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= 035988
(692 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 446 bits (1146), Expect = e-125, Method: Compositional matrix adjust.
Identities = 228/506 (45%), Positives = 325/506 (64%), Gaps = 30/506 (5%)
Query: 73 FEWDSRADDVRLNVFGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREG 132
F W + D+ NVF + +R Q E IN ++G++V ++M GGGKSLCYQLPA+ +G
Sbjct: 26 FPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDG 85
Query: 133 IALVVSPLLSLIQDQVMCLAALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPE 192
LV+ PL+SL++DQ+M L LGI A ML +++SKE K+++ + ELK++YVTPE
Sbjct: 86 FTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPE 145
Query: 193 KISKSKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMA 252
KI+KSK FMS+LEK + A R + I++DE HCCSQWGHDFRPDYK LGILK QFP+ ++
Sbjct: 146 KIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIG 205
Query: 253 LTATATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQESY 312
LTATAT V D ++L I KC F ++ NRPNL+Y VR+K S + I++I K I Y
Sbjct: 206 LTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRY 265
Query: 313 PNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGT 372
+SGI+YCFS+K+ EQV L+ GI A YHA+++ + VH +WS N++QV+V T
Sbjct: 266 -KGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT 324
Query: 373 VAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADVPRQSSMVF 432
VAFGMGI+KPDVRFVIHHS+SKS+E YYQESGRAGRD + ++C+L++ D+ R SSMV
Sbjct: 325 VAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVV 384
Query: 433 YENSGLQNLYDIVRYSQYPLHWNIEKVRLVI----FEKL---QQVNLFCMVV-------- 477
EN G Q LY++V Y Q NI K R V+ F+++ + N C
Sbjct: 385 MENVGQQKLYEMVSYCQ-----NISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDSAFER 439
Query: 478 --LAGHAQCIISLLQDIQDNNQRLTMLQLVD----KMKIKLK---EIDSDLKREEIEQLV 528
+ + + +I +L+ ++ N++LT L+L+D K KL+ + L RE++E+++
Sbjct: 440 KNITEYCRDLIKILKQAEELNEKLTPLKLIDSWMGKGAAKLRVAGVVAPTLPREDLEKII 499
Query: 529 LQLIIDRVLVRIGPFSPGKKIIKLEI 554
+I + L F+ I L+I
Sbjct: 500 AHFLIQQYLKEDYSFTAYATISYLKI 525
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 328 bits (841), Expect = 6e-90, Method: Compositional matrix adjust.
Identities = 159/349 (45%), Positives = 233/349 (66%), Gaps = 13/349 (3%)
Query: 76 DSRADDVRLNVFGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGIAL 135
+S A V FG +R Q+EII+ VLSGRD LV+M GGGKSLCYQ+PA+L G+ +
Sbjct: 10 ESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTV 69
Query: 136 VVSPLLSLIQDQVMCLAALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKIS 195
VVSPL+SL++DQV L A G+ A L ST ++E + + G+ +++LY+ PE++
Sbjct: 70 VVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQ--IRLLYIAPERLM 127
Query: 196 KSKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTA 255
F+ L + L+++DEAHC SQWGHDFRP+Y LG L+ +FP +P MALTA
Sbjct: 128 LDN-FLEHLAHWNPV----LLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTA 182
Query: 256 TATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQESYPNS 315
TA + D++ +L + + +S+ +RPN+ YM+ EK +D++ +Y+QE
Sbjct: 183 TADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKP----LDQLMRYVQEQ--RG 236
Query: 316 ESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAF 375
+SGI+YC SR + E A L+ +GISA YHA ++ N R V ++ ++ LQ++V TVAF
Sbjct: 237 KSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAF 296
Query: 376 GMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
GMGINKP+VRFV+H + +++E+YYQE+GRAGRDGLP+E +LF+ PAD+
Sbjct: 297 GMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADM 345
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 317 bits (811), Expect = 2e-86, Method: Compositional matrix adjust.
Identities = 155/348 (44%), Positives = 226/348 (64%), Gaps = 13/348 (3%)
Query: 76 DSRADDVRLNVFGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGIAL 135
+S A V FG +R Q+EII+ VLSGRD LV+ GGGKSLCYQ+PA+L G+ +
Sbjct: 10 ESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTV 69
Query: 136 VVSPLLSLIQDQVMCLAALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKIS 195
VVSPL+SL +DQV L A G+ A L ST ++E + + G+ +++LY+ PE++
Sbjct: 70 VVSPLISLXKDQVDQLQANGVAAACLNSTQTREQQLEVXTGCRTGQ--IRLLYIAPERLX 127
Query: 196 KSKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTA 255
F+ L + L+++DEAHC SQWGHDFRP+Y LG L+ +FP +P ALTA
Sbjct: 128 LDN-FLEHLAHWNPV----LLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTA 182
Query: 256 TATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQESYPNS 315
TA + D++ +L + + +S+ +RPN+ Y + EK +D++ +Y+QE
Sbjct: 183 TADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYXLXEKFKP----LDQLXRYVQEQ--RG 236
Query: 316 ESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAF 375
+SGI+YC SR + E A L+ +GISA YHA ++ N R V ++ ++ LQ++V TVAF
Sbjct: 237 KSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAF 296
Query: 376 GMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPAD 423
G GINKP+VRFV+H + +++E+YYQE+GRAGRDGLP+E LF+ PAD
Sbjct: 297 GXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPAD 344
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 81/329 (24%), Positives = 141/329 (42%), Gaps = 37/329 (11%)
Query: 96 QQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL--LSLIQDQ 147
Q+E I ++GRD+L G GK+ + +P + L + AL++ P L+L Q
Sbjct: 48 QEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQ 107
Query: 148 VMCLAA--LGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKI-SKSKRFMSKL 204
V+ GI + T T+ D+ I + E + +L TP ++ + R ++ L
Sbjct: 108 VVRTLGKHCGISCMVTTGGTNLRDD--ILRLNET----VHILVGTPGRVLDLASRKVADL 161
Query: 205 EKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTATATQKVQND 264
C SL +DEA DF+ + IL P + +AT V+
Sbjct: 162 SDC------SLFIMDEAD--KMLSRDFKTIIEQ--ILSFLPPTHQSLLFSATFPLTVKEF 211
Query: 265 LMEMLHIRKCIKFVSTINRPNL---FYMVREKSSVGKVVIDEIAKYIQESYPNSESGIVY 321
+++ LH I + + + + V E+ + ++ + +Q + I++
Sbjct: 212 MVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLH--CLNTLFSKLQIN-----QAIIF 264
Query: 322 CFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINK 381
C S E +A+++ G S Y HA M R KV + + K++ +V + GI+
Sbjct: 265 CNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDI 324
Query: 382 PDVRFVIHHSLSKSVETYYQESGRAGRDG 410
V VI+ K+ ETY GR+GR G
Sbjct: 325 QAVNVVINFDFPKTAETYLHRIGRSGRFG 353
>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 = 62.0 bits (149), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 54/93 (58%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
G+V+C ++++ +++A LR G A H D+ + REKV + + K+++++ T
Sbjct: 241 GLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSR 300
Query: 378 GINKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
GI+ D+ VI++ L ++ E+Y GR GR G
Sbjct: 301 GIDVNDLNCVINYHLPQNPESYXHRIGRTGRAG 333
