Sbjct  783  GSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAGDKYYPVVVD  836

Query  626  MMV  628
              V
Sbjct  837  GHV  839


>sp|P0C6T9|R1A_CVBLU Replicase polyprotein 1a OS=Bovine coronavirus 
(strain 98TXSF-110-LUN) OX=233264 GN=1a PE=3 SV=1
Length=4383

 Score = 80.2 bits (196),  Expect = 4e-14, Method: Composition-based stats.
 Identities = 113/663 (17%), Positives = 196/663 (30%), Gaps = 114/663 (17%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLE--------ILQK  276
             FGGCV+           W+P   +++  ++ G+V  G  G    + E         L  
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGCKAIVKETNLICKALYLDY  519

Query  277  EKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKA  336
             +     +   +L     +       +   +   ++ +DY   ++   S   F V     
Sbjct  520  VQHKCGNLHQRELLGVSDVWHKQLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGF  579

Query  337  KKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY  396
                 +    ++      A + +A                         A  I   +   
Sbjct  580  MPFLLDDLVPRAY---YLAVSGQAFC---------------------DYADKICHAVVSK  615

Query  397  SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFK  456
            S  L+D          +    + Y+   +V L +Q  ++   +   K+         K  
Sbjct  616  SKELLDV------SLDSLSAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHFF-----KTF  663

Query  457  EGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFFKLVNKFLALCADSI  513
                 L   W +   +   A  +V   I              Q F  +    L     + 
Sbjct  664  TTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFRSVAKVVLDSLRVTF  722

Query  514  IIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---APKEIIFLEGE  565
            I G +     + +    G       +GL        +   L MP +   A ++ I+L+G 
Sbjct  723  IDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKAKQKPIYLKGS  782

Query  566  TLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPN  625
                 +    V + T  L P         E P V   +CI   + +  K  +KY  +  +
Sbjct  783  GSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAGDKYYPVVVD  836

Query  626  MMV  628
              V
Sbjct  837  GHV  839


>sp|P0C6W9|R1AB_CVBM Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain Mebus) OX=11132 GN=rep PE=3 SV=1
Length=7094

 Score = 80.6 bits (197),  Expect = 4e-14, Method: Composition-based stats.
 Identities = 115/672 (17%), Positives = 197/672 (29%), Gaps = 132/672 (20%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIV  284
             FGGCV+           W+P   +++  ++ G+V  G  G                   
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGC------------------  501

Query  285  GDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVES-CGNFKVTKGKAKKGAW--  341
                                 A V+    +    +   V+  CGN    +       W  
Sbjct  502  --------------------KAIVKETNLICKALYLDYVQHKCGNLHQRELLGVSDVWHK  541

Query  342  ----NIGEQKSILSPLYAFASEAARVVRSIFSRTLETA-----QNSVRVLQKAAITILDG  392
                N G  K +L  +  F    A+     F+   +        + V      A++    
Sbjct  542  QLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGFMPFLLDDLVPRAYYLAVSG-QA  600

Query  393  ISQYSLRLIDAMM-----FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPV  447
               Y+ ++  A++            +    + Y+   +V L +Q  ++   +   K+   
Sbjct  601  FCDYAGKICHAVVSKSKELLDVSLDSLGAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHF  659

Query  448  LDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFFKLVNK  504
                  K       L   W +   +   A  +V   I              Q F  +   
Sbjct  660  F-----KTFTTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFRSVAKV  713

Query  505  FLALCADSIIIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---AP  556
             L     + I G +     + +    G       +GL        +   L MP +     
Sbjct  714  VLDSLRVTFIDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKTK  773

Query  557  KEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDT  616
            ++ I+L+G      +    V + T  L P         E P V   +CI   + +  K  
Sbjct  774  QKPIYLKGSGSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAG  827

Query  617  EKYCALAPNMMV  628
            +KY  +  +  V
Sbjct  828  DKYYPVVVDGHV  839


>sp|P0C6U0|R1A_CVBM Replicase polyprotein 1a OS=Bovine coronavirus 
(strain Mebus) OX=11132 GN=1a PE=3 SV=1
Length=4383

 Score = 79.8 bits (195),  Expect = 5e-14, Method: Composition-based stats.
 Identities = 115/672 (17%), Positives = 197/672 (29%), Gaps = 132/672 (20%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIV  284
             FGGCV+           W+P   +++  ++ G+V  G  G                   
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGC------------------  501

Query  285  GDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVES-CGNFKVTKGKAKKGAW--  341
                                 A V+    +    +   V+  CGN    +       W  
Sbjct  502  --------------------KAIVKETNLICKALYLDYVQHKCGNLHQRELLGVSDVWHK  541

Query  342  ----NIGEQKSILSPLYAFASEAARVVRSIFSRTLETA-----QNSVRVLQKAAITILDG  392
                N G  K +L  +  F    A+     F+   +        + V      A++    
Sbjct  542  QLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGFMPFLLDDLVPRAYYLAVSG-QA  600

Query  393  ISQYSLRLIDAMM-----FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPV  447
               Y+ ++  A++            +    + Y+   +V L +Q  ++   +   K+   
Sbjct  601  FCDYAGKICHAVVSKSKELLDVSLDSLGAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHF  659

Query  448  LDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFFKLVNK  504
                  K       L   W +   +   A  +V   I              Q F  +   
Sbjct  660  F-----KTFTTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFRSVAKV  713

Query  505  FLALCADSIIIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---AP  556
             L     + I G +     + +    G       +GL        +   L MP +     
Sbjct  714  VLDSLRVTFIDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKTK  773

Query  557  KEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDT  616
            ++ I+L+G      +    V + T  L P         E P V   +CI   + +  K  
Sbjct  774  QKPIYLKGSGSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAG  827

Query  617  EKYCALAPNMMV  628
            +KY  +  +  V
Sbjct  828  DKYYPVVVDGHV  839


>sp|P0C6X6|R1AB_CVHOC Replicase polyprotein 1ab OS=Human coronavirus 
OC43 OX=31631 GN=rep PE=3 SV=1
Length=7095

 Score = 77.9 bits (190),  Expect = 2e-13, Method: Composition-based stats.
 Identities = 118/674 (18%), Positives = 200/674 (30%), Gaps = 142/674 (21%)

Query  5    YVDNNFCGPDGY---PLECIKDLLARAGKAS-CTLSEQL--DFIDTKRGVYCCREHEHEI  58
            YVD   C   G     LE   D   +  KA   T S++L  D I               +
Sbjct  252  YVDQYGCDYTGSLADGLEAYADKTLQEMKALFPTWSQELPFDVI---------------V  296

Query  59   AWYTERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPR  107
            AW+  R +  Y   LQ+   I           D  +G      P  V+  +SII      
Sbjct  297  AWHVVR-DPRYVMRLQSAATICSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILRQYNL  355

Query  108  VEKKKLDGFMGR----IRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATC  161
             +   +  F       + + Y VA   +C  +     + C  D C    W  G+ +    
Sbjct  356  FDI--MSHFYMEADTVVNAFYGVA-LKDCGFVMQFGYIDCEQDSCDFKGWIPGNMIDGFA  412

Query  162  E-FCGTENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRK  219
               CG      +    + G LP N V+     A +    G + S   Y            
Sbjct  413  CTTCGHVYEVGDLIAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------  459

Query  220  GGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKV  279
            G   + FGGCV+           W+P   +++  ++  +V  G  G              
Sbjct  460  GQTVVYFGGCVY----WSPARNIWIPILKSSV-KSYDSLVYTGVLGC-------------  501

Query  280  NINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVES-CGNFKVTKGKAKK  338
                                      A V+    +    +   V+  CGN    +     
Sbjct  502  -------------------------KAIVKETNLICKALYLDYVQHKCGNLHQRELLGVS  536

Query  339  GAW------NIGEQKSILSPLYAFASEAARVVRSIFSRTLETA-----QNSVRVLQKAAI  387
              W      N G  K +L  +  F    A+     F+   +        + V      A+
Sbjct  537  DVWHKQLLINRGVYKPLLENIDYFNMRRAKFSLETFTVCADGFMPFLLDDLVPRAYYLAV  596

Query  388  TILDGISQYSLRLIDAMM-----FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYE  442
            +       Y+ +L  A++            +    + Y+   +V L +Q  ++   +   
Sbjct  597  SG-QAFCDYADKLCHAVVSKSKELLDVSLDSLGAAIHYLNSKIVDL-AQHFSDFGTSFVS  654

Query  443  KLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFF  499
            K+         K       L   W +   +   A  +V   I              Q F 
Sbjct  655  KIVHFF-----KTFTTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFQ  708

Query  500  KLVNKFLALCADSIIIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK  554
             +    L     + I G +     + +    G       +GL        +   L MP +
Sbjct  709  SVAKVVLDSLRVTFIDGLSCFKIGRRRICLSGRKIYEVERGLLHSSQLPLDVYDLTMPSQ  768

Query  555  ---APKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLL  611
               A ++ I+L+G      +    V + T  L P         E P V   +CI   + +
Sbjct  769  VQKAKQKPIYLKGSGSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYM  823

Query  612  EIKDTEKYCALAPN  625
              K  +KY  +  +
Sbjct  824  A-KAGDKYYPVVVD  836


>sp|P0C6U7|R1A_CVHOC Replicase polyprotein 1a OS=Human coronavirus 
OC43 OX=31631 GN=1a PE=3 SV=1
Length=4383

 Score = 77.5 bits (189),  Expect = 2e-13, Method: Composition-based stats.
 Identities = 118/674 (18%), Positives = 200/674 (30%), Gaps = 142/674 (21%)

Query  5    YVDNNFCGPDGY---PLECIKDLLARAGKAS-CTLSEQL--DFIDTKRGVYCCREHEHEI  58
            YVD   C   G     LE   D   +  KA   T S++L  D I               +
Sbjct  252  YVDQYGCDYTGSLADGLEAYADKTLQEMKALFPTWSQELPFDVI---------------V  296

Query  59   AWYTERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPR  107
            AW+  R +  Y   LQ+   I           D  +G      P  V+  +SII      
Sbjct  297  AWHVVR-DPRYVMRLQSAATICSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILRQYNL  355

