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= psy18034
(251 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 86.3 bits (212), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 66/105 (62%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F TK V+++ + + A + + ++ D+ R+ +F++G RVL+ TDV ARG
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+P + +INY+ P +L++HR+GR R GR GVA + V +D+
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDD 385
>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 = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 66/105 (62%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F TK V+++ + + A + + ++ D+ R+ +F++G RVL+ TDV ARG
Sbjct: 259 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 318
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+P + +INY+ P +L++HR+GR R GR GVA + V +D+
Sbjct: 319 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDD 363
>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 = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 66/105 (62%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F TK V+++ + + A + + ++ D+ R+ +F++G RVL+ TDV ARG
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+P + +INY+ P +L++HR+GR R GR GVA + V +D+
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDD 385
>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 = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 66/105 (62%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F TK V+++ + + A + + ++ D+ R+ +F++G RVL+ TDV ARG
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+P + +INY+ P +L++HR+GR R GR GVA + V +D+
Sbjct: 340 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDD 384
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 66/105 (62%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F TK V+++ + + A + + ++ D+ R+ +F++G RVL+ TDV ARG
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+P + +INY+ P +L++HR+GR R GR GVA + V +D+
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDD 348
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 66/105 (62%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F TK V+++ + + A + + ++ D+ R+ +F++G RVL+ TDV ARG
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+P + +INY+ P +L++HR+GR R GR GVA + V +D+
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDD 348
>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 = 84.0 bits (206), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 41/106 (38%), Positives = 61/106 (57%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
++VF + V + L AGI++ Y+ ++ R + G++ VLV TDVAAR
Sbjct: 33 SIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAAR 92
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
GIDIP + V N++ P ++HR+GR ARAGR G A SLV + +
Sbjct: 93 GIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHD 138
>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 = 78.2 bits (191), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 39/105 (37%), Positives = 60/105 (57%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+VF TK + + L G + I+ DL + R+ F+ KIR+L+ TDV +RG
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ L+ VINY+ P + + HR+GR RAG+ G A S+++ E
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRRE 346
>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 = 77.8 bits (190), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 36/102 (35%), Positives = 61/102 (59%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F K V+ +H+ L L G+ + I+ D R F+ GK VLV TDVA++G
Sbjct: 58 LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVS 104
+D P++ VINY+ P + + +VHR+GR +G +G+A + ++
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFIN 159
>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 = 76.3 bits (186), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 37/106 (34%), Positives = 62/106 (58%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F + VE + K + G S YI++ + R F+ G R LV TD+ R
Sbjct: 47 SIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTR 106
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
GIDI +++ VIN++FP A+ ++HR+GR R G G+A +L++ D+
Sbjct: 107 GIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDD 152
>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 = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 42/105 (40%), Positives = 58/105 (55%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F TK HV + L G I+ + R +F+ G+ R LV TDVAARG
Sbjct: 39 IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
IDI ++ VINY+ P + + +VHR GR RAG G A S V++ E
Sbjct: 99 IDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFE 143
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 75.5 bits (184), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 39/108 (36%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F ATK ++ L G + ++ DL R F+ G+ +VL+ T+V AR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 62 GIDIPSLDAVINYNFPCKAK------LFVHRVGRCARAGRSGVAYSLV 103
GIDIP++ V+NY+ P A ++HR+GR R GR GVA S V
