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= psy7952
(444 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 184 bits (466), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 127/415 (30%), Positives = 210/415 (50%), Gaps = 55/415 (13%)
Query: 40 LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXIPPGADFI 99
L+ FG+ F+ ++ I +L D V MPT IP +
Sbjct: 17 LQETFGYQQFRPG--QEEIIDTVLSGRDCLVVMPTGGGKSLCYQ--------IPA---LL 63
Query: 100 LNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELR 159
LNG +SP++S K + +++ + S QT+ + ++ R
Sbjct: 64 LNGLTVV----VSPLISLM-------KDQVDQLQANGVAAACLNSTQTREQQLEVMTGCR 112
Query: 160 LVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLG 219
+I+LLY+ PER + ++F L+HL +N + + VDEAHC+S+WGHDFRP Y LG
Sbjct: 113 --TGQIRLLYIAPERLMLDNF---LEHLAHWNPV-LLAVDEAHCISQWGHDFRPEYAALG 166
Query: 220 ELRQ-FTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVIFDDL 277
+LRQ F ++P +ALTATA+ + +QDI+ +L N P + + S+F R N+ Y +
Sbjct: 167 QLRQRFP--TLPFMALTATADDTTRQDIVRLLGLNDP--LIQISSFDRPNIRY------M 216
Query: 278 LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKH 327
L + + + + + + K+ GIIYC +R D A L+ K + +
Sbjct: 217 LMEKFKPLDQLMRYVQEQRGKS---GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENN 273
Query: 328 ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
R+ VQE F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL
Sbjct: 274 VRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLP 333
Query: 388 SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVF 442
+ +++ L ++ + + +E N + + LV+L +
Sbjct: 334 AEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFAEAQTCRRLVLLNY 388
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 176 bits (445), Expect = 3e-44, Method: Compositional matrix adjust.
Identities = 104/293 (35%), Positives = 163/293 (55%), Gaps = 33/293 (11%)
Query: 164 RIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ 223
+I+LLY+ PER ++F L+HL +N + + VDEAHC+S+WGHDFRP Y LG+LRQ
Sbjct: 115 QIRLLYIAPERLXLDNF---LEHLAHWNPV-LLAVDEAHCISQWGHDFRPEYAALGQLRQ 170
Query: 224 -FTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVI--FDDLLK 279
F ++P ALTATA+ + +QDI+ +L N P + + S+F R N+ Y + F L
Sbjct: 171 RFP--TLPFXALTATADDTTRQDIVRLLGLNDP--LIQISSFDRPNIRYXLXEKFKPL-- 224
Query: 280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHER 329
+ ++++ GK GIIYC +R D A L+ K + + R
Sbjct: 225 ---DQLXRYVQEQRGKS------GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVR 275
Query: 330 SRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY 389
+ VQE F R ++ ++ AT++FG GI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL +
Sbjct: 276 ADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAE 335
Query: 390 CRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVF 442
+++ L ++ + + +E N + LV+L +
Sbjct: 336 AXLFYDPADXAWLRRCLEEKPQGQLQDIERHKLNAXGAFAEAQTCRRLVLLNY 388
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 153 bits (386), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 95/268 (35%), Positives = 143/268 (53%), Gaps = 23/268 (8%)
Query: 141 LIVSGQTKTENKAILEELRLVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNKLAYIVVD 199
++ + +K K + E+ +KL+YVTPE+ A ++ F L+ + I VD
Sbjct: 113 MLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVD 172
Query: 200 EAHCVSEWGHDFRPTYRRLGEL-RQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV 258
E HC S+WGHDFRP Y+ LG L RQF S+ I LTATA V D +L K +
Sbjct: 173 EVHCCSQWGHDFRPDYKALGILKRQFPNASL--IGLTATATNHVLTDAQKILCIEKCF-T 229
Query: 259 FKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNK--ANNCGIIYCRTREHTTDL 316
F S R NL+Y+V + ++ ++FIE + N GIIYC +++ + +
Sbjct: 230 FTASFNRPNLYYEV------RQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQV 283
Query: 317 ----------ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWG 366
A A + +++ V + EI V+ AT++FGMGID+ +VRFV+H
Sbjct: 284 TVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHS 343
Query: 367 MPSSIPAYYQESGRAGRDGLQSYCRIYH 394
M S+ YYQESGRAGRD +++ C +Y+
Sbjct: 344 MSKSMENYYQESGRAGRDDMKADCILYY 371
>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
pdb|2HJV|B Chain B, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
