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= 010367
(512 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4ERN|A Chain A, Crystal Structure Of The C-terminal Domain Of Human
Xpb/ercc-3 Excision Repair Protein At 1.80 A
Length = 289
Score = 324 bits (830), Expect = 8e-89, Method: Compositional matrix adjust.
Identities = 179/312 (57%), Positives = 216/312 (69%), Gaps = 33/312 (10%)
Query: 205 LDLVKGGFIANVQCAEVWCPMTKEFFSEYLKKENSKKKQALYVMNPNKFRACEFLIRFHE 264
++L G+IA VQCAEVWCPM+ EF+ EY+ + +KK+ LY MNPNKFRAC+FLI+FHE
Sbjct: 1 MELQNNGYIAKVQCAEVWCPMSPEFYREYVAIK-TKKRILLYTMNPNKFRACQFLIKFHE 59
Query: 265 QQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHVERTKILQAFKCSRDLNTIFLSKVG 324
+ R DKIIVFADN+FAL EYA++L KP IYG TS ER +ILQ FK + +NTIF+SKVG
Sbjct: 60 R-RNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVG 118
Query: 325 DNSIDIPEANVIIQISSHAGSRRQEAQRLGRILRAKGKLEDRMAGGKEEYNAFFYSLVST 384
D S D+PEANV+IQISSH GSRRQEAQRLGR+LRAK + EEYNAFFYSLVS
Sbjct: 119 DTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGM------VAEEYNAFFYSLVSQ 172
Query: 385 DTQEMFYSTKRQQFLIDQGYSFKVITSLPPPDSGADLSYHRLDEQLALLGKVLSAGDDAV 444
DTQEM YSTKRQ+FL+DQGYSFKVIT L + DL++ +EQ LL KVL+A D
Sbjct: 173 DTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATD--- 228
Query: 445 GLEQLDEDADDIA------LHKARRIAGSMSAMSGAQGMVYMEYSTXXXXXXXXXXXXPK 498
LD + + +A +A R G+MS+MSGA VYMEY + K
Sbjct: 229 ----LDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRS----------K 274
Query: 499 DPSKR-HYLFKR 509
PSK H LFKR
Sbjct: 275 APSKHVHPLFKR 286
>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|B Chain B, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|C Chain C, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|D Chain D, Structure Of Archaeoglobus Fulgidis Xpb
Length = 472
Score = 123 bits (308), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 115/406 (28%), Positives = 183/406 (45%), Gaps = 71/406 (17%)
Query: 27 RPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVSAACRIKKSCLCLATNAVSVDQWAF 86
R YQEK+L + + R G IVLP G+GK+ V ++A + L + +QW
Sbjct: 95 RDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKE 151
Query: 87 QFKLWSTIQDDQICRFTSDSKERFRGNAGVVVTTYNMVAFGGXXXXXXXXXXXXXXXXXW 146
+ ++ ++ + F+ KE + V+TY+ +
Sbjct: 152 RLGIFG---EEYVGEFSGRIKEL----KPLTVSTYDSAYVNAEKLGNR-----------F 193
Query: 147 GLLLMDEVHVVPAHMFRKVISLTKSHCKLGLTATLVREDERITDLNFLIGPKLYEANWLD 206
LL+ DEVH +PA + ++ ++ + +LGLTAT RED R L ++G K++E + D
Sbjct: 194 MLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKVFEL-FPD 252
Query: 207 LVKGGFIANVQCAEVWCPMTKEFFSEYLKKENSKKK----QALYVMNPNKF--------- 253
+ G +A ++ P+ ++ EY K+E K+ + + + F
Sbjct: 253 SLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGY 312
Query: 254 --RACEFL--------IRFH------------EQQRGDKIIVFADNLFALTEYAMKLRKP 291
RA E L I F+ E+ R DKII+F + + + P
Sbjct: 313 DERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFLIP 372
Query: 292 MIYGATSHVERTKILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQ 351
I TS ER +IL+ F+ R I S+V D ID+P+ANV + I S +GS R+ Q
Sbjct: 373 AITHRTSREEREEILEGFRTGR-FRAIVSSQVLDEGIDVPDANVGV-IMSGSGSAREYIQ 430
Query: 352 RLGRILR-AKGKLEDRMAGGKEEYNAFFYSLVSTDTQEMFYSTKRQ 396
RLGRILR +KGK E A Y L+S T E+ + +R+
Sbjct: 431 RLGRILRPSKGKKE-----------AVLYELISRGTGEVNTARRRK 465
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 65.5 bits (158), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 51/136 (37%), Positives = 70/136 (51%), Gaps = 17/136 (12%)
Query: 249 NPNKFRACEFLIRFHEQQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHVERTKILQA 308
