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= 043181
         (348 letters)

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

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



>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
          Length = 727

 Score = 29.6 bits (65), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 274 LPSEIGDLKILRYLNFSDAQVETSPESVCKLHNLETLKLQNCNRLQKLFADI 325
           LP+E+G    L+Y  F D  V T P     L NL+ L ++  N L+K F  I
Sbjct: 285 LPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEG-NPLEKQFLKI 335


>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
 pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
 pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
 pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
          Length = 591

 Score = 29.6 bits (65), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 21/98 (21%)

Query: 91  LKEIGEKIVKKCNGLPLASEILGGLLHG---------------------KVDCIDWEDVL 129
           L E    I+K+C G PL   ++G LL                       K    D+E + 
Sbjct: 306 LPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALD 365

Query: 130 NSKAISCHYLLPHLKRCFSYCSIFPEDCKFEEEELILL 167
            + +IS   L   +K  ++  SI  +D K   + L +L
Sbjct: 366 EAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCIL 403


>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
          Length = 1263

 Score = 29.3 bits (64), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 21/98 (21%)

Query: 91  LKEIGEKIVKKCNGLPLASEILGGLLHG---------------------KVDCIDWEDVL 129
           L E    I+K+C G PL   ++G LL                       K    D+E + 
Sbjct: 312 LPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALD 371

Query: 130 NSKAISCHYLLPHLKRCFSYCSIFPEDCKFEEEELILL 167
            + +IS   L   +K  ++  SI  +D K   + L +L
Sbjct: 372 EAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCIL 409


  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
   0.323    0.138    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,133,213
Number of Sequences: 62578
Number of extensions: 399396
Number of successful extensions: 827
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 826
Number of HSP's gapped (non-prelim): 7
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)