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
           570,830 sequences; 206,533,160 total letters

Results from round 1


Query= sp|P0DTD2|ORF9B_SARS2 ORF9b protein OS=Severe acute respiratory
syndrome coronavirus 2 OX=2697049 GN=9b PE=1 SV=1

Length=97
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

sp|P0DTD2|ORF9B_SARS2 ORF9b protein OS=Severe acute respiratory s...  197     3e-66
sp|Q3LZX3|ORF9B_BCHK3 Protein 9b OS=Bat coronavirus HKU3 OX=44273...  147     9e-47
sp|P0C5A6|ORF9B_BC279 Protein 9b OS=Bat coronavirus 279/2005 OX=3...  139     1e-43
sp|P59636|ORF9B_SARS ORF9b protein OS=Severe acute respiratory sy...  139     2e-43
sp|Q3I5I6|ORF9B_BCRP3 Protein 9b OS=Bat coronavirus Rp3/2004 OX=3...  135     5e-42
sp|Q10572|FOX1_CAEEL Sex determination protein fox-1 OS=Caenorhab...  29.6    4.4  
sp|Q05736|PR1_ASPOF Pathogenesis-related protein 1 OS=Asparagus o...  28.9    5.1  
sp|Q8Y866|DEF_LISMO Peptide deformylase OS=Listeria monocytogenes...  28.9    7.0  
sp|B8DCF7|DEF_LISMH Peptide deformylase OS=Listeria monocytogenes...  28.5    7.3  


>sp|P0DTD2|ORF9B_SARS2 ORF9b protein OS=Severe acute respiratory 
syndrome coronavirus 2 OX=2697049 GN=9b PE=1 SV=1
Length=97

 Score = 197 bits (500),  Expect = 3e-66, Method: Compositional matrix adjust.
 Identities = 97/97 (100%), Positives = 97/97 (100%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT
Sbjct  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK
Sbjct  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97


>sp|Q3LZX3|ORF9B_BCHK3 Protein 9b OS=Bat coronavirus HKU3 OX=442736 
GN=9b PE=3 SV=1
Length=97

 Score = 147 bits (372),  Expect = 9e-47, Method: Compositional matrix adjust.
 Identities = 72/97 (74%), Positives = 84/97 (87%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPK++ + PAL LVDPQIQ+ +TRME+AV  DQNN GPKVYPIILRLGS LSL+MA++ 
Sbjct  1   MDPKVNVVPPALHLVDPQIQMTITRMEDAVVHDQNNAGPKVYPIILRLGSQLSLSMAKRN  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           L+SLE +AFQ TPI V+MTKLATTEELPDEFVVVT K
Sbjct  61  LDSLEARAFQSTPIVVKMTKLATTEELPDEFVVVTAK  97


>sp|P0C5A6|ORF9B_BC279 Protein 9b OS=Bat coronavirus 279/2005 
OX=389167 GN=9b PE=3 SV=1
Length=97

 Score = 139 bits (351),  Expect = 1e-43, Method: Compositional matrix adjust.
 Identities = 71/97 (73%), Positives = 80/97 (82%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPK S + PAL LVDPQIQL + RME+AV   Q+N  PKVYPIILRLGS LSL+MAR+ 
Sbjct  1   MDPKTSVVPPALHLVDPQIQLTIIRMEDAVVHGQSNAVPKVYPIILRLGSQLSLSMARRN  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           L+SLE +AFQ TPI V+MTKLATTEELPDEFVVVT K
Sbjct  61  LDSLEARAFQSTPIVVKMTKLATTEELPDEFVVVTAK  97


>sp|P59636|ORF9B_SARS ORF9b protein OS=Severe acute respiratory 
syndrome coronavirus OX=694009 GN=9b PE=1 SV=1
Length=98

 Score = 139 bits (350),  Expect = 2e-43, Method: Compositional matrix adjust.
 Identities = 71/98 (72%), Positives = 83/98 (85%), Gaps = 1/98 (1%)