Length = 163
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRR------KVN----KHERSRVQESFMRGEINVITATISFGMG 353
II+CRT+EH L D L K++ + +R V F RGE + AT G
Sbjct: 39 IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
ID +N+ V+++ +P +Y +GR GR G
Sbjct: 99 IDIENISLVINYDLPLEKESYVHRTGRTGRAG 130
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 54/113 (47%), Gaps = 10/113 (8%)
Query: 303 GIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGM 352
G+++C+T+ T +LA LR +++ +R +V F + +I ++ AT
Sbjct: 241 GLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSR 300
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV 405
GID ++ V+++ +P + +Y GR GR G + + K L Y+
Sbjct: 301 GIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYI 353
>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including
The C-Terminal Reca Domain, The Dimerization Domain, And
The Rna Binding Domain
Length = 300
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 40/146 (27%), Positives = 68/146 (46%), Gaps = 18/146 (12%)
Query: 301 NCGIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISF 350
+ +++ RT+ T ++A L R +++ ER RV +F +GE+ V+ AT
Sbjct: 29 DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVA 88
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV----- 405
G+D V VVH+ MP AY SGR GR G + + ++ +E +
Sbjct: 89 ARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVG 148
Query: 406 ---IKTDTSTKREQLELKFKNYLSML 428
+ + T E LE K+++ L+ L
Sbjct: 149 RRFKRVNPPTPEEVLEAKWRHLLARL 174
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 39/146 (26%), Positives = 68/146 (46%), Gaps = 18/146 (12%)
Query: 301 NCGIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISF 350
+ +++ RT+ T ++A L R +++ ER RV +F +GE+ V+ AT
Sbjct: 32 DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVA 91
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV----- 405
G+D V VVH+ +P AY SGR GR G + + ++ +E +
Sbjct: 92 ARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVG 151
Query: 406 ---IKTDTSTKREQLELKFKNYLSML 428
+ + T E LE K+++ L+ L
Sbjct: 152 RRFKRVNPPTPEEVLEAKWRHLLARL 177
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 58/263 (22%), Positives = 113/263 (42%), Gaps = 39/263 (14%)
Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK-----LAYIVVDEAHC 203
T+ +A + ++ ++P I + TP R L+ L +Y+ + Y V+DEA
Sbjct: 137 TDFRAAMNKMNKLRPNI--VIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEADR 186
Query: 204 VSEWG--HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT 261
+ E G D L E + ++I + +AT + V++ +++ NK +F
Sbjct: 187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM--NKKECLFLD 244
Query: 262 STFRSN------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTD 315
+ ++ + V+ + +S E I+K + K+ +N II+ T + T+
Sbjct: 245 TVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSF 303
Query: 316 LADALRR-------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV 362
L L+ K+ +++R+ + + F + E ++ T G+D NV V
Sbjct: 304 LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEV 363
Query: 363 VHWGMPSSIPAYYQESGRAGRDG 385
+ G+PS + Y GR R G
Sbjct: 364 LQIGVPSELANYIHRIGRTARSG 386
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 58/263 (22%), Positives = 113/263 (42%), Gaps = 39/263 (14%)
Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK-----LAYIVVDEAHC 203
T+ +A + ++ ++P I + TP R L+ L +Y+ + Y V+DEA
Sbjct: 188 TDFRAAMNKMNKLRPNI--VIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEADR 237
Query: 204 VSEWG--HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT 261
+ E G D L E + ++I + +AT + V++ +++ NK +F
Sbjct: 238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM--NKKECLFLD 295
Query: 262 STFRSN------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTD 315
+ ++ + V+ + +S E I+K + K+ +N II+ T + T+
Sbjct: 296 TVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSF 354
Query: 316 LADALRR-------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV 362
L L+ K+ +++R+ + + F + E ++ T G+D NV V
Sbjct: 355 LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEV 414
Query: 363 VHWGMPSSIPAYYQESGRAGRDG 385
+ G+PS + Y GR R G
Sbjct: 415 LQIGVPSELANYIHRIGRTARSG 437
