RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9401
(453 letters)
>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein,
ATPase, RNA binding protein; 3.00A {Methanocaldococcus
jannaschii} SCOP: c.37.1.19 c.37.1.19
Length = 367
Score = 445 bits (1148), Expect = e-156
Identities = 141/394 (35%), Positives = 215/394 (54%), Gaps = 38/394 (9%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGR-DLIVSSQTGSGKTAAFMLPA 59
MNF + L + +L A+ G+ KPT +Q + IP ++ +++ ++TGSGKTA+F +P
Sbjct: 6 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPL 65
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
+ + ++LTPTRELA+QV E
Sbjct: 66 IELVNENNG-----------------------------IEAIILTPTRELAIQVADEIES 96
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
K +K I GG Q++ L +N I++ TPGR++DH+N G +N +++ +LD
Sbjct: 97 LK-GNKNLKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILD 154
Query: 180 EADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKK 239
EAD ML+MGFI D+EKI++A ++ +LFSAT+ + N+A+ D +K
Sbjct: 155 EADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKINA-- 212
Query: 240 QKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPL 299
NI QS + V++ + L LL + +VF TKRD +A L GF A +
Sbjct: 213 --NIEQSYVEVNE-NERFEALCRLL-KNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAI 268
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGR 359
HGDL Q+ R + + ++ +I+IL+ATDV +RGIDV + V NY LP+ PE Y+HRIGR
Sbjct: 269 HGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGR 328
Query: 360 TGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIP 393
TGRAG+ G A+S++N E ++ IER K +I
Sbjct: 329 TGRAGKKGKAISIINRREYKKLRYIERAMKLKIK 362
>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD;
ATP-binding, hydrolase, nucleotide-binding, RNA binding
protein, structural genomics; 1.90A {Sulfolobus
tokodaii}
Length = 337
Score = 442 bits (1139), Expect = e-155
Identities = 120/383 (31%), Positives = 197/383 (51%), Gaps = 47/383 (12%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSK 67
++E + +A+ ++G+ T VQ + IP + G++++V ++TGSGKTAA+ +P L
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 68 NKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKI 127
+ LV+TPTREL QV + G YM
Sbjct: 56 -----------------------------GMKSLVVTPTRELTRQVASHIRDIGRYMD-T 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 GFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSI 247
GFI+DI+ I+ T + T LFSAT+ + + ++ + ++ N+
Sbjct: 145 GFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEACI---GLANVEHKF 201
Query: 248 LFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNA 307
+ V R LR+ + +VF T+ + + A L GDL Q+
Sbjct: 202 VHVK---DDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSV 254
Query: 308 RNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNG 367
RNR ++ R G +L+ TDVA+RG+D+P + V N+D P+ Y+HRIGRTGR GR G
Sbjct: 255 RNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKG 314
Query: 368 FAVSLVNHAERMNIKKIERFTKQ 390
A++ + E K++++ +++
Sbjct: 315 EAITFIL-NEYWLEKEVKKVSQK 336
>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation,
rRNA processing, mRNA splicing, mRNA transport; HET:
ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB:
2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B
2zu6_A
Length = 410
Score = 429 bits (1106), Expect = e-149
Identities = 126/395 (31%), Positives = 200/395 (50%), Gaps = 37/395 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F ++GL E +L+ + G+ KP+ +Q++AI I GRD+I SQ+G+GKTA F + L
Sbjct: 38 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVL- 96
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ L + + + L+L PTRELA+Q+ G
Sbjct: 97 ---------------------------QCLDIQVRETQALILAPTRELAVQIQKGLLALG 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 NITQSILFVDDILHK----NRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
I Q + V+ K L D L + QAV+F TKR D + +++ + F +
Sbjct: 249 GIKQFFVAVEREEWKFDTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREANFTVS 304
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI 357
+HGD+ Q R ++ R G ++L++TDV ARG+DVP ++ + NYDLP E Y+HRI
Sbjct: 305 SMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 364
Query: 358 GRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
GR+GR GR G A++ V + + ++ IE++ QI
Sbjct: 365 GRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQI 399
>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding,
RNA binding protein; 2.10A {Saccharomyces cerevisiae}
SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A
Length = 400
Score = 428 bits (1103), Expect = e-149
Identities = 122/395 (30%), Positives = 201/395 (50%), Gaps = 37/395 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F+ L +L + + G+ KP+ +QE+AIP AI+GRD++ ++ G+GKTAAF++P L
Sbjct: 22 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL- 80
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
E+++ K + + L++ PTRELALQ + G
Sbjct: 81 ---------------------------EKVKPKLNKIQALIMVPTRELALQTSQVVRTLG 113
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
+ I + GG + L+ IL+ TPGR++D + + S + ++DEA
Sbjct: 114 KHCG-ISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEA 172
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ- 240
D+ML F IE+I+ P T Q++LFSAT V P + + ++
Sbjct: 173 DKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL----MEEL 228
Query: 241 --KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAP 298
K ITQ FV++ K L+ L ++ QA++F + +++A ++ G+
Sbjct: 229 TLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYY 287
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
H + Q RN+ R+G+++ LV +D+ RGID+ A+ V N+D PK E Y+HRIG
Sbjct: 288 SHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIG 347
Query: 359 RTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIP 393
R+GR G G A++L+N +R N+ KIE+ +I
Sbjct: 348 RSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIA 382
>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein,
translation; 2.50A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 2vso_A* 2vsx_A*
Length = 394
Score = 426 bits (1097), Expect = e-148
Identities = 122/395 (30%), Positives = 203/395 (51%), Gaps = 38/395 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F + L E +L+ + G+ +P+ +Q++AI I G D++ +Q+G+GKT F + AL
Sbjct: 22 KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAAL- 80
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+R+ P+ L+L PTRELALQ+
Sbjct: 81 ---------------------------QRIDTSVKAPQALMLAPTRELALQIQKVVMALA 113
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
+M IK + +GG ++ + L R+ +I++ TPGR+ D++ + +++ +LDEA
Sbjct: 114 FHMD-IKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEA 171
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML GF I +I P T Q +L SAT+ V + ++P+ + V E +
Sbjct: 172 DEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 231
Query: 242 NITQSILFVDDILHK----NRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
I Q + V++ +K L D + V QAV+F T+R + + +L F +
Sbjct: 232 GIKQFYVNVEEEEYKYECLTDLYDSI----SVTQAVIFCNTRRKVEELTTKLRNDKFTVS 287
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI 357
++ DL Q R+ ++ R G +IL++TD+ ARGIDV ++ V NYDLP E+Y+HRI
Sbjct: 288 AIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRI 347
Query: 358 GRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
GR GR GR G A++ V + + ++++E+F QI
Sbjct: 348 GRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQI 382
>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis,
cell cycle, nucleus, phosph RNA-binding, ATP-binding,
helicase, hydrolase; 3.50A {Homo sapiens}
Length = 414
Score = 425 bits (1096), Expect = e-147
Identities = 123/396 (31%), Positives = 197/396 (49%), Gaps = 38/396 (9%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
+F + L E +L+ + G+ KP+ +Q++AI I G D+I +Q+G+GKTA F + L
Sbjct: 41 SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISIL- 99
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+++ + LVL PTRELA Q+ G
Sbjct: 100 ---------------------------QQIELDLKATQALVLAPTRELAQQIQKVVMALG 132
Query: 122 LYMKKIKAISILGGMPYLRQMQ-LLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM + +GG ++Q L P I++ TPGR+ D +N ++ ++++ VLDE
Sbjct: 133 DYMG-ASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDE 191
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
AD ML GF + I I Q +L SAT+ V + + +DP+ + V E
Sbjct: 192 ADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTL 251
Query: 241 KNITQSILFVDDILHK----NRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLA 296
+ I Q + V+ K L + L + QAV+F T+R D + ++++ F
Sbjct: 252 EGIRQFYINVEREEWKLDTLCDLYETL----TITQAVIFINTRRKVDWLTEKMHARDFTV 307
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHR 356
+ +HGD+ Q R+ + R G ++L+ TD+ ARGIDV ++ V NYDLP E+Y+HR
Sbjct: 308 SAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHR 367
Query: 357 IGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
IGR GR GR G A+++V ++ ++ IE F I
Sbjct: 368 IGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSI 403
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 416 bits (1071), Expect = e-144
Identities = 146/400 (36%), Positives = 213/400 (53%), Gaps = 18/400 (4%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+F + + E+++ + YT+PT VQ+ AIP RDL+ +QTGSGKTAAF+LP L
Sbjct: 15 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 74
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ + + + R + P LVL PTRELA+Q+ ++
Sbjct: 75 SQ----------IYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKF 124
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
Y +++ + GG +Q++ L R +L+ATPGRL+D M GKI + LVLDE
Sbjct: 125 S-YRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDE 183
Query: 181 ADRMLDMGFINDIEKIVDATPV----TRQTMLFSATLDGIVGNMAENITKDPLILKVNSI 236
ADRMLDMGF I +IV+ + R TM+FSAT + +A + + + L V +
Sbjct: 184 ADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRV 243
Query: 237 EKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLA 296
+NITQ +++V++ ++ LLD L + +VF TK+ AD + D L G+
Sbjct: 244 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYAC 303
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHR 356
+HGD Q R L R G+ ILVAT VAARG+D+ + HV N+DLP E+YVHR
Sbjct: 304 TSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHR 363
Query: 357 IGRTGRAGRNGFAVSLVNHAER---MNIKKIERFTKQQIP 393
IGRTGR G G A S N ++ + KQ++P
Sbjct: 364 IGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP 403
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 419 bits (1079), Expect = e-143
Identities = 112/380 (29%), Positives = 179/380 (47%), Gaps = 51/380 (13%)
Query: 27 VQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKI 84
+QE+A+P +S R++I SQ+G+GKTAAF L L
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTML------------------------ 180
Query: 85 YTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQL 144
R+ +P+ + L P+RELA Q+ G Y + +K + +
Sbjct: 181 ----SRVDASVPKPQAICLAPSRELARQIMDVVTEMGKYTE-VKTAFGIKD----SVPKG 231
Query: 145 LSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDM-GFINDIEKIVDATPVT 203
+ +I++ TPG ++D M +++ +++ VLDEAD MLD G + +I P
Sbjct: 232 AKIDAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRN 291
Query: 204 RQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKN----RL 259
Q +LFSAT V AE + +++ + E + I Q + HK L
Sbjct: 292 TQIVLFSATFSERVEKYAERFAPNANEIRLKTEELSVEGIKQLYMDCQSEEHKYNVLVEL 351
Query: 260 LDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGR 319
L +GQ+++F K A+ IA R+ G A L G+L R+ +++ R G
Sbjct: 352 YGLL----TIGQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGT 407
Query: 320 IKILVATDVAARGIDVPAITHVFNYDLPKF------PEDYVHRIGRTGRAGRNGFAVSLV 373
K+LV T+V ARGIDV + V NYD+P P+ Y+HRIGRTGR GR G +++ V
Sbjct: 408 SKVLVTTNVIARGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFV 467
