RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8497
(2355 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 = 347 bits (892), Expect = e-107
Identities = 131/370 (35%), Positives = 197/370 (53%), Gaps = 22/370 (5%)
Query: 10 RTKDVLSNIDVLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGT 69
+T DVL+ FE D +++ + G+ E GF K SPIQ A P + G D + ++K+GT
Sbjct: 11 QTDDVLNTKGNTFE-DFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGT 69
Query: 70 GKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT 129
GK+ FV+ L K +K + + Q +I+ PTRE+A+Q + VVR++G H + GGT
Sbjct: 70 GKTAAFVIPTLEK-VKPKLNKIQALIMVPTRELALQTSQVVRTLGKH-CGISCMVTTGGT 127
Query: 130 ----QVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWI 185
+ R V I+VG+PGR+ + K ++ LFIMDEADK+++ F I I
Sbjct: 128 NLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQI 187
Query: 186 YSQLPPMKQMLVVSATYSHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNP 245
S LPP Q L+ SAT+ + K++ P I + L G+ Q A
Sbjct: 188 LSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYA-------- 238
Query: 246 SLRYVDEEKK---LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQK 302
+V+E +K L L S+ NQ +IF N R E++ + + + + Y Q+
Sbjct: 239 ---FVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQ 295
Query: 303 ARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTR 362
R F++GKVR LV +DL RGID V++VIN + P A TYLHR+GR+GR+G
Sbjct: 296 ERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHL 355
Query: 363 GLVITIVSAE 372
GL I +++
Sbjct: 356 GLAINLINWN 365
>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 = 336 bits (864), Expect = e-103
Identities = 124/358 (34%), Positives = 186/358 (51%), Gaps = 20/358 (5%)
Query: 24 NDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKL 83
D L++ + + + + GF S +Q P + G D + Q+KSG GK+ VFV+A L +
Sbjct: 11 RDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ- 69
Query: 84 IKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPV- 138
++ Q +++ TRE+A QI+ ++ N+ V F GG E K+
Sbjct: 70 LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCP 129
Query: 139 QIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADK-LINTGFVEDITWIYSQLPPMKQMLV 197
IVVG+PGRI + + K LN+ ++ FI+DE DK L D+ I+ P KQ+++
Sbjct: 130 HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMM 189
Query: 198 VSATYSHDNLATLQKYMVDPLLIRPEDATRP-LLGVKQLVALIPECKNPSLRYVDEEK-- 254
SAT S + +K+M DP+ I +D T+ L G++Q + + EK
Sbjct: 190 FSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD----------NEKNR 239
Query: 255 KLVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRG 314
KL LL FNQ VIF R + + L NF A + Q+ RL+ FK
Sbjct: 240 KLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF 299
Query: 315 KVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAE 372
+ RILV T+L RG+D V++ N ++P D+ TYLHR+ RAGR+GT+GL IT VS E
Sbjct: 300 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE 357
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 338 bits (870), Expect = e-102
Identities = 108/341 (31%), Positives = 177/341 (51%), Gaps = 34/341 (9%)
Query: 47 IQMAAFPYVLNGY--DAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAV 104
IQ A P +L+ + I QS+SGTGK+ F + L++ + V +PQ I LAP+RE+A
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSR-VDASVPKPQAICLAPSRELAR 203
Query: 105 QITDVVRSVGAHVKNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRL 164
QI DVV +G + + + I + + K QIV+G+PG + ++K + L+ +++
Sbjct: 204 QIMDVVTEMGKY-TEVKTAFGIKDSVPKGAKIDAQIVIGTPGTVMDLMKRRQLDARDIKV 262
Query: 165 FIMDEADKLINT-GFVEDITWIYSQLPPMKQMLVVSATYSHDNLATLQKYMVDP--LLIR 221
F++DEAD +++ G + I LP Q+++ SAT+S +++ + + ++
Sbjct: 263 FVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSERVEKYAERFAPNANEIRLK 322
Query: 222 PEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK---LVQLLSQTPFNQCVIFSNYQ 275
E+ + G+KQ Y+D EE K LV+L Q +IF +
Sbjct: 323 TEELSVE--GIKQ-------------LYMDCQSEEHKYNVLVELYGLLTIGQSIIFCKKK 367
Query: 276 LRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVD 335
E I + L+G + R A +DSF+ G ++LVTT++ ARGID + V+
Sbjct: 368 DTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQVN 427
Query: 336 LVINLEIP------HDAATYLHRMGRAGRYGTRGLVITIVS 370
LV+N ++P D TYLHR+GR GR+G G+ I V
Sbjct: 428 LVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFVH 468
>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 = 332 bits (855), Expect = e-102