>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 = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 68/355 (19%), Positives = 150/355 (42%), Gaps = 41/355 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL 140
+G A QQ I ++ GRDV+ +G GK+ + + + +RE AL+++P
Sbjct: 34 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT 93
Query: 141 LSL---IQDQVMCLA-ALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L IQ ++ L + + H T+ ++ + L+ G+ ++ TP ++
Sbjct: 94 RELAVQIQKGLLALGDYMNVQCHACIGGTNVGED---IRKLDYGQ---HVVAGTPGRVFD 147
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTAT 256
R S + + ++ +DEA G F+ + + + P ++ ++AT
Sbjct: 148 MIRRRSLRTRA-----IKMLVLDEADEMLNKG--FKEQIYD--VYRYLPPATQVVLISAT 198
Query: 257 -------ATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQ 309
T K D + +L R + T+ F++ E+ + ++ +
Sbjct: 199 LPHEILEMTNKFMTDPIRILVKRDEL----TLEGIKQFFVAVEREEWKFDTLCDLYDTLT 254
Query: 310 ESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVI 369
+ +++C ++++ + + +++R+ + H DM RE + + +V+
Sbjct: 255 IT-----QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 309
Query: 370 VGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
+ T + G++ P V +I++ L + E Y GR+GR G + F + D+
Sbjct: 310 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 364
>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 = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 68/355 (19%), Positives = 150/355 (42%), Gaps = 41/355 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL 140
+G A QQ I ++ GRDV+ +G GK+ + + + +RE AL+++P
Sbjct: 55 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT 114
Query: 141 LSL---IQDQVMCLA-ALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L IQ ++ L + + H T+ ++ + L+ G+ ++ TP ++
Sbjct: 115 RELAVQIQKGLLALGDYMNVQCHACIGGTNVGED---IRKLDYGQ---HVVAGTPGRVFD 168
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTAT 256
R S + + ++ +DEA G F+ + + + P ++ ++AT
Sbjct: 169 MIRRRSLRTRA-----IKMLVLDEADEMLNKG--FKEQIYD--VYRYLPPATQVVLISAT 219
Query: 257 -------ATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQ 309
T K D + +L R + T+ F++ E+ + ++ +
Sbjct: 220 LPHEILEMTNKFMTDPIRILVKRDEL----TLEGIKQFFVAVEREEWKFDTLCDLYDTLT 275
Query: 310 ESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVI 369
+ +++C ++++ + + +++R+ + H DM RE + + +V+
Sbjct: 276 IT-----QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 330
Query: 370 VGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
+ T + G++ P V +I++ L + E Y GR+GR G + F + D+
Sbjct: 331 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 385
>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 = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 68/355 (19%), Positives = 150/355 (42%), Gaps = 41/355 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL 140
+G A QQ I ++ GRDV+ +G GK+ + + + +RE AL+++P
Sbjct: 56 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT 115
Query: 141 LSL---IQDQVMCLA-ALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L IQ ++ L + + H T+ ++ + L+ G+ ++ TP ++
Sbjct: 116 RELAVQIQKGLLALGDYMNVQCHACIGGTNVGED---IRKLDYGQ---HVVAGTPGRVFD 169
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTAT 256
R S + + ++ +DEA G F+ + + + P ++ ++AT
Sbjct: 170 MIRRRSLRTRA-----IKMLVLDEADEMLNKG--FKEQIYD--VYRYLPPATQVVLISAT 220
Query: 257 -------ATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQ 309
T K D + +L R + T+ F++ E+ + ++ +
Sbjct: 221 LPHEILEMTNKFMTDPIRILVKRDEL----TLEGIKQFFVAVEREEWKFDTLCDLYDTLT 276
Query: 310 ESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVI 369
+ +++C ++++ + + +++R+ + H DM RE + + +V+
Sbjct: 277 IT-----QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 331
Query: 370 VGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
+ T + G++ P V +I++ L + E Y GR+GR G + F + D+
Sbjct: 332 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 69/355 (19%), Positives = 149/355 (41%), Gaps = 41/355 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL 140
+G A QQ I ++ GRDV+ +G GK+ + + + +RE AL+++P
Sbjct: 19 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPT 78
Query: 141 LSLIQDQVMCLAALG----IPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L L ALG + +H T+ ++ + L+ G+ ++ TP ++
Sbjct: 79 RELAVQVQKGLLALGDYMNVQSHACIGGTNVGED---IRKLDYGQ---HVVAGTPGRVFD 132
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTAT 256
R S + + ++ +DEA G F+ + + + P ++ ++AT
Sbjct: 133 MIRRRSLRTRA-----IKMLVLDEADEMLNKG--FKEQIYD--VYRYLPPATQVVLISAT 183
Query: 257 -------ATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQ 309
T K D + +L R + T+ F++ E+ + ++ +
Sbjct: 184 LPHEVLEMTNKFMTDPIRILVKRDEL----TLEGIKQFFVAVEREEWKFDTLCDLYDTLT 239
Query: 310 ESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVI 369
+ +++C ++++ + + +++R+ + H DM RE + + +V+
Sbjct: 240 IT-----QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 370 VGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
+ T + G++ P V +I++ L + E Y GR+GR G + F + D+
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>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 = 57.0 bits (136), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 68/355 (19%), Positives = 150/355 (42%), Gaps = 41/355 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL 140
+G A QQ I ++ GRDV+ +G GK+ + + + +RE AL+++P
Sbjct: 56 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT 115
Query: 141 LSL---IQDQVMCLA-ALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L IQ ++ L + + H T+ ++ + L+ G+ ++ TP ++
Sbjct: 116 RELAVQIQKGLLALGDYMNVQCHACIGGTNVGED---IRKLDYGQ---HVVAGTPGRVFD 169
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTAT 256
R S + + ++ +DEA G F+ + + + P ++ ++AT
Sbjct: 170 MIRRRSLRTRA-----IKMLVLDEADEMLNKG--FKEQIYD--VYRYLPPATQVVLISAT 220
Query: 257 -------ATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQ 309
T K D + +L R + T+ F++ E+ + ++ +
Sbjct: 221 LPHEILEMTNKFMTDPIRILVKRDEL----TLEGIKQFFVAVEREEWKFDTLCDLYDTLT 276
Query: 310 ESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVI 369
+ +++C ++++ + + +++R+ + H DM RE + + +V+
Sbjct: 277 IT-----QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 331
Query: 370 VGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
+ T + G++ P V +I++ L + E Y GR+GR G + F + D+
Sbjct: 332 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 386
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 67/355 (18%), Positives = 150/355 (42%), Gaps = 41/355 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV------LREGIALVVSPL 140
+G A QQ I ++ GRDV+ +G GK+ + + + +RE AL+++P
Sbjct: 19 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPT 78
Query: 141 LSL---IQDQVMCLA-ALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L +Q ++ L + + H T+ ++ + L+ G+ ++ TP ++
