BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., 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: Altschul, Stephen F., 
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:
Schaffer, Alejandro A., 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.

Query= gi|254781090|ref|YP_003065503.1| hypothetical protein
CLIBASIA_04960 [Candidatus Liberibacter asiaticus str. psy62]
         (71 letters)

Database: nr 
           14,124,377 sequences; 4,842,793,630 total letters

Searching..................................................done


Results from round 1


>gi|254781090|ref|YP_003065503.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter
          asiaticus str. psy62]
 gi|254040767|gb|ACT57563.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter
          asiaticus str. psy62]
          Length = 71

 Score =  146 bits (369), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 71/71 (100%), Positives = 71/71 (100%)

Query: 1  MKPIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL 60
          MKPIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL
Sbjct: 1  MKPIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL 60

Query: 61 ELENLVTDDIL 71
          ELENLVTDDIL
Sbjct: 61 ELENLVTDDIL 71


>gi|325071179|gb|ADY75699.1| replication initiator protein [Tomato leaf curl New Delhi virus]
          Length = 361

 Score = 34.7 bits (78), Expect = 4.8,   Method: Composition-based stats.
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 10/62 (16%)

Query: 11  WGVNFRFLLDGY--RSG-KTSKDKYQKIVKIGDHAESIKTLADFI-KDYPDCDLELENLV 66
           WGV   F +DG   R G KT+ D Y + +  G+  E++K L +F  KDY    L+  NL+
Sbjct: 113 WGV---FQIDGRSARGGQKTANDAYAQAINTGNKDEALKVLKEFAPKDYV---LQFHNLI 166

Query: 67  TD 68
           T+
Sbjct: 167 TN 168


>gi|331010200|gb|EGH90256.1| hypothetical protein PSYTB_10983 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 642

 Score = 34.3 bits (77), Expect = 5.5,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 3   PIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDLE 61
           P+I LL G G  F  LLD  + G+ ++D+Y+K   + D    + T AD  +++    LE
Sbjct: 510 PLISLLMGRGETFVVLLDDDKEGRKARDRYRKEWILSDQV--VITYADIDQEFSGKALE 566


>gi|257486731|ref|ZP_05640772.1| hypothetical protein PsyrptA_25885 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 642

 Score = 34.3 bits (77), Expect = 5.5,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 3   PIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDLE 61
           P+I LL G G  F  LLD  + G+ ++D+Y+K   + D    + T AD  +++    LE
Sbjct: 510 PLISLLMGRGETFVVLLDDDKEGRKARDRYRKEWILSDQV--VITYADIDQEFSGKALE 566


Searching..................................................done


Results from round 2





CONVERGED!
>gi|254781090|ref|YP_003065503.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter
          asiaticus str. psy62]
 gi|254040767|gb|ACT57563.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter
          asiaticus str. psy62]
          Length = 71

 Score =  147 bits (371), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 71/71 (100%), Positives = 71/71 (100%)

Query: 1  MKPIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL 60
          MKPIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL
Sbjct: 1  MKPIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDL 60

Query: 61 ELENLVTDDIL 71
          ELENLVTDDIL
Sbjct: 61 ELENLVTDDIL 71


>gi|325071179|gb|ADY75699.1| replication initiator protein [Tomato leaf curl New Delhi virus]
          Length = 361

 Score = 34.6 bits (78), Expect = 5.2,   Method: Composition-based stats.
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 10/62 (16%)

Query: 11  WGVNFRFLLDGY--RSG-KTSKDKYQKIVKIGDHAESIKTLADFI-KDYPDCDLELENLV 66
           WGV   F +DG   R G KT+ D Y + +  G+  E++K L +F  KDY    L+  NL+
Sbjct: 113 WGV---FQIDGRSARGGQKTANDAYAQAINTGNKDEALKVLKEFAPKDYV---LQFHNLI 166

Query: 67  TD 68
           T+
Sbjct: 167 TN 168


>gi|210134425|ref|YP_002300864.1| peptide methionine sulfoxide reductase [Helicobacter pylori P12]
 gi|210132393|gb|ACJ07384.1| peptide methionine sulfoxide reductase [Helicobacter pylori P12]
          Length = 359

 Score = 34.2 bits (77), Expect = 6.0,   Method: Composition-based stats.
 Identities = 16/30 (53%), Positives = 21/30 (70%), Gaps = 1/30 (3%)

Query: 21 GYRSGKTSKDKYQKIVKIGDHAESIKTLAD 50
          GY +GKTS   Y+K+ K  DHAES+K + D
Sbjct: 64 GYANGKTSSTNYEKLHK-SDHAESVKVIYD 92


>gi|331010200|gb|EGH90256.1| hypothetical protein PSYTB_10983 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 642

