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= 004900
(724 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 = 311 bits (798), Expect = 6e-85, Method: Compositional matrix adjust.
Identities = 173/414 (41%), Positives = 244/414 (58%), Gaps = 24/414 (5%)
Query: 28 KLLRWHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSPL 87
++L+ FG+ QFR Q + I VLSGRDC +MPTGGGKS+CYQIPAL G+ +VVSPL
Sbjct: 15 QVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPL 74
Query: 88 IALMENQVIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTATPGFM 147
I+LM++QV L+ G+A L+STQT + + ++ +G+ +RLLY+ PE F+
Sbjct: 75 ISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQ--IRLLYIAPERLMLDNFL 132
Query: 148 SKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKV 207
L + L+A+DEAHCIS WGHDFRP Y L LR P +P +ALTATA
Sbjct: 133 EHLAHWNP----VLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTT 188
Query: 208 QKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLKANGDTCAIVYCLE 267
++D++ L L +PL+ SSF+RPN+ Y + K V + G + I+YC
Sbjct: 189 RQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRY--VQEQRGKS-GIIYCNS 245
Query: 268 RTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDV 327
R ++ +A L + GIS AAYHAGL + R+ V + + Q+VVATVAFGMGI++ +V
Sbjct: 246 RAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNV 305
Query: 328 RLVCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRRMEFILXXXXXXXXXXFST 387
R V HF+IP+++E++YQE+GRAGRD LP++++L+Y D M ++
Sbjct: 306 RFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD---MAWLRRCLEEKPQGQLQD 362
Query: 388 RERSSKKSISDFSQMVDYCEGSGCRRKKILESFGE--QIPVSLCKNSCDACKHP 439
ER ++ F+ E CRR +L FGE Q P C N CD C P
Sbjct: 363 IERHKLNAMGAFA------EAQTCRRLVLLNYFGEGRQEP---CGN-CDICLDP 406
>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 = 301 bits (772), Expect = 6e-82, Method: Compositional matrix adjust.
Identities = 157/408 (38%), Positives = 228/408 (55%), Gaps = 21/408 (5%)
Query: 34 FGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSPLIALMEN 93
F +FR QL+ I ++G++ F +MPTGGGKS+CYQ+PAL G LV+ PLI+LME+
Sbjct: 40 FKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMED 99
Query: 94 QVIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTA-TPGFMSKLKK 152
Q++ LK+ GI+ L+++ + + ++ ++ + L+L+YVTPE A + FMS+L+K
Sbjct: 100 QLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK 159
Query: 153 IHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKVQKDVM 212
+ +A+DE HC S WGHDFRP Y+ L L+ P+ ++ LTATA V D
Sbjct: 160 AYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQ 219
Query: 213 ESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLKANG---DTCAIVYCLERT 269
+ LC++ +SFNRPNL+YEVR K L NG I+YC +
Sbjct: 220 KILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKL-INGRYKGQSGIIYCFSQK 278
Query: 270 TCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRL 329
++++ L GI AYHA L + +++V W ++ QVVVATVAFGMGID+ DVR
Sbjct: 279 DSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRF 338
Query: 330 VCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRRMEFILXXXXXXXXXXFSTRE 389
V H ++ KSME +YQESGRAGRD + + +LYYG D R+ ++ +
Sbjct: 339 VIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLY---- 394
Query: 390 RSSKKSISDFSQMVDYCEG-SGCRRKKILESFGEQIPVSLCKNSCDAC 436
+MV YC+ S CRR + + F E C CD C
Sbjct: 395 -----------EMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNC 431
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 298 bits (764), Expect = 5e-81, Method: Compositional matrix adjust.
Identities = 171/414 (41%), Positives = 238/414 (57%), Gaps = 24/414 (5%)
Query: 28 KLLRWHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSPL 87
++L+ FG+ QFR Q + I VLSGRDC + PTGGGKS+CYQIPAL G+ +VVSPL
Sbjct: 15 QVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPL 74
Query: 88 IALMENQVIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTATPGFM 147
I+L ++QV L+ G+A L+STQT + + ++ +G+ +RLLY+ PE F+
Sbjct: 75 ISLXKDQVDQLQANGVAAACLNSTQTREQQLEVXTGCRTGQ--IRLLYIAPERLXLDNFL 132
Query: 148 SKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKV 207
L + L+A+DEAHCIS WGHDFRP Y L LR P +P ALTATA
Sbjct: 133 EHLAHWNP----VLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTATADDTT 188
Query: 208 QKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLKANGDTCAIVYCLE 267
++D++ L L +PL+ SSF+RPN+ Y + K V + G + I+YC
Sbjct: 189 RQDIVRLLGLNDPLIQISSFDRPNIRYXLXEKFKPLDQLXRY--VQEQRGKS-GIIYCNS 245
Query: 268 RTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDV 327
R ++ +A L + GIS AAYHAGL + R+ V + + Q+VVATVAFG GI++ +V
Sbjct: 246 RAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNV 305
Query: 328 RLVCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRRMEFILXXXXXXXXXXFST 387
R V HF+IP+++E++YQE+GRAGRD LP+++ L+Y D + L
Sbjct: 306 RFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLRRCLEEKPQGQLQDI-- 363
Query: 388 RERSSKKSISDFSQMVDYCEGSGCRRKKILESFGE--QIPVSLCKNSCDACKHP 439
ER + F+ E CRR +L FGE Q P C N CD C P
Sbjct: 364 -ERHKLNAXGAFA------EAQTCRRLVLLNYFGEGRQEP---CGN-CDICLDP 406
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 81/326 (24%), Positives = 134/326 (41%), Gaps = 39/326 (11%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPAL--AKP------GIVLVVSPLIALMENQ 94
Q +AI ++GRD G GK+ + IP L KP +++V + +AL +Q
Sbjct: 48 QEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQ 107
Query: 95 VIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTATPGFMSKL--KK 152
V+ K + +T ++ I LRL L TPG + L +K
Sbjct: 108 VVRTLGKHCGISCMVTTGGTNLRDDI----------LRLNETVHILVGTPGRVLDLASRK 157
Query: 153 IHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKVQKDVM 212
+ +L +DEA + S DF+ ++ S +LP L + P K+ M
Sbjct: 158 VADLSDCSLFIMDEADKMLS--RDFKTIIEQILS---FLPPTHQSLLFSATFPLTVKEFM 212
Query: 213 -------ESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLKANGDTCAIVYC 265
+ L L LK + F E R K S L+ N AI++C
Sbjct: 213 VKHLHKPYEINLMEELTLKG-ITQYYAFVEERQKLHCLNTLF---SKLQINQ---AIIFC 265
Query: 266 LERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRK 325
+ L+ ++ G SC HA + + R+ V ++ + + +V + GID +
Sbjct: 266 NSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQ 325
Query: 326 DVRLVCHFNIPKSMEAFYQESGRAGR 351
V +V +F+ PK+ E + GR+GR
Sbjct: 326 AVNVVINFDFPKTAETYLHRIGRSGR 351
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 65.1 bits (157), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 77/342 (22%), Positives = 138/342 (40%), Gaps = 47/342 (13%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAK-----PGIVLVVSPLIALMENQVIG 97
Q AI + RD TG GK+ + +P L++ PG L A+ EN G
Sbjct: 42 QKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPG-----EALRAMKENGRYG 96
Query: 98 LKEKGIAGEFLSSTQTMQVKTK----------------IYEDLDSGKPSLRLLYVTPELT 141
+++ L+ T+ + V+ +Y D G+ L L
Sbjct: 97 RRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLV 156
Query: 142 ATPGFMSKLKKIHSRGLLNL-----VAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPI 196
ATPG +L + RG + L + +DEA + G F P R++ ++ +P +
Sbjct: 157 ATPG---RLVDMMERGKIGLDFCKYLVLDEADRMLDMG--FEPQIRRIVE-QDTMPPKGV 210
