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= psy9401
(453 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 259 bits (661), Expect = 3e-69, Method: Compositional matrix adjust.
Identities = 157/404 (38%), Positives = 219/404 (54%), Gaps = 28/404 (6%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F + + E+++ + YT+PT VQ+ AIP RDL+ +QTGSGKTAAF+LP L
Sbjct: 16 SFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILS 75
Query: 62 KFASSK--NKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
+ S + MK+N K Y P LVL PTRELA+Q+ +
Sbjct: 76 QIYSDGPGEALRAMKENGRYGRRKQY------------PISLVLAPTRELAVQIYEEARK 123
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
+ Y +++ + GG +Q++ L R +L+ATPGRL+D M GKI + LVLD
Sbjct: 124 FS-YRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLD 182
Query: 180 EADRMLDMGFINDIEKIV--DATPV--TRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
EADRMLDMGF I +IV D P R TM+FSAT + +A + + + L V
Sbjct: 183 EADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGR 242
Query: 236 IEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFL 295
+ +NITQ +++V++ ++ LLD L + +VF TK+ AD + D L G+
Sbjct: 243 VGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYA 302
Query: 296 AAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVH 355
+HGD Q R L R G+ ILVAT VAARG+D+ + HV N+DLP E+YVH
Sbjct: 303 CTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVH 362
Query: 356 RIGRTGRAGRNGFAVSLVNHAERMNIKK------IERFTKQQIP 393
RIGRTGR G G A S N +NI K +E KQ++P
Sbjct: 363 RIGRTGRVGNLGLATSFFNE-RNINITKDLLDLLVE--AKQEVP 403
>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 = 239 bits (611), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 138/400 (34%), Positives = 223/400 (55%), Gaps = 36/400 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F S L ++++ + K GY PT +Q+ +IP SGRDL+ +QTGSGKTAAF+LP L
Sbjct: 57 HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILS 116
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
K +++ + +P++++++PTRELA+Q+ ++
Sbjct: 117 KLLEDPHELEL-----------------------GRPQVVIVSPTRELAIQIFNEARKFA 153
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
+ +K + GG + Q + ++R +++ATPGRL+D ++ I F + +VLDEA
Sbjct: 154 -FESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEA 212
Query: 182 DRMLDMGFINDIEKIVDATPVT----RQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
DRMLDMGF D+ +I+ T VT QT++FSAT + MA K+ + + + +
Sbjct: 213 DRMLDMGFSEDMRRIM--THVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVG 270
Query: 238 KKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
++ Q+I V+ +++L++ L ++ +VF TKR AD +A L+ F
Sbjct: 271 GACSDVKQTIYEVNKYAKRSKLIEIL--SEQADGTIVFVETKRGADFLASFLSEKEFPTT 328
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI 357
+HGD Q+ R + L + + G +K+L+AT VA+RG+D+ I HV NYD+P +DYVHRI
Sbjct: 329 SIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRI 388
Query: 358 GRTGRAGRNGFAVSLV----NHAERMNIKKIERFTKQQIP 393
GRTGR G NG A S + A ++ KI + Q +P
Sbjct: 389 GRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVP 428
>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 = 230 bits (586), Expect = 1e-60, Method: Compositional matrix adjust.
Identities = 141/386 (36%), Positives = 214/386 (55%), Gaps = 38/386 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGR-DLIVSSQTGSGKTAAFMLPAL 60
NF + L + +L A+ G+ KPT +Q + IP ++ +++ ++TGSGKTA+F +P +
Sbjct: 7 NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+N+NN ++LTPTRELA+QV E
Sbjct: 67 EL--------------VNENNG---------------IEAIILTPTRELAIQVADEIESL 97
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
K +K I GG Q++ L +N I++ TPGR++DH+N G +N +++ +LDE
Sbjct: 98 K-GNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDE 155
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
AD L+ GFI D+EKI++A ++ +LFSAT + N+A+ D +K K
Sbjct: 156 ADEXLNXGFIKDVEKILNACNKDKRILLFSATXPREILNLAKKYXGDYSFIKA----KIN 211
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
NI QS + V++ + L LL++K +VF TKRD +A L GF A +H
Sbjct: 212 ANIEQSYVEVNE-NERFEALCRLLKNKEF-YGLVFCKTKRDTKELASXLRDIGFKAGAIH 269
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
GDL Q+ R + + ++ +I+IL+ATDV +RGIDV + V NY LP+ PE Y HRIGRT
Sbjct: 270 GDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRT 329
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIER 386
GRAG+ G A+S++N E ++ IER
Sbjct: 330 GRAGKKGKAISIINRREYKKLRYIER 355
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 214 bits (545), Expect = 7e-56, Method: Compositional matrix adjust.
Identities = 125/385 (32%), Positives = 199/385 (51%), Gaps = 33/385 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F+ L +L + + G+ KP+ +QE+AIP AI+GRD++ ++ G+GKTAAF++P L K
Sbjct: 23 FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 82
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
NKI + L++ PTRELALQ + G
Sbjct: 83 VKPKLNKI----------------------------QALIMVPTRELALQTSQVVRTLGK 114
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+ I + GG + L+ IL+ TPGR++D + + S + ++DEAD
Sbjct: 115 HCG-ISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEAD 173
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEK-KQK 241
+ML F IE+I+ P T Q++LFSAT V P ++N +E+ K
Sbjct: 174 KMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPY--EINLMEELTLK 231
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
ITQ FV++ K L+ L ++ QA++F + +++A ++ G+ H
Sbjct: 232 GITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHA 290
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
+ Q RN+ R+G+++ LV +D+ RGID+ A+ V N+D PK E Y+HRIGR+G
Sbjct: 291 RMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSG 350
Query: 362 RAGRNGFAVSLVNHAERMNIKKIER 386
R G G A++L+N +R N+ KIE+
Sbjct: 351 RFGHLGLAINLINWNDRFNLYKIEQ 375
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 214 bits (545), Expect = 7e-56, Method: Compositional matrix adjust.
Identities = 128/391 (32%), Positives = 200/391 (51%), Gaps = 29/391 (7%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVL- 60
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ L + + + L+L PTRELA+QV G
Sbjct: 61 ---------------------------QCLDIQVRETQALILAPTRELAVQVQKGLLALG 93
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM +++ + +GG ++ L ++ TPGR+ D + + +++LVLDEA
Sbjct: 94 DYMN-VQSHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEA 152
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML+ GF I + P Q +L SATL V M DP+ + V E +
Sbjct: 153 DEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLE 212
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q + V+ K L L + QAV+F TKR D + +++ + F + +HG
Sbjct: 213 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG 272
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRIGR+G
Sbjct: 273 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSG 332
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
R GR G AV+ V + + ++ IE++ QI
Sbjct: 333 RYGRKGVAVNFVKNDDIRVLRDIEQYYSTQI 363
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 214 bits (544), Expect = 1e-55, Method: Compositional matrix adjust.
Identities = 127/391 (32%), Positives = 199/391 (50%), Gaps = 29/391 (7%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVL- 60
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ L + + + L+L PTRELA+QV G
Sbjct: 61 ---------------------------QCLDIQVRETQALILAPTRELAVQVQKGLLALG 93
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM ++ + +GG ++ L ++ TPGR+ D + + +++LVLDEA
Sbjct: 94 DYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEA 152
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML+ GF I + P Q +L SATL + M DP+ + V E +
Sbjct: 153 DEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLE 212
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q + V+ K L L + QAV+F TKR D + +++ + F + +HG
Sbjct: 213 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG 272
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRIGR+G
Sbjct: 273 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSG 332
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
R GR G AV+ V + + ++ IE++ QI
Sbjct: 333 RYGRKGVAVNFVKNDDIRVLRDIEQYYSTQI 363
>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 = 213 bits (542), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 125/391 (31%), Positives = 198/391 (50%), Gaps = 29/391 (7%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 38 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 97
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
L + + + L+L PTRELA+Q+ G
Sbjct: 98 C----------------------------LDIQVRETQALILAPTRELAVQIQKGLLALG 129
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM ++ + +GG ++ L ++ TPGR+ D + + +++LVLDEA
Sbjct: 130 DYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEA 188
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML+ GF I + P Q +L SATL + M DP+ + V E +
Sbjct: 189 DEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLE 248
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q + V+ K L L + QAV+F TKR D + +++ + F + +HG
Sbjct: 249 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG 308
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRIGR+G
Sbjct: 309 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSG 368
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
R GR G A++ V + + ++ IE++ QI
Sbjct: 369 RYGRKGVAINFVKNDDIRILRDIEQYYSTQI 399
>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 = 213 bits (541), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 125/391 (31%), Positives = 198/391 (50%), Gaps = 29/391 (7%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 39 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 98
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
L + + + L+L PTRELA+Q+ G
Sbjct: 99 C----------------------------LDIQVRETQALILAPTRELAVQIQKGLLALG 130
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM ++ + +GG ++ L ++ TPGR+ D + + +++LVLDEA
Sbjct: 131 DYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEA 189
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML+ GF I + P Q +L SATL + M DP+ + V E +
Sbjct: 190 DEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLE 249
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q + V+ K L L + QAV+F TKR D + +++ + F + +HG
Sbjct: 250 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG 309
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRIGR+G
Sbjct: 310 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSG 369
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
R GR G A++ V + + ++ IE++ QI
Sbjct: 370 RYGRKGVAINFVKNDDIRILRDIEQYYSTQI 400
>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 = 213 bits (541), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 125/391 (31%), Positives = 198/391 (50%), Gaps = 29/391 (7%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 17 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 76
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
L + + + L+L PTRELA+Q+ G
Sbjct: 77 C----------------------------LDIQVRETQALILAPTRELAVQIQKGLLALG 108
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM ++ + +GG ++ L ++ TPGR+ D + + +++LVLDEA
Sbjct: 109 DYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEA 167
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML+ GF I + P Q +L SATL + M DP+ + V E +
Sbjct: 168 DEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLE 227
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q + V+ K L L + QAV+F TKR D + +++ + F + +HG
Sbjct: 228 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG 287
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRIGR+G
Sbjct: 288 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSG 347
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
R GR G A++ V + + ++ IE++ QI
Sbjct: 348 RYGRKGVAINFVKNDDIRILRDIEQYYSTQI 378
>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 = 213 bits (541), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 125/391 (31%), Positives = 198/391 (50%), Gaps = 29/391 (7%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 39 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 98
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
L + + + L+L PTRELA+Q+ G
Sbjct: 99 C----------------------------LDIQVRETQALILAPTRELAVQIQKGLLALG 130
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM ++ + +GG ++ L ++ TPGR+ D + + +++LVLDEA
Sbjct: 131 DYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEA 189
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML+ GF I + P Q +L SATL + M DP+ + V E +
Sbjct: 190 DEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLE 249
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q + V+ K L L + QAV+F TKR D + +++ + F + +HG
Sbjct: 250 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG 309
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRIGR+G
Sbjct: 310 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSG 369
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
R GR G A++ V + + ++ IE++ QI
Sbjct: 370 RYGRKGVAINFVKNDDIRILRDIEQYYSTQI 400
>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 = 194 bits (492), Expect = 1e-49, Method: Compositional matrix adjust.
