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= 002750
(885 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 = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 94/366 (25%), Positives = 163/366 (44%), Gaps = 60/366 (16%)
Query: 207 ISIFGMGGLGKTTLARK-LYHHNDVKHKFACCA-WVSVSQEYRTEDLLMRIIN------- 257
++I+GM G GK+ LA + + H+ ++ F+ WVS+ ++ ++ LLM++ N
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKS-GLLMKLQNLCMRLDQ 208
Query: 258 --SFNIDSPSNLEKMREEDLERCLYQSLQGYSYLVVIDDVWQKETWESLKRAFPDSKNGS 315
SF+ P N+E+ + D R L S L+++DDVW + W + +AF N
Sbjct: 209 EESFSQRLPLNIEEAK--DRLRVLMLRKHPRS-LLILDDVW--DPW--VLKAF---DNQC 258
Query: 316 RVILTTRIREVAERSDERTHAYELPFLRPDESWKLFCEKAFQSFN-----ADEGLEKLGR 370
+++LTTR + V + H P ES L EK + + E L
Sbjct: 259 QILLTTRDKSVTDSVMGPKHVV------PVES-GLGREKGLEILSLFVNMKKEDLPAEAH 311
Query: 371 EMLEKCGGLPLAIVVLGGLLSKKKPQEW----RIVRDHIWRHLRADSIQISHLLD----L 422
++++C G PL + ++G LL + P W R +++ ++ +R S LD +
Sbjct: 312 SIIKECKGSPLVVSLIGALL-RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSI 370
Query: 423 SFNDLSYQLKLCFLYLGIFPEDADINIERLIRLIVAEGFIDQNEDDQVMEDVAKDILNEL 482
S L +K + L I +D + + L L D E+V +DIL E
Sbjct: 371 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW-----------DLETEEV-EDILQEF 418
Query: 483 INRSLIQIGKISWGRIATCRVHDLLRDLAIQKAK-ELNFFH--ICAQANRQTRPLLVSSC 539
+N+SL+ + G+ +HDL D +K + +L H + Q R +P +S
Sbjct: 419 VNKSLLFCNRN--GKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQFQRYYQPHTLSPD 476
Query: 540 RRQAAY 545
+ Y
Sbjct: 477 QEDCMY 482
>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 = 53.1 bits (126), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 94/366 (25%), Positives = 165/366 (45%), Gaps = 60/366 (16%)
Query: 207 ISIFGMGGLGKTTLARK-LYHHNDVKHKF-ACCAWVSVSQEYRTEDLLMRIIN------- 257
++I GM G GK+ LA + + H+ ++ F WVSV ++ ++ LLM++ N
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKS-GLLMKLQNLCTRLDQ 208
Query: 258 --SFNIDSPSNLEKMREEDLERCLYQSLQGYSYLVVIDDVWQKETWESLKRAFPDSKNGS 315
SF+ P N+E+ + D R L S L+++DDVW ++W + +AF DS+
Sbjct: 209 DESFSQRLPLNIEEAK--DRLRILMLRKHPRS-LLILDDVW--DSW--VLKAF-DSQ--C 258
Query: 316 RVILTTRIREVAERSDERTHAYELPFLRPDESWKLFCEKAFQSFNADEGLEKL-----GR 370
+++LTTR + V + ++ P ES L EK + + ++K
Sbjct: 259 QILLTTRDKSVTDS------VMGPKYVVPVES-SLGKEKGLEILSLFVNMKKADLPEQAH 311
Query: 371 EMLEKCGGLPLAIVVLGGLLSKKKPQEW----RIVRDHIWRHLRADSIQISHLLD----L 422
++++C G PL + ++G LL + P W + +++ ++ +R S LD +
Sbjct: 312 SIIKECKGSPLVVSLIGALL-RDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSI 370
Query: 423 SFNDLSYQLKLCFLYLGIFPEDADINIERLIRLIVAEGFIDQNEDDQVMEDVAKDILNEL 482
S L +K + L I +D + + L L D E+V +DIL E
Sbjct: 371 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW-----------DMETEEV-EDILQEF 418
Query: 483 INRSLIQIGKISWGRIATCRVHDLLRDLAIQK-AKELNFFH--ICAQANRQTRPLLVSSC 539
+N+SL+ + G+ +HDL D +K +L H I Q R +P +S
Sbjct: 419 VNKSLLFCDRN--GKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPD 476
Query: 540 RRQAAY 545
+ Y
Sbjct: 477 QEDCMY 482
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 93/366 (25%), Positives = 162/366 (44%), Gaps = 60/366 (16%)