Identities = 127/354 (35%), Positives = 196/354 (55%), Gaps = 24/354 (6%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+++ + +G+ GF + S IQ A ++ G+D + Q++SGTGK+ F +AAL + I
Sbjct: 28 LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR-IDTS 86
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERPKR---PVQIVVGS 144
V+ PQ ++LAPTRE+A+QI VV ++ H ++ V IGGT QIVVG+
Sbjct: 87 VKAPQALMLAPTRELALQIQKVVMALAFH-MDIKVHACIGGTSFVEDAEGLRDAQIVVGT 145
Query: 145 PGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYSH 204
PGR+ I+ + D +++FI+DEAD+++++GF E I I++ LPP Q++++SAT +
Sbjct: 146 PGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 205
Query: 205 DNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK---LVQ 258
D L K+M +P+ I + L G+KQ YV+ EE K L
Sbjct: 206 DVLEVTTKFMRNPVRILVKKDELTLEGIKQ-------------FYVNVEEEEYKYECLTD 252
Query: 259 LLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRI 318
L Q VIF N + + E + L N F + Q+ R + F+ G RI
Sbjct: 253 LYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI 312
Query: 319 LVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAE 372
L++TDL ARGID V LVIN ++P + Y+HR+GR GR+G +G+ I V+ E
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE 366
>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 = 331 bits (851), Expect = e-101
Identities = 121/355 (34%), Positives = 195/355 (54%), Gaps = 25/355 (7%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+ + + +G+ GF K S IQ A ++ G D I QS+SGTGK+ F ++ L + +
Sbjct: 44 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC-LDIQ 102
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPVQIVVG 143
V++ Q +ILAPTRE+AVQI + ++G + N+ IGGT + + +V G
Sbjct: 103 VRETQALILAPTRELAVQIQKGLLALGDY-MNVQCHACIGGTNVGEDIRKLDYGQHVVAG 161
Query: 144 SPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYS 203
+PGR+ MI+ + L ++++ ++DEAD+++N GF E I +Y LPP Q++++SAT
Sbjct: 162 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 221
Query: 204 HDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK---LV 257
H+ L K+M DP+ I + L G+KQ +V EE K L
Sbjct: 222 HEILEMTNKFMTDPIRILVKRDELTLEGIKQ-------------FFVAVEREEWKFDTLC 268
Query: 258 QLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVR 317
L Q VIF N + + + + E + ANF + G QK R + + F+ G R
Sbjct: 269 DLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR 328
Query: 318 ILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAE 372
+L++TD+ ARG+D V L+IN ++P++ Y+HR+GR+GRYG +G+ I V +
Sbjct: 329 VLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND 383
>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 = 331 bits (851), Expect = e-101
Identities = 122/356 (34%), Positives = 194/356 (54%), Gaps = 26/356 (7%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+ + + +G+ GF K S IQ A + GYD I Q++SGTGK+ F ++ L + I+L
Sbjct: 47 LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ-IELD 105
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVER-----PKRPVQIVV 142
++ Q ++LAPTRE+A QI VV ++G + IGGT V I+V
Sbjct: 106 LKATQALVLAPTRELAQQIQKVVMALGDY-MGASCHACIGGTNVRAEVQKLQMEAPHIIV 164
Query: 143 GSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATY 202
G+PGR+ M+ +YL+ +++F++DEAD++++ GF + I I+ +L Q++++SAT
Sbjct: 165 GTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM 224
Query: 203 SHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK---L 256
D L +K+M DP+ I + L G++Q Y++ EE K L
Sbjct: 225 PSDVLEVTKKFMRDPIRILVKKEELTLEGIRQ-------------FYINVEREEWKLDTL 271
Query: 257 VQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKV 316
L Q VIF N + + + + E + +F + G DQK R + F+ G
Sbjct: 272 CDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS 331
Query: 317 RILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAE 372
R+L+TTDL ARGID V LVIN ++P + Y+HR+GR GR+G +G+ I +V+ E
Sbjct: 332 RVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEE 387
>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 = 325 bits (835), Expect = 3e-99
Identities = 116/364 (31%), Positives = 186/364 (51%), Gaps = 35/364 (9%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNG--YDAIVQSKSGTGKSIVFVVAALNKLIK 85
++ + QG+ GF + S IQ A P +L + I QS+SGTGK+ FV+A L++ ++
Sbjct: 32 LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQ-VE 90
Query: 86 LPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERP-KRPVQIVVGS 144
+ PQ + L+PT E+A+Q V+ +G L + Y + G ++ER K QIV+G+
Sbjct: 91 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGT 150
Query: 145 PGRIKQMI-KLKYLNMDSVRLFIMDEADK-LINTGFVEDITWIYSQLPPMKQMLVVSATY 202