Query  1   MDP-KISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARK  59
           MDP + + + PAL LVDPQIQL +TRME+A+G+ QN+  PKVYPIILRLGS LSL+MAR+
Sbjct  1   MDPNQTNVVPPALHLVDPQIQLTITRMEDAMGQGQNSADPKVYPIILRLGSQLSLSMARR  60

Query  60  TLNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
            L+SLE +AFQ TPI VQMTKLATTEELPDEFVVVT K
Sbjct  61  NLDSLEARAFQSTPIVVQMTKLATTEELPDEFVVVTAK  98


>sp|Q3I5I6|ORF9B_BCRP3 Protein 9b OS=Bat coronavirus Rp3/2004 
OX=349344 GN=9b PE=3 SV=1
Length=97

 Score = 135 bits (341),  Expect = 5e-42, Method: Compositional matrix adjust.
 Identities = 70/97 (72%), Positives = 77/97 (79%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPK S + PAL LVDPQIQL  TRME+AV   QNN   KVYPIILRLGS LSL+M R+ 
Sbjct  1   MDPKTSVVLPALHLVDPQIQLTTTRMEDAVVHGQNNADLKVYPIILRLGSQLSLSMVRRN  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           L+SLE + FQ TPI V+MTKLATTEELPDEFVVVT K
Sbjct  61  LDSLEVRVFQSTPIVVKMTKLATTEELPDEFVVVTAK  97


>sp|Q10572|FOX1_CAEEL Sex determination protein fox-1 OS=Caenorhabditis 
elegans OX=6239 GN=fox-1 PE=1 SV=3
Length=429

 Score = 29.6 bits (65),  Expect = 4.4, Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 21/43 (49%), Gaps = 0/43 (0%)

Query  43   PIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTKLATTE  85
            P+    G PL  N A    N+L+  AF + P AVQ   LA  +
Sbjct  332  PLAQLQGQPLLFNAAALQTNALQQSAFGMDPAAVQAALLANEQ  374


>sp|Q05736|PR1_ASPOF Pathogenesis-related protein 1 OS=Asparagus 
officinalis OX=4686 GN=PR1 PE=2 SV=1
Length=158

 Score = 28.9 bits (63),  Expect = 5.1, Method: Compositional matrix adjust.
 Identities = 14/47 (30%), Positives = 26/47 (55%), Gaps = 0/47 (0%)

Query  19  IQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLE  65
           + +A  RM  A   D +N+GPK+ P  +  GS +S + +  T+  ++
Sbjct  12  VNVAAGRMFKAAMLDWHNLGPKIVPDFIAGGSVVSGDGSVGTIREIK  58


>sp|Q8Y866|DEF_LISMO Peptide deformylase OS=Listeria monocytogenes 
serovar 1/2a (strain ATCC BAA-679 / EGD-e) OX=169963 GN=def 
PE=3 SV=1
Length=183

 Score = 28.9 bits (63),  Expect = 7.0, Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 19/33 (58%), Gaps = 0/33 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRD  33
           MD  + E HPALR V  ++   ++  E  +GRD
Sbjct  4   MDDIVREGHPALREVATEVTFPLSDEEKKLGRD  36


>sp|B8DCF7|DEF_LISMH Peptide deformylase OS=Listeria monocytogenes 
serotype 4a (strain HCC23) OX=552536 GN=def PE=3 SV=1
Length=183

 Score = 28.5 bits (62),  Expect = 7.3, Method: Compositional matrix adjust.
 Identities = 13/33 (39%), Positives = 19/33 (58%), Gaps = 0/33 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRD  33
           MD  + E HPALR V  ++   ++  E  +GRD
Sbjct  4   MDDIVREGHPALREVATEVTFPLSDEEKKLGRD  36



Lambda      K        H        a         alpha
   0.317    0.133    0.364    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: 5048626500
Results from round 2


Query= sp|P0DTD2|ORF9B_SARS2 ORF9b protein OS=Severe acute respiratory
syndrome coronavirus 2 OX=2697049 GN=9b PE=1 SV=1