Query: 207 ISIFGMGGLGKTTLARK-LYHHNDVKHKFACCA-WVSVSQEYRTEDLLMRIIN------- 257
++I+GM G GK+ LA + + H+ ++ F+ WVS+ ++ ++ LLM++ N
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKS-GLLMKLQNLCMRLDQ 215
Query: 258 --SFNIDSPSNLEKMREEDLERCLYQSLQGYSYLVVIDDVWQKETWESLKRAFPDSKNGS 315
SF+ P N+E+ + D R L S L+++DDVW + W + +AF N
Sbjct: 216 EESFSQRLPLNIEEAK--DRLRVLMLRKHPRS-LLILDDVW--DPW--VLKAF---DNQC 265
Query: 316 RVILTTRIREVAERSDERTHAYELPFLRPDESWKLFCEKAFQSFN-----ADEGLEKLGR 370
+++LTT + V + H P ES L EK + + E L
Sbjct: 266 QILLTTSDKSVTDSVMGPKHVV------PVES-GLGREKGLEILSLFVNMKKEDLPAEAH 318
Query: 371 EMLEKCGGLPLAIVVLGGLLSKKKPQEW----RIVRDHIWRHLRADSIQISHLLD----L 422
++++C G PL + ++G LL + P W R +++ ++ +R S LD +
Sbjct: 319 SIIKECKGSPLVVSLIGALL-RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSI 377
Query: 423 SFNDLSYQLKLCFLYLGIFPEDADINIERLIRLIVAEGFIDQNEDDQVMEDVAKDILNEL 482
S L +K + L I +D + + L L D E+V +DIL E
Sbjct: 378 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW-----------DLETEEV-EDILQEF 425
Query: 483 INRSLIQIGKISWGRIATCRVHDLLRDLAIQKAK-ELNFFH--ICAQANRQTRPLLVSSC 539
+N+SL+ + G+ +HDL D +K + +L H + Q R +P +S
Sbjct: 426 VNKSLLFCNRN--GKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQFQRYYQPHTLSPD 483
Query: 540 RRQAAY 545
+ Y
Sbjct: 484 QEDCMY 489
>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 = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 97/375 (25%), Positives = 169/375 (45%), Gaps = 62/375 (16%)
Query: 198 LKEDPRRSVISIFGMGGLGKTTLARK-LYHHNDVKHKF-ACCAWVSVSQEYRTEDLLMRI 255
LK +P ++I GM G GK+ LA + + H+ ++ F WVSV ++ ++ LLM++
Sbjct: 149 LKGEP--GWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKS-GLLMKL 205
Query: 256 IN---------SFNIDSPSNLEKMREEDLERCLYQSLQGYSYLVVIDDVWQKETWESLKR 306
N SF+ P N+E+ + D R L S L+++DDVW ++W + +
Sbjct: 206 QNLCTRLDQDESFSQRLPLNIEEAK--DRLRILMLRKHPRS-LLILDDVW--DSW--VLK 258
Query: 307 AFPDSKNGSRVILTTRIREVAERSDERTHAYELPFLRPDESWKLFCEKAFQSFNADEGLE 366
AF DS+ +++LTTR + V + ++ P ES L EK + + ++
Sbjct: 259 AF-DSQ--CQILLTTRDKSVTDS------VMGPKYVVPVES-SLGKEKGLEILSLFVNMK 308
Query: 367 KL-----GREMLEKCGGLPLAIVVLGGLLSKKKPQEW----RIVRDHIWRHLRADSIQIS 417
K ++++C G PL + ++G LL + P W + +++ ++ +R S
Sbjct: 309 KADLPEQAHSIIKECKGSPLVVSLIGALL-RDFPNRWEYYLKQLQNKQFKRIRKSSSYDY 367
Query: 418 HLLD----LSFNDLSYQLKLCFLYLGIFPEDADINIERLIRLIVAEGFIDQNEDDQVMED 473
LD +S L +K + L I +D + + L L D E+
Sbjct: 368 EALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW-----------DMETEE 416
Query: 474 VAKDILNELINRSLIQIGKISWGRIATCRVHDLLRDLAIQK-AKELNFFH--ICAQANRQ 530
V +DIL E +N+SL+ + G+ +HDL D +K +L H I Q R
Sbjct: 417 V-EDILQEFVNKSLLFCDRN--GKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRY 473
Query: 531 TRPLLVSSCRRQAAY 545
+P +S + Y
Sbjct: 474 HQPHTLSPDQEDCMY 488
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/91 (37%), Positives = 45/91 (49%), Gaps = 19/91 (20%)
Query: 602 TGIFSEFPLPVEIGQLIHLKYLRLRNSPIDNLPPSIEKLQRLQTLDLSDTLCGIPTEISK 661
TGI S LP I L +LK L++RNSP+ L P+I L +L+ LDL
Sbjct: 193 TGIRS---LPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGC---------- 239
Query: 662 LTELRHLIGNFSGYLPIENL-----TNLRTL 687
T LR+ F G P++ L +NL TL
