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= 036584
(919 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 = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 83/332 (25%), Positives = 147/332 (44%), Gaps = 53/332 (15%)
Query: 229 ISIYGMGGLGKTTLARKLYHNNDVKNKFDYC-----AWVSVSQD------YKIKDLLLRI 277
++IYGM G GK+ LA + ++ + + C WVS+ + K+++L +R+
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSL---LEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRL 206
Query: 278 IK--SFNIMXXXXXXXXXXXXXXXRSLRKSLEAYSYLMVIDDIWHKEDWVSLKSAFPENK 335
+ SF+ LRK + L+++DD+W + WV LK AF
Sbjct: 207 DQEESFS-QRLPLNIEEAKDRLRVLMLRKHPRS---LLILDDVW--DPWV-LK-AFDNQ- 257
Query: 336 IGSRVIITTRIKDVAERSDDRNYVHELRF-LRQDESWQLFCERAFRNSKAEKGLENLGRE 394
++++TTR K V + +V + L +++ ++ F N K E L
Sbjct: 258 --CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEIL--SLFVNMKKED-LPAEAHS 312
Query: 395 MVQKCDGLPLAIVVLGGLLSTKRPQEW----REVRNHIWRHLRNDSIQVSYLLD----LS 446
++++C G PL + ++G LL P W R+++N ++ +R S LD +S
Sbjct: 313 IIKECKGSPLVVSLIGALLR-DFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSIS 371
Query: 447 FNDLSHQLKLCFLYLSLFPEDFVINVEKLIRLLVAEGFIRQDEDRTMEEVAKDILDELIN 506
L +K + LS+ +D + + L L D EEV +DIL E +N
Sbjct: 372 VEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW----------DLETEEV-EDILQEFVN 420
Query: 507 RSLIQVEKRCWGRISTCRVHDLLRDLAIQKAK 538
+SL+ + G+ +HDL D +K +
Sbjct: 421 KSLLFCNRN--GKSFCYYLHDLQVDFLTEKNR 450
>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 = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 82/330 (24%), Positives = 146/330 (44%), Gaps = 53/330 (16%)
Query: 229 ISIYGMGGLGKTTLARKLYHNNDVKNKFDYC-----AWVSVSQD------YKIKDLLLRI 277
++I+GM G GK+ LA + ++ + + C WVSV + K+++L R+
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSL---LEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRL 206
Query: 278 IK--SFNIMXXXXXXXXXXXXXXXRSLRKSLEAYSYLMVIDDIWHKEDWVSLKSAFPENK 335
+ SF+ LRK + L+++DD+W + WV LK AF
Sbjct: 207 DQDESFS-QRLPLNIEEAKDRLRILMLRKHPRS---LLILDDVW--DSWV-LK-AFDSQ- 257
Query: 336 IGSRVIITTRIKDVAERSDDRNYVHELRF-LRQDESWQLFCERAFRNSKAEKGLENLGRE 394
++++TTR K V + YV + L +++ ++ F N K + L
Sbjct: 258 --CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEIL--SLFVNMK-KADLPEQAHS 312
Query: 395 MVQKCDGLPLAIVVLGGLLSTKRPQEW----REVRNHIWRHLRNDSIQVSYLLD----LS 446
++++C G PL + ++G LL P W ++++N ++ +R S LD +S
Sbjct: 313 IIKECKGSPLVVSLIGALLRD-FPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSIS 371
Query: 447 FNDLSHQLKLCFLYLSLFPEDFVINVEKLIRLLVAEGFIRQDEDRTMEEVAKDILDELIN 506
L +K + LS+ +D + + L L D EEV +DIL E +N
Sbjct: 372 VEMLREDIKDYYTDLSILQKDVKVPTKVLCILW----------DMETEEV-EDILQEFVN 420
Query: 507 RSLIQVEKRCWGRISTCRVHDLLRDLAIQK 536
+SL+ ++ G+ +HDL D +K
Sbjct: 421 KSLLFCDRN--GKSFRYYLHDLQVDFLTEK 448
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 82/332 (24%), Positives = 146/332 (43%), Gaps = 53/332 (15%)
Query: 229 ISIYGMGGLGKTTLARKLYHNNDVKNKFDYC-----AWVSVSQD------YKIKDLLLRI 277
++IYGM G GK+ LA + ++ + + C WVS+ + K+++L +R+
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSL---LEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRL 213
Query: 278 IK--SFNIMXXXXXXXXXXXXXXXRSLRKSLEAYSYLMVIDDIWHKEDWVSLKSAFPENK 335
+ SF+ LRK + L+++DD+W + WV LK AF
Sbjct: 214 DQEESFS-QRLPLNIEEAKDRLRVLMLRKHPRS---LLILDDVW--DPWV-LK-AFDNQ- 264
Query: 336 IGSRVIITTRIKDVAERSDDRNYVHELRF-LRQDESWQLFCERAFRNSKAEKGLENLGRE 394
++++TT K V + +V + L +++ ++ F N K E L
Sbjct: 265 --CQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEIL--SLFVNMKKED-LPAEAHS 319
Query: 395 MVQKCDGLPLAIVVLGGLLSTKRPQEW----REVRNHIWRHLRNDSIQVSYLLD----LS 446
++++C G PL + ++G LL P W R+++N ++ +R S LD +S
Sbjct: 320 IIKECKGSPLVVSLIGALLR-DFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSIS 378
Query: 447 FNDLSHQLKLCFLYLSLFPEDFVINVEKLIRLLVAEGFIRQDEDRTMEEVAKDILDELIN 506
L +K + LS+ +D + + L L D EEV +DIL E +N