Sbjct: 79 RELAVQVQKGLLALGDYMNVQCHACIGGTNVGED---IRKLDYGQ---HVVAGTPGRVFD 132
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTAT 256
R S + + ++ +DEA G F+ + + + P ++ ++AT
Sbjct: 133 MIRRRSLRTRA-----IKMLVLDEADEMLNKG--FKEQIYD--VYRYLPPATQVVLISAT 183
Query: 257 -------ATQKVQNDLMEMLHIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQ 309
T K D + +L R + T+ F++ E+ + ++ +
Sbjct: 184 LPHEILEMTNKFMTDPIRILVKRDEL----TLEGIKQFFVAVEREEWKFDTLCDLYDTLT 239
Query: 310 ESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVI 369
+ +++C ++++ + + +++R+ + H DM RE + + +V+
Sbjct: 240 IT-----QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 370 VGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
+ T + G++ P V +I++ L + E Y GR+GR G + F + D+
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>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 = 52.8 bits (125), Expect = 6e-07, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 48/98 (48%)
Query: 313 PNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGT 372
P + IV+ R+ ++A LR+ GI+ Y +M R + R ++ ++ V+V T
Sbjct: 28 PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVAT 87
Query: 373 VAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
GI+ PDV V + + +S +TY GR R G
Sbjct: 88 DVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125
>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 = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 45/92 (48%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
I++C S + E +A+++ Q G S Y HA M R +V + + +V T F G
Sbjct: 48 IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
I+ V VI+ K ETY GR+GR G
Sbjct: 108 IDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139
>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 = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 49/105 (46%)
Query: 314 NSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTV 373
N +S I++C +++ Q+ EL G D H M R V + + + + +V T
Sbjct: 34 NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD 93
Query: 374 AFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLF 418
GI+ ++ VI++ L E+Y +GR GR G + + F
Sbjct: 94 VAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISF 138
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 85/395 (21%), Positives = 157/395 (39%), Gaps = 59/395 (14%)
Query: 55 PIQYGGSS-STAVENWSGTFEWDSRADDVRLNVFGIPAYRANQQEIINAVLSGRDVLVIM 113
P++ GS +++++ D D+V + + IP Q+ I + SGRD++
Sbjct: 43 PVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPT--PIQKCSIPVISSGRDLMACA 100
Query: 114 AAGGGKSLCYQLPAVLREGIALVVSPL-LSLIQDQVMCLAALGIPAHMLTSTTSKEDEKF 172
G GK+ + LP + + L+ P L L + QV+ ++ P L E KF
Sbjct: 101 QTGSGKTAAFLLPILSK----LLEDPHELELGRPQVVIVS----PTRELAIQIFNEARKF 152
Query: 173 IYKALEKGEGELKMLYVTPEKISKSKRFMSK--LEKCH----HAGRL------------- 213
+++ K + ++Y S R ++ CH GRL
Sbjct: 153 AFESYLK----IGIVYG-----GTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFED 203
Query: 214 -SLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMALTATATQKVQNDLMEMLHIR 272
+ +DEA G F D + + T P+ + +AT +++Q E L
Sbjct: 204 TRFVVLDEADRMLDMG--FSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFL--- 258
Query: 273 KCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQES------YPNSESGIVYCFSRK 326
K FV+ +V S K I E+ KY + S ++ IV+ +++
Sbjct: 259 KNYVFVA-------IGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKR 311
Query: 327 ECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRF 386
+ +A L ++ H D + RE+ + ++V++ T G++ +++
Sbjct: 312 GADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKH 371
Query: 387 VIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRP 421
VI++ + ++ Y GR GR G FF P
Sbjct: 372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDP 406
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 45/89 (50%)
Query: 314 NSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTV 373
+ + +V+ ++ E E++AQ L + G A H DM RE+V + + +++V+V T
Sbjct: 27 SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD 86
Query: 374 AFGMGINKPDVRFVIHHSLSKSVETYYQE 402
G++ P V V+H+ + E Y
Sbjct: 87 VAARGLDIPQVDLVVHYRMPDRAEAYQHR 115
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 70/331 (21%), Positives = 141/331 (42%), Gaps = 44/331 (13%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI------ALVVSPL 140
+G A QQ I ++ G DVL +G GK+ + + A+ R AL+++P
Sbjct: 40 YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT 99
Query: 141 LSL---IQDQVMCLAA-LGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L IQ VM LA + I H TS F+ A +G + +++ TP ++
Sbjct: 100 RELALQIQKVVMALAFHMDIKVHACIGGTS-----FVEDA--EGLRDAQIVVGTPGRV-- 150
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPD-YKNLGILKTQFPDVPMMALTA 255
F + + ++ + +DEA G F+ Y+ +L P ++ L+A
Sbjct: 151 ---FDNIQRRRFRTDKIKMFILDEADEMLSSG--FKEQIYQIFTLLP---PTTQVVLLSA 202
Query: 256 TATQKVQNDLMEML--HIRKCIKFVSTINRPNL-----FYMVREKSSVGKVVIDEIAKYI 308
T + ND++E+ +R ++ + + L FY+ E+ + ++ I
Sbjct: 203 T----MPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSI 258
Query: 309 QESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQV 368
+ +++C +R++ E++ +LR + ++D+ R+ + + ++
Sbjct: 259 SVT-----QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI 313
Query: 369 IVGTVAFGMGINKPDVRFVIHHSLSKSVETY 399
++ T GI+ V VI++ L + E Y
Sbjct: 314 LISTDLLARGIDVQQVSLVINYDLPANKENY 344
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 32/108 (29%), Positives = 55/108 (50%)
Query: 316 ESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAF 375
+ +V+ ++ E E++AQ L + G A H D+ RE+V + + +++V+V T
Sbjct: 32 DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVA 91
Query: 376 GMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPAD 423
G++ P V V+H+ L E Y SGR GR G +L + P +
Sbjct: 92 ARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRE 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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 80/375 (21%), Positives = 154/375 (41%), Gaps = 52/375 (13%)
Query: 89 IPAYRANQQEIINAVLSGRDVLVIMAA--GGGKSLCYQLPAVLREGI-----------AL 135
P QQ+ I +LS D VI A G GK+ + +P + + I A+
Sbjct: 92 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP-IFQHLINTKFDSQYMVKAV 150
Query: 136 VVSPLLSL---IQDQVMCLAAL--GIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVT 190
+V+P L I+ +V + + G+ + S D ++A +L+ V
Sbjct: 151 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTD----FRAAMNKMNKLRPNIV- 205
Query: 191 PEKISKSKRFMSKLEKCHHA--GRLSLISIDEAHCCSQWGHDFRPDYKNL-GILKTQ--- 244
I+ R + LEK + + +DEA + G FR D + + GIL +
Sbjct: 206 ---IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG--FRDDLETISGILNEKNSK 260
Query: 245 -FPDVPMMALTATATQKVQNDLMEMLHIRKCIKFVSTI--NRPNLFYMVREKSSVGK--- 298
++ + +AT KVQ +++ ++C+ F+ T+ N P + + + +
