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= 017674
         (368 letters)

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

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



>pdb|1RTV|A Chain A, Rmlc (Dtdp-6-Deoxy-D-Xylo-4-Hexulose 3,5-Epimerase)
           Crystal Structure From Pseudomonas Aeruginosa, Apo
           Structure
 pdb|2IXJ|A Chain A, Rmlc P Aeruginosa Native
 pdb|2IXH|A Chain A, Rmlc P Aeruginosa With Dtdp-Rhamnose
 pdb|2IXH|B Chain B, Rmlc P Aeruginosa With Dtdp-Rhamnose
          Length = 184

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 25/47 (53%)

Query: 322 VVNITKGNRDLSPSFLRWLADRNLSSDDRIMRLKEGFAPLFSVLCPY 368
           V ++    R  SP+F +W+ +R  + + R M +  GFA  F VL  Y
Sbjct: 83  VFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEY 129


>pdb|2IXI|A Chain A, Rmlc P Aeruginosa With Dtdp-Xylose
 pdb|2IXI|B Chain B, Rmlc P Aeruginosa With Dtdp-Xylose
 pdb|2IXK|A Chain A, Rmlc P Aeruginosa With Dtdp-4-Keto Rhamnnose (The Product
           Of The Reaction)
 pdb|2IXK|B Chain B, Rmlc P Aeruginosa With Dtdp-4-Keto Rhamnnose (The Product
           Of The Reaction)
          Length = 184

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 25/47 (53%)

Query: 322 VVNITKGNRDLSPSFLRWLADRNLSSDDRIMRLKEGFAPLFSVLCPY 368
           V ++    R  SP+F +W+ +R  + + R M +  GFA  F VL  Y
Sbjct: 83  VFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEY 129


>pdb|1OJ7|A Chain A, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
 pdb|1OJ7|B Chain B, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
 pdb|1OJ7|C Chain C, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
 pdb|1OJ7|D Chain D, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
          Length = 408

 Score = 28.1 bits (61), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 24/46 (52%)

Query: 8  HQLSSGLYVSGRPEQLKERQPTMASRAVPYTGGDVKKSGELGKMFD 53
          H  +  L+  G    L+E+ P  A   + Y GG VKK+G L ++ D
Sbjct: 28 HTPTRILFGKGAIAGLREQIPHDARVLITYGGGSVKKTGVLDQVLD 73


>pdb|1N1X|A Chain A, Crystal Structure Analysis Of The Monomeric [s-
           Carboxyamidomethyl-Cys31, S-Carboxyamidomethyl-Cys32]
           Bovine Seminal Ribonuclease
 pdb|1N3Z|A Chain A, Crystal Structure Of The [s-Carboxyamidomethyl-Cys31, S-
           Carboxyamidomethyl-Cys32] Monomeric Derivative Of The
           Bovine Seminal Ribonuclease In The Liganded State
 pdb|1TQ9|A Chain A, Non-Covalent Swapped Dimer Of Bovine Seminal Ribonuclease
           In Complex With
           2'-Deoxycytidine-2'-Deoxyadenosine-3',5'- Monophosphate
 pdb|1TQ9|B Chain B, Non-Covalent Swapped Dimer Of Bovine Seminal Ribonuclease
           In Complex With
           2'-Deoxycytidine-2'-Deoxyadenosine-3',5'- Monophosphate
          Length = 124

 Score = 27.7 bits (60), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 244 ESSYQRVPRCVYVSTEL--HEYKGCGGKPANPKH 275
           E+   + P C Y +T++  H    CGGKP+ P H
Sbjct: 86  ETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVH 119


  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
   0.318    0.137    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,861,314
Number of Sequences: 62578
Number of extensions: 384473
Number of successful extensions: 763
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 760
Number of HSP's gapped (non-prelim): 11
length of query: 368
length of database: 14,973,337
effective HSP length: 100
effective length of query: 268
effective length of database: 8,715,537
effective search space: 2335763916
effective search space used: 2335763916
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)