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= 000703
         (1342 letters)

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

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



>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 = 35.8 bits (81), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 1/95 (1%)

Query: 726  NGALGVFEVHGRRIRDFRPKWPSSSFISSDGLITAMAYRLPHVVMGDRSGNIRWWDVTTG 785
            NG + ++ V    +             +  G +T + +     ++    G I+WW+V TG
Sbjct: 1154 NGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLISAGGYIKWWNVVTG 1213

Query: 786  HSSQ-FSTHREGIRRIKFSPVVPGDRSRGRIAVLF 819
             SSQ F T+   +++I  SP      +   + +L+
Sbjct: 1214 ESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILY 1248


>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length Murine
            Apaf-1
          Length = 1256

 Score = 34.7 bits (78), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 726  NGALGVFEV-HGRRIRDFRPKWPSSSFISSDGLITAMAYRLPHVVMGDRSGNIRWWDVTT 784
            NG + ++ V  G+ +    P        +  G +T + +      +    G ++WW+V T
Sbjct: 1155 NGEIRIWNVSDGQLLHSCAPISVEEGTATHGGWVTDVCFSPDSKTLVSAGGYLKWWNVAT 1214

Query: 785  GHSSQ-FSTHREGIRRIKFSP 804
            G SSQ F T+   +++I  SP
Sbjct: 1215 GDSSQTFYTNGTNLKKIHVSP 1235


>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
          Length = 1249

 Score = 34.7 bits (78), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 726  NGALGVFEV-HGRRIRDFRPKWPSSSFISSDGLITAMAYRLPHVVMGDRSGNIRWWDVTT 784
            NG + ++ V  G+ +    P        +  G +T + +      +    G ++WW+V T
Sbjct: 1148 NGEIRIWNVSDGQLLHSCAPISVEEGTATHGGWVTDVCFSPDSKTLVSAGGYLKWWNVAT 1207

Query: 785  GHSSQ-FSTHREGIRRIKFSP 804
            G SSQ F T+   +++I  SP
Sbjct: 1208 GDSSQTFYTNGTNLKKIHVSP 1228


>pdb|1VYH|C Chain C, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|D Chain D, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|G Chain G, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|H Chain H, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|K Chain K, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|L Chain L, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|O Chain O, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|P Chain P, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|S Chain S, Paf-Ah Holoenzyme: Lis1ALFA2
 pdb|1VYH|T Chain T, Paf-Ah Holoenzyme: Lis1ALFA2
          Length = 410

 Score = 31.2 bits (69), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 767 HVVMGDRSGNIRWWDVTTGHSSQ-FSTHREGIRRIK 801
           H+V   R   I+ W+V TG+  + F+ HRE +R ++
Sbjct: 206 HIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVR 241


>pdb|1Z9V|A Chain A, Solution Structure Of Mth0776 From Methanobacterium
           Thermoautotrophicum (Strain H)
          Length = 121

 Score = 30.0 bits (66), Expect = 8.9,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 7/82 (8%)

Query: 904 MPLCLPILLPTSHALALQMILQLGVKPSWFNTCSTTIKKRPHLIPGTPSSQKDLRSYMIG 963
           M  CL   L  S    + M      K + F  C+  I+K+   +      +K L + +IG
Sbjct: 21  MTFCLETYLQQSGEYEIHM------KRAGFRECAAMIEKKARRVVHIKPGEKILGARIIG 74

Query: 964 LPPIGDTVVPEMLLKVLEPYRK 985
           +PP+    + E    V+ PY K
Sbjct: 75  IPPV-PIGIDEERSTVMIPYTK 95


  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
   0.318    0.133    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 36,362,029
Number of Sequences: 62578
Number of extensions: 1392725
Number of successful extensions: 3113
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 3094
Number of HSP's gapped (non-prelim): 25
length of query: 1342
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1231
effective length of database: 8,027,179
effective search space: 9881457349
effective search space used: 9881457349
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: 57 (26.6 bits)