RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16633
(540 letters)
>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 = 254 bits (652), Expect = 7e-80
Identities = 109/387 (28%), Positives = 182/387 (47%), Gaps = 41/387 (10%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
TF F + L I + G+ +P+ IQE AIP+ + +D+L RA+ G+GKT AF IP ++
Sbjct: 22 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEP 138
K+ ++ + +AL++ P++EL Q + ++ L + C+ + ++
Sbjct: 82 KV-----KPKLNKIQALIMVPTRELALQTSQVVRTLGK--HCGISCMVTTGGTNLRDDIL 134
Query: 139 LLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK 198
L E I+V TP R L K DL S + I+DEAD + S ++ ++ +L FLP
Sbjct: 135 RLNETVHILVGTPGRVLDLASRKVADL-SDCSLFIMDEADKMLSRDFKTIIEQILSFLPP 193
Query: 199 LYQAILASATLSEDVLSLKHLILRNPVILKLEEPAIAP-VSQLAHYHILAQEDEKATILY 257
+Q++L SAT V L P + L E ++Q Y+ +E +K L
Sbjct: 194 THQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQ---YYAFVEERQKLHCLN 250
Query: 258 TLL-KLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGL 316
TL KL + Q IIF N+ ++ L + S ++ + + R ++F QG
Sbjct: 251 TLFSKLQINQ--AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGK 308
Query: 317 YDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHR 376
++ SD RGID Q V+ VINFDFP + Y+HR
Sbjct: 309 VRTLVCSDLLT-----------------------RGIDIQAVNVVINFDFPKTAETYLHR 345
Query: 377 AGRTARGKNQGTALSFVSLREQDLMND 403
GR+ R + G A++ ++ ++ +
Sbjct: 346 IGRSGRFGHLGLAINLINWNDRFNLYK 372
>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 = 251 bits (643), Expect = 2e-78
Identities = 104/388 (26%), Positives = 196/388 (50%), Gaps = 41/388 (10%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
TF + L+ I G+ +P+ IQ+RAI I++ +DV+ ++++G+GKT F+I ++Q
Sbjct: 38 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 97
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEP 138
+ QV+ET+AL+L+P++EL Q+ K + L +V+C +V
Sbjct: 98 CL-----DIQVRETQALILAPTRELAVQIQKGLLALGDY--MNVQCHACIGGTNVGEDIR 150
Query: 139 LLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK 198
L +V TP R ++ ++L +++++++DEAD + + G+++ + V ++LP
Sbjct: 151 KLDYGQHVVAGTPGRVFDMIRRRSLRT-RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP 209
Query: 199 LYQAILASATLSEDVLSLKHLILRNPVI--LKLEEPAIAPVSQLAHYHILAQEDEKATIL 256
Q +L SATL ++L + + + +P+ +K +E + + Q + + +E+ K L
Sbjct: 210 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQ--FFVAVEREEWKFDTL 267
Query: 257 YTLL-KLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQG 315
L L + Q +IF NT K L + + + ++ ++P K R + +F G
Sbjct: 268 CDLYDTLTITQ--AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG 325
Query: 316 LYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIH 375
V+I++D A RG+D VS +IN+D P + + YIH
Sbjct: 326 ASRVLISTDVWA-----------------------RGLDVPQVSLIINYDLPNNRELYIH 362
Query: 376 RAGRTARGKNQGTALSFVSLREQDLMND 403
R GR+ R +G A++FV + ++ D
Sbjct: 363 RIGRSGRYGRKGVAINFVKNDDIRILRD 390
>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 = 250 bits (641), Expect = 5e-78
Identities = 110/399 (27%), Positives = 192/399 (48%), Gaps = 50/399 (12%)
Query: 16 YFELPFTFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAF 72
+ E+ +F + L+ I G+ +P+ IQ+RAI ++ DV+ +A++G+GKT F
Sbjct: 35 WNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF 94
Query: 73 AIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV------D 126
AI ++Q+I ++ T+ALVL+P++EL Q+ K + L C +
Sbjct: 95 AISILQQI-----ELDLKATQALVLAPTRELAQQIQKVVMALGDYM--GASCHACIGGTN 147
Query: 127 ISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYE 186
+ +V + L +E P I+V TP R L + L +++ ++DEAD + S G++
Sbjct: 148 VRAEV-----QKLQMEAPHIIVGTPGRVFDMLNRRYLSP-KYIKMFVLDEADEMLSRGFK 201
Query: 187 DDMKAVLKFLPKLYQAILASATLSEDVLSLKHLILRNPVI--LKLEEPAIAPVSQLAHYH 244
D + + + L Q +L SAT+ DVL + +R+P+ +K EE + + Q Y
Sbjct: 202 DQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQ--FYI 259
Query: 245 ILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKA 304
+ +E+ K L L + + + +IF+NT K L + + ++ ++ K
Sbjct: 260 NVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE 318
Query: 305 RCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINF 364
R + +F G V+I +D A RGID Q VS VIN+
Sbjct: 319 RDVIMREFRSGSSRVLITTDLLA-----------------------RGIDVQQVSLVINY 355
Query: 365 DFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
D P + + YIHR GR R +G A++ V+ ++ + D
Sbjct: 356 DLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRD 394
>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 = 248 bits (637), Expect = 1e-77
Identities = 114/387 (29%), Positives = 184/387 (47%), Gaps = 40/387 (10%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
F + L+ + G+ EP+ IQ+RAI I++ DVL +A++G+GKTG F+I +Q
Sbjct: 22 KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 81
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEP 138
+I V+ +AL+L+P++EL Q+ K + L D+K
Sbjct: 82 RI-----DTSVKAPQALMLAPTRELALQIQKVVMALAFHM--DIKVHACIGGTSFVEDAE 134
Query: 139 LLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK 198
L IVV TP R +++ + +++ I+DEAD + S G+++ + + LP
Sbjct: 135 GL-RDAQIVVGTPGRVFDNIQRRRFRT-DKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 192
Query: 199 LYQAILASATLSEDVLSLKHLILRNPVI--LKLEEPAIAPVSQLAHYHILAQEDEKATIL 256
Q +L SAT+ DVL + +RNPV +K +E + + Q Y + +E+ K L
Sbjct: 193 TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQ--FYVNVEEEEYKYECL 250
Query: 257 YTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGL 316
L V +IF NT K +L L K + + S+LP + R + +F G
Sbjct: 251 TDLYDSISVTQ-AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGS 309
Query: 317 YDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHR 376
++I++D A RGID Q VS VIN+D P + + YIHR
Sbjct: 310 SRILISTDLLA-----------------------RGIDVQQVSLVINYDLPANKENYIHR 346
Query: 377 AGRTARGKNQGTALSFVSLREQDLMND 403
GR R +G A++FV+ + M +
Sbjct: 347 IGRGGRFGRKGVAINFVTNEDVGAMRE 373
>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 = 248 bits (634), Expect = 2e-75
Identities = 90/402 (22%), Positives = 174/402 (43%), Gaps = 57/402 (14%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNK--DVLVRARTGSGKTGAFAIPMIQKIINLKQTA 87
+AI ++ + T +Q++ I IL ++ DV+ RA+TG+GKT AF IP+ Q +IN K +
Sbjct: 84 HKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS 143
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELT--MKCSRDVKCV------DISEQVDVSVQEPL 139
Q KA++++P+++L Q+ ++++ + CV D +
Sbjct: 144 Q-YMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAA-----MNKM 197
Query: 140 LVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK- 198
RP+IV+ATP R + L+ + ++ ++DEAD + G+ DD++ + L +
Sbjct: 198 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEK 257
Query: 199 ------LYQAILASATLSEDVLSLKHLILRNPVILKL---EEPAIAPVSQLAHYHILAQE 249
+ +L SATL + V L + I+ L L ++ ++ +++++
Sbjct: 258 NSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK 317
Query: 250 DEK-ATILYTLLKLNLVQ----GKTIIFVNT---VDKCYKLKLYLEQFKISTCVLNSELP 301
+K + + K IIF T + + + + ++
Sbjct: 318 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKIT 377
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
R V +F + +++ +D A RG+DF V V
Sbjct: 378 QNKRTSLVKRFKKDESGILVCTDVGA-----------------------RGMDFPNVHEV 414
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
+ P ++ YIHR GRTAR +G+++ F+ E + +
Sbjct: 415 LQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRE 456
>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 = 247 bits (632), Expect = 4e-75
Identities = 90/402 (22%), Positives = 174/402 (43%), Gaps = 57/402 (14%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNK--DVLVRARTGSGKTGAFAIPMIQKIINLKQTA 87
+AI ++ + T +Q++ I IL ++ DV+ RA+TG+GKT AF IP+ Q +IN K +
Sbjct: 33 HKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS 92
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELT--MKCSRDVKCV------DISEQVDVSVQEPL 139
Q KA++++P+++L Q+ ++++ + CV D +
Sbjct: 93 Q-YMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAA-----MNKM 146
Query: 140 LVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK- 198
RP+IV+ATP R + L+ + ++ ++DEAD + G+ DD++ + L +
Sbjct: 147 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEK 206
Query: 199 ------LYQAILASATLSEDVLSLKHLILRNPVILKL---EEPAIAPVSQLAHYHILAQE 249
+ +L SATL + V L + I+ L L ++ ++ +++++
Sbjct: 207 NSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK 266
Query: 250 DEK-ATILYTLLKLNLVQ----GKTIIFVNT---VDKCYKLKLYLEQFKISTCVLNSELP 301
+K + + K IIF T + + + + ++
Sbjct: 267 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKIT 326
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
R V +F + +++ +D A RG+DF V V
Sbjct: 327 QNKRTSLVKRFKKDESGILVCTDVGA-----------------------RGMDFPNVHEV 363
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
+ P ++ YIHR GRTAR +G+++ F+ E + +
Sbjct: 364 LQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRE 405
>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 = 240 bits (614), Expect = 2e-74
Identities = 97/389 (24%), Positives = 179/389 (46%), Gaps = 39/389 (10%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
F F + L+AI G+ P+ +Q IP + DVL +A++G GKT F + +Q
Sbjct: 9 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEP 138
++ + LV+ ++EL Q+ K + + K +VK + + E
Sbjct: 69 QL-----EPVTGQVSVLVMCHTRELAFQISKEYERFS-KYMPNVKVAVFFGGLSIKKDEE 122
Query: 139 LLVER-PDIVVATPARALAHLKAKTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKFL 196
+L + P IVV TP R LA + K+L+L ++ I+DE D ++ D++ + +
Sbjct: 123 VLKKNCPHIVVGTPGRILALARNKSLNL-KHIKHFILDECDKMLEQLDMRRDVQEIFRMT 181
Query: 197 PKLYQAILASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATIL 256
P Q ++ SATLS+++ + +++P+ + +++ + L Y++ +++EK L
Sbjct: 182 PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKL 241
Query: 257 YTLL-KLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQG 315
+ LL L Q +IFV +V +C L L + ++ +P + R QF
Sbjct: 242 FDLLDVLEFNQ--VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF 299
Query: 316 LYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIH 375
+++A++ RG+D + V+ N+D P D Y+H
Sbjct: 300 QRRILVATNLFG-----------------------RGMDIERVNIAFNYDMPEDSDTYLH 336
Query: 376 RAGRTARGKNQGTALSFVSL-REQDLMND 403
R R R +G A++FVS + ++ND
Sbjct: 337 RVARAGRFGTKGLAITFVSDENDAKILND 365
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 241 bits (618), Expect = 1e-73