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFV 353
>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 = 75.5 bits (184), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 39/108 (36%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F ATK ++ L G + ++ DL R F+ G+ +VL+ T+V AR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 62 GIDIPSLDAVINYNFPCKAK------LFVHRVGRCARAGRSGVAYSLV 103
GIDIP++ V+NY+ P A ++HR+GR R GR GVA S V
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFV 353
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 74.7 bits (182), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 39/108 (36%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F ATK ++ L G + ++ DL R F+ G+ +VL+ T+V AR
Sbjct: 38 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 97
Query: 62 GIDIPSLDAVINYNFPCKAK------LFVHRVGRCARAGRSGVAYSLV 103
GIDIP++ V+NY+ P A ++HR+GR R GR GVA S V
Sbjct: 98 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFV 145
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 74.3 bits (181), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 39/108 (36%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F ATK ++ L G + ++ DL R F+ G+ +VL+ T+V AR
Sbjct: 40 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 99
Query: 62 GIDIPSLDAVINYNFPCKAK------LFVHRVGRCARAGRSGVAYSLV 103
GIDIP++ V+NY+ P A ++HR+GR R GR GVA S V
Sbjct: 100 GIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFV 147
>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 = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 39/108 (36%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F ATK ++ L G + ++ DL R F+ G+ +VL+ T+V AR
Sbjct: 39 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 98
Query: 62 GIDIPSLDAVINYNFPCKAK------LFVHRVGRCARAGRSGVAYSLV 103
GIDIP++ V+NY+ P A ++HR+GR R GR GVA S V
Sbjct: 99 GIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFV 146
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 35/105 (33%), Positives = 63/105 (60%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F + VE + K + G S Y ++ + R +F+ GK+R LV +D+ RG
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
IDI +++ VIN++FP A+ ++HR+GR R G G+A +L++ ++
Sbjct: 322 IDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND 366
>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 = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 37/106 (34%), Positives = 59/106 (55%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+VF TK +++ L +T I+ D + R+ F+ G ++VL+ T VA+R
Sbjct: 303 TIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASR 362
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
G+DI ++ VINY+ P K +VHR+GR R G +G A S ++
Sbjct: 363 GLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEK 408
>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 = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 38/104 (36%), Positives = 59/104 (56%)
Query: 1 MTVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAA 60
+T+VF TK + + L G + T I+ D R+ +F++GK +LV T VAA
Sbjct: 48 LTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAA 107
Query: 61 RGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVS 104
RG+DI ++ VIN++ P + +VHR+GR R G G+A S +
Sbjct: 108 RGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN 151
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 73.6 bits (179), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 38/104 (36%), Positives = 59/104 (56%)
Query: 1 MTVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAA 60
+T+VF TK + + L G + T I+ D R+ +F++GK +LV T VAA
Sbjct: 278 LTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAA 337
Query: 61 RGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVS 104
RG+DI ++ VIN++ P + +VHR+GR R G G+A S +
Sbjct: 338 RGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN 381
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 60/104 (57%), Gaps = 4/104 (3%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+VF T+ V + ++ ++ + DL + R N F+ G+ +L+ TDVA+RG
Sbjct: 224 IVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRG 279
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSD 106
+DIP ++ VIN++ P + ++HR+GR R GR G A + + ++
Sbjct: 280 LDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILNE 323
>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 = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 50/149 (33%), Positives = 75/149 (50%), Gaps = 5/149 (3%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+VFT TK E + + L G + ++ DL R+ F+ G++RVLV TDVAAR
Sbjct: 34 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDEXXXXXXXXXXXGRK 121
G+DIP +D V++Y P +A+ + HR GR RAGR G L E GR+
Sbjct: 94 GLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRR 153
Query: 122 -----PVLADDSMKGKIRHQDGMFGKIPQ 145
P ++ ++ K RH ++P+
Sbjct: 154 FKRVNPPTPEEVLEAKWRHLLARLARVPE 182
>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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/149 (32%), Positives = 75/149 (50%), Gaps = 5/149 (3%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+VFT TK E + + L G + ++ D+ R+ F+ G++RVLV TDVAAR
