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= 009285
         (538 letters)

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

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



>pdb|2IYE|A Chain A, Structure Of Catalytic Cpx-atpase Domain Copb-b
 pdb|2IYE|C Chain C, Structure Of Catalytic Cpx-atpase Domain Copb-b
          Length = 263

 Score = 29.3 bits (64), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 461 GVAINGNISSH--EFK--ENQDTISVFRTGDNEVSAN-SEVDGRNEQQSQENLGKEGLEV 515
           G+ + G IS    E K  EN + I+V+  G+   S N S+V   N +   E L  EGL++
Sbjct: 96  GIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKI 155

Query: 516 HARSATTDDKLSE 528
              S   +DK+ E
Sbjct: 156 IILSGDKEDKVKE 168


>pdb|2YJ4|A Chain A, Conformational Changes In The Catalytic Domain Of The Cpx-
           Atpase Copb-B Upon Nucleotide Binding
 pdb|2YJ4|B Chain B, Conformational Changes In The Catalytic Domain Of The Cpx-
           Atpase Copb-B Upon Nucleotide Binding
 pdb|2YJ5|A Chain A, Conformational Changes In The Catalytic Domain Of The Cpx-
           Atpase Copb-B Upon Nucleotide Binding
 pdb|2YJ5|B Chain B, Conformational Changes In The Catalytic Domain Of The Cpx-
           Atpase Copb-B Upon Nucleotide Binding
 pdb|2YJ6|A Chain A, Conformational Changes In The Catalytic Domain Of The
           Cpx-Atpase Copb-B Upon Nucleotide Binding
 pdb|2YJ6|B Chain B, Conformational Changes In The Catalytic Domain Of The
           Cpx-Atpase Copb-B Upon Nucleotide Binding
          Length = 263

 Score = 29.3 bits (64), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 461 GVAINGNISSH--EFK--ENQDTISVFRTGDNEVSAN-SEVDGRNEQQSQENLGKEGLEV 515
           G+ + G IS    E K  EN + I+V+  G+   S N S+V   N +   E L  EGL++
Sbjct: 96  GIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKI 155

Query: 516 HARSATTDDKLSE 528
              S   +DK+ E
Sbjct: 156 IILSGDKEDKVKE 168


>pdb|2YJ3|A Chain A, Conformational Changes In The Catalytic Domain Of The Cpx-
           Atpase Copb-B Upon Nucleotide Binding
          Length = 263

 Score = 29.3 bits (64), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 461 GVAINGNISSH--EFK--ENQDTISVFRTGDNEVSAN-SEVDGRNEQQSQENLGKEGLEV 515
           G+ + G IS    E K  EN + I+V+  G+   S N S+V   N +   E L  EGL++
Sbjct: 96  GIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKI 155

Query: 516 HARSATTDDKLSE 528
              S   +DK+ E
Sbjct: 156 IILSGDKEDKVKE 168


  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
   0.315    0.132    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,388,084
Number of Sequences: 62578
Number of extensions: 552467
Number of successful extensions: 1357
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: 1353
Number of HSP's gapped (non-prelim): 7
length of query: 538
length of database: 14,973,337
effective HSP length: 103
effective length of query: 435
effective length of database: 8,527,803
effective search space: 3709594305
effective search space used: 3709594305
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)