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= 041729
         (744 letters)

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

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



>pdb|1XMJ|A Chain A, Crystal Structure Of Human Deltaf508 Human Nbd1 Domain
           With Atp
          Length = 290

 Score = 29.6 bits (65), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 60/147 (40%), Gaps = 34/147 (23%)

Query: 401 ANELKASLAKW--KPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFL----PCGV 454
           A +L+  ++K+  K N    + G+ L +     + L R      +Y+  D      P G 
Sbjct: 135 ACQLEEDISKFAEKDNIVLGEGGITLSEGQQAKISLAR-----AVYKDADLYLLDSPFGY 189

Query: 455 ENLIVERE-RELQICQNHEEGARLKAIETFHLPDEPLEKTSKA--------------GTL 499
            +++ E+E  E  +C       +L A +T  L    +E   KA              GT 
Sbjct: 190 LDVLTEKEIFESCVC-------KLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTF 242

Query: 500 SEFQNIQSDFGDLKMGNREFELQLEAE 526
           SE QN+Q DF    MG   F+ Q  AE
Sbjct: 243 SELQNLQPDFSSKLMGCDSFD-QFSAE 268


>pdb|2BBO|A Chain A, Human Nbd1 With Phe508
          Length = 291

 Score = 29.6 bits (65), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 60/147 (40%), Gaps = 34/147 (23%)

Query: 401 ANELKASLAKW--KPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFL----PCGV 454
           A +L+  ++K+  K N    + G+ L +     + L R      +Y+  D      P G 
Sbjct: 136 ACQLEEDISKFAEKDNIVLGEGGITLSEGQQAKISLAR-----AVYKDADLYLLDSPFGY 190

Query: 455 ENLIVERE-RELQICQNHEEGARLKAIETFHLPDEPLEKTSKA--------------GTL 499
            +++ E+E  E  +C       +L A +T  L    +E   KA              GT 
Sbjct: 191 LDVLTEKEIFESCVC-------KLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTF 243

Query: 500 SEFQNIQSDFGDLKMGNREFELQLEAE 526
           SE QN+Q DF    MG   F+ Q  AE
Sbjct: 244 SELQNLQPDFSSKLMGCDSFD-QFSAE 269


  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
   0.319    0.137    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,638,575
Number of Sequences: 62578
Number of extensions: 839603
Number of successful extensions: 1772
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1772
Number of HSP's gapped (non-prelim): 5
length of query: 744
length of database: 14,973,337
effective HSP length: 106
effective length of query: 638
effective length of database: 8,340,069
effective search space: 5320964022
effective search space used: 5320964022
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)