PG + KLK+++ +++F++DEAD + G + I LP QML+ SAT+
Sbjct: 151 PGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATF 210
Query: 203 SHDNLATLQKYMVDP--LLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK-- 255
QK + DP + ++ E+ T +KQ YV ++K
Sbjct: 211 EDSVWKFAQKVVPDPNVIKLKREEETLD--TIKQ-------------YYVLCSSRDEKFQ 255
Query: 256 -LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRG 314
L L Q +IF + + + L+ LSG + R A ++ F+ G
Sbjct: 256 ALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREG 315
Query: 315 KVRILVTTDLAARGIDAANVDLVINLEIP------HDAATYLHRMGRAGRYGTRGLVITI 368
K ++LVTT++ ARGID V +VIN ++P D TYLHR+GR GR+G RGL + +
Sbjct: 316 KEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNM 375
Query: 369 VSAE 372
V ++
Sbjct: 376 VDSK 379
>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 = 317 bits (815), Expect = 1e-96
Identities = 97/360 (26%), Positives = 174/360 (48%), Gaps = 34/360 (9%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNG--YDAIVQSKSGTGKSIVFVVAALNKLIK 85
+ + +G+ F K S IQ A P +L+ + I QS+SGTGK+ F + L + +
Sbjct: 12 LAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTR-VN 70
Query: 86 LPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERPKRPVQIVVGSP 145
PQ I LAP+RE+A Q +VV+ +G K + + + + Q++VG+P
Sbjct: 71 PEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQ-LIVPDSFEKNKQINAQVIVGTP 129
Query: 146 GRIKQMIKLKYLNMDSVRLFIMDEADKLINT-GFVEDITWIYSQLPPMKQMLVVSATYSH 204
G + +++ K + + +++F++DEAD +++ G + + LP Q+++ SAT++
Sbjct: 130 GTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFAD 189
Query: 205 DNLATLQKYMVDP--LLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK---L 256
+K + + L ++ + +KQ Y+D E K L
Sbjct: 190 AVRQYAKKIVPNANTLELQTNEVNVD--AIKQ-------------LYMDCKNEADKFDVL 234
Query: 257 VQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKV 316
+L +IF + V+ L + L G + R +D F+ G+
Sbjct: 235 TELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRS 294
Query: 317 RILVTTDLAARGIDAANVDLVINLEIP------HDAATYLHRMGRAGRYGTRGLVITIVS 370
++L+TT++ ARGID V +V+N ++P D ATY+HR+GR GR+G +G+ I+ V
Sbjct: 295 KVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVH 354
>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 = 320 bits (821), Expect = 2e-96
Identities = 118/364 (32%), Positives = 188/364 (51%), Gaps = 35/364 (9%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGY--DAIVQSKSGTGKSIVFVVAALNKLIK 85
++ + QG+ GF + S IQ A P +L + I QS+SGTGK+ FV+A L++ ++
Sbjct: 99 LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQ-VE 157
Query: 86 LPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERP-KRPVQIVVGS 144
+ PQ + L+PT E+A+Q V+ +G L + Y + G ++ER K QIV+G+
Sbjct: 158 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGT 217
Query: 145 PGRIKQMI-KLKYLNMDSVRLFIMDEADKLINT-GFVEDITWIYSQLPPMKQMLVVSATY 202
PG + KLK+++ +++F++DEAD +I T G + I LP QML+ SAT+
Sbjct: 218 PGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATF 277
Query: 203 SHDNLATLQKYMVDP--LLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD---EEKK-- 255
QK + DP + ++ E+ T +KQ YV ++K
Sbjct: 278 EDSVWKFAQKVVPDPNVIKLKREEETLD--TIKQ-------------YYVLCSSRDEKFQ 322
Query: 256 -LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRG 314
L L Q +IF + + + L+ LSG + R A ++ F+ G
Sbjct: 323 ALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREG 382
Query: 315 KVRILVTTDLAARGIDAANVDLVINLEIP------HDAATYLHRMGRAGRYGTRGLVITI 368
K ++LVTT++ ARGID V +VIN ++P D TYLHR+GR GR+G RGL + +
Sbjct: 383 KEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNM 442
Query: 369 VSAE 372
V ++
Sbjct: 443 VDSK 446
>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 = 272 bits (698), Expect = 5e-82
Identities = 92/348 (26%), Positives = 162/348 (46%), Gaps = 28/348 (8%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+ + I Q ++E GF + +Q P +L G + +V++K+G+GK+ + + L
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVE---RPKRPVQIVVGS 144
+++++ PTRE+ Q+ +R +G + + V GG + R IVV +
Sbjct: 56 --GMKSLVVTPTRELTRQVASHIRDIGRY-MDTKVAEVYGGMPYKAQINRVRNADIVVAT 112
Query: 145 PGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYSH 204
PGR+ + +++ S + I+DEAD + GF++DI I +Q K + SAT
Sbjct: 113 PGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPE 172
Query: 205 DNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLVQLLSQTP 264
+ ++ ++ + I V+ + D+ + VQ L +
Sbjct: 173 EIRKVVKDFITNYEEIEAC-IGLAN--VEHKFVHVK----------DDWRSKVQALRENK 219