Query: 374 NHAERMN-IKKIERFTKQQI 392
+ + + I+ + ++ I
Sbjct: 468 HDKKSWEEMNAIQEYFQRPI 487
>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene
regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19
c.37.1.19 PDB: 1xtj_A* 1xtk_A
Length = 391
Score = 410 bits (1056), Expect = e-142
Identities = 112/397 (28%), Positives = 193/397 (48%), Gaps = 33/397 (8%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
F+ L +L+A+V G+ P+ VQ + IP AI G D++ +++G GKTA F+L L
Sbjct: 8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
++L Q +LV+ TRELA Q++ ER+
Sbjct: 68 ----------------------------QQLEPVTGQVSVLVMCHTRELAFQISKEYERF 99
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKINFSHLQILVLD 179
YM +K GG+ + ++L +N P I++ TPGR++ + +N H++ +LD
Sbjct: 100 SKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILD 159
Query: 180 EADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS-IE 237
E D+ML+ + D+++I TP +Q M+FSATL + + +DP+ + V+ +
Sbjct: 160 ECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETK 219
Query: 238 KKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
+ Q + + D KNR L LL Q V+F + + +A L F A
Sbjct: 220 LTLHGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAI 278
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI 357
+H + Q R + + + +ILVAT++ RG+D+ + FNYD+P+ + Y+HR+
Sbjct: 279 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 338
Query: 358 GRTGRAGRNGFAVSLV-NHAERMNIKKIERFTKQQIP 393
R GR G G A++ V + + + ++ + I
Sbjct: 339 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNIS 375
>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex,
ATPase, riken structural genomics/proteomics initiative,
RSGI; HET: ANP; 2.20A {Drosophila melanogaster}
Length = 434
Score = 410 bits (1057), Expect = e-141
Identities = 136/399 (34%), Positives = 218/399 (54%), Gaps = 32/399 (8%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+F S L ++++ + K GY PT +Q+ +IP SGRDL+ +QTGSGKTAAF+LP L
Sbjct: 56 QHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPIL 115
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
K + L +P++++++PTRELA+Q+ ++
Sbjct: 116 SK---------------------LLEDPHELE--LGRPQVVIVSPTRELAIQIFNEARKF 152
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+ +K + GG + Q + ++R +++ATPGRL+D ++ I F + +VLDE
Sbjct: 153 A-FESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDE 211
Query: 181 ADRMLDMGFINDIEKIVDATPVT--RQTMLFSATLDGIVGNMAENITKDPLILKVNSIEK 238
ADRMLDMGF D+ +I+ + QT++FSAT + MA K+ + + + +
Sbjct: 212 ADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGG 271
Query: 239 KQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAP 298
++ Q+I V+ +++L++ L ++ +VF TKR AD +A L+ F
Sbjct: 272 ACSDVKQTIYEVNKYAKRSKLIEIL--SEQADGTIVFVETKRGADFLASFLSEKEFPTTS 329
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
+HGD Q+ R + L + + G +K+L+AT VA+RG+D+ I HV NYD+P +DYVHRIG
Sbjct: 330 IHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIG 389
Query: 359 RTGRAGRNGFAVSLVNHAERMNI----KKIERFTKQQIP 393
RTGR G NG A S + + I KI + Q +P
Sbjct: 390 RTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVP 428
>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA
dependent ATPase, mRNA export, nucleocytoplasmic
transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens}
PDB: 3ews_A* 3g0h_A* 3fhc_B
Length = 412
Score = 403 bits (1039), Expect = e-139
Identities = 120/406 (29%), Positives = 198/406 (48%), Gaps = 50/406 (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 ++ P+ L L+PT ELALQ E+
Sbjct: 86 L----------------------------SQVEPANKYPQCLCLSPTYELALQTGKVIEQ 117
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMN-SGKINFSHLQILVL 178
G + ++K + G R + + +I++ TPG ++D + I+ +++ VL
Sbjct: 118 MGKFYPELKLAYAVRGNKLERGQK---ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 174
Query: 179 DEADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
DEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+ E
Sbjct: 175 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 234
Query: 238 KKQKNITQSILFVDDILHK----NRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISG 293
+ I Q + K L + + QA++F T++ A +A L+ G
Sbjct: 235 ETLDTIKQYYVLCSSRDEKFQALCNLYGAI----TIAQAMIFCHTRKTASWLAAELSKEG 290
Query: 294 FLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP------ 347
A L G++ R +E R G+ K+LV T+V ARGIDV ++ V N+DLP
Sbjct: 291 HQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGN 350
Query: 348 KFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI-KKIERFTKQQI 392
E Y+HRIGRTGR G+ G AV++V+ MNI +I+ ++I
Sbjct: 351 PDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKI 396
>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase,
mRNA-export, nuclear pore, hydrolase-RNA complex; HET:
ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A*
3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A
3pev_A* 3peu_A*
Length = 395
Score = 400 bits (1030), Expect = e-138
Identities = 126/418 (30%), Positives = 204/418 (48%), Gaps = 47/418 (11%)
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-KKIERFTKQ----QIPIEVINGFEPKKR 405
Y+HRIGRTGR GR G A+S V+ NI I+++ ++P + + E +
Sbjct: 333 YIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVK 390
>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA
helicase, DEAD-BOX, ATP-binding, HE hydrolase,
mitochondrion; HET: ANP; 1.90A {Saccharomyces
cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A*
Length = 563
Score = 405 bits (1042), Expect = e-137
Identities = 110/421 (26%), Positives = 192/421 (45%), Gaps = 50/421 (11%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPAL 60
+ L + + KA+ ++ + T VQ++ I +S D+I ++TG+GKT AF++P
Sbjct: 74 LEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIF 133
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
++K + +++ PTR+LALQ+ A ++
Sbjct: 134 QHLINTKFD------------------------SQYMVKAVIVAPTRDLALQIEAEVKKI 169
Query: 121 GLY---MKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKI-NFSHLQI 175
+KK +S++GG + M +++ P I++ATPGRLID + F +
Sbjct: 170 HDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDY 229
Query: 176 LVLDEADRMLDMGFINDIEKIVDATPVTR-------QTMLFSATLDGIVGNMAENITKDP 228
VLDEADR+L++GF +D+E I +T+LFSATLD V +A NI
Sbjct: 230 KVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKK 289
Query: 229 LILKVNSIEKKQK----NITQSILFVDDILHK-----NRLLDYLLRDKRVGQAVVFTATK 279
L +++++K + I QS++ + + + + +A++F T
Sbjct: 290 ECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTV 349
Query: 280 RDADIIADRLNIS---GFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVP 336
+ + L HG + QN R ++ ++ ILV TDV ARG+D P
Sbjct: 350 KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFP 409
Query: 337 AITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEV 396
+ V +P +Y+HRIGRT R+G+ G +V + E ++++E I +
Sbjct: 410 NVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 469
Query: 397 I 397
Sbjct: 470 K 470
>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 3.19A {Homo
sapiens}
Length = 479
Score = 402 bits (1034), Expect = e-137
Identities = 120/406 (29%), Positives = 198/406 (48%), Gaps = 50/406 (12%)
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 ++ P+ L L+PT ELALQ E+
Sbjct: 153 L----------------------------SQVEPANKYPQCLCLSPTYELALQTGKVIEQ 184
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMN-SGKINFSHLQILVL 178
G + ++K + G R + + +I++ TPG ++D + I+ +++ VL
Sbjct: 185 MGKFYPELKLAYAVRGNKLERGQK---ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 241
Query: 179 DEADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
DEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+ E
Sbjct: 242 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 301
Query: 238 KKQKNITQSILFVDDILHK----NRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISG 293
+ I Q + K L + + QA++F T++ A +A L+ G
Sbjct: 302 ETLDTIKQYYVLCSSRDEKFQALCNLYGAI----TIAQAMIFCHTRKTASWLAAELSKEG 357
Query: 294 FLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP------ 347
A L G++ R +E R G+ K+LV T+V ARGIDV ++ V N+DLP
Sbjct: 358 HQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGN 417
Query: 348 KFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI-KKIERFTKQQI 392
E Y+HRIGRTGR G+ G AV++V+ MNI +I+ ++I
Sbjct: 418 PDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKI 463
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 403 bits (1038), Expect = e-136
Identities = 110/421 (26%), Positives = 191/421 (45%), Gaps = 50/421 (11%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISG--RDLIVSSQTGSGKTAAFMLPAL 60
+ L + + KA+ ++ + T VQ++ I +S D+I ++TG+GKT AF++P
Sbjct: 23 LEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIF 82
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
++K + +++ PTR+LALQ+ A ++
Sbjct: 83 QHLINTKFD------------------------SQYMVKAVIVAPTRDLALQIEAEVKKI 118
Query: 121 GLY---MKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKIN-FSHLQI 175
+KK +S++GG + M +++ P I++ATPGRLID + F +
Sbjct: 119 HDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDY 178
Query: 176 LVLDEADRMLDMGFINDIEKIVDATP-------VTRQTMLFSATLDGIVGNMAENITKDP 228
VLDEADR+L++GF +D+E I +T+LFSATLD V +A NI
Sbjct: 179 KVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKK 238
Query: 229 LILKVNSIEKKQK----NITQSILFVDDILHKNRLLDY-----LLRDKRVGQAVVFTATK 279
L +++++K + I QS++ + + + +A++F T
Sbjct: 239 ECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTV 298
Query: 280 RDADIIADRLNIS---GFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVP 336
+ + L HG + QN R ++ ++ ILV TDV ARG+D P
Sbjct: 299 KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFP 358
Query: 337 AITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEV 396
+ V +P +Y+HRIGRT R+G+ G +V + E ++++E I +
Sbjct: 359 NVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE 418
Query: 397 I 397
Sbjct: 419 K 419
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 337 bits (867), Expect = e-113
Identities = 68/430 (15%), Positives = 131/430 (30%), Gaps = 79/430 (18%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSK 67
+E K TG Q + G+ + + TG GKT M+ AL
Sbjct: 6 EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWL----- 60
Query: 68 NKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKI 127
+K + ++ PT L Q ++ +K+
Sbjct: 61 -----ARKG---------------------KKSALVFPTVTLVKQTLERLQKLA--DEKV 92
Query: 128 KAISILGGMPYLRQMQLLSR----NPEILLATPGRLIDHMNSGKINFSHLQILVLDEADR 183
K M + + + IL+ + + + K++ + +D+ D
Sbjct: 93 KIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNR--EKLSQKRFDFVFVDDVDA 150
Query: 184 MLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLI------------- 230
+L D ++ P FS G + +N+ L+
Sbjct: 151 VLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRP 210
Query: 231 --------LKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDA 282
V + +NIT + LL+ + RD ++F T+ +
Sbjct: 211 LLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLE-IFRD----GILIFAQTEEEG 265
Query: 283 DIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV----AARGIDVP-A 337
+ + L F + + E+ + G+I IL+ RG+D+P
Sbjct: 266 KELYEYLKRFKFNVGETWSE-----FEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPER 320
Query: 338 ITHVFNYDLPK--FPEDYVHRIGRTGRAGRNGF--AVSLVNHAERMNIKKIERFTKQQIP 393
I +V + P Y+ GR+ R VS++ + + ++
Sbjct: 321 IKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAE 380
Query: 394 IEVINGFEPK 403
E+I E
Sbjct: 381 EEIIEEAEAN 390
>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic
resolution, AMP complex, ribosome biogenesis,
thermophilic, hydrolase; HET: AMP; 1.20A {Thermus
thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A*
3mwl_A* 3nbf_A* 3nej_A
Length = 207
Score = 273 bits (700), Expect = 8e-91
Identities = 89/233 (38%), Positives = 131/233 (56%), 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+ + +PR LVLTPTRELALQV +
