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= 037567
(374 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 = 290 bits (743), Expect = 7e-79, Method: Compositional matrix adjust.
Identities = 156/374 (41%), Positives = 225/374 (60%), Gaps = 12/374 (3%)
Query: 5 LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
L++ FGY FRP Q+++I ++ RDCLVVM TG GKSLCYQ+P L+ +VVSPLIS
Sbjct: 17 LQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLIS 76
Query: 65 LMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSK 121
LM+DQV L+ G+ A L S QT V T TG +LL++ PE+ ++ +F
Sbjct: 77 LMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPER--LMLDNFLEH 134
Query: 122 LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN 181
L L AVDEAHCIS+WGHDFR EY L +LR +PF+ALTATA + R DI+
Sbjct: 135 LAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVR 194
Query: 182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV 241
L L +P + I+SFDR N+ Y ++ +D+L++ + + +G I+YC + V
Sbjct: 195 LLGLNDPLIQISSFDRPNIRY---MLMEKFKPLDQLMRYVQEQRGKSG--IIYCNSRAKV 249
Query: 242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI 301
E+ + L+ G+ A YH + + R + F RD+++++VAT+AFGMGI+KP+VR V+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 302 HYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLL 361
H+ P+ +ESYYQE+GR GRDG+ + L+Y ++ A C E + + Q I L
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR-RCLEEKPQGQLQDIERHKL 368
Query: 362 AAQ-RYCLLTTCRR 374
A + TCRR
Sbjct: 369 NAMGAFAEAQTCRR 382
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 281 bits (718), Expect = 5e-76, Method: Compositional matrix adjust.
Identities = 154/376 (40%), Positives = 220/376 (58%), Gaps = 16/376 (4%)
Query: 5 LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
L++ FGY FRP Q+++I ++ RDCLVV TG GKSLCYQ+P L+ +VVSPLIS
Sbjct: 17 LQETFGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPLIS 76
Query: 65 LMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSK 121
L +DQV L+ G+ A L S QT V T TG +LL++ PE+ + +F
Sbjct: 77 LXKDQVDQLQANGVAAACLNSTQTREQQLEVXTGCRTGQIRLLYIAPERLXLD--NFLEH 134
Query: 122 LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN 181
L L AVDEAHCIS+WGHDFR EY L +LR +PF ALTATA + R DI+
Sbjct: 135 LAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTATADDTTRQDIVR 194
Query: 182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSF--VDELVQEILKSVAGAGSIIVYCMTIK 239
L L +P + I+SFDR N+ Y + + F +D+L + + + +G I+YC +
Sbjct: 195 LLGLNDPLIQISSFDRPNIRYXLX-----EKFKPLDQLXRYVQEQRGKSG--IIYCNSRA 247
Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
VE+ + L+ G+ A YH + + R + F RD+++++VAT+AFG GI+KP+VR
Sbjct: 248 KVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRF 307
Query: 300 VIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAI-ME 358
V+H+ P+ +ESYYQE+GR GRDG+ + L+Y ++ A C E + + Q I
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLR-RCLEEKPQGQLQDIERH 366
Query: 359 SLLAAQRYCLLTTCRR 374
L A + TCRR
Sbjct: 367 KLNAXGAFAEAQTCRR 382
>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 = 259 bits (663), Expect = 1e-69, Method: Compositional matrix adjust.
Identities = 143/341 (41%), Positives = 204/341 (59%), Gaps = 16/341 (4%)
Query: 5 LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
L+ F FRP Q + I + ++ +VM TG GKSLCYQLP L + LV+ PLIS
Sbjct: 36 LQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLIS 95
Query: 65 LMQDQVMSLKQRGINAEFLGSAQTDSSVQ-TKAE----TGYFQLLFMTPEKACIIPISFW 119
LM+DQ+M LKQ GI+A L ++ + V+ AE +L+++TPEK + F
Sbjct: 96 LMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKM-FM 154
Query: 120 SKLLKA----GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV 175
S+L KA AVDE HC S+WGHDFR +YK L L+ + LTATAT V
Sbjct: 155 SRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHV 214
Query: 176 RIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAG---AGSII 232
D L ++ + ASF+R NL+Y V+ + S ++ +++I+K + G S I
Sbjct: 215 LTDAQKILCIEKCFTFTASFNRPNLYYEVR---QKPSNTEDFIEDIVKLINGRYKGQSGI 271
Query: 233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI 292
+YC + KD E+++ +L+ LG+ AG YH + + + HR + +EI+V+VAT+AFGMGI
Sbjct: 272 IYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGI 331
Query: 293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYA 333
DKPDVR VIH+ K++E+YYQESGR GRD + + C LYY
Sbjct: 332 DKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYG 372
>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 = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 37/92 (40%), Positives = 55/92 (59%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+V+C T +D +E++ L+ +G KAG HG + RE+ RLF + +IR+++AT G
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
ID D+ VI+Y P+ ESY GR GR G
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAG 333
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + V+ +++ +++ + HG M K RE + F RV+++T + G
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
+D P V +I+Y P E Y GR GR G V NF K D
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVA------VNFVKND 347
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 61.2 bits (147), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + V+ +++ +++ + HG M K RE + F RV+++T + G
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
+D P V +I+Y P E Y GR GR G V NF K D
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVA------VNFVKND 347
>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 = 9e-10, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + V+ +++ +++ + HG M K RE + F RV+++T + G
