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= 039430
(308 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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 54/192 (28%), Positives = 88/192 (45%), Gaps = 36/192 (18%)
Query: 52 RYLLVMDYVWNEDLEAWRKFKSLLLGGANGSKILVTTRSRKVA-SIMGTK-----GGSTG 105
R LL++D VW ++W +L + +IL+TTR + V S+MG K S G
Sbjct: 243 RSLLILDDVW----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 293
Query: 106 YNLQGLPFEDCLSLFMKCACKEERDKHPNLIKIAKEIVKKCGGILLAVKTLGSLLYDSTD 165
+GL + LSLF+ K +L + A I+K+C G L V +G+LL D +
Sbjct: 294 KE-KGL---EILSLFVNM-------KKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN 342
Query: 166 EHFWEY----VRDNEIWRLEQKES----GILPALRLSYDQLPPHLKQCVAYCSIFPKDFE 217
WEY +++ + R+ + S + A+ +S + L +K SI KD +
Sbjct: 343 R--WEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVK 400
Query: 218 FDSYSLLFYFKM 229
+ L + M
Sbjct: 401 VPTKVLCILWDM 412
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 54/192 (28%), Positives = 88/192 (45%), Gaps = 36/192 (18%)
Query: 52 RYLLVMDYVWNEDLEAWRKFKSLLLGGANGSKILVTTRSRKVA-SIMGTK-----GGSTG 105
R LL++D VW+ +W +L + +IL+TTR + V S+MG K S G
Sbjct: 237 RSLLILDDVWD----SW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 287
Query: 106 YNLQGLPFEDCLSLFMKCACKEERDKHPNLIKIAKEIVKKCGGILLAVKTLGSLLYDSTD 165
+GL + LSLF+ K +L + A I+K+C G L V +G+LL D +
Sbjct: 288 KE-KGL---EILSLFVNM-------KKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN 336
Query: 166 EHFWEY----VRDNEIWRLEQKES----GILPALRLSYDQLPPHLKQCVAYCSIFPKDFE 217
WEY +++ + R+ + S + A+ +S + L +K SI KD +
Sbjct: 337 R--WEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVK 394
Query: 218 FDSYSLLFYFKM 229
+ L + M
Sbjct: 395 VPTKVLCILWDM 406
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 51/178 (28%), Positives = 80/178 (44%), Gaps = 32/178 (17%)
Query: 52 RYLLVMDYVWNEDLEAWRKFKSLLLGGANGSKILVTTRSRKVA-SIMGTKGGSTGYNLQG 110
R LL++D VW + W +L N +IL+TTR + V S+MG K + G
Sbjct: 237 RSLLILDDVW----DPW-----VLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVES--G 285
Query: 111 LPFE---DCLSLFMKCACKEERDKHPNLIKIAKEIVKKCGGILLAVKTLGSLLYDSTDEH 167
L E + LSLF+ K +L A I+K+C G L V +G+LL D +
Sbjct: 286 LGREKGLEILSLFVNM-------KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNR- 337
Query: 168 FWEY----VRDNEIWRLEQKES----GILPALRLSYDQLPPHLKQCVAYCSIFPKDFE 217
W Y +++ + R+ + S + A+ +S + L +K SI KD +
Sbjct: 338 -WAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVK 394
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 78/184 (42%), Gaps = 44/184 (23%)
Query: 52 RYLLVMDYVWNEDLEAWRKFKSLLLGGANGSKILVTTRSRKVA-SIMGTKGGSTGYNLQG 110
R LL++D VW + W +L N +IL+TT + V S+MG K
Sbjct: 244 RSLLILDDVW----DPW-----VLKAFDNQCQILLTTSDKSVTDSVMGPK--------HV 286
Query: 111 LPFE---------DCLSLFMKCACKEERDKHPNLIKIAKEIVKKCGGILLAVKTLGSLLY 161
+P E + LSLF+ K +L A I+K+C G L V +G+LL
Sbjct: 287 VPVESGLGREKGLEILSLFVNM-------KKEDLPAEAHSIIKECKGSPLVVSLIGALLR 339
Query: 162 DSTDEHFWEY----VRDNEIWRLEQKES----GILPALRLSYDQLPPHLKQCVAYCSIFP 213
D + W Y +++ + R+ + S + A+ +S + L +K SI
Sbjct: 340 DFPNR--WAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQ 397
Query: 214 KDFE 217
KD +
Sbjct: 398 KDVK 401
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 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,097,624
Number of Sequences: 62578
Number of extensions: 366955
Number of successful extensions: 904
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 904
Number of HSP's gapped (non-prelim): 12
length of query: 308
length of database: 14,973,337
effective HSP length: 99
effective length of query: 209
effective length of database: 8,778,115
effective search space: 1834626035
effective search space used: 1834626035
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: 51 (24.3 bits)