Sbjct: 240 -TALRNYPPIFGGRAPLKRLILKDCSNLLTL 269
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 6/84 (7%)
Query: 4 AIVSFVVQKLGDYLIQEAIFLKEVRNEVESLKNTL-GWMQCFVKDAE---EKQDDNPLIR 59
A +S ++ KLG+ L +E K V+ +E L L +K E E+ D +
Sbjct: 1 AAISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQDKL- 59
Query: 60 KWVSEIREIAYDAEDVLDKFLLQV 83
W E+RE++Y EDV+DKFL+QV
Sbjct: 60 -WADEVRELSYVIEDVVDKFLVQV 82
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 33.9 bits (76), Expect = 0.42, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 767 KIEKLPEDIHVILPNLECLSLEDSNLDDDPMPELEKMSNLVILDLSYDSYSGKKLFCTAK 826
+++ LP+ + L NL L+L + L P +K++NL LDLSY+ K
Sbjct: 120 QLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDK 179
Query: 827 GFPRLEILQLLVDELEEWQVEEGAMPRLRGLR 858
+L+ L+L ++L+ V +G RL L+
Sbjct: 180 -LTQLKDLRLYQNQLK--SVPDGVFDRLTSLQ 208
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 32.7 bits (73), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 4/90 (4%)
Query: 608 FPLPVEIGQLIHLKYLRLRNSPIDNLPPSIEKLQRLQTLDLS-DTLCGIPTEISKLTELR 666
F + I + L L L + + LP I+ L L+ LDLS + L +P E+ +L+
Sbjct: 237 FNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLK 296
Query: 667 --HLIGNFSGYLPIENLTNLRTLKYVSVES 694
+ N LP E NL L+++ VE
Sbjct: 297 YFYFFDNMVTTLPWE-FGNLCNLQFLGVEG 325
>pdb|2IUJ|A Chain A, Crystal Structure Of Soybean Lipoxygenase-B
Length = 853
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 234 FACCAWVSVSQEYRTEDLLMRIINSFNIDSPSNLEKMREEDLERC 278
F C +WV S+ Y+T+ + ++P+ L K REE+L+
Sbjct: 139 FICNSWVYNSKHYKTDRIFFANNTYLPSETPAPLVKYREEELKNV 183
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 207 ISIFGMGGLGKTTLARKLYHHNDVKHKFACCAWVSVSQEYRTEDLLM 253
+ ++G G GKT LAR + HH D KF + + Q+Y E M
Sbjct: 185 VILYGPPGTGKTLLARAVAHHTDC--KFIRVSGAELVQKYIGEGSRM 229
>pdb|1Y79|1 Chain 1, Crystal Structure Of The E.Coli Dipeptidyl
Carboxypeptidase Dcp In Complex With A Peptidic
Inhibitor
Length = 680
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 835 QLLVDELEEWQVEEGAMPRLRGLRIPEHLKSR 866
Q+L D+ +W VE+G + R GLR E + SR
Sbjct: 618 QMLADDGYQWFVEQGGLTRENGLRFREAILSR 649
>pdb|4GP6|A Chain A, Polynucleotide Kinase
pdb|4GP6|B Chain B, Polynucleotide Kinase
Length = 171
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 460 GFIDQNEDDQVMEDVAKDILNELINRSLIQIGKISWGRIATCRVHDLLRDLAIQKAKELN 519
G + +E+DQ + A D+L+ ++++ L Q+GK++ + V + R I+ AK+ +
Sbjct: 43 GLVSDDENDQTVTGAAFDVLHYIVSKRL-QLGKLTV--VDATNVQESARKPLIEIAKDYH 99
Query: 520 FFHICAQAN 528
F + N
Sbjct: 100 CFPVAVVFN 108
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 0.138 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,827,563
Number of Sequences: 62578
Number of extensions: 1011918
Number of successful extensions: 2922
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 2889
Number of HSP's gapped (non-prelim): 43
length of query: 885
length of database: 14,973,337
effective HSP length: 107
effective length of query: 778
effective length of database: 8,277,491
effective search space: 6439887998
effective search space used: 6439887998
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)