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= 009411
(535 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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 50/205 (24%), Positives = 89/205 (43%), Gaps = 9/205 (4%)
Query: 167 NPDVHMIGAYGMAGVGKTMLVKEVAR-QAKADKLFDEVVYAEVSQRPDVKKIQGQIADKL 225
N + + YGMAG GK++L E R + + F V+ + D + ++ +
Sbjct: 144 NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLC 203
Query: 226 GLKFYEESESGRAXXXXXXXXXXXXILVILDDIWTNLDLENVGIPFGVRG----CRVLMT 281
EES S R +L++ + L L++V P+ ++ C++L+T
Sbjct: 204 MRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLT 263
Query: 282 ARSQDVLSSKMDCQNNFLI-GVLNESEARDLFKKLVGDKIENNDLKSLAMNIVKACRGLP 340
R + V S M ++ + L + ++ V K E DL + A +I+K C+G P
Sbjct: 264 TRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE--DLPAEAHSIIKECKGSP 321
Query: 341 IAIVTIARALRNKNTFEWKSALREL 365
+ + I LR+ W LR+L
Sbjct: 322 LVVSLIGALLRDFPN-RWAYYLRQL 345
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 49/205 (23%), Positives = 88/205 (42%), Gaps = 9/205 (4%)
Query: 167 NPDVHMIGAYGMAGVGKTMLVKEVAR-QAKADKLFDEVVYAEVSQRPDVKKIQGQIADKL 225
N + + YGMAG GK++L E R + + F V+ + D + ++ +
Sbjct: 151 NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLC 210
Query: 226 GLKFYEESESGRAXXXXXXXXXXXXILVILDDIWTNLDLENVGIPFGVRG----CRVLMT 281
EES S R +L++ + L L++V P+ ++ C++L+T
Sbjct: 211 MRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLT 270
Query: 282 ARSQDVLSSKMDCQNNFLI-GVLNESEARDLFKKLVGDKIENNDLKSLAMNIVKACRGLP 340
+ V S M ++ + L + ++ V K E DL + A +I+K C+G P
Sbjct: 271 TSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE--DLPAEAHSIIKECKGSP 328
Query: 341 IAIVTIARALRNKNTFEWKSALREL 365
+ + I LR+ W LR+L
Sbjct: 329 LVVSLIGALLRDFPN-RWAYYLRQL 352
>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 = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 48/206 (23%), Positives = 87/206 (42%), Gaps = 23/206 (11%)
Query: 173 IGAYGMAGVGKTMLVKEVAR-QAKADKLFDEVVYAEVSQRPDVKKIQGQIADKLGLKFYE 231
+ +GMAG GK++L E R + + F V+ + D + ++ + +
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 215
Query: 232 ESESGRAXXXXXXXXXXXXI---------LVILDDIWTNLDLENVGIPFGVRGCRVLMTA 282
ES S R I L+ILDD+W + L+ C++L+T
Sbjct: 216 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFD-----SQCQILLTT 270
Query: 283 RSQDVLSSKMDCQNNFLIGV---LNESEARDLFKKLVGDKIENNDLKSLAMNIVKACRGL 339
R + V S M +++ V L + + ++ V ++ DL A +I+K C+G
Sbjct: 271 RDKSVTDSVMG--PKYVVPVESSLGKEKGLEILSLFVN--MKKADLPEQAHSIIKECKGS 326
Query: 340 PIAIVTIARALRNKNTFEWKSALREL 365
P+ + I LR+ W+ L++L
Sbjct: 327 PLVVSLIGALLRDFPN-RWEYYLKQL 351
>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 = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 48/206 (23%), Positives = 87/206 (42%), Gaps = 23/206 (11%)
Query: 173 IGAYGMAGVGKTMLVKEVAR-QAKADKLFDEVVYAEVSQRPDVKKIQGQIADKLGLKFYE 231
+ +GMAG GK++L E R + + F V+ + D + ++ + +
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 209
Query: 232 ESESGRAXXXXXXXXXXXXI---------LVILDDIWTNLDLENVGIPFGVRGCRVLMTA 282
ES S R I L+ILDD+W + L+ C++L+T
Sbjct: 210 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFD-----SQCQILLTT 264
Query: 283 RSQDVLSSKMDCQNNFLIGV---LNESEARDLFKKLVGDKIENNDLKSLAMNIVKACRGL 339
R + V S M +++ V L + + ++ V ++ DL A +I+K C+G
Sbjct: 265 RDKSVTDSVMG--PKYVVPVESSLGKEKGLEILSLFVN--MKKADLPEQAHSIIKECKGS 320
Query: 340 PIAIVTIARALRNKNTFEWKSALREL 365
P+ + I LR+ W+ L++L
Sbjct: 321 PLVVSLIGALLRDFPN-RWEYYLKQL 345
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/21 (66%), Positives = 14/21 (66%)
Query: 176 YGMAGVGKTMLVKEVARQAKA 196
YG G GKTMLVK VA KA
Sbjct: 212 YGPPGTGKTMLVKAVANSTKA 232
>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 176 YGMAGVGKTMLVKEVARQAKADKLFDEVVYAEVSQR 211
YG G GKT+L K VA Q A F +V +E+ Q+
Sbjct: 222 YGAPGTGKTLLAKAVANQTSA--TFLRIVGSELIQK 255
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 10/67 (14%)
Query: 144 SIKGYEAFESRMSTLNDVIN-ALKNPDV-HMIGA--------YGMAGVGKTMLVKEVARQ 193
+ G ++ L +VI LKNP++ +G YG G GKT+L K VA
Sbjct: 179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT 238
Query: 194 AKADKLF 200
A+ +F
Sbjct: 239 IGANFIF 245
>pdb|1XI4|A Chain A, Clathrin D6 Coat
pdb|1XI4|B Chain B, Clathrin D6 Coat
pdb|1XI4|C Chain C, Clathrin D6 Coat
pdb|1XI4|D Chain D, Clathrin D6 Coat
pdb|1XI4|E Chain E, Clathrin D6 Coat
pdb|1XI4|F Chain F, Clathrin D6 Coat
pdb|1XI4|G Chain G, Clathrin D6 Coat
pdb|1XI4|H Chain H, Clathrin D6 Coat
pdb|1XI4|I Chain I, Clathrin D6 Coat
pdb|1XI5|A Chain A, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|B Chain B, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|C Chain C, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|D Chain D, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|E Chain E, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|F Chain F, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|G Chain G, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|H Chain H, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|I Chain I, Clathrin D6 Coat With Auxilin J-Domain
pdb|3IYV|A Chain A, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|B Chain B, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|C Chain C, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|D Chain D, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|E Chain E, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|F Chain F, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|G Chain G, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|H Chain H, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|I Chain I, Clathrin D6 Coat As Full-Length Triskelions
Length = 1630
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 145 IKGYEAFESRMSTLNDVINALKNPDVHMIGAYGMAGVGKTMLVKEVARQAKADKLFD 201
+ +++FE L ++N ++PDVH Y A KT +KEV R + +D
Sbjct: 702 FESFKSFEGLFYFLGSIVNFSQDPDVHF--KYIQAAC-KTGQIKEVERICRESNCYD 755
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
0.317 0.133 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,722,340
Number of Sequences: 62578
Number of extensions: 503058
Number of successful extensions: 1377
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1370
Number of HSP's gapped (non-prelim): 21
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)