+ NK R ++ E+ R DKII+F + + + P I TS ER +IL+
Sbjct: 98 SKNKIRKLREIL---ERHRKDKIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEG 154
Query: 309 FKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGRILR-AKGKLEDRM 367
F+ R I S+V D ID+P+ANV + I S +GS R+ QRLGRILR +KGK E
Sbjct: 155 FRTGR-FRAIVSSQVLDEGIDVPDANVGV-IMSGSGSAREYIQRLGRILRPSKGKKE--- 209
Query: 368 AGGKEEYNAFFYSLVS 383
A Y L+S
Sbjct: 210 --------AVLYELIS 217
>pdb|2FZ4|A Chain A, Crystal Structure Of The N-Terminal Half Of Archaeoglobus
Fulgidus Xpb
Length = 237
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 44/161 (27%), Positives = 74/161 (45%), Gaps = 21/161 (13%)
Query: 27 RPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVSAACRIKKSCLCLATNAVSVDQWAF 86
R YQEK+L + + R G IVLP G+GK+ V ++A + L + +QW
Sbjct: 95 RDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKE 151
Query: 87 QFKLWSTIQDDQICRFTSDSKERFRGNAGVVVTTYNMVAFGGXXXXXXXXXXXXXXXXXW 146
+ ++ ++ + F+ KE + V+TY+ +
Sbjct: 152 RLGIFG---EEYVGEFSGRIKEL----KPLTVSTYD-----------SAYVNAEKLGNRF 193
Query: 147 GLLLMDEVHVVPAHMFRKVISLTKSHCKLGLTATLVREDER 187
LL+ DEVH +PA + ++ ++ + +LGLTAT RED R
Sbjct: 194 MLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGR 234
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 36.2 bits (82), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 46/104 (44%), Gaps = 12/104 (11%)
Query: 25 QPRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVS-AACRIKK---SCLCLATNAVS 80
QPR YQE ++ + + +IVLP G GK+L+ + A R+ K L LA
Sbjct: 9 QPRIYQEV----IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPL 64
Query: 81 VDQWAFQFKLWSTIQDDQICRFTSDSKERFR----GNAGVVVTT 120
V Q A F+ + ++I T + R A V+V T
Sbjct: 65 VLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVAT 108
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGRILRAKG 361
IL AFK S D N + + V D IDI + N++I + + G+ + Q GR RA+G
Sbjct: 452 ILDAFKASGDHNILIATSVADEGIDIAQCNLVI-LYEYVGNVIKMIQTRGR-GRARG 506
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGRILRAKG 361
IL AFK S D N + + V D IDI + N++I + + G+ + Q GR RA+G
Sbjct: 443 ILDAFKASGDHNILIATSVADEGIDIAQCNLVI-LYEYVGNVIKMIQTRGR-GRARG 497
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGRILRAKG 361
IL AFK S D N + + V D IDI + N++I + + G+ + Q GR RA+G
Sbjct: 451 ILDAFKASGDHNILIATSVADEGIDIAQCNLVI-LYEYVGNVIKMIQTRGR-GRARG 505
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGR 355
+L+AF+ S D N + + V D IDI E N++I + + G+ + Q GR
Sbjct: 443 VLEAFRASGDNNILIATSVADEGIDIAECNLVI-LYEYVGNVIKXIQTRGR 492
>pdb|3H1T|A Chain A, The Fragment Structure Of A Putative Hsdr Subunit Of A
Type I Restriction Enzyme From Vibrio Vulnificus Yj016
Length = 590
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 53/235 (22%), Positives = 90/235 (38%), Gaps = 42/235 (17%)
Query: 13 NPDLNMELKPHAQ-----PRPYQEKSLSKMFGN---GRARSGIIVLPCGAGKSLVGVSAA 64
+ DL+ L P+ PR YQ+ ++++ + G+ RS +I G GK++V +
Sbjct: 161 DEDLDTLLSPYHHVSGYSPRYYQQIAINRAVQSVLQGKKRS-LITXATGTGKTVVAFQIS 219
Query: 65 CRI------------KKSCLCLATNAVSVDQWAFQFKLWSTIQDDQICRFTSDSKERFRG 112
++ K L LA V VD D + FT R +
Sbjct: 220 WKLWSARWNRTGDYRKPRILFLADRNVLVD-------------DPKDKTFTPFGDARHKI 266
Query: 113 NAGVVVTT---YNMVAFGGXXXXXXXXXXXXXXXXXWGLLLMDEVHVVPAH---MFRKVI 166
G VV + Y + + L+++DE H A +R+++
Sbjct: 267 EGGKVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARDNSNWREIL 326
Query: 167 SLTKSHCKLGLTATLVREDERITDLNFLIGPKLYEANWLDLVKGGFIANVQCAEV 221
+ ++G TAT +RED R T F G +Y + + GF+A + V
Sbjct: 327 EYFEPAFQIGXTATPLREDNRDTYRYF--GNPIYTYSLRQGIDDGFLAPYRVHRV 379
