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= 041647
         (216 letters)

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

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



>pdb|1Z00|A Chain A, Solution Structure Of The C-Terminal Domain Of Ercc1
           Complexed With The C-Terminal Domain Of Xpf
          Length = 89

 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 25/38 (65%)

Query: 71  SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPV 108
           SL  ++ AS EDLA CPG+  +K + L+D  HEPF  V
Sbjct: 41  SLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKV 78


>pdb|2A1J|B Chain B, Crystal Structure Of The Complex Between The C-Terminal
           Domains Of Human Xpf And Ercc1
          Length = 91

 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 25/38 (65%)

Query: 71  SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPV 108
           SL  ++ AS EDLA CPG+  +K + L+D  HEPF  V
Sbjct: 54  SLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKV 91


  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    0.359 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,762,566
Number of Sequences: 62578
Number of extensions: 199785
Number of successful extensions: 439
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 435
Number of HSP's gapped (non-prelim): 7
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)