Query  108  VEKKKLDGFMGR----IRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATC  161
             +   +  F       + + Y VA   +C  +     + C  D C    W  G+ +    
Sbjct  356  FDI--MSHFYMEADTVVNAFYGVA-LKDCGFVMQFGYIDCEQDSCDFKGWIPGNMIDGFA  412

Query  162  E-FCGTENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRK  219
               CG      +    + G LP N V+     A +    G + S   Y            
Sbjct  413  CTTCGHVYEVGDLIAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------  459

Query  220  GGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKV  279
            G   + FGGCV+           W+P   +++  ++  +V  G  G              
Sbjct  460  GQTVVYFGGCVY----WSPARNIWIPILKSSV-KSYDSLVYTGVLGC-------------  501

Query  280  NINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVES-CGNFKVTKGKAKK  338
                                      A V+    +    +   V+  CGN    +     
Sbjct  502  -------------------------KAIVKETNLICKALYLDYVQHKCGNLHQRELLGVS  536

Query  339  GAW------NIGEQKSILSPLYAFASEAARVVRSIFSRTLETA-----QNSVRVLQKAAI  387
              W      N G  K +L  +  F    A+     F+   +        + V      A+
Sbjct  537  DVWHKQLLINRGVYKPLLENIDYFNMRRAKFSLETFTVCADGFMPFLLDDLVPRAYYLAV  596

Query  388  TILDGISQYSLRLIDAMM-----FTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYE  442
            +       Y+ +L  A++            +    + Y+   +V L +Q  ++   +   
Sbjct  597  SG-QAFCDYADKLCHAVVSKSKELLDVSLDSLGAAIHYLNSKIVDL-AQHFSDFGTSFVS  654

Query  443  KLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAK---EIKESVQTFF  499
            K+         K       L   W +   +   A  +V   I              Q F 
Sbjct  655  KIVHFF-----KTFTTSTALAFAWVLFHVL-HGAYIVVESDIYFVKNIPRYASAVAQAFQ  708

Query  500  KLVNKFLALCADSIIIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK  554
             +    L     + I G +     + +    G       +GL        +   L MP +
Sbjct  709  SVAKVVLDSLRVTFIDGLSCFKIGRRRICLSGRKIYEVERGLLHSSQLPLDVYDLTMPSQ  768

Query  555  ---APKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLL  611
               A ++ I+L+G      +    V + T  L P         E P V   +CI   + +
Sbjct  769  VQKAKQKPIYLKGSGSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYM  823

Query  612  EIKDTEKYCALAPN  625
              K  +KY  +  +
Sbjct  824  A-KAGDKYYPVVVD  836


>sp|P0C6X0|R1AB_CVBQ Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain Quebec) OX=11133 GN=rep PE=3 SV=1
Length=7059

 Score = 76.7 bits (187),  Expect = 4e-13, Method: Composition-based stats.
 Identities = 117/672 (17%), Positives = 199/672 (30%), Gaps = 132/672 (20%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIV  284
             FGGCV+           W+P   +++  ++ G+V  G  G                   
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGC------------------  501

Query  285  GDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVES-CGNFKVTKGKAKKGAW--  341
                                 A V+    +    +   V+  CGN    +       W  
Sbjct  502  --------------------KAIVKETNLICKALYLDYVQHKCGNLHQRELLGVSDVWHK  541

Query  342  ----NIGEQKSILSPLYAFASEAARVVRSIFSRTLETA-----QNSVRVLQKAAITILDG  392
                N G  K +L  +  F    A+     F+   +        + V      A++    
Sbjct  542  QLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGFMPFLLDDLVPRAYYLAVSG-QA  600

Query  393  ISQYSLRLIDAMMFTSDLATNNLV-----VMAYITGGVVQLTSQWLTNIFGTVYEKLKPV  447
               Y+ ++  A++  S    +  V      + Y+   +V L +Q  ++   +   K+   
Sbjct  601  FCDYAGKICHAVVSKSKELLDVSVDSLGAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHF  659

Query  448  LDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVT---CAKEIKESVQTFFKLVNK  504
                  K       L   W +   +   A  +V   I       +      Q F      
Sbjct  660  F-----KTFTTSTALAFAWVLFHVL-HGAYIVVESDIYFGKNIPRYASAVAQAFRSGAKV  713

Query  505  FLALCADSIIIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---AP  556
             L     + I G +     + +    G       +GL        +   L MP +     
Sbjct  714  GLDSLRVTFIDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKTK  773

Query  557  KEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDT  616
            ++ I+L+G      +    V + T  L P         E P V   +CI   + +  K  
Sbjct  774  QKGIYLKGSGSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAG  827

Query  617  EKYCALAPNMMV  628
            +KY  +  +  V
Sbjct  828  DKYYPVVVDGHV  839


>sp|P0C6U1|R1A_CVBQ Replicase polyprotein 1a OS=Bovine coronavirus 
(strain Quebec) OX=11133 GN=1a PE=3 SV=1
Length=4383

 Score = 76.3 bits (186),  Expect = 6e-13, Method: Composition-based stats.
 Identities = 117/672 (17%), Positives = 199/672 (30%), Gaps = 132/672 (20%)

Query  5    YVDNNFCGPDG---YPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWY  61
            YVD   C   G     LE   D   +  KA   +  Q    D              +AW+
Sbjct  252  YVDQYGCDYTGGLADGLEAYADKTLQEMKALFPIWSQELPFDVT------------VAWH  299

Query  62   TERSEKSY--ELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
              R +  Y   LQ+   I+          D  +G      P  V+  +SII   Q  +  
Sbjct  300  VVR-DPRYVMRLQSASTIRSVAYVANPTEDLCDGSVVIKEPVHVYADDSIILR-QHNLVD  357

Query  111  KKLDGFMGRIRSVYPVASPN--ECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCG  165
                 +M     V      +  +C  +     + C  D C    W  G+ +       CG
Sbjct  358  IMSCFYMEADAVVNAFYGVDLKDCGFVMQFGYIDCEQDLCDFKGWVPGNMIDGFACTTCG  417

Query  166  TENLTKEGA-TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTI  224
                T +    + G LP N V+     A +    G + S   Y            G   +
Sbjct  418  HVYETGDLLAQSSGVLPVNPVLHTKSAAGYGG-FGCKDSFTLY------------GQTVV  464

Query  225  AFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIV  284
             FGGCV+           W+P   +++  ++ G+V  G  G                   
Sbjct  465  YFGGCVY----WSPARNIWIPILKSSV-KSYDGLVYTGVVGC------------------  501

Query  285  GDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVES-CGNFKVTKGKAKKGAW--  341
                                 A V+    +    +   V+  CGN    +       W  
Sbjct  502  --------------------KAIVKETNLICKALYLDYVQHKCGNLHQRELLGVSDVWHK  541

Query  342  ----NIGEQKSILSPLYAFASEAARVVRSIFSRTLETA-----QNSVRVLQKAAITILDG  392
                N G  K +L  +  F    A+     F+   +        + V      A++    
Sbjct  542  QLLLNRGVYKPLLENIDYFNMRRAKFSLETFTVCADGFMPFLLDDLVPRAYYLAVSG-QA  600

Query  393  ISQYSLRLIDAMMFTSDLATNNLV-----VMAYITGGVVQLTSQWLTNIFGTVYEKLKPV  447
               Y+ ++  A++  S    +  V      + Y+   +V L +Q  ++   +   K+   
Sbjct  601  FCDYAGKICHAVVSKSKELLDVSVDSLGAAIHYLNSKIVDL-AQHFSDFGTSFVSKIVHF  659

Query  448  LDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVT---CAKEIKESVQTFFKLVNK  504
                  K       L   W +   +   A  +V   I       +      Q F      
Sbjct  660  F-----KTFTTSTALAFAWVLFHVL-HGAYIVVESDIYFGKNIPRYASAVAQAFRSGAKV  713

Query  505  FLALCADSIIIGGA-----KLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLK---AP  556
             L     + I G +     + +    G       +GL        +   L MP +     
Sbjct  714  GLDSLRVTFIDGLSCFKIGRRRICLSGSKIYEVERGLLHSSQLPLDVYDLTMPSQVQKTK  773

Query  557  KEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDT  616
            ++ I+L+G      +    V + T  L P         E P V   +CI   + +  K  
Sbjct  774  QKGIYLKGSGSDFSLADSVVEVVTTSLTPCG-----YSEPPKVADKICIVDNVYMA-KAG  827

Query  617  EKYCALAPNMMV  628
            +KY  +  +  V
Sbjct  828  DKYYPVVVDGHV  839


>sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=rep PE=1 SV=1
Length=6684

 Score = 67.9 bits (164),  Expect = 2e-10, Method: Composition-based stats.
 Identities = 65/354 (18%), Positives = 102/354 (29%), Gaps = 78/354 (22%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            YVD   CG DG P+                  +  D+      +      E+  AW T R
Sbjct  113  YVDQYMCGADGKPV---------------IEGDFKDYF-GDEDIIEFEGEEYHCAWTTVR  156

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVY  124
             EK    QT F I+  +       + P      N   + + P V+K          + +Y
Sbjct  157  DEKPLNQQTLFTIQEIQYNLDIPHKLP------NCATRHVAPPVKKNSKIVLSEDYKKLY  210

Query  125  PVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT-CEFCGTENLTKEGATTCGYLPQN  183
                      +  S  M    C    + T  F+ AT    CG+E+      T        
Sbjct  211  ---------DIFGSPFMGNGDCLSKCFDTLHFIAATLRCPCGSESSGVGDWTG-------  254

Query  184  AVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYW  243
               K  C        G   +L +      + T +  G     F  CV  Y G     + W
Sbjct  255  --FKTACCGLSGKVKGV--TLGDIKPGDAVVTSMSAGKGVKFFANCVLQYAGDVEGVSIW  310

Query  244  -------------------------VPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEK  278
                                      P + + + C+       G           +    
Sbjct  311  KVIKTFTVDETVCTPGFEGELNDFIKPESKSLVACSVKRAFITGD----------IDDAV  360

Query  279  VNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVT  332
             +  I G   L+  +   +      T  FV+    L   A+K + E CG+  +T
Sbjct  361  HDCIITGKLDLSTNLFGNVGLLFKKTPWFVQKCGALFVDAWKVVEELCGSLTLT  414


 Score = 40.1 bits (92),  Expect = 0.076, Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 61/175 (35%), Gaps = 13/175 (7%)