Identities = 123/389 (31%), Positives = 193/389 (49%), Gaps = 42/389 (10%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F +GL +LK + + + KP+ +QE+A+P + R++I SQ+G+GKTAAF L
Sbjct: 6 SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L R+ + A P+ + L P+RELA Q +
Sbjct: 66 L----------------------------TRVNPEDASPQAICLAPSRELARQTLEVVQE 97
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
G + K + + +Q+ N ++++ TPG ++D M + ++I VLD
Sbjct: 98 MGKFTKITSQLIVPDSFEKNKQI-----NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLD 152
Query: 180 EADRMLDM-GFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEK 238
EAD MLD G + ++ P Q +LFSAT V A+ I + L++ + E
Sbjct: 153 EADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEV 212
Query: 239 KQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAP 298
I Q + + K +L L +G +++F ATK+ A+++ +L G +
Sbjct: 213 NVDAIKQLYMDCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSI 272
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKF------PED 352
LHGDL R+R +++ R GR K+L+ T+V ARGID+P ++ V NYDLP P
Sbjct: 273 LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPAT 332
Query: 353 YVHRIGRTGRAGRNGFAVSLVNHAERMNI 381
Y+HRIGRTGR GR G A+S V+ NI
Sbjct: 333 YIHRIGRTGRFGRKGVAISFVHDKNSFNI 361
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 194 bits (492), Expect = 1e-49, Method: Compositional matrix adjust.
Identities = 123/389 (31%), Positives = 193/389 (49%), Gaps = 42/389 (10%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F +GL +LK + + + KP+ +QE+A+P + R++I SQ+G+GKTAAF L
Sbjct: 6 SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L R+ + A P+ + L P+RELA Q +
Sbjct: 66 L----------------------------TRVNPEDASPQAICLAPSRELARQTLEVVQE 97
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
G + K + + +Q+ N ++++ TPG ++D M + ++I VLD
Sbjct: 98 MGKFTKITSQLIVPDSFEKNKQI-----NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLD 152
Query: 180 EADRMLDM-GFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEK 238
EAD MLD G + ++ P Q +LFSAT V A+ I + L++ + E
Sbjct: 153 EADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEV 212
Query: 239 KQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAP 298
I Q + + K +L L +G +++F ATK+ A+++ +L G +
Sbjct: 213 NVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSI 272
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKF------PED 352
LHGDL R+R +++ R GR K+L+ T+V ARGID+P ++ V NYDLP P
Sbjct: 273 LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPAT 332
Query: 353 YVHRIGRTGRAGRNGFAVSLVNHAERMNI 381
Y+HRIGRTGR GR G A+S V+ NI
Sbjct: 333 YIHRIGRTGRFGRKGVAISFVHDKNSFNI 361
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 192 bits (488), Expect = 3e-49, Method: Compositional matrix adjust.
Identities = 126/371 (33%), Positives = 196/371 (52%), Gaps = 56/371 (15%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSK 67
++E + +A+ ++G+ T VQ + IP + G++++V ++TGSGKTAA+ +P L S
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKS- 59
Query: 68 NKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKI 127
LV+TPTREL QV + G YM
Sbjct: 60 ---------------------------------LVVTPTRELTRQVASHIRDIGRYMDT- 85
Query: 128 KAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDM 187
K + GGMPY Q+ + RN +I++ATPGRL+D + G I+ S +I+++DEAD M +M
Sbjct: 86 KVAEVYGGMPYKAQINRV-RNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEM 144
Query: 188 GFINDIEKIVDATPVTRQTMLFSATLD----GIVGNMAENITKDPLILKVNSIEKKQKNI 243
GFI+DI+ I+ T + T LFSAT+ +V + N + + + ++E K ++
Sbjct: 145 GFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEACIGLANVEHKFVHV 204
Query: 244 TQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATK-RDADIIADRLNISGFLAAPLHGD 302
DD K + L R+ + +VF T+ R A ++ N A L GD
Sbjct: 205 K------DDWRSKVQAL----RENKDKGVIVFVRTRNRVAKLVRLFDN-----AIELRGD 249
Query: 303 LHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
L Q+ RNR ++ R G +L+ TDVA+RG+D+P + V N+D P+ Y+HRIGRTGR
Sbjct: 250 LPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGR 309
Query: 363 AGRNGFAVSLV 373
GR G A++ +
Sbjct: 310 MGRKGEAITFI 320
>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 = 184 bits (468), Expect = 7e-47, Method: Compositional matrix adjust.
Identities = 122/390 (31%), Positives = 202/390 (51%), Gaps = 30/390 (7%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F + L E +L+ + G+ +P+ +Q++AI I G D++ +Q+G+GKT F + AL +
Sbjct: 24 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 83
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
+S P+ L+L PTRELALQ+
Sbjct: 84 IDTSVKA----------------------------PQALMLAPTRELALQIQKVVMALAF 115
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+M IK + +GG ++ + L R+ +I++ TPGR+ D++ + +++ +LDEAD
Sbjct: 116 HM-DIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEAD 173
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKN 242
ML GF I +I P T Q +L SAT+ V + ++P+ + V E +
Sbjct: 174 EMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEG 233
Query: 243 ITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGD 302
I Q + V++ +K L L V QAV+F T+R + + +L F + ++ D
Sbjct: 234 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 293
Query: 303 LHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
L Q R+ ++ R G +IL++TD+ ARGIDV ++ V NYDLP E+Y+HRIGR GR
Sbjct: 294 LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 353
Query: 363 AGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
GR G A++ V + + ++++E+F QI
Sbjct: 354 FGRKGVAINFVTNEDVGAMRELEKFYSTQI 383
>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 = 184 bits (466), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 127/399 (31%), Positives = 202/399 (50%), Gaps = 33/399 (8%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F + L E +L+ + G+ KP+ +Q++AI I G D+I +Q+G+GKTA F + L
Sbjct: 15 SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 74
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ L K Q LVL PTRELA Q+ G
Sbjct: 75 QI--------------------------ELDLKATQA--LVLAPTRELAQQIQKVVMALG 106
Query: 122 LYMKKIKAISILGGMPYLRQMQLLS-RNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM + +GG ++Q L P I++ TPGR+ D +N ++ ++++ VLDE
Sbjct: 107 DYMGA-SCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDE 165
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
AD ML GF + I I Q +L SAT+ V + + +DP+ + V E
Sbjct: 166 ADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTL 225
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ I Q + V+ K L L + QAV+F T+R D + ++++ F + +H
Sbjct: 226 EGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMH 285
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
GD+ Q R+ + R G ++L+ TD+ ARGIDV ++ V NYDLP E+Y+HRIGR
Sbjct: 286 GDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG 345
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIERF---TKQQIPIEV 396
GR GR G A+++V ++ ++ IE F + +++P+ V
Sbjct: 346 GRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNV 384
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 183 bits (464), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 127/401 (31%), Positives = 203/401 (50%), Gaps = 33/401 (8%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F + L E +L+ + G+ KP+ +Q++AI I G D+I +Q+G+GKTA F + L
Sbjct: 41 SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 100
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ L K Q LVL PTRELA Q+ G
Sbjct: 101 QI--------------------------ELDLKATQA--LVLAPTRELAQQIQKVVMALG 132
Query: 122 LYMKKIKAISILGGMPYLRQMQLLS-RNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM + +GG ++Q L P I++ TPGR+ D +N ++ ++++ VLDE
Sbjct: 133 DYMGA-SCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDE 191
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
AD ML GF + I I Q +L SAT+ V + + +DP+ + V E
Sbjct: 192 ADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTL 251
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ I Q + V+ K L L + QAV+F T+R D + ++++ F + +H
Sbjct: 252 EGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMH 311
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
GD+ Q R+ + R G ++L+ TD+ ARGIDV ++ V NYDLP E+Y+HRIGR
Sbjct: 312 GDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG 371
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIERF---TKQQIPIEVIN 398
GR GR G A+++V ++ ++ IE F + +++P+ V +
Sbjct: 372 GRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVAD 412
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 182 bits (462), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 111/374 (29%), Positives = 184/374 (49%), Gaps = 30/374 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F+ L +L+A+V G+ P+ VQ + IP AI G D++ +++G GKTA F+L L +
Sbjct: 9 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 68
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
++ V LV+ TRELA Q++ ER+
Sbjct: 69 LEPVTGQVSV----------------------------LVMCHTRELAFQISKEYERFSK 100
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM +K GG+ + ++L +N P I++ TPGR++ + +N H++ +LDEA
Sbjct: 101 YMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEA 160
Query: 182 DRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
D+ML+ + D+++I TP +Q M+FSATL + + +DP+ + V+ K
Sbjct: 161 DKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLT 220
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ Q KNR L LL Q V+F + + +A L F A +H
Sbjct: 221 LHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIH 280
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
+ Q R + + + +ILVAT++ RG+D+ + FNYD+P+ + Y+HR+ R
Sbjct: 281 RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARA 340
Query: 361 GRAGRNGFAVSLVN 374
GR G G A++ V+
Sbjct: 341 GRFGTKGLAITFVS 354
>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 = 182 bits (461), Expect = 5e-46, Method: Compositional matrix adjust.