Sbjct: 61 ERLAPSQER-------------------------GRKPRALVLTPTRELALQVASELTAV 95
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+K +++ GG Y +Q + L R + ++ATPGR +D++ G ++ S +++ VLDE
Sbjct: 96 A---PHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDE 152
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
AD ML MGF ++E ++ ATP +RQT+LFSATL +AE K+P+++ V
Sbjct: 153 ADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural
genomics, structural GEN consortium, SGC, ATP-binding,
hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}
Length = 249
Score = 272 bits (697), Expect = 1e-89
Identities = 88/236 (37%), Positives = 134/236 (56%), Gaps = 30/236 (12%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
FK +G+ +++ +A ++G+TKPT +Q +AIP A+ GRD+I ++TGSGKT AF LP L
Sbjct: 43 KTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPIL 102
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ L P + LVLTPTRELA Q++ E
Sbjct: 103 N----------------------------ALLETPQRLFALVLTPTRELAFQISEQFEAL 134
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGK-INFSHLQILVLD 179
G + +++ I+GG+ + Q L++ P I++ATPGRLIDH+ + K N L+ LV+D
Sbjct: 135 GSSIG-VQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMD 193
Query: 180 EADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
EADR+L+M F +++KI+ P R+T LFSAT+ V + K+P+ V+S
Sbjct: 194 EADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVSS 249
>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity
A; hydrolase inhibitor-hydrolase complex, DEAD box RNA
helicase; 2.90A {Escherichia coli}
Length = 170
Score = 266 bits (682), Expect = 1e-88
Identities = 67/169 (39%), Positives = 102/169 (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 TGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIRT 408
T RAGR G A+SLV + + + K+ R+ ++ I VI+ PK R +
Sbjct: 121 TARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVIDELRPKTRAPS 169
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 262 bits (671), Expect = 3e-86
Identities = 66/244 (27%), Positives = 118/244 (48%), Gaps = 34/244 (13%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F +++A+ + + KPT +QE+ IP A+ G ++ SQTG+GKT A++LP +
Sbjct: 5 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM- 63
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
E+++ + A+ + ++ PTRELA Q+ T +
Sbjct: 64 ---------------------------EKIKPERAEVQAVITAPTRELATQIYHETLKIT 96
Query: 122 LYMKKIKAISIL---GGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVL 178
+ K + I GG + ++ L+ P I++ TPGR+ D + ++ ILV+
Sbjct: 97 KFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVV 156
Query: 179 DEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEK 238
DEAD MLDMGFI D+++I P Q ++FSAT+ + + ++P + + +
Sbjct: 157 DEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVH---VLE 213
Query: 239 KQKN 242
+
Sbjct: 214 HHHH 217
>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA,
N project on protein structural and functional analyses;
2.40A {Dugesia japonica} SCOP: c.37.1.19
Length = 253
Score = 260 bits (668), Expect = 3e-85
Identities = 80/251 (31%), Positives = 136/251 (54%), Gaps = 24/251 (9%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
NF + L + ++ Y +PT +Q+ AIPA + RD++ +QTGSGKTAAF++P +
Sbjct: 23 ENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII 82
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ ++ ++LNQ K A P+ L+L PTRELA+Q+ + ++++
Sbjct: 83 NH---------LVCQDLNQQRYS----------KTAYPKCLILAPTRELAIQILSESQKF 123
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+++ + GG Q++ + +L+ATPGRL+D + KI+ + +VLDE
Sbjct: 124 S-LNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDE 182
Query: 181 ADRMLDMGFINDIEKIVDA----TPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSI 236
ADRMLDMGF I KI++ + + RQT++FSAT + +A + + + + V +
Sbjct: 183 ADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRV 242
Query: 237 EKKQKNITQSI 247
+I Q I
Sbjct: 243 GSTSDSIKQEI 253
>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding
protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19
Length = 206
Score = 246 bits (630), Expect = 3e-80
Identities = 65/227 (28%), Positives = 114/227 (50%), Gaps = 28/227 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F+ L +L + ++G+ KP+ +QE++IP A+SGRD++ ++ G+GK+ A+++P L
Sbjct: 4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ K+ + +V+ PTRELALQV+ +
Sbjct: 64 RLDLKKDN----------------------------IQAMVIVPTRELALQVSQICIQVS 95
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
+M K ++ GG + L +++ATPGR++D + G H+Q++VLDEA
Sbjct: 96 KHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEA 155
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDP 228
D++L F+ +E I+ P RQ +L+SAT V + + P
Sbjct: 156 DKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKP 202
>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural
genomics, structural genomic consortium, SGC, hydrolase;
HET: ADP; 2.15A {Homo sapiens}
Length = 236
Score = 244 bits (625), Expect = 4e-79
Identities = 77/236 (32%), Positives = 119/236 (50%), Gaps = 29/236 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F L + LK L + Y T +Q+Q I A+ G+D++ +++TGSGKT AF++P L
Sbjct: 26 RFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLE 85
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQP-RMLVLTPTRELALQVTAATERY 120
RL++ +L+++PTRELA Q +
Sbjct: 86 ALY-------------------------RLQWTSTDGLGVLIISPTRELAYQTFEVLRKV 120
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHM-NSGKINFSHLQILVLD 179
G A I+GG + + + N IL+ TPGRL+ HM + + + LQ+LVLD
Sbjct: 121 GKNHD-FSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLD 178
Query: 180 EADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
EADR+LDMGF + + +++ P RQT+LFSAT V ++A K+P + V+
Sbjct: 179 EADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE 234
>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA
processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP:
c.37.1.19
Length = 220
Score = 240 bits (616), Expect = 5e-78
Identities = 70/234 (29%), Positives = 118/234 (50%), Gaps = 30/234 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F+ L +L+A+V G+ P+ VQ + IP AI G D++ +++G GKTA F+L L
Sbjct: 15 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL- 73
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
++L Q +LV+ TRELA Q++ ER+
Sbjct: 74 ---------------------------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 106
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRN-PEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM +K GG+ + ++L +N P I++ TPGR++ + +N H++ +LDE
Sbjct: 107 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 166
Query: 181 ADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
D+ML+ + D+++I TP +Q M+FSATL + + +DP+ + V
Sbjct: 167 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220
>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX,
structural genomics, structural genomi consortium, SGC,
ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}
Length = 228
Score = 239 bits (613), Expect = 2e-77
Identities = 87/234 (37%), Positives = 125/234 (53%), Gaps = 25/234 (10%)
Query: 1 MNFK-SIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPA 59
FK + + +LK++++VG KPT +Q QA P + G DLIV +QTG+GKT ++++P
Sbjct: 19 CRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPG 78
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
S R + P MLVLTPTRELAL V A +
Sbjct: 79 FIHLDSQ----------------------PISREQRNGPGMLVLTPTRELALHVEAECSK 116
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
Y K +K+I I GG Q++ +S+ +I++ATPGRL D + +N + LV+D
Sbjct: 117 YS--YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVID 174
Query: 180 EADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
EAD+MLDM F I KI+ RQT++ SAT V +A + KDP+I+ V
Sbjct: 175 EADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228
>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural
genomics, structural genomics consortium, SGC,
hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*
Length = 230
Score = 236 bits (604), Expect = 4e-76
Identities = 65/236 (27%), Positives = 114/236 (48%), Gaps = 30/236 (12%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+F+S+ L VL+ L G+ +P+ VQ +AIP G DLIV +++G+GKT F AL
Sbjct: 24 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIAL 83
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ L + ++L+L PTRE+A+Q+ +
Sbjct: 84 ----------------------------DSLVLENLSTQILILAPTREIAVQIHSVITAI 115
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
G+ M+ ++ +GG P + L + I + +PGR+ + +N +++ +LDE
Sbjct: 116 GIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDE 174
Query: 181 ADRMLDMG-FINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS 235
AD++L+ G F I I + P ++Q + SAT + N +DP +++NS
Sbjct: 175 ADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLNS 230
>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics,
structural genomics consort ATP-binding, hydrolase,
nucleotide-binding, RNA-B; 2.80A {Homo sapiens}
Length = 262
Score = 237 bits (607), Expect = 5e-76
Identities = 83/234 (35%), Positives = 130/234 (55%), Gaps = 31/234 (13%)
Query: 1 MNFKSIG--LHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLP 58
+F S+ ++E LKA+ ++G+T T +Q ++I + GRDL+ +++TGSGKT AF++P
Sbjct: 52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIP 111
Query: 59 ALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQP-RMLVLTPTRELALQVTAAT 117
A+ +LRF P +L+L+PTRELA+Q
Sbjct: 112 AVELIV-------------------------KLRFMPRNGTGVLILSPTRELAMQTFGVL 146
Query: 118 ERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHM-NSGKINFSHLQIL 176
+ + I+GG + Q L I++ATPGRL+DHM N+ + +LQ L
Sbjct: 147 KELMTHHV-HTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCL 205
Query: 177 VLDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAE-NITKDPL 229
V+DEADR+LD+GF ++++I+ P RQTMLFSAT V ++A ++ K+PL
Sbjct: 206 VIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPL 259
>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding,
hydrolase, nucleotide- RNA-binding, methylation, mRNA
processing, mRNA S nucleus; HET: ADP; 2.60A {Homo
sapiens}
Length = 242
Score = 233 bits (598), Expect = 6e-75
Identities = 88/237 (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
++ + + + P LVL PTRELA QV Y
Sbjct: 89 -----------------------VHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEY 125
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
++K+ I GG P Q++ L R EI +ATPGRLID + GK N LVLDE
Sbjct: 126 C-RACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDE 184
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
ADRMLDMGF I KIVD RQT+++SAT V +AE+ KD + + + ++E
Sbjct: 185 ADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALE 241
>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family,
gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 1qva_A
Length = 224
Score = 230 bits (588), Expect = 9e-74
Identities = 68/243 (27%), Positives = 117/243 (48%), Gaps = 35/243 (14%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
F + L E +L+ + G+ +P+ +Q++AI I G D++ +Q+G+GKT F + AL
Sbjct: 15 KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 74
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
+ +S P+ L+L PTRELALQ+
Sbjct: 75 RIDTSVKA----------------------------PQALMLAPTRELALQIQKVVMALA 106
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
+M IK + +GG ++ + L R+ +I++ TPGR+ D++ + +++ +LDEA
Sbjct: 107 FHMD-IKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEA 164
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQK 241
D ML GF I +I P T Q +L SAT+ V + ++P+ + V K+
Sbjct: 165 DEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV-----KKD 219
Query: 242 NIT 244
+T
Sbjct: 220 ELT 222
>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX,
