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= 039283
(600 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 60/232 (25%), Positives = 103/232 (44%), Gaps = 39/232 (16%)
Query: 296 VLDDVWNENYNSWRALSCPFGAGASGSKIVVTHRNQGVAETMRAVSTKTLKE--LSDDDC 353
+LDDVW+ SW A S +I++T R++ V +++ E L +
Sbjct: 241 ILDDVWD----SW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKG 291
Query: 354 LRVLIQHSLGARDFNIPQS-LKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEIVL- 411
L +L + N+ ++ L E A I+K+CKG PL +G LLR D N WE L
Sbjct: 292 LEIL------SLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLR--DFPNRWEYYLK 343
Query: 412 ---NANIWDLQE----DKCDIIPALRVSYHFLPPQLKQCFAYISLFPKDYEFEEEQIILL 464
N +++ D + A+ +S L +K + +S+ KD + + + +L
Sbjct: 344 QLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCIL 403
Query: 465 WTAEGFLDQEYNGRKMEDLGRQFVRELHSRSLFQLSSKDTSRFVMHDLINDL 516
W E ++ED+ ++FV + LF + + R+ +HDL D
Sbjct: 404 WDME--------TEEVEDILQEFVNK---SLLFCDRNGKSFRYYLHDLQVDF 444
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 60/232 (25%), Positives = 103/232 (44%), Gaps = 39/232 (16%)
Query: 296 VLDDVWNENYNSWRALSCPFGAGASGSKIVVTHRNQGVAETMRAVSTKTLKE--LSDDDC 353
+LDDVW+ SW A S +I++T R++ V +++ E L +
Sbjct: 247 ILDDVWD----SW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKG 297
Query: 354 LRVLIQHSLGARDFNIPQS-LKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEIVL- 411
L +L + N+ ++ L E A I+K+CKG PL +G LLR D N WE L
Sbjct: 298 LEIL------SLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLR--DFPNRWEYYLK 349
Query: 412 ---NANIWDLQE----DKCDIIPALRVSYHFLPPQLKQCFAYISLFPKDYEFEEEQIILL 464
N +++ D + A+ +S L +K + +S+ KD + + + +L
Sbjct: 350 QLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCIL 409
Query: 465 WTAEGFLDQEYNGRKMEDLGRQFVRELHSRSLFQLSSKDTSRFVMHDLINDL 516
W E ++ED+ ++FV + LF + + R+ +HDL D
Sbjct: 410 WDME--------TEEVEDILQEFVNK---SLLFCDRNGKSFRYYLHDLQVDF 450
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 67/154 (43%), Gaps = 21/154 (13%)
Query: 371 QSLKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEIVL----NANIWDLQE----DK 422
+ L A I+K+CKG PL +G LLR D N W L N +++ D
Sbjct: 304 EDLPAEAHSIIKECKGSPLVVSLIGALLR--DFPNRWAYYLRQLQNKQFKRIRKSSSYDY 361
Query: 423 CDIIPALRVSYHFLPPQLKQCFAYISLFPKDYEFEEEQIILLWTAEGFLDQEYNGRKMED 482
+ A+ +S L +K + +S+ KD + + + +LW E ++ED
Sbjct: 362 EALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--------TEEVED 413
Query: 483 LGRQFVRELHSRSLFQLSSKDTSRFVMHDLINDL 516
+ ++FV + LF + + + +HDL D
Sbjct: 414 ILQEFVNK---SLLFCNRNGKSFCYYLHDLQVDF 444
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 67/154 (43%), Gaps = 21/154 (13%)
Query: 371 QSLKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEIVL----NANIWDLQE----DK 422
+ L A I+K+CKG PL +G LLR D N W L N +++ D
Sbjct: 311 EDLPAEAHSIIKECKGSPLVVSLIGALLR--DFPNRWAYYLRQLQNKQFKRIRKSSSYDY 368
Query: 423 CDIIPALRVSYHFLPPQLKQCFAYISLFPKDYEFEEEQIILLWTAEGFLDQEYNGRKMED 482
+ A+ +S L +K + +S+ KD + + + +LW E ++ED
Sbjct: 369 EALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--------TEEVED 420
Query: 483 LGRQFVRELHSRSLFQLSSKDTSRFVMHDLINDL 516
+ ++FV + LF + + + +HDL D
Sbjct: 421 ILQEFVNK---SLLFCNRNGKSFCYYLHDLQVDF 451
>pdb|1DLC|A Chain A, Crystal Structure Of Insecticidal Delta-Endotoxin From
Bacillus Thuringiensis At 2.5 Angstroms Resolution
Length = 584
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 40 WKGMLEMIQAVLADAEDRKTKDKAVKKWLDNLQNLAYDAEDVLDELET 87
WK +E ++A++ D+K D A K L LQ L + ED + L +
Sbjct: 46 WKAFMEQVEALM----DQKIADYAKNKALAELQGLQNNVEDYVSALSS 89
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
0.319 0.135 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,016,982
Number of Sequences: 62578
Number of extensions: 619552
Number of successful extensions: 1538
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1533
Number of HSP's gapped (non-prelim): 11
length of query: 600
length of database: 14,973,337
effective HSP length: 104
effective length of query: 496
effective length of database: 8,465,225
effective search space: 4198751600
effective search space used: 4198751600
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)