Query  463  RDGWEIVKFISTCACEIV--GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
            +  +E+V  + T A  IV      V     +K+ V    K++ K   +    I I G + 
Sbjct  416  KQIYEVVASLCTSAFTIVNYKPTFVVPDNRVKDLVDKCVKVLVKAFDVFTQIITIAGIEA  475

Query  521  KALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKT  580
            K   LG  ++  +  L            L+      K+   LE     T ++   V +  
Sbjct  476  KCFVLGAKYLLFNNAL----------VKLVSVKILGKKQKGLECAFFATSLVGATVNVTP  525

Query  581  GDLQPLEQPTSEAVEAPLVGT-PVCINGLMLLEIKDTEKYCALAPNMMVTNNTFT  634
               +      ++  +    G   + I G M         +   +PN ++TNN F 
Sbjct  526  KRTETATISLNKVDDVVAPGEGYIVIVGDMAFYKSGEYYFMMSSPNFVLTNNVFK  580


>sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=1a PE=1 SV=1
Length=4017

 Score = 67.9 bits (164),  Expect = 3e-10, Method: Composition-based stats.
 Identities = 65/354 (18%), Positives = 102/354 (29%), Gaps = 78/354 (22%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            YVD   CG DG P+                  +  D+      +      E+  AW T R
Sbjct  113  YVDQYMCGADGKPV---------------IEGDFKDYF-GDEDIIEFEGEEYHCAWTTVR  156

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVY  124
             EK    QT F I+  +       + P      N   + + P V+K          + +Y
Sbjct  157  DEKPLNQQTLFTIQEIQYNLDIPHKLP------NCATRHVAPPVKKNSKIVLSEDYKKLY  210

Query  125  PVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT-CEFCGTENLTKEGATTCGYLPQN  183
                      +  S  M    C    + T  F+ AT    CG+E+      T        
Sbjct  211  ---------DIFGSPFMGNGDCLSKCFDTLHFIAATLRCPCGSESSGVGDWTG-------  254

Query  184  AVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYW  243
               K  C        G   +L +      + T +  G     F  CV  Y G     + W
Sbjct  255  --FKTACCGLSGKVKGV--TLGDIKPGDAVVTSMSAGKGVKFFANCVLQYAGDVEGVSIW  310

Query  244  -------------------------VPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEK  278
                                      P + + + C+       G           +    
Sbjct  311  KVIKTFTVDETVCTPGFEGELNDFIKPESKSLVACSVKRAFITGD----------IDDAV  360

Query  279  VNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVT  332
             +  I G   L+  +   +      T  FV+    L   A+K + E CG+  +T
Sbjct  361  HDCIITGKLDLSTNLFGNVGLLFKKTPWFVQKCGALFVDAWKVVEELCGSLTLT  414


 Score = 40.1 bits (92),  Expect = 0.075, Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 61/175 (35%), Gaps = 13/175 (7%)

Query  463  RDGWEIVKFISTCACEIV--GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL  520
            +  +E+V  + T A  IV      V     +K+ V    K++ K   +    I I G + 
Sbjct  416  KQIYEVVASLCTSAFTIVNYKPTFVVPDNRVKDLVDKCVKVLVKAFDVFTQIITIAGIEA  475

Query  521  KALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKT  580
            K   LG  ++  +  L            L+      K+   LE     T ++   V +  
Sbjct  476  KCFVLGAKYLLFNNAL----------VKLVSVKILGKKQKGLECAFFATSLVGATVNVTP  525

Query  581  GDLQPLEQPTSEAVEAPLVGT-PVCINGLMLLEIKDTEKYCALAPNMMVTNNTFT  634
               +      ++  +    G   + I G M         +   +PN ++TNN F 
Sbjct  526  KRTETATISLNKVDDVVAPGEGYIVIVGDMAFYKSGEYYFMMSSPNFVLTNNVFK  580


>sp|P0C6X8|R1AB_CVM2 Replicase polyprotein 1ab OS=Murine coronavirus 
(strain 2) OX=76344 GN=rep PE=3 SV=1
Length=7124

 Score = 65.9 bits (159),  Expect = 1e-09, Method: Composition-based stats.
 Identities = 86/538 (16%), Positives = 164/538 (30%), Gaps = 102/538 (19%)

Query  5    YVDNNFC---GPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCR-EHEHEIAW  60
            ++D   C   G     LE   D         CTL E  +       V+C   ++E  +AW
Sbjct  253  FLDQYGCDYTGRLAKGLEDYGD---------CTLEEMKELFP----VWCDSLDNEVVVAW  299

Query  61   YTERSEKSYEL-QTPFEIKLA-----KKFDTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
            + +R  ++    QT   I+          D  +G+     P  +   N+I+K + PR+ +
Sbjct  300  HVDRDPRAVMRLQTLATIRSIGYVGQPTEDLVDGDVVVREPAHLLAANAIVKRL-PRLVE  358

Query  111  KKLDGFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTE  167
              L          Y      +C  +     + C  D C    W  G+ +       C   
Sbjct  359  TMLYTDSSVTEFCY-KTKLCDCGFITQFGYVDCCGDACDFRGWVPGNMMDGFLCPGCSKS  417

Query  168  NLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAF  226
             +  E  A + G +P+  V+        +++     S   Y            G   + F
Sbjct  418  YMPWELEAQSSGVIPKGGVL-----FTQSTDTVNRESFKLY------------GHAVVPF  460

Query  227  GGCVF--SYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNI--N  282
            G  V+   Y G       W+P   +++  ++  +   G  G    +++       ++  +
Sbjct  461  GSAVYWSPYPG------MWLPVIWSSV-KSYADLTYTGVVGC-KAIVQETDAICRSLYMD  512

Query  283  IVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWN  342
             V     N E   IL               GLD    +Q++       V +G       N
Sbjct  513  YVQHKCGNLEQRAIL---------------GLDDVYHRQLL-------VNRGDYSLLLEN  550

Query  343  IGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQ----YSL  398
            +              +E A    +     +    + +       I      +     +S 
Sbjct  551  VDL-------FVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSMMVNFSH  603

Query  399  RLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEG  458
             + D  M  + L  +++ V       V    +     +   V  K+    D   +     
Sbjct  604  EVTDMCMDMALLFMHDVKVATKYVKKVTGKLAVRFKALGVAVVRKITEWFDLAVDTAASA  663

Query  459  VEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIG  516
              +L         +      +  G I   +  + E V+ F      F  +  DS+ + 
Sbjct  664  AGWL------CYQLVNGLFAVANGGITFLSD-VPELVKNFVDKFKVFFKVLIDSMSVS  714


>sp|P0C6Y4|R1AB_PEDV7 Replicase polyprotein 1ab OS=Porcine epidemic 
diarrhea virus (strain CV777) OX=229032 GN=rep PE=1 SV=1
Length=6781

 Score = 65.6 bits (158),  Expect = 1e-09, Method: Composition-based stats.
 Identities = 42/191 (22%), Positives = 67/191 (35%), Gaps = 28/191 (15%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERS  65
            VD   CG DG P+     L     + +   ++  D      G+   +      AW  ERS
Sbjct  115  VDQYMCGADGKPV-----LQESEWEYTDFFADSEDGQLNIAGITYVK------AWIVERS  163

Query  66   EKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTI-QPRVEK-----KKLDGFMGR  119
            + SY  Q    IK      T+        F   + +K    P+++K     + L      
Sbjct  164  DVSYASQNLTSIKSITYCSTYE-----HTFLDGTAMKVARTPKIKKNVVLSEPLATIYRE  218

Query  120  IRSVYPVASPNECNQM----CLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGAT  175
            I S +     +  + +     L   +KC  CG   W  GD+       CG +        
Sbjct  219  IGSPFVDNGSDARSIIRRPVFLHAFVKCK-CGSYHWTVGDWTSYVSTCCGFK-CKPVLVA  276

Query  176  TCGYLPQNAVV  186
            +C  +P + VV
Sbjct  277  SCSAMPGSVVV  287


>sp|P0C6V6|R1A_PEDV7 Replicase polyprotein 1a OS=Porcine epidemic 
diarrhea virus (strain CV777) OX=229032 GN=1a PE=1 SV=1
Length=4117

 Score = 65.6 bits (158),  Expect = 1e-09, Method: Composition-based stats.
 Identities = 42/191 (22%), Positives = 67/191 (35%), Gaps = 28/191 (15%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERS  65
            VD   CG DG P+     L     + +   ++  D      G+   +      AW  ERS
Sbjct  115  VDQYMCGADGKPV-----LQESEWEYTDFFADSEDGQLNIAGITYVK------AWIVERS  163

Query  66   EKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTI-QPRVEK-----KKLDGFMGR  119
            + SY  Q    IK      T+        F   + +K    P+++K     + L      
Sbjct  164  DVSYASQNLTSIKSITYCSTYE-----HTFLDGTAMKVARTPKIKKNVVLSEPLATIYRE  218

Query  120  IRSVYPVASPNECNQM----CLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGAT  175
            I S +     +  + +     L   +KC  CG   W  GD+       CG +        
Sbjct  219  IGSPFVDNGSDARSIIRRPVFLHAFVKCK-CGSYHWTVGDWTSYVSTCCGFK-CKPVLVA  276

Query  176  TCGYLPQNAVV  186
            +C  +P + VV
Sbjct  277  SCSAMPGSVVV  287


>sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavirus 
(strain 2) OX=76344 GN=1a PE=3 SV=1
Length=4416

 Score = 65.2 bits (157),  Expect = 2e-09, Method: Composition-based stats.
 Identities = 86/538 (16%), Positives = 164/538 (30%), Gaps = 102/538 (19%)

Query  5    YVDNNFC---GPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCR-EHEHEIAW  60
            ++D   C   G     LE   D         CTL E  +       V+C   ++E  +AW
Sbjct  253  FLDQYGCDYTGRLAKGLEDYGD---------CTLEEMKELFP----VWCDSLDNEVVVAW  299

Query  61   YTERSEKSYEL-QTPFEIKLA-----KKFDTFNGEC----PNFVFPLNSIIKTIQPRVEK  110
            + +R  ++    QT   I+          D  +G+     P  +   N+I+K + PR+ +
Sbjct  300  HVDRDPRAVMRLQTLATIRSIGYVGQPTEDLVDGDVVVREPAHLLAANAIVKRL-PRLVE  358