Identities = 130/406 (32%), Positives = 205/406 (50%), Gaps = 52/406 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F+ + L +L+ + +G+ +P+ +QE A+P ++ ++LI SQ+G+GKTAAF+L
Sbjct: 26 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L + + NK P+ L L+PT ELALQ E+
Sbjct: 86 LSQVEPA-NKY---------------------------PQCLCLSPTYELALQTGKVIEQ 117
Query: 120 YGLYMKKIK-AISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQILV 177
G + ++K A ++ G L + Q +S +I++ TPG ++D + K I+ +++ V
Sbjct: 118 MGKFYPELKLAYAVRGNK--LERGQKISE--QIVIGTPGTVLDWCSKLKFIDPKKIKVFV 173
Query: 178 LDEADRML-DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSI 236
LDEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+
Sbjct: 174 LDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 233
Query: 237 EKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLA 296
E+ I Q + K + L L + QA++F T++ A +A L+ G
Sbjct: 234 EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQV 293
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP------KFP 350
A L G++ R +E R G+ K+LV T+V ARGIDV ++ V N+DLP
Sbjct: 294 ALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDN 353
Query: 351 EDYVHRIGRTGRAGRNGFAVSLVNHAERMNI---------KKIERF 387
E Y+HRIGRTGR G+ G AV++V+ MNI KKIER
Sbjct: 354 ETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 399
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 181 bits (460), Expect = 5e-46, Method: Compositional matrix adjust.
Identities = 127/405 (31%), Positives = 202/405 (49%), Gaps = 50/405 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F+ + L +L+ + +G+ +P+ +QE A+P ++ ++LI SQ+G+GKTAAF+L
Sbjct: 42 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 101
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L + + NK P+ L L+PT ELALQ E+
Sbjct: 102 LSQVEPA-NKY---------------------------PQCLCLSPTYELALQTGKVIEQ 133
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQILVL 178
G + ++K + G R ++ + +I++ TPG ++D + K I+ +++ VL
Sbjct: 134 MGKFYPELKLAYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 190
Query: 179 DEADRML-DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
DEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+ E
Sbjct: 191 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 250
Query: 238 KKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
+ I Q + K + L L + QA++F T++ A +A L+ G A
Sbjct: 251 ETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVA 310
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP------KFPE 351
L G++ R +E R G+ K+LV T+V ARGIDV ++ V N+DLP E
Sbjct: 311 LLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE 370
Query: 352 DYVHRIGRTGRAGRNGFAVSLVNHAERMNI---------KKIERF 387
Y+HRIGRTGR G+ G AV++V+ MNI KKIER
Sbjct: 371 TYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 415
>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 = 181 bits (460), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 127/407 (31%), Positives = 202/407 (49%), Gaps = 54/407 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F+ + L +L+ + +G+ +P+ +QE A+P ++ ++LI SQ+G+GKTAAF+L
Sbjct: 93 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQ--PRMLVLTPTRELALQVTAAT 117
L + +PA P+ L L+PT ELALQ
Sbjct: 153 LSQ------------------------------VEPANKYPQCLCLSPTYELALQTGKVI 182
Query: 118 ERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQIL 176
E+ G + ++K + G R ++ + +I++ TPG ++D + K I+ +++
Sbjct: 183 EQMGKFYPELKLAYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVF 239
Query: 177 VLDEADRML-DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
VLDEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+
Sbjct: 240 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR 299
Query: 236 IEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFL 295
E+ I Q + K + L L + QA++F T++ A +A L+ G
Sbjct: 300 EEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQ 359
Query: 296 AAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP------KF 349
A L G++ R +E R G+ K+LV T+V ARGIDV ++ V N+DLP
Sbjct: 360 VALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPD 419
Query: 350 PEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI---------KKIERF 387
E Y+HRIGRTGR G+ G AV++V+ MNI KKIER
Sbjct: 420 NETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 466
>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 = 181 bits (460), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 127/405 (31%), Positives = 202/405 (49%), Gaps = 50/405 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F+ + L +L+ + +G+ +P+ +QE A+P ++ ++LI SQ+G+GKTAAF+L
Sbjct: 63 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 122
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L + + NK P+ L L+PT ELALQ E+
Sbjct: 123 LSQVEPA-NKY---------------------------PQCLCLSPTYELALQTGKVIEQ 154
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQILVL 178
G + ++K + G R ++ + +I++ TPG ++D + K I+ +++ VL
Sbjct: 155 MGKFYPELKLAYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 211
Query: 179 DEADRML-DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
DEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+ E
Sbjct: 212 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 271
Query: 238 KKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
+ I Q + K + L L + QA++F T++ A +A L+ G A
Sbjct: 272 ETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVA 331
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP------KFPE 351
L G++ R +E R G+ K+LV T+V ARGIDV ++ V N+DLP E
Sbjct: 332 LLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE 391
Query: 352 DYVHRIGRTGRAGRNGFAVSLVNHAERMNI---------KKIERF 387
Y+HRIGRTGR G+ G AV++V+ MNI KKIER
Sbjct: 392 TYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL 436
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 181 bits (459), Expect = 7e-46, Method: Compositional matrix adjust.
Identities = 110/374 (29%), Positives = 183/374 (48%), Gaps = 30/374 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F+ L +L+A+V G+ P+ VQ + IP AI G D++ +++G GKTA F+L L +
Sbjct: 10 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 69
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
++ V LV+ TRELA Q++ ER+
Sbjct: 70 LEPVTGQVSV----------------------------LVMCHTRELAFQISKEYERFSK 101
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM +K GG+ + ++L +N P I++ TPGR++ + +N H++ +LDE
Sbjct: 102 YMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEC 161
Query: 182 DRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
D+ML+ + D+++I TP +Q M+FSATL + + +DP+ + V+ K
Sbjct: 162 DKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLT 221
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ Q KNR L LL Q V+F + + +A L F A +H
Sbjct: 222 LHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIH 281
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
+ Q R + + + +ILVAT++ RG+D+ + FNYD+P+ + Y+HR+ R
Sbjct: 282 RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARA 341
Query: 361 GRAGRNGFAVSLVN 374
GR G G A++ V+
Sbjct: 342 GRFGTKGLAITFVS 355
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 181 bits (459), Expect = 7e-46, Method: Compositional matrix adjust.
Identities = 110/374 (29%), Positives = 183/374 (48%), Gaps = 30/374 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F+ L +L+A+V G+ P+ VQ + IP AI G D++ +++G GKTA F+L L +
Sbjct: 10 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 69
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
++ V LV+ TRELA Q++ ER+
Sbjct: 70 LEPVTGQVSV----------------------------LVMCHTRELAFQISKEYERFSK 101
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
YM +K GG+ + ++L +N P I++ TPGR++ + +N H++ +LDE
Sbjct: 102 YMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEC 161
Query: 182 DRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
D+ML+ + D+++I TP +Q M+FSATL + + +DP+ + V+ K
Sbjct: 162 DKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLT 221
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ Q KNR L LL Q V+F + + +A L F A +H
Sbjct: 222 LHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIH 281
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
+ Q R + + + +ILVAT++ RG+D+ + FNYD+P+ + Y+HR+ R
Sbjct: 282 RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARA 341
Query: 361 GRAGRNGFAVSLVN 374
GR G G A++ V+
Sbjct: 342 GRFGTKGLAITFVS 355
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 175 bits (444), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 120/390 (30%), Positives = 194/390 (49%), Gaps = 30/390 (7%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F L E +L+ + G+ +P+ +Q++AI I G D++ +Q+G+GKT F + AL +
Sbjct: 23 FDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
+S P+ L L PTRELALQ+
Sbjct: 83 IDTSVKA----------------------------PQALXLAPTRELALQIQKVVXALAF 114
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+ IK + +GG ++ + L R+ +I++ TPGR+ D++ + ++ +LDEAD
Sbjct: 115 HXD-IKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEAD 172
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKN 242
L GF I +I P T Q +L SAT V + ++P+ + V E +
Sbjct: 173 EXLSSGFKEQIYQIFTLLPPTTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEG 232
Query: 243 ITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGD 302
I Q + V++ +K L L V QAV+F T+R + + +L F + ++ D
Sbjct: 233 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 292
Query: 303 LHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
L Q R+ + R G +IL++TD+ ARGIDV ++ V NYDLP E+Y+HRIGR GR
Sbjct: 293 LPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 352
Query: 363 AGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
GR G A++ V + + +++E+F QI
Sbjct: 353 FGRKGVAINFVTNEDVGAXRELEKFYSTQI 382
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 162 bits (411), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 94/233 (40%), Positives = 136/233 (58%), Gaps = 28/233 (12%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
M FK L +L+AL G T PT +Q A+P A+ G+DLI ++TG+GKT AF LP
Sbjct: 1 MEFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIA 60
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ A S+ ER R +PR LVLTPTRELALQV A+E
Sbjct: 61 ERLAPSQ---------------------ERGR----KPRALVLTPTRELALQV--ASELT 93
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+ +K +++ GG Y +Q + L R + ++ATPGR +D++ G ++ S +++ VLDE
Sbjct: 94 AV-APHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDE 152
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
AD ML MGF ++E ++ ATP +RQT+LFSATL +AE K+P+++ V
Sbjct: 153 ADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 162 bits (409), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 116/366 (31%), Positives = 180/366 (49%), Gaps = 45/366 (12%)
Query: 27 VQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKI 84
+QE+A+P +S R++I SQ+G+GKTAAF L L + +S +P