Identities = 101/375 (26%), Positives = 172/375 (45%), Gaps = 56/375 (14%)
Query: 44 IQERAIPLILQN--KDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSK 101
IQE+A+PL+L N ++++ ++++G+GKT AFA+ M+ ++ A V + +A+ L+PS+
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRV-----DASVPKPQAICLAPSR 199
Query: 102 ELCNQLHKNIQELTMKCSRDVKCV-DISEQVDVSVQEPLLVERPDIVVATPARALAHLKA 160
EL Q+ + E+ +VK I + IV+ TP + +K
Sbjct: 200 ELARQIMDVVTEMGKYT--EVKTAFGIKDS-----VPKGAKIDAQIVIGTPGTVMDLMKR 252
Query: 161 KTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKHL 219
+ LD +++ ++DEAD ++ G D + LP+ Q +L SAT SE V
Sbjct: 253 RQLDA-RDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSERVEKYAER 311
Query: 220 ILRNPVILKL--EEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVD 277
N ++L EE ++ + QL Y E+ K +L L L L G++IIF D
Sbjct: 312 FAPNANEIRLKTEELSVEGIKQL--YMDCQSEEHKYNVLVELYGL-LTIGQSIIFCKKKD 368
Query: 278 KCYKL--KLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINS 335
++ ++ + ++ L L R + F G V++ ++ A
Sbjct: 369 TAEEIARRMTADGHTVA--CLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIA-------- 418
Query: 336 TNNRKRKRDKESGVSRGIDFQFVSNVINFDFPL------DIQCYIHRAGRTARGKNQGTA 389
RGID V+ V+N+D PL D Q Y+HR GRT R G +
Sbjct: 419 ---------------RGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVS 463
Query: 390 LSFVSLREQ-DLMND 403
++FV ++ + MN
Sbjct: 464 INFVHDKKSWEEMNA 478
>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 = 228 bits (584), Expect = 3e-70
Identities = 100/379 (26%), Positives = 178/379 (46%), Gaps = 49/379 (12%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNK-DVLVRARTGSGKTGAFAIPMIQKIINLKQTAQ 88
L AI G+ +PT IQ + IPL L ++ +++ +ARTGSGKT +FAIP+I+ + N +
Sbjct: 18 LNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELV-NENNGIE 76
Query: 89 VQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV----DISEQVDVSVQEPLLVERP 144
A++L+P++EL Q+ I+ L + + + I Q+ ++
Sbjct: 77 -----AIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIK-------ALKNA 124
Query: 145 DIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAIL 204
+IVV TP R L H+ TL+L +++ I+DEAD + + G+ D++ +L K + +L
Sbjct: 125 NIVVGTPGRILDHINRGTLNL-KNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILL 183
Query: 205 ASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNL 264
SAT+ ++L+L + + +K + + ++ E+E+ L LLK
Sbjct: 184 FSATMPREILNLAKKYMGDYSFIK-----AKINANIEQSYVEVNENERFEALCRLLKNK- 237
Query: 265 VQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASD 324
+ ++F T +L L ++ +L R + F Q ++IA+D
Sbjct: 238 -EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD 296
Query: 325 EKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGK 384
+ RGID ++ VIN+ P + + Y+HR GRT R
Sbjct: 297 VMS-----------------------RGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAG 333
Query: 385 NQGTALSFVSLREQDLMND 403
+G A+S ++ RE +
Sbjct: 334 KKGKAISIINRREYKKLRY 352
>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 = 226 bits (580), Expect = 5e-70
Identities = 118/374 (31%), Positives = 186/374 (49%), Gaps = 50/374 (13%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
QAI ++G+ T +Q + IPL+LQ K+V+VRA+TGSGKT A+AIP+++ +
Sbjct: 6 EQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGM-------- 57
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
K+LV++P++EL Q+ +I+++ D K ++ + Q + DIVVA
Sbjct: 58 ---KSLVVTPTRELTRQVASHIRDIGRY--MDTKVAEVYGGMPYKAQINRV-RNADIVVA 111
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP R L +DL SS EIVIIDEADL+F G+ DD+K +L L SAT+
Sbjct: 112 TPGRLLDLWSKGVIDL-SSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATI 170
Query: 210 SEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKT 269
E++ + + N ++ +A V + ++D ++ L+ N +G
Sbjct: 171 PEEIRKVVKDFITNYEEIEA-CIGLANVEH---KFVHVKDDWRS--KVQALRENKDKG-V 223
Query: 270 IIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALE 329
I+FV T ++ KL + + L +LP R + F +G YD++I +D +
Sbjct: 224 IVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS-- 277
Query: 330 TPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTA 389
RG+D V VINFD P D++ YIHR GRT R +G A
Sbjct: 278 ---------------------RGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEA 316
Query: 390 LSFVSLREQDLMND 403
++F+ E L +
Sbjct: 317 ITFIL-NEYWLEKE 329
>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 = 225 bits (575), Expect = 2e-68
Identities = 101/388 (26%), Positives = 183/388 (47%), Gaps = 64/388 (16%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQN--KDVLVRARTGSGKTGAFAIPMIQKIINLKQTA 87
LQ + +G+ P+ IQE A+PL+L ++++ ++++G+GKT AF + M+ ++
Sbjct: 37 LQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV-----EP 91
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV------DISEQVDVSVQEPLLV 141
+ + L LSP+ EL Q K I+++ K ++K + +S Q
Sbjct: 92 ANKYPQCLCLSPTYELALQTGKVIEQMG-KFYPELKLAYAVRGNKLERGQKISEQ----- 145
Query: 142 ERPDIVVATPARALAHL-KAKTLDLKSSLEIVIIDEADLVFSF-GYEDDMKAVLKFLPKL 199
IV+ TP L K K +D +++ ++DEAD++ + G++D + + LP+
Sbjct: 146 ----IVIGTPGTVLDWCSKLKFIDP-KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN 200
Query: 200 YQAILASATLSEDVLSLKHLILRNPVILKL--EEPAIAPVSQLAHYHILAQEDEKATILY 257
Q +L SAT + V ++ +P ++KL EE + + Q +Y + + DEK L
Sbjct: 201 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQ--YYVLCSSRDEKFQALC 258
Query: 258 TLLKLNLVQGKTIIFVNTVDKCYKL--KLYLEQFKISTCVLNSELPAKARCHAVYQFNQG 315
L + + +IF +T L +L E +++ +L+ E+ + R + +F +G
Sbjct: 259 NLYGAITI-AQAMIFCHTRKTASWLAAELSKEGHQVA--LLSGEMMVEQRAAVIERFREG 315
Query: 316 LYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQC--- 372
V++ ++ A RGID + VS VINFD P+D
Sbjct: 316 KEKVLVTTNVCA-----------------------RGIDVEQVSVVINFDLPVDKDGNPD 352
Query: 373 ---YIHRAGRTARGKNQGTALSFVSLRE 397
Y+HR GRT R +G A++ V +
Sbjct: 353 NETYLHRIGRTGRFGKRGLAVNMVDSKH 380
>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 = 222 bits (569), Expect = 1e-67
Identities = 106/387 (27%), Positives = 178/387 (45%), Gaps = 63/387 (16%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQN--KDVLVRARTGSGKTGAFAIPMIQKIINLKQTA 87
L+ I + + +P+ IQERA+PL+L N ++++ ++++G+GKT AF++ M+ ++
Sbjct: 17 LKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV-----NP 71
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV-------DISEQVDVSVQEPLL 140
+ +A+ L+PS+EL Q + +QE+ + + ++Q+
Sbjct: 72 EDASPQAICLAPSRELARQTLEVVQEMGKFT--KITSQLIVPDSFEKNKQI--------- 120
Query: 141 VERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKFLPKL 199
++V TP L ++ K + L ++I ++DEAD ++ G D V +FLPK
Sbjct: 121 --NAQVIVGTPGTVLDLMRRKLMQL-QKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKD 177
Query: 200 YQAILASATLSEDVLSLKHLILRNPVILKL--EEPAIAPVSQLAHYHILAQEDEKATILY 257
Q +L SAT ++ V I+ N L+L E + + QL Y E +K +L
Sbjct: 178 TQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQL--YMDCKNEADKFDVLT 235
Query: 258 TLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLY 317
L L + G +IIFV T L L+ +L+ +L + R + F +G
Sbjct: 236 ELYGLMTI-GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRS 294
Query: 318 DVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPL------DIQ 371
V+I ++ A RGID VS V+N+D P D
Sbjct: 295 KVLITTNVLA-----------------------RGIDIPTVSMVVNYDLPTLANGQADPA 331
Query: 372 CYIHRAGRTARGKNQGTALSFVSLREQ 398
YIHR GRT R +G A+SFV +
Sbjct: 332 TYIHRIGRTGRFGRKGVAISFVHDKNS 358
>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 = 222 bits (567), Expect = 2e-66
Identities = 101/388 (26%), Positives = 183/388 (47%), Gaps = 64/388 (16%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQN--KDVLVRARTGSGKTGAFAIPMIQKIINLKQTA 87
LQ + +G+ P+ IQE A+PL+L ++++ ++++G+GKT AF + M+ ++
Sbjct: 104 LQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV-----EP 158
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV------DISEQVDVSVQEPLLV 141
+ + L LSP+ EL Q K I+++ K ++K + +S Q
Sbjct: 159 ANKYPQCLCLSPTYELALQTGKVIEQMG-KFYPELKLAYAVRGNKLERGQKISEQ----- 212
Query: 142 ERPDIVVATPARALAHL-KAKTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKFLPKL 199
IV+ TP L K K +D +++ ++DEAD ++ + G++D + + LP+
Sbjct: 213 ----IVIGTPGTVLDWCSKLKFIDP-KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN 267
Query: 200 YQAILASATLSEDVLSLKHLILRNPVILKL--EEPAIAPVSQLAHYHILAQEDEKATILY 257
Q +L SAT + V ++ +P ++KL EE + + Q +Y + + DEK L
Sbjct: 268 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQ--YYVLCSSRDEKFQALC 325
Query: 258 TLLKLNLVQGKTIIFVNTVDKCYKL--KLYLEQFKISTCVLNSELPAKARCHAVYQFNQG 315
L + + +IF +T L +L E +++ +L+ E+ + R + +F +G
Sbjct: 326 NLYGA-ITIAQAMIFCHTRKTASWLAAELSKEGHQVA--LLSGEMMVEQRAAVIERFREG 382
Query: 316 LYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQC--- 372
V++ ++ A RGID + VS VINFD P+D
Sbjct: 383 KEKVLVTTNVCA-----------------------RGIDVEQVSVVINFDLPVDKDGNPD 419
Query: 373 ---YIHRAGRTARGKNQGTALSFVSLRE 397
Y+HR GRT R +G A++ V +
Sbjct: 420 NETYLHRIGRTGRFGKRGLAVNMVDSKH 447
>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 = 187 bits (478), Expect = 5e-54
Identities = 95/373 (25%), Positives = 169/373 (45%), Gaps = 37/373 (9%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
+ + K G+ PT IQ+ +IP+I +D++ A+TGSGKT AF +P++ K++ ++
Sbjct: 68 IDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELEL 127
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
+ +++SP++EL Q+ ++ S +K + Q + +V+A
Sbjct: 128 GRPQVVIVSPTRELAIQIFNEARKFA-FESY-LKIGIVYGGTSFRHQNECITRGCHVVIA 185
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKF--LPKLYQAILASA 207
TP R L + + V++DEAD + G+ +DM+ ++ + +Q ++ SA
Sbjct: 186 TPGRLLDFVDRTFITF-EDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSA 244
Query: 208 TLSEDVLSLKHLILRNPVILKL--EEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLV 265
T E++ + L+N V + + A + V Q + + K + L + L+
Sbjct: 245 TFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYE---VNKYAKRSKLIEI--LSEQ 299
Query: 266 QGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDE 325
TI+FV T L +L + + T ++ + R A+ F G V+IA+
Sbjct: 300 ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS- 358
Query: 326 KALETPQINSTNNRKRKRDKESGV-SRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGK 384
V SRG+D + + +VIN+D P I Y+HR GRT R
Sbjct: 359 -----------------------VASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
Query: 385 NQGTALSFVSLRE 397
N G A SF +
Sbjct: 396 NNGRATSFFDPEK 408
>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 = 181 bits (461), Expect = 8e-54