structural genomics, helic binding, HOST-virus
interaction, hydrolase; 1.85A {Homo sapiens} PDB:
2g9n_A*
Length = 237
Score = 226 bits (579), Expect = 3e-72
Identities = 71/233 (30%), Positives = 114/233 (48%), Gaps = 30/233 (12%)
Query: 2 NFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALH 61
NF + L E +L+ + G+ KP+ +Q++AI I G D+I +Q+G+GKTA F + L
Sbjct: 31 NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISIL- 89
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
++L + + + LVL PTRELA Q+ G
Sbjct: 90 ---------------------------QQLEIEFKETQALVLAPTRELAQQIQKVILALG 122
Query: 122 LYMKKIKAISILGGMPYLRQMQLL-SRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
YM + +GG +MQ L + P I++ TPGR+ D +N ++ +++ VLDE
Sbjct: 123 DYMG-ATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDE 181
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
AD ML GF + I +I + Q +L SAT+ V + + +DP+ + V
Sbjct: 182 ADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILV 234
>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural
genomics, structural GEN consortium, SGC, rRNA,
ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}
Length = 245
Score = 226 bits (578), Expect = 6e-72
Identities = 60/244 (24%), Positives = 106/244 (43%), Gaps = 39/244 (15%)
Query: 1 MNFKSI----GLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFM 56
F+ + ++ +L+ ++ G+ PT +Q QAIP + GR+L+ S+ TGSGKT AF
Sbjct: 25 ATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFS 84
Query: 57 LPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAA 116
+P L + NK R L+++PTRELA Q+
Sbjct: 85 IPILMQLKQPANK---------------------------GFRALIISPTRELASQIHRE 117
Query: 117 TERYGLYMKKIKAISILGGMPYLRQ-MQLLSRNPEILLATPGRLIDHMNSGK--INFSHL 173
+ + I ++ S+ +IL+ TP RLI + I+ + +
Sbjct: 118 LIKIS-EGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASV 176
Query: 174 QILVLDEADRMLD---MGFINDIEKIVDA-TPVTRQTMLFSATLDGIVGNMAENITKDPL 229
+ LV+DE+D++ + GF + + I A T + +FSAT V + + +
Sbjct: 177 EWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVI 236
Query: 230 ILKV 233
+ +
Sbjct: 237 SVSI 240
>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 2.51A {Homo
sapiens}
Length = 300
Score = 218 bits (558), Expect = 2e-68
Identities = 64/236 (27%), Positives = 114/236 (48%), Gaps = 35/236 (14%)
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 ++ P+ L L+PT ELALQ E+
Sbjct: 153 L----------------------------SQVEPANKYPQCLCLSPTYELALQTGKVIEQ 184
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMN-SGKINFSHLQILVL 178
G + ++K + G R + + +I++ TPG ++D + I+ +++ VL
Sbjct: 185 MGKFYPELKLAYAVRGNKLERGQK---ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 241
Query: 179 DEADRMLD-MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKV 233
DEAD M+ G + +I P Q +LFSAT + V A+ + DP ++K+
Sbjct: 242 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 205 bits (524), Expect = 5e-65
Identities = 58/152 (38%), Positives = 83/152 (54%), Gaps = 1/152 (0%)
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
NI +++ V + +K LL +L + ++F TK + + D L+ G+ +HG
Sbjct: 9 NIEHAVIQVRE-ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHG 67
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
+ Q R + +RG + LVATDVAARGID+ I+ V NYDLP E YVHR GRTG
Sbjct: 68 GMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTG 127
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQIP 393
RAG G A+S V E+ + IE + +I
Sbjct: 128 RAGNKGKAISFVTAFEKRFLADIEEYIGFEIQ 159
>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer,
ATP-binding, helicase, hydrolase, nucleotide-binding;
2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A
Length = 212
Score = 197 bits (503), Expect = 3e-61
Identities = 60/156 (38%), Positives = 82/156 (52%), Gaps = 1/156 (0%)
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
+ + + +L LL +A+VFT TK + + IA L G A LHG
Sbjct: 5 TYEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHG 63
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
DL Q R R L R+G +++LVATDVAARG+D+P + V +Y LP E Y HR GRTG
Sbjct: 64 DLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTG 123
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVI 397
RAGR G V L ER +++ +ER ++
Sbjct: 124 RAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNP 159
>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA
recognition motif, ATP-BIND helicase,
nucleotide-binding; 2.80A {Thermus thermophilus}
Length = 300
Score = 198 bits (504), Expect = 3e-60
Identities = 57/152 (37%), Positives = 82/152 (53%), Gaps = 1/152 (0%)
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
+ + + +L LL +A+VFT TK + + IA L G A LHG
Sbjct: 2 TYEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHG 60
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
D+ Q R R + R+G +++LVATDVAARG+D+P + V +Y +P E Y HR GRTG
Sbjct: 61 DMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTG 120
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQIP 393
RAGR G V L ER +++ +ER ++
Sbjct: 121 RAGRGGRVVLLYGPRERRDVEALERAVGRRFK 152
>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural
genomics, structural consortium, SGC, alternative
initiation, ATP-binding, devel protein; 2.80A {Homo
sapiens}
Length = 175
Score = 181 bits (462), Expect = 1e-55
Identities = 52/158 (32%), Positives = 81/158 (51%), Gaps = 6/158 (3%)
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
NI Q + + K + L + +GQA++F T+R+A + + G + L
Sbjct: 6 NNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLS 65
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKF------PEDYV 354
G+L R ++ R G+ K+L+ T+V ARGIDV +T V N+DLP E Y+
Sbjct: 66 GELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYL 125
Query: 355 HRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
HRIGRTGR G+ G A +++ E ++ KI+ I
Sbjct: 126 HRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSI 163
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 181 bits (462), Expect = 2e-55
Identities = 60/172 (34%), Positives = 90/172 (52%), Gaps = 6/172 (3%)
Query: 228 PLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIAD 287
L S+ ++ Q + +V + LL+ L K ++F K D D I +
Sbjct: 15 TENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECL--QKTPPPVLIFAEKKADVDAIHE 72
Query: 288 RLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP 347
L + G A +HG Q R + +E R G+ +LVATDVA++G+D PAI HV NYD+P
Sbjct: 73 YLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMP 132
Query: 348 KFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNI----KKIERFTKQQIPIE 395
+ E+YVHRIGRTG +G G A + +N A ++ K + KQ++P
Sbjct: 133 EEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPV 184
>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation,
nucleotide-binding, hydrolase, RNA-binding, ATP-binding,
DNA-binding, nuclear protein; 1.91A {Homo sapiens}
Length = 185
Score = 180 bits (459), Expect = 5e-55
Identities = 62/156 (39%), Positives = 87/156 (55%), Gaps = 3/156 (1%)
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---MNIKKIERFTKQQIP 393
GR G G A S N ++ + KQ++P
Sbjct: 138 GRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVP 173
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 174 bits (443), Expect = 5e-53
Identities = 55/153 (35%), Positives = 88/153 (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 GRAGRNGFAVSLVNHAERMNIKKIERFTKQQIP 393
GR GR G A++ V + + ++++E+F QI
Sbjct: 122 GRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 154
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase;
RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo
sapiens} SCOP: c.37.1.19
Length = 172
Score = 173 bits (441), Expect = 1e-52
Identities = 42/154 (27%), Positives = 73/154 (47%), Gaps = 2/154 (1%)
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+ Q + + D KNR L LL Q V+F + + +A L F A +H
Sbjct: 4 HGLQQYYVKLKDN-EKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIH 62
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
+ Q R + + + +ILVAT++ RG+D+ + FNYD+P+ + Y+HR+ R
Sbjct: 63 RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARA 122
Query: 361 GRAGRNGFAVSLV-NHAERMNIKKIERFTKQQIP 393
GR G G A++ V + + + ++ + I
Sbjct: 123 GRFGTKGLAITFVSDENDAKILNDVQDRFEVNIS 156
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 102 bits (254), Expect = 1e-23
Identities = 56/323 (17%), Positives = 105/323 (32%), Gaps = 26/323 (8%)
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPR---MLVLTPTRELALQVTAATER 119
S+ KI + NL + + + + + + E
Sbjct: 166 PGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREM 225
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
+K + +L + + R +I+ + + + + L L
Sbjct: 226 LRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAM--ALKLH 283
Query: 180 EADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKK 239
A +L+ ++ + + + A+ + I D + K S+ +
Sbjct: 284 HAIELLETQGLSALRAYIKKLYEEAKAGSTKAS---------KEIFSDKRMKKAISLLVQ 334
Query: 240 QKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPL 299
K I + ++ L+ K+ + +VFT + A I + L G A
Sbjct: 335 AKEIGLDH---PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRF 391
Query: 300 HGD--------LHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPE 351
G L Q + L+ RG +LVAT V G+DVP + V Y+
Sbjct: 392 VGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAI 451
Query: 352 DYVHRIGRTGRAGRNGFAVSLVN 374
+ R GRTGR G + L+
Sbjct: 452 RSIQRRGRTGRH-MPGRVIILMA 473
Score = 79.5 bits (195), Expect = 4e-16
Identities = 40/265 (15%), Positives = 96/265 (36%), Gaps = 34/265 (12%)
Query: 16 LVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKK 75
+++ +P QE + ++ TG GKT M+ + +
Sbjct: 2 VLRRDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMM--------------IAEY 46
Query: 76 NLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGG 135
L + K+ L+L PT+ L LQ + R + K +++ G
Sbjct: 47 RLTKYGGKV----------------LMLAPTKPLVLQHAESFRRL-FNLPPEKIVALTGE 89
Query: 136 MPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEK 195
+ + +R ++++ATP + + + +G+I+ + ++V DEA R + I +
Sbjct: 90 KSPEERSKAWARA-KVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAR 148
Query: 196 IVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILH 255
+ +A+ + E I + I + + ++ + +
Sbjct: 149 EYKRQAKNPLVIGLTASPGSTPEKIMEVI-NNLGIEHIEYRSENSPDVRPYVKGIRFEWV 207
Query: 256 KNRLLDYLLRDKRVGQAVVFTATKR 280
+ L + +++ + ++ A K
Sbjct: 208 RVDLPEIYKEVRKLLREMLRDALKP 232
>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA
compl protease/ntpase/helicase, hydrolase; 1.95A
{Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A*
1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A*
3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A
Length = 666
Score = 98.2 bits (244), Expect = 5e-22
Identities = 63/360 (17%), Positives = 110/360 (30%), Gaps = 97/360 (26%)
Query: 27 VQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYT 86
S + + + TGSGK+ + A
Sbjct: 221 DNSSPPAVPQSFQVAHLHAPTGSGKSTK-VPAAYAAQG---------------------- 257
Query: 87 HKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLR-QMQLL 145
++LVL P+ L A YM K G P +R ++ +
Sbjct: 258 -----------YKVLVLNPSVAATLGFGA-------YMSK-----AHGIDPNIRTGVRTI 294
Query: 146 SRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQ 205
+ + +T G+ + + I++ DE D I I ++D
Sbjct: 295 TTGAPVTYSTYGKFLADGGCSGGAYD---IIICDECHST-DSTTILGIGTVLDQAETAGA 350
Query: 206 TMLF--SATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYL 263
++ +AT G V NI + L S + K ++ +
Sbjct: 351 RLVVLATATPPGSVTVPHPNIEEVAL-----SNTGE-----------IPFYGKAIPIEAI 394
Query: 264 LRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKIL 323
R G+ ++F +K+ D +A +L+ G A + L + + ++
Sbjct: 395 ----RGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGL-------DVSVIPTIGDVVV 443
Query: 324 VATDVAARG--IDV-------PAITHVFNYD--------LPKFPEDYVHRIGRTGRAGRN 366