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDAS---VP------------- 188
Query: 85 YTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQL 144
+P+ + L P+RELA Q+ G Y + A I +P ++
Sbjct: 189 ------------KPQAICLAPSRELARQIMDVVTEMGKYTEVKTAFGIKDSVPKGAKI-- 234
Query: 145 LSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIE-KIVDATPVT 203
+ +I++ TPG ++D M +++ +++ VLDEAD MLD + D +I P
Sbjct: 235 ---DAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRN 291
Query: 204 RQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYL 263
Q +LFSAT V AE + +++ + E + I Q + HK +L L
Sbjct: 292 TQIVLFSATFSERVEKYAERFAPNANEIRLKTEELSVEGIKQLYMDCQSEEHKYNVLVEL 351
Query: 264 LRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKIL 323
+GQ+++F K A+ IA R+ G A L G+L R+ +++ R G K+L
Sbjct: 352 YGLLTIGQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVL 411
Query: 324 VATDVAARGIDVPAITHVFNYDLP------KFPEDYVHRIGRTGRAGRNGFAVSLVN--- 374
V T+V ARGIDV + V NYD+P P+ Y+HRIGRTGR GR G +++ V+
Sbjct: 412 VTTNVIARGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFVHDKK 471
Query: 375 HAERMN 380
E MN
Sbjct: 472 SWEEMN 477
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 161 bits (407), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 93/233 (39%), Positives = 136/233 (58%), Gaps = 28/233 (12%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
M FK L +L+AL G T PT ++ A+P A+ G+DLI ++TG+GKT AF LP
Sbjct: 1 MEFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIA 60
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ A S+ ER R +PR LVLTPTRELALQV A+E
Sbjct: 61 ERLAPSQ---------------------ERGR----KPRALVLTPTRELALQV--ASELT 93
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+ +K +++ GG Y +Q + L R + ++ATPGR +D++ G ++ S +++ VLDE
Sbjct: 94 AV-APHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDE 152
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
AD ML MGF ++E ++ ATP +RQT+LFSATL +AE K+P+++ V
Sbjct: 153 ADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 160 bits (405), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 124/430 (28%), Positives = 212/430 (49%), Gaps = 58/430 (13%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRD--LIVSSQTGSGKTAAFMLPALHKFAS 65
L + + KA+ ++ + T VQ++ I +S D +I ++TG+GKT AF++P +
Sbjct: 28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 66 SKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER-----Y 120
+K M K +++ PTR+LALQ+ A ++ Y
Sbjct: 88 TKFDSQYMVK------------------------AVIVAPTRDLALQIEAEVKKIHDMNY 123
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSR-NPEILLATPGRLIDHMN--SGKINFSHLQILV 177
GL KK +S++GG + M +++ P I++ATPGRLID + S K F + V
Sbjct: 124 GL--KKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKF-FRFVDYKV 180
Query: 178 LDEADRMLDMGFINDIEKIV-------DATPVTRQTMLFSATLDGIVGNMAENITKDPLI 230
LDEADR+L++GF +D+E I + +T+LFSATLD V +A NI
Sbjct: 181 LDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 240
Query: 231 LKVNSIEKKQ----KNITQSIL----FVDDILHKNRLLDYLLRDKRVG-QAVVFTATKRD 281
L +++++K + + I QS++ F + I + ++++ +A++F T +
Sbjct: 241 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 300
Query: 282 ADIIADRLNISGFLAAPL---HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAI 338
+ L P+ HG + QN R ++ ++ ILV TDV ARG+D P +
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 360
Query: 339 THVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVIN 398
V +P +Y+HRIGRT R+G+ G +V + E ++++E + I I
Sbjct: 361 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE--DAKNIVIAKQE 418
Query: 399 GFEPKKRIRT 408
+EP + I++
Sbjct: 419 KYEPSEEIKS 428
>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 = 159 bits (402), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 124/430 (28%), Positives = 212/430 (49%), Gaps = 58/430 (13%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRD--LIVSSQTGSGKTAAFMLPALHKFAS 65
L + + KA+ ++ + T VQ++ I +S D +I ++TG+GKT AF++P +
Sbjct: 79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 66 SKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER-----Y 120
+K M K +++ PTR+LALQ+ A ++ Y
Sbjct: 139 TKFDSQYMVK------------------------AVIVAPTRDLALQIEAEVKKIHDMNY 174
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSR-NPEILLATPGRLIDHMN--SGKINFSHLQILV 177
GL KK +S++GG + M +++ P I++ATPGRLID + S K F + V
Sbjct: 175 GL--KKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKF-FRFVDYKV 231
Query: 178 LDEADRMLDMGFINDIEKIV-------DATPVTRQTMLFSATLDGIVGNMAENITKDPLI 230
LDEADR+L++GF +D+E I + +T+LFSATLD V +A NI
Sbjct: 232 LDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 291
Query: 231 LKVNSIEKKQ----KNITQSIL----FVDDILHKNRLLDYLLRDKRVG-QAVVFTATKRD 281
L +++++K + + I QS++ F + I + ++++ +A++F T +
Sbjct: 292 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 351
Query: 282 ADIIADRLNISGFLAAPL---HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAI 338
+ L P+ HG + QN R ++ ++ ILV TDV ARG+D P +
Sbjct: 352 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 411
Query: 339 THVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVIN 398
V +P +Y+HRIGRT R+G+ G +V + E ++++E + I I
Sbjct: 412 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE--DAKNIVIAKQE 469
Query: 399 GFEPKKRIRT 408
+EP + I++
Sbjct: 470 KYEPSEEIKS 479
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 159 bits (401), Expect = 4e-39, Method: Compositional matrix adjust.
Identities = 124/430 (28%), Positives = 212/430 (49%), Gaps = 58/430 (13%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRD--LIVSSQTGSGKTAAFMLPALHKFAS 65
L + + KA+ ++ + T VQ++ I +S D +I ++TG+GKT AF++P +
Sbjct: 28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 66 SKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER-----Y 120
+K M K +++ PTR+LALQ+ A ++ Y
Sbjct: 88 TKFDSQYMVK------------------------AVIVAPTRDLALQIEAEVKKIHDMNY 123
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSR-NPEILLATPGRLIDHMN--SGKINFSHLQILV 177
GL KK +S++GG + M +++ P I++ATPGRLID + S K F + V
Sbjct: 124 GL--KKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKF-FRFVDYKV 180
Query: 178 LDEADRMLDMGFINDIEKIV-------DATPVTRQTMLFSATLDGIVGNMAENITKDPLI 230
LDEADR+L++GF +D+E I + +T+LFSATLD V +A NI
Sbjct: 181 LDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 240
Query: 231 LKVNSIEKKQ----KNITQSIL----FVDDILHKNRLLDYLLRDKRVG-QAVVFTATKRD 281
L +++++K + + I QS++ F + I + ++++ +A++F T +
Sbjct: 241 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 300
Query: 282 ADIIADRLNISGFLAAPL---HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAI 338
+ L P+ HG + QN R ++ ++ ILV TDV ARG+D P +
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 360
Query: 339 THVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVIN 398
V +P +Y+HRIGRT R+G+ G +V + E ++++E + I I
Sbjct: 361 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE--DAKNIVIAKQE 418
Query: 399 GFEPKKRIRT 408
+EP + I++
Sbjct: 419 KYEPSEEIKS 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 = 152 bits (385), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 90/237 (37%), Positives = 125/237 (52%), Gaps = 24/237 (10%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+NF V+ + + +T+PT +Q Q P A+SG D++ +QTGSGKT +++LPA+
Sbjct: 29 LNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAI 88
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
N P +++ P LVL PTRELA QV Y
Sbjct: 89 VHI----NHQPFLERGDG-------------------PICLVLAPTRELAQQVQQVAAEY 125
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
++K+ I GG P Q++ L R EI +ATPGRLID + GK N LVLDE
Sbjct: 126 -CRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDE 184
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
ADRMLDMGF I KIVD RQT+++SAT V +AE+ KD + + + ++E
Sbjct: 185 ADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALE 241
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 151 bits (381), Expect = 9e-37, Method: Compositional matrix adjust.
Identities = 89/227 (39%), Positives = 119/227 (52%), Gaps = 24/227 (10%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+NF V+ + + +T+PT +Q Q P A+SG D++ +QTGSGKT +++LPA+
Sbjct: 43 LNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAI 102
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
N P +++ P LVL PTRELA QV Y
Sbjct: 103 VHI----NHQPFLERGDG-------------------PICLVLAPTRELAQQVQQVAAEY 139
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
++K+ I GG P Q++ L R EI +ATPGRLID + GK N LVLDE
Sbjct: 140 -CRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDE 198
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKD 227
ADRMLDMGF I KIVD RQT+++SAT V +AE+ KD
Sbjct: 199 ADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKD 245
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 150 bits (379), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 89/235 (37%), Positives = 135/235 (57%), Gaps = 30/235 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
FK +G+ +++ +A ++G+TKPT +Q +AIP A+ GRD+I ++TGSGKT AF LP L
Sbjct: 44 TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPIL- 102
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
N + +RL LVLTPTRELA Q++ E G
Sbjct: 103 --------------------NALLETPQRLF-------ALVLTPTRELAFQISEQFEALG 135
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHM-NSGKINFSHLQILVLDE 180
+ +++ I+GG+ + Q L++ P I++ATPGRLIDH+ N+ N L+ LV+DE
Sbjct: 136 SSIG-VQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDE 194
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
ADR+L+M F +++KI+ P R+T LFSAT+ V + K+P+ V+S
Sbjct: 195 ADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVSS 249
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 143 bits (361), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 81/250 (32%), Positives = 135/250 (54%), Gaps = 24/250 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
NF + L + ++ Y +PT +Q+ AIPA + RD++ +QTGSGKTAAF++P ++
Sbjct: 24 NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
++LNQ K A P+ L+L PTRELA+Q+ + ++++
Sbjct: 84 HLVC---------QDLNQQRYS----------KTAYPKCLILAPTRELAIQILSESQKFS 124
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
L +++ + GG Q++ + +L+ATPGRL+D + KI+ + +VLDEA
Sbjct: 125 LN-TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEA 183
Query: 182 DRMLDMGFINDIEKIVD----ATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
DRMLDMGF I KI++ + + RQT++FSAT + +A + + + + V +
Sbjct: 184 DRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVG 243
Query: 238 KKQKNITQSI 247
+I Q I
Sbjct: 244 STSDSIKQEI 253
>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain
pdb|3IUY|B Chain B, Crystal Structure Of Ddx53 Dead-Box Domain
Length = 228
Score = 138 bits (348), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 88/223 (39%), Positives = 126/223 (56%), Gaps = 26/223 (11%)
Query: 12 VLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIP 71