Query: 265 FNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDL 324
++F R L A L G Q R ++D+F+ G+ +L+TTD+
Sbjct: 220 DKGVIVFV----RTRNRVAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDV 275
Query: 325 AARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAE 372
A+RG+D V+ VIN + P D TY+HR+GR GR G +G IT + E
Sbjct: 276 ASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILNE 323
>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 = 269 bits (689), Expect = 3e-80
Identities = 108/348 (31%), Positives = 182/348 (52%), Gaps = 22/348 (6%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNG-YDAIVQSKSGTGKSIVFVVAALNKLIKL 86
+ I ++ GF K + IQM P LN Y+ + Q+++G+GK+ F + + +
Sbjct: 13 LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVN-- 70
Query: 87 PVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPVQIVV 142
+ IIL PTRE+A+Q+ D + S+ + KNL + GG Q++ K IVV
Sbjct: 71 ENNGIEAIILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIKALKNA-NIVV 128
Query: 143 GSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATY 202
G+PGRI I LN+ +V+ FI+DEAD+++N GF++D+ I + K++L+ SAT
Sbjct: 129 GTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATM 188
Query: 203 SHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLVQLLSQ 262
+ L +KYM D I+ + ++Q + E + + L +LL
Sbjct: 189 PREILNLAKKYMGDYSFIKAKINAN----IEQSYVEVNE--------NERFEALCRLLKN 236
Query: 263 TPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTT 322
F ++F + + + L + F A + G Q R + FK+ K+RIL+ T
Sbjct: 237 KEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIAT 295
Query: 323 DLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVS 370
D+ +RGID +++ VIN +P + +Y+HR+GR GR G +G I+I++
Sbjct: 296 DVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIIN 343
>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 = 258 bits (662), Expect = 4e-74
Identities = 115/570 (20%), Positives = 214/570 (37%), Gaps = 68/570 (11%)
Query: 18 IDVLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNG--YDAIVQSKSGTGKSIVF 75
+D L E + +++K I + + F +P+Q +L+ +D I ++K+GTGK+ F
Sbjct: 19 LDSLLE-EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAF 77
Query: 76 VVAALNKLIKL---PVQQPQTIILAPTREIAVQITDVVRSVGAH---VKNLHVDYFIGGT 129
++ LI + +I+APTR++A+QI V+ + +K +GGT
Sbjct: 78 LIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGT 137
Query: 130 QVER-----PKRPVQIVVGSPGRIKQMIKLKYLNM-DSVRLFIMDEADKLINTGFVEDIT 183
K IV+ +PGR+ +++ V ++DEAD+L+ GF +D+
Sbjct: 138 DFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLE 197
Query: 184 WIYSQLP-------PMKQMLVVSATYSHD--NLATLQKYMVDPLLIR----PEDATRPLL 230
I L + L+ SAT LA M + ++
Sbjct: 198 TISGILNEKNSKSADNIKTLLFSATLDDKVQKLA--NNIMNKKECLFLDTVDKNEPEAHE 255
Query: 231 GVKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANAN- 289
+ Q V + + N V+ KK Q+ + + +IF+ +C L N
Sbjct: 256 RIDQSVVISEKFANSIFAAVEHIKK--QIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK 313
Query: 290 --FGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAA 347
G Q R + + FK+ + ILV TD+ ARG+D NV V+ + +P + A
Sbjct: 314 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 373
Query: 348 TYLHRMGRAGRYGTRGLVITIVSAESLVKFHSLMGEINLDHAFN---------------- 391
Y+HR+GR R G G + + + L L N+ A
Sbjct: 374 NYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEA 433
Query: 392 VGLVPDNLTGDQINWTQRVQTLLAKPLDQ------------AQEREDVEQTAEESSKVEN 439
V P++++ I+ ++ + + D + S + +
Sbjct: 434 VTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLD 493
Query: 440 TKPLRGAPSKEVTKKGASKEGTKWNLTDGQSEEESDSENDGKPDENGSQRGSKRSKEFKT 499
L +P + + N +++S+ G ++N + R R + +
Sbjct: 494 KLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRG--NKNYNNRSQNRDYDDEP 551
Query: 500 QEKCVKGAGEDENGDRKASKDEQKIDGANS 529
+ + R K+ +N
Sbjct: 552 FR---RSNNNRRSFSRSNDKNNYSSRNSNI 578
>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 = 253 bits (647), Expect = 2e-72
Identities = 95/382 (24%), Positives = 163/382 (42%), Gaps = 35/382 (9%)
Query: 19 DVLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNG--YDAIVQSKSGTGKSIVFV 76
D L E + +++K I + + F +P+Q +L+ +D I ++K+GTGK+ F+
Sbjct: 71 DSLLE-EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL 129
Query: 77 VAALNKLIKL---PVQQPQTIILAPTREIAVQITDVVRSVGAH---VKNLHVDYFIGGTQ 130
+ LI + +I+APTR++A+QI V+ + +K +GGT
Sbjct: 130 IPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTD 189
Query: 131 VER-----PKRPVQIVVGSPGRIKQMIKLKYLNM-DSVRLFIMDEADKLINTGFVEDITW 184
K IV+ +PGR+ +++ V ++DEAD+L+ GF +D+