VATD G D +T ++ P+D V R R GR GR
Sbjct: 444 VATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRG 503
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 79.1 bits (195), Expect = 8e-16
Identities = 83/454 (18%), Positives = 145/454 (31%), Gaps = 108/454 (23%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAI-SGRDLIVSSQTGSGKTAAFMLPA 59
M + + E + L + G Q +A+ + I G++ ++S T SGKT +
Sbjct: 1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAM 60
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
+H+ + K +Y + P + LA + +
Sbjct: 61 VHRILTQGGKA-------------VY-----------------IVPLKALAEEKFQEFQD 90
Query: 120 YGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD 179
+ ++ + G + L +I++AT + + G ++ILV D
Sbjct: 91 WEKIGLRVA---MATGDYDSKDEWL--GKYDIIIATAEKFDSLLRHGSSWIKDVKILVAD 145
Query: 180 E----ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNM--------AENITKD 227
E R D G +E I+ Q + SAT+ GN AE I D
Sbjct: 146 EIHLIGSR--DRGAT--LEVILAHMLGKAQIIGLSATI----GNPEELAEWLNAELIVSD 197
Query: 228 ----PLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDAD 283
L V Q +T +D L+ +R K A++F +R A+
Sbjct: 198 WRPVKLRRGV----FYQGFVTWEDGSIDRFSSWEELVYDAIRKK--KGALIFVNMRRKAE 251
Query: 284 IIADRL---------------------------------NISGFLAAPLHGDLHQNARNR 310
+A L A H L ++ R
Sbjct: 252 RVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVL 311
Query: 311 TLENLRRGRIKILVATDVAARGIDVPA----ITHVFNYDLPKFPE----DYVHRIGRTGR 362
EN R+G IK +VAT + GI+ PA I ++ Y + +GR GR
Sbjct: 312 VEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGR 371
Query: 363 AGRNGFAVSLVNHAERMNIKKIER-FTKQQIPIE 395
+ ++ + + + +
Sbjct: 372 PKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLF 405
>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding,
viral nucleoprotein, endoplasmic reticulum, helicase,
hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A*
2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A
2bhr_A
Length = 451
Score = 78.0 bits (192), Expect = 9e-16
Identities = 54/360 (15%), Positives = 99/360 (27%), Gaps = 93/360 (25%)
Query: 30 QAIPAAIS-GRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHK 88
+ R I+ G+GKT LP++ + A +
Sbjct: 10 EVDEDIFRKKRLTIMDLHPGAGKTKRI-LPSIVREALLRRL------------------- 49
Query: 89 ERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRN 148
R L+L PTR +A ++ ++ + +
Sbjct: 50 ----------RTLILAPTRVVAAEM-------EEALRGLP-----IRYQTPAVKSDHTGR 87
Query: 149 PEILLATPGRLIDHMNSGKINFSHLQILVLDEA-----DRMLDMGFINDIEKIVDATPVT 203
+ L + S + ++V+DEA + G+I+ ++ +A +
Sbjct: 88 EIVDLMCHATFTTRLLSST-RVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAI- 145
Query: 204 RQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYL 263
+AT G + + P+ I ++ N +
Sbjct: 146 ----FMTATPPGSTDPFPQ--SNSPIEDIEREIPERSWNTGFDWI--------------- 184
Query: 264 LRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKIL 323
G+ V F + + + IA+ L SG L +T +
Sbjct: 185 --TDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDW----DFV 238
Query: 324 VATDVAARG--IDV-------PAITHVFNYD-------LPKFPEDYVHRIGRTGRAGRNG 367
V TD++ G + V D P R GR GRN
Sbjct: 239 VTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNP 298
>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic
subunit]; helicase, flavivirus, DEAD-BOX, ATPase,
rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP:
c.37.1.14 c.37.1.14 PDB: 1ymf_A*
Length = 440
Score = 68.7 bits (168), Expect = 1e-12
Identities = 56/354 (15%), Positives = 99/354 (27%), Gaps = 99/354 (27%)
Query: 38 GRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQ 97
G ++ G+GKT LP + + +
Sbjct: 8 GMTTVLDFHPGAGKTRR-FLPQILAECARRRL---------------------------- 38
Query: 98 PRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLL----SRNPEILL 153
R LVL PTR + ++ A G+ Q S I
Sbjct: 39 -RTLVLAPTRVVLSEMKEA----------------FHGLDVKFHTQAFSAHGSGREVIDA 81
Query: 154 ATPGRLIDHMNSGKINFSHLQILVLDE-----ADRMLDMGFINDIEKIVDATPVTRQTML 208
L M + +++++DE + G+ + ++ T+L
Sbjct: 82 MCHATLTYRMLEP-TRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESA-----TIL 135
Query: 209 FSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKR 268
+AT G T D IE Q +I + + +
Sbjct: 136 MTATPPG---------TSDEFPHSNGEIEDVQTDI-----PSEPWNTGHDWIL-----AD 176
Query: 269 VGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV 328
F + R A+++A L +G L+ + +++ + ++ATD+
Sbjct: 177 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFERE----YPTIKQKKPDFILATDI 232
Query: 329 AARG--IDV-------PAITHVFNYD------LPKFPEDYVHRIGRTGRAGRNG 367
A G + V A V + R GR GRN
Sbjct: 233 AEMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNP 286
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 69.2 bits (168), Expect = 1e-12
Identities = 58/424 (13%), Positives = 129/424 (30%), Gaps = 36/424 (8%)
Query: 41 LIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRM 100
L S G+ K + + S + + N + + +K + + + R+
Sbjct: 413 LTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRI 472
Query: 101 LVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLI 160
P + + + TE + + +S + Q +L
Sbjct: 473 H--NPFAAIISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLE 530
Query: 161 DHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNM 220
D +I + + + D I++ +I+DA F +
Sbjct: 531 DKEEESRICRALFICT--EHLRKYNDALIISEDARIIDAL---SYLTEFFTNVKNGPYTE 585
Query: 221 AENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKR 280
E K + K+ T + +LD R + ++F T+
Sbjct: 586 LEQHLTAKFQEKEPELIALSKDETNEN---PKLEELVCILDDAYRYNPQTRTLLFAKTRA 642
Query: 281 DADIIADRLN----ISGFLAAPLHG--------DLHQNARNRTLENLRRGRI-KILVATD 327
+ + ++ L G + ++ L+ + + ++L+AT
Sbjct: 643 LVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATS 702
Query: 328 VAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERF 387
VA GID+ V Y+ + GR GRA + + + E + +K R+
Sbjct: 703 VADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNRY 760
Query: 388 TKQQIPIEVINGFEPKKRIRTYYSRYRFNNNNWKTHNINKSNITKRFYRQIKKTSISASS 447
++ + K + ++ K HN+ R R+ +
Sbjct: 761 KEEMM----------NKAVEK-IQKWDEETFAKKIHNLQMKERVLRDSRRKEIKPKVVEG 809
Query: 448 KNSI 451
+ ++
Sbjct: 810 QKNL 813
Score = 41.5 bits (96), Expect = 6e-04
Identities = 36/229 (15%), Positives = 77/229 (33%), Gaps = 39/229 (17%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q + AI+G++ ++ + TGSGKT +L H F
Sbjct: 253 QIELAQPAINGKNALICAPTGSGKTFVSILICEHHF------------------------ 288
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+ + +++ L + Q + + + I G ++ +
Sbjct: 289 --QNMPAGRKAKVVFLATKVPVYEQQKNVFKHH-FERQGYSVQGISGENFSNVSVEKVIE 345
Query: 148 NPEILLATPGRLIDHMNSGKI-NFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQT 206
+ +I++ TP L++ G + + S +++ DE N + +
Sbjct: 346 DSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSAS 405
Query: 207 MLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILH 255
L I+G +T + +IE+ ++I S+ DI
Sbjct: 406 QLPQ-----ILG-----LTASVGVGNAKNIEETIEHI-CSLCSYLDIQA 443
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 68.6 bits (168), Expect = 1e-12
Identities = 95/473 (20%), Positives = 163/473 (34%), Gaps = 131/473 (27%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAI-SGRDLIVSSQTGSGKTAAFMLPA 59
M + + L V++ + K G K Q +A+ + G L+++S TGSGKT +
Sbjct: 8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGI 67
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATER 119
+ + K IY TP R AL E+
Sbjct: 68 ISFLLKNGGKA-------------IYV-----------------TPLR--AL----TNEK 91
Query: 120 YGLYMKKIKAISIL-----GGMPYLRQMQLLSRNPEILLATPGRLIDHM-NSGKINFSHL 173
Y K + I G L + + I++ T +L D + + +
Sbjct: 92 YL-TFKDWELIGFKVAMTSGDYD-TDDAWLKNYD--IIITTYEKL-DSLWRHRPEWLNEV 146
Query: 174 QILVLDE------ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNM------- 220
VLDE +R G + +E + R + SAT+ N
Sbjct: 147 NYFVLDELHYLNDPER----GPV--VESVT-IRAKRRNLLALSATI----SNYKQIAKWL 195
Query: 221 -AENITKD--PLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRD-----KRVGQA 272
AE + + P+ L I ++K +++F D+ K D ++ + GQ
Sbjct: 196 GAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQV 255
Query: 273 VVFTATKRD----ADIIADRLNISGFLAAPL----------------------------- 299
+VF +++ A IA+ +N L
Sbjct: 256 LVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGV 315
Query: 300 ---HGDLHQNARNRTLENL-RRGRIKILVATDVAARGIDVPA---I---THVFNYDLPKF 349
H L + R +E R+ +IK++VAT A G+++PA I + FN + +
Sbjct: 316 AYHHAGLSKALR-DLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGY 374
Query: 350 -----PEDYVHRIGRTGRAGRN--GFAVSLVNHAERMNIKKIERFTKQQIPIE 395
+Y GR GR G + G ++ +V E ++ + PIE
Sbjct: 375 YDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIE 427
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 66.0 bits (161), Expect = 1e-11
Identities = 74/448 (16%), Positives = 147/448 (32%), Gaps = 109/448 (24%)
Query: 7 GLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASS 66
+ + L + G + Q +A+ SG++L+++ T +GKT + + +
Sbjct: 9 SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68
Query: 67 KNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKK 126
+ L + P R LA + + +++ +
Sbjct: 69 G-------------------------------KSLYVVPLRALAGEKYESFKKWEKIGLR 97
Query: 127 IKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLD 186
I + G Y + + L I++ T + + + + LV+DE
Sbjct: 98 IGIST--GD--YESRDEHLGDCD-IIVTTSEKADSLIRNRASWIKAVSCLVVDE------ 146
Query: 187 MGFIND------IEKIVDATPVTRQTMLF---SATLDGIVGNM--------AENITKD-- 227
+ ++ +E +V + + SAT N+ A+ D
Sbjct: 147 IHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATA----PNVTEIAEWLDADYYVSDWR 202
Query: 228 --PLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADII 285
PL+ V + + L++ + + G +VF +T+R A+
Sbjct: 203 PVPLVEGVLCEGTLELFDGAFSTSRRVKFEE--LVEECVAEN--GGVLVFESTRRGAEKT 258
Query: 286 ADRL--------NISGFLAAPL----------------------HGDLHQNARNRTLENL 315
A +L G A L H L R +
Sbjct: 259 AVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAF 318
Query: 316 RRGRIKILVATDVAARGIDVPAI------THVFNYDLPKFPE-DYVHRIGRTGRAGRNGF 368
RRG IK++VAT A G+++PA + F+ + +Y GR GR G +
Sbjct: 319 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDER 378
Query: 369 AVSLVNHAERMNIKKIERF-TKQQIPIE 395
+++ +R ++R+ + I
Sbjct: 379 GEAIIIVGKRDREIAVKRYIFGEPERIT 406
>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase,
ATP-binding, reticulum, nucleotidyltransferase,
multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4}
PDB: 2vbc_A 2wzq_A
Length = 618
Score = 65.7 bits (160), Expect = 1e-11
Identities = 57/368 (15%), Positives = 103/368 (27%), Gaps = 93/368 (25%)
Query: 22 TKPTGVQEQAIPAAIS-GRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQN 80
+ + R I+ G+GKT LP++ + A +
Sbjct: 169 ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRI-LPSIVREALKRRL----------- 216
Query: 81 NNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLR 140
R L+L PTR +A ++ +
Sbjct: 217 ------------------RTLILAPTRVVA-------AEMEEALRGLP-----IRYQTPA 246
Query: 141 QMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE-----ADRMLDMGFINDIEK 195
+ + L + S + ++V+DE + G+I+ +
Sbjct: 247 VKSDHTGREIVDLMCHATFTTRLLS-STRVPNYNLIVMDEAHFTDPCSVAARGYISTRVE 305
Query: 196 IVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILH 255
+ +A + +AT G + DP + IE ++ I +
Sbjct: 306 MGEAAAI-----FMTATPPG---------STDPFPQSNSPIEDIEREIPERS-------- 343
Query: 256 KNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENL 315
N D++ + G+ V F + + + IA+ L SG L +T
Sbjct: 344 WNTGFDWITDYQ--GKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTD 401
Query: 316 RRGRIKILVATDVAARG--IDV-------PAITHVFNYD-------LPKFPEDYVHRIGR 359
+V TD++ G + V D P R
Sbjct: 402 W----DFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQR 457
Query: 360 TGRAGRNG 367
GR GRN
Sbjct: 458 RGRIGRNP 465
>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane,
nucleotide-binding, RNA replication, transmembrane,
