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= 042891
(423 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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 307 LKEIGEKIVKKCNGLPLVAKSLGGLLRVKYDPNDWE 342
L E I+K+C G PLV +G LLR PN WE
Sbjct: 312 LPEQAHSIIKECKGSPLVVSLIGALLRDF--PNRWE 345
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 40/92 (43%), Gaps = 17/92 (18%)
Query: 257 QIVITTRNLCVVEKTGTLPAY------PLKELSNNDCLSVFTQHSLGEKDFSTHPSLKEI 310
QI++TTR+ V + P Y L + + LS+F + L E
Sbjct: 259 QILLTTRDKSVTDSVMG-PKYVVPVESSLGKEKGLEILSLFVNMKKAD--------LPEQ 309
Query: 311 GEKIVKKCNGLPLVAKSLGGLLRVKYDPNDWE 342
I+K+C G PLV +G LLR PN WE
Sbjct: 310 AHSIIKECKGSPLVVSLIGALLRDF--PNRWE 339
>pdb|1E6Y|C Chain C, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
pdb|1E6Y|F Chain F, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
Length = 247
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 279 LKELSNNDCLSVFTQHSLGEKDFSTHPSLKEIGEKIVKKCNGLPLVAKSLGGLLRVKY 336
L+E+S+ D +V + G STHP L E+GE + + G RV+Y
Sbjct: 28 LREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGEPAXSTRENVAATPGAAAG-DRVRY 84
>pdb|4GP6|A Chain A, Polynucleotide Kinase
pdb|4GP6|B Chain B, Polynucleotide Kinase
Length = 171
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 53/120 (44%), Gaps = 23/120 (19%)
Query: 187 LSVIPIIGMGGIGKTTLAQLVYNDVRVHNHFDLKSWTCVSEDFDIIWVTKSILKSIASDQ 246
LS++ +IG G GK+T A+ HF K +S DF + ++ +DQ
Sbjct: 9 LSLVVLIGSSGSGKSTFAK---------KHF--KPTEVISSDF-----CRGLVSDDENDQ 52
Query: 247 LVDDRDLNLLQIVITTR----NLCVVEKTGTLPAY--PLKELSNN-DCLSVFTQHSLGEK 299
V ++L +++ R L VV+ T + PL E++ + C V +L EK
Sbjct: 53 TVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEK 112
>pdb|1HBM|C Chain C, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBM|F Chain F, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBN|C Chain C, Methyl-Coenzyme M Reductase
pdb|1HBN|F Chain F, Methyl-Coenzyme M Reductase
pdb|1HBO|C Chain C, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBO|F Chain F, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBU|C Chain C, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|1HBU|F Chain F, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|3M1V|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M1V|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
Length = 248
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 257 QIVITTRNLCVVEKTGTLPAYPL---KELSNNDCLSVFTQHSLGEKDFSTHPSLKEIGE 312
++ RN C P Y L +E+S+ D + + + GE+ S HP L+E+ E
Sbjct: 9 KVAQNRRNFCN-------PEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDE 60
>pdb|3POT|C Chain C, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
pdb|3POT|F Chain F, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
Length = 249
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 257 QIVITTRNLCVVEKTGTLPAYPL---KELSNNDCLSVFTQHSLGEKDFSTHPSLKEIGE 312
++ RN C P Y L +E+S+ D + + + GE+ S HP L+E+ E
Sbjct: 10 KVAQNRRNFCN-------PEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDE 61
>pdb|1MRO|C Chain C, Methyl-Coenzyme M Reductase
pdb|1MRO|F Chain F, Methyl-Coenzyme M Reductase
Length = 247
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 257 QIVITTRNLCVVEKTGTLPAYPL---KELSNNDCLSVFTQHSLGEKDFSTHPSLKEIGE 312
++ RN C P Y L +E+S+ D + + + GE+ S HP L+E+ E
Sbjct: 9 KVAQNRRNFCN-------PEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDE 60
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 254 NLLQIVITTRNLCVVEKT-GTLPAYPLKE-LSNNDCLSVFTQHSLGEKDFSTHPSLKEIG 311
N QI++TTR+ V + G P++ L L + + +K+ L
Sbjct: 256 NQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEA 310
Query: 312 EKIVKKCNGLPLVAKSLGGLLRVKYDPNDW 341
I+K+C G PLV +G LLR PN W
Sbjct: 311 HSIIKECKGSPLVVSLIGALLRDF--PNRW 338
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 311 GEKIVKKCNGLPLVAKSLGGLLRVKYDPNDW 341
I+K+C G PLV +G LLR PN W
Sbjct: 317 AHSIIKECKGSPLVVSLIGALLRDF--PNRW 345
>pdb|2YNM|A Chain A, Structure Of The Adpxalf3-stabilized Transition State Of
The Nitrogenase-like Dark-operative Protochlorophyllide
Oxidoreductase Complex From Prochlorococcus Marinus With
Its Substrate Protochlorophyllide A
pdb|2YNM|B Chain B, Structure Of The Adpxalf3-stabilized Transition State Of
The Nitrogenase-like Dark-operative Protochlorophyllide
Oxidoreductase Complex From Prochlorococcus Marinus With
Its Substrate Protochlorophyllide A
Length = 301
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 153 TTSLVNEAKVYGRDKEKEETVELLLSDDLRTDDGLSVIPIIGMGGIGKTT 202
TT+L N + E +V++ L + ++G VI + G GGIGK+T
Sbjct: 7 TTTLANRP-------DGEGSVQVKLDPKVNIEEGALVIAVYGKGGIGKST 49
>pdb|4GP7|A Chain A, Polynucleotide Kinase
pdb|4GP7|B Chain B, Polynucleotide Kinase
Length = 171
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 51/120 (42%), Gaps = 23/120 (19%)
Query: 187 LSVIPIIGMGGIGKTTLAQLVYNDVRVHNHFDLKSWTCVSEDFDIIWVTKSILKSIASDQ 246
LS++ +IG G GK+T A+ HF K +S DF + + +DQ
Sbjct: 9 LSLVVLIGSSGSGKSTFAK---------KHF--KPTEVISSDF-----CRGLXSDDENDQ 52
Query: 247 LVDDRDLNLLQIVITTR----NLCVVEKTGTLPAY--PLKELSNN-DCLSVFTQHSLGEK 299
V ++L +++ R L VV+ T + PL E + + C V +L EK
Sbjct: 53 TVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEXAKDYHCFPVAVVFNLPEK 112
>pdb|1F48|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1IHU|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase In Complex With
Mg-Adp-Alf3
pdb|1II0|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II0|B Chain B, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II9|A Chain A, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
pdb|1II9|B Chain B, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
Length = 589
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 163 YGRDKEKEETVELLLSDDLRTDDGLSVIPIIGMGGIGKTTLAQLV 207
Y + + ++ L+ D R + GL I ++G GG+GKTT+A +
Sbjct: 305 YLQQRPDIPSLSALVDDIARNEHGL--IMLMGKGGVGKTTMAAAI 347
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
0.318 0.134 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,781,532
Number of Sequences: 62578
Number of extensions: 481917
Number of successful extensions: 1356
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1346
Number of HSP's gapped (non-prelim): 22
length of query: 423
length of database: 14,973,337
effective HSP length: 101
effective length of query: 322
effective length of database: 8,652,959
effective search space: 2786252798
effective search space used: 2786252798
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: 53 (25.0 bits)