Sbjct: 190 FRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLET 249
Query: 185 IYSQLP-------PMKQMLVVSATYSHD--NLATLQKYMVDPLLIR----PEDATRPLLG 231
I L + L+ SAT LA M + ++
Sbjct: 250 ISGILNEKNSKSADNIKTLLFSATLDDKVQKLA--NNIMNKKECLFLDTVDKNEPEAHER 307
Query: 232 VKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANAN-- 289
+ Q V + + N V+ KK Q+ + + +IF+ +C L N
Sbjct: 308 IDQSVVISEKFANSIFAAVEHIKK--QIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK 365
Query: 290 -FGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAAT 348
G Q R + + FK+ + ILV TD+ ARG+D NV V+ + +P + A
Sbjct: 366 DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELAN 425
Query: 349 YLHRMGRAGRYGTRGLVITIVS 370
Y+HR+GR R G G + +
Sbjct: 426 YIHRIGRTARSGKEGSSVLFIC 447
>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 = 231 bits (591), Expect = 4e-69
Identities = 108/216 (50%), Positives = 135/216 (62%), Gaps = 6/216 (2%)
Query: 10 RTKDVLSNIDVLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGT 69
RT DVL FE +L+ +P+ +GL+ GF + SP+Q+ A P G D IVQ+KSGT
Sbjct: 14 RTGDVLLAEPADFE-SLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGT 72
Query: 70 GKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT 129
GK+ VF AL+ + L Q +ILAPTREIAVQI V+ ++G ++ L FIGGT
Sbjct: 73 GKTCVFSTIALDS-LVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGT 131
Query: 130 QVERPKR---PVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTG-FVEDITWI 185
+ + K I VGSPGRIKQ+I+L YLN S+RLFI+DEADKL+ G F E I WI
Sbjct: 132 PLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWI 191
Query: 186 YSQLPPMKQMLVVSATYSHDNLATLQKYMVDPLLIR 221
YS LP KQML VSATY L KYM DP +R
Sbjct: 192 YSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVR 227
>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 = 225 bits (577), Expect = 2e-64
Identities = 94/357 (26%), Positives = 180/357 (50%), Gaps = 30/357 (8%)
Query: 32 IRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLI----KLP 87
I + ++G+ +PIQ + P + +G D + +++G+GK+ F++ L+KL+ +L
Sbjct: 67 IIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELE 126
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPVQIVVG 143
+ +PQ +I++PTRE+A+QI + R L + GGT Q E R +V+
Sbjct: 127 LGRPQVVIVSPTRELAIQIFNEARKFA-FESYLKIGIVYGGTSFRHQNECITRGCHVVIA 185
Query: 144 SPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQ--LPPMKQMLVVSAT 201
+PGR+ + ++ + R ++DEAD++++ GF ED+ I + + P Q L+ SAT
Sbjct: 186 TPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSAT 245
Query: 202 YSHD--NLATLQKYMVDPLLI---RPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKL 256
+ + +A +++ + + + A VKQ + + + + KL
Sbjct: 246 FPEEIQRMA--GEFLKNYVFVAIGIVGGACS---DVKQTIYEVNK--------YAKRSKL 292
Query: 257 VQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKV 316
+++LS+ + ++F + + + L+ F + G + Q R +L FK G +
Sbjct: 293 IEILSEQA-DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSM 351
Query: 317 RILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAES 373
++L+ T +A+RG+D N+ VIN ++P Y+HR+GR GR G G + E
Sbjct: 352 KVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEK 408
>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 = 213 bits (544), Expect = 9e-63
Identities = 74/197 (37%), Positives = 122/197 (61%), Gaps = 5/197 (2%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+++ + +G+ GF + S IQ A ++ G+D + Q++SGTGK+ F +AAL + I
Sbjct: 21 LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR-IDTS 79
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERPKRP---VQIVVGS 144
V+ PQ ++LAPTRE+A+QI VV ++ H ++ V IGGT QIVVG+
Sbjct: 80 VKAPQALMLAPTRELALQIQKVVMALAFH-MDIKVHACIGGTSFVEDAEGLRDAQIVVGT 138
Query: 145 PGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYSH 204
PGR+ I+ + D +++FI+DEAD+++++GF E I I++ LPP Q++++SAT +
Sbjct: 139 PGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 198
Query: 205 DNLATLQKYMVDPLLIR 221
D L K+M +P+ I
Sbjct: 199 DVLEVTTKFMRNPVRIL 215
>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 = 213 bits (545), Expect = 9e-63
Identities = 68/199 (34%), Positives = 117/199 (58%), Gaps = 7/199 (3%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+++ + +G+ GF K S IQ A + GYD I Q++SGTGK+ F ++ L + +++
Sbjct: 37 LKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQ-LEIE 95
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVER-----PKRPVQIVV 142
++ Q ++LAPTRE+A QI V+ ++G + IGGT V IVV
Sbjct: 96 FKETQALVLAPTRELAQQIQKVILALGDY-MGATCHACIGGTNVRNEMQKLQAEAPHIVV 154
