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= 017346
         (373 letters)

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

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



>pdb|1XHX|A Chain A, Phi29 Dna Polymerase, Orthorhombic Crystal Form
 pdb|1XHX|B Chain B, Phi29 Dna Polymerase, Orthorhombic Crystal Form
 pdb|1XHX|C Chain C, Phi29 Dna Polymerase, Orthorhombic Crystal Form
 pdb|1XHX|D Chain D, Phi29 Dna Polymerase, Orthorhombic Crystal Form
 pdb|1XHZ|A Chain A, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
           Complex
 pdb|1XHZ|B Chain B, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
           Complex
 pdb|1XHZ|C Chain C, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
           Complex
 pdb|1XHZ|D Chain D, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
           Complex
 pdb|1XI1|A Chain A, Phi29 Dna Polymerase Ssdna Complex, Monoclinic Crystal
           Form
 pdb|1XI1|B Chain B, Phi29 Dna Polymerase Ssdna Complex, Monoclinic Crystal
           Form
 pdb|2EX3|A Chain A, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
           Protein
 pdb|2EX3|C Chain C, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
           Protein
 pdb|2EX3|E Chain E, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
           Protein
 pdb|2EX3|G Chain G, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
           Protein
 pdb|2EX3|I Chain I, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
           Protein
 pdb|2EX3|K Chain K, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
           Protein
 pdb|2PY5|A Chain A, Phi29 Dna Polymerase Complexed With Single-stranded Dna
 pdb|2PY5|B Chain B, Phi29 Dna Polymerase Complexed With Single-stranded Dna
 pdb|2PYJ|A Chain A, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           And Incoming Nucleotide Substrates (Ternary Complex)
 pdb|2PYJ|B Chain B, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           And Incoming Nucleotide Substrates (Ternary Complex)
 pdb|2PYL|A Chain A, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           And Incoming Nucleotide Substrates (Ternary Complex)
 pdb|2PZS|A Chain A, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           (Post-Translocation Binary Complex)
 pdb|2PZS|B Chain B, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           (Post-Translocation Binary Complex)
 pdb|2PZS|C Chain C, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           (Post-Translocation Binary Complex)
 pdb|2PZS|D Chain D, Phi29 Dna Polymerase Complexed With Primer-Template Dna
           (Post-Translocation Binary Complex)
          Length = 575

 Score = 28.5 bits (62), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 4/35 (11%)

Query: 53  AYEGRWVYDESYPLYDSSACPNIRKEFDCNECGRP 87
            +EG++V+DE YPL+      +IR EF+  E   P
Sbjct: 270 VFEGKYVWDEDYPLH----IQHIRCEFELKEGYIP 300


  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    0.139    0.458 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,762,941
Number of Sequences: 62578
Number of extensions: 494163
Number of successful extensions: 967
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 961
Number of HSP's gapped (non-prelim): 8
length of query: 373
length of database: 14,973,337
effective HSP length: 100
effective length of query: 273
effective length of database: 8,715,537
effective search space: 2379341601
effective search space used: 2379341601
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: 52 (24.6 bits)