+LK++++VG KPT +Q QA P + G DLIV +QTG+GKT ++++P S P
Sbjct: 31 LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQ----P 86
Query: 72 VMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAIS 131
+ ++ N P MLVLTPTRELAL V A +Y K +K+I
Sbjct: 87 ISREQRNG------------------PGMLVLTPTRELALHVEAECSKYS--YKGLKSIC 126
Query: 132 ILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFIN 191
I GG Q++ +S+ +I++ATPGRL D + +N + LV+DEAD+MLDM F
Sbjct: 127 IYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEP 186
Query: 192 DIEKI-VDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
I KI +D P RQT++ SAT V +A + KDP+I+ V
Sbjct: 187 QIRKILLDVRP-DRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228
>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 = 133 bits (335), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 67/166 (40%), Positives = 101/166 (60%)
Query: 240 QKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPL 299
+K I Q DD+ HK LL +LL+ +++VF + +A+ L +G L
Sbjct: 1 RKKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYL 60
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGR 359
G++ Q RN ++ L GR+ +LVATDVAARGID+P ++HVFN+D+P+ + Y+HRIGR
Sbjct: 61 EGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGR 120
Query: 360 TGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKR 405
T RAGR G A+SLV + + + K+ R+ ++ I VI+ PK R
Sbjct: 121 TARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVIDELRPKTR 166
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 85/233 (36%), Positives = 129/233 (55%), Gaps = 45/233 (19%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSK 67
++E LKA+ ++G+T T +Q ++I + GRDL+ +++TGSGKT AF++PA+
Sbjct: 61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIV--- 117
Query: 68 NKIPVMKKNLNQNNNKIYTHKERLRFKPAQPR-MLVLTPTRELALQ--------VTAATE 118
+LRF P +L+L+PTRELA+Q +T
Sbjct: 118 ----------------------KLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVH 155
Query: 119 RYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHM-NSGKINFSHLQILV 177
YGL I+GG + Q L I++ATPGRL+DHM N+ + +LQ LV
Sbjct: 156 TYGL---------IMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLV 206
Query: 178 LDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAE-NITKDPL 229
+DEADR+LD+GF ++++I+ P RQTMLFSAT V ++A ++ K+PL
Sbjct: 207 IDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPL 259
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Uap56
Length = 220
Score = 123 bits (309), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 68/230 (29%), Positives = 115/230 (50%), Gaps = 30/230 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F+ L +L+A+V G+ P+ VQ + IP AI G D++ +++G GKTA F+L L
Sbjct: 15 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ ++ V LV+ TRELA Q++ ER+
Sbjct: 75 QLEPVTGQVSV----------------------------LVMCHTRELAFQISKEYERFS 106
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM +K GG+ + ++L +N P I++ TPGR++ + +N H++ +LDE
Sbjct: 107 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 166
Query: 181 ADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPL 229
D+ML+ + D+++I TP +Q M+FSATL + + +DP+
Sbjct: 167 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPM 216
>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 = 122 bits (305), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 66/212 (31%), Positives = 111/212 (52%), Gaps = 28/212 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F+ L +L + ++G+ KP+ +QE++IP A+SGRD++ ++ G+GK+ A+++P L
Sbjct: 4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL- 62
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
ERL K + +V+ PTRELALQV+ +
Sbjct: 63 ---------------------------ERLDLKKDNIQAMVIVPTRELALQVSQICIQVS 95
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
+M K ++ GG + L +++ATPGR++D + G H+Q++VLDEA
Sbjct: 96 KHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEA 155
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATL 213
D++L F+ +E I+ P RQ +L+SAT
Sbjct: 156 DKLLSQDFVQIMEDIILTLPKNRQILLYSATF 187
>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 = 116 bits (291), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 68/160 (42%), Positives = 92/160 (57%), Gaps = 11/160 (6%)
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+NITQ +++V++ ++ LLD L + +VF TK+ AD + D L G+ +H
Sbjct: 18 ENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIH 77
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
GD Q R L R G+ ILVAT VAARG+D+ + HV N+DLP E+YVHRIGRT
Sbjct: 78 GDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRT 137
Query: 361 GRAGRNGFAVSLVNHAER-MNIKK------IERFTKQQIP 393
GR G G A S N ER +NI K +E KQ++P
Sbjct: 138 GRVGNLGLATSFFN--ERNINITKDLLDLLVE--AKQEVP 173
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 114 bits (284), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 52/119 (43%), Positives = 75/119 (63%), Gaps = 6/119 (5%)
Query: 269 VGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV 328
+G +++F ATK+ A+++ +L G + LHGDL R+R +++ R GR K+L+ T+V
Sbjct: 35 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV 94
Query: 329 AARGIDVPAITHVFNYDLPKF------PEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI 381
ARGID+P ++ V NYDLP P Y+HRIGRTGR GR G A+S V+ NI
Sbjct: 95 LARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNI 153
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 113 bits (283), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 52/119 (43%), Positives = 75/119 (63%), Gaps = 6/119 (5%)
Query: 269 VGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV 328
+G +++F ATK+ A+++ +L G + LHGDL R+R +++ R GR K+L+ T+V
Sbjct: 37 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV 96
Query: 329 AARGIDVPAITHVFNYDLPKF------PEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI 381
ARGID+P ++ V NYDLP P Y+HRIGRTGR GR G A+S V+ NI
Sbjct: 97 LARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNI 155
>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 = 113 bits (283), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 52/119 (43%), Positives = 75/119 (63%), Gaps = 6/119 (5%)
Query: 269 VGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV 328
+G +++F ATK+ A+++ +L G + LHGDL R+R +++ R GR K+L+ T+V
Sbjct: 36 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV 95
Query: 329 AARGIDVPAITHVFNYDLPKF------PEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI 381
ARGID+P ++ V NYDLP P Y+HRIGRTGR GR G A+S V+ NI
Sbjct: 96 LARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNI 154
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 111 bits (277), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 72/229 (31%), Positives = 111/229 (48%), Gaps = 30/229 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
NF + L E +L+ + G+ KP+ +Q++AI I G D+I +Q+G+GKTA F + L
Sbjct: 31 NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ 90
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ + FK Q LVL PTRELA Q+ G
Sbjct: 91 QL--------------------------EIEFKETQA--LVLAPTRELAQQIQKVILALG 122
Query: 122 LYMKKIKAISILGGMPYLRQMQ-LLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM + +GG +MQ L + P I++ TPGR+ D +N ++ +++ VLDE
Sbjct: 123 DYMGA-TCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDE 181
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPL 229
AD ML GF + I +I + Q +L SAT+ V + + +DP+
Sbjct: 182 ADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPI 230
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 111 bits (277), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 77/229 (33%), Positives = 119/229 (51%), Gaps = 31/229 (13%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F L + LK L + Y T +Q+Q I A+ G+D++ +++TGSGKT AF++P L
Sbjct: 27 FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEA 86
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQP-RMLVLTPTRELALQVTAATERYG 121
RL++ +L+++PTRELA Q + G
Sbjct: 87 LY-------------------------RLQWTSTDGLGVLIISPTRELAYQTFEVLRKVG 121
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINF--SHLQILVLD 179
A I+GG + + ++ N IL+ TPGRL+ HM+ ++F + LQ+LVLD
Sbjct: 122 -KNHDFSAGLIIGGKDLKHEAERIN-NINILVCTPGRLLQHMDE-TVSFHATDLQMLVLD 178
Query: 180 EADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDP 228
EADR+LDMGF + + +++ P RQT+LFSAT V ++A K+P
Sbjct: 179 EADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNP 227
>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 = 110 bits (276), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/156 (37%), Positives = 88/156 (56%), Gaps = 6/156 (3%)
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
++ Q + +V + LL+ L K ++F K D D I + L + G A +HG
Sbjct: 29 DVIQEVEYVKEEAKMVYLLECL--QKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG 86
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
Q R + +E R G+ +LVATDVA++G+D PAI HV NYD+P+ E+YVHRIGRTG
Sbjct: 87 GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTG 146
Query: 362 RAGRNGFAVSLVNHAER----MNIKKIERFTKQQIP 393
+G G A + +N A M++K + KQ++P
Sbjct: 147 CSGNTGIATTFINKACDESVLMDLKALLLEAKQKVP 182
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 107 bits (268), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 65/227 (28%), Positives = 111/227 (48%), Gaps = 30/227 (13%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F + L E +L+ + G+ +P+ +Q++AI I G D++ +Q+G+GKT F + AL +
Sbjct: 23 FDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
+S P+ L+L PTRELALQ+
Sbjct: 83 IDTSVKA----------------------------PQALMLAPTRELALQIQKVVMALAF 114
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+M IK + +GG ++ + L R+ +I++ TPGR+ D++ + +++ +LDEAD
Sbjct: 115 HM-DIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEAD 172
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPL 229
ML GF I +I P T Q +L SAT+ V + ++P+
Sbjct: 173 EMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPV 219
>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 = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 65/227 (28%), Positives = 111/227 (48%), Gaps = 30/227 (13%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F + L E +L+ + G+ +P+ +Q++AI I G D++ +Q+G+GKT F + AL +
Sbjct: 16 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 75
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
+S P+ L+L PTRELALQ+
Sbjct: 76 IDTSVKA----------------------------PQALMLAPTRELALQIQKVVMALAF 107
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+M IK + +GG ++ + L R+ +I++ TPGR+ D++ + +++ +LDEAD
Sbjct: 108 HM-DIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEAD 165
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPL 229
ML GF I +I P T Q +L SAT+ V + ++P+
Sbjct: 166 EMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPV 212
>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 = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 54/161 (33%), Positives = 93/161 (57%), Gaps = 4/161 (2%)