Query: 143 GSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATY 202
G+PGR+ M+ +YL+ +++F++DEAD++++ GF + I I+ +L Q++++SAT
Sbjct: 155 GTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM 214
Query: 203 SHDNLATLQKYMVDPLLIR 221
D L +K+M DP+ I
Sbjct: 215 PTDVLEVTKKFMRDPIRIL 233
>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 = 210 bits (538), Expect = 3e-62
Identities = 62/197 (31%), Positives = 109/197 (55%), Gaps = 5/197 (2%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+++ + G+ E G+ K SPIQ + P L+G D + ++K+GTGKS +++ L + + L
Sbjct: 10 LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER-LDLK 68
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPVQIVVG 143
Q +++ PTRE+A+Q++ + V H+ V GGT + R V +V+
Sbjct: 69 KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIA 128
Query: 144 SPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYS 203
+PGRI +IK +D V++ ++DEADKL++ FV+ + I LP +Q+L+ SAT+
Sbjct: 129 TPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFP 188
Query: 204 HDNLATLQKYMVDPLLI 220
+ ++ P I
Sbjct: 189 LSVQKFMNSHLEKPYEI 205
>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 = 207 bits (529), Expect = 9e-61
Identities = 66/204 (32%), Positives = 106/204 (51%), Gaps = 7/204 (3%)
Query: 24 NDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKL 83
D L++ + + + + GF S +Q P + G D + Q+KSG GK+ VFV+A L +
Sbjct: 17 RDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ- 75
Query: 84 IKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPV- 138
++ Q +++ TRE+A QI+ ++ N+ V F GG E K+
Sbjct: 76 LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCP 135
Query: 139 QIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADK-LINTGFVEDITWIYSQLPPMKQMLV 197
IVVG+PGRI + + K LN+ ++ FI+DE DK L D+ I+ P KQ+++
Sbjct: 136 HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMM 195
Query: 198 VSATYSHDNLATLQKYMVDPLLIR 221
SAT S + +K+M DP+ I
Sbjct: 196 FSATLSKEIRPVCRKFMQDPMEIF 219
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 210 bits (536), Expect = 3e-59
Identities = 98/386 (25%), Positives = 183/386 (47%), Gaps = 55/386 (14%)
Query: 30 KPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPV- 88
+ I ++ + + +P+Q A P + D + +++G+GK+ F++ L+++
Sbjct: 24 EIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPG 83
Query: 89 ----------------QQPQTIILAPTREIAVQITDVVR--SVGAHVKNLHVDYFIGGT- 129
Q P +++LAPTRE+AVQI + R S + V+ V GG
Sbjct: 84 EALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVV---YGGAD 140
Query: 130 ---QVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIY 186
Q+ +R ++V +PGR+ M++ + +D + ++DEAD++++ GF I I
Sbjct: 141 IGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIV 200
Query: 187 SQL--PP--MKQMLVVSATYSHD--NLATLQKYMVDPLLI---RPEDATRPLLGVKQLVA 237
Q PP ++ ++ SAT+ + LA + ++ + + + R + + Q V
Sbjct: 201 EQDTMPPKGVRHTMMFSATFPKEIQMLA--RDFLDEYIFLAVGRVGSTS---ENITQKVV 255
Query: 238 LIPECKNPSLRYVDEEKKLVQLLSQTPFNQCV-IFSNYQLRPEVICENLANANFGAEYLS 296
+ E D+ L+ LL+ T + +F + + + + L + + +
Sbjct: 256 WVEE--------SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIH 307
Query: 297 GAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRA 356
G + Q+ R +L F+ GK ILV T +AARG+D +NV VIN ++P D Y+HR+GR
Sbjct: 308 GDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRT 367
Query: 357 GRYGTRGLVITIVS------AESLVK 376
GR G GL + + + L+
Sbjct: 368 GRVGNLGLATSFFNERNINITKDLLD 393
>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 = 205 bits (524), Expect = 5e-59
Identities = 69/199 (34%), Positives = 112/199 (56%), Gaps = 6/199 (3%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGY--DAIVQSKSGTGKSIVFVVAALNKLIK 85
++ + QG+ GF + S IQ A P +L + I QS+SGTGK+ FV+A L++ ++
Sbjct: 99 LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQ-VE 157
Query: 86 LPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERP-KRPVQIVVGS 144
+ PQ + L+PT E+A+Q V+ +G L + Y + G ++ER K QIV+G+
Sbjct: 158 PANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGT 217
Query: 145 PGRIKQMI-KLKYLNMDSVRLFIMDEADKLINT-GFVEDITWIYSQLPPMKQMLVVSATY 202
PG + KLK+++ +++F++DEAD +I T G + I LP QML+ SAT+
Sbjct: 218 PGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATF 277
Query: 203 SHDNLATLQKYMVDPLLIR 221
QK + DP +I+
Sbjct: 278 EDSVWKFAQKVVPDPNVIK 296
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 200 bits (511), Expect = 6e-56
Identities = 66/437 (15%), Positives = 142/437 (32%), Gaps = 60/437 (13%)
