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= 014672
         (420 letters)

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

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



>pdb|3AYX|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
           Hydrogenovibrio Marinus In An H2-Reduced Condition
 pdb|3AYX|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
           Hydrogenovibrio Marinus In An H2-Reduced Condition
 pdb|3AYY|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
           Hydrogenovibrio Marinus In A Ferricyanide-Oxidized
           Condition
 pdb|3AYY|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
           Hydrogenovibrio Marinus In A Ferricyanide-Oxidized
           Condition
 pdb|3AYZ|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
           Hydrogenovibrio Marinus In An Air-Oxidized Condition
 pdb|3AYZ|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
           Hydrogenovibrio Marinus In An Air-Oxidized Condition
          Length = 596

 Score = 32.3 bits (72), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 15/88 (17%)

Query: 196 LGLFKSPIAQGLQFKSSV------------QDFIICIEMAIASIVHLYVFPAKPYEQMGE 243
           L   KS I QG  F ++V            +D++    ++  +++    +P  PY++  +
Sbjct: 259 LNFVKSLIEQGRTFNTNVYVPDVIAIAAFYRDWLYGGGLSATNVMDYGAYPKTPYDKSTD 318

Query: 244 CFSGDISVLGDYSADCPLDPDEIRDSER 271
              G   + GD+    P+DP   RD E+
Sbjct: 319 QLPGGAIINGDWGKIHPVDP---RDPEQ 343


>pdb|1AJ8|A Chain A, Citrate Synthase From Pyrococcus Furiosus
 pdb|1AJ8|B Chain B, Citrate Synthase From Pyrococcus Furiosus
          Length = 371

 Score = 31.2 bits (69), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 30/102 (29%), Positives = 43/102 (42%), Gaps = 19/102 (18%)

Query: 167 IKPLAKFLTFKSIVFLTWWQGVAIALLYSLGLFKSPIAQGLQFKSSVQDFIICIEMAIAS 226
           ++ LA+  TF+ +V+L WW    +  L  L  FK  +A+       V    I I  A+  
Sbjct: 32  VEELAELSTFEEVVYLLWWG--KLPSLSELENFKKELAKSRGLPKEV----IEIMEALPK 85

Query: 227 IVHLYVFPAKPYEQMGECFSGDISVLG--DYSADCPLDPDEI 266
             H           MG      IS LG  D S D P+ P+E+
Sbjct: 86  NTH----------PMG-ALRTIISYLGNIDDSGDIPVTPEEV 116


>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
 pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
           Extrusion (Mate) Transporter
          Length = 460

 Score = 28.1 bits (61), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 6/42 (14%)

Query: 132 GCGYPYMAVVLNFSQSWALYCLIQFYTVTKDELAHIKPLAKF 173
           GCG     V       W +  L+ FY VT   LAH+K    F
Sbjct: 194 GCGVATAIV------YWIMLLLLLFYIVTSKRLAHVKVFETF 229


  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
   0.324    0.140    0.436 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,760,958
Number of Sequences: 62578
Number of extensions: 452979
Number of successful extensions: 632
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 632
Number of HSP's gapped (non-prelim): 3
length of query: 420
length of database: 14,973,337
effective HSP length: 101
effective length of query: 319
effective length of database: 8,652,959
effective search space: 2760293921
effective search space used: 2760293921
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)