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= 043779
(581 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 = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 82/361 (22%), Positives = 154/361 (42%), Gaps = 54/361 (14%)
Query: 151 GSVVAQPEVY-GREEDKEKIVERLVKDVAGSDDISIYPIVGMGGLGKTTLA-QLVFNDDR 208
G V +P V+ R++ I ++L K ++I+ GM G GK+ LA + V +
Sbjct: 117 GGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIH---GMAGCGKSVLAAEAVRDHSL 173
Query: 209 IKRHFEFRI-WVFVFED------FNVRRLMTDIITSSGGNVSEAWNLDLLQRRLKDMLDG 261
++ F + WV V + ++ L T + + N++ + RL+ ++
Sbjct: 174 LEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLR 233
Query: 262 K--RYLLVLDDVWNEDQEKWDQLKCTLTCGSKGSSVVVTTRLAKVA-SIVGTLPVYRL-- 316
K R LL+LDDVW+ W L +++TTR V S++G P Y +
Sbjct: 234 KHPRSLLILDDVWDS----W-----VLKAFDSQCQILLTTRDKSVTDSVMG--PKYVVPV 282
Query: 317 -SDLSEDDCWLLFKQRAFGNDTEPPMNILAIAKEIVKKCKGVPLAAKTLGSLMHFKSNEN 375
S L ++ + + P A I+K+CKG PL +G+L+ N
Sbjct: 283 ESSLGKEKGLEILSLFVNMKKADLPEQ----AHSIIKECKGSPLVVSLIGALLRDFPNRW 338
Query: 376 EWL--HVKDSELWNLPQEEN----SILPALRLSYANLPVELRQCFAFCAVFPKNAEIKKE 429
E+ +++ + + + + ++ A+ +S L +++ + ++ K+ ++ +
Sbjct: 339 EYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTK 398
Query: 430 RLIHLWMANGFISSKGSLEAEAVGNEIFNELYWRSLIQDFAGDNGSTYNQIYKMHDLVHD 489
L LW +E E V +I E +SL+ F NG ++ Y +HDL D
Sbjct: 399 VLCILW----------DMETEEV-EDILQEFVNKSLL--FCDRNGKSFR--YYLHDLQVD 443
Query: 490 L 490
Sbjct: 444 F 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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 82/361 (22%), Positives = 154/361 (42%), Gaps = 54/361 (14%)
Query: 151 GSVVAQPEVY-GREEDKEKIVERLVKDVAGSDDISIYPIVGMGGLGKTTLA-QLVFNDDR 208
G V +P V+ R++ I ++L K ++I+ GM G GK+ LA + V +
Sbjct: 123 GGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIH---GMAGCGKSVLAAEAVRDHSL 179
Query: 209 IKRHFEFRI-WVFVFED------FNVRRLMTDIITSSGGNVSEAWNLDLLQRRLKDMLDG 261
++ F + WV V + ++ L T + + N++ + RL+ ++
Sbjct: 180 LEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLR 239
Query: 262 K--RYLLVLDDVWNEDQEKWDQLKCTLTCGSKGSSVVVTTRLAKVA-SIVGTLPVYRL-- 316
K R LL+LDDVW + W L +++TTR V S++G P Y +
Sbjct: 240 KHPRSLLILDDVW----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMG--PKYVVPV 288
Query: 317 -SDLSEDDCWLLFKQRAFGNDTEPPMNILAIAKEIVKKCKGVPLAAKTLGSLMHFKSNEN 375
S L ++ + + P A I+K+CKG PL +G+L+ N
Sbjct: 289 ESSLGKEKGLEILSLFVNMKKADLPEQ----AHSIIKECKGSPLVVSLIGALLRDFPNRW 344
Query: 376 EWL--HVKDSELWNLPQEEN----SILPALRLSYANLPVELRQCFAFCAVFPKNAEIKKE 429
E+ +++ + + + + ++ A+ +S L +++ + ++ K+ ++ +
Sbjct: 345 EYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTK 404