Sbjct: 259 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 318
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
+D P V +I+Y P E Y GR GR G V NF K D
Sbjct: 319 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 362
>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 = 9e-10, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + V+ +++ +++ + HG M K RE + F RV+++T + G
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
+D P V +I+Y P E Y GR GR G V NF K D
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 384
>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 = 9e-10, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + V+ +++ +++ + HG M K RE + F RV+++T + G
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
+D P V +I+Y P E Y GR GR G V NF K D
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 384
>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 = 9e-10, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + V+ +++ +++ + HG M K RE + F RV+++T + G
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
+D P V +I+Y P E Y GR GR G V NF K D
Sbjct: 340 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 383
>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 = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 40/131 (30%), Positives = 62/131 (47%), Gaps = 3/131 (2%)
Query: 193 ASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG 252
A +N+ + V + F L++++L + S I++C T + V +++ L LG
Sbjct: 3 AGLTTRNIEHAVIQVREENKF--SLLKDVLMT-ENPDSCIIFCRTKEHVNQLTDELDDLG 59
Query: 253 VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESY 312
HG M + R + F R E R +VAT GID ++ VI+Y P ESY
Sbjct: 60 YPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESY 119
Query: 313 YQESGRCGRDG 323
+GR GR G
Sbjct: 120 VHRTGRTGRAG 130
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 82/331 (24%), Positives = 133/331 (40%), Gaps = 34/331 (10%)
Query: 10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP------PLVTGKTALVVSPL- 62
G+ P Q++ I I RD L G+GK+ + +P P + AL++ P
Sbjct: 40 GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR 99
Query: 63 -ISLMQDQVMSL--KQRGINAEFL-GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF 118
++L QV+ K GI+ G + ET +L TP + +
Sbjct: 100 ELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNET--VHILVGTPGRVLDLASRK 157
Query: 119 WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
+ L + LF +DEA + DF+ +Q+ L +L +AT + +
Sbjct: 158 VADL--SDCSLFIMDEADKM--LSRDFKTIIEQI----LSFLPPTHQSLLFSATFPLTVK 209
Query: 179 IINSLKLKNPYVTIASFDRKNLF--YGVKVINRGQSFVDELVQ----EILKSVAGAGSII 232
L PY NL +K I + +FV+E + L S I
Sbjct: 210 EFMVKHLHKPY-------EINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAI 262
Query: 233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI 292
++C + VE ++K + LG H +M + R + F + ++R +V + GI
Sbjct: 263 IFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGI 322
Query: 293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
D V VI++ PKT E+Y GR GR G
Sbjct: 323 DIQAVNVVINFDFPKTAETYLHRIGRSGRFG 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 = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 45/91 (49%)
Query: 225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA 284
VA +V+ T + EEI++ L +LG A HG M RE F + E+RV+VA
Sbjct: 25 VASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVA 84
Query: 285 TMAFGMGIDKPDVRHVIHYGCPKTLESYYQE 315
T G+D P V V+HY P E+Y
Sbjct: 85 TDVAARGLDIPQVDLVVHYRMPDRAEAYQHR 115
>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 = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 45/91 (49%)
Query: 225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA 284
VA +V+ T + EEI++ L +LG A HG + RE F + E+RV+VA
Sbjct: 28 VASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVA 87
Query: 285 TMAFGMGIDKPDVRHVIHYGCPKTLESYYQE 315
T G+D P V V+HY P E+Y
Sbjct: 88 TDVAARGLDIPQVDLVVHYRLPDRAEAYQHR 118
>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 = 3e-08, Method: Compositional matrix adjust.
Identities = 31/117 (26%), Positives = 52/117 (44%)
Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
++L + +V+ T K + + L G + HG + REEA F +
Sbjct: 38 DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 97
Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN 336
++VAT G+D +V+HVI++ P +E Y GR GR G + ++ N
Sbjct: 98 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN 154
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 76/326 (23%), Positives = 132/326 (40%), Gaps = 33/326 (10%)
Query: 7 KYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLM 66
+ G+ F Q I +++ ++ +V TGSGK+ Y +P L G +LVV+P L
Sbjct: 10 REMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELT 69
Query: 67 QDQVMSLKQRGINAEFLGS--AQTDSSVQTKAETGYFQ---LLFMTPEKACIIPISFWSK 121
+ ++ G ++ + A+ + KA+ + ++ TP + + WSK
Sbjct: 70 RQVASHIRDIG---RYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRL----LDLWSK 122
Query: 122 --LLKAGVCLFAVDEAHCISEWG--HDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI 177
+ + + +DEA + E G D ++ Q + L F A KV
Sbjct: 123 GVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGL---FSATIPEEIRKVVK 179
Query: 178 DIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
D I + + + +A+ + K F VK + +S V L + K V IV+ T
Sbjct: 180 DFITNYEEIEACIGLANVEHK--FVHVK--DDWRSKVQALRENKDKGV------IVFVRT 229
Query: 238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
V ++ + A G + R F E +++ T G+D P V