viral protein; 1.80A {Japanese encephalitis virus} PDB:
2v8o_A 2qeq_A
Length = 459
Score = 65.2 bits (159), Expect = 1e-11
Identities = 55/369 (14%), Positives = 103/369 (27%), Gaps = 101/369 (27%)
Query: 24 PTGVQEQAIPAAIS-GRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNN 82
+ P + + ++ GSGKT +LP + K A +
Sbjct: 6 GGQQMGRGSPNMLRKRQMTVLDLHPGSGKTRK-ILPQIIKDAIQQRL------------- 51
Query: 83 KIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMP----Y 138
R VL PTR +A ++ A L G+P
Sbjct: 52 ----------------RTAVLAPTRVVAAEMAEA----------------LRGLPVRYQT 79
Query: 139 LRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE-----ADRMLDMGFINDI 193
+ N + + L H + + V+DE + G+I
Sbjct: 80 SAVQREHQGNEIVDVMCHATLT-HRLMSPNRVPNYNLFVMDEAHFTDPASIAARGYIATK 138
Query: 194 EKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDI 253
++ +A + +AT G + + P+ + I + + +
Sbjct: 139 VELGEAAAI-----FMTATPPGTTDPFPD--SNAPIHDLQDEIPDRAWSSGYEWI----- 186
Query: 254 LHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLE 313
+ G+ V F A+ + + IA L +G L+ + +
Sbjct: 187 ------------TEYAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRKSYDTEYPKCKN 234
Query: 314 NLRRGRIKILVATDVAARG--IDV-------PAITHVFNYD-------LPKFPEDYVHRI 357
G ++ TD++ G ++ + P
Sbjct: 235 ----GDWDFVITTDISEMGANFGASRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAA 290
Query: 358 GRTGRAGRN 366
R GR GRN
Sbjct: 291 QRRGRVGRN 299
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 65.3 bits (158), Expect = 1e-11
Identities = 47/359 (13%), Positives = 113/359 (31%), Gaps = 27/359 (7%)
Query: 48 GSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTR 107
G+ K + + S + + N + + +K + + + R+
Sbjct: 179 GNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRI-----HN 233
Query: 108 ELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLID-HMNSG 166
A ++ M+ I ++ L + ++ RL+
Sbjct: 234 PFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEE 293
Query: 167 KINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITK 226
+ + + + D I++ +I+DA F + E
Sbjct: 294 ESRICRALFICTEHLRKYNDALIISEDARIIDAL---SYLTEFFTNVKNGPYTELEQHLT 350
Query: 227 DPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIA 286
K + K+ T +++++ +LD R + ++F T+ +
Sbjct: 351 AKFQEKEPELIALSKDETNENPKLEELV---CILDDAYRYNPQTRTLLFAKTRALVSALK 407
Query: 287 DRLN------------ISGFLAAPLHGDLHQNARNRTLENLRRGRI-KILVATDVAARGI 333
+ + G + ++ L+ + + ++L+AT VA GI
Sbjct: 408 KCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI 467
Query: 334 DVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQI 392
D+ V Y+ + GR GRA + + + E + +K R+ ++ +
Sbjct: 468 DIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNRYKEEMM 524
Score = 44.9 bits (105), Expect = 4e-05
Identities = 24/160 (15%), Positives = 56/160 (35%), Gaps = 28/160 (17%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q + AI+G++ ++ + TGSGKT +L + + H
Sbjct: 12 QIELAQPAINGKNALICAPTGSGKTFVSIL--------------ICE------------H 45
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+ + +++ L + Q + + + I G ++ +
Sbjct: 46 HFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHH-FERQGYSVQGISGENFSNVSVEKVIE 104
Query: 148 NPEILLATPGRLIDHMNSGKIN-FSHLQILVLDEADRMLD 186
+ +I++ TP L++ G + S +++ DE
Sbjct: 105 DSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTG 144
>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix,
helix-turn-helix, ATP binding, Zn(2+) binding,
hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43
c.37.1.19 c.37.1.19 PDB: 1oyy_A*
Length = 523
Score = 63.7 bits (156), Expect = 4e-11
Identities = 36/114 (31%), Positives = 61/114 (53%), Gaps = 8/114 (7%)
Query: 256 KNRLLDYLLRDKRVGQA-VVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLEN 314
++L+ Y+ ++ G++ +++ ++ + A RL G AA H L N R E
Sbjct: 224 LDQLMRYV--QEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEK 281
Query: 315 LRRGRIKILVATDVA-ARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNG 367
+R ++I+VAT VA GI+ P + V ++D+P+ E Y TGRAGR+G
Sbjct: 282 FQRDDLQIVVAT-VAFGMGINKPNVRFVVHFDIPRNIESYYQ---ETGRAGRDG 331
Score = 33.3 bits (77), Expect = 0.17
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 5 SIGLHELVLKALVKV-GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+ L + L + GY + QE+ I +SGRD +V TG GK+ + +PAL
Sbjct: 6 VLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL 62
Score = 28.6 bits (65), Expect = 4.8
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 287 DRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKIL-VA 325
D+L +G AA L+ + + + R G+I++L +A
Sbjct: 83 DQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIA 122
>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch
repair, nucleotide-binding, DNA-binding, polymorphism,
nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens}
PDB: 2wwy_A*
Length = 591
Score = 62.7 bits (153), Expect = 1e-10
Identities = 33/135 (24%), Positives = 62/135 (45%), Gaps = 16/135 (11%)
Query: 235 SIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQA-VVFTATKRDADIIADRLNISG 293
+ +K N F++DI+ L+ + GQ+ +++ +++D++ + L G
Sbjct: 242 EVRQKPSNTED---FIEDIVK-------LINGRYKGQSGIIYCFSQKDSEQVTVSLQNLG 291
Query: 294 FLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVA-ARGIDVPAITHVFNYDLPKFPED 352
A H +L + I+++VAT VA GID P + V ++ + K E+
Sbjct: 292 IHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT-VAFGMGIDKPDVRFVIHHSMSKSMEN 350
Query: 353 YVHRIGRTGRAGRNG 367
Y +GRAGR+
Sbjct: 351 YYQ---ESGRAGRDD 362
Score = 37.3 bits (87), Expect = 0.011
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 12 VLKALVKV-GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
V L V K +Q + I ++G+++ + TG GK+ + LPAL
Sbjct: 32 VKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPAL 81
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 62.7 bits (151), Expect = 1e-10
Identities = 50/366 (13%), Positives = 115/366 (31%), Gaps = 27/366 (7%)
Query: 41 LIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRM 100
L S G+ K + + S + + N + + +K + + + R+
Sbjct: 413 LTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRI 472
Query: 101 LVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLI 160
A ++ M+ I ++ L + ++ RL+
Sbjct: 473 -----HNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLL 527
Query: 161 DHMNSGKINFSHLQILVLDEA-DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGN 219
+ + + + + E + D I++ +I+D F +
Sbjct: 528 QLEDKEEESRICRALFICTEHLRKYNDALIISEDARIID---ALSYLTEFFTNVKNGPYT 584
Query: 220 MAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATK 279
E K + K+ T + +LD R + ++F T+
Sbjct: 585 ELEQHLTAKFQEKEPELIALSKDETNEN---PKLEELVCILDDAYRYNPQTRTLLFAKTR 641
Query: 280 RDADIIADRL----NISGFLAAPLHG--------DLHQNARNRTLENLRRGRI-KILVAT 326
+ + ++ L G + ++ L+ + + ++L+AT
Sbjct: 642 ALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIAT 701
Query: 327 DVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIER 386
VA GID+ V Y+ + GR GRA + + + E + +K R
Sbjct: 702 SVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNR 759
Query: 387 FTKQQI 392
+ ++ +
Sbjct: 760 YKEEMM 765
Score = 46.1 bits (108), Expect = 2e-05
Identities = 27/183 (14%), Positives = 60/183 (32%), Gaps = 28/183 (15%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q + AI+G++ ++ + TGSGKT +L H F
Sbjct: 253 QIELAQPAINGKNALICAPTGSGKTFVSILICEHHF------------------------ 288
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+ + +++ L + Q + + + I G ++ +
Sbjct: 289 --QNMPAGRKAKVVFLATKVPVYEQQKNVFKHH-FERQGYSVQGISGENFSNVSVEKVIE 345
Query: 148 NPEILLATPGRLIDHMNSGKI-NFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQT 206
+ +I++ TP L++ G + + S +++ DE N + +
Sbjct: 346 DSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSAS 405
Query: 207 MLF 209
L
Sbjct: 406 QLP 408
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 61.5 bits (148), Expect = 2e-10
Identities = 33/213 (15%), Positives = 69/213 (32%), Gaps = 22/213 (10%)
Query: 257 NRLLDYLLRDKRVGQAVVFTATKRDADIIADRLN----ISGFLAAPLHG--------DLH 304
+L ++F T+ D + + + +S L G +
Sbjct: 386 CFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMT 445
Query: 305 QNARNRTLENLR-RGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRA 363
A+ L+ + G IL+AT VA GID+ V Y+ + GR
Sbjct: 446 LPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRA- 504
Query: 364 GRNGFAVSLVN-----HAERMNIKKIERFTKQQIPIEVINGFEPKKRIRTYYSRYRFNNN 418
R L + E++N+ K + + ++ + +++I + +F +
Sbjct: 505 -RGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRD 563
Query: 419 NWKTHNINKSNITKRFYRQIKKTSISASSKNSI 451
+ + K+ +K A +
Sbjct: 564 SQEKPKPVPDKENKKLLC--RKCKALACYTADV 594
Score = 45.7 bits (107), Expect = 2e-05
Identities = 27/169 (15%), Positives = 60/169 (35%), Gaps = 28/169 (16%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q + A+ G++ I+ + TG GKT +L + + +L
Sbjct: 18 QLELALPAMKGKNTIICAPTGCGKTFVSLL--------------ICEHHL---------- 53
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+ + + +++ + Q + +Y + I G ++ +
Sbjct: 54 --KKFPQGQKGKVVFFANQIPVYEQNKSVFSKY-FERHGYRVTGISGATAENVPVEQIVE 110
Query: 148 NPEILLATPGRLIDHMNSGKIN-FSHLQILVLDEADRMLDMGFINDIEK 195
N +I++ TP L++++ G I S +++ DE N I
Sbjct: 111 NNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMF 159
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 61.0 bits (148), Expect = 3e-10
Identities = 29/149 (19%), Positives = 50/149 (33%), Gaps = 11/149 (7%)
Query: 219 NMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT 278
+ D + ++ + I + +K R L +L R + ++FT
Sbjct: 305 KIVMASGYDERAYEALRAWEEARRI------AFNSKNKIRKLREILERHRKDKIIIFTRH 358
Query: 279 KRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAI 338
I+ I + R LE R GR + +V++ V GIDVP
Sbjct: 359 NELVYRISKVFLIPAI-----THRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDA 413
Query: 339 THVFNYDLPKFPEDYVHRIGRTGRAGRNG 367
+Y+ R+GR R +
Sbjct: 414 NVGVIMSGSGSAREYIQRLGRILRPSKGK 442
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 59.7 bits (144), Expect = 1e-09
Identities = 26/112 (23%), Positives = 44/112 (39%), Gaps = 3/112 (2%)
Query: 256 KNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNIS-GFLAAPLHGDLHQNARNRTLEN 314
+ L L R + +V A A + L G AA H + R+R
Sbjct: 490 RVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAW 549
Query: 315 LRR--GRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAG 364
++L+ +++ + G + +H+ +DLP P+ RIGR R G
Sbjct: 550 FAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIG 601
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 58.4 bits (140), Expect = 2e-09
Identities = 44/263 (16%), Positives = 82/263 (31%), Gaps = 21/263 (7%)
Query: 143 QLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPV 202
Q + + + L + D I++ ++ DA
Sbjct: 269 QKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDALIISEDAQMTDAL-- 326
Query: 203 TRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDY 262
F + + E K+ +EK ++ + + +L
Sbjct: 327 -NYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNEN---PKLRDLYLVLQE 382
Query: 263 LLRDKRVGQAVVFTATKRDADIIADRLN----ISGFLAAPLHG--------DLHQNARNR 310
K + ++F T+ D + + +S L G + A+
Sbjct: 383 EYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKC 442
Query: 311 TLENLR-RGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFA 369
LE R G IL+AT VA GID+ V Y+ + GR GRA R+
Sbjct: 443 VLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKC 500
Query: 370 VSLVNHAERMNIKKIERFTKQQI 392
L + A+ + +K ++ +
Sbjct: 501 FLLTSSADVIEKEKANMIKEKIM 523
Score = 47.6 bits (112), Expect = 6e-06
Identities = 33/167 (19%), Positives = 57/167 (34%), Gaps = 28/167 (16%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q + A G++ I+ + TG GKT +L H +KK K+
Sbjct: 9 QLELALPAKKGKNTIICAPTGCGKTFVSLLICEH----------HLKKFPCGQKGKV--- 55
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+ + Q RY SI G +Q +
Sbjct: 56 -------------VFFANQIPVYEQQATVFSRY-FERLGYNIASISGATSDSVSVQHIIE 101
