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= 008685
(557 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana
Length = 176
Score = 125 bits (315), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 72/159 (45%), Positives = 97/159 (61%), Gaps = 5/159 (3%)
Query: 4 FLSFRGEDTRDNFASHLFSALSQKSIETFIDD-QLNRGDEISESLMNAIEASAISLIIFS 62
FLSFRG DTR NF S L+ L ++SI TF DD +L G S L + IE S ++++ S
Sbjct: 12 FLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVS 71
Query: 63 EGYASSRWCLDELLKILDCRKEYAQIVIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKEN 122
E YA+S WCLDEL+ I+D K+ + V+P+FY V+P+ VR QTG + F K R E+
Sbjct: 72 ENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASR--ED 129
Query: 123 SVKLQTWRNALREAASLSGFHSLNIRPESKLVKEVVNHI 161
K+ WR AL A LSG S + +SKLV ++ N I
Sbjct: 130 PEKVLKWRQALTNFAQLSGDCSGD--DDSKLVDKIANEI 166
>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
pdb|3OZI|B Chain B, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
Length = 204
Score = 122 bits (306), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 63/142 (44%), Positives = 93/142 (65%), Gaps = 4/142 (2%)
Query: 4 FLSFRGEDTRDNFASHLFSALSQKSIETF-IDDQLNRGDEISESLMNAIEASAISLIIFS 62
FLSFRG DTR+ F L+ +L + I TF DD+L +G EI +L+ AI+ S I + I S
Sbjct: 39 FLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIIS 98
Query: 63 EGYASSRWCLDELLKILDCRKEYA-QIVIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKE 121
GYA S+WCL EL +I+ ++E +I++P+FY VDPSDVR+QTG + +F K +F
Sbjct: 99 SGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANKFDG 158
Query: 122 NSVKLQTWRNALREAASLSGFH 143
++ Q W++AL++ L G+H
Sbjct: 159 QTI--QNWKDALKKVGDLKGWH 178
>pdb|3H16|A Chain A, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|B Chain B, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|C Chain C, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|D Chain D, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
Length = 154
Score = 36.6 bits (83), Expect = 0.041, Method: Composition-based stats.
Identities = 24/111 (21%), Positives = 46/111 (41%), Gaps = 2/111 (1%)
Query: 4 FLSFRGEDTRDNFASHLFSALSQKSIETFIDD-QLNRGDEISESLMNAIEASAISLIIFS 62
F+S ED D F L L E + DD L GD + S+ + +S +++ S
Sbjct: 24 FISHAWEDKAD-FVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLS 82
Query: 63 EGYASSRWCLDELLKILDCRKEYAQIVIPVFYRVDPSDVRNQTGSFGDSFS 113
+ W EL + ++P++++V +V + + + D +
Sbjct: 83 THFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLA 133
>pdb|3RGW|L Chain L, Crystal Structure At 1.5 A Resolution Of An H2-Reduced,
O2-Tolerant Hydrogenase From Ralstonia Eutropha Unmasks
A Novel Iron-Sulfur Cluster
Length = 603
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%)
Query: 66 ASSRWCLDELLKILDCRKEYAQIVIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKENSVK 125
A+ R L ++I D R E Q V+P + P D + Q G+F S E V+
Sbjct: 527 AAPRGALGHWIRIKDGRIENYQCVVPTTWNGSPRDYKGQIGAFEASLMNTPMVNPEQPVE 586
Query: 126 L 126
+
Sbjct: 587 I 587
>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 = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 75/294 (25%), Positives = 121/294 (41%), Gaps = 61/294 (20%)
Query: 268 LSFRRLSRRKVLIVFDDVSCFNQIESLIGSLDWFTPRSTIIITTRDKQVLRN-WGVKKIY 326
L R+ R L++ DDV +S + L F + I++TTRDK V + G K +
Sbjct: 236 LMLRKHPRS--LLILDDV-----WDSWV--LKAFDSQCQILLTTRDKSVTDSVMGPKYVV 286
Query: 327 EME-ALEYDHALELFSRHAFKQIHPAVGYEELSSKVMEYAQGVPLALKVLGCFL--FGRE 383