Sbjct: 261 SADNIKTLLFSATLDDKVQKLANNIMNKKECL-FLDTVDKNEPEAHERIDQSVVISEKFA 319
Query: 299 ----VVIDEIAKYIQESYPNSESGIVYC----FSRKECEQVAQELRQRGISADYYHADMD 350
++ I K I+E N ++ I++ F+ C + E + + + +H +
Sbjct: 320 NSIFAAVEHIKKQIKERDSNYKA-IIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKIT 377
Query: 351 INAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
N R + R+ K++ ++V T G++ P+V V+ + + Y GR R G
Sbjct: 378 QNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 437
Query: 411 LPSECLLFFRPADVP 425
+LF ++P
Sbjct: 438 KEGSSVLFICKDELP 452
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 80/375 (21%), Positives = 154/375 (41%), Gaps = 52/375 (13%)
Query: 89 IPAYRANQQEIINAVLSGRDVLVIMAA--GGGKSLCYQLPAVLREGI-----------AL 135
P QQ+ I +LS D VI A G GK+ + +P + + I A+
Sbjct: 41 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP-IFQHLINTKFDSQYMVKAV 99
Query: 136 VVSPLLSL---IQDQVMCLAAL--GIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVT 190
+V+P L I+ +V + + G+ + S D ++A +L+ V
Sbjct: 100 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTD----FRAAMNKMNKLRPNIV- 154
Query: 191 PEKISKSKRFMSKLEKCHHA--GRLSLISIDEAHCCSQWGHDFRPDYKNL-GILKTQ--- 244
I+ R + LEK + + +DEA + G FR D + + GIL +
Sbjct: 155 ---IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG--FRDDLETISGILNEKNSK 209
Query: 245 -FPDVPMMALTATATQKVQNDLMEMLHIRKCIKFVSTI--NRPNLFYMVREKSSVGK--- 298
++ + +AT KVQ +++ ++C+ F+ T+ N P + + + +
Sbjct: 210 SADNIKTLLFSATLDDKVQKLANNIMNKKECL-FLDTVDKNEPEAHERIDQSVVISEKFA 268
Query: 299 ----VVIDEIAKYIQESYPNSESGIVYC----FSRKECEQVAQELRQRGISADYYHADMD 350
++ I K I+E N ++ I++ F+ C + E + + + +H +
Sbjct: 269 NSIFAAVEHIKKQIKERDSNYKA-IIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKIT 326
Query: 351 INAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
N R + R+ K++ ++V T G++ P+V V+ + + Y GR R G
Sbjct: 327 QNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 386
Query: 411 LPSECLLFFRPADVP 425
+LF ++P
Sbjct: 387 KEGSSVLFICKDELP 401
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 69/331 (20%), Positives = 135/331 (40%), Gaps = 44/331 (13%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI------ALVVSPL 140
+G A QQ I ++ G DVL +G GK+ + + A+ R AL ++P
Sbjct: 39 YGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALXLAPT 98
Query: 141 LSL---IQDQVMCLAA-LGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISK 196
L IQ V LA I H TS F+ A +G + +++ TP ++
Sbjct: 99 RELALQIQKVVXALAFHXDIKVHACIGGTS-----FVEDA--EGLRDAQIVVGTPGRV-- 149
Query: 197 SKRFMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPD-YKNLGILKTQFPDVPMMALTA 255
F + + ++ +DEA G F+ Y+ +L P ++ L+A
Sbjct: 150 ---FDNIQRRRFRTDKIKXFILDEADEXLSSG--FKEQIYQIFTLLP---PTTQVVLLSA 201
Query: 256 TATQKVQNDLMEML--HIRKCIKFVSTINRPNL-----FYMVREKSSVGKVVIDEIAKYI 308
T ND++E+ R ++ + + L FY+ E+ + ++ I
Sbjct: 202 TXP----NDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSI 257
Query: 309 QESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQV 368
+ +++C +R++ E++ +LR + ++D+ R+ + + ++
Sbjct: 258 SVT-----QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRI 312
Query: 369 IVGTVAFGMGINKPDVRFVIHHSLSKSVETY 399
++ T GI+ V VI++ L + E Y
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENY 343
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 80/375 (21%), Positives = 154/375 (41%), Gaps = 52/375 (13%)
Query: 89 IPAYRANQQEIINAVLSGRDVLVIMAA--GGGKSLCYQLPAVLREGI-----------AL 135
P QQ+ I +LS D VI A G GK+ + +P + + I A+
Sbjct: 41 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP-IFQHLINTKFDSQYMVKAV 99
Query: 136 VVSPLLSL---IQDQVMCLAAL--GIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVT 190
+V+P L I+ +V + + G+ + S D ++A +L+ V
Sbjct: 100 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTD----FRAAMNKMNKLRPNIV- 154
Query: 191 PEKISKSKRFMSKLEKCHHA--GRLSLISIDEAHCCSQWGHDFRPDYKNL-GILKTQ--- 244
I+ R + LEK + + +DEA + G FR D + + GIL +
Sbjct: 155 ---IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG--FRDDLETISGILNEKNSK 209
Query: 245 -FPDVPMMALTATATQKVQNDLMEMLHIRKCIKFVSTI--NRPNLFYMVREKSSVGK--- 298
++ + +AT KVQ +++ ++C+ F+ T+ N P + + + +
Sbjct: 210 SADNIKTLLFSATLDDKVQKLANNIMNKKECL-FLDTVDKNEPEAHERIDQSVVISEKFA 268
Query: 299 ----VVIDEIAKYIQESYPNSESGIVYC----FSRKECEQVAQELRQRGISADYYHADMD 350
++ I K I+E N ++ I++ F+ C + E + + + +H +
Sbjct: 269 NSIFAAVEHIKKQIKERDSNYKA-IIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKIT 326
Query: 351 INAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
N R + R+ K++ ++V T G++ P+V V+ + + Y GR R G
Sbjct: 327 QNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 386
Query: 411 LPSECLLFFRPADVP 425
+LF ++P
Sbjct: 387 KEGSSVLFICKDELP 401
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 6/99 (6%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++C +RK +A EL + G +M + R V R+ + K +V+V T
Sbjct: 336 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR 395
Query: 378 GINKPDVRFVIHHSL------SKSVETYYQESGRAGRDG 410
GI+ V VI+ L + ETY GR GR G
Sbjct: 396 GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 434
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 6/99 (6%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++C +RK +A EL + G +M + R V R+ + K +V+V T
Sbjct: 285 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR 344
Query: 378 GINKPDVRFVIHHSL------SKSVETYYQESGRAGRDG 410
GI+ V VI+ L + ETY GR GR G
Sbjct: 345 GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 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 = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 6/99 (6%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++C +RK +A EL + G +M + R V R+ + K +V+V T
Sbjct: 269 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR 328
Query: 378 GINKPDVRFVIHHSL------SKSVETYYQESGRAGRDG 410
GI+ V VI+ L + ETY GR GR G
Sbjct: 329 GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 6/99 (6%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++C +RK +A EL + G +M + R V R+ + K +V+V T
Sbjct: 306 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR 365
Query: 378 GINKPDVRFVIHHSL------SKSVETYYQESGRAGRDG 410
GI+ V VI+ L + ETY GR GR G
Sbjct: 366 GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 404
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 43/101 (42%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+V+ ++K + + L G + H D RE+ ++ K ++V T G
Sbjct: 280 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARG 339
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFF 419
++ +V+ VI+ L +E Y GR GR G FF
Sbjct: 340 LDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFF 380
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 45/106 (42%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+V+ ++K + + L G + H D RE+ ++ K ++V T G
