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= 011147
         (492 letters)

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

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



>pdb|3JTF|A Chain A, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
           Efflux Protein From Bordetella Parapertussis In Complex
           With Amp
 pdb|3JTF|B Chain B, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
           Efflux Protein From Bordetella Parapertussis In Complex
           With Amp
          Length = 129

 Score = 32.0 bits (71), Expect = 0.74,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 204 QKTAKDAMTAMSKIFSLDINSRLDEKTMGLIISNGHSRVPIYVGTPTNIIGAILG 258
           ++T  D     S+   LDI+  L +  +  II   HSR P+Y     NIIG +L 
Sbjct: 4   ERTVADIXVPRSRXDLLDISQPLPQ-LLATIIETAHSRFPVYEDDRDNIIGILLA 57


>pdb|3LHH|A Chain A, The Crystal Structure Of Cbs Domain Protein From
           Shewanella Oneidensis Mr-1
          Length = 172

 Score = 28.9 bits (63), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 181 EAGKGGELTHDETTIITGALDMTQKTAKDAMTAMSKIFSLDINSRLDEKTMGLIISNGHS 240
           E    G + H+E   +     + ++T        S I  LD+N  LD   +  +  + HS
Sbjct: 18  EGSSAGVIEHNEHAXVKNVFRLDERTISSLXVPRSDIVFLDLNLPLD-ANLRTVXQSPHS 76

Query: 241 RVPIYVGTPTNIIGAI 256
           R P+      + +G I
Sbjct: 77  RFPVCRNNVDDXVGII 92


>pdb|2P9M|A Chain A, Crystal Structure Of Conserved Hypothetical Protein Mj0922
           From Methanocaldococcus Jannaschii Dsm 2661
 pdb|2P9M|B Chain B, Crystal Structure Of Conserved Hypothetical Protein Mj0922
           From Methanocaldococcus Jannaschii Dsm 2661
 pdb|2P9M|C Chain C, Crystal Structure Of Conserved Hypothetical Protein Mj0922
           From Methanocaldococcus Jannaschii Dsm 2661
 pdb|2P9M|D Chain D, Crystal Structure Of Conserved Hypothetical Protein Mj0922
           From Methanocaldococcus Jannaschii Dsm 2661
          Length = 138

 Score = 28.5 bits (62), Expect = 8.3,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 2/41 (4%)

Query: 350 KISKEELESLPSVDEE--VIGIITLEDVMEELLQEEILDET 388
           K  K ++ SLP +D+E  VIGI+T  D+   L++++   ET
Sbjct: 33  KXLKYKISSLPVIDDENKVIGIVTTTDIGYNLIRDKYTLET 73


>pdb|3LV9|A Chain A, Crystal Structure Of Cbs Domain Of A Putative Transporter
           From Clostridium Difficile 630
          Length = 148

 Score = 28.5 bits (62), Expect = 8.5,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 24/35 (68%), Gaps = 2/35 (5%)

Query: 350 KISKEELESLPSVDEE--VIGIITLEDVMEELLQE 382
           +I KE+L+    VDE     G++T+ED++EE++ E
Sbjct: 112 RIRKEKLQLAIVVDEYGGTSGVVTIEDILEEIVGE 146


  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    0.133    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,889,429
Number of Sequences: 62578
Number of extensions: 480602
Number of successful extensions: 1075
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1071
Number of HSP's gapped (non-prelim): 11
length of query: 492
length of database: 14,973,337
effective HSP length: 103
effective length of query: 389
effective length of database: 8,527,803
effective search space: 3317315367
effective search space used: 3317315367
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: 53 (25.0 bits)