Query: 226 KDPLILKVNSIEK-KQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADI 284
+DP ++N +E+ K +TQ +V + K L+ L ++ Q+++F + + ++
Sbjct: 3 QDPY--EINLMEELTLKGVTQYYAYVTE-RQKVHCLNTLFSRLQINQSIIFCNSSQRVEL 59
Query: 285 IADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNY 344
+A +++ G+ +H + Q RNR + R G + LV TD+ RGID+ A+ V N+
Sbjct: 60 LAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINF 119
Query: 345 DLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIE 385
D PK E Y+HRIGR+GR G G A++L+ + +R N+K IE
Sbjct: 120 DFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIE 160
>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain
pdb|1Q0U|B Chain B, Crystal Structure Of The Bstdead N-Terminal Domain
Length = 219
Score = 107 bits (266), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 65/235 (27%), Positives = 111/235 (47%), Gaps = 31/235 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F +++A+ + + KPT +QE+ IP A+ G + SQTG+GKT A++LP
Sbjct: 5 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXE 64
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
K + ++ + ++ PTRELA Q+ T +
Sbjct: 65 KIKPERAEV----------------------------QAVITAPTRELATQIYHETLKIT 96
Query: 122 LYMKK---IKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVL 178
+ K I A ++GG + ++ L+ P I++ TPGR+ D + ++ ILV+
Sbjct: 97 KFCPKDRXIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVV 156
Query: 179 DEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
DEAD LD GFI D+++I P Q ++FSAT+ + + ++P + V
Sbjct: 157 DEADLXLDXGFITDVDQIAARXPKDLQXLVFSATIPEKLKPFLKKYXENPTFVHV 211
>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 = 102 bits (253), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 58/152 (38%), Positives = 84/152 (55%), Gaps = 1/152 (0%)
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+NI +++ V + +K LL +L + ++F TK + + D L+ G+ +H
Sbjct: 8 RNIEHAVIQVRE-ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIH 66
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
G + Q R + +RG + LVATDVAARGID+ I+ V NYDLP E YVHR GRT
Sbjct: 67 GGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRT 126
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
GRAG G A+S V E+ + IE + +I
Sbjct: 127 GRAGNKGKAISFVTAFEKRFLADIEEYIGFEI 158
>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|2OXC|B Chain B, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|3B7G|A Chain A, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
pdb|3B7G|B Chain B, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
Length = 230
Score = 101 bits (251), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 70/240 (29%), Positives = 121/240 (50%), Gaps = 40/240 (16%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F+S+ L VL+ L G+ +P+ VQ +AIP G DLIV +++G+GKT F AL
Sbjct: 25 DFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALD 84
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
++ +NL+ ++L+L PTRE+A+Q+ + G
Sbjct: 85 S---------LVLENLST-------------------QILILAPTREIAVQIHSVITAIG 116
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRL-----IDHMNSGKINFSHLQIL 176
+ M+ ++ +GG P L Q + + I + +PGR+ +D++N G I ++
Sbjct: 117 IKMEGLECHVFIGGTP-LSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSI-----RLF 170
Query: 177 VLDEADRMLDMG-FINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
+LDEAD++L+ G F I I + P ++Q + SAT + N +DP +++NS
Sbjct: 171 ILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLNS 230
>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
pdb|2G9N|B Chain B, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
Length = 221
Score = 98.6 bits (244), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 65/229 (28%), Positives = 104/229 (45%), Gaps = 30/229 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F + L E +L+ + G+ P+ +Q++AI I G D+I +Q+G+G TA F + L
Sbjct: 16 SFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISIL- 74
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+++ + LVL PTRELA Q+ G
Sbjct: 75 ---------------------------QQIELDLXATQALVLAPTRELAQQIQXVVMALG 107
Query: 122 LYMKKIKAISILGGMPYLRQMQLLS-RNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM + +GG ++Q L P I++ TPGR+ D +N ++ ++ + VLDE
Sbjct: 108 DYMGA-SCHACIGGTNVRAEVQXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDE 166
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPL 229
AD ML GF + I I Q +L SAT+ V + +DP+
Sbjct: 167 ADEMLSRGFXDQIYDIFQXLNSNTQVVLLSATMPSDVLEVTXXFMRDPI 215
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 92.8 bits (229), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 71/242 (29%), Positives = 123/242 (50%), Gaps = 37/242 (15%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAIS--GRDLIVSSQTGSGKTAAFMLPA 59
+F+ + L +L+ + +G+ +P+ +QE A+P ++ ++LI SQ+G+GKTAAF+L
Sbjct: 26 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L + + NK P+ L L+PT ELALQ E+
Sbjct: 86 LSQVEPA-NKY---------------------------PQCLCLSPTYELALQTGKVIEQ 117
Query: 120 YGLYMKKIK-AISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQILV 177
G + ++K A ++ G L + Q +S +I++ TPG ++D + K I+ +++ V
Sbjct: 118 MGKFYPELKLAYAVRGNK--LERGQKISE--QIVIGTPGTVLDWCSKLKFIDPKKIKVFV 173
Query: 178 LDEADRML-DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSI 236
LDEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+
Sbjct: 174 LDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 233
Query: 237 EK 238
E+
Sbjct: 234 EE 235
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 92.0 bits (227), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 37/237 (15%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F+ + L +L+ + +G+ +P+ +QE A+P ++ ++LI SQ+G+GKTAAF+L
Sbjct: 93 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
L + + NK P+ L L+PT ELALQ E+
Sbjct: 153 LSQVEPA-NKY---------------------------PQCLCLSPTYELALQTGKVIEQ 184
Query: 120 YGLYMKKIK-AISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQILV 177
G + ++K A ++ G L + Q +S +I++ TPG ++D + K I+ +++ V
Sbjct: 185 MGKFYPELKLAYAVRGN--KLERGQKISE--QIVIGTPGTVLDWCSKLKFIDPKKIKVFV 240
Query: 178 LDEADRML-DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
LDEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+
Sbjct: 241 LDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297
>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 = 89.4 bits (220), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 47/123 (38%), Positives = 73/123 (59%), Gaps = 6/123 (4%)
Query: 269 VGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV 328
+GQA++F T+R+A + + G + L G+L R ++ R G+ K+L+ T+V
Sbjct: 34 IGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV 93
Query: 329 AARGIDVPAITHVFNYDLP----KFP--EDYVHRIGRTGRAGRNGFAVSLVNHAERMNIK 382
ARGIDV +T V N+DLP + P E Y+HRIGRTGR G+ G A +++ E ++
Sbjct: 94 CARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLM 153
Query: 383 KIE 385
KI+
Sbjct: 154 KIQ 156
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 64/226 (28%), Positives = 104/226 (46%), Gaps = 36/226 (15%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPA 59
+F +GL +LK + + + KP+ +QE+A+P + R++I SQ+G+GKTAAF L
Sbjct: 23 SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL-- 80
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
T R+ + A P+ + L P+RELA Q +
Sbjct: 81 --------------------------TMLTRVNPEDASPQAICLAPSRELARQTLEVVQE 114
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
G + K + + +Q+ N ++++ TPG ++D M + ++I VLD
Sbjct: 115 MGKFTKITSQLIVPDSFEKNKQI-----NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLD 169
Query: 180 EADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENI 224
EAD MLD G + ++ P Q +LFSAT V A+ I
Sbjct: 170 EADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKI 215
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 55/152 (36%), Positives = 88/152 (57%)
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ I Q + V++ +K L L V QAV+F T+R + + +L F + ++
Sbjct: 2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIY 61
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
DL Q R+ ++ R G +IL++TD+ ARGIDV ++ V NYDLP E+Y+HRIGR
Sbjct: 62 SDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRG 121
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
GR GR G A++ V + + ++++E+F QI
Sbjct: 122 GRFGRKGVAINFVTNEDVGAMRELEKFYSTQI 153
>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 = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 57/116 (49%), Positives = 73/116 (62%)
Query: 271 QAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAA 330
+A+VFT TK + + IA L G A LHGDL Q R R L R+G +++LVATDVAA
Sbjct: 33 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA 92
Query: 331 RGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIER 386
RG+D+P + V +Y LP E Y HR GRTGRAGR G V L ER +++ +ER
Sbjct: 93 RGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALER 148
>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 = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 54/116 (46%), Positives = 73/116 (62%)
Query: 271 QAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAA 330
+A+VFT TK + + IA L G A LHGD+ Q R R + R+G +++LVATDVAA
Sbjct: 30 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA 89
Query: 331 RGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIER 386
RG+D+P + V +Y +P E Y HR GRTGRAGR G V L ER +++ +ER
Sbjct: 90 RGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALER 145
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 95/381 (24%), Positives = 159/381 (41%), Gaps = 67/381 (17%)
Query: 20 GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASS---KNKIPVMKKN 76
GY + QE+ I +SGRD +V TG GK+ + +PAL + I +MK
Sbjct: 22 GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQ 81
Query: 77 LNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGM 136
++Q L+ L T TRE L+V R G
Sbjct: 82 VDQ-----------LQANGVAAACLNSTQTREQQLEVMTGC-RTG--------------- 114
Query: 137 PYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQ--ILVLDEADRMLDMGFINDIE 194
Q++LL PE L+ ++H+ +H +L +DEA + G +D
Sbjct: 115 ----QIRLLYIAPERLMLD--NFLEHL-------AHWNPVLLAVDEAHCISQWG--HDFR 159
Query: 195 KIVDATPVTRQ---TMLFSATLDGIVGNMAENITK-----DPLILKVNSIEKKQKNITQS 246
A RQ T+ F A ++I + DPLI +++S ++ +
Sbjct: 160 PEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLI-QISSFDRP------N 212
Query: 247 ILFVDDILHKNRLLDYLLR---DKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDL 303
I ++ ++ K + LD L+R ++R +++ ++ + A RL G AA H L
Sbjct: 213 IRYM--LMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGL 270
Query: 304 HQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRA 363
N R E +R ++I+VAT GI+ P + V ++D+P+ E Y GR GR
Sbjct: 271 ENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRD 330
Query: 364 GRNGFAVSLVNHAERMNIKKI 384
G A+ + A+ +++