Query: 197 ---LALTATAAPKVQ---KDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXC 250
+ +AT ++Q +D ++ V + N+ +V +
Sbjct: 211 RHTMMFSATFPKEIQMLARDFLDEYIFLA--VGRVGSTSENITQKVVW-VEESDKRSFLL 267
Query: 251 SVLKANG-DTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRK 309
+L A G D+ +V+ + D L +L G +C + H + + R L + S +
Sbjct: 268 DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 327
Query: 310 QVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
++VAT G+D +V+ V +F++P +E + GR GR
Sbjct: 328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGR 369
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 73/344 (21%), Positives = 144/344 (41%), Gaps = 43/344 (12%)
Query: 29 LLR--WHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP 86
LLR + +G + Q AI+ ++ GRD +G GK+ + I L I + +
Sbjct: 48 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQ 107
Query: 87 LIALMENQVIGLK-EKGIAGEFLSSTQTMQVK-------TKIYEDLDSGKPSLRLLYVTP 138
+ L + + ++ +KG+ L+ M V+ T + ED+ +L Y
Sbjct: 108 ALILAPTRELAVQIQKGL----LALGDYMNVQCHACIGGTNVGEDIR------KLDYGQH 157
Query: 139 ELTATPGF---MSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVP 195
+ TPG M + + + +R + LV +DEA + + G ++ + YLP
Sbjct: 158 VVAGTPGRVFDMIRRRSLRTRAIKMLV-LDEADEMLNKGFK-----EQIYDVYRYLPPAT 211
Query: 196 ILALTATAAP--------KVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXX 247
+ L + P K D + L ++ L L+ F V +
Sbjct: 212 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGI---KQFFVAVEREEWKFDTL- 267
Query: 248 XXCSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISS 307
C + T A+++C + D L+ + + ++ H + K R S++ ++ S
Sbjct: 268 --CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 325
Query: 308 RKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
+V+++T + G+D V L+ ++++P + E + GR+GR
Sbjct: 326 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 369
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 73/344 (21%), Positives = 144/344 (41%), Gaps = 43/344 (12%)
Query: 29 LLR--WHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP 86
LLR + +G + Q AI+ ++ GRD +G GK+ + I L I + +
Sbjct: 49 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQ 108
Query: 87 LIALMENQVIGLK-EKGIAGEFLSSTQTMQVK-------TKIYEDLDSGKPSLRLLYVTP 138
+ L + + ++ +KG+ L+ M V+ T + ED+ +L Y
Sbjct: 109 ALILAPTRELAVQIQKGL----LALGDYMNVQCHACIGGTNVGEDIR------KLDYGQH 158
Query: 139 ELTATPGF---MSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVP 195
+ TPG M + + + +R + LV +DEA + + G ++ + YLP
Sbjct: 159 VVAGTPGRVFDMIRRRSLRTRAIKMLV-LDEADEMLNKGFK-----EQIYDVYRYLPPAT 212
Query: 196 ILALTATAAP--------KVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXX 247
+ L + P K D + L ++ L L+ F V +
Sbjct: 213 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGI---KQFFVAVEREEWKFDTL- 268
Query: 248 XXCSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISS 307
C + T A+++C + D L+ + + ++ H + K R S++ ++ S
Sbjct: 269 --CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 326
Query: 308 RKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
+V+++T + G+D V L+ ++++P + E + GR+GR
Sbjct: 327 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 370
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 73/344 (21%), Positives = 144/344 (41%), Gaps = 43/344 (12%)
Query: 29 LLR--WHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP 86
LLR + +G + Q AI+ ++ GRD +G GK+ + I L I + +
Sbjct: 49 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQ 108
Query: 87 LIALMENQVIGLK-EKGIAGEFLSSTQTMQVK-------TKIYEDLDSGKPSLRLLYVTP 138
+ L + + ++ +KG+ L+ M V+ T + ED+ +L Y
Sbjct: 109 ALILAPTRELAVQIQKGL----LALGDYMNVQCHACIGGTNVGEDIR------KLDYGQH 158
Query: 139 ELTATPGF---MSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVP 195
+ TPG M + + + +R + LV +DEA + + G ++ + YLP
Sbjct: 159 VVAGTPGRVFDMIRRRSLRTRAIKMLV-LDEADEMLNKGFK-----EQIYDVYRYLPPAT 212
Query: 196 ILALTATAAP--------KVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXX 247
+ L + P K D + L ++ L L+ F V +
Sbjct: 213 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGI---KQFFVAVEREEWKFDTL- 268
Query: 248 XXCSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISS 307
C + T A+++C + D L+ + + ++ H + K R S++ ++ S
Sbjct: 269 --CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 326
Query: 308 RKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
+V+++T + G+D V L+ ++++P + E + GR+GR
Sbjct: 327 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 370
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 71/337 (21%), Positives = 141/337 (41%), Gaps = 29/337 (8%)
Query: 29 LLR--WHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP 86
LLR + +G + Q AI+ ++ GRD +G GK+ + I L I + +
Sbjct: 27 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQ 86
Query: 87 LIALMENQVIGLK-EKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTATPG 145
+ L + + ++ +KG+ L +Q I + G+ +L Y + TPG
Sbjct: 87 ALILAPTRELAVQIQKGLLA--LGDYMNVQCHACI-GGTNVGEDIRKLDYGQHVVAGTPG 143
Query: 146 F---MSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTAT 202
M + + + +R + LV +DEA + + G ++ + YLP + L +
Sbjct: 144 RVFDMIRRRSLRTRAIKMLV-LDEADEMLNKGFK-----EQIYDVYRYLPPATQVVLISA 197
Query: 203 AAP--------KVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLK 254
P K D + L ++ L L+ F V + C +
Sbjct: 198 TLPHEILEMTNKFMTDPIRILVKRDELTLEGI---KQFFVAVEREEWKFDTL---CDLYD 251
Query: 255 ANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVA 314
T A+++C + D L+ + + ++ H + K R S++ ++ S +V+++
Sbjct: 252 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLIS 311
Query: 315 TVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
T + G+D V L+ ++++P + E + GR+GR
Sbjct: 312 TDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 348
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 70/340 (20%), Positives = 145/340 (42%), Gaps = 35/340 (10%)
Query: 29 LLR--WHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP 86
LLR + +G + Q AI+ ++ GRD +G GK+ + + L I + +
Sbjct: 12 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQ 71
Query: 87 LIALMENQVIGLK-EKGIA--GEFLSSTQTMQVK-TKIYEDLDSGKPSLRLLYVTPELTA 142
+ L + + ++ +KG+ G++++ + T + ED+ +L Y +
Sbjct: 72 ALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIR------KLDYGQHVVAG 125
Query: 143 TPGF---MSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILAL 199
TPG M + + + +R + LV +DEA + + G ++ + YLP + L
Sbjct: 126 TPGRVFDMIRRRSLRTRAIKMLV-LDEADEMLNKGFK-----EQIYDVYRYLPPATQVVL 179
Query: 200 TATAAP--------KVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCS 251
+ P K D + L ++ L L+ F V + C
Sbjct: 180 ISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGI---KQFFVAVEREEWKFDTL---CD 233
Query: 252 VLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQV 311
+ T A+++C + D L+ + + ++ H + K R S++ ++ S +V
Sbjct: 234 LYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 293
Query: 312 VVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
+++T + G+D V L+ ++++P + E + GR+GR
Sbjct: 294 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 333
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 70/337 (20%), Positives = 141/337 (41%), Gaps = 29/337 (8%)