Query  111  KKLDGFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTE  167
              L          Y      +C  +     + C  D C    W  G+ +       C   
Sbjct  359  TMLYTDSSVTEFCY-KTKLCDCGFITQFGYVDCCGDACDFRGWVPGNMMDGFLCPGCSKS  417

Query  168  NLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAF  226
             +  E  A + G +P+  V+        +++     S   Y            G   + F
Sbjct  418  YMPWELEAQSSGVIPKGGVL-----FTQSTDTVNRESFKLY------------GHAVVPF  460

Query  227  GGCVF--SYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNI--N  282
            G  V+   Y G       W+P   +++  ++  +   G  G    +++       ++  +
Sbjct  461  GSAVYWSPYPG------MWLPVIWSSV-KSYADLTYTGVVGC-KAIVQETDAICRSLYMD  512

Query  283  IVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWN  342
             V     N E   IL               GLD    +Q++       V +G       N
Sbjct  513  YVQHKCGNLEQRAIL---------------GLDDVYHRQLL-------VNRGDYSLLLEN  550

Query  343  IGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQ----YSL  398
            +              +E A    +     +    + +       I      +     +S 
Sbjct  551  VDL-------FVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSMMVNFSH  603

Query  399  RLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEG  458
             + D  M  + L  +++ V       V    +     +   V  K+    D   +     
Sbjct  604  EVTDMCMDMALLFMHDVKVATKYVKKVTGKLAVRFKALGVAVVRKITEWFDLAVDTAASA  663

Query  459  VEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIG  516
              +L         +      +  G I   +  + E V+ F      F  +  DS+ + 
Sbjct  664  AGWL------CYQLVNGLFAVANGGITFLSD-VPELVKNFVDKFKVFFKVLIDSMSVS  714


>sp|P0C6Y0|R1AB_CVMJH Replicase polyprotein 1ab OS=Murine coronavirus 
(strain JHM) OX=11144 GN=rep PE=1 SV=1
Length=7180

 Score = 64.4 bits (155),  Expect = 3e-09, Method: Composition-based stats.
 Identities = 78/530 (15%), Positives = 165/530 (31%), Gaps = 86/530 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G    C+   L   G  + +  ++L  +          ++E  +AW+ +R
Sbjct  253  FVDQYGCDYTG----CLAKGLEDYGDLTLSEMKELSPVWRDSL-----DNEVVVAWHVDR  303

Query  65   SEKSYEL-QTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
              ++    QT   ++  +       D  +G+     P  +   N+I+K + PR+ +  L 
Sbjct  304  DPRAVMRLQTLATVRSIEYVGQPIEDMVDGDVVMREPAHLLAPNAIVKRL-PRLVETMLY  362

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                     Y      +C  +     + C  D CG   W  G+ +       C    +  
Sbjct  363  TDSSVTEFCY-KTKLCDCGFITQFGYVDCCGDTCGFRGWVPGNMMDGFPCPGCCKSYMPW  421

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+  V+        +++     S   Y            G   + FGG  
Sbjct  422  ELEAQSSGVIPEGGVL-----FTQSTDTVNRESFKLY------------GHAVVPFGGA-  463

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
             +Y   +     W+P   +++  +++ +   G  G    + E         + +  F   
Sbjct  464  -AYWSPYPGM--WLPVIWSSV-KSYSYLTYTGVVGCKAIVQE--------TDAICRFLYM  511

Query  291  EEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSIL  350
            + +     +           + GLD    +Q++       V +G       N+       
Sbjct  512  DYVQHKCGNLE------QRAILGLDDVYHRQLL-------VNRGDYSLLLENVDL-----  553

Query  351  SPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQ----YSLRLIDAMMF  406
                   +E A    +     +    + +       I      +     +S  ++D  M 
Sbjct  554  --FVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSLMVNFSREVVDMCMD  611

Query  407  TSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGW  466
             + L  +++ V       V    +     +   V  K+    D   +       +L    
Sbjct  612  MALLFMHDVKVATKYVKKVTGKVAVRFKALGIAVVRKITEWFDLAVDTAASAAGWL----  667

Query  467  EIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIG  516
                 +      +  G I    + + E V+ F      F  +  DS+ + 
Sbjct  668  --CYQLVNGLFAVANGVITFIQE-VPELVKNFVDKFKTFFKVLIDSMSVS  714


>sp|P0C6V1|R1A_CVMJH Replicase polyprotein 1a OS=Murine coronavirus 
(strain JHM) OX=11144 GN=1a PE=1 SV=1
Length=4474

 Score = 64.0 bits (154),  Expect = 4e-09, Method: Composition-based stats.
 Identities = 78/530 (15%), Positives = 165/530 (31%), Gaps = 86/530 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G    C+   L   G  + +  ++L  +          ++E  +AW+ +R
Sbjct  253  FVDQYGCDYTG----CLAKGLEDYGDLTLSEMKELSPVWRDSL-----DNEVVVAWHVDR  303

Query  65   SEKSYEL-QTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
              ++    QT   ++  +       D  +G+     P  +   N+I+K + PR+ +  L 
Sbjct  304  DPRAVMRLQTLATVRSIEYVGQPIEDMVDGDVVMREPAHLLAPNAIVKRL-PRLVETMLY  362

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                     Y      +C  +     + C  D CG   W  G+ +       C    +  
Sbjct  363  TDSSVTEFCY-KTKLCDCGFITQFGYVDCCGDTCGFRGWVPGNMMDGFPCPGCCKSYMPW  421

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+  V+        +++     S   Y            G   + FGG  
Sbjct  422  ELEAQSSGVIPEGGVL-----FTQSTDTVNRESFKLY------------GHAVVPFGGA-  463

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
             +Y   +     W+P   +++  +++ +   G  G    + E         + +  F   
Sbjct  464  -AYWSPYPGM--WLPVIWSSV-KSYSYLTYTGVVGCKAIVQE--------TDAICRFLYM  511

Query  291  EEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSIL  350
            + +     +           + GLD    +Q++       V +G       N+       
Sbjct  512  DYVQHKCGNLE------QRAILGLDDVYHRQLL-------VNRGDYSLLLENVDL-----  553

Query  351  SPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQ----YSLRLIDAMMF  406
                   +E A    +     +    + +       I      +     +S  ++D  M 
Sbjct  554  --FVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSLMVNFSREVVDMCMD  611

Query  407  TSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGW  466
             + L  +++ V       V    +     +   V  K+    D   +       +L    
Sbjct  612  MALLFMHDVKVATKYVKKVTGKVAVRFKALGIAVVRKITEWFDLAVDTAASAAGWL----  667

Query  467  EIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIG  516
                 +      +  G I    + + E V+ F      F  +  DS+ + 
Sbjct  668  --CYQLVNGLFAVANGVITFIQE-VPELVKNFVDKFKTFFKVLIDSMSVS  714


>sp|P0C6X2|R1AB_CVHN1 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N1) OX=443239 GN=rep PE=3 SV=1
Length=7182

 Score = 62.5 bits (150),  Expect = 1e-08, Method: Composition-based stats.
 Identities = 99/608 (16%), Positives = 188/608 (31%), Gaps = 99/608 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G   +C   L A    +   + ++                   +AW+  R
Sbjct  228  FVDQYGCDYSGKLADC---LQAYGHYSLQDMRQKQSVWLANCDFDIV------VAWHVVR  278

Query  65   -SEKSYELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
             S     LQT   I   K       D  +G+     P  +   ++I+  + P + K    
Sbjct  279  DSRFVMRLQTIATICGIKYVAQPTEDVVDGDVVIREPVHLLSADAIVLKL-PSLMKVMTH  337

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                 I+S+Y V    +C  +     + C  D+C    W +G+ +       C T   + 
Sbjct  338  MDDFSIKSIYNVD-LCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMDGFSCPLCCTVYDSS  396

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+N V+        NS     H     +           G     FG C+
Sbjct  397  EVKAQSSGVIPENPVLFT------NSTDTVNHDSFNLY-----------GYSVTPFGSCI  439

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
            +       +   W+P   +++  ++  +V  G  G                +IV +  L 
Sbjct  440  Y----WSPRPGLWIPIIKSSV-KSYDDLVYSGVVGCK--------------SIVKETALI  480

Query  291  EEIAIILASFSASTSAFVET-VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSI  349
               A+ L           +  + G++    +Q++ + G++ +          NI      
Sbjct  481  -THALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLK-------NIDLFVKR  532

Query  350  LSPL-YAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTS  408
             +     FA      V  +    +  +   +    ++ I     +SQ+S  + D  +   
Sbjct  533  RADFACKFAVCGDGFVPFLLDGLIPRSYYLI----QSGIFFTSLMSQFSQEVSDMCLKMC  588

Query  409  DLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI  468
             L  + + V  +     V         +  T+  K+    + + +       +L      
Sbjct  589  ILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVNKMVNWFNTMLDASAPATGWL------  642

Query  469  VKFISTCACEIVGGQIVTCA---KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNL  525
            +  +      +        A      K  V  F+      L      ++     LK +N 
Sbjct  643  LYQLLNGLFVVSQANFNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING  702

Query  526  -----GETFVTHSKGLYRKCVKSREETGLLMPLKAP-KEIIFLEGETLPTEVLTEEVVLK  579
                 G  F   S GL           G ++P  A  ++I F EG      V  + +   
Sbjct  703  LVCIVGNKFYNVSTGLIP---------GFVLPCNAQEQQIYFFEGVAESVIVEDDVIENV  753

Query  580  TGDLQPLE  587
               L   E
Sbjct  754  KSSLSSYE  761


>sp|P0C6U3|R1A_CVHN1 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N1) OX=443239 GN=1a PE=1 SV=1
Length=4471

 Score = 62.5 bits (150),  Expect = 1e-08, Method: Composition-based stats.
 Identities = 99/608 (16%), Positives = 188/608 (31%), Gaps = 99/608 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G   +C   L A    +   + ++                   +AW+  R
Sbjct  228  FVDQYGCDYSGKLADC---LQAYGHYSLQDMRQKQSVWLANCDFDIV------VAWHVVR  278

Query  65   -SEKSYELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
             S     LQT   I   K       D  +G+     P  +   ++I+  + P + K    
Sbjct  279  DSRFVMRLQTIATICGIKYVAQPTEDVVDGDVVIREPVHLLSADAIVLKL-PSLMKVMTH  337

