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= 011568
(483 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 = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 82/325 (25%), Positives = 138/325 (42%), Gaps = 52/325 (16%)
Query: 166 IGVWGMGGIGKTTIMSNINNKLHEKPNKFND-VIWVTVSQPLD---LIKLQT-----EIA 216
+ ++GM G GK+ + + F+ V WV++ + L+KLQ +
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 209
Query: 217 TALKQSLPENEDKVSRAGRLLRMLKAKEKFVLILDDMWEAFPLEEVGIPEPNEENGCKLV 276
+ Q LP N ++ R+L ML+ + +LILDD+W+ + L+ +N C+++
Sbjct: 210 ESFSQRLPLNIEEAKDRLRVL-MLRKHPRSLLILDDVWDPWVLKAF-------DNQCQIL 261
Query: 277 ITTRSCRVCRSMKCKQ----VEIELLSKK--EALNLFIDKVGSSILQVPTLNEGIINEVV 330
+TTR V S+ + VE L +K E L+LF++ + P II
Sbjct: 262 LTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDL---PAEAHSII---- 314
Query: 331 EECGRLPLAIVTVAASMSGEEEIYEWQNALNELRG----RLRSLNDVDAKVLGR-LEFSY 385
+EC PL + + A + W L +L+ R+R + D + L + S
Sbjct: 315 KECKGSPLVVSLIGALLRDFPN--RWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISV 372
Query: 386 HRLKDEKLRQCFLDCALYPEDFPILKDELIEYWIAEGFIEEVKDVQAKYDRGHTILNRLV 445
L+ E ++ + D ++ +D + L W E EEV+D IL V
Sbjct: 373 EMLR-EDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--TEEVED----------ILQEFV 419
Query: 446 NCCLLESAEDGS--CVKMHDLIRDM 468
N LL +G C +HDL D
Sbjct: 420 NKSLLFCNRNGKSFCYYLHDLQVDF 444
>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 = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 87/375 (23%), Positives = 156/375 (41%), Gaps = 53/375 (14%)
Query: 122 TSYVSDAPSTSGMTLSTTRNLAGKRTGKIVKEIWEDLMGDKVSKIGVWGMGGIGKTTIMS 181
TSYV G+ + K+ +++ L G+ + + GM G GK+ + +
Sbjct: 107 TSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEP-GWVTIHGMAGCGKSVLAA 165
Query: 182 NINNKLHEKPNKF-NDVIWVTVSQPLD---LIKLQT-----EIATALKQSLPENEDKVSR 232
F V WV+V + L+KLQ + + Q LP N ++
Sbjct: 166 EAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKD 225
Query: 233 AGRLLRMLKAKEKFVLILDDMWEAFPLEEVGIPEPNEENGCKLVITTRSCRVCRSMKCKQ 292
R+L ML+ + +LILDD+W+++ L+ ++ C++++TTR V S+ +
Sbjct: 226 RLRIL-MLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSVMGPK 277
Query: 293 ----VEIELLSKK--EALNLFIDKVGSSILQVPTLNEGIINEVVEECGRLPLAIVTVAAS 346
VE L +K E L+LF++ + + + + +++EC PL + + A
Sbjct: 278 YVVPVESSLGKEKGLEILSLFVNMKKADLPEQA-------HSIIKECKGSPLVVSLIGAL 330
Query: 347 MSGEEEIYEWQNALNELRG----RLRSLNDVDAKVLGR-LEFSYHRLKDEKLRQCFLDCA 401
+ W+ L +L+ R+R + D + L + S L+ E ++ + D +
Sbjct: 331 LRDFPN--RWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLR-EDIKDYYTDLS 387
Query: 402 LYPEDFPILKDELIEYWIAEGFIEEVKDVQAKYDRGHTILNRLVNCCLLESAEDGSCVK- 460
+ +D + L W E EEV+D IL VN LL +G +
Sbjct: 388 ILQKDVKVPTKVLCILWDME--TEEVED----------ILQEFVNKSLLFCDRNGKSFRY 435
Query: 461 -MHDLIRDMQGRTPC 474
+HDL D C
Sbjct: 436 YLHDLQVDFLTEKNC 450
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 87/375 (23%), Positives = 156/375 (41%), Gaps = 53/375 (14%)
Query: 122 TSYVSDAPSTSGMTLSTTRNLAGKRTGKIVKEIWEDLMGDKVSKIGVWGMGGIGKTTIMS 181
TSYV G+ + K+ +++ L G+ + + GM G GK+ + +
Sbjct: 113 TSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEP-GWVTIHGMAGCGKSVLAA 171
Query: 182 NINNKLHEKPNKF-NDVIWVTVSQPLD---LIKLQT-----EIATALKQSLPENEDKVSR 232
F V WV+V + L+KLQ + + Q LP N ++
Sbjct: 172 EAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKD 231
Query: 233 AGRLLRMLKAKEKFVLILDDMWEAFPLEEVGIPEPNEENGCKLVITTRSCRVCRSMKCKQ 292
R+L ML+ + +LILDD+W+++ L+ ++ C++++TTR V S+ +
Sbjct: 232 RLRIL-MLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSVMGPK 283
Query: 293 ----VEIELLSKK--EALNLFIDKVGSSILQVPTLNEGIINEVVEECGRLPLAIVTVAAS 346
VE L +K E L+LF++ + + + + +++EC PL + + A