Query: 430 RLIHLWMANGFISSKGSLEAEAVGNEIFNELYWRSLIQDFAGDNGSTYNQIYKMHDLVHD 489
L LW +E E V +I E +SL+ F NG ++ Y +HDL D
Sbjct: 405 VLCILW----------DMETEEV-EDILQEFVNKSLL--FCDRNGKSFR--YYLHDLQVD 449
Query: 490 L 490
Sbjct: 450 F 450
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 81/361 (22%), Positives = 153/361 (42%), Gaps = 54/361 (14%)
Query: 151 GSVVAQPEVY-GREEDKEKIVERLVKDVAGSDDISIYPIVGMGGLGKTTLA-QLVFNDDR 208
G V +P ++ R++ I ++L K ++IY GM G GK+ LA + V +
Sbjct: 117 GGVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIY---GMAGCGKSVLAAEAVRDHSL 173
Query: 209 IKRHFEFRI-WVFVFED------FNVRRLMTDIITSSGGNVSEAWNLDLLQRRLKDMLDG 261
++ F + WV + + ++ L + + N++ + RL+ ++
Sbjct: 174 LEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLR 233
Query: 262 K--RYLLVLDDVWNEDQEKWDQLKCTLTCGSKGSSVVVTTRLAKVA-SIVGTLPVYRL-S 317
K R LL+LDDVW + W L +++TTR V S++G V + S
Sbjct: 234 KHPRSLLILDDVW----DPW-----VLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVES 284
Query: 318 DLSEDDCWLLFKQRAFGNDTEPPMNILAIAKEIVKKCKGVPLAAKTLGSLMHFKSNENEW 377
L + + + P A A I+K+CKG PL +G+L+ + N W
Sbjct: 285 GLGREKGLEILSLFVNMKKEDLP----AEAHSIIKECKGSPLVVSLIGALL--RDFPNRW 338
Query: 378 LH----VKDSELWNLPQEEN----SILPALRLSYANLPVELRQCFAFCAVFPKNAEIKKE 429
+ +++ + + + + ++ A+ +S L +++ + ++ K+ ++ +
Sbjct: 339 AYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTK 398
Query: 430 RLIHLWMANGFISSKGSLEAEAVGNEIFNELYWRSLIQDFAGDNGSTYNQIYKMHDLVHD 489
L LW LE E V +I E +SL+ F NG ++ Y +HDL D
Sbjct: 399 VLCVLW----------DLETEEV-EDILQEFVNKSLL--FCNRNGKSF--CYYLHDLQVD 443
Query: 490 L 490
Sbjct: 444 F 444
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 82/367 (22%), Positives = 154/367 (41%), Gaps = 66/367 (17%)
Query: 151 GSVVAQPEVY-GREEDKEKIVERLVKDVAGSDDISIYPIVGMGGLGKTTLA-QLVFNDDR 208
G V +P ++ R++ I ++L K ++IY GM G GK+ LA + V +
Sbjct: 124 GGVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIY---GMAGCGKSVLAAEAVRDHSL 180
Query: 209 IKRHFEFRI-WVFVFED------FNVRRLMTDIITSSGGNVSEAWNLDLLQRRLKDMLDG 261
++ F + WV + + ++ L + + N++ + RL+ ++
Sbjct: 181 LEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLR 240
Query: 262 K--RYLLVLDDVWNEDQEKW------DQLKCTLTCGSKG--SSVVVTTRLAKVASIVGTL 311
K R LL+LDDVW + W +Q + LT K SV+ + V S +G
Sbjct: 241 KHPRSLLILDDVW----DPWVLKAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGRE 296
Query: 312 PVYRLSDLSEDDCWLLFKQRAFGNDTEPPMNILAIAKEIVKKCKGVPLAAKTLGSLMHFK 371
+ L F N + ++ A A I+K+CKG PL +G+L+ +
Sbjct: 297 KGLEILSL-------------FVNMKKE--DLPAEAHSIIKECKGSPLVVSLIGALL--R 339
Query: 372 SNENEWLH----VKDSELWNLPQEEN----SILPALRLSYANLPVELRQCFAFCAVFPKN 423
N W + +++ + + + + ++ A+ +S L +++ + ++ K+