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                 I+S+Y V    +C  +     + C  D+C    W +G+ +       C T   + 
Sbjct  338  MDDFSIKSIYNVD-LCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMDGFSCPLCCTVYDSS  396

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+N V+        NS     H     +           G     FG C+
Sbjct  397  EVKAQSSGVIPENPVLFT------NSTDTVNHDSFNLY-----------GYSVTPFGSCI  439

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
            +       +   W+P   +++  ++  +V  G  G                +IV +  L 
Sbjct  440  Y----WSPRPGLWIPIIKSSV-KSYDDLVYSGVVGCK--------------SIVKETALI  480

Query  291  EEIAIILASFSASTSAFVET-VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSI  349
               A+ L           +  + G++    +Q++ + G++ +          NI      
Sbjct  481  -THALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLK-------NIDLFVKR  532

Query  350  LSPL-YAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTS  408
             +     FA      V  +    +  +   +    ++ I     +SQ+S  + D  +   
Sbjct  533  RADFACKFAVCGDGFVPFLLDGLIPRSYYLI----QSGIFFTSLMSQFSQEVSDMCLKMC  588

Query  409  DLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI  468
             L  + + V  +     V         +  T+  K+    + + +       +L      
Sbjct  589  ILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVNKMVNWFNTMLDASAPATGWL------  642

Query  469  VKFISTCACEIVGGQIVTCA---KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNL  525
            +  +      +        A      K  V  F+      L      ++     LK +N 
Sbjct  643  LYQLLNGLFVVSQANFNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING  702

Query  526  -----GETFVTHSKGLYRKCVKSREETGLLMPLKAP-KEIIFLEGETLPTEVLTEEVVLK  579
                 G  F   S GL           G ++P  A  ++I F EG      V  + +   
Sbjct  703  LVCIVGNKFYNVSTGLIP---------GFVLPCNAQEQQIYFFEGVAESVIVEDDVIENV  753

Query  580  TGDLQPLE  587
               L   E
Sbjct  754  KSSLSSYE  761


>sp|P0C6U4|R1A_CVHN2 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N2) OX=443240 GN=1a PE=3 SV=1
Length=4441

 Score = 61.3 bits (147),  Expect = 3e-08, Method: Composition-based stats.
 Identities = 97/608 (16%), Positives = 186/608 (31%), Gaps = 99/608 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G   +C   L A    +   + ++                   +AW+  R
Sbjct  228  FVDQYGCDYSGKLADC---LQAYGHYSLQDMRQKQSVWLANCDFDIV------VAWHVVR  278

Query  65   -SEKSYELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
             S     LQT   I   K       D  +G      P  +   ++I+  + P + K    
Sbjct  279  DSRFVMRLQTIATICGIKYVAQPTEDVVDGAVVIREPVHLLSADAIVLKL-PSLMKVMTH  337

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                 I+S+Y V    +C  +     + C  D+C    W +G+ +       C T   + 
Sbjct  338  MDDFSIKSIYNVD-LCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMDGFSCPLCCTVYDSS  396

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+N V+        N +    +                 G     FG C+
Sbjct  397  EVKAQSSGVIPENPVLFTNSTDTVNPDSFNLY-----------------GYSVTPFGSCI  439

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
            +       +   W+P   +++  ++  +V  G  G                +IV +  L 
Sbjct  440  Y----WSPRPGLWIPIIKSSV-KSYDDLVYSGVVGCK--------------SIVKETALI  480

Query  291  EEIAIILASFSASTSAFVET-VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSI  349
               A+ L           +  + G++    +Q++ + G++ +          NI      
Sbjct  481  -THALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLK-------NIDLFVKR  532

Query  350  LSPL-YAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTS  408
             +     FA      V  +    +  +   +    ++ I     +SQ+S  + D  +   
Sbjct  533  RADFACKFAVCGDGFVPFLLDGLIPRSYYLI----QSGIFFTSLMSQFSQEVSDMCLKMC  588

Query  409  DLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI  468
             L  + + V  +     V         +  T+  K+    + + +       +L      
Sbjct  589  ILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVNKMVNWFNTMLDASAPATGWL------  642

Query  469  VKFISTCACEIVGGQIVTCA---KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNL  525
            +  +      +        A      K  V  F+      L      ++     LK +N 
Sbjct  643  LYQLLNGLFVVSQANFNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING  702

Query  526  -----GETFVTHSKGLYRKCVKSREETGLLMPLKAP-KEIIFLEGETLPTEVLTEEVVLK  579
                 G  F   S GL           G ++P  A  ++I F EG      V  + +   
Sbjct  703  LVCIVGNKFYNVSTGLIP---------GFVLPCNAQEQQIYFFEGVAESVIVEDDVIENV  753

Query  580  TGDLQPLE  587
               L   E
Sbjct  754  KSSLSSYE  761


>sp|P0C6X3|R1AB_CVHN2 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N2) OX=443240 GN=rep PE=3 SV=1
Length=7152

 Score = 61.3 bits (147),  Expect = 3e-08, Method: Composition-based stats.
 Identities = 97/608 (16%), Positives = 186/608 (31%), Gaps = 99/608 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G   +C   L A    +   + ++                   +AW+  R
Sbjct  228  FVDQYGCDYSGKLADC---LQAYGHYSLQDMRQKQSVWLANCDFDIV------VAWHVVR  278

Query  65   -SEKSYELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
             S     LQT   I   K       D  +G      P  +   ++I+  + P + K    
Sbjct  279  DSRFVMRLQTIATICGIKYVAQPTEDVVDGAVVIREPVHLLSADAIVLKL-PSLMKVMTH  337

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                 I+S+Y V    +C  +     + C  D+C    W +G+ +       C T   + 
Sbjct  338  MDDFSIKSIYNVD-LCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMDGFSCPLCCTVYDSS  396

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+N V+        N +    +                 G     FG C+
Sbjct  397  EVKAQSSGVIPENPVLFTNSTDTVNPDSFNLY-----------------GYSVTPFGSCI  439

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
            +       +   W+P   +++  ++  +V  G  G                +IV +  L 
Sbjct  440  Y----WSPRPGLWIPIIKSSV-KSYDDLVYSGVVGCK--------------SIVKETALI  480

Query  291  EEIAIILASFSASTSAFVET-VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSI  349
               A+ L           +  + G++    +Q++ + G++ +          NI      
Sbjct  481  -THALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLK-------NIDLFVKR  532

Query  350  LSPL-YAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTS  408
             +     FA      V  +    +  +   +    ++ I     +SQ+S  + D  +   
Sbjct  533  RADFACKFAVCGDGFVPFLLDGLIPRSYYLI----QSGIFFTSLMSQFSQEVSDMCLKMC  588

Query  409  DLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI  468
             L  + + V  +     V         +  T+  K+    + + +       +L      
Sbjct  589  ILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVNKMVNWFNTMLDASAPATGWL------  642

Query  469  VKFISTCACEIVGGQIVTCA---KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNL  525
            +  +      +        A      K  V  F+      L      ++     LK +N 
Sbjct  643  LYQLLNGLFVVSQANFNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING  702

Query  526  -----GETFVTHSKGLYRKCVKSREETGLLMPLKAP-KEIIFLEGETLPTEVLTEEVVLK  579
                 G  F   S GL           G ++P  A  ++I F EG      V  + +   
Sbjct  703  LVCIVGNKFYNVSTGLIP---------GFVLPCNAQEQQIYFFEGVAESVIVEDDVIENV  753

Query  580  TGDLQPLE  587
               L   E
Sbjct  754  KSSLSSYE  761


>sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronavirus 
(strain FIPV WSU-79/1146) OX=33734 GN=rep PE=1 SV=2
Length=6709

 Score = 60.2 bits (144),  Expect = 6e-08, Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 70/240 (29%), Gaps = 43/240 (18%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            YVD   CG DG P+                  E  D+      V      E+  AW T R
Sbjct  113  YVDQYMCGADGKPV---------------IEGEFKDYF-GDEDVIIYEGEEYHCAWLTVR  156

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVY  124
             EK    QT   I+  +       + P      N  I+ + P V+K          R +Y
Sbjct  157  DEKPLWQQTLLTIREIQYNLDIPHKLP------NCAIREVAPPVKKNSKVVLSEEYRKLY  210

Query  125  PVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT-CEFCGTENLTKEGATTCGYLPQN  183
                      +  S  M       T + +  F+ AT    CG E+      T        
Sbjct  211  ---------DIFGSPFMGNGDSLNTCFDSLHFIAATLKCPCGAESSGVGDWTG-------  254

Query  184  AVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYW  243
               K  C   H    G   +L        + T +  G     F   V  Y G     + W
Sbjct  255  --FKTACCGLHGKVKGV--TLGAVKPGDAIVTSMSAGKGVKFFANSVLQYAGDVENVSVW  310


 Score = 43.6 bits (101),  Expect = 0.007, Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 83/238 (35%), Gaps = 24/238 (10%)

Query  402  DAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEF  461
            D ++      + NL   A     ++     W     G ++     V++ L    K   + 
Sbjct  362  DCIIAGKLDLSTNLFGSA----NLLFKKMPWFVQKCGAIFADAWKVVEELLCSLKLTYKQ  417

Query  462  LRDGWEIVKFISTCACEIVGGQ--IVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAK  519
            + D   +V  + T A  I+  +   V  +  +K+ V    K++ K   +   +I I G +
Sbjct  418  IYD---VVASLCTSAFTIMDYKPVFVVSSNSVKDLVDKCVKILVKAFDVFTQTITIAGVE  474

Query  520  LKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLK  579
             K   LG  ++  +  L            L+      K    L+     T ++   V + 
Sbjct  475  AKCFVLGSKYLLFNNAL----------VKLVSVKILGKRQKGLDSAFFATNLIGATVNVT  524

Query  580  TGDLQPLEQPTSEA--VEAPLVGTPVCINGLMLLEIKDTEKYCAL-APNMMVTNNTFT  634
                +      ++   V  P  G  V I  +     K  E Y  + +P+ ++ NN F 
Sbjct  525  PQRTESAYISLNKVDDVVTPGGGHIVIIGDMAFY--KSEEYYFMMASPDSVLVNNVFK  580