Length=97
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value
Sequences used in model and found again:

sp|Q3LZX3|ORF9B_BCHK3 Protein 9b OS=Bat coronavirus HKU3 OX=44273...  162     2e-52
sp|P0C5A6|ORF9B_BC279 Protein 9b OS=Bat coronavirus 279/2005 OX=3...  159     3e-51
sp|P59636|ORF9B_SARS ORF9b protein OS=Severe acute respiratory sy...  156     4e-50
sp|Q3I5I6|ORF9B_BCRP3 Protein 9b OS=Bat coronavirus Rp3/2004 OX=3...  156     4e-50
sp|P0DTD2|ORF9B_SARS2 ORF9b protein OS=Severe acute respiratory s...  152     1e-48

Sequences not found previously or not previously below threshold:

sp|A0A0C1EFK1|OPAE_ASPUT Epimerase opaE OS=Aspergillus ustus OX=4...  32.4    0.36 
sp|Q98IH6|ADC2_RHILO Acetoacetate decarboxylase 2 OS=Mesorhizobiu...  31.6    0.81 
sp|Q98AN6|ADC1_RHILO Acetoacetate decarboxylase 1 OS=Mesorhizobiu...  29.7    3.3  
sp|Q7NSA6|ADC_CHRVO Acetoacetate decarboxylase OS=Chromobacterium...  28.9    6.2  


>sp|Q3LZX3|ORF9B_BCHK3 Protein 9b OS=Bat coronavirus HKU3 OX=442736 
GN=9b PE=3 SV=1
Length=97

 Score = 162 bits (409),  Expect = 2e-52, Method: Composition-based stats.
 Identities = 72/97 (74%), Positives = 84/97 (87%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPK++ + PAL LVDPQIQ+ +TRME+AV  DQNN GPKVYPIILRLGS LSL+MA++ 
Sbjct  1   MDPKVNVVPPALHLVDPQIQMTITRMEDAVVHDQNNAGPKVYPIILRLGSQLSLSMAKRN  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           L+SLE +AFQ TPI V+MTKLATTEELPDEFVVVT K
Sbjct  61  LDSLEARAFQSTPIVVKMTKLATTEELPDEFVVVTAK  97


>sp|P0C5A6|ORF9B_BC279 Protein 9b OS=Bat coronavirus 279/2005 
OX=389167 GN=9b PE=3 SV=1
Length=97

 Score = 159 bits (401),  Expect = 3e-51, Method: Composition-based stats.
 Identities = 71/97 (73%), Positives = 80/97 (82%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPK S + PAL LVDPQIQL + RME+AV   Q+N  PKVYPIILRLGS LSL+MAR+ 
Sbjct  1   MDPKTSVVPPALHLVDPQIQLTIIRMEDAVVHGQSNAVPKVYPIILRLGSQLSLSMARRN  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           L+SLE +AFQ TPI V+MTKLATTEELPDEFVVVT K
Sbjct  61  LDSLEARAFQSTPIVVKMTKLATTEELPDEFVVVTAK  97


>sp|P59636|ORF9B_SARS ORF9b protein OS=Severe acute respiratory 
syndrome coronavirus OX=694009 GN=9b PE=1 SV=1
Length=98

 Score = 156 bits (394),  Expect = 4e-50, Method: Composition-based stats.
 Identities = 71/98 (72%), Positives = 83/98 (85%), Gaps = 1/98 (1%)

Query  1   MDP-KISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARK  59
           MDP + + + PAL LVDPQIQL +TRME+A+G+ QN+  PKVYPIILRLGS LSL+MAR+
Sbjct  1   MDPNQTNVVPPALHLVDPQIQLTITRMEDAMGQGQNSADPKVYPIILRLGSQLSLSMARR  60

Query  60  TLNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
            L+SLE +AFQ TPI VQMTKLATTEELPDEFVVVT K
Sbjct  61  NLDSLEARAFQSTPIVVQMTKLATTEELPDEFVVVTAK  98


>sp|Q3I5I6|ORF9B_BCRP3 Protein 9b OS=Bat coronavirus Rp3/2004 
OX=349344 GN=9b PE=3 SV=1
Length=97