Sbjct: 50 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARG 109
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLFFRPADV 424
++ +V+ VI+ L +E Y GR GR G FF ++
Sbjct: 110 LDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI 155
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 46/91 (50%), Gaps = 12/91 (13%)
Query: 332 AQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHS 391
+ L +RGI+ +H + +E + + +SK ++V+ T F MG+N P R VI S
Sbjct: 394 TRSLLERGIAV--HHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLP-TRTVIFSS 450
Query: 392 LSK---------SVETYYQESGRAGRDGLPS 413
+ K + + Q +GRAGR GL S
Sbjct: 451 IRKHDGNGLRELTPGEFTQMAGRAGRRGLDS 481
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 6/100 (6%)
Query: 317 SGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFG 376
S I++ ++K + +L+ G H D+ R+++ + + + +V++ T
Sbjct: 245 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA 304
Query: 377 MGINKPDVRFVIHHSLSKSVE------TYYQESGRAGRDG 410
GI+ P V V+++ L TY GR GR G
Sbjct: 305 RGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 344
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 6/100 (6%)
Query: 317 SGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFG 376
S I++ ++K + +L+ G H D+ R+++ + + + +V++ T
Sbjct: 245 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA 304
Query: 377 MGINKPDVRFVIHHSLSKSVE------TYYQESGRAGRDG 410
GI+ P V V+++ L TY GR GR G
Sbjct: 305 RGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 344
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 43/92 (46%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+++ + + + + + L +G+ A H D R K + + K V+V T G
Sbjct: 58 LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
++ P ++ VI++ + + +E Y GR G G
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTGCSG 149
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 13/94 (13%)
Query: 329 EQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVI 388
+++ + L +G++ Y+HA + R+ + + + K++VIV T G+N P +I
Sbjct: 304 KELLKSLISKGVA--YHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVII 361
Query: 389 H--HSLSKSVETYYQE---------SGRAGRDGL 411
+ +K + YY E SGRAGR G
Sbjct: 362 GDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGF 395
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 73/343 (21%), Positives = 137/343 (39%), Gaps = 46/343 (13%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI-ALVVSPLLSLIQ 145
G + Q + I +L G++V+V G GK+ Y +P +L G+ +LVV+P L +
Sbjct: 12 MGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIP-ILELGMKSLVVTPTRELTR 70
Query: 146 DQVMCLAALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKI----SKSKRFM 201
+ +G + + ++ YKA ++ TP ++ SK +
Sbjct: 71 QVASHIRDIG---RYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDL 127
Query: 202 SKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLGILKTQFPDVPMMAL-TATATQK 260
S E ++ IDEA + G F D K I+ Q + + L +AT ++
Sbjct: 128 SSFE---------IVIIDEADLMFEMG--FIDDIK---IILAQTSNRKITGLFSATIPEE 173
Query: 261 VQNDLMEML----HIRKCIKFVSTINRPNLFYMVREKSSVGKVVIDEIAKYIQESYPNSE 316
++ + + + I CI N + F V+ D+ +Q N +
Sbjct: 174 IRKVVKDFITNYEEIEACIGLA---NVEHKFVHVK----------DDWRSKVQALRENKD 220
Query: 317 SG-IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAF 375
G IV+ +R ++ + +A D+ + R + + + + +++ T
Sbjct: 221 KGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVA 276
Query: 376 GMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLF 418
G++ P V VI+ + + TY GR GR G E + F
Sbjct: 277 SRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITF 319
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 45/100 (45%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+++ S + C +AQ L ++ A H M R + ++ + +++V T FG G
Sbjct: 253 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 312
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLF 418
++ V ++ + + +TY RAGR G + F
Sbjct: 313 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 352
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 46/108 (42%), Gaps = 6/108 (5%)
Query: 317 SGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFG 376
S I++ ++K + +L+ G H D+ R+++ + + + +V++ T
Sbjct: 37 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA 96
Query: 377 MGINKPDVRFVIHHSLSKSVE------TYYQESGRAGRDGLPSECLLF 418
GI+ P V V+++ L TY GR GR G + F
Sbjct: 97 RGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 144
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 45/100 (45%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+++ S + C +AQ L ++ A H M R + ++ + +++V T FG G
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLF 418
++ V ++ + + +TY RAGR G + F
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 353
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 45/100 (45%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+++ S + C +AQ L ++ A H M R + ++ + +++V T FG G
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLF 418
++ V ++ + + +TY RAGR G + F
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 353
>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
pdb|2RB4|B Chain B, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
Length = 175
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 52/130 (40%), Gaps = 6/130 (4%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
I++C +R+ + + E+ Q G ++ + R + R+ K +V++ T
Sbjct: 37 AIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCAR 96
Query: 378 GINKPDVRFVIHHSL------SKSVETYYQESGRAGRDGLPSECLLFFRPADVPRQSSMV 431
GI+ V V++ L ETY GR GR G ++P +
Sbjct: 97 GIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQ 156
Query: 432 FYENSGLQNL 441
+ NS ++ L
Sbjct: 157 DHFNSSIKQL 166
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 45/100 (45%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMG 378
+++ S + C +AQ L ++ A H M R + ++ + +++V T FG G
Sbjct: 35 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 94
Query: 379 INKPDVRFVIHHSLSKSVETYYQESGRAGRDGLPSECLLF 418
++ V ++ + + +TY RAGR G + F
Sbjct: 95 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF 134
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 341 SADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIH-------HSLS 393
A ++HA + R V + + ++V+V T G+N P R ++ +S
Sbjct: 298 GAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKR 357
Query: 394 KSVETYYQESGRAGRDGL 411
V Y Q +GRAGR G+
Sbjct: 358 IKVSEYKQMAGRAGRPGM 375
Score = 32.3 bits (72), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 88 GIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI----ALVVSPLLSL 143
GI Q E + V SG+++L+ M GK+L ++ A++RE I +L V PL +L
Sbjct: 22 GIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEM-AMVREAIKGGKSLYVVPLRAL 80