Sbjct: 379 VEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW----------DLETEEV-EDILQEFVN 427
Query: 507 RSLIQVEKRCWGRISTCRVHDLLRDLAIQKAK 538
+SL+ + G+ +HDL D +K +
Sbjct: 428 KSLLFCNRN--GKSFCYYLHDLQVDFLTEKNR 457
>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 = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 82/330 (24%), Positives = 146/330 (44%), Gaps = 53/330 (16%)
Query: 229 ISIYGMGGLGKTTLARKLYHNNDVKNKFDYC-----AWVSVSQD------YKIKDLLLRI 277
++I+GM G GK+ LA + ++ + + C WVSV + K+++L R+
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSL---LEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRL 212
Query: 278 IK--SFNIMXXXXXXXXXXXXXXXRSLRKSLEAYSYLMVIDDIWHKEDWVSLKSAFPENK 335
+ SF+ LRK + L+++DD+W + WV LK AF
Sbjct: 213 DQDESFS-QRLPLNIEEAKDRLRILMLRKHPRS---LLILDDVW--DSWV-LK-AFDSQ- 263
Query: 336 IGSRVIITTRIKDVAERSDDRNYVHELRF-LRQDESWQLFCERAFRNSKAEKGLENLGRE 394
++++TTR K V + YV + L +++ ++ F N K + L
Sbjct: 264 --CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEIL--SLFVNMK-KADLPEQAHS 318
Query: 395 MVQKCDGLPLAIVVLGGLLSTKRPQEW----REVRNHIWRHLRNDSIQVSYLLD----LS 446
++++C G PL + ++G LL P W ++++N ++ +R S LD +S
Sbjct: 319 IIKECKGSPLVVSLIGALLR-DFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSIS 377
Query: 447 FNDLSHQLKLCFLYLSLFPEDFVINVEKLIRLLVAEGFIRQDEDRTMEEVAKDILDELIN 506
L +K + LS+ +D + + L L D EEV +DIL E +N
Sbjct: 378 VEMLREDIKDYYTDLSILQKDVKVPTKVLCILW----------DMETEEV-EDILQEFVN 426
Query: 507 RSLIQVEKRCWGRISTCRVHDLLRDLAIQK 536
+SL+ ++ G+ +HDL D +K
Sbjct: 427 KSLLFCDRN--GKSFRYYLHDLQVDFLTEK 454
>pdb|3QFL|A Chain A, Coiled-Coil Domain-Dependent Homodimerization Of
Intracellular Mla Immune Receptors Defines A Minimal
Functional Module For Triggering Cell Death
Length = 115
Score = 47.0 bits (110), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 50/85 (58%), Gaps = 2/85 (2%)
Query: 4 AVVSYVVETLGDYLIQEVNFLQGVRDEVESLKKELEWMQ-SFIKDAEA-KQAGNNLIRRW 61
A +S ++ LG+ L +E +GV+ +E L KELE + IK E ++ ++ + W
Sbjct: 1 AAISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQDKLW 60
Query: 62 VSDIRDIAYDAEDVLGKYMLSVHGV 86
++R+++Y EDV+ K+++ V G+
Sbjct: 61 ADEVRELSYVIEDVVDKFLVQVDGI 85
>pdb|4FHO|A Chain A, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
pdb|4FHO|B Chain B, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
Length = 231
Score = 33.5 bits (75), Expect = 0.51, Method: Composition-based stats.
Identities = 45/180 (25%), Positives = 79/180 (43%), Gaps = 19/180 (10%)
Query: 619 EADLDRESTLMHWSNRLS--EKIGDLIHLKYLGLRNSNIGILPSSIVKLQRLQTLDFSGD 676
+ADLD +TL ++ ++ E I L +L L L+++ I L + + L ++ L+ SG+
Sbjct: 43 QADLDGIATLSAFNTGVTTIEGIQYLNNLIGLELKDNQITDL-TPLKNLTKITELELSGN 101
Query: 677 VGCPVELPIEINMMQELRHL---IGNFKGTLPIENLTNLQTLKYVQSKSWNKVNTAKLVN 733
P++ I +Q ++ L P+ L+NLQ L ++ N A L N
Sbjct: 102 ---PLKNVSAIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVLYLDLNQITNISPLAGLTN 158
Query: 734 LRDLHIXXXXXXXXXXTVFSFESIAKLKNLRFLSVKLLDANSFASLQPLSHCQCLVDLRL 793
L+ L I + L NL L+ D N + + PL+ L+++ L
Sbjct: 159 LQYLSIGNN----------QVNDLTPLANLSKLTTLRADDNKISDISPLASLPNLIEVHL 208
>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 = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 223 EQRRLVISIYGMGGLGKTTLARKL 246
E+ LVI++YG GG+GK+T + L
Sbjct: 31 EEGALVIAVYGKGGIGKSTTSSNL 54
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 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,364,667
Number of Sequences: 62578
Number of extensions: 998982
Number of successful extensions: 2542
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2529
Number of HSP's gapped (non-prelim): 16
length of query: 919
length of database: 14,973,337
effective HSP length: 108
effective length of query: 811
effective length of database: 8,214,913
effective search space: 6662294443
effective search space used: 6662294443
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)