+E +L + LE+ S F + A E+ S + E +G PL + ++G L F
Sbjct: 287 PVESSLGKEKGLEILS--LFVNMKKADLPEQAHSIIKE-CKGSPLVVSLIGALLRDFPNR 343
Query: 384 KEVWKSA--------INKLKSILHPSIQEILKISYDGLDDKEKNIFLDVACFFKGEDVYS 435
E + I K S + ++ E + IS + L + K+ + D++ K DV
Sbjct: 344 WEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQK--DVKV 401
Query: 436 VMKFL----DASGFYPEIGISVLVDKSLIVISNND---RITMHDL------------LQE 476
K L D E + V+KSL+ N R +HDL LQ+
Sbjct: 402 PTKVLCILWDMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQD 461
Query: 477 LGRDIVLQ-------ESVNPGNRSRLWHHEDIYGVLTYNMVSI-----LLGLLF 518
L + I+ Q +++P ++ Y L Y+M S L L+F
Sbjct: 462 LHKKIITQFQRYHQPHTLSPDQEDCMY----WYNFLAYHMASAKMHKELCALMF 511
>pdb|3F0W|A Chain A, Human Numb-Like Protein, Phosphotyrosine Interaction
Domain
Length = 168
Score = 33.1 bits (74), Expect = 0.43, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 382 REKEVWKSAINKLKSILHPSIQEILKISYDGL---DDKEKNIFLD 423
R V + A+ KLK++ S++ +L +S DGL DDK K++ +D
Sbjct: 58 RGMHVCEDAVKKLKAMGRKSVKSVLWVSADGLRVVDDKTKDLLVD 102
>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 = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 64/252 (25%), Positives = 104/252 (41%), Gaps = 47/252 (18%)
Query: 298 LDWFTPRSTIIITTRDKQVLRN-WGVKKIYEME-ALEYDHALELFSRHAFKQIHPAVGYE 355
L F + I++TTRDK V + G K + +E +L + LE+ S F + A E
Sbjct: 251 LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILS--LFVNMKKADLPE 308
Query: 356 ELSSKVMEYAQGVPLALKVLGCFL--FGREKEVWKSA--------INKLKSILHPSIQEI 405
+ S + E +G PL + ++G L F E + I K S + ++ E
Sbjct: 309 QAHSIIKE-CKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA 367
Query: 406 LKISYDGLDDKEKNIFLDVACFFKGEDVYSVMKFL----DASGFYPEIGISVLVDKSLIV 461
+ IS + L + K+ + D++ K DV K L D E + V+KSL+
Sbjct: 368 MSISVEMLREDIKDYYTDLSILQK--DVKVPTKVLCILWDMETEEVEDILQEFVNKSLLF 425
Query: 462 ISNND---RITMHDL------------LQELGRDIVLQ-------ESVNPGNRSRLWHHE 499
N R +HDL LQ+L + I+ Q +++P ++
Sbjct: 426 CDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDCMY--- 482
Query: 500 DIYGVLTYNMVS 511
Y L Y+M S
Sbjct: 483 -WYNFLAYHMAS 493
>pdb|1Z05|A Chain A, Crystal Structure Of The Rok Family Transcriptional
Regulator, Homolog Of E.Coli Mlc Protein
Length = 429
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 13/56 (23%)
Query: 365 AQGVPLALKV---LGCFL----------FGREKEVWKSAINKLKSILHPSIQEILK 407
A G PLA+ V LG +L F EK + IN+ KSIL+PSI++ ++
Sbjct: 328 ADGDPLAVDVIQQLGRYLGAAIAIVINLFNPEKILIGGVINQAKSILYPSIEQCIR 383
>pdb|2J67|A Chain A, The Tir Domain Of Human Toll-Like Receptor 10 (Tlr10)
pdb|2J67|B Chain B, The Tir Domain Of Human Toll-Like Receptor 10 (Tlr10)
Length = 178
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 34 DDQLNRGDEISESLMNAIEASAISLIIFSEGYASSRWCLDEL 75
+ + G ISE++++ IE S S+ + S + + WC E
Sbjct: 71 ESYFDPGKSISENIVSFIEKSYKSIFVLSPNFVQNEWCHYEF 112
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
0.322 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,799,795
Number of Sequences: 62578
Number of extensions: 573543
Number of successful extensions: 1549
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1539
Number of HSP's gapped (non-prelim): 15
length of query: 557
length of database: 14,973,337
effective HSP length: 104
effective length of query: 453
effective length of database: 8,465,225
effective search space: 3834746925
effective search space used: 3834746925
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)