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 32.0 bits (71), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 26/111 (23%), Positives = 49/111 (44%), Gaps = 8/111 (7%)
Query: 252 KFRACEFLIRFHEQQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHVE-----RTKIL 306
KF+ + L+R+ ++QRG I++ ++ + + A +L+ I A H R +
Sbjct: 220 KFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQ 279
Query: 307 QAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQ--ISSHAGSRRQEAQRLGR 355
+ F+ DL + + I+ P ++ I + S QE R GR
Sbjct: 280 EKFQ-RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR 329
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGR 355
+L AFK S+D + + V D IDI + N+++ + ++G+ + Q GR
Sbjct: 685 VLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV-LYEYSGNVTKMIQVRGR 734
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGR 355
+L AFK S+D + + V D IDI + N+++ + ++G+ + Q GR
Sbjct: 685 VLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV-LYEYSGNVTKMIQVRGR 734
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/111 (23%), Positives = 48/111 (43%), Gaps = 8/111 (7%)
Query: 252 KFRACEFLIRFHEQQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHVE-----RTKIL 306
KF+ + L R+ ++QRG I++ ++ + + A +L+ I A H R +
Sbjct: 220 KFKPLDQLXRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQ 279
Query: 307 QAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQ--ISSHAGSRRQEAQRLGR 355
+ F+ DL + + I+ P ++ I + S QE R GR
Sbjct: 280 EKFQ-RDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGR 329
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 305 ILQAFKCSRDLNTIFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGR 355
+L AFK S+D + + V D IDI + N+++ + ++G+ + Q GR
Sbjct: 444 VLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV-LYEYSGNVTKMIQVRGR 493
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 38/169 (22%), Positives = 70/169 (41%), Gaps = 28/169 (16%)
Query: 281 LTEYAMKLRKPMIYGATSHVERTKILQAFKCSRDLNTIFLSKVGDNSIDIPEAN-VIIQI 339
L E + R + +G E +++ F R N + + + + IDIP AN +II+
Sbjct: 832 LAELVPEARIAIGHGQMRERELERVMNDFHHQR-FNVLVCTTIIETGIDIPTANTIIIER 890
Query: 340 SSHAGSRRQEAQRLGRILRAKGKLEDRMAGGKEEYNAFFYSLVSTDTQEMFYSTKRQQFL 399
+ H G L ++ + +G++ G+ + A+ + L + KR
Sbjct: 891 ADHFG--------LAQLHQLRGRV------GRSHHQAYAWLLTPHPKAMTTDAQKR---- 932
Query: 400 IDQGYSFKVITSLPPPDSGADLSYHRLDEQLA--LLGKVLSAGDDAVGL 446
+ I SL +G L+ H L+ + A LLG+ S + +G
Sbjct: 933 ------LEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGF 975
>pdb|2VUG|A Chain A, The Structure Of An Archaeal Homodimeric Rna Ligase
pdb|2VUG|B Chain B, The Structure Of An Archaeal Homodimeric Rna Ligase
Length = 389
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 18/105 (17%)
Query: 147 GLLLMDEVHVVPAHMFRKVISLTKSHCKLGLTATLVREDERITDLNFLIGPKLYEANWLD 206
G +++DE +V+P K I +S + +E++ N + +Y+ L
Sbjct: 62 GTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDGYNVRV--VMYKGKMLG 119
Query: 207 LVKGGFIANVQCAEVWCPMTKEFFSEYLKKENSKKKQALYVMNPN 251
+ +GGFI CP T E +++ +E K NPN
Sbjct: 120 ITRGGFI---------CPFTTERIPDFVPQEFFKD-------NPN 148
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 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,003,752
Number of Sequences: 62578
Number of extensions: 541238
Number of successful extensions: 953
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 930
Number of HSP's gapped (non-prelim): 21
length of query: 512
length of database: 14,973,337
effective HSP length: 103
effective length of query: 409
effective length of database: 8,527,803
effective search space: 3487871427
effective search space used: 3487871427
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)