BLASTP 2.2.26 [Sep-21-2011]


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.

Query= 039857
         (285 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|2BSJ|A Chain A, Native Crystal Structure Of The Type Iii Secretion
           Chaperone Syct From Yersinia Enterocolitica
 pdb|2BSJ|B Chain B, Native Crystal Structure Of The Type Iii Secretion
           Chaperone Syct From Yersinia Enterocolitica
          Length = 133

 Score = 28.5 bits (62), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 81  RLGNHEVSWHRKELMKCNVSEGQDWSARLYSQNWNIEQRKASSNLTWPAN 130
           RL    + W ++ L+  ++ E Q W  R      +IEQRK   N  +  N
Sbjct: 79  RLDGKSILWSQQSLVGLDIDEMQAWLERFID---DIEQRKEPQNTKFQPN 125


>pdb|2BSH|A Chain A, Crystal Structure Of The Type Iii Secretion Chaperone Syct
           From Yersinia Enterocolitica (Crystal Form 2)
 pdb|2BSH|B Chain B, Crystal Structure Of The Type Iii Secretion Chaperone Syct
           From Yersinia Enterocolitica (Crystal Form 2)
 pdb|2BSI|A Chain A, Crystal Structure Of The Type Iii Secretion Chaperone Syct
           From Yersinia Enterocolitica (Crystal Form 1)
 pdb|2BSI|B Chain B, Crystal Structure Of The Type Iii Secretion Chaperone Syct
           From Yersinia Enterocolitica (Crystal Form 1)
          Length = 125

 Score = 28.5 bits (62), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 81  RLGNHEVSWHRKELMKCNVSEGQDWSARLYSQNWNIEQRKASSNLTWPAN 130
           RL    + W ++ L+  ++ E Q W  R      +IEQRK   N  +  N
Sbjct: 79  RLDGKSILWSQQSLVGLDIDEXQAWLERFID---DIEQRKEPQNTKFQPN 125


>pdb|3IEB|A Chain A, Crystal Structure Of 3-Keto-L-Gulonate-6-Phosphate
           Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str.
           N16961
 pdb|3IEB|B Chain B, Crystal Structure Of 3-Keto-L-Gulonate-6-Phosphate
           Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str.
           N16961
 pdb|3IEB|C Chain C, Crystal Structure Of 3-Keto-L-Gulonate-6-Phosphate
           Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str.
           N16961
 pdb|3IEB|D Chain D, Crystal Structure Of 3-Keto-L-Gulonate-6-Phosphate
           Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str.
           N16961
 pdb|3IEB|E Chain E, Crystal Structure Of 3-Keto-L-Gulonate-6-Phosphate
           Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str.
           N16961
 pdb|3JR2|A Chain A, X-Ray Crystal Structure Of The Mg-Bound
           3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio
           Cholerae O1 Biovar El Tor Str. N16961
 pdb|3JR2|B Chain B, X-Ray Crystal Structure Of The Mg-Bound
           3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio
           Cholerae O1 Biovar El Tor Str. N16961
 pdb|3JR2|C Chain C, X-Ray Crystal Structure Of The Mg-Bound
           3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio
           Cholerae O1 Biovar El Tor Str. N16961
 pdb|3JR2|D Chain D, X-Ray Crystal Structure Of The Mg-Bound
           3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio
           Cholerae O1 Biovar El Tor Str. N16961
          Length = 218

 Score = 28.1 bits (61), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 50  YFRWIHKDLRPWVHTGITREMIERGREPGYFRLG 83
           Y  W  +D + WV  GIT+ +  R R+     +G
Sbjct: 117 YGNWTXQDAKAWVDLGITQAIYHRSRDAELAGIG 150


>pdb|2BHO|A Chain A, Crystal Structure Of The Yersinia Enterocolitica Type Iii
           Secretion Chaperone Syct
          Length = 130

 Score = 28.1 bits (61), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 81  RLGNHEVSWHRKELMKCNVSEGQDWSARLYSQNWNIEQRKASSNLTWPAN 130
           RL    + W ++ L+  ++ E Q W  R      +IEQRK   N  +  N
Sbjct: 76  RLDGKPILWSQQSLVGLDIDEMQAWLERFID---DIEQRKEPQNTKFQPN 122


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.316    0.133    0.437 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,904,265
Number of Sequences: 62578
Number of extensions: 430797
Number of successful extensions: 871
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 869
Number of HSP's gapped (non-prelim): 6
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)