Sbjct: 331 GLPAEAMLFYDPADMAWLRRC 351
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 73.2 bits (178), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 94/378 (24%), Positives = 153/378 (40%), Gaps = 61/378 (16%)
Query: 20 GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQ 79
GY + QE+ I +SGRD +V TG GK+ + +PAL + P++ +Q
Sbjct: 22 GYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPLISLXKDQ 81
Query: 80 NNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYL 139
++L+ L T TRE L+V R G
Sbjct: 82 --------VDQLQANGVAAACLNSTQTREQQLEVXTGC-RTG------------------ 114
Query: 140 RQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQ--ILVLDEADRMLDMGFINDIEKIV 197
Q++LL PE L ++H+ +H +L +DEA + G +D
Sbjct: 115 -QIRLLYIAPERLXLD--NFLEHL-------AHWNPVLLAVDEAHCISQWG--HDFRPEY 162
Query: 198 DATPVTRQ---TMLFSATLDGIVGNMAENITK-----DPLILKVNSIEKKQKNITQSILF 249
A RQ T+ F A ++I + DPLI +++S ++ NI +
Sbjct: 163 AALGQLRQRFPTLPFXALTATADDTTRQDIVRLLGLNDPLI-QISSFDRP--NIRYXLX- 218
Query: 250 VDDILHKNRLLDYLLR---DKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQN 306
K + LD L R ++R +++ ++ + A RL G AA H L N
Sbjct: 219 -----EKFKPLDQLXRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENN 273
Query: 307 ARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRN 366
R E +R ++I+VAT GI+ P + V ++D+P+ E Y GR GR G
Sbjct: 274 VRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLP 333
Query: 367 GFAVSLVNHAERMNIKKI 384
A + A+ +++
Sbjct: 334 AEAXLFYDPADXAWLRRC 351
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 72.0 bits (175), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 61/212 (28%), Positives = 102/212 (48%), Gaps = 41/212 (19%)
Query: 12 VLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIP 71
+L+ ++ G+ PT +Q QAIP + GR+L+ S+ TGSGKT AF +P L +
Sbjct: 40 LLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQ--------- 90
Query: 72 VMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQV----TAATERYGLYMKKI 127
L Q NK + R L+++PTRELA Q+ +E G + I
Sbjct: 91 -----LKQPANKGF-------------RALIISPTRELASQIHRELIKISEGTGFRIHMI 132
Query: 128 KAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHM--NSGKINFSHLQILVLDEADRML 185
++ + S+ +IL+ TP RLI + + I+ + ++ LV+DE+D++
Sbjct: 133 HKAAVAAKKFGPKS----SKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLF 188
Query: 186 D---MGFINDIEKIVDATPVTR-QTMLFSATL 213
+ GF + + I A + + +FSAT
Sbjct: 189 EDGKTGFRDQLASIFLACTSHKVRRAMFSATF 220
>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 = 71.6 bits (174), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 36/110 (32%), Positives = 59/110 (53%), Gaps = 2/110 (1%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
HG + QN R ++ ++ ILV TDV ARG+D P + V +P +Y+HRIG
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 359 RTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIRT 408
RT R+G+ G +V + E ++++E + I I +EP + I++
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE--DAKNIVIAKQEKYEPSEEIKS 173
>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 = 71.6 bits (174), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 36/110 (32%), Positives = 59/110 (53%), Gaps = 2/110 (1%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
HG + QN R ++ ++ ILV TDV ARG+D P + V +P +Y+HRIG
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 359 RTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIRT 408
RT R+G+ G +V + E ++++E + I I +EP + I++
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE--DAKNIVIAKQEKYEPSEEIKS 173
>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 = 71.6 bits (174), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 36/110 (32%), Positives = 59/110 (53%), Gaps = 2/110 (1%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
HG + QN R ++ ++ ILV TDV ARG+D P + V +P +Y+HRIG
Sbjct: 66 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 359 RTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIRT 408
RT R+G+ G +V + E ++++E + I I +EP + I++
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE--DAKNIVIAKQEKYEPSEEIKS 173
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 39/120 (32%), Positives = 62/120 (51%)
Query: 255 HKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLEN 314
KNR L LL Q V+F + + +A L F A +H + Q R +
Sbjct: 17 EKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQ 76
Query: 315 LRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVN 374
+ + +ILVAT++ RG+D+ + FNYD+P+ + Y+HR+ R GR G G A++ V+
Sbjct: 77 FKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVS 136
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 54/247 (21%), Positives = 106/247 (42%), Gaps = 49/247 (19%)
Query: 168 INFSHLQILVLDEADR--------MLDMGFINDIEKIVDATPVTRQTML-FSATLDGIVG 218
++F +L ++++DE R +++ G + D ++ ATP+ R L F LD V
Sbjct: 486 VHFKNLGLVIIDEQHRFGVKQREALMNKGKMVDT-LVMSATPIPRSMALAFYGDLDVTV- 543
Query: 219 NMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRD-KRVGQAVVFTA 277
++ + +K + ++ +D + N + +++ ++ R GQA +
Sbjct: 544 --------------IDEMPPGRKEVQTMLVPMDRV---NEVYEFVRQEVMRGGQAFIVYP 586
Query: 278 TKRDADIIADRLNISG---------------FLAAPLHGDLHQNARNRTLENLRRGRIKI 322
++D +LN+ F +HG L Q ++R + GR I
Sbjct: 587 LIEESD----KLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDI 642
Query: 323 LVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI-GRTGRAGRNGFAVSLVNHAERMNI 381
LV+T V GIDVP + + +F +H++ GR GR G+ + +V +
Sbjct: 643 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAM 702
Query: 382 KKIERFT 388
+++ FT
Sbjct: 703 ERLRFFT 709
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 53/115 (46%), Gaps = 8/115 (6%)
Query: 249 FVDDILHKNRLLDYLLRDKRVGQA-VVFTATKRDADIIADRLNISGFLAAPLHGDLHQNA 307
F++DI+ L+ + GQ+ +++ +++D++ + L G A H +L
Sbjct: 253 FIEDIVK-------LINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPED 305
Query: 308 RNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
+ I+++VAT GID P + V ++ + K E+Y GR GR
Sbjct: 306 KTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGR 360
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 12 VLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+L+ + K+ +P +Q + I ++G+++ + TG GK+ + LPAL
Sbjct: 35 ILQNVFKLEKFRP--LQLETINVTMAGKEVFLVMPTGGGKSLCYQLPAL 81
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 33/107 (30%), Positives = 46/107 (42%), Gaps = 8/107 (7%)
Query: 264 LRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGD--------LHQNARNRTLENL 315
L+ K+ + +VFT + A I + L G A G L Q + L+
Sbjct: 356 LQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEF 415
Query: 316 RRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
RG +LVAT V G+DVP + V Y+ + R GRTGR
Sbjct: 416 ARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 46/86 (53%), Gaps = 4/86 (4%)
Query: 99 RMLVLTPTRELALQVTAATER-YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPG 157
++L+L PT+ L LQ + R + L +KI A++ G + ++++ATP
Sbjct: 54 KVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALT---GEKSPEERSKAWARAKVIVATPQ 110
Query: 158 RLIDHMNSGKINFSHLQILVLDEADR 183
+ + + +G+I+ + ++V DEA R
Sbjct: 111 TIENDLLAGRISLEDVSLIVFDEAHR 136
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 58/120 (48%), Gaps = 7/120 (5%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+DD++ + R R +R + +V T TK+ A+ + D L +G A LH ++ R
Sbjct: 431 IDDLIGEIRE-----RVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 485
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
+ +LR G+ +LV ++ G+D+P ++ V + D F I GRA RN
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 58/120 (48%), Gaps = 7/120 (5%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+DD++ + R R +R + +V T TK+ A+ + D L +G A LH ++ R
Sbjct: 430 IDDLIGEIRE-----RVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 484
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
+ +LR G+ +LV ++ G+D+P ++ V + D F I GRA RN
Sbjct: 485 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 544
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 58/120 (48%), Gaps = 7/120 (5%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+DD++ + R R +R + +V T TK+ A+ + D L +G A LH ++ R
Sbjct: 431 IDDLIGEIRE-----RVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 485
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
+ +LR G+ +LV ++ G+D+P ++ V + D F I GRA RN
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 58/120 (48%), Gaps = 7/120 (5%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+DD++ + R R +R + +V T TK+ A+ + D L +G A LH ++ R
Sbjct: 431 IDDLIGEIRE-----RVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERI 485
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
+ +LR G+ +LV ++ G+D+P ++ V + D F I GRA RN
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 51/105 (48%), Gaps = 2/105 (1%)
Query: 265 RDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILV 324
R +R + +V T TK+ A+ + D L +G A LH ++ R + +LR G+ +LV
Sbjct: 466 RVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLV 525
Query: 325 ATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
++ G+D+P ++ V + D F I GRA RN
Sbjct: 526 GINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 570
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/135 (23%), Positives = 58/135 (42%), Gaps = 17/135 (12%)
Query: 256 KNRLLDYLLRDKRVGQAVVFTATKRDADIIA------DRLNISGFLAAPLHGDLH----- 304
+N +++ R + + ++FT T++ A ++ ++ G A L G H
Sbjct: 387 RNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFK 446
Query: 305 ---QNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
QN + + R G+I +L+AT VA G+D+ V Y L + + + G
Sbjct: 447 PMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVT---NEIAMVQARG 503
Query: 362 RAGRNGFAVSLVNHA 376
RA + LV H+
Sbjct: 504 RARADESTYVLVAHS 518
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 14/105 (13%)
Query: 256 KNRLLDYLLRDKRVGQAVVFTATKRDA----DIIADRLNIS--GFLAAPLHGDLH----- 304
+N + ++ R + + ++FT T++ A I D + G A L G H
Sbjct: 137 RNTIXEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFK 196
Query: 305 ---QNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDL 346
QN + + R G+I +L+AT VA G+D+ V Y L
Sbjct: 197 PXTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 49/105 (46%), Gaps = 2/105 (1%)
Query: 265 RDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILV 324
R +R + +V T TK+ ++ + D L G LH ++ R + +LR G+ +LV
Sbjct: 447 RIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLV 506
Query: 325 ATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
++ G+D+P ++ V + D F I GRA RN
Sbjct: 507 GINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 49/105 (46%), Gaps = 2/105 (1%)
Query: 265 RDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILV 324
R +R + +V T TK+ ++ + D L G LH ++ R + +LR G+ +LV
Sbjct: 441 RIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLV 500
Query: 325 ATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRNG 367