Query: 30 KPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQ 89
+ R ++ + Q ++ G + + +G GK+ ++ AL K
Sbjct: 8 EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK---- 63
Query: 90 QPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKR----PVQIV 141
++ ++ PT + Q + ++ + + + F + + K I+
Sbjct: 64 GKKSALVFPTVTLVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEKSFEEDDYHIL 121
Query: 142 VGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSAT 201
V S + + L+ +D+ D ++ D + +P S
Sbjct: 122 VFSTQFV--SKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTI 179
Query: 202 YSHDNLATLQKYMVDPLLI-----RPEDATRPLLGVKQLVALIPECKNPSLR-------Y 249
+ L++ +P L + L+ R
Sbjct: 180 KQGKIYERPKNLKPGILVVSSATAKPRGIRPLLF--RDLLNFTVGRLVSVARNITHVRIS 237
Query: 250 VDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLD 309
++KLV+LL + +IF+ + + + E L F ++ + +
Sbjct: 238 SRSKEKLVELLEIFR-DGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEK-----NFE 291
Query: 310 SFKRGKVRILVTTD----LAARGIDAAN-VDLVINLEIPH--DAATYLHRMGRAGRYGTR 362
FK GK+ IL+ RG+D + VI P D TY+ GR+ R
Sbjct: 292 DFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNG 351
Query: 363 GL--VITIVSAESLVKFHSLMGEINLDHAFNVGLVPDNLTGDQINWTQRVQTLLAKPLDQ 420
L ++++ E F SL + L + + + + + +
Sbjct: 352 VLVKGVSVIFEEDEEIFESLKTRLLLI--------------AEEEIIEEAEANWKELVHE 397
Query: 421 AQE-REDVEQTAEESSK 436
+E R E+ ++S+
Sbjct: 398 VEESRRRSERELTDTSR 414
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 193 bits (492), Expect = 7e-56
Identities = 62/201 (30%), Positives = 104/201 (51%), Gaps = 8/201 (3%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+ I + ++ F K + IQ P L G + QS++GTGK+ +++ + K IK
Sbjct: 11 FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEK-IKPE 69
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHV---KNLHVDYFIGGT----QVERPKRPVQI 140
+ Q +I APTRE+A QI + + + IGGT +E+ I
Sbjct: 70 RAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHI 129
Query: 141 VVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSA 200
V+G+PGRI I+ + L++ + + ++DEAD +++ GF+ D+ I +++P QMLV SA
Sbjct: 130 VIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSA 189
Query: 201 TYSHDNLATLQKYMVDPLLIR 221
T L+KYM +P +
Sbjct: 190 TIPEKLKPFLKKYMENPTFVH 210
>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 = 176 bits (449), Expect = 3e-50
Identities = 65/200 (32%), Positives = 110/200 (55%), Gaps = 9/200 (4%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKL--IK 85
++ I + L G +PIQ AA P L G D I Q+++GTGK++ F + +L +
Sbjct: 8 LKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ 67
Query: 86 LPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPVQIV 141
++P+ ++L PTRE+A+Q+ + +V H+K + V GGT Q E R V
Sbjct: 68 ERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAV---YGGTGYGKQKEALLRGADAV 124
Query: 142 VGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSAT 201
V +PGR ++ L++ V + ++DEAD++++ GF E++ + S PP +Q L+ SAT
Sbjct: 125 VATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSAT 184
Query: 202 YSHDNLATLQKYMVDPLLIR 221
++YM +P+LI
Sbjct: 185 LPSWAKRLAERYMKNPVLIN 204
>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 = 155 bits (394), Expect = 2e-42
Identities = 53/199 (26%), Positives = 106/199 (53%), Gaps = 9/199 (4%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
+ + + + G+ K + IQ+ A P L G D I +++G+GK+ F + LN L++ P
Sbjct: 50 VTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP 109
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGG----TQVERPKRPVQIVVG 143
Q+ ++L PTRE+A QI++ ++G+ + + +GG +Q + I++
Sbjct: 110 -QRLFALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKKPHIIIA 167
Query: 144 SPGR-IKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATY 202
+PGR I + K N+ +++ +MDEAD+++N F ++ I +P ++ + SAT
Sbjct: 168 TPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATM 227
Query: 203 SHDNLATLQK-YMVDPLLI 220
+ + LQ+ + +P+
Sbjct: 228 T-KKVQKLQRAALKNPVKC 245
>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 = 149 bits (378), Expect = 3e-41
Identities = 51/128 (39%), Positives = 71/128 (55%), Gaps = 3/128 (2%)
Query: 249 YVDEEKK---LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARL 305
+ + +K L LL FNQ VIF R + + L NF A + Q+ RL
Sbjct: 12 KLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERL 71
Query: 306 ASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLV 365
+ FK + RILV T+L RG+D V++ N ++P D+ TYLHR+ RAGR+GT+GL