Identities = 67/205 (32%), Positives = 113/205 (55%), Gaps = 6/205 (2%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+ + + + T IQ++ I L LQ KDVL A+TGSGKT AF +P+++ + L+ T+
Sbjct: 37 LKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTST- 95
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
L++SP++EL Q + ++++ K + D I D+ + + +I+V
Sbjct: 96 DGLGVLIISPTRELAYQTFEVLRKV-GK-NHDFSAGLIIGGKDLKHEAERI-NNINILVC 152
Query: 150 TPARALAHLK-AKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASAT 208
TP R L H+ + L+++++DEAD + G+ D M AV++ LPK Q +L SAT
Sbjct: 153 TPGRLLQHMDETVSFHAT-DLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSAT 211
Query: 209 LSEDVLSLKHLILRNPVILKLEEPA 233
++ V L L L+NP + + E A
Sbjct: 212 QTKSVKDLARLSLKNPEYVWVHEKA 236
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 185 bits (471), Expect = 3e-53
Identities = 104/403 (25%), Positives = 181/403 (44%), Gaps = 68/403 (16%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKII-------- 81
+ I + PT +Q+ AIP+I + +D++ A+TGSGKT AF +P++ +I
Sbjct: 27 MGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEAL 86
Query: 82 -----NLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSR--DVKCV------DIS 128
N + + Q +LVL+P++EL Q I E K S V+ DI
Sbjct: 87 RAMKENGRYGRRKQYPISLVLAPTRELAVQ----IYEEARKFSYRSRVRPCVVYGGADIG 142
Query: 129 EQVDVSVQEPLLVER-PDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYED 187
+Q+ +ER ++VATP R + ++ + L + +++DEAD + G+E
Sbjct: 143 QQIRD-------LERGCHLLVATPGRLVDMMERGKIGL-DFCKYLVLDEADRMLDMGFEP 194
Query: 188 DMKAVLKFL---PKLY-QAILASATLSEDVLSLKHLILRNPVILKL--EEPAIAPVSQLA 241
++ +++ PK ++ SAT +++ L L + L + ++Q
Sbjct: 195 QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKV 254
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
+ +E +K + L LL T++FV T L+ +L + ++ +
Sbjct: 255 VW---VEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRS 311
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGV-SRGIDFQFVSN 360
+ R A++QF G +++A+ V +RG+D V +
Sbjct: 312 QRDREEALHQFRSGKSPILVATA------------------------VAARGLDISNVKH 347
Query: 361 VINFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
VINFD P DI+ Y+HR GRT R N G A SF + R ++ D
Sbjct: 348 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKD 390
>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 = 179 bits (457), Expect = 3e-53
Identities = 72/197 (36%), Positives = 117/197 (59%), Gaps = 9/197 (4%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
+A +LGW +PT IQ AIPL LQ +D++ A TGSGKTGAFA+P++ ++ Q
Sbjct: 55 CEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLF- 113
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
ALVL+P++EL Q+ + + L S V+ I +D Q L ++P I++A
Sbjct: 114 ----ALVLTPTRELAFQISEQFEALGS--SIGVQSAVIVGGIDSMSQSLALAKKPHIIIA 167
Query: 150 TPARALAHLK-AKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASAT 208
TP R + HL+ K +L +L+ +++DEAD + + +E ++ +LK +P+ + L SAT
Sbjct: 168 TPGRLIDHLENTKGFNL-RALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSAT 226
Query: 209 LSEDVLSLKHLILRNPV 225
+++ V L+ L+NPV
Sbjct: 227 MTKKVQKLQRAALKNPV 243
>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 = 170 bits (432), Expect = 5e-50
Identities = 57/207 (27%), Positives = 109/207 (52%), Gaps = 10/207 (4%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
F +C+ L I ++GW +P+ IQE +IP+ L +D+L RA+ G+GK+GA+ IP+++
Sbjct: 4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEP 138
++ + +A+V+ P++EL Q+ + +++ K K + + ++
Sbjct: 64 RL-----DLKKDNIQAMVIVPTRELALQVSQICIQVS-KHMGGAKVMATTGGTNLRDDIM 117
Query: 139 LLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK 198
L + +V+ATP R L +K + ++++++DEAD + S + M+ ++ LPK
Sbjct: 118 RLDDTVHVVIATPGRILDLIKKGVAKV-DHVQMIVLDEADKLLSQDFVQIMEDIILTLPK 176
Query: 199 LYQAILASATLSEDVLSLKHLILRNPV 225
Q +L SAT V + L P
Sbjct: 177 NRQILLYSATFPLSVQKFMNSHLEKPY 203
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 170 bits (433), Expect = 5e-50
Identities = 57/204 (27%), Positives = 109/204 (53%), Gaps = 8/204 (3%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
++AI L + +PT IQER IP L+ + ++ +++TG+GKT A+ +P+++KI +
Sbjct: 16 IEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKI-----KPER 70
Query: 90 QETKALVLSPSKELCNQLHKNIQELT--MKCSRDVKCVDISEQVDVSVQEPLLVERPDIV 147
E +A++ +P++EL Q++ ++T R + + D L +P IV
Sbjct: 71 AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIV 130
Query: 148 VATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASA 207
+ TP R ++ + LD+ + I+++DEADL+ G+ D+ + +PK Q ++ SA
Sbjct: 131 IGTPGRINDFIREQALDV-HTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSA 189
Query: 208 TLSEDVLSLKHLILRNPVILKLEE 231
T+ E + + NP + + E
Sbjct: 190 TIPEKLKPFLKKYMENPTFVHVLE 213
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 176 bits (447), Expect = 7e-50
Identities = 65/403 (16%), Positives = 129/403 (32%), Gaps = 72/403 (17%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
K + T Q I+Q K + A TG GKT + +
Sbjct: 11 RSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-------- 62
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLL----VERPD 145
+ K+ ++ P+ L Q + +Q+L VK + +E +
Sbjct: 63 KGKKSALVFPTVTLVKQTLERLQKL---ADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYH 119
Query: 146 IVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILA 205
I+V + + + L + V +D+ D V D ++ +P+
Sbjct: 120 ILVFSTQFVSKNR--EKLSQ-KRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAF 176
Query: 206 SATLSEDVLSLKHLILRNPVILK-------------LEEPAIAPVSQLAHYH-------I 245
S + + +++ + V +L I
Sbjct: 177 STIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRI 236
Query: 246 LAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKAR 305
++ EK L L + + +IF T ++ +L YL++FK + SE
Sbjct: 237 SSRSKEKLVEL-----LEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----F 286
Query: 306 CHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDF-QFVSNVINF 364
F G +++I ++RG+D + + VI +
Sbjct: 287 EKNFEDFKVGKINILIGVQA-------------------YYGKLTRGVDLPERIKYVIFW 327
Query: 365 DFP--LDIQCYIHRAGRTARGKNQG--TALSFVSLREQDLMND 403
P D+ YI +GR++R N +S + ++++
Sbjct: 328 GTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFES 370
>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 = 170 bits (432), Expect = 2e-49
Identities = 67/196 (34%), Positives = 109/196 (55%), Gaps = 5/196 (2%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+AI ++G+ T IQ ++I +L+ +D+L A+TGSGKT AF IP ++ I+ L+ +
Sbjct: 66 LKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPR- 124
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
T L+LSP++EL Q ++EL M I + S + L +I+VA
Sbjct: 125 NGTGVLILSPTRELAMQTFGVLKEL-MT-HHVHTYGLIMGGSNRSAEAQKLGNGINIIVA 182
Query: 150 TPARALAHLK-AKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASAT 208
TP R L H++ K +L+ ++IDEAD + G+E+++K ++K LP Q +L SAT
Sbjct: 183 TPGRLLDHMQNTPGFMYK-NLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSAT 241
Query: 209 LSEDVLSLKHLILRNP 224
+ V L + L+
Sbjct: 242 QTRKVEDLARISLKKE 257
>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 = 167 bits (425), Expect = 6e-49
Identities = 71/199 (35%), Positives = 117/199 (58%), Gaps = 7/199 (3%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+A+ G PT IQ A+PL L+ KD++ +ARTG+GKT AFA+P+ +++ +
Sbjct: 13 LEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL--APSQERG 70
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
++ +ALVL+P++EL Q+ + + + +K V + Q+ L+ D VVA
Sbjct: 71 RKPRALVLTPTRELALQVASELTAV----APHLKVVAVYGGTGYGKQKEALLRGADAVVA 126
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP RAL +L+ LDL S +E+ ++DEAD + S G+E++++A+L P Q +L SATL
Sbjct: 127 TPGRALDYLRQGVLDL-SRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATL 185
Query: 210 SEDVLSLKHLILRNPVILK 228
L ++NPV++
Sbjct: 186 PSWAKRLAERYMKNPVLIN 204
>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 = 164 bits (418), Expect = 1e-47
Identities = 62/205 (30%), Positives = 111/205 (54%), Gaps = 15/205 (7%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+ I G+ +P+ IQ+RAI ++ DV+ +A++G+GKT FAI ++Q++ +
Sbjct: 42 LRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQL-----EIEF 96
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV----DISEQVDVSVQEPLLVERPD 145
+ET+ALVL+P++EL Q+ K I L ++ ++ + L E P
Sbjct: 97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEM-----QKLQAEAPH 151
Query: 146 IVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILA 205
IVV TP R L + L +++ ++DEAD + S G++D + + + L Q +L
Sbjct: 152 IVVGTPGRVFDMLNRRYLSP-KWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLL 210
Query: 206 SATLSEDVLSLKHLILRNPVILKLE 230
SAT+ DVL + +R+P+ + ++
Sbjct: 211 SATMPTDVLEVTKKFMRDPIRILVK 235
>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 = 163 bits (416), Expect = 2e-47
Identities = 51/215 (23%), Positives = 102/215 (47%), Gaps = 12/215 (5%)
Query: 20 PFTFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPM 76
P F + L+ + G+ P+ +Q +AIPL D++V+A++G+GKT F+
Sbjct: 23 PADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIA 82
Query: 77 IQKIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQ 136
+ + + T+ L+L+P++E+ Q+H I + ++C +S
Sbjct: 83 LDSL-----VLENLSTQILILAPTREIAVQIHSVITAIG-IKMEGLECHVFIGGTPLSQD 136
Query: 137 EPLLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFG-YEDDMKAVLKF 195
+ L ++ I V +P R ++ L+ S+ + I+DEAD + G +++ + +
Sbjct: 137 KTRL-KKCHIAVGSPGRIKQLIELDYLNP-GSIRLFILDEADKLLEEGSFQEQINWIYSS 194
Query: 196 LPKLYQAILASATLSEDVLSLKHLILRNPVILKLE 230
LP Q + SAT E + + +R+P ++L
Sbjct: 195 LPASKQMLAVSATYPEFLANALTKYMRDPTFVRLN 229
>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 = 162 bits (413), Expect = 4e-47
Identities = 63/201 (31%), Positives = 107/201 (53%), Gaps = 9/201 (4%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+ + G+ EP+ IQ+RAI I++ DVL +A++G+GKTG F+I +Q+I V
Sbjct: 26 LRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI-----DTSV 80
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
+ +AL+L+P++EL Q+ K + L D+K L IVV
Sbjct: 81 KAPQALMLAPTRELALQIQKVVMALAFHM--DIKVHACIGGTSFVEDAEGL-RDAQIVVG 137
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP R +++ + +++ I+DEAD + S G+++ + + LP Q +L SAT+
Sbjct: 138 TPGRVFDNIQRRRFRT-DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATM 196
Query: 210 SEDVLSLKHLILRNPVILKLE 230