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 56/258 (21%), Positives = 111/258 (43%), Gaps = 29/258 (11%)
Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG 208
T+ +A + ++ ++P I + TP R + + R+ + Y V+DEA + E G
Sbjct: 137 TDFRAAMNKMNKLRPNI--VIATPGRLI-DVLEKYSNKFFRF--VDYKVLDEADRLLEIG 191
Query: 209 --HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS 266
D L E + ++I + +AT + V++ +++ NK +F + ++
Sbjct: 192 FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM--NKKECLFLDTVDKN 249
Query: 267 N------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADAL 320
+ V+ + +S E I+K + K+ +N II+ T + T+ L L
Sbjct: 250 EPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSIL 308
Query: 321 RR-------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM 367
+ K+ +++R+ + + F + E ++ T G+D NV V+ G+
Sbjct: 309 KNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGV 368
Query: 368 PSSIPAYYQESGRAGRDG 385
PS + Y GR R G
Sbjct: 369 PSELANYIHRIGRTARSG 386
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+ +R + F G + V+ AT G+D +N++ V+++ MPS I Y GR GR G
Sbjct: 336 QSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 10/95 (10%)
Query: 301 NCGIIYCRTREHTTDLADAL----------RRKVNKHERSRVQESFMRGEINVITATISF 350
N II+C + LA + ++ + ER++V F +G++ + +
Sbjct: 259 NQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLL 318
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
GID Q V V+++ P + Y GR+GR G
Sbjct: 319 TRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFG 353
>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain
pdb|2P6N|B Chain B, Human Dead-box Rna Helicase Ddx41, Helicase Domain
Length = 191
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%)
Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
A A+ ++ ER++ E+F G+ +V+ AT G+D ++ V+++ MP I Y
Sbjct: 81 AVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVH 140
Query: 377 ESGRAGRDG 385
GR G G
Sbjct: 141 RIGRTGCSG 149
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 53/246 (21%), Positives = 101/246 (41%), Gaps = 29/246 (11%)
Query: 154 ILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRP 213
I +++R ++ LL TP R V + + + + Y+V+DEA + + G F P
Sbjct: 141 IGQQIRDLERGCHLLVATPGRLVD----MMERGKIGLDFCKYLVLDEADRMLDMG--FEP 194
Query: 214 TYRRLGELRQFTGNSIPIIALTATAEPS----VKQDIISVLKFNKPYKVFKTSTFRSNLF 269
RR+ E + + + P + +D + F +V TS N+
Sbjct: 195 QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTS---ENIT 251
Query: 270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKV----- 324
V++ + + + F+ L K ++ +++ T++ L D L +
Sbjct: 252 QKVVWVE-----ESDKRSFLLDLLNATGK-DSLTLVFVETKKGADSLEDFLYHEGYACTS 305
Query: 325 -----NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
++ +R F G+ ++ AT G+D NV+ V+++ +PS I Y G
Sbjct: 306 IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIG 365
Query: 380 RAGRDG 385
R GR G
Sbjct: 366 RTGRVG 371
>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAX|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
Length = 193
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 40/95 (42%), Gaps = 10/95 (10%)
Query: 301 NCGIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISF 350
N II+C + + LA + + K+ + R+RV F G + T F
Sbjct: 45 NQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLF 104
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
GID Q V V+++ P Y GR+GR G
Sbjct: 105 TRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139
>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
Length = 170
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
I++ R RE +LA+ LR ++ + +R+ + G +NV+ AT G
Sbjct: 34 IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
ID +V V ++ MP S Y GR R G
Sbjct: 94 IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/257 (20%), Positives = 102/257 (39%), Gaps = 50/257 (19%)
Query: 181 HYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ---FTGNSIP------- 230
H L+Q V + L +++DE H +G R G++ + IP
Sbjct: 479 HALIQEDVHFKNLGLVIIDEQH---RFGVKQREALMNKGKMVDTLVMSATPIPRSMALAF 535
Query: 231 -------IIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN---LFYDVI--FDDLL 278
+I V+ ++ + + N+ Y+ + R + Y +I D L
Sbjct: 536 YGDLDVTVIDEMPPGRKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLN 595