Sbjct: 31 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDEXXXXXXXXXXXGRK 121
G+DIP +D V++Y P +A+ + HR GR RAGR G L E GR+
Sbjct: 91 GLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRR 150
Query: 122 -----PVLADDSMKGKIRHQDGMFGKIPQ 145
P ++ ++ K RH ++P+
Sbjct: 151 FKRVNPPTPEEVLEAKWRHLLARLARVPE 179
>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 = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 62/111 (55%), Gaps = 6/111 (5%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F T+ + +++ + G + + +L R +F+ GK +VL+ T+V ARG
Sbjct: 38 IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 63 IDIPSLDAVINYNFPCKA------KLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ + V+N++ P K + ++HR+GR R G+ G+A++++ DE
Sbjct: 98 IDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDE 148
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 35/105 (33%), Positives = 65/105 (61%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F T+ V+++ + + + + ++ D+D R + +F++G RVL+ TD+ ARG
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ + VINY+ P + ++HR+GR R GR GVA ++V+ ++
Sbjct: 344 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEED 388
>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 = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 35/105 (33%), Positives = 65/105 (61%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F T+ V+++ + + + + ++ D+D R + +F++G RVL+ TD+ ARG
Sbjct: 258 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 317
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ + VINY+ P + ++HR+GR R GR GVA ++V+ ++
Sbjct: 318 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEED 362
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 32/108 (29%), Positives = 56/108 (51%), Gaps = 6/108 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+++F K E + + + G + + +L+ R F+ G +VLV T+V AR
Sbjct: 360 SIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIAR 419
Query: 62 GIDIPSLDAVINYNFPCKA------KLFVHRVGRCARAGRSGVAYSLV 103
GID+ ++ V+NY+ P + ++HR+GR R GR GV+ + V
Sbjct: 420 GIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFV 467
>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 = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 6/109 (5%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F T+ ++ L G + ++ R +F+ GK +VLV T+V ARG
Sbjct: 307 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 366
Query: 63 IDIPSLDAVINYNFPCKA------KLFVHRVGRCARAGRSGVAYSLVSS 105
ID+ + VIN++ P + ++HR+GR R G+ G+A ++V S
Sbjct: 367 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 415
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 6/109 (5%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F T+ ++ L G + ++ R +F+ GK +VLV T+V ARG
Sbjct: 286 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 345
Query: 63 IDIPSLDAVINYNFPCKA------KLFVHRVGRCARAGRSGVAYSLVSS 105
ID+ + VIN++ P + ++HR+GR R G+ G+A ++V S
Sbjct: 346 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 394
>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 = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 6/109 (5%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F T+ ++ L G + ++ R +F+ GK +VLV T+V ARG
Sbjct: 270 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 329
Query: 63 IDIPSLDAVINYNFPCKA------KLFVHRVGRCARAGRSGVAYSLVSS 105
ID+ + VIN++ P + ++HR+GR R G+ G+A ++V S
Sbjct: 330 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 378
>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 = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 6/109 (5%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F T+ ++ L G + ++ R +F+ GK +VLV T+V ARG
Sbjct: 337 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 396
Query: 63 IDIPSLDAVINYNFPCKA------KLFVHRVGRCARAGRSGVAYSLVSS 105
ID+ + VIN++ P + ++HR+GR R G+ G+A ++V S
Sbjct: 397 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 445
>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 = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 39/105 (37%), Positives = 62/105 (59%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F T+ VE + L + + IYSDL R +F++G R+L+ TD+ ARG
Sbjct: 264 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 323
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ + VINY+ P + ++HR+GR R GR GVA + V++++
Sbjct: 324 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED 368
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 39/105 (37%), Positives = 62/105 (59%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F T+ VE + L + + IYSDL R +F++G R+L+ TD+ ARG
Sbjct: 34 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ + VINY+ P + ++HR+GR R GR GVA + V++++
Sbjct: 94 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED 138
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 39/105 (37%), Positives = 62/105 (59%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
V+F T+ VE + L + + IYSDL R +F++G R+L+ TD+ ARG
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARG 322