DVL + +RNPV + ++
Sbjct: 197 PNDVLEVTTKFMRNPVRILVK 217
>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 = 157 bits (399), Expect = 5e-45
Identities = 56/212 (26%), Positives = 104/212 (49%), Gaps = 12/212 (5%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
F F + L+AI G+ P+ +Q IP + DVL +A++G GKT F + +Q
Sbjct: 15 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEP 138
++ + LV+ ++EL Q+ K + + K +VK + + E
Sbjct: 75 QL-----EPVTGQVSVLVMCHTRELAFQISKEYERFS-KYMPNVKVAVFFGGLSIKKDEE 128
Query: 139 LLVER-PDIVVATPARALAHLKAKTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKFL 196
+L + P IVV TP R LA + K+L+L ++ I+DE D ++ D++ + +
Sbjct: 129 VLKKNCPHIVVGTPGRILALARNKSLNL-KHIKHFILDECDKMLEQLDMRRDVQEIFRMT 187
Query: 197 PKLYQAILASATLSEDVLSLKHLILRNPVILK 228
P Q ++ SATLS+++ + +++P+ +
Sbjct: 188 PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF 219
>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 = 154 bits (390), Expect = 6e-43
Identities = 56/211 (26%), Positives = 108/211 (51%), Gaps = 26/211 (12%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQN--KDVLVRARTGSGKTGAFAIPMIQKIINLKQTA 87
LQ + +G+ P+ IQE A+PL+L ++++ ++++G+GKT AF + M+ ++
Sbjct: 104 LQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV-----EP 158
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV------DISEQVDVSVQEPLLV 141
+ + L LSP+ EL Q K I+++ K ++K + +S Q
Sbjct: 159 ANKYPQCLCLSPTYELALQTGKVIEQMG-KFYPELKLAYAVRGNKLERGQKISEQ----- 212
Query: 142 ERPDIVVATPARALAHL-KAKTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKFLPKL 199
IV+ TP L K K +D +++ ++DEAD ++ + G++D + + LP+
Sbjct: 213 ----IVIGTPGTVLDWCSKLKFIDP-KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN 267
Query: 200 YQAILASATLSEDVLSLKHLILRNPVILKLE 230
Q +L SAT + V ++ +P ++KL+
Sbjct: 268 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLK 298
>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 = 145 bits (368), Expect = 3e-40
Identities = 60/222 (27%), Positives = 115/222 (51%), Gaps = 12/222 (5%)
Query: 10 PTLIQVYFELPFTFTLFCIPLQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKT 69
P I + +L + + LQ I G+ PT IQ +AIP++L +++L A TGSGKT
Sbjct: 21 PDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKT 80
Query: 70 GAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISE 129
AF+IP++ ++ + + +AL++SP++EL +Q+H+ + +++ + + + I +
Sbjct: 81 LAFSIPILMQL----KQPANKGFRALIISPTRELASQIHRELIKIS-EGTG-FRIHMIHK 134
Query: 130 QVDVSVQEPLLVERP-DIVVATPARALAHLKAKTLDLK-SSLEIVIIDEADLVF---SFG 184
+ + + DI+V TP R + LK + +S+E +++DE+D +F G
Sbjct: 135 AAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTG 194
Query: 185 YEDDMKAVLKFL-PKLYQAILASATLSEDVLSLKHLILRNPV 225
+ D + ++ + + SAT + DV L L N +
Sbjct: 195 FRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVI 236
>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 = 139 bits (353), Expect = 2e-38
Identities = 56/205 (27%), Positives = 109/205 (53%), Gaps = 17/205 (8%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L++I ++G L+PT IQ +A P+ILQ D++V A+TG+GKT ++ +P + Q
Sbjct: 32 LKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL--DSQPISR 89
Query: 90 QETK---ALVLSPSKELCNQLHKNIQELTMKCSRDVKCV----DISEQVDVSVQEPLLVE 142
++ LVL+P++EL + + + K + + C+ + + Q++ + +
Sbjct: 90 EQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSI-CIYGGRNRNGQIED------ISK 142
Query: 143 RPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQA 202
DI++ATP R +++L S+ ++IDEAD + +E ++ +L + Q
Sbjct: 143 GVDIIIATPGRLNDLQMNNSVNL-RSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQT 201
Query: 203 ILASATLSEDVLSLKHLILRNPVIL 227
++ SAT + V L L++P+I+
Sbjct: 202 VMTSATWPDTVRQLALSYLKDPMIV 226
>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 = 130 bits (330), Expect = 6e-35
Identities = 55/217 (25%), Positives = 108/217 (49%), Gaps = 14/217 (6%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
F + I + PT IQ+ AIP IL+++D++ A+TGSGKT AF IP+I
Sbjct: 24 NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83
Query: 79 KII----NLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVS 134
++ N ++ ++ K L+L+P++EL Q+ Q+ + + ++ + D
Sbjct: 84 HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFS-LNTP-LRSCVVYGGADTH 141
Query: 135 VQEPLLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLK 194
Q + ++VATP R + ++ + L + +++DEAD + G+E ++ +++
Sbjct: 142 SQIREVQMGCHLLVATPGRLVDFIEKNKISL-EFCKYIVLDEADRMLDMGFEPQIRKIIE 200
Query: 195 F--LPKLY--QAILASATLSEDVLSLKHLILRNPVIL 227
+P Q ++ SAT +++ L L N + +
Sbjct: 201 ESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 237
>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 = 126 bits (318), Expect = 3e-33
Identities = 55/214 (25%), Positives = 100/214 (46%), Gaps = 16/214 (7%)
Query: 22 TFTLFCIP---LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQ 78
F P + IA+ + EPT IQ + P+ L D++ A+TGSGKT ++ +P I
Sbjct: 30 NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 89
Query: 79 KIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCV----DISEQVDVS 134
I + + LVL+P++EL Q+ + E C C+ Q+
Sbjct: 90 HINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRD- 148
Query: 135 VQEPLLVER-PDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVL 193
+ER +I +ATP R + L+ +L+ +++DEAD + G+E ++ ++
Sbjct: 149 ------LERGVEICIATPGRLIDFLECGKTNLR-RTTYLVLDEADRMLDMGFEPQIRKIV 201
Query: 194 KFLPKLYQAILASATLSEDVLSLKHLILRNPVIL 227
+ Q ++ SAT ++V L L++ + +
Sbjct: 202 DQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHI 235
>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 = 96.9 bits (242), Expect = 1e-23
Identities = 44/196 (22%), Positives = 77/196 (39%), Gaps = 42/196 (21%)
Query: 237 VSQLAHYHILAQEDEKATILYTLL-KLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCV 295
+ L Y++ +++EK L+ LL L Q +IFV +V +C L L +
Sbjct: 3 LHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQ--VVIFVKSVQRCIALAQLLVEQNFPAIA 60
Query: 296 LNSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDF 355
++ +P + R QF +++A++ RG+D
Sbjct: 61 IHRGMPQEERLSRYQQFKDFQRRILVATNLFG-----------------------RGMDI 97
Query: 356 QFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMNDGTALSFVSLREQ 415
+ V+ N+D P D Y+HR R R +G A++FVS +
Sbjct: 98 ERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN----------------DA 141
Query: 416 DLMNDVNEYLMTNLHE 431
++NDV + N+ E
Sbjct: 142 KILNDVQDRFEVNISE 157
>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 = 94.6 bits (236), Expect = 7e-23
Identities = 47/162 (29%), Positives = 74/162 (45%), Gaps = 24/162 (14%)
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
Y+ + K +L LLK ++I+FV ++ ++L +L + I+ C L E+
Sbjct: 7 WYYRADDLEHKTALLVHLLKQPEAT-RSIVFVRKRERVHELANWLREAGINNCYLEGEMV 65
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
R A+ + +G +V++A+D A RGID VS+V
Sbjct: 66 QGKRNEAIKRLTEGRVNVLVATDVAA-----------------------RGIDIPDVSHV 102
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
NFD P Y+HR GRTAR +GTA+S V + L+
Sbjct: 103 FNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGK 144
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 93.4 bits (233), Expect = 2e-22
Identities = 46/162 (28%), Positives = 72/162 (44%), Gaps = 24/162 (14%)
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
Y + +E+ K L L + + +IF NT K +L L K + + S+LP
Sbjct: 7 FYVNVEEEEYKYECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLP 65
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
+ R + +F G ++I++D A RGID Q VS V
Sbjct: 66 QQERDTIMKEFRSGSSRILISTDLLA-----------------------RGIDVQQVSLV 102
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
IN+D P + + YIHR GR R +G A++FV+ + M +
Sbjct: 103 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRE 144
>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 = 92.3 bits (230), Expect = 6e-22
Identities = 44/160 (27%), Positives = 71/160 (44%), Gaps = 25/160 (15%)
Query: 245 ILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKA 304
+ +E +K + L LL T++FV T L+ +L + ++ + +
Sbjct: 25 VWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRD 84
Query: 305 RCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGV-SRGIDFQFVSNVIN 363
R A++QF G +++A+ V +RG+D V +VIN
Sbjct: 85 REEALHQFRSGKSPILVATA------------------------VAARGLDISNVKHVIN 120
Query: 364 FDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
FD P DI+ Y+HR GRT R N G A SF + R ++ D
Sbjct: 121 FDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKD 160
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 89.9 bits (224), Expect = 2e-21
Identities = 45/162 (27%), Positives = 74/162 (45%), Gaps = 24/162 (14%)
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
H I +E+ K ++L +L IIF T + +L L+ ++ +
Sbjct: 12 HAVIQVREENKFSLLKDVLMTENPD-SCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMI 70
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
+ R + +F +G Y ++A+D A RGID + +S V
Sbjct: 71 QEDRFDVMNEFKRGEYRYLVATDVAA-----------------------RGIDIENISLV 107
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
IN+D PL+ + Y+HR GRT R N+G A+SFV+ E+ + D
Sbjct: 108 INYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLAD 149
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 90.0 bits (224), Expect = 5e-21
Identities = 38/153 (24%), Positives = 64/153 (41%), Gaps = 28/153 (18%)
Query: 248 QEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCH 307
+E+ K L L+ +IF + YL + ++ + R
Sbjct: 38 KEEAKMVYLLECLQKT--PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTK 95
Query: 308 AVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGV-SRGIDFQFVSNVINFDF 366
A+ F +G DV++A+D V S+G+DF + +VIN+D
Sbjct: 96 AIEAFREGKKDVLVATD------------------------VASKGLDFPAIQHVINYDM 131
Query: 367 PLDIQCYIHRAGRTARGKNQGTALSFVSLREQD 399
P +I+ Y+HR GRT N G A +F++ + D
Sbjct: 132 PEEIENYVHRIGRTGCSGNTGIATTFIN-KACD 163
>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 = 87.7 bits (218), Expect = 2e-20
Identities = 40/167 (23%), Positives = 66/167 (39%), Gaps = 30/167 (17%)
Query: 243 YHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPA 302
Y + +K L + + G+ IIF T L + + Q +L+ EL
Sbjct: 12 YVLCEHRKDKYQALCNIYGS-ITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTV 70
Query: 303 KARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVI 362
+ R + +F G V+I ++ A RGID + V+ V+
