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= 041692
         (73 letters)

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

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



>pdb|1S3A|A Chain A, Nmr Solution Structure Of Subunit B8 From Human Nadh-
          Ubiquinone Oxidoreductase Complex I (Ci-B8)
          Length = 102

 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 37/55 (67%)

Query: 19 SMKELRILLCQXXXXXXXXXXFVERNYKELKTLNPKLPILIRECSGIEPQLWARY 73
           ++E+RI LCQ          F+E+ Y ELK  NP LPILIRECS ++P+LWARY
Sbjct: 18 GLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARY 72


>pdb|3U60|A Chain A, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
           Clamp, Dna And Atp Analog
          Length = 195

 Score = 26.6 bits (57), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 16/22 (72%)

Query: 44  NYKELKTLNPKLPILIRECSGI 65
           NYK + T N KLP++++E  G+
Sbjct: 139 NYKSILTKNGKLPLVLKELKGL 160


>pdb|3U5Z|A Chain A, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
           Clamp, Primer-Template Dna, And Atp Analog
 pdb|3U5Z|K Chain K, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
           Clamp, Primer-Template Dna, And Atp Analog
 pdb|3U61|A Chain A, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
           Clamp, Dna And Atp Analog And Adp
          Length = 199

 Score = 26.6 bits (57), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 16/22 (72%)

Query: 44  NYKELKTLNPKLPILIRECSGI 65
           NYK + T N KLP++++E  G+
Sbjct: 139 NYKSILTKNGKLPLVLKELKGL 160


  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
   0.322    0.135    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,709,315
Number of Sequences: 62578
Number of extensions: 38723
Number of successful extensions: 82
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 79
Number of HSP's gapped (non-prelim): 3
length of query: 73
length of database: 14,973,337
effective HSP length: 43
effective length of query: 30
effective length of database: 12,282,483
effective search space: 368474490
effective search space used: 368474490
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: 45 (21.9 bits)