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= 009652
         (529 letters)

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

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



>pdb|3UPU|A Chain A, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
 pdb|3UPU|B Chain B, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
 pdb|3UPU|C Chain C, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
          Length = 459

 Score = 30.8 bits (68), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 1/32 (3%)

Query: 430 SNAPSVMSYAVDVRRGKVGENRVVDAHLLRLF 461
           SNAP ++  A DVR GK   ++VVD H +R F
Sbjct: 199 SNAP-IIDVATDVRNGKWIYDKVVDGHGVRGF 229


>pdb|1IK9|A Chain A, Crystal Structure Of A Xrcc4-Dna Ligase Iv Complex
 pdb|1IK9|B Chain B, Crystal Structure Of A Xrcc4-Dna Ligase Iv Complex
          Length = 213

 Score = 29.6 bits (65), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 29/113 (25%), Positives = 49/113 (43%), Gaps = 19/113 (16%)

Query: 397 LVTSAGSSPVRGLSPSR----------VRNTAMGMNSSNLISVSNAPSVM----SYAVDV 442
           L++ AG + V   + S+          +++ +  + S NL  V N   V+    +YA+D 
Sbjct: 74  LLSGAGPADVYTFNFSKESAYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDT 133

Query: 443 RRGKVGENRVVDAHLLRLFHNRLLQWRFVNARANAALSAQRLNAERSLYNAWI 495
               + EN+  + HL +     L  W  V  R   A+SA+    E  LY  +I
Sbjct: 134 ----IAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKE-ALETDLYKRFI 181


  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
   0.314    0.127    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,803,007
Number of Sequences: 62578
Number of extensions: 352953
Number of successful extensions: 485
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 484
Number of HSP's gapped (non-prelim): 3
length of query: 529
length of database: 14,973,337
effective HSP length: 103
effective length of query: 426
effective length of database: 8,527,803
effective search space: 3632844078
effective search space used: 3632844078
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)