Sbjct: 71 EQRASIIQRFRDGKEKVLITTNVCA-----------------------RGIDVKQVTIVV 107
Query: 363 NFDFPL------DIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
NFD P+ D + Y+HR GRT R +G A + + + E +
Sbjct: 108 NFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMK 154
>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 = 83.1 bits (206), Expect = 2e-18
Identities = 33/162 (20%), Positives = 59/162 (36%), Gaps = 24/162 (14%)
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
+ A + +L LL + + ++F T + ++ L + L+ +L
Sbjct: 8 EEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLS 66
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
R + F QG V++A+D A RG+D V V
Sbjct: 67 QGERERVLGAFRQGEVRVLVATDVAA-----------------------RGLDIPQVDLV 103
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
+++ P + Y HR+GRT R G + RE+ +
Sbjct: 104 VHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEA 145
>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 = 83.6 bits (207), Expect = 5e-18
Identities = 32/162 (19%), Positives = 59/162 (36%), Gaps = 24/162 (14%)
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
+ A + +L LL + + ++F T + ++ L + L+ ++
Sbjct: 5 EEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMS 63
Query: 302 AKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNV 361
R + F QG V++A+D A RG+D V V
Sbjct: 64 QGERERVMGAFRQGEVRVLVATDVAA-----------------------RGLDIPQVDLV 100
Query: 362 INFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMND 403
+++ P + Y HR+GRT R G + RE+ +
Sbjct: 101 VHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEA 142
>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 = 57.5 bits (139), Expect = 1e-09
Identities = 34/138 (24%), Positives = 58/138 (42%), Gaps = 9/138 (6%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
Q L+ K++++ TGSGKT I K K+ + K +VL L
Sbjct: 38 QMEVAQPALEGKNIIICLPTGSGKT--RVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLV 95
Query: 105 NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATP---ARALAHLKAK 161
QL + + +K V + Q+ +S E +V+ DI+++T +L +L+
Sbjct: 96 EQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPE--VVKSCDIIISTAQILENSLLNLENG 153
Query: 162 TLDLK--SSLEIVIIDEA 177
S ++IIDE
Sbjct: 154 EDAGVQLSDFSLIIIDEC 171
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 60.0 bits (144), Expect = 1e-09
Identities = 31/140 (22%), Positives = 59/140 (42%), Gaps = 5/140 (3%)
Query: 39 LEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS 98
+P Q ++ K+ ++ A TG GKT + +LK+ Q Q+ K + +
Sbjct: 12 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEH---HLKKFPQGQKGKVVFFA 68
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHL 158
+ Q + + V + + +V V++ +VE DI++ TP + +L
Sbjct: 69 NQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQ--IVENNDIIILTPQILVNNL 126
Query: 159 KAKTLDLKSSLEIVIIDEAD 178
K T+ S ++I DE
Sbjct: 127 KKGTIPSLSIFTLMIFDECH 146
Score = 36.1 bits (82), Expect = 0.030
Identities = 29/184 (15%), Positives = 63/184 (34%), Gaps = 25/184 (13%)
Query: 352 GIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMNDGTALSFVS 411
GID + VI +++ ++ I GR R + L + + ++
Sbjct: 474 GIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLTSNAGVIEKEQ-------IN 525
Query: 412 LREQDLMNDVNEYLMTNLHEDDFIIKPYQFNLDEVKGFEYRAKDAWRSNYFEDNPTDLET 471
+ ++ +MND L T + + ++ + F +++ + ++N L
Sbjct: 526 MYKEKMMNDSILRLQTWDEA---VFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCR 582
Query: 472 LRHDKALYTVRIQSHLADVPDYIVPPALKKLARIEDDGDEDVRAEPITDEEYNKQYEEYK 531
A YT ++ + + Y V D KQ+ ++
Sbjct: 583 KCKALACYTADVR--VIEDCHYTVLG------------DAFKECFVSRPHPKPKQFSSFE 628
Query: 532 KRSK 535
KR+K
Sbjct: 629 KRAK 632
>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 = 59.0 bits (142), Expect = 2e-09
Identities = 36/200 (18%), Positives = 71/200 (35%), Gaps = 13/200 (6%)
Query: 33 IAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQET 92
+ + ++P + QE + + L+ TG GKT + ++
Sbjct: 2 VLRRDLIQPRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYRLTKYGG------- 53
Query: 93 KALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPA 152
K L+L+P+K L Q ++ + L + + + + + R ++VATP
Sbjct: 54 KVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKA---WARAKVIVATPQ 110
Query: 153 RALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSED 212
L A + L + +++ DEA + K K I +A+
Sbjct: 111 TIENDLLAGRISL-EDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGST 169
Query: 213 VLSLKHLILRNPVILKLEEP 232
+ +I N I +E
Sbjct: 170 PEKIMEVI-NNLGIEHIEYR 188
Score = 57.9 bits (139), Expect = 4e-09
Identities = 28/169 (16%), Positives = 56/169 (33%), Gaps = 35/169 (20%)
Query: 237 VSQLAHYHILAQEDEKATILYTLLKLNL---VQGKTIIFVNTVDKCYKLKLYLEQFKIST 293
+S L + + K L +++ L K I+F N + K+ L + I
Sbjct: 329 ISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKA 388
Query: 294 CVL--------NSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDK 345
+ L + + + +F +G ++V++A+
Sbjct: 389 KRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSV-------------------- 428
Query: 346 ESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTALSFVS 394
G+D V V+ ++ I R GRT R G + ++
Sbjct: 429 ---GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR-HMPGRVIILMA 473
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 59.1 bits (142), Expect = 2e-09
Identities = 29/139 (20%), Positives = 57/139 (41%), Gaps = 5/139 (3%)
Query: 39 LEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS 98
L+P Q + K+ ++ A TG GKT ++ + + LK+ Q+ K + +
Sbjct: 3 LKPRNYQLELALPAKKGKNTIICAPTGCGKT-FVSLLICEHH--LKKFPCGQKGKVVFFA 59
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHL 158
+ Q + ++ + + VSVQ ++E DI++ TP + +L
Sbjct: 60 NQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQH--IIEDNDIIILTPQILVNNL 117
Query: 159 KAKTLDLKSSLEIVIIDEA 177
+ S ++I DE
Sbjct: 118 NNGAIPSLSVFTLMIFDEC 136
Score = 33.3 bits (75), Expect = 0.23
Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 12/92 (13%)
Query: 352 GIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKN--------QGTALSF--VSLREQDLM 401
GID + VI +++ ++ I GR R ++ + ++ ++ +M
Sbjct: 465 GIDIAECNLVILYEYVGNVIKMIQTRGR-GRARDSKCFLLTSSADVIEKEKANMIKEKIM 523
Query: 402 NDGTALSFVSLREQDLMNDVNEYLMTNLHEDD 433
N+ + L + E V+ + D
Sbjct: 524 NE-SILRLQTWDEMKFGKTVHRIQVNEKLLRD 554
>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 = 59.7 bits (144), Expect = 2e-09
Identities = 51/311 (16%), Positives = 98/311 (31%), Gaps = 75/311 (24%)
Query: 5 LGWLE-PTLI--QVYF-ELPFTFTLFCIPLQ-----AIAKLGWLEPTLIQERAIPLILQN 55
L WLE P+ + Y +P + L + +Q AKL P ++ +
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGV-IQLAHYVVTAKLLGFTPGELRSYLKGATGHS 274
Query: 56 KDVLVRARTGSGKTGAFAIPMIQKIINL--------KQTAQVQETKALVLSPSKE----- 102
+ ++ + ++K I + + +L S E
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 103 ----LC------NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPD-IVVATP 151
L Q+ + + + +QV++S LV +VV+ P
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTN-------SHLPAGKQVEIS-----LVNGAKNLVVSGP 382
Query: 152 ARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVL--KFLPKLYQAILA---S 206
++L L K+ +D++ + FS + K +FLP + + S
Sbjct: 383 PQSLYGLNLTLRKAKAPSG---LDQSRIPFS-----ERKLKFSNRFLP-----VASPFHS 429
Query: 207 ATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQ 266
L + +++N V ++ I PV Y D + L + +V
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQI-PV-----YDTFDGSDLRV--LSGSISERIVD 481
Query: 267 GKTIIFVNTVD 277
I V
Sbjct: 482 ---CIIRLPVK 489
Score = 58.5 bits (141), Expect = 4e-09
Identities = 109/628 (17%), Positives = 182/628 (28%), Gaps = 241/628 (38%)
Query: 50 PLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTA-QVQET-KALVLSPSKELCNQL 107
PL L + GS + +P A Q+QE ++ P++
Sbjct: 8 PLTLSH---------GSLEH-VLLVP-----TASFFIASQLQEQFNKILPEPTEGFAADD 52
Query: 108 H-KNIQELTMK----CSRDVKCVDIS--EQV----------------DV-SVQEPLLVER 143
EL K S V+ + +QV D+ ++ LL E
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEN 112
Query: 144 PDIVVATPARALAHLKAKTLDLK-------SSL-EIVIIDEADLVFSFG-------YEDD 188
+V T ++ A+ + + S+L V A LV FG Y ++
Sbjct: 113 DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEE 172
Query: 189 MKAVLKFLPKLYQAIL------ASATLSE----------------DVLSLKHLILRNPVI 226
L+ L + Y ++ ++ TLSE ++L L NP
Sbjct: 173 ----LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW----LENPS- 223
Query: 227 LKLEEP-----AIAPVS-------QLAHYHILAQEDEKAT-ILYTLLKLNLVQGKTII-- 271
P P+S QLAHY + A+ L + LK + ++
Sbjct: 224 ---NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA 280
Query: 272 -----------FVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVI 320
F +V K + L F I RC+ Y N L I
Sbjct: 281 VAIAETDSWESFFVSVRKAITV-L----FFIG-----------VRCYEAYP-NTSLPPSI 323
Query: 321 IASDEKALE---TPQINSTNNRKRKRDKESGVSRGIDFQFVSNVI---NFDFPLDIQCYI 374
+ + E +P + + + + V + + N P Q I
Sbjct: 324 LEDSLENNEGVPSPML--------------SI-SNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 375 HRAGRTARGKNQGTALSFV------SLREQDLMNDGTALSFVSLR--------EQ----- 415
N A + V SL L+ ++LR +Q
Sbjct: 369 SL-------VN--GAKNLVVSGPPQSLY---------GLN-LTLRKAKAPSGLDQSRIPF 409
Query: 416 --------------------DLMNDVNEYLMTNLHEDDFIIKPYQFNL---DEVKGFEYR 452
L+ ++ + +L +++ + D G + R
Sbjct: 410 SERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLR 469
Query: 453 AKDAWRSNYFED-------NPTDLETLRHDKALYTVRIQSHLADV-PDYIVPPALKKL-A 503
+ E P ET KA +H+ D P L L
Sbjct: 470 VLSG---SISERIVDCIIRLPVKWETTTQFKA-------THILDFGPGGA--SGLGVLTH 517
Query: 504 RIED-DGDEDVRA---EPITDEEY-NKQ 526
R +D G + A + D++Y KQ
Sbjct: 518 RNKDGTGVRVIVAGTLDINPDDDYGFKQ 545
Score = 46.2 bits (109), Expect = 3e-05
Identities = 73/456 (16%), Positives = 128/456 (28%), Gaps = 166/456 (36%)
Query: 13 IQVYF-EL--------PFTFTLFCI---PLQAIAK---------------LGWLEPTLIQ 45
YF EL L L + + L WLE
Sbjct: 166 TDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE----N 221
Query: 46 ERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQET-KALVLSPSKELC 104
P +KD L+ + P+I + Q A T K L +P
Sbjct: 222 PSNTP----DKDYLLSI--------PISCPLIG----VIQLAHYVVTAKLLGFTPG---- 261
Query: 105 NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLD 164
+L ++ T S+ +V A A+A + +
Sbjct: 262 -ELRSYLKGATG-HSQG------------------------LVTAV---AIAE--TDSWE 290
Query: 165 --LKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKH---- 218
S + + ++F G + P L + L + SL++