Query: 279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMR 338
S + E++ K + + K G+++ R +++ E+ RV F
Sbjct: 596 VKSAVEMYEYLSKEVFPEFK---LGLMHGR---------------LSQEEKDRVMLEFAE 637
Query: 339 GEINVITATISFGMGID--RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 396
G +++ +T +GID R NV V+ + +Q GR GR G ++YC + +
Sbjct: 638 GRYDILVSTTVIEVGIDVPRANV-MVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD 696
Query: 397 HSKKSLE----YVIKTD 409
++++E + + TD
Sbjct: 697 VGEEAMERLRFFTLNTD 713
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 56/127 (44%), Gaps = 14/127 (11%)
Query: 272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR--------- 322
V+ + +S E I+K + K+ +N II+ T + T+ L L+
Sbjct: 6 VVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPIL 64
Query: 323 ----KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQES 378
K+ +++R+ + + F + E ++ T G+D NV V+ G+PS + Y
Sbjct: 65 EFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 124
Query: 379 GRAGRDG 385
GR R G
Sbjct: 125 GRTARSG 131
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 50/111 (45%), Gaps = 14/111 (12%)
Query: 278 LKDSYAHVKE--FIEKCLGK--DNKANNCGIIYCRTREHTTDLADALRRK---------- 323
+K Y +V+E + +CL D+ + +I+C TR +L LR
Sbjct: 4 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 63
Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY 374
+ + ER + + F G ++ +T GID Q V V+++ +P++ Y
Sbjct: 64 LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 114
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 56/127 (44%), Gaps = 14/127 (11%)
Query: 272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR--------- 322
V+ + +S E I+K + K+ +N II+ T + T+ L L+
Sbjct: 6 VVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPIL 64
Query: 323 ----KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQES 378
K+ +++R+ + + F + E ++ T G+D NV V+ G+PS + Y
Sbjct: 65 EFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 124
Query: 379 GRAGRDG 385
GR R G
Sbjct: 125 GRTARSG 131
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 56/127 (44%), Gaps = 14/127 (11%)
Query: 272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR--------- 322
V+ + +S E I+K + K+ +N II+ T + T+ L L+
Sbjct: 6 VVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPIL 64
Query: 323 ----KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQES 378
K+ +++R+ + + F + E ++ T G+D NV V+ G+PS + Y
Sbjct: 65 EFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 124
Query: 379 GRAGRDG 385
GR R G
Sbjct: 125 GRTARSG 131
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 50/111 (45%), Gaps = 14/111 (12%)
Query: 278 LKDSYAHVKE--FIEKCLGK--DNKANNCGIIYCRTREHTTDLADALRRK---------- 323
+K Y +V+E + +CL D+ + +I+C TR +L LR
Sbjct: 233 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 292
Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY 374
+ + ER + + F G ++ +T GID Q V V+++ +P++ Y
Sbjct: 293 LPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 343
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 50/111 (45%), Gaps = 14/111 (12%)
Query: 278 LKDSYAHVKE--FIEKCLGK--DNKANNCGIIYCRTREHTTDLADALRRK---------- 323
+K Y +V+E + +CL D+ + +I+C TR +L LR
Sbjct: 234 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 293
Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY 374
+ + ER + + F G ++ +T GID Q V V+++ +P++ Y
Sbjct: 294 LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 344
>pdb|2JGN|A Chain A, Ddx3 Helicase Domain
pdb|2JGN|B Chain B, Ddx3 Helicase Domain
pdb|2JGN|C Chain C, Ddx3 Helicase Domain
Length = 185
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD 384
++ +R F G+ ++ AT G+D NV+ V+++ +PS I Y GR GR
Sbjct: 81 SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV 140
Query: 385 G 385
G
Sbjct: 141 G 141
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 258 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 317
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
G+D V ++++ +P++ Y GR+GR G
Sbjct: 318 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 350
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 280 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 339