Query: 29 LLR--WHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP 86
LLR + +G + Q AI+ ++ GRD +G GK+ + + L I + +
Sbjct: 12 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQ 71
Query: 87 LIALMENQVIGLK-EKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTATPG 145
+ L + + ++ +KG+ L +Q I + G+ +L Y + TPG
Sbjct: 72 ALILAPTRELAVQVQKGLLA--LGDYMNVQCHACI-GGTNVGEDIRKLDYGQHVVAGTPG 128
Query: 146 F---MSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTAT 202
M + + + +R + LV +DEA + + G ++ + YLP + L +
Sbjct: 129 RVFDMIRRRSLRTRAIKMLV-LDEADEMLNKGFK-----EQIYDVYRYLPPATQVVLISA 182
Query: 203 AAP--------KVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLK 254
P K D + L ++ L L+ F V + C +
Sbjct: 183 TLPHEILEMTNKFMTDPIRILVKRDELTLEGI---KQFFVAVEREEWKFDTL---CDLYD 236
Query: 255 ANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVA 314
T A+++C + D L+ + + ++ H + K R S++ ++ S +V+++
Sbjct: 237 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLIS 296
Query: 315 TVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
T + G+D V L+ ++++P + E + GR+GR
Sbjct: 297 TDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 333
>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 = 56.2 bits (134), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 50/101 (49%), Gaps = 1/101 (0%)
Query: 252 VLKANG-DTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQ 310
+L A G D+ +V+ + D L +L G +C + H + + R L + S +
Sbjct: 39 LLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP 98
Query: 311 VVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
++VAT G+D +V+ V +F++P +E + GR GR
Sbjct: 99 ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGR 139
>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 = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 61/124 (49%), Gaps = 1/124 (0%)
Query: 250 CSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRK 309
C +LK N + +V+C + EL++ L G A H L+ R V+ + +
Sbjct: 231 CRLLK-NKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI 289
Query: 310 QVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRR 369
++++AT GID D+ V ++++P++ E++ GR GR K++ + ++
Sbjct: 290 RILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKK 349
Query: 370 MEFI 373
+ +I
Sbjct: 350 LRYI 353
>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 = 55.8 bits (133), Expect = 8e-08, Method: Composition-based stats.
Identities = 29/117 (24%), Positives = 61/117 (52%), Gaps = 1/117 (0%)
Query: 252 VLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQV 311
++ N D+C I++C + ++L+ L G C H G+ + R V++++ +
Sbjct: 30 LMTENPDSC-IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRY 88
Query: 312 VVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRR 368
+VAT GID +++ LV ++++P E++ +GR GR K++ + ++R
Sbjct: 89 LVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKR 145
>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 = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 75/351 (21%), Positives = 136/351 (38%), Gaps = 46/351 (13%)
Query: 33 HFGHAQFRDKQLD----------------AIQAVLSGRDCFCLMPTGGGKSMCYQIPALA 76
HF A RD +D +I + SGRD TG GK+ + +P L+
Sbjct: 57 HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILS 116
Query: 77 KPGIVLVVSPL-IALMENQVIGLK-EKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLR-- 132
K L+ P + L QV+ + + +A + + + ++ + + G S R
Sbjct: 117 K----LLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQ 172
Query: 133 ---LLYVTPELTATPGFMSKLKKIHSRGLLNL-----VAIDEAHCISSWGHDFRPSYRKL 184
+ + ATPG +L R + V +DEA + G F R++
Sbjct: 173 NECITRGCHVVIATPG---RLLDFVDRTFITFEDTRFVVLDEADRMLDMG--FSEDMRRI 227
Query: 185 SSLRNYLPDVPILALTATAAPKVQKDVMESL----CLQNPLVLKSSFNRPNLFYEVRYKX 240
+ P+ L +AT ++Q+ E L + +V + + YEV
Sbjct: 228 MTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVN--- 284
Query: 241 XXXXXXXXXCSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSV 300
+L D IV+ + D L+++LS + H R
Sbjct: 285 -KYAKRSKLIEILSEQAD-GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQA 342
Query: 301 LDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
L D+ + +V++AT G+D K+++ V ++++P ++ + GR GR
Sbjct: 343 LRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGR 393
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 74/337 (21%), Positives = 141/337 (41%), Gaps = 48/337 (14%)
Query: 29 LLRWHFGHAQFRDK---QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVS 85
LLR FG+ F + Q AI ++ G D +G GK+ + I AL + +
Sbjct: 33 LLRGVFGYG-FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAP 91
Query: 86 PLIALMENQVIGLKEKGIAGEFLSSTQTMQVK-------TKIYEDLDSGKPSLRLLYVTP 138
+ L + + L+ + + ++ M +K T ED + + + ++
Sbjct: 92 QALMLAPTRELALQIQKVV---MALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVV---- 144
Query: 139 ELTATPG--FMSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPI 196
TPG F + ++ + + +DEA + S G F+ ++ +L LP
Sbjct: 145 ---GTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG--FKEQIYQIFTL---LPPTTQ 196
Query: 197 LALTATAAPKVQKDVMESLC--LQNP---LVLKSSFNRPNL--FY----EVRYKXXXXXX 245
+ L + P DV+E ++NP LV K + FY E YK
Sbjct: 197 VVLLSATMPN---DVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 253
Query: 246 XXXXCSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWI 305
SV T A+++C R +EL+ L + +A ++ L + R +++ ++
Sbjct: 254 LYDSISV------TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFR 307
Query: 306 SSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAF 342
S +++++T GID + V LV ++++P + E +
Sbjct: 308 SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 344
>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 = 53.5 bits (127), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 47/91 (51%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++C + L+ +S G SC HA + + R+ V D+ + + +V T F
Sbjct: 47 SIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTR 106
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
GID + V +V +F+ PK E + GR+GR
Sbjct: 107 GIDIQAVNVVINFDFPKLAETYLHRIGRSGR 137
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 74/335 (22%), Positives = 137/335 (40%), Gaps = 44/335 (13%)
Query: 29 LLRWHFGHAQFRDK---QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVS 85
LLR FG+ F + Q AI ++ G D +G GK+ + I AL + +
Sbjct: 32 LLRGVFGYG-FEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAP 90
Query: 86 PLIALMENQVIGLKEKGIAGEFLSSTQTMQVK-----TKIYEDLDSGKPSLRLLYVTPEL 140
+ L + + L+ + + L+ ++V T ED + + + ++
Sbjct: 91 QALXLAPTRELALQIQKVVXA-LAFHXDIKVHACIGGTSFVEDAEGLRDAQIVV------ 143
Query: 141 TATPG--FMSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILA 198
TPG F + ++ + +DEA S G F+ ++ +L LP +
Sbjct: 144 -GTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSG--FKEQIYQIFTL---LPPTTQVV 197
Query: 199 LTATAAPKVQKDVMESLC--LQNP---LVLKSSFNRPNL--FY----EVRYKXXXXXXXX 247
L + P DV+E +NP LV K + FY E YK
Sbjct: 198 LLSATXPN---DVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY 254
Query: 248 XXCSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISS 307