Sbjct: 230 RNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLV 285
Query: 298 RHVIHYGCPKTLESYYQESGRCGRDG 323
VI++ P+ L +Y GR GR G
Sbjct: 286 EKVINFDAPQDLRTYIHRIGRTGRMG 311
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 31/118 (26%), Positives = 52/118 (44%)
Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
++L + +V+ T K + + L G + HG + REEA F +
Sbjct: 268 DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 327
Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNF 337
++VAT G+D +V+HVI++ P +E Y GR GR G + ++ N
Sbjct: 328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI 385
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 22/40 (55%)
Query: 11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL 50
Y+ P QK I I EKRD + TGSGK+ + LP L
Sbjct: 35 YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 74
>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 = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 46/92 (50%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
IV+ + V E++ L++ G+ G+M R EA + + V+VAT G
Sbjct: 34 IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
ID PDV HV ++ P++ ++Y GR R G
Sbjct: 94 IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/129 (26%), Positives = 61/129 (47%), Gaps = 8/129 (6%)
Query: 231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM 290
++++ DV+ I + L GV+A HG + R +A F + V+VAT
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTE 350
G+D P ++HVI+Y P+ +E+Y GR G G + + ++ C ES
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKA--------CDESVLM 168
Query: 351 NQRTAIMES 359
+ + ++E+
Sbjct: 169 DLKALLLEA 177
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 47/96 (48%)
Query: 228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA 287
A IV+ T + + ++ L + + HG RE+A R F ++V++AT
Sbjct: 300 ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSV 359
Query: 288 FGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
G+D +++HVI+Y P ++ Y GR GR G
Sbjct: 360 ASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 21/41 (51%)
Query: 10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL 50
GY + P QK I I RD + TGSGK+ + LP L
Sbjct: 75 GYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPIL 115
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 44/92 (47%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
I++C + + VE ++K + QLG H +M + R F R +V T F G
Sbjct: 48 IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
ID V VI++ PK E+Y GR GR G
Sbjct: 108 IDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 48/185 (25%), Positives = 73/185 (39%), Gaps = 19/185 (10%)
Query: 164 FVALTATATEKVR------IDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL 217
V +AT + VR + N+L+L+ V + + K L+ K N F D L
Sbjct: 180 LVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAI--KQLYMDCK--NEADKF-DVL 234
Query: 218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD 277
+ L V GS I++ T K + LK G + HG + ++ R+ F
Sbjct: 235 TE--LYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREG 292
Query: 278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLY 331
+V++ T GID P V V++Y P +Y GR GR G V +
Sbjct: 293 RSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
Query: 332 YARSN 336
N
Sbjct: 353 VHDKN 357
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 78/327 (23%), Positives = 138/327 (42%), Gaps = 35/327 (10%)
Query: 5 LKKYFGYSVFRP--YQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL------VTGKTA 56
L+ FGY P Q+ I IIE D L +G+GK+ + + L V A
Sbjct: 34 LRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQA 93
Query: 57 LVVSPLISL---MQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-- 111
L+++P L +Q VM+L ++ + S V+ Q++ TP +
Sbjct: 94 LMLAPTRELALQIQKVVMALAFH-MDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFD 152
Query: 112 CIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP---FVALT 168
I F + +K +F +DEA + G F+ + Q+ F L P V L+
Sbjct: 153 NIQRRRFRTDKIK----MFILDEADEMLSSG--FKEQIYQI-----FTLLPPTTQVVLLS 201
Query: 169 ATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVK---VINRGQSFVDELVQEILKSV 225
AT V +++ ++NP + D L G+K V + + E + ++ S+
Sbjct: 202 ATMPNDV-LEVTTKF-MRNPVRILVKKDELTL-EGIKQFYVNVEEEEYKYECLTDLYDSI 258
Query: 226 AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT 285
+ ++I +C T + VEE++ L+ + + + R+ + F R++++T
Sbjct: 259 SVTQAVI-FCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILIST 317
Query: 286 MAFGMGIDKPDVRHVIHYGCPKTLESY 312
GID V VI+Y P E+Y
Sbjct: 318 DLLARGIDVQQVSLVINYDLPANKENY 344
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
+HG++ R + F +DE ++V T G+D P+V V+ G P L +Y G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 318 RCGRDGIASVCWLY 331
R R G L+
Sbjct: 381 RTARSGKEGSSVLF 394
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
+HG++ R + F +DE ++V T G+D P+V V+ G P L +Y G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 318 RCGRDGIASVCWLY 331
R R G L+
Sbjct: 126 RTARSGKEGSSVLF 139
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
+HG++ R + F +DE ++V T G+D P+V V+ G P L +Y G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 318 RCGRDGIASVCWLY 331
R R G L+
Sbjct: 126 RTARSGKEGSSVLF 139
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
+HG++ R + F +DE ++V T G+D P+V V+ G P L +Y G
Sbjct: 372 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 431
Query: 318 RCGRDGIASVCWLY 331
R R G L+
Sbjct: 432 RTARSGKEGSSVLF 445