Sbjct: 291 SFFVSVRKAI-----TVLFFIGVR-----CYEAYPNTS---LPPSILED---SLENNEGV 334
Query: 219 ----LILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIFVN 274
L + N ++++ + + H+ ++ I +LV G V
Sbjct: 335 PSPMLSISNLTQEQVQD-YVNKTNS----HL--PAGKQVEI-------SLVNGAKN-LVV 379
Query: 275 T--VDKCYKLKLYLEQFKISTC-----VLNSE---------LPAKARCH------AVYQF 312
+ Y L L L + K + + SE LP + H A
Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 313 NQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINF-------- 364
N+ L ++ + K ++ P + T + R +S I + + +
Sbjct: 440 NKDLVKNNVSFNAKDIQIP-VYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKA 498
Query: 365 ----DF-PLDIQCYIHRAGR-TARGKNQGTALSFVS 394
DF P G T R K GT + +
Sbjct: 499 THILDFGPGG----ASGLGVLTHRNK-DGTGVRVIV 529
Score = 43.1 bits (101), Expect = 2e-04
Identities = 43/237 (18%), Positives = 76/237 (32%), Gaps = 54/237 (22%)
Query: 153 RALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSED 212
RA H K T S L+IVI + +L FG E + + +++ I+ +E
Sbjct: 1648 RADNHFK-DTYGF-SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEK 1705
Query: 213 VL-----SLKHLILRNP-VILKLEE---PAIAPVSQLAHYHILAQE---DEKATI----L 256
+ R+ +L + PA+ + A + L + AT L
Sbjct: 1706 IFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME-KAAFEDLKSKGLIPADATFAGHSL 1764
Query: 257 --YTLL-----------KLNLVQ--GKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
Y L + +V G T+ D+ + + +
Sbjct: 1765 GEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE 1824
Query: 302 A-KARCHAVYQ----------FN----QGLYDVIIASDEKALETPQINSTNNRKRKR 343
A + V + +N Q + A D +AL+T N N K ++
Sbjct: 1825 ALQYVVERVGKRTGWLVEIVNYNVENQQ----YVAAGDLRALDTV-TNVLNFIKLQK 1876
Score = 34.3 bits (78), Expect = 0.12
Identities = 29/171 (16%), Positives = 52/171 (30%), Gaps = 76/171 (44%)
Query: 48 AIPLILQNKDV--LVRARTGSGKTGAFAIP----------MIQKIINLKQTAQVQETKAL 95
+ + + + +V R G T A+P MI IN + A +AL
Sbjct: 1776 VMSI----ESLVEVVFYR---GMTMQVAVPRDELGRSNYGMIA--INPGRVAASFSQEAL 1826
Query: 96 VLSPSKELCNQLHKNIQELTMKCSRDVKCVDI------SEQVDVSVQEPLLVERPDIVVA 149
+ + ++ K L V+I ++Q V A
Sbjct: 1827 -----QYVVERVGKRTGWL----------VEIVNYNVENQQ---------------YVAA 1856
Query: 150 TPARALA-------HLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVL 193
RAL +K + +D+ +L S E +++ L
Sbjct: 1857 GDLRALDTVTNVLNFIKLQKIDI-----------IELQKSLSLE-EVEGHL 1895
>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 = 58.8 bits (141), Expect = 3e-09
Identities = 30/140 (21%), Positives = 57/140 (40%), Gaps = 5/140 (3%)
Query: 39 LEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS 98
+ Q + K+ L+ A TGSGKT +I + + + ++ K + L+
Sbjct: 247 KKARSYQIELAQPAINGKNALICAPTGSGKT-FVSILICEHH--FQNMPAGRKAKVVFLA 303
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHL 158
+ Q + + V+ + +VSV++ ++E DI+V TP +
Sbjct: 304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEK--VIEDSDIIVVTPQILVNSF 361
Query: 159 KAKTLDLKSSLEIVIIDEAD 178
+ TL S ++I DE
Sbjct: 362 EDGTLTSLSIFTLMIFDECH 381
Score = 34.6 bits (78), Expect = 0.087
Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 8/81 (9%)
Query: 352 GIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMNDGTALSFVS 411
GID + V+ +++ ++ I GR R L + +
Sbjct: 707 GIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEK-------CN 758
Query: 412 LREQDLMNDVNEYLMTNLHED 432
++++MN E + E
Sbjct: 759 RYKEEMMNKAVEKIQKWDEET 779
>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 = 58.3 bits (140), Expect = 5e-09
Identities = 90/573 (15%), Positives = 170/573 (29%), Gaps = 177/573 (30%)
Query: 12 LIQVYFELPFTFTLFCIPLQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGA 71
++ V FE F C +Q + K +++ + I I+ +KD +
Sbjct: 21 ILSV-FEDAFVDNFDCKDVQDMPK------SILSKEEIDHIIMSKDAVSGTL-------- 65
Query: 72 FAIPMIQKIINLKQTAQVQETKALVLSPSKE-LCNQLHKNIQELTMKCSRDVKCVDISEQ 130
+ + KQ VQ+ VL + + L + + ++ +M ++ D
Sbjct: 66 ----RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 131 VDVSVQEPLLVERPDIVVATPARALAHLK-AKTLDL-------KSSLEIVIIDEADL--- 179
D V V R + +AL L+ AK + + K+ + + + +
Sbjct: 122 -DNQVFAKYNVSRLQPYLKL-RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK 179
Query: 180 ----VF--SFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKHLILRNPVILKLEEPA 233
+F + + + VL+ L KL I + T D S + L++
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS--------NIKLRIHS-- 229
Query: 234 IAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKIST 293
Q +L + + LL L VQ F +
Sbjct: 230 ----IQAELRRLLKSKPYENC----LLVLLNVQNAKAW---------------NAFNL-- 264
Query: 294 CVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGI 353
C K L T T R K+
Sbjct: 265 -----------SC-------------------KILLT-----T------RFKQ------- 276
Query: 354 DFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTAL--SFVSLREQDL---MNDGT--A 406
F+S LD H T ++ +L ++ R QDL +
Sbjct: 277 VTDFLSAATTTHISLDH----HSMTLT---PDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329
Query: 407 LSFVSLREQDLMNDVNEYLMTNLHEDDFIIKPYQFNLDEVKGFEYRAKDAWRSNYFEDNP 466
LS ++ +D + + + N + II+ +L+ ++ EYR F+
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIE---SSLNVLEPAEYRK-------MFD--- 376
Query: 467 TDLETLRHDKALYTVRIQSHL-----ADVPDYIVPPALKKLAR---IEDDGDE------- 511
L I + L DV V + KL + +E E
Sbjct: 377 -RLSVFPPS-----AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 512 ---DVRAEPITDEEYNK----QYEEYKKRSKEN 537
+++ + + ++ Y K ++
Sbjct: 431 IYLELKVKLENEYALHRSIVDHYNIPKTFDSDD 463
Score = 49.1 bits (116), Expect = 3e-06
Identities = 38/245 (15%), Positives = 75/245 (30%), Gaps = 63/245 (25%)
Query: 8 LEPTLIQVYFELPFTFTLF----CIPLQAIAKLGWLEPTLIQERAIPLILQNKDVLVRAR 63
LEP + F+ ++F IP ++ + W + + L ++ +
Sbjct: 366 LEPAEYRKMFD---RLSVFPPSAHIPTILLSLI-WFDVIKSDVMVVVNKLHKYSLVEK-- 419
Query: 64 TGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNI----QELTMKCS 119
K +IP I L+ +++ A LH++I S
Sbjct: 420 --QPKESTISIPSIY----LELKVKLENEYA------------LHRSIVDHYNIPKTFDS 461
Query: 120 RD--VKCVD------------ISEQVDVSVQEPLL------VERPDIVVATPARALAHLK 159
D +D E + ++ +E+ +T A +
Sbjct: 462 DDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSIL 521
Query: 160 AKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKHL 219
LK + ++ YE + A+L FLPK+ + ++ S L +
Sbjct: 522 NTLQQLKFYKPYICDNDPK------YERLVNAILDFLPKIEENLICS-----KYTDLLRI 570
Query: 220 ILRNP 224
L
Sbjct: 571 ALMAE 575
Score = 39.5 bits (91), Expect = 0.003
Identities = 40/313 (12%), Positives = 94/313 (30%), Gaps = 81/313 (25%)
Query: 43 LIQERAIP---LIL---QNKDVL----VRART-------------GSGKTGAFAIPMIQK 79
L++ + L+L QN + + + T ++
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 80 IINLKQT----AQVQETKALVLSPSKELCNQLH-----KNIQE--LTMKCSRDVKCVDIS 128
+ + + + + L N ++I++ T + V C ++
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLT 356
Query: 129 EQVDVSV--QEPLLVER--------PDIVVATPARALAHLKAKTL-----DLKSSLEIVI 173
++ S+ EP + P H+ L D+ S +V+
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVFPPSA---------HIPTILLSLIWFDVIKSDVMVV 407
Query: 174 IDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSL-KHLILRNPVILKLEEP 232
+++ L E K +P +Y + E+ +L + ++ + +
Sbjct: 408 VNK--LHKYSLVEKQPKESTISIPSIYLELKVKL---ENEYALHRSIVDHYNIPKTFDSD 462
Query: 233 AIAPVSQ----LAH--YHILAQEDEKATILYTLLKLNL--VQGKTIIFVNTVDKCYK--- 281
+ P +H +H+ E + L+ ++ L+ ++ K I +T
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK-IRHDSTAWNASGSIL 521
Query: 282 -----LKLYLEQF 289
LK Y
Sbjct: 522 NTLQQLKFYKPYI 534
>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 = 57.6 bits (138), Expect = 6e-09
Identities = 30/139 (21%), Positives = 57/139 (41%), Gaps = 5/139 (3%)
Query: 39 LEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS 98
+ Q + K+ L+ A TGSGKT +I + + + ++ K + L+
Sbjct: 6 KKARSYQIELAQPAINGKNALICAPTGSGKT-FVSILICEHHF--QNMPAGRKAKVVFLA 62
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHL 158
+ Q + + V+ + +VSV++ ++E DI+V TP +
Sbjct: 63 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEK--VIEDSDIIVVTPQILVNSF 120
Query: 159 KAKTLDLKSSLEIVIIDEA 177
+ TL S ++I DE
Sbjct: 121 EDGTLTSLSIFTLMIFDEC 139
Score = 34.1 bits (77), Expect = 0.13
Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 8/81 (9%)
Query: 352 GIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMNDGTALSFVS 411
GID + V+ +++ ++ I GR R L + +
Sbjct: 466 GIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEK-------CN 517
Query: 412 LREQDLMNDVNEYLMTNLHED 432
++++MN E + E
Sbjct: 518 RYKEEMMNKAVEKIQKWDEET 538
>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 = 57.3 bits (137), Expect = 1e-08
Identities = 30/140 (21%), Positives = 57/140 (40%), Gaps = 5/140 (3%)
Query: 39 LEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS 98
+ Q + K+ L+ A TGSGKT +I + + + ++ K + L+
Sbjct: 247 KKARSYQIELAQPAINGKNALICAPTGSGKT-FVSILICEHH--FQNMPAGRKAKVVFLA 303
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHL 158
+ Q + + V+ + +VSV++ ++E DI+V TP +
Sbjct: 304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEK--VIEDSDIIVVTPQILVNSF 361
Query: 159 KAKTLDLKSSLEIVIIDEAD 178
+ TL S ++I DE
Sbjct: 362 EDGTLTSLSIFTLMIFDECH 381
Score = 33.0 bits (74), Expect = 0.32
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 9/94 (9%)
Query: 352 GIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTALSFVSLREQDLMNDGTALSFVS 411
GID + V+ +++ ++ I GR R L + +
Sbjct: 707 GIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEK-------CN 758
Query: 412 LREQDLMNDVNEYLMTNLHEDDFIIKPYQFNLDE 445
++++MN E + E+ F K + + E
Sbjct: 759 RYKEEMMNKAVEKIQ-KWDEETFAKKIHNLQMKE 791
>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 = 54.5 bits (131), Expect = 6e-08
Identities = 56/254 (22%), Positives = 102/254 (40%), Gaps = 34/254 (13%)
Query: 44 IQERAIP-LILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
Q A+ IL+ K+ L+ T SGKT I M+ +I+ KA+ + P K
Sbjct: 27 PQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGG-------KAVYIVPLKA 79
Query: 103 LCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKT 162
L + + Q+ ++ + D + + + DI++AT + + L
Sbjct: 80 LAEEKFQEFQDWE---KIGLRVAMATGDYDSKDEW---LGKYDIIIATAEKFDS-LLRHG 132
Query: 163 LDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLS--EDVLS-LK-H 218
++I++ DE L+ S ++ +L + Q I SAT+ E++ L
Sbjct: 133 SSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNPEELAEWLNAE 192
Query: 219 LILRN--PVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKL---NLVQGK-TIIF 272