SV T A+++C R +EL+ L + +A ++ L + R ++ ++ S
Sbjct: 255 DSISV------TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSG 308
Query: 308 RKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAF 342
+++++T GID + V LV ++++P + E +
Sbjct: 309 SSRILISTDLLARGIDVQQVSLVINYDLPANKENY 343
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 47/97 (48%), Gaps = 6/97 (6%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++C ++ T +E++ ++A G + A L R +++D + +V+V T
Sbjct: 360 SIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIAR 419
Query: 321 GIDRKDVRLVCHFNIPKSM------EAFYQESGRAGR 351
GID V LV ++++P + + GR GR
Sbjct: 420 GIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGR 456
>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
pdb|3FHT|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
Length = 412
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 67/273 (24%), Positives = 114/273 (41%), Gaps = 37/273 (13%)
Query: 108 LSSTQTMQVKT-KIYEDLDSGKPSLRLLYVT-------------PELTATPG----FMSK 149
LS T + ++T K+ E + P L+L Y + TPG + SK
Sbjct: 101 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSK 160
Query: 150 LKKIHSRGLLNLVAIDEAHC-ISSWGHDFRPSYRKLSSLRNYLP-DVPILALTATAAPKV 207
LK I + + + +DEA I++ GH + S R ++ LP + +L +AT V
Sbjct: 161 LKFIDPKKI-KVFVLDEADVMIATQGHQDQ-SIR----IQRMLPRNCQMLLFSATFEDSV 214
Query: 208 QKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKX---XXXXXXXXXCSVLKANGDTCAIVY 264
K + +P V+K L +Y C++ A A+++
Sbjct: 215 WK--FAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIF 272
Query: 265 CLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDR 324
C R T L+A LS G A + + R++V++ + +++V+V T GID
Sbjct: 273 CHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDV 332
Query: 325 KDVRLVCHFNIP------KSMEAFYQESGRAGR 351
+ V +V +F++P E + GR GR
Sbjct: 333 EQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR 365
>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
pdb|3EWS|B Chain B, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
Length = 445
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 67/273 (24%), Positives = 115/273 (42%), Gaps = 37/273 (13%)
Query: 108 LSSTQTMQVKT-KIYEDLDSGKPSLRLLYVT-------------PELTATPG----FMSK 149
LS T + ++T K+ E + P L+L Y + TPG + SK
Sbjct: 138 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSK 197
Query: 150 LKKIHSRGLLNLVAIDEAHC-ISSWGHDFRPSYRKLSSLRNYLP-DVPILALTATAAPKV 207
LK I + + + +DEA I++ GH + S R ++ LP + +L +AT V
Sbjct: 198 LKFIDPKKI-KVFVLDEADVMIATQGHQDQ-SIR----IQRMLPRNCQMLLFSATFEDSV 251
Query: 208 QKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKX---XXXXXXXXXCSVLKANGDTCAIVY 264
K + + +P V+K L +Y C++ A A+++
Sbjct: 252 WKFAQK--VVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIF 309
Query: 265 CLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDR 324
C R T L+A LS G A + + R++V++ + +++V+V T GID
Sbjct: 310 CHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDV 369
Query: 325 KDVRLVCHFNIP------KSMEAFYQESGRAGR 351
+ V +V +F++P E + GR GR
Sbjct: 370 EQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR 402
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 67/273 (24%), Positives = 115/273 (42%), Gaps = 37/273 (13%)
Query: 108 LSSTQTMQVKT-KIYEDLDSGKPSLRLLYVT-------------PELTATPG----FMSK 149
LS T + ++T K+ E + P L+L Y + TPG + SK
Sbjct: 117 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSK 176
Query: 150 LKKIHSRGLLNLVAIDEAHC-ISSWGHDFRPSYRKLSSLRNYLP-DVPILALTATAAPKV 207
LK I + + + +DEA I++ GH + S R ++ LP + +L +AT V
Sbjct: 177 LKFIDPKKI-KVFVLDEADVMIATQGHQDQ-SIR----IQRMLPRNCQMLLFSATFEDSV 230
Query: 208 QKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKX---XXXXXXXXXCSVLKANGDTCAIVY 264
K + + +P V+K L +Y C++ A A+++
Sbjct: 231 WKFAQK--VVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIF 288
Query: 265 CLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDR 324
C R T L+A LS G A + + R++V++ + +++V+V T GID
Sbjct: 289 CHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDV 348
Query: 325 KDVRLVCHFNIP------KSMEAFYQESGRAGR 351
+ V +V +F++P E + GR GR
Sbjct: 349 EQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR 381
>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|D Chain D, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 479
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 67/273 (24%), Positives = 115/273 (42%), Gaps = 37/273 (13%)
Query: 108 LSSTQTMQVKT-KIYEDLDSGKPSLRLLYVT-------------PELTATPG----FMSK 149
LS T + ++T K+ E + P L+L Y + TPG + SK
Sbjct: 168 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSK 227
Query: 150 LKKIHSRGLLNLVAIDEAHC-ISSWGHDFRPSYRKLSSLRNYLP-DVPILALTATAAPKV 207
LK I + + + +DEA I++ GH + S R ++ LP + +L +AT V
Sbjct: 228 LKFIDPKKI-KVFVLDEADVMIATQGHQDQ-SIR----IQRMLPRNCQMLLFSATFEDSV 281
Query: 208 QKDVMESLCLQNPLVLKSSFNRPNLFYEVRYK---XXXXXXXXXXCSVLKANGDTCAIVY 264
K + + +P V+K L +Y C++ A A+++
Sbjct: 282 WKFAQK--VVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIF 339
Query: 265 CLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDR 324
C R T L+A LS G A + + R++V++ + +++V+V T GID
Sbjct: 340 CHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDV 399
Query: 325 KDVRLVCHFNIP------KSMEAFYQESGRAGR 351
+ V +V +F++P E + GR GR
Sbjct: 400 EQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR 432
>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 = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 46/89 (51%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++ ++ D + YL G+ A H G + + R+ ++ + +K V+VAT G
Sbjct: 58 LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117
Query: 322 IDRKDVRLVCHFNIPKSMEAFYQESGRAG 350
+D ++ V ++++P+ +E + GR G
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTG 146
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 47/93 (50%)
Query: 250 CSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRK 309
C + + T A+++ R D L+ + A + +A H ++ K R ++ ++ S
Sbjct: 272 CDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS 331
Query: 310 QVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAF 342
+V++ T GID + V LV ++++P + E +
Sbjct: 332 RVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 47/84 (55%)
Query: 259 TCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAF 318
T A+++C R +EL+ L + +A ++ L + R +++ ++ S +++++T
Sbjct: 31 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL 90
Query: 319 GMGIDRKDVRLVCHFNIPKSMEAF 342
GID + V LV ++++P + E +
Sbjct: 91 ARGIDVQQVSLVINYDLPANKENY 114
>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 = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 47/93 (50%)
Query: 250 CSVLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRK 309
C + + T A+++ R D L+ + A + +A H ++ K R ++ ++ S
Sbjct: 246 CDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS 305
Query: 310 QVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAF 342
+V++ T GID + V LV ++++P + E +
Sbjct: 306 RVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
>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 = 45.8 bits (107), Expect = 9e-05, Method: Composition-based stats.
