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= 042290
(425 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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 57/230 (24%), Positives = 92/230 (40%), Gaps = 42/230 (18%)
Query: 128 VLDDMWSENYDVRANLCKPFKAGLPGSKIIVTTRNEGVSSMVTTPG----AAHSLGNLLR 183
+LDD+W KA +I++TTR++ V+ V P SLG
Sbjct: 247 ILDDVWDSWV---------LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKG 297
Query: 184 DGCLRIFVQHSLRRTDFVAHQYLSEIGEKIVDRCNGSPLAAKTLGGLLRDKYDPKDWEDV 243
L +FV ++++ D L E I+ C GSPL +G LLRD P WE
Sbjct: 298 LEILSLFV--NMKKAD------LPEQAHSIIKECKGSPLVVSLIGALLRDF--PNRWEYY 347
Query: 244 L----NSKIWDLDE----DKSGIMRALRVSYYYLPSHVKRCFAHCSLLPKGYEFDERQIV 295
L N + + + D + A+ +S L +K + S+L K + + +
Sbjct: 348 LKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLC 407
Query: 296 LLWMAEGLLQHKTDGMEMEELGRKSFQVLHSRSFFQRSKIDASRFLMHDL 345
+LW ME EE+ + ++ F + R+ +HDL
Sbjct: 408 ILW-----------DMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDL 446
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 57/230 (24%), Positives = 92/230 (40%), Gaps = 42/230 (18%)
Query: 128 VLDDMWSENYDVRANLCKPFKAGLPGSKIIVTTRNEGVSSMVTTPG----AAHSLGNLLR 183
+LDD+W KA +I++TTR++ V+ V P SLG
Sbjct: 241 ILDDVWDSWV---------LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKG 291
Query: 184 DGCLRIFVQHSLRRTDFVAHQYLSEIGEKIVDRCNGSPLAAKTLGGLLRDKYDPKDWEDV 243
L +FV ++++ D L E I+ C GSPL +G LLRD P WE
Sbjct: 292 LEILSLFV--NMKKAD------LPEQAHSIIKECKGSPLVVSLIGALLRDF--PNRWEYY 341
Query: 244 L----NSKIWDLDE----DKSGIMRALRVSYYYLPSHVKRCFAHCSLLPKGYEFDERQIV 295
L N + + + D + A+ +S L +K + S+L K + + +
Sbjct: 342 LKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLC 401
Query: 296 LLWMAEGLLQHKTDGMEMEELGRKSFQVLHSRSFFQRSKIDASRFLMHDL 345
+LW ME EE+ + ++ F + R+ +HDL
Sbjct: 402 ILW-----------DMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDL 440
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 81/190 (42%), Gaps = 39/190 (20%)
Query: 128 VLDDMWSENYDVRA--NLCKPFKAGLPGSKIIVTTRNEGVSSMVTTPG----AAHSLGNL 181
+LDD+W + + ++A N C+ I++TTR++ V+ V P LG
Sbjct: 241 ILDDVW-DPWVLKAFDNQCQ----------ILLTTRDKSVTDSVMGPKHVVPVESGLGRE 289
Query: 182 LRDGCLRIFVQHSLRRTDFVAHQYLSEIGEKIVDRCNGSPLAAKTLGGLLRD-------- 233
L +FV ++++ D A + I+ C GSPL +G LLRD
Sbjct: 290 KGLEILSLFV--NMKKEDLPAEAH------SIIKECKGSPLVVSLIGALLRDFPNRWAYY 341
Query: 234 --KYDPKDWEDVLNSKIWDLDEDKSGIMRALRVSYYYLPSHVKRCFAHCSLLPKGYEFDE 291
+ K ++ + S +D + + A+ +S L +K + S+L K +
Sbjct: 342 LRQLQNKQFKRIRKSSSYDYE----ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPT 397
Query: 292 RQIVLLWMAE 301
+ + +LW E
Sbjct: 398 KVLCVLWDLE 407
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 80/190 (42%), Gaps = 39/190 (20%)
Query: 128 VLDDMWSENYDVRA--NLCKPFKAGLPGSKIIVTTRNEGVSSMVTTPG----AAHSLGNL 181
+LDD+W + + ++A N C+ I++TT ++ V+ V P LG
Sbjct: 248 ILDDVW-DPWVLKAFDNQCQ----------ILLTTSDKSVTDSVMGPKHVVPVESGLGRE 296
Query: 182 LRDGCLRIFVQHSLRRTDFVAHQYLSEIGEKIVDRCNGSPLAAKTLGGLLRD-------- 233
L +FV ++++ D A + I+ C GSPL +G LLRD
Sbjct: 297 KGLEILSLFV--NMKKEDLPAEAH------SIIKECKGSPLVVSLIGALLRDFPNRWAYY 348
Query: 234 --KYDPKDWEDVLNSKIWDLDEDKSGIMRALRVSYYYLPSHVKRCFAHCSLLPKGYEFDE 291
+ K ++ + S +D + + A+ +S L +K + S+L K +
Sbjct: 349 LRQLQNKQFKRIRKSSSYDYE----ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPT 404
Query: 292 RQIVLLWMAE 301
+ + +LW E
Sbjct: 405 KVLCVLWDLE 414
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
0.322 0.138 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,558,749
Number of Sequences: 62578
Number of extensions: 518192
Number of successful extensions: 1191
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1182
Number of HSP's gapped (non-prelim): 12
length of query: 425
length of database: 14,973,337
effective HSP length: 102
effective length of query: 323
effective length of database: 8,590,381
effective search space: 2774693063
effective search space used: 2774693063
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)