LI+ + PV KL + + + ED + +L + + K +IF
Sbjct: 193 LIVSDWRPV--KLRR-------GVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIF 243
Query: 273 VNTVDKCYKLKLYL 286
VN K ++ L L
Sbjct: 244 VNMRRKAERVALEL 257
>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 = 53.7 bits (129), Expect = 9e-08
Identities = 41/256 (16%), Positives = 92/256 (35%), Gaps = 35/256 (13%)
Query: 44 IQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKEL 103
Q A+ + K++L+ T +GKT + M+++ I K+L + P + L
Sbjct: 29 PQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG--------KSLYVVPLRAL 80
Query: 104 CNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTL 163
+ +++ ++ ++ + + + + DI+V T +A L
Sbjct: 81 AGEKYESFKKWE---KIGLRIGISTGDYESRDEH---LGDCDIIVTTSEKA-DSLIRNRA 133
Query: 164 DLKSSLEIVIIDEADLVFSFGYEDDMKAVL-------KFLPKLYQAILASATLS--EDV- 213
++ +++DE L+ + A L + + K + I SAT ++
Sbjct: 134 SWIKAVSCLVVDEIHLLD----SEKRGATLEILVTKMRRMNKALRVIGLSATAPNVTEIA 189
Query: 214 --LSLKHLILR-NPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTI 270
L + + PV L E + + L + + + + G +
Sbjct: 190 EWLDADYYVSDWRPV--PLVEGVLCEGT-LELFDGAFSTSRRVKFEELVEECVAENGGVL 246
Query: 271 IFVNTVDKCYKLKLYL 286
+F +T K + L
Sbjct: 247 VFESTRRGAEKTAVKL 262
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 50.1 bits (120), Expect = 1e-06
Identities = 25/136 (18%), Positives = 53/136 (38%), Gaps = 19/136 (13%)
Query: 44 IQERAIP-LILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
Q A+ +L+ +L+ + TGSGKT + +I ++ KA+ ++P +
Sbjct: 34 PQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGG-------KAIYVTPLRA 86
Query: 103 LCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATP--ARALAHLKA 160
L N+ + ++ K S D ++ DI++ T +L
Sbjct: 87 LTNEKYLTFKDWE---LIGFKVAMTSGDYDTDDAW---LKNYDIIITTYEKLDSLWR--- 137
Query: 161 KTLDLKSSLEIVIIDE 176
+ + + ++DE
Sbjct: 138 HRPEWLNEVNYFVLDE 153
>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 = 50.2 bits (119), Expect = 2e-06
Identities = 34/170 (20%), Positives = 64/170 (37%), Gaps = 28/170 (16%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
Q+ AI I + + VLV A T +GKT +AI + + + + SP K
Sbjct: 91 QDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQ----------SLKNKQRVIYTSPIKA 140
Query: 103 LCNQLHKNIQELTMKCSRDVKCVDISE-QVDVSVQEPLLVERPDIVVATPARALAHLKAK 161
L NQ ++ + V + + ++ LV +I R++ + ++
Sbjct: 141 LSNQKYRELLAE-------FGDVGLMTGDITINPDAGCLVMTTEI-----LRSMLYRGSE 188
Query: 162 TLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSE 211
+ + VI DE + + + LP + + SAT+
Sbjct: 189 VMR---EVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPN 235
>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 = 49.5 bits (117), Expect = 2e-06
Identities = 34/170 (20%), Positives = 64/170 (37%), Gaps = 28/170 (16%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
Q+ AI I + + VLV A T +GKT +AI + + + + SP K
Sbjct: 189 QDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQ----------SLKNKQRVIYTSPIKA 238
Query: 103 LCNQLHKNIQELTMKCSRDVKCVDISE-QVDVSVQEPLLVERPDIVVATPARALAHLKAK 161
L NQ ++ + V + + ++ LV +I R++ + ++
Sbjct: 239 LSNQKYRELLAE-------FGDVGLMTGDITINPDAGCLVMTTEI-----LRSMLYRGSE 286
Query: 162 TLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSE 211
+ + VI DE + + + LP + + SAT+
Sbjct: 287 VMR---EVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPN 333
>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 = 48.7 bits (116), Expect = 3e-06
Identities = 52/342 (15%), Positives = 97/342 (28%), Gaps = 99/342 (28%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
QE+A+ L +K + TGSGKT AI + L++ P+
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELST-------------PTLIVVPTLA 144
Query: 103 LCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKT 162
L Q + + + V + E + V+T A + +
Sbjct: 145 LAEQWKERLGIFGEE---YVGEFSGRIK-----------ELKPLTVSTYDSAYVNAE--- 187
Query: 163 LDLKSSLEIVIIDEADLVFSFGY---------------------EDDMKAVLKFL--PKL 199
L + ++I DE + + Y ED +LK + K+
Sbjct: 188 -KLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKV 246
Query: 200 YQAIL----------------------------------ASATLSEDVLSLKHLILRNPV 225
++ L ++L+ N +
Sbjct: 247 FELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKI 306
Query: 226 ILKLEEPAIAPVSQLAH---YHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKL 282
++ A + A I K L +L+ + K IIF + Y++
Sbjct: 307 VMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILE-RHRKDKIIIFTRHNELVYRI 365
Query: 283 KLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASD 324
I+ + R + F G + I++S
Sbjct: 366 SKVFLIPAIT-----HRTSREEREEILEGFRTGRFRAIVSSQ 402
>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 = 42.3 bits (99), Expect = 3e-04
Identities = 59/359 (16%), Positives = 99/359 (27%), Gaps = 91/359 (25%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
+ + + A TGSGK+ +P Q K LVL+PS
Sbjct: 222 NSSPPAVPQSFQVAHLHAPTGSGKSTK--VP--AAYAA-------QGYKVLVLNPSVAAT 270
Query: 105 NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLD 164
+ + ++ + + +T + LA
Sbjct: 271 LGFGAYMSKA------------HGIDPNIRTGVRTITTGAPVTYSTYGKFLAD---GGCS 315
Query: 165 LKSSLEIVIIDEA-----DLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKHL 219
+ +I+I DE + G + + +LA+AT V
Sbjct: 316 GGA-YDIIICDECHSTDSTTILGIGT---VLDQAETAGARL-VVLATATPPGSVTV---- 366
Query: 220 ILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKC 279
P E + + E + G+ +IF ++ KC
Sbjct: 367 ----PHPNIEEVALSNTGEIPFYGKAIPIEAIR-------------GGRHLIFCHSKKKC 409
Query: 280 YKLKLYLEQFKISTCVLN-----SELPAKARCHAVYQFNQGLYDVIIASDEKALE---TP 331
+L L I+ S +P V++A+D AL T
Sbjct: 410 DELAAKLSGLGINAVAYYRGLDVSVIPTIGD------------VVVVATD--ALMTGYTG 455
Query: 332 QINS---TNNRKRKR-DKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQ 386
+S N + D + I+ V P D R GRT RG+
Sbjct: 456 DFDSVIDCNTCVTQTVDFSLDPTFTIETTTV--------PQDAVSRSQRRGRTGRGRRG 506
>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 = 39.7 bits (93), Expect = 0.001
Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 22/93 (23%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
QE+A+ L +K + TGSGKT AI + L++ P+
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELST-------------PTLIVVPTLA 144
Query: 103 LCNQLHKNIQELTMKC-------SRDVKCVDIS 128
L Q + + + +++K + +S
Sbjct: 145 LAEQWKERLGIFGEEYVGEFSGRIKELKPLTVS 177
>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 = 39.1 bits (91), Expect = 0.003
Identities = 44/283 (15%), Positives = 86/283 (30%), Gaps = 54/283 (19%)
Query: 51 LILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKN 110
++ + ++ G+GKT F ++ + + + LVL+P++ + +++ +
Sbjct: 4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRRL-------RTLVLAPTRVVLSEMKEA 56
Query: 111 IQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLDLKSSLE 170
L VK + S R I A L + + + + E
Sbjct: 57 FHGLD------VKFHTQAFSAHGS-------GREVIDAMCHA-TLTYRMLEPTRV-VNWE 101
Query: 171 IVIIDEA---DLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKHLILRNPVIL 227
++I+DEA D IL +AT H N I
Sbjct: 102 VIIMDEAHFLDPASIAARGWAAHRARANESAT---ILMTATPPGTSDEFPH---SNGEIE 155
Query: 228 KLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLE 287
++ I + + + T F+ ++ + L
Sbjct: 156 DVQT-DIPSEPWNTGHDWILADK----------------RPTAWFLPSIRAANVMAASLR 198
Query: 288 QFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALET 330
+ S VLN + + Q D I+A+D E
Sbjct: 199 KAGKSVVVLNRKTFER----EYPTIKQKKPDFILATD--IAEM 235
>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 = 39.3 bits (91), Expect = 0.003
Identities = 25/140 (17%), Positives = 44/140 (31%), Gaps = 27/140 (19%)
Query: 246 LAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKL-KLYLEQFKISTCVLNSELPAKA 304
D + L L + K ++ +L ++ E+ I V + +
Sbjct: 484 WWNFDPRVEWLMGYLT-SHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIE 542
Query: 305 RCHAVYQFNQGLYDV--IIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVI 362
R A F + ++ S+ S G +FQF S+++
Sbjct: 543 RDRAAAWFAEEDTGAQVLLCSE-----------------------IGSEGRNFQFASHMV 579
Query: 363 NFDFPLDIQCYIHRAGRTAR 382
FD P + R GR R
Sbjct: 580 MFDLPFNPDLLEQRIGRLDR 599
Score = 28.1 bits (62), Expect = 8.9
Identities = 22/120 (18%), Positives = 41/120 (34%), Gaps = 24/120 (20%)
Query: 65 GSGKTGAFAIPMIQKIINLKQTAQVQETK-ALVLSPSKELCNQLHKNIQELTMKCSRDVK 123
G GKT I+ + L Q + L++ P + L +Q E+ + +
Sbjct: 180 GLGKT-------IEAGMILHQQLLSGAAERVLIIVP-ETLQHQWL---VEMLRRFNLRFA 228
Query: 124 CVDISEQVDVSVQEPLLVERPDIVVAT------PARALAHLKAKTLDLKSSLEIVIIDEA 177
D + + +V+ + + L HL DL +++DEA
Sbjct: 229 LFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDL------LVVDEA 282
>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 = 38.7 bits (90), Expect = 0.004
Identities = 50/360 (13%), Positives = 110/360 (30%), Gaps = 88/360 (24%)
Query: 44 IQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKEL 103
E + + + ++ G+GKT + + ++ + A ++ + L+L+P++ +
Sbjct: 8 DYEVDEDIFRKKRLTIMDLHPGAGKT-------KRILPSIVREALLRRLRTLILAPTRVV 60
Query: 104 CNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTL 163
++ + ++ L ++ + + D + +E + + A L + T
Sbjct: 61 AAEMEEALRGLP------IRYQTPAVKSDHTGREI-------VDLMCHATFTTRLLSST- 106
Query: 164 DLKSSLEIVIIDEA-----DLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKH 218
+ + ++++DEA V + GY + + AI +AT
Sbjct: 107 RV-PNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAA-----AIFMTATPPGSTDPFP- 159
Query: 219 LILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDK 278
N I +E P + + GKT+ FV ++
Sbjct: 160 --QSNSPIEDIERE--IPERSWNTGFDWITDYQ---------------GKTVWFVPSIKA 200
Query: 279 CYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNN 338
+ L + L+ + +D ++ +D E
Sbjct: 201 GNDIANCLRKSGKRVIQLSRKTFDTEYPKTK----LTDWDFVVTTD--ISEM-------- 246
Query: 339 RKRKRDKES---GVSRGIDFQF-VSNVINFDFPLDIQCY----------IHRAGRTARGK 384
R ID + + VI D P + R GR R
Sbjct: 247 --------GANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNP 298
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 37.9 bits (87), Expect = 0.008
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSKE 102
Q+ A+ + Q V V A T +GKT +AI M A TK + SP K
Sbjct: 44 QKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAM----------AHRNMTKTIYTSPIKA 93
Query: 103 LCNQLHKNIQE 113
L NQ ++ +E
Sbjct: 94 LSNQKFRDFKE 104
>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 = 37.4 bits (87), Expect = 0.014
