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= psy5919
         (387 letters)

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

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



>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
          Length = 919

 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 47/184 (25%), Positives = 78/184 (42%), Gaps = 18/184 (9%)

Query: 89  VIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGY-KDS 147
           V+R FG   EG      V G   YLY+P  +            A+  + +N  + Y  ++
Sbjct: 70  VVRFFGVTSEGHSVLCNVTGFKNYLYVPAPNSS---------DANDQEQINKFVHYLNET 120

Query: 148 VQHVF-HISICKKFPMYGYHADER-TFLKILLYEPYHMSKLEDLLLNGAV-FNERFQPYE 204
             H    I +  K  ++GY  D +  F KI +  P+ ++KL      G + FN  F    
Sbjct: 121 FDHAIDSIEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFSNGT 180

Query: 205 S---HIPYILQFCIDYNLYGMSNIEFNMVKFRSDSETSLPKLSHCQLEADVKAESIVVDM 261
           +   +I Y L+  +D  + GMS I     K+      +  ++S CQLE  +   +++   
Sbjct: 181 TTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNN--RVSSCQLEVSINYRNLIAHP 238

Query: 262 AAND 265
           A  D
Sbjct: 239 AEGD 242


  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
   0.325    0.140    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,382,532
Number of Sequences: 62578
Number of extensions: 456967
Number of successful extensions: 1119
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: 1118
Number of HSP's gapped (non-prelim): 4
length of query: 387
length of database: 14,973,337
effective HSP length: 101
effective length of query: 286
effective length of database: 8,652,959
effective search space: 2474746274
effective search space used: 2474746274
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)