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= 006687
         (635 letters)

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

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



>pdb|3SKX|A Chain A, Crystal Structure Of The Atp Binding Domain Of
           Archaeoglobus Fulgidus Copb
          Length = 280

 Score = 29.3 bits (64), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 5/122 (4%)

Query: 67  PDSGVMQENSTRSLYGINTVGIIRAPRGDGKEAIVLVTPYNAVKGGVRETLSLGIAYSVF 126
           P +  + E + +  +G+  V   RA  G G E IV    Y  V  G    L +    SV 
Sbjct: 58  PIAAAIVEEAEKRGFGLTEVEEFRAIPGKGVEGIVNGRRYMVVSPGYIRELGIKTDESVE 117

Query: 127 SLLTRVTWLAKDIIWLVADSQYGEYAPVAAWLRDYHTPAFSNLDSLNTETCHV-GNNNFE 185
            L  +     K +++++ + +      +A  +R     A S L ++  +   + G+N F 
Sbjct: 118 KLKQQ----GKTVVFILKNGEVSGVIALADRIRPESREAISKLKAIGIKCMMLTGDNRFV 173

Query: 186 SK 187
           +K
Sbjct: 174 AK 175


  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
   0.321    0.136    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,185,726
Number of Sequences: 62578
Number of extensions: 729755
Number of successful extensions: 1552
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: 1552
Number of HSP's gapped (non-prelim): 3
length of query: 635
length of database: 14,973,337
effective HSP length: 105
effective length of query: 530
effective length of database: 8,402,647
effective search space: 4453402910
effective search space used: 4453402910
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)