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= 048809
(878 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 = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 11/100 (11%)
Query: 4 CKVLLTARSHDVLSSKMDCQKNIFVDVLNAKEA----WSLFEKMTGDCIENGELKSVATE 59
C++LLT R V S M + + V+ KE SLF M + +L A
Sbjct: 258 CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHS 312
Query: 60 IVKECAGLPIAILPVAKALKNKSSLYVWKDALRQLKNKSL 99
I+KEC G P+ + + L++ + W+ L+QL+NK
Sbjct: 313 IIKECKGSPLVVSLIGALLRDFPNR--WEYYLKQLQNKQF 350
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 37.7 bits (86), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 11/100 (11%)
Query: 4 CKVLLTARSHDVLSSKMDCQKNIFVDVLNAKEA----WSLFEKMTGDCIENGELKSVATE 59
C++LLT R V S M + + V+ +E SLF M + +L + A
Sbjct: 258 CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEAHS 312
Query: 60 IVKECAGLPIAILPVAKALKNKSSLYVWKDALRQLKNKSL 99
I+KEC G P+ + + L++ + W LRQL+NK
Sbjct: 313 IIKECKGSPLVVSLIGALLRDFPNR--WAYYLRQLQNKQF 350
>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 = 37.7 bits (86), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 11/100 (11%)
Query: 4 CKVLLTARSHDVLSSKMDCQKNIFVDVLNAKEA----WSLFEKMTGDCIENGELKSVATE 59
C++LLT R V S M + + V+ KE SLF M + +L A
Sbjct: 264 CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHS 318
Query: 60 IVKECAGLPIAILPVAKALKNKSSLYVWKDALRQLKNKSL 99
I+KEC G P+ + + L++ + W+ L+QL+NK
Sbjct: 319 IIKECKGSPLVVSLIGALLRDFPNR--WEYYLKQLQNKQF 356
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 46/100 (46%), Gaps = 11/100 (11%)
Query: 4 CKVLLTARSHDVLSSKMDCQKNIFVDVLNAKEA----WSLFEKMTGDCIENGELKSVATE 59
C++LLT V S M + + V+ +E SLF M + +L + A
Sbjct: 265 CQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEAHS 319
Query: 60 IVKECAGLPIAILPVAKALKNKSSLYVWKDALRQLKNKSL 99
I+KEC G P+ + + L++ + W LRQL+NK
Sbjct: 320 IIKECKGSPLVVSLIGALLRDFPNR--WAYYLRQLQNKQF 357
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 34.3 bits (77), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 217 LTSWPDK--DVLKDCTAISLNNSNINELPQGF--ECPQLKYFRIHNDHSLKIPDNFFTGM 272
L S P + D L T +SL + + LP+G + LK R++N+ ++P+ F +
Sbjct: 121 LKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNNQLKRVPEGAFDKL 180
Query: 273 TELRVL 278
TEL+ L
Sbjct: 181 TELKTL 186
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 30.4 bits (67), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 224 DVLKDCTAISLNNSNINELPQGF--ECPQLKYFRIHNDHSLKIPDNFFTGMTEL 275
D L + T + L+N+ + LP+G + QLK ++++ +PD F +T L
Sbjct: 154 DKLTNLTRLDLDNNQLQSLPEGVFDKLTQLKQLSLNDNQLKSVPDGVFDRLTSL 207
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 224 DVLKDCTAISLNNSNINELPQGF--ECPQLKYFRIHNDHSLKIPDNFFTGMTELRVL 278
D L + T + L+ + + LP+G + QLK R++ + +PD F +T L+ +
Sbjct: 154 DKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYI 210
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
0.321 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,389,374
Number of Sequences: 62578
Number of extensions: 901390
Number of successful extensions: 2009
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2006
Number of HSP's gapped (non-prelim): 10
length of query: 878
length of database: 14,973,337
effective HSP length: 107
effective length of query: 771
effective length of database: 8,277,491
effective search space: 6381945561
effective search space used: 6381945561
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: 56 (26.2 bits)