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 47/185 (25%), Positives = 73/185 (39%), Gaps = 19/185 (10%)
Query: 164 FVALTATATEKVR------IDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL 217
V +AT + VR + N+L+L+ V + + K L+ K N F D L
Sbjct: 180 LVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAI--KQLYMDCK--NEADKF-DVL 234
Query: 218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD 277
+ L + GS I++ T K + LK G + HG + ++ R+ F
Sbjct: 235 TE--LYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREG 292
Query: 278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLY 331
+V++ T GID P V V++Y P +Y GR GR G V +
Sbjct: 293 RSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
Query: 332 YARSN 336
N
Sbjct: 353 VHDKN 357
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
+HG++ R + F +DE ++V T G+D P+V V+ G P L +Y G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 318 RCGRDGIASVCWLY 331
R R G L+
Sbjct: 126 RTARSGKEGSSVLF 139
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
+HG++ R + F +DE ++V T G+D P+V V+ G P L +Y G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 318 RCGRDGIASVCWLY 331
R R G L+
Sbjct: 381 RTARSGKEGSSVLF 394
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
L V ++++ +++ +++ L + A H M + R ++ F + R+
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
+VAT FG G+D V +Y P+ ++Y R GR G + + + N AK
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 361
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
L V ++++ +++ +++ L + A H M + R ++ F + R+
Sbjct: 25 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 84
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
+VAT FG G+D V +Y P+ ++Y R GR G + + + N AK
Sbjct: 85 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 142
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
L V ++++ +++ +++ L + A H M + R ++ F + R+
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
+VAT FG G+D V +Y P+ ++Y R GR G + + + N AK
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 361
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
L V ++++ +++ +++ L + A H M + R ++ F + R+
Sbjct: 243 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 302
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
+VAT FG G+D V +Y P+ ++Y R GR G + + + N AK
Sbjct: 303 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 360
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 47/121 (38%), Gaps = 6/121 (4%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
L V GS I++ T K + LK G + HG + ++ R+ F +V
Sbjct: 30 LYGVXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKV 89
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLYYARS 335
++ T GID P V V++Y P +Y GR GR G V +
Sbjct: 90 LITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 149
Query: 336 N 336
N
Sbjct: 150 N 150
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 45/114 (39%), Gaps = 6/114 (5%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
GS I++ T K + LK G + HG + ++ R+ F +V++ T
Sbjct: 38 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 97
Query: 289 GMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLYYARSN 336
GID P V V++Y P +Y GR GR G V + N
Sbjct: 98 ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 151
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 45/114 (39%), Gaps = 6/114 (5%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
GS I++ T K + LK G + HG + ++ R+ F +V++ T
Sbjct: 36 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 95
Query: 289 GMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLYYARSN 336
GID P V V++Y P +Y GR GR G V + N
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 149
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 49/122 (40%), Gaps = 17/122 (13%)
Query: 219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG-----VKAGTYHGQMGSKAREEAHRL 273
+ IL+ + G VY + DVE I KA ++L + HGQM + E
Sbjct: 803 EAILREILRGGQ--VYYL-YNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMND 859
Query: 274 FIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDGIASVC 328
F V+V T GID P +I H+G L +Q GR GR +
Sbjct: 860 FHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFG----LAQLHQLRGRVGRSHHQAYA 915
Query: 329 WL 330
WL
Sbjct: 916 WL 917
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + VEE++ L+ + + + R+ + F R++++T G
Sbjct: 34 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 292 IDKPDVRHVIHYGCPKTLESY 312
ID V VI+Y P E+Y
Sbjct: 94 IDVQQVSLVINYDLPANKENY 114
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++C T + VEE++ L+ + + + R+ + F R++++T G
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARG 322
Query: 292 IDKPDVRHVIHYGCPKTLESY 312
ID V VI+Y P E+Y
Sbjct: 323 IDVQQVSLVINYDLPANKENY 343
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 36/81 (44%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++ T + V+ +++ + HG M K R+ R F RV++ T G
Sbjct: 258 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 317
Query: 292 IDKPDVRHVIHYGCPKTLESY 312
ID V VI+Y P E+Y
Sbjct: 318 IDVQQVSLVINYDLPTNRENY 338
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 36/81 (44%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
+++ T + V+ +++ + HG M K R+ R F RV++ T G
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343
Query: 292 IDKPDVRHVIHYGCPKTLESY 312
ID V VI+Y P E+Y
Sbjct: 344 IDVQQVSLVINYDLPTNRENY 364
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 45/150 (30%), Positives = 65/150 (43%), Gaps = 21/150 (14%)
Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQM------GSKAR 267
+ E+++E L+ + IIV+ + ++I L + G+KA + GQ G R
Sbjct: 348 LKEIIREQLQRKQNS-KIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQR 406
Query: 268 EEAHRL--FIRDEIRVMVATMAFGMGIDKPDVRHVIHY-GCPKTLESYYQESGRCGRDGI 324
E+ L F R E V+VAT G+D P+V V+ Y P + S Q GR GR
Sbjct: 407 EQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRS-IQRRGRTGRHMP 465
Query: 325 ASVCWLYYARSNFAKGD----FYCGESQTE 350
V L AKG +Y Q E
Sbjct: 466 GRVIIL------MAKGTRDEAYYWSSRQKE 489
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 52/210 (24%), Positives = 85/210 (40%), Gaps = 24/210 (11%)
Query: 127 VCLFAVDEAHC-ISEWGHD---FRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS 182
+ +F +DEA I+ GH R++ + L F +KV D N
Sbjct: 185 IKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NV 243
Query: 183 LKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSI---IVYCMTIK 239
+KLK T+ + + Y V +R + F + L ++ GA +I +++C T K
Sbjct: 244 IKLKREEETLDTIKQ----YYVLCSSRDEKF------QALCNLYGAITIAQAMIFCHTRK 293
Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
++ L + G + G+M + R F + +V+V T GID V
Sbjct: 294 TASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSV 353
Query: 300 VIHYGCP------KTLESYYQESGRCGRDG 323
VI++ P E+Y GR GR G
Sbjct: 354 VINFDLPVDKDGNPDNETYLHRIGRTGRFG 383
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 52/210 (24%), Positives = 85/210 (40%), Gaps = 24/210 (11%)
Query: 127 VCLFAVDEAHC-ISEWGHD---FRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS 182
+ +F +DEA I+ GH R++ + L F +KV D N
Sbjct: 169 IKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NV 227
Query: 183 LKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSI---IVYCMTIK 239
+KLK T+ + + Y V +R + F + L ++ GA +I +++C T K
Sbjct: 228 IKLKREEETLDTIKQ----YYVLCSSRDEKF------QALCNLYGAITIAQAMIFCHTRK 277
Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
++ L + G + G+M + R F + +V+V T GID V
Sbjct: 278 TASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSV 337
Query: 300 VIHYGCP------KTLESYYQESGRCGRDG 323
VI++ P E+Y GR GR G
Sbjct: 338 VINFDLPVDKDGNPDNETYLHRIGRTGRFG 367
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 52/210 (24%), Positives = 85/210 (40%), Gaps = 24/210 (11%)
Query: 127 VCLFAVDEAHC-ISEWGHD---FRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS 182
+ +F +DEA I+ GH R++ + L F +KV D N
Sbjct: 206 IKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NV 264
Query: 183 LKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSI---IVYCMTIK 239
+KLK T+ + + Y V +R + F + L ++ GA +I +++C T K
Sbjct: 265 IKLKREEETLDTIKQ----YYVLCSSRDEKF------QALCNLYGAITIAQAMIFCHTRK 314
Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
++ L + G + G+M + R F + +V+V T GID V
Sbjct: 315 TASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSV 374
Query: 300 VIHYGCP------KTLESYYQESGRCGRDG 323
VI++ P E+Y GR GR G
Sbjct: 375 VINFDLPVDKDGNPDNETYLHRIGRTGRFG 404
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 53/121 (43%), Gaps = 5/121 (4%)
Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRL 273
+D+L+ EI + ++V +T K E+++ LK++G+K H ++ + R E R
Sbjct: 437 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRD 496
Query: 274 FIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDGIASVC 328
+ V+V G+D P+V V G ++ S Q GR R+ V
Sbjct: 497 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVI 556
Query: 329 W 329
Sbjct: 557 M 557
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 53/121 (43%), Gaps = 5/121 (4%)
Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRL 273
+D+L+ EI + ++V +T K E+++ LK++G+K H ++ + R E R
Sbjct: 431 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRD 490
Query: 274 FIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDGIASVC 328
+ V+V G+D P+V V G ++ S Q GR R+ V
Sbjct: 491 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVI 550
Query: 329 W 329
Sbjct: 551 M 551
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 7/126 (5%)
Query: 209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE 268
+GQ +D+L+ EI + V +V +T K E+++ LK+ G+K H ++ + R
Sbjct: 427 KGQ--IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 484
Query: 269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDG 323
E R + V+V G+D P+V V G ++ S Q GR R+
Sbjct: 485 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 544
Query: 324 IASVCW 329
V
Sbjct: 545 NGHVIM 550
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 7/126 (5%)
Query: 209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE 268
+GQ +D+L+ EI + V +V +T K E+++ LK+ G+K H ++ + R
Sbjct: 428 KGQ--IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 485
Query: 269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDG 323
E R + V+V G+D P+V V G ++ S Q GR R+
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
Query: 324 IASVCW 329
V
Sbjct: 546 NGHVIM 551
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 7/126 (5%)
Query: 209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE 268
+GQ +D+L+ EI + V +V +T K E+++ LK+ G+K H ++ + R
Sbjct: 428 KGQ--IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 485
Query: 269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDG 323
E R + V+V G+D P+V V G ++ S Q GR R+
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
Query: 324 IASVCW 329
V
Sbjct: 546 NGHVIM 551
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 7/126 (5%)
Query: 209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE 268