Identities = 29/100 (29%), Positives = 46/100 (46%)
Query: 252 VLKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQV 311
+LK T +IV+ +R EL+ +L GI+ + R+ + R V
Sbjct: 24 LLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNV 83
Query: 312 VVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
+VAT GID DV V +F++P+S + + GR R
Sbjct: 84 LVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTAR 123
>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 = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 35/111 (31%), Positives = 53/111 (47%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
A+V+ + +E++ L G A H L+ R VL + +V+VAT
Sbjct: 34 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRRME 371
G+D V LV H+ +P EA+ SGR GR + +L YG +RR +E
Sbjct: 94 GLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVE 144
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 6/97 (6%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++ + T + L L + G + H L + R ++DD+ R +V++ T
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 321 GIDRKDVRLVCHFNIPKSMEA------FYQESGRAGR 351
GID V +V ++++P + GR GR
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGR 342
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 6/97 (6%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++ + T + L L + G + H L + R ++DD+ R +V++ T
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 321 GIDRKDVRLVCHFNIPKSMEA------FYQESGRAGR 351
GID V +V ++++P + GR GR
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGR 342
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 71/334 (21%), Positives = 126/334 (37%), Gaps = 50/334 (14%)
Query: 33 HFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSPLIALME 92
G F + Q I +L G++ TG GK+ Y IP L LVV+P L
Sbjct: 11 EMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELTR 70
Query: 93 NQVIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKP---SLRLLYVTPELTATPGFMSK 149
+++ G ++ TK+ E + G P + + + ATPG +
Sbjct: 71 QVASHIRD---IGRYMD--------TKVAE-VYGGMPYKAQINRVRNADIVVATPG---R 115
Query: 150 LKKIHSRGLLNL-----VAIDEAHCISSWGH--DFR-----PSYRKLSSLRNYLPDVPIL 197
L + S+G+++L V IDEA + G D + S RK++ L
Sbjct: 116 LLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGL---------- 165
Query: 198 ALTATAAPKVQKDVMESLCLQNPLVLKSSFNRPNLFYEVRYKXXXXXXXXXXCSVLKANG 257
+AT +++K V + + N +++ N+ ++ + L+ N
Sbjct: 166 -FSATIPEEIRKVVKDFIT--NYEEIEACIGLANVEHKFVH---VKDDWRSKVQALRENK 219
Query: 258 DTCAIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVA 317
D IV+ R +L + L R+ +D + +++ T
Sbjct: 220 DKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDV 275
Query: 318 FGMGIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
G+D V V +F+ P+ + + GR GR
Sbjct: 276 ASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGR 309
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 43/91 (47%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+++ C L+ L A H G+ + R S + +++++VAT FG
Sbjct: 252 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 311
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
G+D + V + ++++P+ + + RAGR
Sbjct: 312 GMDIERVNIAFNYDMPEDSDTYLHRVARAGR 342
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 43/91 (47%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+++ C L+ L A H G+ + R S + +++++VAT FG
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
G+D + V + ++++P+ + + RAGR
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 43/91 (47%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+++ C L+ L A H G+ + R S + +++++VAT FG
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
G+D + V + ++++P+ + + RAGR
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 54/113 (47%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
A+V+ + +E++ L G A H ++ R V+ + +V+VAT
Sbjct: 31 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRRMEFI 373
G+D V LV H+ +P EA+ SGR GR + +L YG +RR +E +
Sbjct: 91 GLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEAL 143
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 6/97 (6%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++ + T + L L + G + H L + R ++DD+ R +V++ T
Sbjct: 38 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 97
Query: 321 GIDRKDVRLVCHFNIPKSMEA------FYQESGRAGR 351
GID V +V ++++P + GR GR
Sbjct: 98 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGR 134
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 21/90 (23%), Positives = 43/90 (47%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++ C L+ L A H G+ + R S + +++++VAT FG G
Sbjct: 35 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 94
Query: 322 IDRKDVRLVCHFNIPKSMEAFYQESGRAGR 351
+D + V + ++++P+ + + RAGR
Sbjct: 95 MDIERVNIAFNYDMPEDSDTYLHRVARAGR 124
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 6/97 (6%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++ + T + L L + G + H L + R ++DD+ R +V++ T
Sbjct: 39 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 98
Query: 321 GIDRKDVRLVCHFNIPKSMEA------FYQESGRAGR 351
GID V V ++++P + GR GR
Sbjct: 99 GIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGR 135
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 6/97 (6%)
Query: 261 AIVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGM 320
+I++ + T + L L + G + H L + R ++DD+ R +V++ T
Sbjct: 40 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 99
Query: 321 GIDRKDVRLVCHFNIPKSMEA------FYQESGRAGR 351
GID V V ++++P + GR GR
Sbjct: 100 GIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGR 136
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 56/186 (30%), Positives = 84/186 (45%), Gaps = 19/186 (10%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSP--LIALMENQVIGLKE 100
Q++AI L GRD L TG GK+ + +P L L+ +P L AL+ L
Sbjct: 70 QIEAIPLALQGRDIIGLAETGSGKTGAFALPILN----ALLETPQRLFALVLTPTRELAF 125
Query: 101 KGIAGEFLSSTQTMQVKTK-IYEDLDSGKPSLRLLYVTPELTATPG----FMSKLKKIHS 155
+ I+ +F + ++ V++ I +DS SL L + ATPG + K +
Sbjct: 126 Q-ISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNL 184
Query: 156 RGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKVQKDVMESL 215
R L LV +DEA I DF K+ L+ D +AT KVQK ++
Sbjct: 185 RALKYLV-MDEADRI--LNMDFETEVDKI--LKVIPRDRKTFLFSATMTKKVQK--LQRA 237
Query: 216 CLQNPL 221
L+NP+
Sbjct: 238 ALKNPV 243
>pdb|2ZJO|A Chain A, Crystal Structure Of Hepatitis C Virus Ns3 Helicase With A