Sbjct: 340 DFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKD 399
Query: 424 AEIKKERLIHLWMANGFISSKGSLEAEAVGNEIFNELYWRSLIQDFAGDNGSTYNQIYKM 483
++ + L LW LE E V +I E +SL+ F NG ++ Y +
Sbjct: 400 VKVPTKVLCVLW----------DLETEEV-EDILQEFVNKSLL--FCNRNGKSF--CYYL 444
Query: 484 HDLVHDL 490
HDL D
Sbjct: 445 HDLQVDF 451
>pdb|2A5Y|B Chain B, Structure Of A Ced-4CED-9 Complex
pdb|2A5Y|C Chain C, Structure Of A Ced-4CED-9 Complex
pdb|3LQQ|A Chain A, Structure Of The Ced-4 Apoptosome
pdb|3LQQ|B Chain B, Structure Of The Ced-4 Apoptosome
pdb|3LQR|A Chain A, Structure Of Ced-4:ced-3 Complex
pdb|3LQR|B Chain B, Structure Of Ced-4:ced-3 Complex
Length = 549
Score = 35.4 bits (80), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 72/318 (22%), Positives = 131/318 (41%), Gaps = 62/318 (19%)
Query: 151 GSVVAQPEVYGREEDKEKIVERLVKDVAGSDDISIYPIVGMGGLGKTTLAQ--LVFNDDR 208
G+V Q Y RE ++++++L ++ D ++ + G G GK+ +A L +D
Sbjct: 122 GNVPKQMTCYIREYHVDRVIKKL-DEMCDLDSFFLF-LHGRAGSGKSVIASQALSKSDQL 179
Query: 209 IKRHFEFRIWVFVFEDFNVRR-----LMTDIITS--------SGGNVSEAWNLDLLQRRL 255
I +++ +W+ +D L TDI+ + +V ++ L +
Sbjct: 180 IGINYDSIVWL---KDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMIC 236
Query: 256 KDMLDGKRYLLVLDDVWNEDQEKWDQ---LKCTLTCGSKGSSVVVTTRLAKVASIVG-TL 311
++D L V DDV E+ +W Q L+C +VTTR ++++ T
Sbjct: 237 NALIDRPNTLFVFDDVVQEETIRWAQELRLRC-----------LVTTRDVEISNAASQTC 285
Query: 312 PVYRLSDLSEDDCWLLFKQRAFGNDTEPPMNILAIAKEIVKKCKGVPLAAKTLGSL-MHF 370
++ L D+C+ + A+G PM + ++++ K + L++ +L M F
Sbjct: 286 EFIEVTSLEIDECYDFLE--AYGM----PMPVGEKEEDVLN--KTIELSSGNPATLMMFF 337
Query: 371 KSNENEWLHVKDSELWN-------------LPQEENSILPALRLSYANLPVELRQCFAFC 417
KS E + K ++L N P S+ AL+ L E R AF
Sbjct: 338 KSCEPKTFE-KMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFA 396
Query: 418 AVFPKNAEIKKERLIHLW 435
V P +I + LW
Sbjct: 397 VVMPPGVDIP----VKLW 410
>pdb|1W5S|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
pdb|1W5S|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
pdb|1W5T|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
pdb|1W5T|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
pdb|1W5T|C Chain C, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
Length = 412
Score = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 59/129 (45%), Gaps = 20/129 (15%)
Query: 157 PEVYGREEDKEKI----VERLVKDVAGSDDISIYPIVGMGGLGKTTLAQLVFNDDRIKRH 212
PE+ R + E + + RL+ SD IY +G G+GKTTLA+ +KR
Sbjct: 22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFT-----VKRV 76
Query: 213 FEF---------RIWVFVFEDFNVRRLMTDIITSSGG--NVSEAWNLDLLQRRLKDMLDG 261
E + +V F N+ +++ I+ +G V A LD+L+ + ++