Query: 144 IQDQ 147
++
Sbjct: 81 AGEK 84
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++ +R++ + + +++ R + H DMD R+ + + +V++ T
Sbjct: 283 AVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLAR 342
Query: 378 GINKPDVRFVIHHSLSKSVETY 399
GI+ V VI++ L + E Y
Sbjct: 343 GIDVQQVSLVINYDLPTNRENY 364
>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 = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ I+E +E +V ++K E + L++ GI Y H+++ R ++
Sbjct: 431 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRD 490
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 491 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 6/100 (6%)
Query: 317 SGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFG 376
S I++ ++K + +L+ G H D+ R+++ + + + +V++ T
Sbjct: 39 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA 98
Query: 377 MGINKPDVRFVIHHSL------SKSVETYYQESGRAGRDG 410
GI+ P V V+++ L TY GR GR G
Sbjct: 99 RGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFG 138
>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 = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 6/100 (6%)
Query: 317 SGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFG 376
S I++ ++K + +L+ G H D+ R+++ + + + +V++ T
Sbjct: 38 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA 97
Query: 377 MGINKPDVRFVIHHSL------SKSVETYYQESGRAGRDG 410
GI+ P V V+++ L TY GR GR G
Sbjct: 98 RGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFG 137
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ I+E +E +V ++K E + L++ GI Y H+++ R ++
Sbjct: 431 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRD 490
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 491 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ I+E +E +V ++K E + L++ GI Y H+++ R ++
Sbjct: 430 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRD 489
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 490 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 544
>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 = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++ +R++ + + +++ R + H DMD R+ + + +V++ T
Sbjct: 257 AVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLAR 316
Query: 378 GINKPDVRFVIHHSLSKSVETY 399
GI+ V VI++ L + E Y
Sbjct: 317 GIDVQQVSLVINYDLPTNRENY 338
>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 = 0.019, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ I+E +E +V ++K E + L++ GI Y H+++ R ++
Sbjct: 431 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRD 490
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 491 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 16/82 (19%), Positives = 40/82 (48%)
Query: 318 GIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGM 377
+++C +R++ E++ +LR + ++D+ R+ + + ++++ T
Sbjct: 33 AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR 92
Query: 378 GINKPDVRFVIHHSLSKSVETY 399
GI+ V VI++ L + E Y
Sbjct: 93 GIDVQQVSLVINYDLPANKENY 114
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 49/115 (42%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ I E +E +V ++K E + L++ GI Y H+++ R ++
Sbjct: 456 IDDLIGEIHERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRD 515
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 516 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 570
>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 = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ IQ +E +V ++K E + L++ GI +Y H+++ R ++
Sbjct: 437 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRD 496
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 497 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 551
>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 = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 5/115 (4%)
Query: 301 IDEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMR 360
ID++ IQ +E +V ++K E + L++ GI +Y H+++ R ++
Sbjct: 431 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRD 490
Query: 361 WSKNKLQVIVGTVAFGMGINKPDVRFVI-----HHSLSKSVETYYQESGRAGRDG 410
K V+VG G++ P+V V +S + Q GRA R+
Sbjct: 491 LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>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 = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%)
Query: 345 YHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESG 404
+H + N R + R+ K++ ++V T G++ P+V V+ + + Y G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 405 RAGRDGLPSECLLFFRPADVP 425
R R G +LF ++P
Sbjct: 126 RTARSGKEGSSVLFICKDELP 146
>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 = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%)
Query: 345 YHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESG 404
+H + N R + R+ K++ ++V T G++ P+V V+ + + Y G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 405 RAGRDGLPSECLLFFRPADVP 425
R R G +LF ++P
Sbjct: 126 RTARSGKEGSSVLFICKDELP 146
>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 = 35.8 bits (81), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%)
Query: 345 YHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESG 404
+H + N R + R+ K++ ++V T G++ P+V V+ + + Y G
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 405 RAGRDGLPSECLLFFRPADVP 425
R R G +LF ++P
Sbjct: 126 RTARSGKEGSSVLFICKDELP 146
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 12/86 (13%)
Query: 335 LRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSK 394
L +RGI +H+ + +E + + + + L+V+ T F +G+N P + V+ S+ K
Sbjct: 502 LLRRGIGI--HHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMP-AKTVVFTSVRK 558
Query: 395 ---------SVETYYQESGRAGRDGL 411
S Y Q SGRAGR GL
Sbjct: 559 WDGQQFRWVSGGEYIQMSGRAGRRGL 584
>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 = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 12/86 (13%)
Query: 335 LRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSK 394
L +RGI +H+ + +E + + + + L+V+ T F +G+N P + V+ S+ K
Sbjct: 404 LLRRGIGI--HHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMP-AKTVVFTSVRK 460
Query: 395 ---------SVETYYQESGRAGRDGL 411
S Y Q SGRAGR GL
Sbjct: 461 WDGQQFRWVSGGEYIQMSGRAGRRGL 486
>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 = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 75/379 (19%), Positives = 139/379 (36%), Gaps = 85/379 (22%)
Query: 88 GIPAYRANQQEII-NAVLSGRDVLVIMAAGGGKSLCYQLPAVLR----EGIALVVSPLLS 142
GI ++ Q E + + +L G++ L+ + GK+L ++ V R G A+ + PL +
Sbjct: 20 GIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKA 79
Query: 143 LIQDQVMCL---AALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISKSKR 199
L +++ +G+ M T +DE G+ ++ T EK R
Sbjct: 80 LAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWL---------GKYDIIIATAEKFDSLLR 130