+GQ +D+L+ EI + V +V +T K E+++ LK+ G+K H ++ + R
Sbjct: 428 KGQ--IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 485
Query: 269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDG 323
E R + V+V G+D P+V V G ++ S Q GR R+
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
Query: 324 IASVCW 329
V
Sbjct: 546 NGHVIM 551
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 91/386 (23%), Positives = 149/386 (38%), Gaps = 82/386 (21%)
Query: 10 GYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPP----LVTGKTALVVSPLIS 64
G P Q + +++ ++E L+ TGSGK+L ++ L G A+ V+PL +
Sbjct: 27 GIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRA 86
Query: 65 LMQDQVMSLKQRGINAEFLG--SAQTDSSVQTK-AETGYFQLLFMTPEKACIIPISFWSK 121
L ++ ++ K + E +G A T T A + ++ T EK S W
Sbjct: 87 LTNEKYLTFK----DWELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLD----SLWRH 138
Query: 122 LLK--AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI-- 177
+ V F +DE H +++ +E + R LL AL+AT + +I
Sbjct: 139 RPEWLNEVNYFVLDELHYLNDPERGPVVESVTIRAKRRNLL-----ALSATISNYKQIAK 193
Query: 178 ----DIINSLKLKNPYVTIASF-DRKNLFYGVKVINRGQSFV---DELVQEILKSVAGAG 229
+ + + P + + +RK Y V + V D ++ L S++ G
Sbjct: 194 WLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNG 253
Query: 230 SIIVYCMTIK------------------DVEEISKALKQLG-----------------VK 254
++V+ + K D +S+ LKQL K
Sbjct: 254 QVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISK 313
Query: 255 AGTYHGQMGSKA-REEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH---YGCPKTLE 310
YH SKA R+ F + +I+V+VAT G++ P R VI Y K +
Sbjct: 314 GVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLP-ARTVIIGDIYRFNKKIA 372
Query: 311 SYYQE---------SGRCGRDGIASV 327
YY E SGR GR G +
Sbjct: 373 GYYDEIPIMEYKQMSGRAGRPGFDQI 398
>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 = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 52/210 (24%), Positives = 85/210 (40%), Gaps = 24/210 (11%)
Query: 127 VCLFAVDEAHC-ISEWGH---DFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS 182
+ +F +DEA I+ GH R++ + L F +KV D N
Sbjct: 236 IKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NV 294
Query: 183 LKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSI---IVYCMTIK 239
+KLK T+ + + Y V +R + F + L ++ GA +I +++C T K
Sbjct: 295 IKLKREEETLDTIKQ----YYVLCSSRDEKF------QALCNLYGAITIAQAMIFCHTRK 344
Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
++ L + G + G+M + R F + +V+V T GID V
Sbjct: 345 TASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSV 404
Query: 300 VIHYGCP------KTLESYYQESGRCGRDG 323
VI++ P E+Y GR GR G
Sbjct: 405 VINFDLPVDKDGNPDNETYLHRIGRTGRFG 434
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 7/126 (5%)
Query: 209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE 268
+GQ +D+L+ EI + V +V +T K E+++ LK+ G+K H ++ + R
Sbjct: 453 KGQ--IDDLIGEIHERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 510
Query: 269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDG 323
E R + V+V G+D P+V V G ++ S Q GR R+
Sbjct: 511 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 570
Query: 324 IASVCW 329
V
Sbjct: 571 NGHVIM 576
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 59/144 (40%), Gaps = 11/144 (7%)
Query: 10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP-------PLVTGKTALVVSP- 61
G+ + P Q I ++ R+ L TGSGK+L + +P P G AL++SP
Sbjct: 48 GFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPT 107
Query: 62 --LISLMQDQVMSLKQ-RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF 118
L S + +++ + + G + A + + F +L TP + +
Sbjct: 108 RELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQD 167
Query: 119 WSKLLKAGVCLFAVDEAHCISEWG 142
+ A V VDE+ + E G
Sbjct: 168 PPGIDLASVEWLVVDESDKLFEDG 191
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 43/97 (44%), Gaps = 10/97 (10%)
Query: 239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR 298
+D+ +I K L +HG + +E LF + I+V+ AT F MG++ P R
Sbjct: 386 RDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLP-TR 444
Query: 299 HVIHYGCPK---------TLESYYQESGRCGRDGIAS 326
VI K T + Q +GR GR G+ S
Sbjct: 445 TVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDS 481
>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 = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 85/378 (22%), Positives = 153/378 (40%), Gaps = 79/378 (20%)
Query: 3 STLKKYFGYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPP----LVTGKTAL 57
STLK+ G F P Q + ++ I+E ++ L+ + T SGK+L ++ L G A+
Sbjct: 14 STLKER-GIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAV 72
Query: 58 VVSPLISLMQDQVMSLKQRGINAEFLG--SAQTDSSVQTKAE-TGYFQLLFMTPEK--AC 112
+ PL +L +++ + + E +G A +K E G + ++ T EK +
Sbjct: 73 YIVPLKALAEEKFQEFQ----DWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSL 128
Query: 113 IIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLG-VPFVALTATA 171
+ S W K V + DE H I R L+ + +LG + L+AT
Sbjct: 129 LRHGSSWIK----DVKILVADEIHLIGS-----RDRGATLEVILAHMLGKAQIIGLSATI 179
Query: 172 TEKVRI-DIINSLKLKNPYVTIASFDRKNLFYGVKV------INRGQSFVDELVQEILKS 224
+ + +N+ + + + + R+ +FY V I+R S+ +ELV + ++
Sbjct: 180 GNPEELAEWLNAELIVSDWRPVKL--RRGVFYQGFVTWEDGSIDRFSSW-EELVYDAIRK 236
Query: 225 VAGAGSIIVYCMTIKDVE----EISKALKQL---------------------------GV 253
GA +++ + E E+SK +K L +
Sbjct: 237 KKGA---LIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAI 293
Query: 254 KAGT--YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH-------YG 304