Query: 148 NPEILLATPGRLIDHMNSGKIN-FSHLQILVLDEADRMLDMGFINDI 193
+ +I++ TP L++++N+G I S +++ DE N I
Sbjct: 102 DNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQI 148
>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication,
viral replication, nucleotide-binding; 2.10A {Kokobera
virus} PDB: 2v6j_A
Length = 431
Score = 57.5 bits (139), Expect = 4e-09
Identities = 54/351 (15%), Positives = 100/351 (28%), Gaps = 97/351 (27%)
Query: 38 GRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQ 97
++ G+GKT LP L + A K
Sbjct: 2 RELTVLDLHPGAGKTRRV-LPQLVREAVKKRL---------------------------- 32
Query: 98 PRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLL----SRNPEILL 153
R ++L PTR +A ++ A L G P + + N +
Sbjct: 33 -RTVILAPTRVVASEMYEA----------------LRGEPIRYMTPAVQSERTGNEIVDF 75
Query: 154 ATPGRLIDHMNSGKINFSHLQILVLDEA-----DRMLDMGFINDIEKIVDATPVTRQTML 208
+ G + + + ++DEA + G+I + DA +
Sbjct: 76 MCHSTFTMKLLQG-VRVPNYNLYIMDEAHFLDPASVAARGYIETRVSMGDAGAI-----F 129
Query: 209 FSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKR 268
+AT G + + P+I + I K N + +
Sbjct: 130 MTATPPGTTEAFPPSNS--PIIDEETRIPDKAWNSGYEWI-----------------TEF 170
Query: 269 VGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDV 328
G+ V F + + I L +G L+ ++ + + + ++ TD+
Sbjct: 171 DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRKTFESEYPKC----KSEKWDFVITTDI 226
Query: 329 AARG--IDVPAI----THVFNYDL-PKFPEDYVHRIG------RTGRAGRN 366
+ G + + L + I R GR GRN
Sbjct: 227 SEMGANFKADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRN 277
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 54.8 bits (132), Expect = 7e-09
Identities = 26/161 (16%), Positives = 56/161 (34%), Gaps = 34/161 (21%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTA-AFMLPALHKFASSKNKIPVMKKNLNQNNNKIYT 86
Q + A+ G+++I+ TGSGKT A +
Sbjct: 38 QMEVAQPALEGKNIIICLPTGSGKTRVAVYI--------------------------AKD 71
Query: 87 HKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLS 146
H ++ + +++VL L Q E K + I + G +
Sbjct: 72 HLDKKKKASEPGKVIVLVNKVLLVEQ-LFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVV 130
Query: 147 RNPEILLATPGRLIDHMNS------GKINFSHLQILVLDEA 181
++ +I+++T L + + + + S ++++DE
Sbjct: 131 KSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDEC 171
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 56.4 bits (135), Expect = 1e-08
Identities = 69/466 (14%), Positives = 144/466 (30%), Gaps = 101/466 (21%)
Query: 37 SGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPA 96
+++++ GSGKT + K+ + + KI+ L K
Sbjct: 149 PAKNVLIDGVLGSGKT------WVALDVCLSYKV------QCKMDFKIFW----LNLKNC 192
Query: 97 QPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATP 156
VL ++L Q+ + IK + I LR++ LL
Sbjct: 193 NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK-LRIHSIQAELRRLLKSKPYENCLL--- 248
Query: 157 GRLIDHMNSGKI----NFSHLQILVL--DE--ADRMLDMGFINDIEKIVDATPVT-RQTM 207
++ ++ + K N +IL+ + D L I + +T +
Sbjct: 249 --VLLNVQNAKAWNAFNL-SCKILLTTRFKQVTDF-LSAATTTHISLDHHSMTLTPDEVK 304
Query: 208 -LFSATLDGIVGNMAENITK-DPLILKV-----------------NSIEKKQKNITQSIL 248
L LD ++ + +P L + + +K I S+
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364
Query: 249 FVDDILHKNRLLDY--LLRDKRVGQAVV----FTATKRDADIIADRLNISGFLAA----- 297
++ ++ + ++ F K D ++ ++L+ +
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES 424
Query: 298 --PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPED--- 352
+ ++ + LEN + +V + D + DL D
Sbjct: 425 TISIP-SIYLELK-VKLENEYALH-RSIVDHYNIPKTFD--------SDDLIPPYLDQYF 473
Query: 353 YVHRIGRTGRAGRNGFAVSLVNHAERMNI-KKIE---RFTKQQIPIEVINGFEPKKRIRT 408
Y H I G + + H ERM + + + RF +Q+I + + T
Sbjct: 474 YSH-I---------GHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNT 523
Query: 409 -----YYSRYRFNNNNWKTHNINKSNITKRFYRQIKKTSISASSKN 449
+Y Y +N+ +N F +I++ I + +
Sbjct: 524 LQQLKFYKPYICDNDPKYERLVNA---ILDFLPKIEENLICSKYTD 566
Score = 46.0 bits (108), Expect = 2e-05
Identities = 20/147 (13%), Positives = 41/147 (27%), Gaps = 38/147 (25%)
Query: 216 IVGNMAENITKDPLILKVNSIEKKQKNITQS-----ILFVDDILHKNRLLDYLLRDKRVG 270
I+ + + ++ K+I I+ D + L + L K+
Sbjct: 21 ILSVFEDAFVDN---FDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEE 77
Query: 271 QAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAA 330
F + FL +P+ + Q + + +R R+
Sbjct: 78 MVQKFVEEVLRINY--------KFLMSPIKTEQRQPSMMTRMYIEQRDRL---------- 119
Query: 331 RGIDVPAITHVFNYDLPKFPEDYVHRI 357
+N D F + V R+
Sbjct: 120 -----------YN-DNQVFAKYNVSRL 134
>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3
catalytic subunit; nucleotide-binding, capsid protein;
2.75A {Murray valley encephalitis virus}
Length = 673
Score = 54.6 bits (131), Expect = 4e-08
Identities = 46/293 (15%), Positives = 85/293 (29%), Gaps = 70/293 (23%)
Query: 99 RMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMP----YLRQMQLLSRNPEILLA 154
R VL PTR +A ++ A L G+P + S N + +
Sbjct: 272 RTAVLAPTRVVAAEMAEA----------------LRGLPVRYLTPAVQREHSGNEIVDVM 315
Query: 155 TPGRLIDHMNSGKINFSHLQILVLDE-----ADRMLDMGFINDIEKIVDATPVTRQTMLF 209
L H + + + V+DE + G+I + +A +
Sbjct: 316 CHATLT-HRLMSPLRVPNYNLFVMDEAHFTDPASIAARGYIATRVEAGEAAAI-----FM 369
Query: 210 SATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRV 269
+AT G + T P+ + I + + +
Sbjct: 370 TATPPGTSDPFPD--TNSPVHDVSSEIPDRAWSSGFEWITDYA----------------- 410
Query: 270 GQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVA 329
G+ V F A+ + ++ IA L +G L+ + + G ++ TD++
Sbjct: 411 GKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRKSYDTEYPKCKN----GDWDFVITTDIS 466
Query: 330 ARG--IDVP-------AITHVFNYD-------LPKFPEDYVHRIGRTGRAGRN 366
G ++ + R GR GRN
Sbjct: 467 EMGANFGASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRN 519
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 51.2 bits (122), Expect = 6e-07
Identities = 52/257 (20%), Positives = 85/257 (33%), Gaps = 78/257 (30%)
Query: 177 VLDEADRML--DMGFINDIEKIVDATPVTRQTMLFSATLDGIVGN-MAEN---ITKDPLI 230
V + AD GF I IV P T+ F G G + EN + + ++
Sbjct: 1645 VWNRADNHFKDTYGF--SILDIVINNP-VNLTIHF----GGEKGKRIRENYSAMIFETIV 1697
Query: 231 LKVNSIEKKQKNITQ---SILFVDDILHKNRLLDYLLRDKRVGQAVVFTATK------RD 281
EK K I + S F + LL + Q + K +
Sbjct: 1698 DGKLKTEKIFKEINEHSTSYTFRSE--------KGLLSATQFTQPALTLMEKAAFEDLKS 1749
Query: 282 ADIIADRLNISGF-------LAAPLHGDLHQNARNRTLENL-----RRGR-IKILVATDV 328
+I +G LA+ A ++E+L RG +++ V D
Sbjct: 1750 KGLIPADATFAGHSLGEYAALASL--------ADVMSIESLVEVVFYRGMTMQVAVPRDE 1801
Query: 329 AARG------IDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIK 382
R I+ + F+ + + V R+G+ R G+ V +VN+ N++
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEA---LQYVVERVGK-----RTGWLVEIVNY----NVE 1849
Query: 383 KIERFTKQQIPIEVING 399
QQ V G
Sbjct: 1850 ------NQQY---VAAG 1857
Score = 49.3 bits (117), Expect = 2e-06
Identities = 69/469 (14%), Positives = 137/469 (29%), Gaps = 140/469 (29%)
Query: 10 ELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPA-LHKFASS-- 66
ELV K L GY V P+ + D +++ + ++ +H A+
Sbjct: 59 ELVGKFL---GY-----VSSLVEPSKVGQFDQVLNLCLTEFENC-YLEGNDIHALAAKLL 109
Query: 67 -KNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMK 125
+N ++K + K Y + +P AL L
Sbjct: 110 QENDTTLVKT---KELIKNYITARIMAKRP-------FDKKSNSALFRAVGEGNAQLV-- 157
Query: 126 KIKAISILGG----MPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLD-- 179
+I GG Y +++ L + +L+ G LI L L+
Sbjct: 158 -----AIFGGQGNTDDYFEELRDLYQTYHVLV---GDLIKFS------AETLSELIRTTL 203
Query: 180 EADRMLDMGFINDIEKIVDATPVTR--QTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
+A+++ G +I + ++ P + L S + PLI
Sbjct: 204 DAEKVFTQGL--NILEWLE-NPSNTPDKDYLLSIPISC------------PLI------- 241
Query: 238 KKQKNITQSILFVDDILHKNRLLDY---LLRDKRVGQAVVFTATKRDADIIADRLNISGF 294
+ Q +V +LL + LR G AT ++ +
Sbjct: 242 ----GVIQLAHYVVTA----KLLGFTPGELRSYLKG------ATGHSQGLVT-----AVA 282
Query: 295 LAAPLHGD-LHQNARN----------RTLENLRRGRIKILVATDVAARGIDVP----AIT 339
+A + + R R E + + D VP +I+
Sbjct: 283 IAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS 342
Query: 340 HVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVING 399
+L + + ++ + N +Q+ I ++NG
Sbjct: 343 -----NLTQ---------------------EQVQDYVNKTNSHLPAG---KQVEISLVNG 373
Query: 400 FEPKKRIRTYYSR--YRFNNNNWKTHNINKSNITKRFYRQIKKTSISAS 446
K + + + Y N K + + ++ + + +K S
Sbjct: 374 --AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSE-RKLKFSNR 419
Score = 44.3 bits (104), Expect = 8e-05
Identities = 72/359 (20%), Positives = 118/359 (32%), Gaps = 122/359 (33%)
Query: 79 QNNNKIYTHKERLR--FKPAQPRMLVLTPT-----RELALQVTAATERY--GL------- 122
Q N Y +E LR ++ + L EL A + + GL
Sbjct: 163 QGNTDDYF-EE-LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE 220
Query: 123 ---------YMKKIKAISILGGMPYLRQMQLLS--RNPEILLATPGRLIDHMNSGKINFS 171
Y+ I IS P + +QL ++L TPG L ++ G
Sbjct: 221 NPSNTPDKDYLLSI-PIS----CPLIGVIQLAHYVVTAKLLGFTPGELRSYL-KGAT--G 272
Query: 172 HLQILV--------------LDEADRMLDMGFINDIEKI----VDATPVT--RQTMLFSA 211
H Q LV + + + F I +A P T ++L
Sbjct: 273 HSQGLVTAVAIAETDSWESFFVSVRKAITVLFF-----IGVRCYEAYPNTSLPPSIL-ED 326
Query: 212 TLDGIVGN---MA--ENITKDPL---ILKVNSIEKKQKNITQSI-L------FVDDI--- 253
+L+ G M N+T++ + + K NS K + I L V +
Sbjct: 327 SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQV--EISLVNGAKNLV--VSGP 382
Query: 254 ---LHKNRLLDYLLRDKRVG----QA-VVFTATKRDADIIADRLNIS-GFL--AAPLHGD 302
L+ L+ LR + Q+ + F+ +R +L S FL A+P H
Sbjct: 383 PQSLY---GLNLTLRKAKAPSGLDQSRIPFS--ER-------KLKFSNRFLPVASPFHSH 430
Query: 303 LHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFN----YDLPKFPEDYVHRI 357
L A + ++L + + A+ I +P V++ DL RI
Sbjct: 431 LLVPASDLINKDLVKNNVSF------NAKDIQIP----VYDTFDGSDLRVLSGSISERI 479
Score = 34.6 bits (79), Expect = 0.086
Identities = 30/210 (14%), Positives = 53/210 (25%), Gaps = 59/210 (28%)
Query: 228 PLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT--KRDADII 285
PL L S+E +L V L+++ F +
Sbjct: 8 PLTLSHGSLE-------HVLL-VPTASFFIAS---QLQEQ-------FNKILPEPTEGFA 49
Query: 286 ADRLNIS---------GFLAAPLHGDLHQNARNRTLEN-LRRGRIKILVATDVAARGIDV 335
AD + G++++ + ++ L L L G D+
Sbjct: 50 ADDEPTTPAELVGKFLGYVSSLVE-PSKVGQFDQVLNLCLTEFENCYL-------EGNDI 101
Query: 336 PAITHVFNYDLPKFPED-----------YVHRIGRTGRAGRNGFAVSLVNHAERMNIKKI 384
H L + + Y+ R +L N + +
Sbjct: 102 ----HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 385 ERFTKQQIPIEVINGFEPKKRIRTYYSRYR 414
F Q + FE +R Y Y
Sbjct: 158 AIFGGQGNTDDY---FE---ELRDLYQTYH 181
Score = 31.2 bits (70), Expect = 0.92
Identities = 23/168 (13%), Positives = 48/168 (28%), Gaps = 46/168 (27%)
Query: 58 PALHKFASSKNKIPVMKKNLNQNNNKI--------YT----HKERLRFKPAQPRMLVLTP 105
PAL K +K + Y + + + + +
Sbjct: 1734 PAL--TLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESL----VEVVF 1787
Query: 106 TRELALQVTA-----ATERYGLYMKKIKAISILGGMPYLRQM--QLLSRNPEIL------ 152
R + +QV YG+ ++ L+ + ++ R ++
Sbjct: 1788 YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN 1847
Query: 153 --------------LATPGRLIDHMNSGKINFSHLQI-LVLDEADRML 185
L T +++ + KI+ LQ L L+E + L
Sbjct: 1848 VENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
>3h1t_A Type I site-specific restriction-modification system, R
(restriction) subunit; hydrolase, restriction enzyme
HSDR, ATP-binding; 2.30A {Vibrio vulnificus}
Length = 590
Score = 48.2 bits (115), Expect = 4e-06
Identities = 20/103 (19%), Positives = 32/103 (31%), Gaps = 12/103 (11%)
Query: 249 FVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDL----- 303
D L D++ R R + +VF + AD + LN + H D
Sbjct: 421 RTDAFAKH--LTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVT 478
Query: 304 -----HQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHV 341
+ L IL + + G+D P +V
Sbjct: 479 SEEGKIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNV 521
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 48.1 bits (115), Expect = 5e-06