>sp|P0C6X4|R1AB_CVHN5 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N5) OX=443241 GN=rep PE=3 SV=1
Length=7132

 Score = 59.4 bits (142),  Expect = 1e-07, Method: Composition-based stats.
 Identities = 97/608 (16%), Positives = 188/608 (31%), Gaps = 99/608 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G   +C   L A    +   + ++                   +AW+  R
Sbjct  228  FVDQYGCDYSGKLADC---LQAYGHYSLQDMRQKQSVWLANCDFDIV------VAWHVVR  278

Query  65   -SEKSYELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
             S     LQT   I   K       D  +G+     P  +   ++I+  + P + K    
Sbjct  279  DSRFVMRLQTIATICGIKYVAQPTEDVVDGDVVIREPVHLLSADAIVLKL-PSLMKVMTH  337

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                 I+S+Y V    +C  +     + C  D+C    W +G+ +       C T   + 
Sbjct  338  MDDFSIKSIYNVD-LCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMDGFSCPLCCTVYDSS  396

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+N V+        N +    +                 G     FG C+
Sbjct  397  EVKAQSSGVIPENPVLFTNSTDTVNPDSFNLY-----------------GYSVTPFGSCI  439

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
            +       +   W+P   +++  ++  +V  G  G                +IV +  L 
Sbjct  440  Y----WSPRPGLWIPIIKSSV-KSYDDLVYSGVVGCK--------------SIVKETALI  480

Query  291  EEIAIILASFSASTSAFVET-VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSI  349
               A+ L           +  + G++    +Q++ + G++ +          NI      
Sbjct  481  -THALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLK-------NIDLFVKR  532

Query  350  LSPL-YAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTS  408
             +     FA      V  +    +  +   +    ++ I     +SQ+S  + D  +   
Sbjct  533  RADFACKFAVCGDGFVPFLLDGLIPRSYYLI----QSGIFFTSLMSQFSQEVSDMCLKMC  588

Query  409  DLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI  468
             L  + + V  +     V         +  T+  K+    + + +       +L      
Sbjct  589  ILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVNKMVNWFNTMLDASAPATGWL------  642

Query  469  VKFISTCACEIVGGQIVTCA---KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNL  525
            +  +      +    +   A      K  V  F+      L      ++     LK +N 
Sbjct  643  LYQLLNGFFVVSQANLNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING  702

Query  526  -----GETFVTHSKGLYRKCVKSREETGLLMPLKAP-KEIIFLEGETLPTEVLTEEVVLK  579
                 G  F   S GL           G ++P  A  ++I F EG      V  + +   
Sbjct  703  LVCIVGNKFYNVSTGLIP---------GFVLPCNAQEQQIYFFEGVAESVIVEDDVIENV  753

Query  580  TGDLQPLE  587
               L   E
Sbjct  754  KSSLSSYE  761


>sp|P0C6U5|R1A_CVHN5 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N5) OX=443241 GN=1a PE=3 SV=1
Length=4421

 Score = 59.4 bits (142),  Expect = 1e-07, Method: Composition-based stats.
 Identities = 97/608 (16%), Positives = 188/608 (31%), Gaps = 99/608 (16%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G   +C   L A    +   + ++                   +AW+  R
Sbjct  228  FVDQYGCDYSGKLADC---LQAYGHYSLQDMRQKQSVWLANCDFDIV------VAWHVVR  278

Query  65   -SEKSYELQTPFEIKLAKKF-----DTFNGEC----PNFVFPLNSIIKTIQPRVEKKKLD  114
             S     LQT   I   K       D  +G+     P  +   ++I+  + P + K    
Sbjct  279  DSRFVMRLQTIATICGIKYVAQPTEDVVDGDVVIREPVHLLSADAIVLKL-PSLMKVMTH  337

Query  115  GFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTENLTK  171
                 I+S+Y V    +C  +     + C  D+C    W +G+ +       C T   + 
Sbjct  338  MDDFSIKSIYNVD-LCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMDGFSCPLCCTVYDSS  396

Query  172  E-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCV  230
            E  A + G +P+N V+        N +    +                 G     FG C+
Sbjct  397  EVKAQSSGVIPENPVLFTNSTDTVNPDSFNLY-----------------GYSVTPFGSCI  439

Query  231  FSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLN  290
            +       +   W+P   +++  ++  +V  G  G                +IV +  L 
Sbjct  440  Y----WSPRPGLWIPIIKSSV-KSYDDLVYSGVVGCK--------------SIVKETALI  480

Query  291  EEIAIILASFSASTSAFVET-VKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSI  349
               A+ L           +  + G++    +Q++ + G++ +          NI      
Sbjct  481  -THALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLK-------NIDLFVKR  532

Query  350  LSPL-YAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTS  408
             +     FA      V  +    +  +   +    ++ I     +SQ+S  + D  +   
Sbjct  533  RADFACKFAVCGDGFVPFLLDGLIPRSYYLI----QSGIFFTSLMSQFSQEVSDMCLKMC  588

Query  409  DLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI  468
             L  + + V  +     V         +  T+  K+    + + +       +L      
Sbjct  589  ILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVNKMVNWFNTMLDASAPATGWL------  642

Query  469  VKFISTCACEIVGGQIVTCA---KEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNL  525
            +  +      +    +   A      K  V  F+      L      ++     LK +N 
Sbjct  643  LYQLLNGFFVVSQANLNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING  702

Query  526  -----GETFVTHSKGLYRKCVKSREETGLLMPLKAP-KEIIFLEGETLPTEVLTEEVVLK  579
                 G  F   S GL           G ++P  A  ++I F EG      V  + +   
Sbjct  703  LVCIVGNKFYNVSTGLIP---------GFVLPCNAQEQQIYFFEGVAESVIVEDDVIENV  753

Query  580  TGDLQPLE  587
               L   E
Sbjct  754  KSSLSSYE  761


>sp|P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab OS=Human coronavirus 
NL63 OX=277944 GN=rep PE=1 SV=1
Length=6729

 Score = 57.9 bits (138),  Expect = 3e-07, Method: Composition-based stats.
 Identities = 37/173 (21%), Positives = 55/173 (32%), Gaps = 30/173 (17%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   CG DG P+                + E  D+ +            +++AW   R
Sbjct  114  FVDKYMCGFDGKPV------------LPKNMWEFRDYFNNNTDSIVIGGVTYQLAWDVIR  161

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVY  124
             + SYE Q    I+      T               +   +P     K+    G   +VY
Sbjct  162  KDLSYEQQNVLAIESIHYLGTTG-----HTLKSGCKLTNAKPPKYSSKV-VLSGEWNAVY  215

Query  125  -PVASPNECNQM----------CLSTLMKCDHCGETSWQTGDFVKATCEFCGT  166
                SP   N M            +  +KC+ CG  SW  G +       CGT
Sbjct  216  RAFGSPFITNGMSLLDIIVKPVFFNAFVKCN-CGSESWSVGAWDGYLSSCCGT  267


>sp|P0C6U6|R1A_CVHNL Replicase polyprotein 1a OS=Human coronavirus 
NL63 OX=277944 GN=1a PE=1 SV=1
Length=4060

 Score = 57.9 bits (138),  Expect = 3e-07, Method: Composition-based stats.
 Identities = 37/173 (21%), Positives = 55/173 (32%), Gaps = 30/173 (17%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   CG DG P+                + E  D+ +            +++AW   R
Sbjct  114  FVDKYMCGFDGKPV------------LPKNMWEFRDYFNNNTDSIVIGGVTYQLAWDVIR  161

Query  65   SEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVY  124
             + SYE Q    I+      T               +   +P     K+    G   +VY
Sbjct  162  KDLSYEQQNVLAIESIHYLGTTG-----HTLKSGCKLTNAKPPKYSSKV-VLSGEWNAVY  215

Query  125  -PVASPNECNQM----------CLSTLMKCDHCGETSWQTGDFVKATCEFCGT  166
                SP   N M            +  +KC+ CG  SW  G +       CGT
Sbjct  216  RAFGSPFITNGMSLLDIIVKPVFFNAFVKCN-CGSESWSVGAWDGYLSSCCGT  267


>sp|P0C6X9|R1AB_CVMA5 Replicase polyprotein 1ab OS=Murine coronavirus 
(strain A59) OX=11142 GN=rep PE=1 SV=1
Length=7176

 Score = 56.7 bits (135),  Expect = 6e-07, Method: Composition-based stats.
 Identities = 83/535 (16%), Positives = 161/535 (30%), Gaps = 96/535 (18%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G    C+   L   G    TLSE  +     R      + E  +AW+ +R
Sbjct  253  FVDQYGCDYTG----CLAKGLEDYGDL--TLSEMKELFPVWRDSL---DSEVLVAWHVDR  303

Query  65   SEKSYELQTPFEIKLAKKFDTFNGEC-------------PNFVFPLNSIIKTIQPRVEKK  111
              ++       +     +   + G+              P  +   N+I+K + PR+ + 
Sbjct  304  DPRAAMR---LQTLATVRCIDYVGQPTEDVVDGDVVVREPAHLLAANAIVKRL-PRLVET  359

Query  112  KLDGFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTEN  168
             L          Y      EC  +     + C  D C    W  G+ +       C    
Sbjct  360  MLYTDSSVTEFCY-KTKLCECGFITQFGYVDCCGDTCDFRGWVAGNMMDGFPCPGCTKNY  418

Query  169  LTKE-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFG  227
            +  E  A + G +P+  V+        +++     S   Y            G   + FG
Sbjct  419  MPWELEAQSSGVIPEGGVL-----FTQSTDTVNRESFKLY------------GHAVVPFG  461

Query  228  GCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNI--NIVG  285
              V+ +  C      W+P   +++  +++G+   G  G    +++       ++  + V 
Sbjct  462  SAVY-WSPCPG---MWLPVIWSSV-KSYSGLTYTGVVGC-KAIVQETDAICRSLYMDYVQ  515

Query  286  DFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE  345
                N E   IL               GLD    +Q++       V +G       N+  
Sbjct  516  HKCGNLEQRAIL---------------GLDDVYHRQLL-------VNRGDYSLLLENVDL  553

Query  346  QKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQ----YSLRLI  401
                        +E A    +     +    + +       I      +     +S  + 
Sbjct  554  -------FVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSMMVNFSHEVT  606