+ G +H +G R F + I+ +VAT GI+ P R +I +G
Sbjct: 294 RGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFG 353
Query: 305 CPK-TLESYYQESGRCGR 321
+ + +Q GR GR
Sbjct: 354 MERIPIIEVHQMLGRAGR 371
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 6/106 (5%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
G I++C EEI++ + G G + R+ F +V+V T
Sbjct: 358 GQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVI 417
Query: 289 GMGIDKPDVRHVIHYGCP------KTLESYYQESGRCGRDGIASVC 328
GID V V++Y P ++Y GR GR G V
Sbjct: 418 ARGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVS 463
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 43/168 (25%), Positives = 70/168 (41%), Gaps = 18/168 (10%)
Query: 3 STLK--KYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV--------- 51
+TLK K G++ Q I+ ++E RD L TGSGK+L + +P +
Sbjct: 64 NTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMP 123
Query: 52 -TGKTALVVSPLISLMQDQVMSLKQ---RGINAEFLGSAQTDSSVQTKAETGYFQLLFMT 107
G L++SP L LK+ ++ L ++ S + + ++ T
Sbjct: 124 RNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVAT 183
Query: 108 PEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKL 155
P + + + K CL +DEA I + G F E KQ+ KL
Sbjct: 184 PGRLLDHMQNTPGFMYKNLQCL-VIDEADRILDVG--FEEELKQIIKL 228
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 35.0 bits (79), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 47/105 (44%), Gaps = 17/105 (16%)
Query: 233 VYCMTIKDVEEISKALKQLGVKAGTYHGQM--GSKAREEAHRLFIRDEIRVMVATMAFGM 290
+ C + D+ +S+ ++ G+++ +G + G+K + D +++VAT A GM
Sbjct: 325 IVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGM 384
Query: 291 GIDKPDVRHVIHYGC--------------PKTLESYYQESGRCGR 321
G++ +R +I Y P T Q +GR GR
Sbjct: 385 GLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGR 428
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 34.7 bits (78), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 254 KAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKT--LES 311
K G HG++ + ++ F ++V+T +GID P +V+ P+ L
Sbjct: 615 KLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRA-NVMVIENPERFGLAQ 673
Query: 312 YYQESGRCGRDGIASVCWL 330
+Q GR GR G + C+L
Sbjct: 674 LHQLRGRVGRGGQEAYCFL 692
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 34.7 bits (78), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 17/140 (12%)
Query: 11 YSVFRPYQKDVIQRIIEKRDCLVVMA-TGSGKSLCYQLPPL-----VTGKTALVVSPLIS 64
+ F P Q V + D + V A TGSGK++C + L + + ++P+ +
Sbjct: 924 FPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEA 983
Query: 65 LMQDQVMSLKQR---GINAEFL---GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF 118
L + M ++ +N + + G TD + K ++ TPEK I+ +
Sbjct: 984 LAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKG-----NIIISTPEKWDILSRRW 1038
Query: 119 WSKLLKAGVCLFAVDEAHCI 138
+ + LF VDE H I
Sbjct: 1039 KQRKNVQNINLFVVDEVHLI 1058
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 34.7 bits (78), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 17/140 (12%)
Query: 11 YSVFRPYQKDVIQRIIEKRDCLVVMA-TGSGKSLCYQLPPL-----VTGKTALVVSPLIS 64
+ F P Q V + D + V A TGSGK++C + L + + ++P+ +
Sbjct: 924 FPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEA 983
Query: 65 LMQDQVMSLKQR---GINAEFL---GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF 118
L + M ++ +N + + G TD + K ++ TPEK I+ +
Sbjct: 984 LAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKG-----NIIISTPEKWDILSRRW 1038
Query: 119 WSKLLKAGVCLFAVDEAHCI 138
+ + LF VDE H I
Sbjct: 1039 KQRKNVQNINLFVVDEVHLI 1058
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 16 PYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP 48
P QK+ I I+E RD + TGSGK+ + +P
Sbjct: 48 PIQKNAIPAILEHRDIMACAQTGSGKTAAFLIP 80
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 60/133 (45%), Gaps = 16/133 (12%)
Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
+L++ I + A +V +T++ EE++ L + G++A H ++ + R+ I
Sbjct: 428 DLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQ----ALI 483
Query: 276 RDEIRV-----MVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDGIA 325
RD +R+ +V G+D P+V V G ++ S Q GR R+
Sbjct: 484 RD-LRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARG 542
Query: 326 SVCWLYYARSNFA 338
V WLY R + A
Sbjct: 543 EV-WLYADRVSEA 554
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 60/133 (45%), Gaps = 16/133 (12%)
Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
+L++ I + A +V +T++ EE++ L + G++A H ++ + R+ I
Sbjct: 427 DLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQ----ALI 482
Query: 276 RDEIRV-----MVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDGIA 325
RD +R+ +V G+D P+V V G ++ S Q GR R+
Sbjct: 483 RD-LRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARG 541
Query: 326 SVCWLYYARSNFA 338
V WLY R + A
Sbjct: 542 EV-WLYADRVSEA 553
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL----------VTGKTALVVS 60
Y + QK I ++ +D L TGSGK+L + +P L G L++S
Sbjct: 45 YRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIIS 104
Query: 61 PLISLMQDQVMSLKQRGINAEF 82
P L L++ G N +F
Sbjct: 105 PTRELAYQTFEVLRKVGKNHDF 126
>pdb|1M3U|A Chain A, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|B Chain B, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|C Chain C, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|D Chain D, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|E Chain E, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|F Chain F, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|G Chain G, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|H Chain H, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|I Chain I, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