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
G+D V ++++ +P++ Y GR+GR G
Sbjct: 340 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 243 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 302
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
G+D V ++++ +P++ Y GR+GR G
Sbjct: 303 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 279 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 338
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
G+D V ++++ +P++ Y GR+GR G
Sbjct: 339 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 371
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 280 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 339
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
G+D V ++++ +P++ Y GR+GR G
Sbjct: 340 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
+I+C T+ L + +R + + ER + + F G V+ +T +
Sbjct: 243 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 302
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
G+D V ++++ +P++ Y GR+GR G
Sbjct: 303 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%)
Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
A A+ R + + ER + F + ++ AT FG G+D + V ++ MP Y
Sbjct: 277 AIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLH 336
Query: 377 ESGRAGRDGLQSYCRIYHSEHS 398
RAGR G + + S+ +
Sbjct: 337 RVARAGRFGTKGLAITFVSDEN 358
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%)
Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
A A+ R + + ER + F + ++ AT FG G+D + V ++ MP Y
Sbjct: 276 AIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLH 335
Query: 377 ESGRAGRDGLQSYCRIYHSEHS 398
RAGR G + + S+ +
Sbjct: 336 RVARAGRFGTKGLAITFVSDEN 357
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 47/105 (44%), Gaps = 14/105 (13%)
Query: 296 DNKANNCGIIYCRTREHTTDLADALRRKVNKH-------ERSRVQESFMRGEINVITATI 348
+N+ I+ E + LA+ +R+ H +R V+++F RG I V+ AT
Sbjct: 271 ENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATP 330
Query: 349 SFGMGIDRQNVRFVVH-------WGMPSSIPAYYQESGRAGRDGL 386
+ G++ R +V + + Y Q +GRAGR G+
Sbjct: 331 TLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGM 375
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%)
Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
A A+ R + + ER + F + ++ AT FG G+D + V ++ MP Y
Sbjct: 277 AIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLH 336
Query: 377 ESGRAGRDGLQSYCRIYHSEHS 398
RAGR G + + S+ +
Sbjct: 337 RVARAGRFGTKGLAITFVSDEN 358
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 38/86 (44%)
Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
A A+ R + + ER + F + ++ AT FG G+D + V ++ MP Y
Sbjct: 58 AIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLH 117
Query: 377 ESGRAGRDGLQSYCRIYHSEHSKKSL 402
RAGR G + + S+ + +
Sbjct: 118 RVARAGRFGTKGLAITFVSDENDAKI 143
>pdb|3OIY|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3OIY|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 414
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 12/92 (13%)
Query: 304 IIYCRTREHTTDLADALRR-KVNKHER----SRVQESFMRGEINVITATISF----GMGI 354
+I+ +T E +L + L+R K N E + E F G+IN++ ++ G+
Sbjct: 256 LIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGV 315
Query: 355 DR-QNVRFVVHWGMPSS--IPAYYQESGRAGR 383
D + +++V+ WG PS + Y Q SGR+ R
Sbjct: 316 DLPERIKYVIFWGTPSGPDVYTYIQASGRSSR 347
>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3P4X|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 413
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 12/92 (13%)
Query: 304 IIYCRTREHTTDLADALRR-KVNKHER----SRVQESFMRGEINVITATISF----GMGI 354
+I+ +T E +L + L+R K N E + E F G+IN++ ++ G+
Sbjct: 255 LIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGV 314
Query: 355 DR-QNVRFVVHWGMPSS--IPAYYQESGRAGR 383
D + +++V+ WG PS + Y Q SGR+ R
Sbjct: 315 DLPERIKYVIFWGTPSGPDVYTYIQASGRSSR 346
>pdb|3P4Y|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
- P2 Form
Length = 415
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 12/92 (13%)
Query: 304 IIYCRTREHTTDLADALRR-KVNKHER----SRVQESFMRGEINVITATISF----GMGI 354
+I+ +T E +L + L+R K N E + E F G+IN++ ++ G+
Sbjct: 257 LIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGV 316
