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= 009629
         (530 letters)

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

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



>pdb|2GP4|A Chain A, Structure Of [fes]cluster-free Apo Form Of
           6-phosphogluconate Dehydratase From Shewanella
           Oneidensis
 pdb|2GP4|B Chain B, Structure Of [fes]cluster-free Apo Form Of
           6-phosphogluconate Dehydratase From Shewanella
           Oneidensis
          Length = 628

 Score = 30.4 bits (67), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 84  GQLSNILAPAGPVAETIPAKRKENT-ESLAEGQAKDKHVVEAEKNS 128
           G L  +  PAGP    IP K K    +  A+G+     ++EAE  S
Sbjct: 189 GHLPXLFVPAGPXKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQS 234


>pdb|3EWK|A Chain A, Structure Of The Redox Sensor Domain Of Methylococcus
           Capsulatus (Bath) Mmos
          Length = 227

 Score = 29.3 bits (64), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 13/94 (13%)

Query: 193 YAKGKWVVDDSRPLYSGAHCKQWLSQMWACRLMQRTDFAYERLRWQPKDCQMEEFEGSQF 252
           Y + + V  D R + SG H K ++  MW  R + R +       WQ + C   + +G+++
Sbjct: 24  YGREELVGQDHRIVNSGYHGKAYIRDMW--RTISRGNI------WQGEFCNRRK-DGTRY 74

Query: 253 LTRMQDRTLAFIGDSLGR-QQFQSLMCMVTGGKE 285
                D T+  + D+ G+ +Q+ S+   +T  KE
Sbjct: 75  WV---DSTIVPLMDNAGKPRQYISIRRDITAQKE 105


  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
   0.319    0.133    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,641,260
Number of Sequences: 62578
Number of extensions: 647834
Number of successful extensions: 1739
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1736
Number of HSP's gapped (non-prelim): 5
length of query: 530
length of database: 14,973,337
effective HSP length: 103
effective length of query: 427
effective length of database: 8,527,803
effective search space: 3641371881
effective search space used: 3641371881
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: 54 (25.4 bits)