pdb|1M3U|J Chain J, Crystal Structure Of Ketopantoate Hydroxymethyltransferase
Complexed The Product Ketopantoate
Length = 264
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 199 NLFYGVKVINRGQSFVDELVQEILK-SVAGAGSIIVYCMTIKDVEEISKAL--KQLGVKA 255
N+F G KV RG D+L+ + L AGA +++ C+ ++ + I++AL +G+ A
Sbjct: 145 NIFGGYKVQGRGDEAGDQLLSDALALEAAGAQLLVLECVPVELAKRITEALAIPVIGIGA 204
Query: 256 GT 257
G
Sbjct: 205 GN 206
>pdb|3B6E|A Chain A, Crystal Structure Of Human Dech-Box Rna Helicase Mda5
(Melanoma Differentiation-Associated Protein 5),
Dech-Domain
Length = 216
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 14 FRPYQKDVIQRIIEKRDCLVVMATGSGKS 42
RPYQ +V Q +E ++ ++ + TGSGK+
Sbjct: 34 LRPYQMEVAQPALEGKNIIICLPTGSGKT 62
>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|B Chain B, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|C Chain C, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|D Chain D, Structure Of Archaeoglobus Fulgidis Xpb
Length = 472
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 8 YFGYSV-FRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISL 65
YF + R YQ+ ++R +++KR C +V+ TGSGK+ L+V P ++L
Sbjct: 87 YFDAEISLRDYQEKALERWLVDKRGC-IVLPTGSGKTHVAMAAINELSTPTLIVVPTLAL 145
Query: 66 MQ 67
+
Sbjct: 146 AE 147
>pdb|2FZ4|A Chain A, Crystal Structure Of The N-Terminal Half Of Archaeoglobus
Fulgidus Xpb
Length = 237
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 8 YFGYSV-FRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISL 65
YF + R YQ+ ++R +++KR C +V+ TGSGK+ L+V P ++L
Sbjct: 87 YFDAEISLRDYQEKALERWLVDKRGC-IVLPTGSGKTHVAMAAINELSTPTLIVVPTLAL 145
Query: 66 MQ 67
+
Sbjct: 146 AE 147
>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 = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 19/94 (20%)
Query: 221 ILKSVAGAGSIIVYCMTIKDVEEISKALK---QLGVKAGTYHGQMGSKAREEAHRLFIRD 277
IL+ + G I+Y T ++ EEI ++LK ++G+ T G + F+
Sbjct: 270 ILEKLGTGG--IIYARTGEEAEEIYESLKNKFRIGIVTATKKGD---------YEKFVEG 318
Query: 278 EIRVMVATMAF----GMGIDKPD-VRHVIHYGCP 306
EI ++ T + G+D P+ +R + GCP
Sbjct: 319 EIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP 352
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 19/94 (20%)
Query: 221 ILKSVAGAGSIIVYCMTIKDVEEISKALK---QLGVKAGTYHGQMGSKAREEAHRLFIRD 277
IL+ + G I+Y T ++ EEI ++LK ++G+ T G + F+
Sbjct: 270 ILEKLGTGG--IIYARTGEEAEEIYESLKNKFRIGIVTATKKGD---------YEKFVEG 318
Query: 278 EIRVMVATMAF----GMGIDKPD-VRHVIHYGCP 306
EI ++ T + G+D P+ +R + GCP
Sbjct: 319 EIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP 352
>pdb|2PG0|A Chain A, Crystal Structure Of Acyl-Coa Dehydrogenase From
Geobacillus Kaustophilus
pdb|2PG0|B Chain B, Crystal Structure Of Acyl-Coa Dehydrogenase From
Geobacillus Kaustophilus
Length = 385
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 24/100 (24%)
Query: 109 EKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEY-----KQLDKLRTFLLGV- 162
EK IIP SFW+K+ + G VDE + G + Y ++L+K+ + L+G+
Sbjct: 37 EKRGIIPRSFWAKMGENGFLCPWVDEKYG----GLNADFAYSVVINEELEKVGSSLVGIG 92
Query: 163 -------PFVALTATATEK-------VRIDIINSLKLKNP 188
P++A T +K V ++I ++ + P
Sbjct: 93 LHNDIVTPYIASYGTEEQKQKWLPKCVTGELITAIAMTEP 132
>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 = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 14 FRPYQKDVIQRIIEKRDCLVVMATGSGKS 42
RPYQ +V Q +E ++ ++ + TG GK+
Sbjct: 8 LRPYQMEVAQPALEGKNIIICLPTGCGKT 36
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 10/105 (9%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
+I + T +++ +I L L G +H + +E LF ++V+ AT F
Sbjct: 383 NAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETF 442
Query: 289 GMGIDKPDVRHVIHYGCPK---------TLESYYQESGRCGRDGI 324
+G++ P + V+ K + Y Q SGR GR G+
Sbjct: 443 SIGLNMP-AKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGL 486
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 10/105 (9%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
+I + T +++ +I L L G +H + +E LF ++V+ AT F
Sbjct: 481 NAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETF 540
Query: 289 GMGIDKPDVRHVIHYGCPK---------TLESYYQESGRCGRDGI 324
+G++ P + V+ K + Y Q SGR GR G+
Sbjct: 541 SIGLNMP-AKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGL 584
>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain
pdb|3IUY|B Chain B, Crystal Structure Of Ddx53 Dead-Box Domain
Length = 228
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 16 PYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP 48
P Q I++ D +VV TG+GK+L Y +P
Sbjct: 45 PIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMP 77
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
0.324 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,213,456
Number of Sequences: 62578
Number of extensions: 401513
Number of successful extensions: 1451
Number of sequences better than 100.0: 86
Number of HSP's better than 100.0 without gapping: 65
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1353
Number of HSP's gapped (non-prelim): 109
length of query: 374
length of database: 14,973,337
effective HSP length: 100
effective length of query: 274
effective length of database: 8,715,537
effective search space: 2388057138
effective search space used: 2388057138
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)