Query: 355 DR-QNVRFVVHWGMPSS--IPAYYQESGRAGR 383
D + +++V+ WG PS + Y Q SGR+ R
Sbjct: 317 DLPERIKYVIFWGTPSGPDVYTYIQASGRSSR 348
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 48/111 (43%), Gaps = 7/111 (6%)
Query: 282 YAHVKE-FIEKCLGKDNKANNCGIIYCRTREHTTDL------ADALRRKVNKHERSRVQE 334
+ HVK+ + K + I++ RTR L A LR + + R+R +
Sbjct: 201 FVHVKDDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRLFDNAIELRGDLPQSVRNRNID 260
Query: 335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+F GE +++ T G+D V V+++ P + Y GR GR G
Sbjct: 261 AFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMG 311
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 322 RKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRA 381
+ + ++E+ V F G+IN++ AT G+D + V+ +G+ ++ A Q GRA
Sbjct: 446 KPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRA 505
Query: 382 GRDGLQSYCRIYHS 395
D +Y + HS
Sbjct: 506 RADE-STYVLVAHS 518
>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 = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 322 RKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHW-GMPSSIPAYYQESGR 380
R +++ E+ + + F RGE NV+ AT G+D V VV + +PS+I + Q GR
Sbjct: 401 RGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRS-IQRRGR 459
Query: 381 AGR 383
GR
Sbjct: 460 TGR 462
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 57/150 (38%), Gaps = 28/150 (18%)
Query: 304 IIYCRTREHTTDLA----------DALRRKVNKHERSRVQESFMRGEINVITATISFGMG 353
II+C+ ++ ++A L + +R + +SF G V+ T G
Sbjct: 361 IIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARG 420
Query: 354 IDRQNVRFVVHWGMP---SSIP---AYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK 407
ID V VV++ MP + P Y GR GR G + H KKS E +
Sbjct: 421 IDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVS--INFVHDKKSWEEMNA 478
Query: 408 TDTSTKR----------EQLELKFKNYLSM 427
+R E+LE KN L M
Sbjct: 479 IQEYFQRPITRVPTDDYEELEKVVKNALKM 508
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 316 LADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH--W- 365
LA A+R V H ER V+E+F +G I + AT + GI+ R ++ W
Sbjct: 289 LAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWR 348
Query: 366 ----GMPS-SIPAYYQESGRAGR 383
GM I +Q GRAGR
Sbjct: 349 YSDFGMERIPIIEVHQMLGRAGR 371
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 32.0 bits (71), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 297 NKANNCGIIYCRTREHTTDLADALRRK----VNKHERSRVQESFMRGEINVITATI---- 348
K GIIY RT E ++ ++L+ K + + E F+ GEI+ + T
Sbjct: 272 EKLGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYG 331
Query: 349 SFGMGID-RQNVRFVVHWGMPS 369
+ G+D + +RF V G PS
Sbjct: 332 TLVRGLDLPERIRFAVFVGCPS 353
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%)
Query: 319 ALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY 374
A+ +++ ER + F G V+ T GID Q V V+++ +P++ Y
Sbjct: 283 AMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 31.6 bits (70), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 297 NKANNCGIIYCRTREHTTDLADALRRK----VNKHERSRVQESFMRGEINVITATI---- 348
K GIIY RT E ++ ++L+ K + + E F+ GEI+ + T
Sbjct: 272 EKLGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYG 331
Query: 349 SFGMGID-RQNVRFVVHWGMPS 369
+ G+D + +RF V G PS
Sbjct: 332 TLVRGLDLPERIRFAVFVGCPS 353
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 31.6 bits (70), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%)
Query: 319 ALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY 374
A+ +++ ER + F G V+ T GID Q V V+++ +P++ Y
Sbjct: 309 AMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 12/105 (11%)
Query: 336 FMRGEINVITATISFGMGIDR-------QNVRFVVHWGMPSSIPA-YYQESGRAGRDGLQ 387
F +G I V+ AT +F MG++ ++R G+ P + Q +GRAGR GL
Sbjct: 421 FSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLD 480
Query: 388 SYCRI----YHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSML 428
S + Y+S S + + V + + Q L + L++L
Sbjct: 481 STGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLL 525
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/109 (24%), Positives = 44/109 (40%), Gaps = 11/109 (10%)
Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH--WGMPSSIPAYYQE---- 377