Novel Inhibitor
Length = 482
Score = 37.0 bits (84), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LSA GI AY+ GL+ SV+ +S VVVAT A G
Sbjct: 210 LIFCHSKKKCDELAAKLSALGIHAVAYYRGLD----VSVIP---ASGNVVVVATDALMTG 262
Query: 322 I 322
Sbjct: 263 F 263
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 36.6 bits (83), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPAL------AKPGI-VLVVSP 86
Q+ AI +L GR+ PTG GK++ + IP L A G L++SP
Sbjct: 56 QMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISP 106
>pdb|8OHM|A Chain A, Crystal Structure Of Rna Helicase From Genotype 1b
Hepatitis C Virus: Mechanism Of Unwinding Duplex Rna
Length = 435
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LSA G++ AY+ GL+ SV+ +S VVVAT A G
Sbjct: 176 LIFCHSKKKCDELAAKLSALGLNAVAYYRGLD----VSVIP---TSGDVVVVATDALMTG 228
>pdb|4B75|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B75|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
Length = 666
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS GI+ AY+ GL+ ++ D VVVAT A G
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGD-------VVVVATDALMTG 452
>pdb|1CU1|A Chain A, Crystal Structure Of An Enzyme Complex From Hepatitis C
Virus
pdb|1CU1|B Chain B, Crystal Structure Of An Enzyme Complex From Hepatitis C
Virus
Length = 645
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS GI+ AY+ GL+ ++ D VVVAT A G
Sbjct: 379 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGD-------VVVVATDALMTG 431
>pdb|4B6E|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B6E|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B6F|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B6F|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
Length = 683
Score = 35.8 bits (81), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS GI+ AY+ GL+ ++ D VVVAT A G
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGD-------VVVVATDALMTG 452
>pdb|3O8B|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8B|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8C|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8C|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8D|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8D|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8R|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8R|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|4B71|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B71|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B73|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B73|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B74|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B74|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B76|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B76|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
Length = 666
Score = 35.8 bits (81), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS GI+ AY+ GL+ ++ D VVVAT A G
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGD-------VVVVATDALMTG 452
>pdb|4A92|A Chain A, Full-Length Hcv Ns3-4a Protease-Helicase In Complex With A
Macrocyclic Protease Inhibitor.
pdb|4A92|B Chain B, Full-Length Hcv Ns3-4a Protease-Helicase In Complex With A
Macrocyclic Protease Inhibitor
Length = 666
Score = 35.8 bits (81), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS GI+ AY+ GL+ ++ D VVVAT A G
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGD-------VVVVATDALMTG 452
>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 = 35.8 bits (81), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 45/198 (22%), Positives = 82/198 (41%), Gaps = 40/198 (20%)
Query: 40 RDKQLDAIQAVLSGRDCFCLMPTGGGKS-----MCYQ----IPALAKPGIVLVVSPLIAL 90
R Q++ Q ++G++ PTG GK+ +C +PA K +V + + +
Sbjct: 9 RSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVY 68
Query: 91 MENQVI--------GLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTA 142
+ + + G +GI+GE S+ K+ ED D ++ VTP++
Sbjct: 69 EQQKNVFKHHFERQGYSVQGISGENFSNVSV----EKVIEDSD-------IIVVTPQILV 117
Query: 143 TP---GFMSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRP-SYRKLSSLRNYLPDVP-IL 197
G ++ L + L+ DE H ++ H + R L N +P IL
Sbjct: 118 NSFEDGTLTSL------SIFTLMIFDECHN-TTGNHPYNVLMTRYLEQKFNSASQLPQIL 170
Query: 198 ALTATAAPKVQKDVMESL 215
LTA+ K++ E++
Sbjct: 171 GLTASVGVGNAKNIEETI 188
>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 = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 54/124 (43%), Gaps = 11/124 (8%)
Query: 253 LKANGDTCAIVYCLERTTCDELSAYLSAGGISCAAYHA--------GLNDKARSSVLDDW 304
L+ ++ IV+ R T ++ L GI + GL+ + + +LD++
Sbjct: 356 LQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEF 415
Query: 305 ISSRKQVVVATVAFGMGIDRKDVRLVCHFN-IPKSMEAFYQESGRAGRDQLPSKSLLYYG 363
V+VAT G+D +V LV + +P ++ + Q GR GR +P + ++
Sbjct: 416 ARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSI-QRRGRTGR-HMPGRVIILMA 473
Query: 364 MDDR 367
R
Sbjct: 474 KGTR 477
>pdb|1JR6|A Chain A, Solution Structure Of An Engineered Arginine-Rich
Subdomain 2 Of The Hepatitis C Virus Ns3 Rna Helicase
pdb|1ONB|A Chain A, Solution Structure Of An Engineered Arginine-Rich
Subdomain 2 Of The Hepatitis C Virus Ns3 Rna Helicase
Length = 142
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLN 293
+++C + CDEL+A L A GI+ AY+ GL+
Sbjct: 43 LIFCHSKKKCDELAAKLVALGINAVAYYRGLD 74
>pdb|1A1V|A Chain A, Hepatitis C Virus Ns3 Helicase Domain Complexed With
Single Stranded Sdna
Length = 476
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A L A GI+ AY+ GL+ SV+ +S VVVAT A G
Sbjct: 200 LIFCHSKKKCDELAAKLVALGINAVAYYRGLD----VSVIP---TSGDVVVVATDALMTG 252
>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 = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 45/198 (22%), Positives = 82/198 (41%), Gaps = 40/198 (20%)
Query: 40 RDKQLDAIQAVLSGRDCFCLMPTGGGKS-----MCYQ----IPALAKPGIVLVVSPLIAL 90
R Q++ Q ++G++ PTG GK+ +C +PA K +V + + +
Sbjct: 250 RSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVY 309
Query: 91 MENQVI--------GLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTA 142
+ + + G +GI+GE S+ K+ ED D ++ VTP++
Sbjct: 310 EQQKNVFKHHFERQGYSVQGISGENFSNVSV----EKVIEDSD-------IIVVTPQILV 358
Query: 143 TP---GFMSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRP-SYRKLSSLRNYLPDVP-IL 197