++ G+D+P ++ V + D F I GRA RN
Sbjct: 501 GINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 545
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 1/89 (1%)
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI-G 358
HG + + R + + R +LV T + GID+P + F +H++ G
Sbjct: 845 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRG 904
Query: 359 RTGRAGRNGFAVSLVNHAERMNIKKIERF 387
R GR+ +A L H + M +R
Sbjct: 905 RVGRSHHQAYAWLLTPHPKAMTTDAQKRL 933
>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 = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 9/73 (12%)
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPA-------ITHVFNYDLPKFPED 352
H L ++ R EN R+G IK +VAT + GI+ PA I ++ + + P
Sbjct: 301 HAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPII 360
Query: 353 YVHRIGRTGRAGR 365
VH++ GRAGR
Sbjct: 361 EVHQM--LGRAGR 371
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 32/125 (25%), Positives = 60/125 (48%), Gaps = 18/125 (14%)
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHV------FNYDLPKFPE-- 351
H L + R+ E R+ +IK++VAT A G+++PA T + FN + + +
Sbjct: 319 HAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEI 378
Query: 352 ---DYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKI-ERFTKQQI-PIEVINGFEPKKRI 406
+Y GR GR G + S+V ++ ++ ++ +++ + PIE G E
Sbjct: 379 PIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIESKLGSE----- 433
Query: 407 RTYYS 411
R +Y+
Sbjct: 434 RAFYT 438
>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 = 35.8 bits (81), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 42/93 (45%), Gaps = 11/93 (11%)
Query: 296 AAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFP----- 350
AA H L R + RRG IK++VAT A G+++PA V L +F
Sbjct: 299 AAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPA-RRVIVRSLYRFDGYSKR 357
Query: 351 ---EDYVHRIGRTGRAGRN--GFAVSLVNHAER 378
+Y GR GR G + G A+ +V +R
Sbjct: 358 IKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR 390
>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 = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 315 LRRGRIKILVATDVAARGIDVPAITHVFN----YDLPKFPE----DYVHRIGRTGRAGRN 366
+ G +K+L AT+ + G+++PA T VF +D +F +Y+ GR GR G +
Sbjct: 428 FQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLD 487
Query: 367 GFAVSLVNHAERMN 380
+ ++ E+M
Sbjct: 488 DRGIVIMMIDEKME 501
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 315 LRRGRIKILVATDVAARGIDVPAITHVFN----YDLPKFPE----DYVHRIGRTGRAGRN 366
+ G +K+L AT+ + G+++PA T VF +D +F +Y+ GR GR G +
Sbjct: 526 FQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLD 585
Query: 367 GFAVSLVNHAERM 379
+ ++ E+M
Sbjct: 586 DRGIVIMMIDEKM 598
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 28/66 (42%)
Query: 294 FLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDY 353
FL + + R LE R GR + +V++ V GIDVP +Y
Sbjct: 134 FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREY 193
Query: 354 VHRIGR 359
+ R+GR
Sbjct: 194 IQRLGR 199
>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 = 32.3 bits (72), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 28/66 (42%)
Query: 294 FLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDY 353
FL + + R LE R GR + +V++ V GIDVP +Y
Sbjct: 369 FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREY 428
Query: 354 VHRIGR 359
+ R+GR
Sbjct: 429 IQRLGR 434
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 36/158 (22%), Positives = 68/158 (43%), Gaps = 17/158 (10%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+ D+ + L LR+ V+ T ++ ++ L GF A H + + R
Sbjct: 337 IRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGF--AIHHAGMTRVDRT 394
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAI------THVFNYDLPKFPE----DYVHRIGR 359
+ I++LV+T A G+++PA T V++ + ++ E D + +GR
Sbjct: 395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGR 454
Query: 360 TGRAGRN--GFAVSLVNHAERMNIKKIERFTKQQIPIE 395
GR + G + + +H E ++ QQ+PIE
Sbjct: 455 AGRPQYDTKGEGILITSHGE---LQYYLSLLNQQLPIE 489
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 36/158 (22%), Positives = 68/158 (43%), Gaps = 17/158 (10%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+ D+ + L LR+ V+ T ++ ++ L GF A H + + R
Sbjct: 337 IRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGF--AIHHAGMTRVDRT 394
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAI------THVFNYDLPKFPE----DYVHRIGR 359
+ I++LV+T A G+++PA T V++ + ++ E D + +GR
Sbjct: 395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGR 454
Query: 360 TGRAGRN--GFAVSLVNHAERMNIKKIERFTKQQIPIE 395
GR + G + + +H E ++ QQ+PIE
Sbjct: 455 AGRPQYDTKGEGILITSHGE---LQYYLSLLNQQLPIE 489
>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
Length = 968
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 321 KILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGR 365
++L+ +++ + G + +H +DLP P+ RIGR R G+
Sbjct: 558 QVLLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQ 602
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 13/66 (19%)
Query: 23 KPTGVQ-EQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH---KFASSK--------NKI 70
KP Q E A+PA + G++ I+ + TG GKT +L H KF + N+I
Sbjct: 13 KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI 71
Query: 71 PVMKKN 76
PV ++N
Sbjct: 72 PVYEQN 77
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 13/66 (19%)
Query: 23 KPTGVQ-EQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH---KFASSK--------NKI 70
KP Q E A+PA + G++ I+ + TG GKT +L H KF + N+I
Sbjct: 4 KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI 62
Query: 71 PVMKKN 76
PV ++N
Sbjct: 63 PVYEQN 68
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 25 TGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPV 72
T +Q +G+D++V++ GSGKTA + + K + +N I V
Sbjct: 10 TWTDDQWNAIVSTGQDILVAAAAGSGKTAVLVERMIRKITAEENPIDV 57
>pdb|1PEM|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|1PEO|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|1PEQ|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|1PEU|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|2BQ1|E Chain E, Ribonucleotide Reductase Class 1b Holocomplex R1e,R2f From
Salmonella Typhimurium
pdb|2BQ1|F Chain F, Ribonucleotide Reductase Class 1b Holocomplex R1e,R2f From
Salmonella Typhimurium
Length = 714
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 99 RMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYL 139
R + PTRE+ L++ RYG+Y + ++A+ G + Y+
Sbjct: 555 RSGITLPTREMWLKLRDDVMRYGIYNQNLQAVPPTGSISYI 595
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 317 RGRIKILVATDVAARGIDVPAITHVFN----YDLPKF----PEDYVHRIGRTGRAGRNGF 368
+G IK+L AT+ A G+++P T +F+ +D P ++ GR GR G +
Sbjct: 423 KGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDST 482
Query: 369 AVSLV 373
+V
Sbjct: 483 GTVIV 487
>pdb|2BYJ|A Chain A, Ornithine Aminotransferase Mutant Y85i
pdb|2BYJ|B Chain B, Ornithine Aminotransferase Mutant Y85i
pdb|2BYJ|C Chain C, Ornithine Aminotransferase Mutant Y85i
Length = 439
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 19/86 (22%)
Query: 219 NMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT 278
N+AEN K +IL+ N + K ++ ++ R K + A+V T
Sbjct: 344 NLAENADKLGIILR-NELMKLPSDVVTAV-----------------RGKGLLNAIVIKET 385
Query: 279 K-RDADIIADRLNISGFLAAPLHGDL 303
K DA + RL +G LA P HGD+
Sbjct: 386 KDWDAWKVCLRLRDNGLLAKPTHGDI 411
>pdb|1OAT|A Chain A, Ornithine Aminotransferase
pdb|1OAT|B Chain B, Ornithine Aminotransferase
pdb|1OAT|C Chain C, Ornithine Aminotransferase
pdb|2OAT|A Chain A, Ornithine Aminotransferase Complexed With
5-Fluoromethylornithine
pdb|2OAT|B Chain B, Ornithine Aminotransferase Complexed With
5-Fluoromethylornithine
pdb|2OAT|C Chain C, Ornithine Aminotransferase Complexed With
5-Fluoromethylornithine
Length = 439
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 19/86 (22%)
Query: 219 NMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT 278
N+AEN K +IL+ N + K ++ ++ R K + A+V T
Sbjct: 344 NLAENADKLGIILR-NELMKLPSDVVTAV-----------------RGKGLLNAIVIKET 385
Query: 279 K-RDADIIADRLNISGFLAAPLHGDL 303
K DA + RL +G LA P HGD+
Sbjct: 386 KDWDAWKVCLRLRDNGLLAKPTHGDI 411
>pdb|2BYL|A Chain A, Structure Of Ornithine Aminotransferase Triple Mutant Y85i
Y55a G320f
pdb|2BYL|B Chain B, Structure Of Ornithine Aminotransferase Triple Mutant Y85i
Y55a G320f
pdb|2BYL|C Chain C, Structure Of Ornithine Aminotransferase Triple Mutant Y85i
Y55a G320f
Length = 439
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 19/86 (22%)
Query: 219 NMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT 278
N+AEN K +IL+ N + K ++ ++ R K + A+V T
Sbjct: 344 NLAENADKLGIILR-NELMKLPSDVVTAV-----------------RGKGLLNAIVIKET 385
Query: 279 K-RDADIIADRLNISGFLAAPLHGDL 303
K DA + RL +G LA P HGD+
Sbjct: 386 KDWDAWKVCLRLRDNGLLAKPTHGDI 411
>pdb|2CAN|A Chain A, Human Ornithine Aminotransferase Complexed With L-Canaline
pdb|2CAN|B Chain B, Human Ornithine Aminotransferase Complexed With L-Canaline
pdb|2CAN|C Chain C, Human Ornithine Aminotransferase Complexed With L-Canaline
pdb|1GBN|A Chain A, Human Ornithine Aminotransferase Complexed With The
Neurotoxin Gabaculine
pdb|1GBN|B Chain B, Human Ornithine Aminotransferase Complexed With The
Neurotoxin Gabaculine
pdb|1GBN|C Chain C, Human Ornithine Aminotransferase Complexed With The
Neurotoxin Gabaculine
Length = 402
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 19/86 (22%)
Query: 219 NMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT 278
N+AEN K +IL+ N + K ++ ++ R K + A+V T
Sbjct: 307 NLAENADKLGIILR-NELMKLPSDVVTAV-----------------RGKGLLNAIVIKET 348
Query: 279 K-RDADIIADRLNISGFLAAPLHGDL 303
K DA + RL +G LA P HGD+
Sbjct: 349 KDWDAWKVCLRLRDNGLLAKPTHGDI 374
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 35 AISGRDLIVSSQTGSGKTAAFMLPALHKF 63
AI+G++ ++ + TGSGKT +L H F
Sbjct: 19 AINGKNALICAPTGSGKTFVSILICEHHF 47
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 35 AISGRDLIVSSQTGSGKTAAFMLPALHKF 63
AI+G++ ++ + TGSGKT +L H F
Sbjct: 260 AINGKNALICAPTGSGKTFVSILICEHHF 288
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 35 AISGRDLIVSSQTGSGKTAAFMLPALHKF 63
AI+G++ ++ + TGSGKT +L H F
Sbjct: 260 AINGKNALICAPTGSGKTFVSILICEHHF 288
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.137 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,690,090
Number of Sequences: 62578
Number of extensions: 461023
Number of successful extensions: 1550
Number of sequences better than 100.0: 107
Number of HSP's better than 100.0 without gapping: 91
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1278
Number of HSP's gapped (non-prelim): 156
length of query: 453
length of database: 14,973,337
effective HSP length: 102
effective length of query: 351
effective length of database: 8,590,381
effective search space: 3015223731
effective search space used: 3015223731
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)