 Score = 34.2 bits (77), Expect = 6.1,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 3   PIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDLE 61
           P+I LL G G  F  LLD  + G+ ++D+Y+K   + D    + T AD  +++    LE
Sbjct: 510 PLISLLMGRGETFVVLLDDDKEGRKARDRYRKEWILSDQV--VITYADIDQEFSGKALE 566


>gi|257486731|ref|ZP_05640772.1| hypothetical protein PsyrptA_25885 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 642

 Score = 34.2 bits (77), Expect = 6.1,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 3   PIIHLLNGWGVNFRFLLDGYRSGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDLE 61
           P+I LL G G  F  LLD  + G+ ++D+Y+K   + D    + T AD  +++    LE
Sbjct: 510 PLISLLMGRGETFVVLLDDDKEGRKARDRYRKEWILSDQV--VITYADIDQEFSGKALE 566


>gi|227500467|ref|ZP_03930529.1| peptide-methionine (R)-S-oxide reductase [Anaerococcus tetradius
          ATCC 35098]
 gi|227217530|gb|EEI82849.1| peptide-methionine (R)-S-oxide reductase [Anaerococcus tetradius
          ATCC 35098]
          Length = 161

 Score = 34.2 bits (77), Expect = 7.0,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 11/60 (18%)

Query: 1  MKPIIHLLNG--WGVNFRF-----LLD---GYRSGKTSKDKYQKIVKIGDHAESIKTLAD 50
          MK II+L  G  WGV+  F     +L+    Y +GKT K  Y+ + K  DHAE++K   D
Sbjct: 1  MKKIIYLAGGCFWGVDAYFSSIKGVLETETAYANGKTKKTYYENL-KTTDHAETVKITYD 59


>gi|293390351|ref|ZP_06634685.1| peptide methionine sulfoxide reductase MsrA/msrB [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950885|gb|EFE01004.1| peptide methionine sulfoxide reductase MsrA/msrB [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 356

 Score = 33.8 bits (76), Expect = 7.6,   Method: Composition-based stats.
 Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 1/32 (3%)

Query: 19  LDGYRSGKTSKDKYQKIVKIGDHAESIKTLAD 50
           + GY +GK+ K  YQKI  I DHAE++K   D
Sbjct: 72  ISGYANGKSDKTNYQKI-GITDHAETVKVTYD 102


>gi|261867936|ref|YP_003255858.1| peptide methionine sulfoxide reductase MsrA/msrB [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|20455137|sp|Q9AL99|MSRAB_AGGAC RecName: Full=Peptide methionine sulfoxide reductase MsrA/MsrB;
           Includes: RecName: Full=Peptide methionine sulfoxide
           reductase MsrA; Short=Protein-methionine-S-oxide
           reductase; AltName: Full=Peptide-methionine (S)-S-oxide
           reductase; Short=Peptide Met(O) reductase; Includes:
           RecName: Full=Peptide methionine sulfoxide reductase
           MsrB; AltName: Full=Peptide-methionine (R)-S-oxide
           reductase
 gi|12963881|gb|AAK07680.1| methionine sulfoxide reductase [Aggregatibacter
           actinomycetemcomitans]
 gi|261413268|gb|ACX82639.1| peptide methionine sulfoxide reductase MsrA/msrB [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 356

 Score = 33.8 bits (76), Expect = 7.6,   Method: Composition-based stats.
 Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 1/32 (3%)

Query: 19  LDGYRSGKTSKDKYQKIVKIGDHAESIKTLAD 50
           + GY +GK+ K  YQKI  I DHAE++K   D
Sbjct: 72  ISGYANGKSDKTNYQKI-GITDHAETVKVTYD 102


  Database: nr
    Posted date:  May 22, 2011 12:22 AM
  Number of letters in database: 999,999,966
  Number of sequences in database:  2,987,313
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 22, 2011 12:30 AM
  Number of letters in database: 999,999,796
  Number of sequences in database:  2,903,041
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 22, 2011 12:36 AM
  Number of letters in database: 999,999,281
  Number of sequences in database:  2,904,016
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 22, 2011 12:41 AM
  Number of letters in database: 999,999,960
  Number of sequences in database:  2,935,328
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 22, 2011 12:46 AM
  Number of letters in database: 842,794,627
  Number of sequences in database:  2,394,679
  
Lambda     K      H
   0.321    0.144    0.434 

Lambda     K      H
   0.267   0.0472    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,528,825,180
Number of Sequences: 14124377
Number of extensions: 53093864
Number of successful extensions: 151073
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 151053
Number of HSP's gapped (non-prelim): 32
length of query: 71
length of database: 4,842,793,630
effective HSP length: 43
effective length of query: 28
effective length of database: 4,235,445,419
effective search space: 118592471732
effective search space used: 118592471732
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 76 (33.7 bits)