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= 040597
(515 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 36/110 (32%), Positives = 52/110 (47%), Gaps = 22/110 (20%)
Query: 243 FLLLDDVWDGDYNKWEPFFFCVKNGLHGSKILVTTRNESVA-RMMGSTNIIFIEQ-LTEE 300
L+LDDVWD + +K + +IL+TTR++SV +MG +++ +E L E
Sbjct: 239 LLILDDVWDP---------WVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGRE 289
Query: 301 ---ECWSLFKRLAFFDRSFEDYEKLEPIGRKIAHKCKGLPLAAKVIGILL 347
E SLF + E L I +CKG PL +IG LL
Sbjct: 290 KGLEILSLFVNMK--------KEDLPAEAHSIIKECKGSPLVVSLIGALL 331
>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 = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 36/110 (32%), Positives = 51/110 (46%), Gaps = 22/110 (20%)
Query: 243 FLLLDDVWDGDYNKWEPFFFCVKNGLHGSKILVTTRNESVA-RMMGSTNIIFIEQ-LTEE 300
L+LDDVWD + +K +IL+TTR++SV +MG ++ +E L +E
Sbjct: 239 LLILDDVWDS---------WVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKE 289
Query: 301 ---ECWSLFKRLAFFDRSFEDYEKLEPIGRKIAHKCKGLPLAAKVIGILL 347
E SLF + D L I +CKG PL +IG LL
Sbjct: 290 KGLEILSLFVNMKKAD--------LPEQAHSIIKECKGSPLVVSLIGALL 331
>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 = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 36/110 (32%), Positives = 51/110 (46%), Gaps = 22/110 (20%)
Query: 243 FLLLDDVWDGDYNKWEPFFFCVKNGLHGSKILVTTRNESVA-RMMGSTNIIFIEQ-LTEE 300
L+LDDVWD + +K +IL+TTR++SV +MG ++ +E L +E
Sbjct: 245 LLILDDVWDS---------WVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKE 295
Query: 301 ---ECWSLFKRLAFFDRSFEDYEKLEPIGRKIAHKCKGLPLAAKVIGILL 347
E SLF + D L I +CKG PL +IG LL
Sbjct: 296 KGLEILSLFVNMKKAD--------LPEQAHSIIKECKGSPLVVSLIGALL 337
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 35/110 (31%), Positives = 51/110 (46%), Gaps = 22/110 (20%)
Query: 243 FLLLDDVWDGDYNKWEPFFFCVKNGLHGSKILVTTRNESVA-RMMGSTNIIFIEQ-LTEE 300
L+LDDVWD + +K + +IL+TT ++SV +MG +++ +E L E
Sbjct: 246 LLILDDVWDP---------WVLKAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGRE 296
Query: 301 ---ECWSLFKRLAFFDRSFEDYEKLEPIGRKIAHKCKGLPLAAKVIGILL 347
E SLF + E L I +CKG PL +IG LL
Sbjct: 297 KGLEILSLFVNMK--------KEDLPAEAHSIIKECKGSPLVVSLIGALL 338
>pdb|1ZYN|A Chain A, Oxidized Structure Of The N-Terminal Domain Of Salmonella
Typhimurium Ahpf
pdb|1ZYN|B Chain B, Oxidized Structure Of The N-Terminal Domain Of Salmonella
Typhimurium Ahpf
pdb|1ZYP|A Chain A, Synchrotron Reduced Form Of The N-Terminal Domain Of
Salmonella Typhimurium Ahpf
pdb|1ZYP|B Chain B, Synchrotron Reduced Form Of The N-Terminal Domain Of
Salmonella Typhimurium Ahpf
Length = 202
Score = 28.9 bits (63), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 88 DIAVKIREINEKLDDVASQKDRFKFVENLSNNVKKPERVRTTSFIDEGEVFSG 140
D + K EI E L ++A D+ F E+ + V+KP + T +G F+G
Sbjct: 28 DDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAG 80
>pdb|1HYU|A Chain A, Crystal Structure Of Intact Ahpf
Length = 521
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 88 DIAVKIREINEKLDDVASQKDRFKFVENLSNNVKKPERVRTTSFIDEGEVFSG 140
D + K EI E L ++A D+ F E+ + V+KP + T +G F+G
Sbjct: 28 DDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAG 80
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 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,237,663
Number of Sequences: 62578
Number of extensions: 482820
Number of successful extensions: 1273
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1266
Number of HSP's gapped (non-prelim): 12
length of query: 515
length of database: 14,973,337
effective HSP length: 103
effective length of query: 412
effective length of database: 8,527,803
effective search space: 3513454836
effective search space used: 3513454836
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: 54 (25.4 bits)