 Score = 156 bits (394),  Expect = 4e-50, Method: Composition-based stats.
 Identities = 70/97 (72%), Positives = 77/97 (79%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPK S + PAL LVDPQIQL  TRME+AV   QNN   KVYPIILRLGS LSL+M R+ 
Sbjct  1   MDPKTSVVLPALHLVDPQIQLTTTRMEDAVVHGQNNADLKVYPIILRLGSQLSLSMVRRN  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           L+SLE + FQ TPI V+MTKLATTEELPDEFVVVT K
Sbjct  61  LDSLEVRVFQSTPIVVKMTKLATTEELPDEFVVVTAK  97


>sp|P0DTD2|ORF9B_SARS2 ORF9b protein OS=Severe acute respiratory 
syndrome coronavirus 2 OX=2697049 GN=9b PE=1 SV=1
Length=97

 Score = 152 bits (384),  Expect = 1e-48, Method: Composition-based stats.
 Identities = 97/97 (100%), Positives = 97/97 (100%), Gaps = 0/97 (0%)

Query  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60
           MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT
Sbjct  1   MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT  60

Query  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
           LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK
Sbjct  61  LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97


>sp|A0A0C1EFK1|OPAE_ASPUT Epimerase opaE OS=Aspergillus ustus 
OX=40382 GN=opaE PE=1 SV=1
Length=274

 Score = 32.4 bits (72),  Expect = 0.36, Method: Composition-based stats.
 Identities = 16/91 (18%), Positives = 38/91 (42%), Gaps = 6/91 (7%)

Query  7    EMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLED  66
             +   L   DP   + +T + N +G +Q    P + P++      + L   ++  + L  
Sbjct  29   VVETVLNHKDPSTHVTITSLANRIGGNQTLAYPSIRPLLYGEMIRVCLQARKENYDVLII  88

Query  67   KAFQLTPIAVQMTKLATTEELPDEFVVVTVK  97
              F   P+  ++ ++A      D+ V++  +
Sbjct  89   NCF-GDPMVDELQQIAG-----DDMVILGAR  113


>sp|Q98IH6|ADC2_RHILO Acetoacetate decarboxylase 2 OS=Mesorhizobium 
japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) 
OX=266835 GN=adc2 PE=3 SV=1
Length=261

 Score = 31.6 bits (70),  Expect = 0.81, Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 21/48 (44%), Gaps = 2/48 (4%)

Query  2   DPKI--SEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILR  47
           DPK   S +   L L +P ++    RM ++ G        +V P+  R
Sbjct  40  DPKKLRSLVPEPLELSEPLVKFEFIRMPDSTGFGNYTESGQVIPVTFR  87


>sp|Q98AN6|ADC1_RHILO Acetoacetate decarboxylase 1 OS=Mesorhizobium 
japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) 
OX=266835 GN=adc1 PE=3 SV=1
Length=247

 Score = 29.7 bits (65),  Expect = 3.3, Method: Composition-based stats.
 Identities = 10/45 (22%), Positives = 21/45 (47%), Gaps = 2/45 (4%)

Query  2   DPKI--SEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPI  44
           DP+     +   L++ +P ++    RM ++ G      G +V P+
Sbjct  40  DPQKLRDLVPEPLQVCEPMVKFEFIRMPDSTGFGDYTEGGQVIPV  84


>sp|Q7NSA6|ADC_CHRVO Acetoacetate decarboxylase OS=Chromobacterium 
violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 
12614 / NCIMB 9131 / NCTC 9757) OX=243365 GN=adc PE=1 SV=1
Length=246

 Score = 28.9 bits (63),  Expect = 6.2, Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 24/52 (46%), Gaps = 1/52 (2%)

Query  6   SEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMA  57
           + +   L++ +P ++    RM ++ G    +   +V P+  R G   S  +A
Sbjct  46  AVLPEPLQMAEPVVRYEFIRMPDSTGFGDYSESGQVIPVTFR-GERGSYTLA  96



Lambda      K        H        a         alpha
   0.311    0.125    0.341    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0383    0.140     1.90     42.6     43.6 

Effective search space used: 5048626500

Search has CONVERGED!


  Database: uniprot_sprot.fasta
    Posted date:  Feb 9, 2024  7:20 PM
  Number of letters in database: 206,533,160
  Number of sequences in database:  570,830



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40