G ++ L + L+ DE H ++ H + R L N +P IL
Sbjct: 359 NSFEDGTLTSL------SIFTLMIFDECHN-TTGNHPYNVLMTRYLEQKFNSASQLPQIL 411
Query: 198 ALTATAAPKVQKDVMESL 215
LTA+ K++ E++
Sbjct: 412 GLTASVGVGNAKNIEETI 429
>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 = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 45/198 (22%), Positives = 82/198 (41%), Gaps = 40/198 (20%)
Query: 40 RDKQLDAIQAVLSGRDCFCLMPTGGGKS-----MCYQ----IPALAKPGIVLVVSPLIAL 90
R Q++ Q ++G++ PTG GK+ +C +PA K +V + + +
Sbjct: 250 RSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVY 309
Query: 91 MENQVI--------GLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTA 142
+ + + G +GI+GE S+ K+ ED D ++ VTP++
Sbjct: 310 EQQKNVFKHHFERQGYSVQGISGENFSNVSV----EKVIEDSD-------IIVVTPQILV 358
Query: 143 TP---GFMSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRP-SYRKLSSLRNYLPDVP-IL 197
G ++ L + L+ DE H ++ H + R L N +P IL
Sbjct: 359 NSFEDGTLTSL------SIFTLMIFDECHN-TTGNHPYNVLMTRYLEQKFNSASQLPQIL 411
Query: 198 ALTATAAPKVQKDVMESL 215
LTA+ K++ E++
Sbjct: 412 GLTASVGVGNAKNIEETI 429
>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 = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPAL---AKPGIVLVVSPLIAL 90
Q +A++ V SG++ MPT GK++ ++ + K G L V PL AL
Sbjct: 30 QAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRAL 80
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 9/92 (9%)
Query: 285 CAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGID----RKDVRLVCHFN-IPKSM 339
A +HAGL + R V D + +VVVAT G++ R VR + F+ K +
Sbjct: 299 AAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRI 358
Query: 340 EA--FYQESGRAGRDQLPSK--SLLYYGMDDR 367
+ + Q +GRAGR + + +++ G DR
Sbjct: 359 KVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR 390
>pdb|3KQH|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQH|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQK|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQK|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
Length = 436
Score = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS G++ AY+ GL+ SV+ +S +VVAT A G
Sbjct: 177 LIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD----VSVIP---TSGDVIVVATDALMTG 229
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 40/158 (25%), Positives = 63/158 (39%), Gaps = 25/158 (15%)
Query: 34 FGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPA---------LAKPGI-VLV 83
G + Q +I+ +L GRD TG GK++ + IPA + + G VL+
Sbjct: 72 MGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLI 131
Query: 84 VSPLIALMENQVIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTP----- 138
+SP L Q G+ ++ + + M + E G + ++ TP
Sbjct: 132 LSPTREL-AMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGN-GINIIVATPGRLLD 189
Query: 139 ELTATPGFMSKLKKIHSRGLLNLVAIDEAHCISSWGHD 176
+ TPGFM K L + IDEA I G +
Sbjct: 190 HMQNTPGFMYK--------NLQCLVIDEADRILDVGFE 219
>pdb|3KQL|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQL|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQN|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|C Chain C, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|D Chain D, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|E Chain E, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|F Chain F, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
Length = 437
Score = 33.9 bits (76), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A LS G++ AY+ GL+ SV+ +S +VVAT A G
Sbjct: 177 LIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD----VSVIP---TSGDVIVVATDALMTG 229
>pdb|1HEI|A Chain A, Structure Of The Hepatitis C Virus Rna Helicase Domain
pdb|1HEI|B Chain B, Structure Of The Hepatitis C Virus Rna Helicase Domain
Length = 451
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLN 293
+++C + CDEL+A L A GI+ AY+ GL+
Sbjct: 186 LIFCHSKKKCDELAAKLVALGINAVAYYRGLD 217
>pdb|2F55|A Chain A, Two Hepatitis C Virus Ns3 Helicase Domains Complexed With
The Same Strand Of Dna
pdb|2F55|B Chain B, Two Hepatitis C Virus Ns3 Helicase Domains Complexed With
The Same Strand Of Dna
pdb|2F55|C Chain C, Two Hepatitis C Virus Ns3 Helicase Domains Complexed With
The Same Strand Of Dna
Length = 435
Score = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 262 IVYCLERTTCDELSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVATVAFGMG 321
+++C + CDEL+A L+ G++ AY+ GL+ + D VVVAT A G
Sbjct: 176 LIFCHSKKKCDELAAKLTGLGLNAVAYYRGLDVSVIPPIGD-------VVVVATDALMTG 228
>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 = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 288 YHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESG 347
+H + R+S++ + ++V T G+D +V V +P + + G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 348 RAGRDQLPSKSLLYYGMDD 366
R R S+L+ D+
Sbjct: 126 RTARSGKEGSSVLFICKDE 144
>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 = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 288 YHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESG 347
+H + R+S++ + ++V T G+D +V V +P + + G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 348 RAGRDQLPSKSLLYYGMDD 366
R R S+L+ D+
Sbjct: 126 RTARSGKEGSSVLFICKDE 144
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 47/100 (47%), Gaps = 17/100 (17%)
Query: 266 LERTTCDE---LSAYLSAGGISCAAYHAGLNDKARSSVLDDWISSRKQVVVA--TVAFGM 320
+E DE L + +S G A +HAGL+ R + + + + +V+VA T+A G+
Sbjct: 296 IEEGGSDEKELLKSLISKG---VAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGV 352
Query: 321 GIDRKDVRLVCHFNIPKSMEAFYQE---------SGRAGR 351
+ + V + + K + +Y E SGRAGR
Sbjct: 353 NLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGR 392
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 288 YHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESG 347
+H + R+S++ + ++V T G+D +V V +P + + G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 348 RAGRDQLPSKSLLYYGMDD 366
R R S+L+ D+
Sbjct: 126 RTARSGKEGSSVLFICKDE 144
>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
pdb|1VEC|B Chain B, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
Length = 206
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 63/145 (43%), Gaps = 21/145 (14%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAK--------PGIVLVVSPLIALMENQ 94
Q ++I LSGRD G GKS Y IP L + +V+V + +AL +Q
Sbjct: 30 QEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQ 89