Query: 200 FMSKLEKCHHAGRLSLISIDEAHCCSQWGHDFRPDYKNLG-----ILKTQFPDVPMMALT 254
S K + ++ DE H ++ G IL ++ L+
Sbjct: 131 HGSSWIKD-----VKILVADEIHLIGS---------RDRGATLEVILAHMLGKAQIIGLS 176
Query: 255 ATATQKVQNDLMEMLHIRKCIKFVSTIN-RPNLFY---MVREKSSVGKVVIDEIAKYIQE 310
AT +L E L+ + + R +FY + E S+ + + + +
Sbjct: 177 ATIGN--PEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDR--FSSWEELVYD 232
Query: 311 SYPNSESGIVYCFSRKECEQVAQELRQRGIS-------------AD-------------- 343
+ + +++ R++ E+VA EL ++ S AD
Sbjct: 233 AIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKA 292
Query: 344 ------YYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKS-- 395
++HA + + R V + K ++ +V T GIN P R +I S
Sbjct: 293 IRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDF 352
Query: 396 ------VETYYQESGRAGR 408
+ +Q GRAGR
Sbjct: 353 GMERIPIIEVHQMLGRAGR 371
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 53/116 (45%), Gaps = 18/116 (15%)
Query: 310 ESYPNSESG-IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWS--KNKL 366
ES N G + CFS+ + V++++ RG+ + + + + +++ +
Sbjct: 314 ESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPC 373
Query: 367 QVIVGTVAFGMGINKPDVRFVIHHSLSK--------------SVETYYQESGRAGR 408
+++V T A GMG+N +R +I +SL K + Q +GRAGR
Sbjct: 374 KILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGR 428
>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 = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 28/129 (21%), Positives = 59/129 (45%), Gaps = 11/129 (8%)
Query: 301 IDEIAKYIQESYPNSESG--IVYCFSRKECEQVAQELRQRGISADYY------HADMDIN 352
+D++ + I+E ++ IV+ R+ +++ EL + GI A + D ++
Sbjct: 345 MDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLS 404
Query: 353 AREK--VHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGRDG 410
RE+ + +++ + V+V T G++ P+V V+ + S Q GR GR
Sbjct: 405 QREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH- 463
Query: 411 LPSECLLFF 419
+P ++
Sbjct: 464 MPGRVIILM 472
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 36/146 (24%), Positives = 60/146 (41%), Gaps = 25/146 (17%)
Query: 97 QEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLR----EGIALVVSPLLSLIQDQVMCLA 152
QE+I A + L+++ G GK+L + A R G L+++P L+
Sbjct: 14 QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFR 73
Query: 153 AL-GIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKISKSKRFMSKLEKCHHAG 211
L +P + + T ++ + KA + K++ TP+ I E AG
Sbjct: 74 RLFNLPPEKIVALTGEKSPEERSKAWARA----KVIVATPQTI----------ENDLLAG 119
Query: 212 RL-----SLISIDEAH-CCSQWGHDF 231
R+ SLI DEAH + + F
Sbjct: 120 RISLEDVSLIVFDEAHRAVGNYAYVF 145
>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 = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVS 433
>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 = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVS 433
>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 = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVS 433
>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 = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVS 433
>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 = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 379 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVS 412
>pdb|1A1V|A Chain A, Hepatitis C Virus Ns3 Helicase Domain Complexed With
Single Stranded Sdna
Length = 476
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 200 LIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS 233
>pdb|2ZJO|A Chain A, Crystal Structure Of Hepatitis C Virus Ns3 Helicase With A
Novel Inhibitor
Length = 482
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 24/34 (70%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI A Y+ +D++
Sbjct: 210 LIFCHSKKKCDELAAKLSALGIHAVAYYRGLDVS 243
>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 = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 186 LIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS 219
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 32.7 bits (73), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 96 QQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAV 128
Q + I +L GRD+L G GK+L + +PAV
Sbjct: 81 QHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAV 113
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 32.7 bits (73), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 33/142 (23%), Positives = 60/142 (42%), Gaps = 9/142 (6%)
Query: 276 KFVSTINRPN--LFYMVREKSSVGKVVIDEIAKYIQESYPNSESGIVYCFSRKECEQVAQ 333
+ V I RP L +VR K + +++ ++ + I+E E +V + + E++
Sbjct: 401 RVVEQIIRPTGLLDPLVRVKPTENQIL--DLMEGIRERAARGERTLVTVLTVRMAEELTS 458
Query: 334 ELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVI----- 388
L + GI A Y H ++D R+ + +VG G++ P+V V
Sbjct: 459 FLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD 518
Query: 389 HHSLSKSVETYYQESGRAGRDG 410
+S + Q GRA R+
Sbjct: 519 KEGFLRSERSLIQTIGRAARNA 540
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 32.7 bits (73), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 33/142 (23%), Positives = 60/142 (42%), Gaps = 9/142 (6%)
Query: 276 KFVSTINRPN--LFYMVREKSSVGKVVIDEIAKYIQESYPNSESGIVYCFSRKECEQVAQ 333
+ V I RP L +VR K + +++ ++ + I+E E +V + + E++
Sbjct: 400 RVVEQIIRPTGLLDPLVRVKPTENQIL--DLMEGIRERAARGERTLVTVLTVRMAEELTS 457
Query: 334 ELRQRGISADYYHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVI----- 388
L + GI A Y H ++D R+ + +VG G++ P+V V
Sbjct: 458 FLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD 517
Query: 389 HHSLSKSVETYYQESGRAGRDG 410
+S + Q GRA R+
Sbjct: 518 KEGFLRSERSLIQTIGRAARNA 539
>pdb|8OHM|A Chain A, Crystal Structure Of Rna Helicase From Genotype 1b
Hepatitis C Virus: Mechanism Of Unwinding Duplex Rna
Length = 435
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L G++A Y+ +D++
Sbjct: 176 LIFCHSKKKCDELAAKLSALGLNAVAYYRGLDVS 209
>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 = 32.3 bits (72), Expect = 0.80, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L GI+A Y+ +D++
Sbjct: 43 LIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS 76
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 40/88 (45%), Gaps = 19/88 (21%)
Query: 104 LSGRDVLVIMAAGGGKSLCYQLPAV--------LREG---IALVVSPLLSLIQDQVMCLA 152
LSG D++ + G GK+L Y LPA+ L G I LV++P L Q QV +A
Sbjct: 78 LSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQ-QVQQVA 136
Query: 153 ALGIPAHMLTSTTSKEDEKFIYKALEKG 180
A A L ST IY KG
Sbjct: 137 AEYCRACRLKSTC-------IYGGAPKG 157
>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 = 32.3 bits (72), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L G++A Y+ +D++
Sbjct: 177 LIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVS 210
>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 = 32.3 bits (72), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L G++A Y+ +D++