Query  402  DAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEF  461
            D  M  + L  +++ V       V    +     +   V  K+    D   +       +
Sbjct  607  DMCMDMALLFMHDVKVATKYVKKVTGKLAVRFKALGVAVVRKITEWFDLAVDIAASAAGW  666

Query  462  LRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIG  516
            L         +      +  G I    + + E V+ F      F  +  DS+ + 
Sbjct  667  L------CYQLVNGLFAVANGVITFVQE-VPELVKNFVDKFKAFFKVLIDSMSVS  714


>sp|P0C6V0|R1A_CVMA5 Replicase polyprotein 1a OS=Murine coronavirus 
(strain A59) OX=11142 GN=1a PE=1 SV=1
Length=4468

 Score = 56.3 bits (134),  Expect = 9e-07, Method: Composition-based stats.
 Identities = 83/535 (16%), Positives = 161/535 (30%), Gaps = 96/535 (18%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            +VD   C   G    C+   L   G    TLSE  +     R      + E  +AW+ +R
Sbjct  253  FVDQYGCDYTG----CLAKGLEDYGDL--TLSEMKELFPVWRDSL---DSEVLVAWHVDR  303

Query  65   SEKSYELQTPFEIKLAKKFDTFNGEC-------------PNFVFPLNSIIKTIQPRVEKK  111
              ++       +     +   + G+              P  +   N+I+K + PR+ + 
Sbjct  304  DPRAAMR---LQTLATVRCIDYVGQPTEDVVDGDVVVREPAHLLAANAIVKRL-PRLVET  359

Query  112  KLDGFMGRIRSVYPVASPNECNQMCLSTLMKC--DHCGETSWQTGDFVKATCE-FCGTEN  168
             L          Y      EC  +     + C  D C    W  G+ +       C    
Sbjct  360  MLYTDSSVTEFCY-KTKLCECGFITQFGYVDCCGDTCDFRGWVAGNMMDGFPCPGCTKNY  418

Query  169  LTKE-GATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFG  227
            +  E  A + G +P+  V+        +++     S   Y            G   + FG
Sbjct  419  MPWELEAQSSGVIPEGGVL-----FTQSTDTVNRESFKLY------------GHAVVPFG  461

Query  228  GCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNI--NIVG  285
              V+ +  C      W+P   +++  +++G+   G  G    +++       ++  + V 
Sbjct  462  SAVY-WSPCPG---MWLPVIWSSV-KSYSGLTYTGVVGC-KAIVQETDAICRSLYMDYVQ  515

Query  286  DFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE  345
                N E   IL               GLD    +Q++       V +G       N+  
Sbjct  516  HKCGNLEQRAIL---------------GLDDVYHRQLL-------VNRGDYSLLLENVDL  553

Query  346  QKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQ----YSLRLI  401
                        +E A    +     +    + +       I      +     +S  + 
Sbjct  554  -------FVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSMMVNFSHEVT  606

Query  402  DAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEF  461
            D  M  + L  +++ V       V    +     +   V  K+    D   +       +
Sbjct  607  DMCMDMALLFMHDVKVATKYVKKVTGKLAVRFKALGVAVVRKITEWFDLAVDIAASAAGW  666

Query  462  LRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIG  516
            L         +      +  G I    + + E V+ F      F  +  DS+ + 
Sbjct  667  L------CYQLVNGLFAVANGVITFVQE-VPELVKNFVDKFKAFFKVLIDSMSVS  714


>sp|P0C6X1|R1AB_CVH22 Replicase polyprotein 1ab OS=Human coronavirus 
229E OX=11137 GN=rep PE=1 SV=1
Length=6758

 Score = 48.6 bits (114),  Expect = 2e-04, Method: Composition-based stats.
 Identities = 75/498 (15%), Positives = 143/498 (29%), Gaps = 91/498 (18%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            Y D   CG DG P+             S  L + +D       +     H +  AW T+R
Sbjct  115  YTDQYLCGADGKPV------------MSEDLWQFVDHFGENEEIII-NGHTYVCAWLTKR  161

Query  65   SEKSYELQTPFEIKLA--KKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS  122
                Y+ Q    I+       D  +      V  +   +KT    V    LD    ++  
Sbjct  162  KPLDYKRQNNLAIEEIEYVHGDALHTLRNGSVLEMAKEVKTSSKVVLSDALD----KLYK  217

Query  123  VYPVASPNECNQM--------CLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGA  174
            V+        + +         +S L++C  CG  SW  GD+                  
Sbjct  218  VFGSPVMTNGSNILEAFTKPVFISALVQCT-CGTKSWSVGDWTG--------------FK  262

Query  175  TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYV  234
            ++C  +  N +  +         V P  ++          T  + G     F G    +V
Sbjct  263  SSCCNVISNKLCVVP------GNVKPGDAVI---------TTQQAGAGIKYFCGMTLKFV  307

Query  235  GCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIA  294
                  + W       I           S  + +  +  +     N+       + +E  
Sbjct  308  ANIEGVSVW-----RVIALQSVDCFVASSTFVEEEHVNRMDTFCFNVR----NSVTDECR  358

Query  295  IILASFSASTSAFVETVKGLD------YKAFKQIVESCGNFKVTKGKAKKG-AWNIGEQK  347
            + +     +++   +   G+       +  +  I      + V K +   G  W+     
Sbjct  359  LAMLGAEMTSNVRRQVASGVIDISTGWFDVYDDIFAESKPWFVRKAEDIFGPCWS--ALA  416

Query  348  SILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSL---RLIDAM  404
            S L  L     E  R V+SI +  +     ++++L       L+    +      + D  
Sbjct  417  SALKQLKVTTGELVRFVKSICNSAVAVVGGTIQILASVPEKFLNAFDVFVTAIQTVFDCA  476

Query  405  -------------MFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWL  451
                         +F   L  N LV +       V+            V    + V    
Sbjct  477  VETCTIAGKAFDKVFDYVLLDNALVKLVTTKLKGVRERGLNKVKYATVVVGSTEEVKSSR  536

Query  452  EEKFKEGVEFLRDGWEIV  469
             E+    +    +  ++ 
Sbjct  537  VERSTAVLTIANNYSKLF  554


>sp|P0C6U2|R1A_CVH22 Replicase polyprotein 1a OS=Human coronavirus 
229E OX=11137 GN=1a PE=1 SV=1
Length=4085

 Score = 48.6 bits (114),  Expect = 2e-04, Method: Composition-based stats.
 Identities = 75/498 (15%), Positives = 143/498 (29%), Gaps = 91/498 (18%)

Query  5    YVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTER  64
            Y D   CG DG P+             S  L + +D       +     H +  AW T+R
Sbjct  115  YTDQYLCGADGKPV------------MSEDLWQFVDHFGENEEIII-NGHTYVCAWLTKR  161

Query  65   SEKSYELQTPFEIKLA--KKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS  122
                Y+ Q    I+       D  +      V  +   +KT    V    LD    ++  
Sbjct  162  KPLDYKRQNNLAIEEIEYVHGDALHTLRNGSVLEMAKEVKTSSKVVLSDALD----KLYK  217

Query  123  VYPVASPNECNQM--------CLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGA  174
            V+        + +         +S L++C  CG  SW  GD+                  
Sbjct  218  VFGSPVMTNGSNILEAFTKPVFISALVQCT-CGTKSWSVGDWTG--------------FK  262

Query  175  TTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYV  234
            ++C  +  N +  +         V P  ++          T  + G     F G    +V
Sbjct  263  SSCCNVISNKLCVVP------GNVKPGDAVI---------TTQQAGAGIKYFCGMTLKFV  307

Query  235  GCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIA  294
                  + W       I           S  + +  +  +     N+       + +E  
Sbjct  308  ANIEGVSVW-----RVIALQSVDCFVASSTFVEEEHVNRMDTFCFNVR----NSVTDECR  358

Query  295  IILASFSASTSAFVETVKGLD------YKAFKQIVESCGNFKVTKGKAKKG-AWNIGEQK  347
            + +     +++   +   G+       +  +  I      + V K +   G  W+     
Sbjct  359  LAMLGAEMTSNVRRQVASGVIDISTGWFDVYDDIFAESKPWFVRKAEDIFGPCWS--ALA  416

Query  348  SILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSL---RLIDAM  404
            S L  L     E  R V+SI +  +     ++++L       L+    +      + D  
Sbjct  417  SALKQLKVTTGELVRFVKSICNSAVAVVGGTIQILASVPEKFLNAFDVFVTAIQTVFDCA  476

Query  405  -------------MFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWL  451
                         +F   L  N LV +       V+            V    + V    
Sbjct  477  VETCTIAGKAFDKVFDYVLLDNALVKLVTTKLKGVRERGLNKVKYATVVVGSTEEVKSSR  536

Query  452  EEKFKEGVEFLRDGWEIV  469
             E+    +    +  ++ 
Sbjct  537  VERSTAVLTIANNYSKLF  554


>sp|P0C6W0|R1AB_BC512 Replicase polyprotein 1ab OS=Bat coronavirus 
512/2005 OX=693999 GN=rep PE=3 SV=1
Length=6793

 Score = 42.4 bits (98),  Expect = 0.014, Method: Composition-based stats.
 Identities = 32/169 (19%), Positives = 53/169 (31%), Gaps = 30/169 (18%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERS  65
            VD   CG DG P       + + G  +      +D+       +      +  AW  +R 
Sbjct  115  VDQFMCGADGAP-------VIQEGDWTF-----MDYFQ-DSNQFTLNGITYVKAWDVDRK  161

Query  66   EKSYELQTPFEIKLA--------KKFDTFNGECPNFVFPLNSIIKTIQP--RVEKKKLDG  115
               Y  Q    I+             D    +       +N  +    P  ++ K+    
Sbjct  162  PNDYAKQNVTCIRRITYITDHRHVLADGTTMKTARHP-KVNKSVVLDSPFDQIYKEVGSP  220

Query  116  FMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFC  164
            FMG   +   V    +        L+ C+ CG + W  GD+ K     C
Sbjct  221  FMGNGSTF--VEMLKDPAFFH--ALITCE-CGRSEWTVGDW-KGYNSLC  263