Sbjct: 77 SEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVE 136
Query: 262 KRYLLVLDD 270
YLLV+ D
Sbjct: 137 NHYLLVILD 145
>pdb|3L5Z|A Chain A, Crystal Structure Of Transcriptional Regulator, Gntr
Family From Bacillus Cereus
pdb|3L5Z|B Chain B, Crystal Structure Of Transcriptional Regulator, Gntr
Family From Bacillus Cereus
Length = 156
Score = 32.0 bits (71), Expect = 0.86, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 9/72 (12%)
Query: 8 VVLDNLNSLIKNELGLLHGVEKEMEKLSSTLSTIQAVLEDAEEKQLKDKALQNWLRKLKD 67
V+ +++ S I+N+LGL K+ +++ ++ + D +EKQ + Q++L +++
Sbjct: 70 VLEESIYSYIQNKLGL---------KVGTSVVRVKGIRPDDKEKQFXNLTNQDFLXRVEQ 120
Query: 68 AAYEVDDLLDEY 79
AY D EY
Sbjct: 121 VAYLTDGRTFEY 132
>pdb|3LHE|A Chain A, The Crystal Structure Of The C-Terminal Domain Of A Gntr
Family Transcriptional Regulator From Bacillus Anthracis
Str. Sterne
Length = 143
Score = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 9/74 (12%)
Query: 6 LQVVLDNLNSLIKNELGLLHGVEKEMEKLSSTLSTIQAVLEDAEEKQLKDKALQNWLRKL 65
+ V+ +++ S I+N+LGL ++ +++ ++ + D +EKQ + Q++L ++
Sbjct: 68 VSVLEESIYSHIQNKLGL---------QVGTSVVRVKGIRPDDKEKQFXNLTNQDFLXRV 118
Query: 66 KDAAYEVDDLLDEY 79
+ AY D EY
Sbjct: 119 EQVAYLTDGRTFEY 132
>pdb|2CWJ|A Chain A, Crystal Structure Of Ape1501, A Putative Endonuclease From
Aeropyrum Pernix
Length = 123
Score = 30.0 bits (66), Expect = 4.2, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 45 LEDAEEKQLKDKALQNWLRKLKDAAYEVDDLLD--EYKTEASRLADDNKVHAAYLTCFRP 102
LE+ K+ +AL N ++ A Y +DD++ Y T+ SR ++ N+V+ Y RP
Sbjct: 36 LEEGGFKESAKRALDNLKAIVEGAGYSMDDIVKVTVYITDISRFSEFNEVYREYFN--RP 93
>pdb|4GFP|A Chain A, 2.7 Angstrom Resolution Structure Of 3-Phosphoshikimate 1-
Carboxyvinyltransferase (Aroa) From Coxiella Burnetii In
A Second Conformational State
Length = 462
Score = 28.5 bits (62), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 490 LAQSIAGDECCITKAERPSDHLSRQTRHVTFTLSKDSFTI 529
LA A + CIT+ DH R +H +TL KD +I
Sbjct: 200 LAGLYARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSI 239
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
0.320 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,803,387
Number of Sequences: 62578
Number of extensions: 685095
Number of successful extensions: 2090
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 2077
Number of HSP's gapped (non-prelim): 27
length of query: 581
length of database: 14,973,337
effective HSP length: 104
effective length of query: 477
effective length of database: 8,465,225
effective search space: 4037912325
effective search space used: 4037912325
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)