Query: 95 VIGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPELTATPGFMSKL--KK 152
+ K + G + +T T + +D+ +RL + ATPG + L K
Sbjct: 90 ICIQVSKHMGGAKVMATTG---GTNLRDDI------MRLDDTVHVVIATPGRILDLIKKG 140
Query: 153 IHSRGLLNLVAIDEAHCISSWGHDF 177
+ + ++ +DEA + S DF
Sbjct: 141 VAKVDHVQMIVLDEADKLLS--QDF 163
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 47/177 (26%), Positives = 77/177 (43%), Gaps = 20/177 (11%)
Query: 46 AIQA-----VLSGRDCFCLMPTGGGKSMCYQIPALA----KPGIVLVVSPL-IALMENQV 95
AIQA LSG D + TG GK++ Y +PA+ +P + P+ + L +
Sbjct: 68 AIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRE 127
Query: 96 IGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPEL-TATPGFMSKLKKIH 154
+ + + +A E+ + + T IY G P +R L E+ ATPG + +
Sbjct: 128 LAQQVQQVAAEYCRACRLK--STCIYGGAPKG-PQIRDLERGVEICIATPGRLIDFLECG 184
Query: 155 SRGL--LNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKVQK 209
L + +DEA + G F P RK+ + PD L +AT +V++
Sbjct: 185 KTNLRRTTYLVLDEADRMLDMG--FEPQIRKI--VDQIRPDRQTLMWSATWPKEVRQ 237
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 288 YHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESG 347
+H + R+S++ + ++V T G+D +V V +P + + G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 348 RAGRDQLPSKSLLYYGMDD 366
R R S+L+ D+
Sbjct: 381 RTARSGKEGSSVLFICKDE 399
>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 = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 288 YHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESG 347
+H + R+S++ + ++V T G+D +V V +P + + G
Sbjct: 372 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 431
Query: 348 RAGRDQLPSKSLLYYGMDD 366
R R S+L+ D+
Sbjct: 432 RTARSGKEGSSVLFICKDE 450
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 288 YHAGLNDKARSSVLDDWISSRKQVVVATVAFGMGIDRKDVRLVCHFNIPKSMEAFYQESG 347
+H + R+S++ + ++V T G+D +V V +P + + G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 348 RAGRDQLPSKSLLYYGMDD 366
R R S+L+ D+
Sbjct: 381 RTARSGKEGSSVLFICKDE 399
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 47/189 (24%), Positives = 73/189 (38%), Gaps = 35/189 (18%)
Query: 43 QLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPALAKPGIVLVVSPLIALMENQ-------- 94
Q +AI A+L RD TG GK+ + IP +++ L+ NQ
Sbjct: 50 QKNAIPAILEHRDIMACAQTGSGKTAAFLIP---------IINHLVCQDLNQQRYSKTAY 100
Query: 95 ---VIGLKEKGIAGEFLSSTQTMQVKTK-----IYEDLDSGKPSLRLLYVTPELTATPG- 145
+I + +A + LS +Q + T +Y D+ + L ATPG
Sbjct: 101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGR 160
Query: 146 ---FMSKLKKIHSRGLLNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDV--PILALT 200
F+ K K S + +DEA + G F P RK+ N + L +
Sbjct: 161 LVDFIEKNKI--SLEFCKYIVLDEADRMLDMG--FEPQIRKIIEESNMPSGINRQTLMFS 216
Query: 201 ATAAPKVQK 209
AT ++QK
Sbjct: 217 ATFPKEIQK 225
>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
pdb|3FE2|B Chain B, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
Length = 242
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 47/177 (26%), Positives = 77/177 (43%), Gaps = 20/177 (11%)
Query: 46 AIQA-----VLSGRDCFCLMPTGGGKSMCYQIPALA----KPGIVLVVSPL-IALMENQV 95
AIQA LSG D + TG GK++ Y +PA+ +P + P+ + L +
Sbjct: 54 AIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRE 113
Query: 96 IGLKEKGIAGEFLSSTQTMQVKTKIYEDLDSGKPSLRLLYVTPEL-TATPGFMSKLKKIH 154
+ + + +A E+ + + T IY G P +R L E+ ATPG + +
Sbjct: 114 LAQQVQQVAAEYCRACRLK--STCIYGGAPKG-PQIRDLERGVEICIATPGRLIDFLECG 170
Query: 155 SRGL--LNLVAIDEAHCISSWGHDFRPSYRKLSSLRNYLPDVPILALTATAAPKVQK 209
L + +DEA + G F P RK+ + PD L +AT +V++
Sbjct: 171 KTNLRRTTYLVLDEADRMLDMG--FEPQIRKI--VDQIRPDRQTLMWSATWPKEVRQ 223
>pdb|3UIT|A Chain A, Overall Structure Of PatjPALS1MALS COMPLEX
pdb|3UIT|B Chain B, Overall Structure Of PatjPALS1MALS COMPLEX
pdb|3UIT|C Chain C, Overall Structure Of PatjPALS1MALS COMPLEX
pdb|3UIT|D Chain D, Overall Structure Of PatjPALS1MALS COMPLEX
Length = 265
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 34/78 (43%), Gaps = 15/78 (19%)
Query: 18 KPLHEKEA--LVKLLRWHFGHAQFRDKQLDAIQAVLSGRDCFCLMPTGGGKSMCYQIPAL 75
KP+H KE L LL IQA+L D GGG + +Q PAL
Sbjct: 156 KPVHHKEGQELTALLNT------------PHIQALLLAHDKVAEQEMGGGLEVLFQGPAL 203
Query: 76 AKP-GIVLVVSPLIALME 92
+P G+ VS + L+E
Sbjct: 204 VEPLGLERDVSRAVELLE 221
>pdb|2E46|A Chain A, Crystal Structure Analysis Of The Clock Protein Ea4
Length = 157
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 24/38 (63%)
Query: 438 HPNLLAKYLGELTSAVLQKNHFSQIFISSQDMTDGGQY 475
HPN + +++G+L + V +NH+S+I + ++ G +
Sbjct: 78 HPNDVNRHVGDLGNVVFDENHYSRIDLVDDQISLSGPH 115
>pdb|2E47|A Chain A, Crystal Structure Analysis Of The Clock Protein Ea4
(Glycosylation Form)
pdb|2E47|B Chain B, Crystal Structure Analysis Of The Clock Protein Ea4
(Glycosylation Form)
Length = 156
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 24/38 (63%)
Query: 438 HPNLLAKYLGELTSAVLQKNHFSQIFISSQDMTDGGQY 475
HPN + +++G+L + V +NH+S+I + ++ G +
Sbjct: 77 HPNDVNRHVGDLGNVVFDENHYSRIDLVDDQISLSGPH 114
>pdb|2KS6|A Chain A, Nmr Solution Structure Of Alg13 --- Obtained With
Iterative Cs-Rosetta From Backbone Nmr Data
Length = 201
Score = 29.3 bits (64), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 33/125 (26%), Positives = 49/125 (39%), Gaps = 11/125 (8%)
Query: 327 VRLVCHF--NIPKSMEAFYQESGRAGRDQLPSKSLLYYGMDDRRRMEFILXXXXXXXXXX 384
VRL+ F N E QE R G+ + + +G D R ++
Sbjct: 40 VRLIIQFGRNYSSEFEHLVQE--RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFD 97
Query: 385 FSTRERSSKKSISDFSQMVDYCEGSGCRRKKILESFGEQIPVSLCKNSCDACKHPNLLAK 444
FST+ +S I D+S +V G+G IL+S P+ +C N H +A
Sbjct: 98 FSTKMQS---IIRDYSDLVISHAGTG----SILDSLRLNKPLIVCVNDSLMDNHQQQIAD 150
Query: 445 YLGEL 449
EL
Sbjct: 151 KFVEL 155
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
0.316 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,176,635
Number of Sequences: 62578
Number of extensions: 735582
Number of successful extensions: 1574
Number of sequences better than 100.0: 78
Number of HSP's better than 100.0 without gapping: 65
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1469
Number of HSP's gapped (non-prelim): 99
length of query: 724
length of database: 14,973,337
effective HSP length: 106
effective length of query: 618
effective length of database: 8,340,069
effective search space: 5154162642
effective search space used: 5154162642
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)