Identities = 63/350 (18%), Positives = 116/350 (33%), Gaps = 74/350 (21%)
Query: 23 KPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNN 82
+P +Q+ + ++ TG GKT+ + +L F + K K
Sbjct: 56 EPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSL--FLALKGK------------- 100
Query: 83 KIYTHKERLRFKPAQPRMLVLTPTRELALQV----TAATERYGLYMKKIKAISILGGMPY 138
R V+ PT L +Q E+ G+ + G +P
Sbjct: 101 ----------------RCYVIFPTSLLVIQAAETIRKYAEKAGVG-TENLIGYYHGRIPK 143
Query: 139 LRQMQLLSR--NPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLD---------- 186
+ + N +I++ T L H H + +D+ D +L
Sbjct: 144 REKENFMQNLRNFKIVITTTQFLSKHYR----ELGHFDFIFVDDVDAILKASKNVDKLLH 199
Query: 187 -MGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQ 245
+GF D++ M+ +AT G AE + + L + S +N+
Sbjct: 200 LLGFHYDLKTKSWVGEARGCLMVSTATAKK--GKKAE-LFRQLLNFDIGSSRITVRNVED 256
Query: 246 SILFVDDILHKNRLLDYLLRDKRVGQ-AVVFTATKRDADIIADRLNISGFLAAPLHGDLH 304
+ + I + L L +++G +++ T +A+ I + L + F +
Sbjct: 257 VAVNDESI---STLSSIL---EKLGTGGIIYARTGEEAEEIYESLK-NKFRIGIVT---- 305
Query: 305 QNARNRTLENLRRGRIKILVAT----DVAARGIDVP-AITHVFNYDLPKF 349
+ E G I L+ T RG+D+P I P F
Sbjct: 306 -ATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSF 354
>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant
helicase, T4-bacteriophage, recombination, hydrolase;
2.70A {Enterobacteria phage T4}
Length = 510
Score = 46.1 bits (108), Expect = 2e-05
Identities = 55/360 (15%), Positives = 107/360 (29%), Gaps = 39/360 (10%)
Query: 97 QPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATP 156
+ ++L++ PT L Q+ Y L+ + I GG + + + +++ T
Sbjct: 157 EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK-IGGGASKDDKYKN---DAPVVVGTW 212
Query: 157 GRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDA------TPVTRQTMLFS 210
++ F +++ DE + I + + + R
Sbjct: 213 QTVVKQPKEWFSQFG---MMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANI 269
Query: 211 ATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKN----RLLDYLLRD 266
G+ G + + +T L+ E K +I K + +
Sbjct: 270 MQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGL 329
Query: 267 KRV---------------GQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRT 311
+ A V I D + + G++ RN
Sbjct: 330 SKRNKWIAKLAIKLAQKDENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIM 389
Query: 312 LENLRRGRIKILVAT-DVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAV 370
G+ I+VA+ V + GI V + HV K + IGR R +
Sbjct: 390 KTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIA 449
Query: 371 SLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIRTY------YSRYRFNNNNWKTHN 424
++ + + +K TK++ RI+ Y Y N H+
Sbjct: 450 TVWDLIDDAGVKPKSANTKKKYVHLNYLLKHGIDRIQRYADEKFNYVMKTVNLLEHHHHH 509
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 39.8 bits (92), Expect = 0.002
Identities = 27/150 (18%), Positives = 56/150 (37%), Gaps = 20/150 (13%)
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKF------- 349
H L + + G +K+L AT+ + G+++PA T VF + K+
Sbjct: 508 GIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFT-SVRKWDGQQFRW 566
Query: 350 --PEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIR 407
+Y+ GR GR G + + ++ E+M + + K + +
Sbjct: 567 VSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKG----------QADRLDS 616
Query: 408 TYYSRYRFNNNNWKTHNINKSNITKRFYRQ 437
++ Y N + I+ + + + Q
Sbjct: 617 AFHLGYNMILNLMRVEGISPEFMLEHSFFQ 646
Score = 36.4 bits (83), Expect = 0.025
Identities = 36/190 (18%), Positives = 69/190 (36%), Gaps = 47/190 (24%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q+ AI G ++VS+ T +GKT + A ++A + ++L IYT
Sbjct: 189 QDTAISCIDRGESVLVSAHTSAGKT----VVA--EYA--------IAQSLKNKQRVIYT- 233
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+P + L+ Q +Y + + + ++ G ++
Sbjct: 234 ----------------SPIKALSNQ------KYRELLAEFGDVGLMTGD--------ITI 263
Query: 148 NPE--ILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQ 205
NP+ L+ T L + G + ++ DE M D E+ + P +
Sbjct: 264 NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVR 323
Query: 206 TMLFSATLDG 215
+ SAT+
Sbjct: 324 YVFLSATIPN 333
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 39.0 bits (90), Expect = 0.003
Identities = 27/150 (18%), Positives = 56/150 (37%), Gaps = 20/150 (13%)
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKF------- 349
H L + + G +K+L AT+ + G+++PA T VF + K+
Sbjct: 410 GIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFT-SVRKWDGQQFRW 468
Query: 350 --PEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIR 407
+Y+ GR GR G + + ++ E+M + + K + +
Sbjct: 469 VSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKG----------QADRLDS 518
Query: 408 TYYSRYRFNNNNWKTHNINKSNITKRFYRQ 437
++ Y N + I+ + + + Q
Sbjct: 519 AFHLGYNMILNLMRVEGISPEFMLEHSFFQ 548
Score = 36.7 bits (84), Expect = 0.018
Identities = 36/190 (18%), Positives = 69/190 (36%), Gaps = 47/190 (24%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
Q+ AI G ++VS+ T +GKT + A ++A + ++L IYT
Sbjct: 91 QDTAISCIDRGESVLVSAHTSAGKT----VVA--EYA--------IAQSLKNKQRVIYT- 135
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+P + L+ Q +Y + + + ++ G ++
Sbjct: 136 ----------------SPIKALSNQ------KYRELLAEFGDVGLMTGD--------ITI 165
Query: 148 NPE--ILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQ 205
NP+ L+ T L + G + ++ DE M D E+ + P +
Sbjct: 166 NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVR 225
Query: 206 TMLFSATLDG 215
+ SAT+
Sbjct: 226 YVFLSATIPN 235
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 34.4 bits (78), Expect = 0.084
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 300 HGDLHQNARNRTLENL-RRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
H +E L +G IK+L AT+ A G+++P T +F+ + K + R
Sbjct: 405 HHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIFS-SIRKHDGNG-LREL 462
Query: 359 R-------TGRAGRNGF 368
GRAGR G
Sbjct: 463 TPGEFTQMAGRAGRRGL 479
Score = 28.3 bits (62), Expect = 6.0
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTA 53
Q++A+ G + V++ T +GKT
Sbjct: 44 QKEAVYHLEQGDSVFVAAHTSAGKTV 69
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 34.5 bits (80), Expect = 0.084
Identities = 17/38 (44%), Positives = 22/38 (57%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVP 336
+HG L Q ++R + GR ILV+T V GIDVP
Sbjct: 619 MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVP 656
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 0.51
Identities = 12/53 (22%), Positives = 17/53 (32%), Gaps = 25/53 (47%)
Query: 67 KNKIPVMKKNLNQNNNKIYTHKERLRFKP-AQPRMLVLTPTRELALQVTAATE 118
K + KK L Q + K+Y + P AL + A E
Sbjct: 19 KQAL---KK-L-QASLKLYA--------DDSAP-----------ALAIKATME 47
Score = 29.9 bits (66), Expect = 1.0
Identities = 5/27 (18%), Positives = 10/27 (37%), Gaps = 4/27 (14%)
Query: 377 ERMNIKKIER----FTKQQIPIEVING 399
E+ +KK++ + P I
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKA 44
>3soz_A ORF 245 protein, cytoplasmic protein STM1381; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
2.60A {Salmonella enterica subsp}
Length = 248
Score = 30.2 bits (67), Expect = 1.4
Identities = 11/37 (29%), Positives = 15/37 (40%)
Query: 20 GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFM 56
GY K + + A I+G L+V GK F
Sbjct: 181 GYNKLIAKENSQVLAEINGDPLLVMGTYHKGKVCCFA 217
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 30.1 bits (67), Expect = 1.4
Identities = 9/58 (15%), Positives = 17/58 (29%), Gaps = 9/58 (15%)
Query: 364 GRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIRTYYSRYRFNNNNWK 421
G G A+ VN++ + + + + P RI + K
Sbjct: 114 GSVGMAIQ-VNYSSEV--------KENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKK 162
>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase,
hypertherm protein, replication; HET: DNA BOG; 1.50A
{Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB:
1d2m_A*
Length = 664
Score = 30.2 bits (69), Expect = 1.4
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+ D++ R + R +R +V T R A+ + L G A LH +L R
Sbjct: 425 ILDLMEGIR--ERAARGERT---LVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQ 479
Query: 310 RTLENLRRGRIKILVATDVAARGIDVP 336
+ +LR G LV ++ G+D+P
Sbjct: 480 ALIRDLRLGHYDCLVGINLLREGLDIP 506
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 1.6
Identities = 14/87 (16%), Positives = 27/87 (31%), Gaps = 22/87 (25%)
Query: 373 VNHAERMN-----IKK-IERFTKQQIPIEVINGFEPKKRIRT----------YYSRYRFN 416
+ A+R+ I+K E K+ ++ ++ + R +
Sbjct: 74 IAQADRLTQEPESIRKWREEQRKR---LQELDAASKVMEQEWREKAKKDLEEWNQRQ--S 128
Query: 417 NNNWKTHNINKSNITKRFYRQIKKTSI 443
K N+ K FY+Q I
Sbjct: 129 EQVEKNKINNRIA-DKAFYQQPDADII 154
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 29.7 bits (67), Expect = 2.5
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 34 AAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKI 70
+ + + S TGSGKT + AL + K K+
Sbjct: 18 SLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKV 54
>2gk3_A Putative cytoplasmic protein; STM3548, structural genomics, PSI, P
structure initiative; 2.25A {Salmonella typhimurium}
SCOP: c.23.16.9
Length = 256
Score = 28.6 bits (63), Expect = 3.8
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 20 GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFM 56
GY + + + I+ L+V + GKTA FM
Sbjct: 188 GYNQAVARDDADVVLTINNDPLLVFGEYQQGKTACFM 224
>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex,
hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus
subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A*
1d9x_A 2d7d_B* 2nmv_B*
Length = 661
Score = 28.7 bits (65), Expect = 5.1
Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
+DD++ + + + R++RV +V T TK+ ++ + D L G LH ++ R
Sbjct: 431 IDDLIGEIQ--ARIERNERV---LVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERI 485
Query: 310 RTLENLRRGRIKILVATDVAARGIDVP 336
+ +LR G+ +LV ++ G+D+P
Sbjct: 486 EIIRDLRLGKYDVLVGINLLREGLDIP 512
>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition
domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus
fulgidus} SCOP: c.37.1.19
Length = 237
Score = 28.1 bits (63), Expect = 5.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKT 52
QE+A+ + + + TGSGKT
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKT 122
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease,
double strand DNA repair, protein-DNA CO hydrolase-DNA
complex; HET: DNA; 2.80A {Bacillus subtilis} PDB:
3u44_A*
Length = 1232
Score = 28.0 bits (62), Expect = 7.7
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 22 TKPTGV-----QEQAIPAAISGRDLIVSSQTGSGKTA 53
KP Q AI + +G+D++V++ GSGKTA
Sbjct: 4 PKPADSTWTDDQWNAIVS--TGQDILVAAAAGSGKTA 38
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 27.6 bits (61), Expect = 9.6
Identities = 28/165 (16%), Positives = 53/165 (32%), Gaps = 14/165 (8%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVM-KKNLNQNNNKIYT 86
Q A+ + ++ G+GKT H K++I V N+ ++
Sbjct: 365 QSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKL 424
Query: 87 HKERLRF--KPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMP--YLRQM 142
L+ A+ R V + LAL G +K +G + ++
Sbjct: 425 RDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRF 484
Query: 143 QLLSRNPEILLATPGRLIDHMNSG------KINFSHLQILVLDEA 181
L R E + ++ G F +++DE+
Sbjct: 485 VKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRT---VLIDES 526
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.136 0.382
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,919,854
Number of extensions: 444754
Number of successful extensions: 1530
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1348
Number of HSP's successfully gapped: 123
Length of query: 453
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 356
Effective length of database: 3,993,456
Effective search space: 1421670336
Effective search space used: 1421670336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.0 bits)