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
ID+ + VINY+ P + ++HR+GR R GR GVA + V++++
Sbjct: 323 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED 367
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + +LV TDV ARG+D P++ V+ P + ++HR+GR AR+G+ G + +
Sbjct: 387 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 446
Query: 104 SSDE 107
DE
Sbjct: 447 CKDE 450
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + +LV TDV ARG+D P++ V+ P + ++HR+GR AR+G+ G + +
Sbjct: 336 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 395
Query: 104 SSDE 107
DE
Sbjct: 396 CKDE 399
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + +LV TDV ARG+D P++ V+ P + ++HR+GR AR+G+ G + +
Sbjct: 336 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 395
Query: 104 SSDE 107
DE
Sbjct: 396 CKDE 399
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + +LV TDV ARG+D P++ V+ P + ++HR+GR AR+G+ G + +
Sbjct: 81 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140
Query: 104 SSDE 107
DE
Sbjct: 141 CKDE 144
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + +LV TDV ARG+D P++ V+ P + ++HR+GR AR+G+ G + +
Sbjct: 81 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140
Query: 104 SSDE 107
DE
Sbjct: 141 CKDE 144
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + +LV TDV ARG+D P++ V+ P + ++HR+GR AR+G+ G + +
Sbjct: 81 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140
Query: 104 SSDE 107
DE
Sbjct: 141 CKDE 144
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ + R+LV T++ RG+DI ++ NY+ P + ++HRV R R G G+A + V
Sbjct: 76 QFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFV 135
Query: 104 SSD 106
S +
Sbjct: 136 SDE 138
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 51/105 (48%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
V+F + + ++L + I+ + R +F+ + R+LV T++ R
Sbjct: 252 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 311
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSD 106
G+DI ++ NY+ P + ++HRV R R G G+A + VS +
Sbjct: 312 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE 356
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 51/105 (48%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
V+F + + ++L + I+ + R +F+ + R+LV T++ R
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSD 106
G+DI ++ NY+ P + ++HRV R R G G+A + VS +
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE 357
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 51/105 (48%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
V+F + + ++L + I+ + R +F+ + R+LV T++ R
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSD 106
G+DI ++ NY+ P + ++HRV R R G G+A + VS +
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE 357
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 33/89 (37%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 16 HKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYN 75
H ++G AG SS + + +K +KF+TGKI +L+ T VA G+DI + VI Y
Sbjct: 434 HHLIG-AGHSSEF--KPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYG 490
Query: 76 FPCKAKLFVHRVGRCARAGRSGVAYSLVS 104
V GR ARA S Y LV+
Sbjct: 491 LVTNEIAMVQARGR-ARADES--TYVLVA 516
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 44/92 (47%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ ++ VE L GIS+ ++ L+ R KFQ ++++V T G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAG 94
I+ P++ V++++ P + + GR R G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 44/92 (47%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ ++ VE L GIS+ ++ L+ R KFQ ++++V T G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAG 94
I+ P++ V++++ P + + GR R G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T TK E + L AGI Y++S++ R + GK VLV ++
Sbjct: 473 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 532
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCAR 92
G+DIP SL A+++ + F + + +GR AR
Sbjct: 533 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 568
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T TK E + L AGI Y++S++ R + GK VLV ++
Sbjct: 447 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 506
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCAR 92
G+DIP SL A+++ + F + + +GR AR
Sbjct: 507 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 542
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T TK E + L AGI Y++S++ R + GK VLV ++
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCAR 92
G+DIP SL A+++ + F + + +GR AR
Sbjct: 508 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 543
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T TK E + L AGI Y++S++ R + GK VLV ++
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCAR 92
G+DIP SL A+++ + F + + +GR AR
Sbjct: 508 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 543
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T TK E + L AGI Y++S++ R + GK VLV ++
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCAR 92
G+DIP SL A+++ + F + + +GR AR
Sbjct: 508 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 543