Sbjct: 177 LIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVS 210
>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 = 32.3 bits (72), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 25/34 (73%)
Query: 319 IVYCFSRKECEQVAQELRQRGISADYYHADMDIN 352
+++C S+K+C+++A +L G++A Y+ +D++
Sbjct: 176 LIFCHSKKKCDELAAKLTGLGLNAVAYYRGLDVS 209
>pdb|3RC3|A Chain A, Human Mitochondrial Helicase Suv3
Length = 677
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 52/116 (44%), Gaps = 18/116 (15%)
Query: 310 ESYPNSESG-IVYCFSRKECEQVAQELRQRGISADYYHADMDINAREKVHMRWS--KNKL 366
ES N G + CFS+ + V++++ RG+ + + + + +++ +
Sbjct: 314 ESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPC 373
Query: 367 QVIVGTVAFGMGINKPDVRFVIHHSLSK--------------SVETYYQESGRAGR 408
+++V T A G G+N +R +I +SL K + Q +GRAGR
Sbjct: 374 KILVATDAIGXGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGR 428
>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 = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 40/88 (45%), Gaps = 19/88 (21%)
Query: 104 LSGRDVLVIMAAGGGKSLCYQLPAV--------LREG---IALVVSPLLSLIQDQVMCLA 152
LSG D++ + G GK+L Y LPA+ L G I LV++P L Q QV +A
Sbjct: 64 LSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQ-QVQQVA 122
Query: 153 ALGIPAHMLTSTTSKEDEKFIYKALEKG 180
A A L ST IY KG
Sbjct: 123 AEYCRACRLKSTC-------IYGGAPKG 143
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 55/110 (50%), Gaps = 16/110 (14%)
Query: 96 QQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLR------EGI-ALVVSP---LLSLIQ 145
Q + I +L GR++L G GK+L + +P +++ +G AL++SP L S I
Sbjct: 56 QMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIH 115
Query: 146 DQVMCLA-ALGIPAHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKI 194
+++ ++ G HM+ + +KF K+ +K +L TP ++
Sbjct: 116 RELIKISEGTGFRIHMI-HKAAVAAKKFGPKSSKK----FDILVTTPNRL 160
>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation
Initiation Factor 4a From Saccharomyces Cerevisiae-The
Prototype Of The Dead Box Protein Family
Length = 224
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 10/90 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI------ALVVSPL 140
+G A QQ I ++ G DVL +G GK+ + + A+ R AL+++P
Sbjct: 32 YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT 91
Query: 141 LSL---IQDQVMCLAA-LGIPAHMLTSTTS 166
L IQ VM LA + I H TS
Sbjct: 92 RELALQIQKVVMALAFHMDIKVHACIGGTS 121
>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 = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 96 QQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI------ALVVSP 139
Q+E I LSGRD+L G GKS Y +P + R + A+V+ P
Sbjct: 30 QEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVP 79
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 345 YHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESG 404
+HA M R V ++ +QV+V T G+N P H + K + Y E G
Sbjct: 384 HHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLP-----AHTVIIKGTQVYSPEKG 438
Query: 405 R 405
R
Sbjct: 439 R 439
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 345 YHADMDINAREKVHMRWSKNKLQVIVGTVAFGMGINKPDVRFVIHHSLSKSVETYYQESG 404
+HA M R V ++ +QV+V T G+N P H + K + Y E G
Sbjct: 384 HHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLP-----AHTVIIKGTQVYSPEKG 438
Query: 405 R 405
R
Sbjct: 439 R 439
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 10/90 (11%)
Query: 87 FGIPAYRANQQEIINAVLSGRDVLVIMAAGGGKSLCYQLPAVLREGI------ALVVSPL 140
+G A QQ I ++ G DVL +G GK+ + + A+ R AL+++P
Sbjct: 39 YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT 98
Query: 141 LSL---IQDQVMCLAA-LGIPAHMLTSTTS 166
L IQ VM LA + I H TS
Sbjct: 99 RELALQIQKVVMALAFHMDIKVHACIGGTS 128
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 32/102 (31%), Positives = 44/102 (43%), Gaps = 17/102 (16%)
Query: 68 NWSGTFEWDSRADDVRLN---VFGIPAY-----RANQQEIINAVLSGRDVLVIMAAGGGK 119
NW+ E DD+ L + GI AY A QQ I + G DV+ +G GK
Sbjct: 24 NWN---EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGK 80
Query: 120 SLCY------QLPAVLREGIALVVSPLLSLIQDQVMCLAALG 155
+ + QL +E ALV++P L Q + ALG
Sbjct: 81 TATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALG 122
>pdb|3DIN|A Chain A, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
pdb|3DIN|B Chain B, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
Length = 871
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 31/135 (22%), Positives = 58/135 (42%), Gaps = 20/135 (14%)
Query: 302 DEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGI-----SADYYHADMDINAREK 356
++I + I++ Y + +V S ++ E ++ L+++GI +A Y+ + +I A+
Sbjct: 461 EKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAK-- 518
Query: 357 VHMRWSKNKLQVIVGT--------VAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGR 408
+ K V + T + G G+ + +I +S Q GRAGR
Sbjct: 519 -----AGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGR 573
Query: 409 DGLPSECLLFFRPAD 423
G P E + F D
Sbjct: 574 QGDPGESIFFLSLED 588
>pdb|3JUX|A Chain A, Structure Of The Translocation Atpase Seca From Thermotoga
Maritima
Length = 822
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 31/135 (22%), Positives = 58/135 (42%), Gaps = 20/135 (14%)
Query: 302 DEIAKYIQESYPNSESGIVYCFSRKECEQVAQELRQRGI-----SADYYHADMDINAREK 356
++I + I++ Y + +V S ++ E ++ L+++GI +A Y+ + +I A+
Sbjct: 461 EKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAK-- 518
Query: 357 VHMRWSKNKLQVIVGT--------VAFGMGINKPDVRFVIHHSLSKSVETYYQESGRAGR 408
+ K V + T + G G+ + +I +S Q GRAGR
Sbjct: 519 -----AGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGR 573
Query: 409 DGLPSECLLFFRPAD 423
G P E + F D
Sbjct: 574 QGDPGESIFFLSLED 588
>pdb|2B39|A Chain A, Structure Of Mammalian C3 With An Intact Thioester At 3a
Resolution
pdb|2B39|B Chain B, Structure Of Mammalian C3 With An Intact Thioester At 3a
Resolution
Length = 1661
Score = 28.9 bits (63), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 158 AHMLTSTTSKEDEKFIYKALEKGEGELKMLYVTPEKI 194
A +L S +KE+E+F KA KG+G L ++ V K+
Sbjct: 1315 ASLLRSEETKENERFTVKAEGKGQGTLSVVTVYHAKL 1351
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
0.317 0.133 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,404,261
Number of Sequences: 62578
Number of extensions: 729430
Number of successful extensions: 2424
Number of sequences better than 100.0: 101
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 2303
Number of HSP's gapped (non-prelim): 129
length of query: 692
length of database: 14,973,337
effective HSP length: 106
effective length of query: 586
effective length of database: 8,340,069
effective search space: 4887280434
effective search space used: 4887280434
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)