Identities = 48/304 (15%), Positives = 101/304 (33%), Gaps = 53/304 (17%)
Query: 40 EPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSP 99
EP IQ+ IL+ + A TG GKT +F + M + + + V+ P
Sbjct: 56 EPRAIQKMWAKRILRKESFAATAPTGVGKT-SFGLAMSLFLALKGK-------RCYVIFP 107
Query: 100 SKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERP----DIVVATPARAL 155
+ L Q + I++ K + + + +E + IV+ T
Sbjct: 108 TSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFL- 166
Query: 156 AHLKAKTLDLKSSLEIVIIDEAD-----------LVFSFGYEDDMKAVLKFLPKLYQAIL 204
+K + + +D+ D L+ G+ D+K ++
Sbjct: 167 ----SKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMV 222
Query: 205 ASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHY-----HILAQEDEKATILYTL 259
++AT + K + R +L + + + ++ +T+ L
Sbjct: 223 STATAKK---GKKAELFRQ--LLNFD------IGSSRITVRNVEDVAVNDESISTLSSIL 271
Query: 260 LKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDV 319
KL II+ T ++ ++ L+ + + +F +G D
Sbjct: 272 EKLG---TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDH 322
Query: 320 IIAS 323
+I +
Sbjct: 323 LIGT 326
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 35.7 bits (82), Expect = 0.035
Identities = 42/322 (13%), Positives = 90/322 (27%), Gaps = 68/322 (21%)
Query: 52 ILQNKDVLVRARTGSGKTGA---FAIPMIQKIINLKQTAQVQET----------KALVLS 98
+ K +L+ A+ G GKT + + +K++ +T ++ K L
Sbjct: 23 LKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHSQLDSIYKNAKLLGLKTGFLI 82
Query: 99 PSKELCNQLHKNIQELTMKCSRD---VKCVDISEQVDVSVQEPL--------------LV 141
C + + + CS+ K I ++ + E +
Sbjct: 83 GKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANL 142
Query: 142 ERPDIVVAT------PARALAHLKAKTLDLKSSLEIVIIDEA----DLVFSFGYE----- 186
+ D++ T + K LK +++IDEA + F +
Sbjct: 143 KDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLEADKWFTRKISRKM 202
Query: 187 -----DDMKAVLKFLPKLYQAILASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLA 241
+++ V + + + L D +S R + + P +L
Sbjct: 203 LERALKEIEIVERLNRIDAKKVKDYINLLIDYMSKLIKDGRCHELSLMPLPDRETNGELI 262
Query: 242 HYHILAQEDEKATILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELP 301
++ + + LK + FV Y L + L +
Sbjct: 263 VVTRAYLNIDEGPVKKSSLK------SLLKFVEMKGDLYNCNGSLVKVPSDVNQLIEDAL 316
Query: 302 AKARCHAVYQFNQGLYDVIIAS 323
++ S
Sbjct: 317 NVKTF------------KVLMS 326
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.7 bits (79), Expect = 0.042
Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 12/57 (21%)
Query: 496 PPALKKL-----ARIE--DDGDEDVRAEPITD-----EEYNKQYEEYKKRSKENERN 540
P +++K R++ D + + E EE+N++ E +++K N R
Sbjct: 84 PESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRI 140
>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 = 34.2 bits (77), Expect = 0.045
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 15/41 (36%)
Query: 215 SLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATI 255
+LK L LKL AP LA I KAT+
Sbjct: 21 ALKKLQAS----LKLYADDSAPA--LA---I------KATM 46
Score = 29.9 bits (66), Expect = 1.2
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 27/52 (51%)
Query: 158 LKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
LK K L++SL++ Y DD A P L AI AT+
Sbjct: 22 LK-K---LQASLKL-------------YADD-SA-----PAL--AI--KATM 46
Score = 29.1 bits (64), Expect = 2.2
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 7/28 (25%)
Query: 482 RIQSHL---ADVPDYIVPPALKKLARIE 506
++Q+ L A D PAL A +E
Sbjct: 24 KLQASLKLYA--DD--SAPALAIKATME 47
Score = 27.2 bits (59), Expect = 8.8
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 14/43 (32%)
Query: 129 EQVDVS-VQEPLLVERPDIVVATPARALAHLKAKTLDLKSSLE 170
E+ + +Q L + D + PA LA +K+++E
Sbjct: 18 EKQALKKLQASLKLYADD---SAPA--LA--------IKATME 47
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 35.2 bits (81), Expect = 0.062
Identities = 33/150 (22%), Positives = 58/150 (38%), Gaps = 21/150 (14%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
Q A+ +LQ L++ G+GKT + + A+ LV +PS
Sbjct: 185 QVYAVKTVLQRPLSLIQGPPGTGKT-------VTSATIVYHLARQGNGPVLVCAPSNIAV 237
Query: 105 NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVER-PDIVVATPARALAHLKAKTL 163
+QL + I + +K R C E +D V L + ++ + L LK +T
Sbjct: 238 DQLTEKIHQTGLKVVRL--CAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETG 295
Query: 164 D-----------LKSSLEIVIIDEADLVFS 182
+ LK + E ++ AD++
Sbjct: 296 ELSSADEKRYRALKRTAERELLMNADVICC 325
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 34.5 bits (79), Expect = 0.093
Identities = 33/150 (22%), Positives = 58/150 (38%), Gaps = 21/150 (14%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
Q A+ +LQ L++ G+GKT + + A+ LV +PS
Sbjct: 361 QVYAVKTVLQRPLSLIQGPPGTGKT-------VTSATIVYHLARQGNGPVLVCAPSNIAV 413
Query: 105 NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVER-PDIVVATPARALAHLKAKTL 163
+QL + I + +K R C E +D V L + ++ + L LK +T
Sbjct: 414 DQLTEKIHQTGLKVVRL--CAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETG 471
Query: 164 D-----------LKSSLEIVIIDEADLVFS 182
+ LK + E ++ AD++
Sbjct: 472 ELSSADEKRYRALKRTAERELLMNADVICC 501
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 32.2 bits (73), Expect = 0.44
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
Q A+ +LQ L++ G+GKT I+ +++ + + LV +PS
Sbjct: 365 QSNAVSHVLQRPLSLIQGPPGTGKT-----VTSATIV--YHLSKIHKDRILVCAPSNVAV 417
Query: 105 NQLHKNIQELTMKCSR 120
+ L +++L +K R
Sbjct: 418 DHLAAKLRDLGLKVVR 433
>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer
aging, hydrolase; HET: FLC; 2.00A {Sulfolobus
acidocaldarius} PDB: 3crw_1*
Length = 551
Score = 31.5 bits (71), Expect = 0.70
Identities = 25/164 (15%), Positives = 55/164 (33%), Gaps = 38/164 (23%)
Query: 52 ILQNKDVLVRARTGSGKTGAFAIPMIQ---KII--------------NLKQTAQVQETKA 94
+ N V + A TGSGKT + ++ K++ +L + + +
Sbjct: 19 LRNNFLVALNAPTGSGKTLFSLLVSLEVKPKVLFVVRTHNEFYPIYRDLTKIREKRNITF 78
Query: 95 LVLSPSKELCNQLHKNIQELTMKCSRD---VKCVDI-SEQVDVSVQEPL----------- 139
L C K + + C V++ ++ +S+ + L
Sbjct: 79 SFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCP 138
Query: 140 ------LVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEA 177
+ + D++ T + +D+ +++IDEA
Sbjct: 139 YYSLLNSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEA 182
>1gcy_A Glucan 1,4-alpha-maltotetrahydrolase; beta-alpha-barrel, beta
sheet; 1.60A {Pseudomonas stutzeri} SCOP: b.71.1.1
c.1.8.1 PDB: 1jdc_A* 1jda_A* 1jdd_A* 1qi5_A* 1qi3_A*
1qi4_A* 2amg_A 1qpk_A*
Length = 527
Score = 31.2 bits (70), Expect = 0.88
Identities = 15/97 (15%), Positives = 23/97 (23%), Gaps = 26/97 (26%)
Query: 415 QDLMNDVNEYLMTNLHEDDFIIKPYQFNL------DEVKGFEYRAKDAWRSNY--FEDNP 466
Q + + + DF + + D G WR F DN
Sbjct: 240 QIIKDWSDRAKCPVF---DF---ALKERMQNGSIADWKHGLNGNPDPRWREVAVTFVDN- 292
Query: 467 TDLETLRHDKALYTVRIQSHLADVPDYIVPPALKKLA 503
HD T + + L + A
Sbjct: 293 -------HD----TGYSPGQNGGQHHWALQDGLIRQA 318
>1ri5_A MRNA capping enzyme; methyltransferase, M7G, messenger RNA CAP,
structural genomics, PSI, protein structure initiative;
2.10A {Encephalitozoon cuniculi} SCOP: c.66.1.34 PDB:
1ri2_A* 1ri3_A* 1ri1_A* 1ri4_A 1z3c_A* 2hv9_A*
Length = 298
Score = 28.5 bits (63), Expect = 6.0
Identities = 9/91 (9%), Positives = 26/91 (28%), Gaps = 8/91 (8%)
Query: 451 YRAKDAWRSNYFEDNPTDLETLRHDKALYTVRIQSHLADVPDYIVP-PALKKLARIEDDG 509
Y+ Y + + Y + + + +Y V +
Sbjct: 184 YKQGRMSNDFYKIELEKMEDVPMESVREYRFTLLDSVNNCIEYFVDFTRMVDGF------ 237
Query: 510 DEDVRAEPITDEEYNKQYEEYKKRSKENERN 540
+ + + + + YE+ +R+ E +
Sbjct: 238 -KRLGLSLVERKGFIDFYEDEGRRNPELSKK 267
>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 = 28.4 bits (63), Expect = 6.9
Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 6/52 (11%)
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVAT 150
S ++ N++ + +Q + V ++ + D V+ T
Sbjct: 418 ASVKMSNEIAQCLQRAGKR----VIQLNRKSYD--TEYPKCKNGDWDFVITT 463
>2bi7_A UDP-galactopyranose mutase; FAD, flavoprotein, isomerase,
lipopolysaccharide biosynthesi; HET: FAD; 2.0A
{Klebsiella pneumoniae} SCOP: c.4.1.3 d.16.1.7 PDB:
2bi8_A* 1wam_A* 3inr_A* 3gf4_A* 3int_A* 3kyb_A*
Length = 384
Score = 28.1 bits (62), Expect = 7.5
Identities = 5/30 (16%), Positives = 10/30 (33%)
Query: 509 GDEDVRAEPITDEEYNKQYEEYKKRSKENE 538
+ D+ PI E+Y ++
Sbjct: 307 EENDIPYYPIRQMGEMALLEKYLSLAENET 336
>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial
conjugation, F1-ATPase-like quaternary structure, ring
helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB:
1e9s_A 1gki_A* 1gl7_A* 1gl6_A*
Length = 437
Score = 28.3 bits (63), Expect = 7.5
Identities = 10/64 (15%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 40 EPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSP 99
+ + +P + + +LV TG+GK+ + L T ++ + +++ P
Sbjct: 38 KQVTVAGVPMPRDAEPRHLLVNGATGTGKS--------VLLRELAYTGLLRGDRMVIVDP 89
Query: 100 SKEL 103
+ ++
Sbjct: 90 NGDM 93
>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET:
DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11
PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*
Length = 296
Score = 28.0 bits (63), Expect = 7.7
Identities = 20/130 (15%), Positives = 42/130 (32%), Gaps = 14/130 (10%)
Query: 53 LQNKD-VLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS---PSKELCNQLH 108
+ + ++V + +G GK+ F + K + +E L
Sbjct: 32 ARGGEVIMVTSGSGMGKS-TFVRQQALQW------GTAMGKKVGLAMLEESVEETAEDLI 84
Query: 109 KNIQELTMKCSRDVKCVDIS-EQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLDLKS 167
+ ++ S +K I + D E + + + L AK ++S
Sbjct: 85 GLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRS 144
Query: 168 SLEI--VIID 175
L +I+D
Sbjct: 145 GLGCDVIILD 154
>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 = 28.0 bits (63), Expect = 9.9
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 45 QERAIPLILQNKDVLVRARTGSGK 68
Q I + + K+V + TG GK
Sbjct: 49 QLETINVTMAGKEVFLVMPTGGGK 72
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
0.319 0.136 0.386
Gapped
Lambda K H
0.267 0.0478 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,170,795
Number of extensions: 510854
Number of successful extensions: 1466
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1284
Number of HSP's successfully gapped: 114
Length of query: 540
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 442
Effective length of database: 3,965,535
Effective search space: 1752766470
Effective search space used: 1752766470
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: 60 (27.5 bits)