>sp|P0C6F6|R1A_BC512 Replicase polyprotein 1a OS=Bat coronavirus 
512/2005 OX=693999 GN=1a PE=3 SV=1
Length=4128

 Score = 42.4 bits (98),  Expect = 0.015, Method: Composition-based stats.
 Identities = 32/169 (19%), Positives = 53/169 (31%), Gaps = 30/169 (18%)

Query  6    VDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERS  65
            VD   CG DG P       + + G  +      +D+       +      +  AW  +R 
Sbjct  115  VDQFMCGADGAP-------VIQEGDWTF-----MDYFQ-DSNQFTLNGITYVKAWDVDRK  161

Query  66   EKSYELQTPFEIKLA--------KKFDTFNGECPNFVFPLNSIIKTIQP--RVEKKKLDG  115
               Y  Q    I+             D    +       +N  +    P  ++ K+    
Sbjct  162  PNDYAKQNVTCIRRITYITDHRHVLADGTTMKTARHP-KVNKSVVLDSPFDQIYKEVGSP  220

Query  116  FMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFC  164
            FMG   +   V    +        L+ C+ CG + W  GD+ K     C
Sbjct  221  FMGNGSTF--VEMLKDPAFFH--ALITCE-CGRSEWTVGDW-KGYNSLC  263


>sp|Q3C251|ARGJ_CITLA Arginine biosynthesis bifunctional protein 
ArgJ, chloroplastic OS=Citrullus lanatus OX=3654 PE=1 SV=1
Length=460

 Score = 40.9 bits (94),  Expect = 0.031, Method: Composition-based stats.
 Identities = 34/160 (21%), Positives = 67/160 (42%), Gaps = 20/160 (13%)

Query  218  RKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEI-LQK  276
            + GG TI  GG     +   +   +  P  +  +G   T  V      +   +++I + +
Sbjct  215  QVGGSTIRIGG-----MAKGSGMIH--PNMATMLGVVTTDAVVACD--VWRKMVQISVDR  265

Query  277  EKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKA  336
                I + GD   N+ +  + +  S   S  + ++K  +    ++ ++      V +G A
Sbjct  266  SFNQITVDGDTSTNDTVIALSSGLSGFNSNIISSLKSREAGQLQECLD-----VVMQGLA  320

Query  337  KKGAWNIGEQKS----ILSPLYAFASEAARVVRSIFSRTL  372
            K  AW+ GE  +    I     +  +EAA+V RS+   +L
Sbjct  321  KSIAWD-GEGATCLIEITVSGASTEAEAAKVARSVAGSSL  359


>sp|Q9KIP9|AGAS_ECOLX D-galactosamine-6-phosphate deaminase AgaS 
OS=Escherichia coli OX=562 GN=agaS PE=1 SV=1
Length=384

 Score = 35.1 bits (79),  Expect = 2.2, Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 56/155 (36%), Gaps = 14/155 (9%)

Query  243  WVPRASAN-IGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFS  301
            +VP      I CN  G + + +   ++    ++  E  +        +   +A  LA F+
Sbjct  129  FVPECYHLPITCNEAGALYQNAINSDNAFALLMPAETHDRGFAMTSSITTMMASCLAVFA  188

Query  302  ASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSIL----SPLYAFA  357
              T         ++ + F+ + + C     T G   +G +     K I+      L   A
Sbjct  189  PET---------INSQTFRDVADRCQAILTTLGDFSEGVFGYAPWKRIVYLGSGGLQGAA  239

Query  358  SEAARVVRSIFSRTLETAQNSVRVLQKAAITILDG  392
             E+A  V  + +  L    +S    +    +++D 
Sbjct  240  RESALKVLELTAGKLAAFYDSPTGFRHGPKSLVDD  274


>sp|Q6P6T1|C1S_RAT Complement C1s subcomponent OS=Rattus norvegicus 
OX=10116 GN=C1s PE=2 SV=2
Length=688

 Score = 34.4 bits (77),  Expect = 4.0, Method: Composition-based stats.
 Identities = 20/92 (22%), Positives = 29/92 (32%), Gaps = 16/92 (17%)

Query  89   ECPNFVFPLNS-IIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDH-C  146
                F FP N   +        +++  GF     + Y     NEC      T + C H C
Sbjct  95   TVEEFQFPYNRLQVVFTSDFSNEERFTGF----AAYYSAVDVNECTDF---TDVPCSHFC  147

Query  147  GETSWQTGDFVKATCEFCGTENLTKEGATTCG  178
                    +F+      C  E    +   TCG
Sbjct  148  N-------NFIGGYFCSCPPEYFLHDDMRTCG  172


>sp|Q9ZUR7|ARGJ_ARATH Arginine biosynthesis bifunctional protein 
ArgJ, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=At2g37500 
PE=1 SV=2
Length=468

 Score = 34.4 bits (77),  Expect = 4.0, Method: Composition-based stats.
 Identities = 32/151 (21%), Positives = 60/151 (40%), Gaps = 15/151 (10%)

Query  227  GGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEI-LQKEKVNINIVG  285
            GG      G         P  +  +G   T  + E    +   ++++ + +    I + G
Sbjct  227  GGIKIRVGGMAKGSGMIHPNMATMLGVITTDALVESD--IWRKMVKVAVNRSFNQITVDG  284

Query  286  DFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGE  345
            D   N+ +  + +  S S S      K          +++C +  V +G AK  AW+ GE
Sbjct  285  DTSTNDTVIALASGLSGSPSISSLNCKEAAQ------LQACLD-AVMQGLAKSIAWD-GE  336

Query  346  QKSILSPLYA----FASEAARVVRSIFSRTL  372
              + L  +        +EAA++ RS+ S +L
Sbjct  337  GATCLIEVTVKGTETEAEAAKIARSVASSSL  367


>sp|Q18823|LAM2_CAEEL Laminin-like protein lam-2 OS=Caenorhabditis 
elegans OX=6239 GN=lam-2 PE=1 SV=3
Length=1633

 Score = 34.4 bits (77),  Expect = 4.1, Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 25/83 (30%), Gaps = 4/83 (5%)

Query  136  CLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHN  195
              +    C+ C    +  GD ++ T E C       +G   C       V+   CP  + 
Sbjct  756  HNTAGDTCERCARGYY--GDALQGTEEDCQKCPCPNDGP--CILHADGDVICTECPNGYT  811

Query  196  SEVGPEHSLAEYHNESGLKTILR  218
                 E S   + N       + 
Sbjct  812  GRRCDECSDGYFGNPKDGTECVE  834


>sp|Q9Y7Q9|YCX2_SCHPO Probable metabolite transporter C2H8.02 
OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 
GN=SPCC2H8.02 PE=1 SV=1
Length=583

 Score = 34.0 bits (76),  Expect = 5.5, Method: Composition-based stats.
 Identities = 11/88 (13%), Positives = 22/88 (25%), Gaps = 4/88 (5%)

Query  149  TSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYH  208
             +W+T             +     G  T  ++    V      A  +             
Sbjct  449  GTWETISTGGRFACVALAQFFFNFGPNTTCFVIPAEVFPSRVRAFSHGICAACGKAGAIL  508

Query  209  NESGLKTILRKGGRTIAFGGCVFSYVGC  236
            +      +    G    FG  ++ + GC
Sbjct  509  SALLFNKLTEVIG----FGNVLWIFFGC  532


>sp|P42907|AGAS_ECOLI Putative D-galactosamine-6-phosphate deaminase 
AgaS OS=Escherichia coli (strain K12) OX=83333 GN=agaS 
PE=1 SV=1
Length=384

 Score = 33.2 bits (74),  Expect = 7.1, Method: Composition-based stats.
 Identities = 26/155 (17%), Positives = 56/155 (36%), Gaps = 14/155 (9%)

Query  243  WVPRASAN-IGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFS  301
            +VP      I CN  G + + +   ++    ++  E  +        +   +A  LA F+
Sbjct  129  FVPECYHLPITCNEAGALYQNAINSDNAFALLMPAETHDRGFAMTSSITTMMASCLAVFA  188

Query  302  ASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSIL----SPLYAFA  357
              T         ++ + F+ + + C     + G   +G +     K I+      L   A
Sbjct  189  PET---------INSQTFRDVADRCQAILTSLGDFSEGVFGYAPWKRIVYLGSGGLQGAA  239

Query  358  SEAARVVRSIFSRTLETAQNSVRVLQKAAITILDG  392
             E+A  V  + +  L    +S    +    +++D 
Sbjct  240  RESALKVLELTAGKLAAFYDSPTGFRHGPKSLVDD  274


>sp|Q8U221|SYM_PYRFU Methionine--tRNA ligase OS=Pyrococcus furiosus 
(strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 
GN=metG PE=3 SV=1
Length=724

 Score = 33.6 bits (75),  Expect = 7.8, Method: Composition-based stats.
 Identities = 15/54 (28%), Positives = 22/54 (41%), Gaps = 2/54 (4%)

Query  145  HCGETS-WQTGDFVKATCEFCGTENLTKEGATTCGY-LPQNAVVKIYCPACHNS  196
            +C     +    FV  TC +CG EN   +    CG  L    +++  C  C N 
Sbjct  126  YCEHDKRFLPDRFVIGTCPYCGAENQRGDQCEVCGRPLTPEILIEPRCAFCKNP  179


>sp|Q1LVF0|LAMC1_DANRE Laminin subunit gamma-1 OS=Danio rerio 
OX=7955 GN=lamc1 PE=2 SV=2
Length=1593

 Score = 33.2 bits (74),  Expect = 9.1, Method: Composition-based stats.
 Identities = 15/61 (25%), Positives = 23/61 (38%), Gaps = 5/61 (8%)

Query  132  CNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQ-NAVVKIYC  190
            CN    +  + C+ C +  +  GD    +   C           TC  +P+ N VV   C
Sbjct  724  CNCQHNTAGLSCERCKDGFY--GDSTVGSSSDCKA--CPCPAGATCAVVPKTNEVVCTNC  779

Query  191  P  191
            P
Sbjct  780  P  780



Lambda      K        H        a         alpha
   0.318    0.126    0.315    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0385    0.140     1.90     42.6     43.6 

Effective search space used: 68552451906


  Database: uniprot_sprot.fasta
    Posted date:  Feb 13, 2021  1:23 PM
  Number of letters in database: 203,340,877
  Number of sequences in database:  564,277



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40