++K R ++E F + +I VI AT + G++ ++ + I YY E
Sbjct: 322 LSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIM 381
Query: 378 -----SGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKF 421
SGRAGR G K+ ++ V K + E +E K
Sbjct: 382 EYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIESKL 430
>pdb|1YN9|A Chain A, Crystal Structure Of Baculovirus Rna 5'-Phosphatase
Complexed With Phosphate
pdb|1YN9|B Chain B, Crystal Structure Of Baculovirus Rna 5'-Phosphatase
Complexed With Phosphate
pdb|1YN9|C Chain C, Crystal Structure Of Baculovirus Rna 5'-Phosphatase
Complexed With Phosphate
Length = 169
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 50/112 (44%), Gaps = 19/112 (16%)
Query: 237 TAEPSVKQD--IISVLKFNKPYKVFKTSTF-RSNLFYDVI--------FDDLLKDSYAHV 285
TAE VKQ+ I +++ K + F R+ L Y I + ++++ V
Sbjct: 45 TAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTV 104
Query: 286 KEFIEKCLGK------DNKANNCGIIYCRTREHTTDLADALRRKVNKHERSR 331
KEF EKC G + N G + CR HT L A + +++ E++R
Sbjct: 105 KEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHT--LGIAPQEAIDRFEKAR 154
>pdb|1VRM|A Chain A, Crystal Structure Of The Apbe Protein (Tm1553) From
Thermotoga Maritima Msb8 At 1.58 A Resolution
Length = 325
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 138 QLELIVSGQ---TKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLA 194
+ ++VS Q +T +AILE+ + + + T ER+V + + V ++
Sbjct: 29 SVRIVVSSQKINPRTIAEAILEDXKRITYKFSF---TDERSVVKKINDHPNEWVEVDEET 85
Query: 195 YIVVDEAHCVSEWGHD-FRPTYRRLGELRQFTGN 227
Y ++ A +E F PT RL EL FTGN
Sbjct: 86 YSLIKAACAFAELTDGAFDPTVGRLLELWGFTGN 119
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 304 IIYCRTREHTTDLADALRR-KVNKHER----SRVQESFMRGEINVITATISF----GMGI 354
+I+ +T E +L + L+R K N E + E F G+IN++ ++ G+
Sbjct: 313 LIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGV 372
Query: 355 D-RQNVRFVVHWGMPS 369
D + +++V+ WG PS
Sbjct: 373 DLPERIKYVIFWGTPS 388
>pdb|3PXI|A Chain A, Structure Of Meca108:clpc
pdb|3PXI|B Chain B, Structure Of Meca108:clpc
pdb|3PXI|C Chain C, Structure Of Meca108:clpc
Length = 758
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 44/191 (23%), Positives = 70/191 (36%), Gaps = 43/191 (22%)
Query: 162 KPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH--DFRPTYRRLG 219
KP +L E+A + F+ LLQ V+++ G DFR T
Sbjct: 578 KPYSVVLLDAIEKAHPDVFNILLQ-----------VLEDGRLTDSKGRTVDFRNT----- 621
Query: 220 ELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLK 279
I+ +T+ S K ++ LK + F+ F + + ++F L K
Sbjct: 622 -----------ILIMTSNVGASEKDKVMGELK-----RAFRPE-FINRIDEIIVFHSLEK 664
Query: 280 DSYAHVKEFIEKCLGKDNKANNCGI-----IYCRTREHTTDL---ADALRRKVNKHERSR 331
+ + L K K + I + E DL A LRR + KH R
Sbjct: 665 KHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLRRAIQKHVEDR 724
Query: 332 VQESFMRGEIN 342
+ E +RG I+
Sbjct: 725 LSEELLRGNIH 735
>pdb|1WGY|A Chain A, Ra Domain Of Guanine Nucleotide Exchange Factor For Rap1
Length = 104
Score = 28.5 bits (62), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 379 GRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLV 438
G +G G + +C +Y +EHS S +K S+ +++ K ++Y E+ LV
Sbjct: 1 GSSGSSGEEIFCHVYITEHSYVS----VKAKVSSIAQEI---LKVVAEKIQYAEEDLALV 53
Query: 439 ILVF 442
+ F
Sbjct: 54 AITF 57
>pdb|2ET6|A Chain A, (3r)-Hydroxyacyl-Coa Dehydrogenase Domain Of Candida
Tropicalis Peroxisomal Multifunctional Enzyme Type 2
Length = 604
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 11/68 (16%)
Query: 276 DLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQES 335
D+ KDS A +K I+K D NN GI+ R+ K++K E VQ+
Sbjct: 377 DVAKDSEAIIKNVIDKYGTIDILVNNAGILRDRSFA-----------KMSKQEWDSVQQV 425
Query: 336 FMRGEINV 343
+ G N+
Sbjct: 426 HLIGTFNL 433
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 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,275,924
Number of Sequences: 62578
Number of extensions: 487164
Number of successful extensions: 1151
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 40
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1095
Number of HSP's gapped (non-prelim): 61
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
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: 53 (25.0 bits)