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 45 FQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAG---RSGVAYS 101
F+TG+ R +V + V GID+P + + + A+ ++ R+GR R + V Y
Sbjct: 390 FRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE 449
Query: 102 LVS 104
L+S
Sbjct: 450 LIS 452
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 45 FQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCAR---AGRSGVAYS 101
F+TG+ R +V + V GID+P + + + A+ ++ R+GR R + V Y
Sbjct: 155 FRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE 214
Query: 102 LVS 104
L+S
Sbjct: 215 LIS 217
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 33 LDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCAR 92
L +K+ +F G+ VLV T V G+D+P +D V+ Y A + R GR R
Sbjct: 403 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462
Query: 93 --AGRSGVAYSLVSSDE 107
GR + + + DE
Sbjct: 463 HMPGRVIILMAKGTRDE 479
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 15 VHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINY 74
H ++G AG SS + + I +KF+TGKI +L+ T VA G+DI + VI Y
Sbjct: 183 AHHLIG-AGHSSEFKPXTQNEQREVI--SKFRTGKINLLIATTVAEEGLDIKECNIVIRY 239
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 5/102 (4%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T E + L GI + Y++ +LD R+ + G LV ++
Sbjct: 442 TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 501
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCARAGRSGV 98
G+DIP SL A+++ + F + + +GR AR R V
Sbjct: 502 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEV 543
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 5/102 (4%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+V T E + L GI + Y++ +LD R+ + G LV ++
Sbjct: 443 TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 502
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCARAGRSGV 98
G+DIP SL A+++ + F + + +GR AR R V
Sbjct: 503 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEV 544
>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 = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 46/101 (45%), Gaps = 5/101 (4%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+V T TK E + L GI Y++S++ R + GK VLV ++ G
Sbjct: 455 LVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 514
Query: 63 IDIP--SLDAVINYN---FPCKAKLFVHRVGRCARAGRSGV 98
+DIP SL A+++ + F + + +GR AR V
Sbjct: 515 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRV 555
>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 = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 46/101 (45%), Gaps = 5/101 (4%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+V T TK E + L GI Y++S++ R + GK VLV ++ G
Sbjct: 449 LVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 63 IDIP--SLDAVINYN---FPCKAKLFVHRVGRCARAGRSGV 98
+DIP SL A+++ + F + + +GR AR V
Sbjct: 509 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRV 549
>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 = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 42/90 (46%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ ++ E V L GI + +++L+P + K+ +I+V+V T G
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG 330
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCAR 92
ID P + VI+++ + + GR R
Sbjct: 331 IDKPDVRFVIHHSMSKSMENYYQESGRAGR 360
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRV-GRCARAGRSGVAYSL 102
+F G+ +LV T V GID+P + ++ N +H++ GR R G+ + +
Sbjct: 634 EFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLV 693
Query: 103 VSS 105
V
Sbjct: 694 VGD 696
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 8 TKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQ--TGKIRVLVVTDVAARGIDI 65
+K + V + + + G+ S IY L P + A KF ++LV TD G+++
Sbjct: 329 SKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL 388
Query: 66 PSLDAVINYNF 76
S+ +I Y+
Sbjct: 389 -SIRRIIFYSL 398
>pdb|3RC3|A Chain A, Human Mitochondrial Helicase Suv3
Length = 677
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 8 TKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQ--TGKIRVLVVTDVAARGIDI 65
+K + V + + + G+ S IY L P + A KF ++LV TD G+++
Sbjct: 329 SKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGXGLNL 388
Query: 66 PSLDAVINYNF 76
S+ +I Y+
Sbjct: 389 -SIRRIIFYSL 398
>pdb|4FQ2|H Chain H, Crystal Structure Of 10-1074 Fab
Length = 244
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 29/65 (44%)
Query: 173 NNAYKKYVKSRPGASVESVKKVKELELATMQVHPLFRNIGSAEQEKFNLLTKMSEYRPPS 232
NN Y +++ PG +E + + + E AT R + S + K L K++ P
Sbjct: 30 NNYYWTWIRQSPGKGLEWIGYISDRESATYNPSLNSRVVISRDTSKNQLSLKLNSVTPAD 89
Query: 233 TVLEF 237
T + +
Sbjct: 90 TAVYY 94
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
0.320 0.135 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,574,538
Number of Sequences: 62578
Number of extensions: 235426
Number of successful extensions: 690
Number of sequences better than 100.0: 71
Number of HSP's better than 100.0 without gapping: 68
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 611
Number of HSP's gapped (non-prelim): 71
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)