Sbjct: 284 YVVPVESSLGKEKGLEILSLFVNMKKADLPEQA-------HSIIKECKGSPLVVSLIGAL 336
Query: 347 MSGEEEIYEWQNALNELRG----RLRSLNDVDAKVLGR-LEFSYHRLKDEKLRQCFLDCA 401
+ W+ L +L+ R+R + D + L + S L+ E ++ + D +
Sbjct: 337 LRDFPN--RWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLR-EDIKDYYTDLS 393
Query: 402 LYPEDFPILKDELIEYWIAEGFIEEVKDVQAKYDRGHTILNRLVNCCLLESAEDGSCVK- 460
+ +D + L W E EEV+D IL VN LL +G +
Sbjct: 394 ILQKDVKVPTKVLCILWDME--TEEVED----------ILQEFVNKSLLFCDRNGKSFRY 441
Query: 461 -MHDLIRDMQGRTPC 474
+HDL D C
Sbjct: 442 YLHDLQVDFLTEKNC 456
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 81/325 (24%), Positives = 137/325 (42%), Gaps = 52/325 (16%)
Query: 166 IGVWGMGGIGKTTIMSNINNKLHEKPNKFND-VIWVTVSQPLD---LIKLQT-----EIA 216
+ ++GM G GK+ + + F+ V WV++ + L+KLQ +
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 216
Query: 217 TALKQSLPENEDKVSRAGRLLRMLKAKEKFVLILDDMWEAFPLEEVGIPEPNEENGCKLV 276
+ Q LP N ++ R+L ML+ + +LILDD+W+ + L+ +N C+++
Sbjct: 217 ESFSQRLPLNIEEAKDRLRVL-MLRKHPRSLLILDDVWDPWVLKAF-------DNQCQIL 268
Query: 277 ITTRSCRVCRSMKCKQ----VEIELLSKK--EALNLFIDKVGSSILQVPTLNEGIINEVV 330
+TT V S+ + VE L +K E L+LF++ + P II
Sbjct: 269 LTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDL---PAEAHSII---- 321
Query: 331 EECGRLPLAIVTVAASMSGEEEIYEWQNALNELRG----RLRSLNDVDAKVLGR-LEFSY 385
+EC PL + + A + W L +L+ R+R + D + L + S
Sbjct: 322 KECKGSPLVVSLIGALLRDFPN--RWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISV 379
Query: 386 HRLKDEKLRQCFLDCALYPEDFPILKDELIEYWIAEGFIEEVKDVQAKYDRGHTILNRLV 445
L+ E ++ + D ++ +D + L W E EEV+D IL V
Sbjct: 380 EMLR-EDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--TEEVED----------ILQEFV 426
Query: 446 NCCLLESAEDGS--CVKMHDLIRDM 468
N LL +G C +HDL D
Sbjct: 427 NKSLLFCNRNGKSFCYYLHDLQVDF 451
>pdb|3HVE|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Gigaxoninbtb3-Box
Length = 256
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 306 LFIDKVGSSILQVPTLNEGIINEVVEECGRLPLA 339
L++ + SS L+ LNE ++ E+V+EC +PL+
Sbjct: 223 LWVSGLDSSYLREQXLNEPLVREIVKECSNIPLS 256
>pdb|3HVE|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Gigaxoninbtb3-Box
Length = 256
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 306 LFIDKVGSSILQVPTLNEGIINEVVEECGRLPLA 339
L++ + SS L+ LNE ++ E+V+EC +PL+
Sbjct: 223 LWVSGLDSSYLREQXLNEPLVREIVKECSNIPLS 256
>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
Bound To Origin Dna (From S. Solfataricus)
Length = 386
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 52/101 (51%), Gaps = 7/101 (6%)
Query: 161 DKVSKIGVWGMGGIGKTTIMSNINNKLHEK-PNKFNDVIWVTVSQPLDLIKLQTEIATAL 219
+K + I ++G+ G GKT ++ + +KLH+K KF V ++ Q ++ ++ +L
Sbjct: 43 EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHV-YINTRQIDTPYRVLADLLESL 101
Query: 220 KQSLPENEDKVSRAGRLLRMLKAKEKF---VLILDDMWEAF 257
+P ++ R R++KA + V+I+ D +AF
Sbjct: 102 DVKVPFTGLSIAELYR--RLVKAVRDYGSQVVIVLDEIDAF 140
>pdb|1CP2|A Chain A, Nitrogenase Iron Protein From Clostridium Pasteurianum
pdb|1CP2|B Chain B, Nitrogenase Iron Protein From Clostridium Pasteurianum
Length = 269
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 165 KIGVWGMGGIGKTTIMSNINNKLH 188
++ ++G GGIGK+T N+ + LH
Sbjct: 3 QVAIYGKGGIGKSTTTQNLTSGLH 26
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 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,822,161
Number of Sequences: 62578
Number of extensions: 555718
Number of successful extensions: 1953
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1945
Number of HSP's gapped (non-prelim): 15
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
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)