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= psy17186
         (100 letters)

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

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



>pdb|2ZXH|A Chain A, Structure Of Aquifex Aeolicus Gida In The Form I Crystal
 pdb|2ZXH|B Chain B, Structure Of Aquifex Aeolicus Gida In The Form I Crystal
 pdb|2ZXI|A Chain A, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
 pdb|2ZXI|B Chain B, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
 pdb|2ZXI|C Chain C, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
 pdb|2ZXI|D Chain D, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
          Length = 637

 Score = 27.3 bits (59), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/95 (24%), Positives = 49/95 (51%), Gaps = 10/95 (10%)

Query: 12  TVSESCDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHYVMTEIAKRLN------AII 65
           T++ + D +KE+F +   Q+   K EVE  ++ +  ++R   + E  K+L        I 
Sbjct: 530 TMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDID 589

Query: 66  VQIMPFLSQEHQQQVATALERAKQVTMTELNAIIG 100
              +P L++E +++    L++ K +T+ + + I G
Sbjct: 590 YDKIPGLTKEAREK----LKKFKPITVGQASRIDG 620


>pdb|1Y4T|A Chain A, Ferric Binding Protein From Campylobacter Jejuni
 pdb|1Y4T|D Chain D, Ferric Binding Protein From Campylobacter Jejuni
 pdb|3E13|X Chain X, Iron Reconstituted Ferric Binding Protein From
          Campylobacter Jejuni
          Length = 322

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 23 EFNFLQAQYHNAKMEVEKLIQEKTEMQRHYVM---TEIAKRLN 62
          E N   A+++NA  E+ K  +EKT ++ ++     +E+ KRL+
Sbjct: 3  ELNIYSARHYNADFEIIKKFEEKTGIKVNHTQAKASELIKRLS 45


>pdb|1S2X|A Chain A, Crystal Structure Of Cag-Z From Helicobacter Pylori
          Length = 206

 Score = 26.6 bits (57), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 54  MTEIAKRLNAIIVQI-MPFLSQEHQQQVATALERAKQVTMTELN 96
           + +  K+LN I+  I   ++     +   T+LERAK +T  +LN
Sbjct: 161 IDDFGKKLNEIVQDIGTKYIILSKNKTYLTSLERAKLITQLKLN 204


>pdb|1VR5|A Chain A, Crystal Structure Of Oligopeptide Abc Transporter,
           Periplasmic Oligopeptide-Binding (Tm1223) From
           Thermotoga Maritima At 1.73 A Resolution
 pdb|1VR5|B Chain B, Crystal Structure Of Oligopeptide Abc Transporter,
           Periplasmic Oligopeptide-Binding (Tm1223) From
           Thermotoga Maritima At 1.73 A Resolution
          Length = 547

 Score = 26.2 bits (56), Expect = 4.5,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 28/55 (50%)

Query: 18  DRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHYVMTEIAKRLNAIIVQIMPFL 72
           D ++ E+++       A  EVE L+ E         + E+  +L+ I+++ +PF+
Sbjct: 443 DAVESEYSYSGNFGKYANPEVETLLDELNRSNDDAKIKEVVAKLSEILLKDLPFI 497


>pdb|2GAI|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
           Maritima In Triclinic Crystal Form
 pdb|2GAI|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
           Maritima In Triclinic Crystal Form
 pdb|2GAJ|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
           Maritima In Monoclinic Crystal Form
 pdb|2GAJ|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
           Maritima In Monoclinic Crystal Form
          Length = 633

 Score = 25.8 bits (55), Expect = 6.9,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 12  TVSESCDRIKEEFNFLQAQYHNAKMEVEKLIQEKTEMQRHYVMTEIAKRLNAI 64
           T+   CDR +E   F+  +YH   +  + L  E    ++ +   E  K + +I
Sbjct: 172 TLKLVCDREREILRFVPKKYHRITVNFDGLTAEIDVKEKKFFDAETLKEIQSI 224


  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    0.130    0.359 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,391,883
Number of Sequences: 62578
Number of extensions: 65928
Number of successful extensions: 238
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 234
Number of HSP's gapped (non-prelim): 7
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)