Sbjct: 72 SRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLA 131
Query: 366 ITIVSAES 373
IT VS E+
Sbjct: 132 ITFVSDEN 139
>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 = 151 bits (384), Expect = 3e-41
Identities = 57/203 (28%), Positives = 104/203 (51%), Gaps = 12/203 (5%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKL- 86
+ K +GLQE + + IQ L G D + +K+G+GK++ F+V L L +L
Sbjct: 32 LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQ 91
Query: 87 --PVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGG----TQVERPKRPVQI 140
+I++PTRE+A Q +V+R VG + + IGG + ER I
Sbjct: 92 WTSTDGLGVLIISPTRELAYQTFEVLRKVGKN-HDFSAGLIIGGKDLKHEAERINNI-NI 149
Query: 141 VVGSPGRIKQ-MIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVS 199
+V +PGR+ Q M + + +++ ++DEAD++++ GF + + + LP +Q L+ S
Sbjct: 150 LVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFS 209
Query: 200 ATYSHDNLATLQK-YMVDPLLIR 221
AT + ++ L + + +P +
Sbjct: 210 ATQT-KSVKDLARLSLKNPEYVW 231
>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 = 140 bits (356), Expect = 2e-37
Identities = 57/210 (27%), Positives = 105/210 (50%), Gaps = 15/210 (7%)
Query: 22 FENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALN 81
F++ + + + G +K +PIQ A+P +L G D IV +++GTGK++ +++
Sbjct: 21 FKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFI 80
Query: 82 KLIKLPVQQ-----PQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVE 132
L P+ + P ++L PTRE+A+ + K L GG Q+E
Sbjct: 81 HLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIE 138
Query: 133 RPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPM 192
+ V I++ +PGR+ + +N+ S+ ++DEADK+++ F I I + P
Sbjct: 139 DISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPD 198
Query: 193 KQMLVVSATYSHD--NLATLQKYMVDPLLI 220
+Q ++ SAT+ LA Y+ DP+++
Sbjct: 199 RQTVMTSATWPDTVRQLA--LSYLKDPMIV 226
>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 = 142 bits (359), Expect = 2e-37
Identities = 55/208 (26%), Positives = 110/208 (52%), Gaps = 16/208 (7%)
Query: 25 DVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLI 84
L+ + + ++E GF + IQ + +L G D + +K+G+GK++ F++ A+ ++
Sbjct: 58 CNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIV 117
Query: 85 KLPVQQPQT---IILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGG----TQVERPKRP 137
KL +IL+PTRE+A+Q V++ + H +GG + ++
Sbjct: 118 KLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNG 176
Query: 138 VQIVVGSPGRIKQ-MIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQML 196
+ I+V +PGR+ M +++ ++DEAD++++ GF E++ I LP +Q +
Sbjct: 177 INIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTM 236
Query: 197 VVSATYSH--DNLA--TLQKYMVDPLLI 220
+ SAT + ++LA +L+K +PL +
Sbjct: 237 LFSATQTRKVEDLARISLKK---EPLYV 261
>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 = 140 bits (355), Expect = 3e-37
Identities = 46/206 (22%), Positives = 97/206 (47%), Gaps = 16/206 (7%)
Query: 28 IEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLP 87
I + Q + + GF +PIQM A P +L+G + + + +G+GK++ F + L +L +
Sbjct: 36 INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA 95
Query: 88 VQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERP-----KRPVQIVV 142
+ + +I++PTRE+A QI + + + + + I+V
Sbjct: 96 NKGFRALIISPTRELASQIHRELIKISEG-TGFRIHMIHKAAVAAKKFGPKSSKKFDILV 154
Query: 143 GSPGRIKQMIKLK--YLNMDSVRLFIMDEADKL---INTGFVEDITWIYSQL-PPMKQML 196
+P R+ ++K +++ SV ++DE+DKL TGF + + I+ +
Sbjct: 155 TTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRA 214
Query: 197 VVSATYSHD--NLATLQKYMVDPLLI 220
+ SAT+++D + + + + +
Sbjct: 215 MFSATFAYDVEQWC--KLNLDNVISV 238
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 135 bits (341), Expect = 3e-36
Identities = 49/130 (37%), Positives = 68/130 (52%), Gaps = 6/130 (4%)
Query: 249 YVD---EEKK---LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQK 302
YV+ EE K L L Q VIF N + + E + L N F + Q+
Sbjct: 8 YVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQ 67
Query: 303 ARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTR 362
R + F+ G RIL++TDL ARGID V LVIN ++P + Y+HR+GR GR+G +
Sbjct: 68 ERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRK 127
Query: 363 GLVITIVSAE 372
G+ I V+ E
Sbjct: 128 GVAINFVTNE 137
>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 = 135 bits (342), Expect = 2e-35
Identities = 52/200 (26%), Positives = 99/200 (49%), Gaps = 13/200 (6%)
Query: 31 PIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQ 90
+ + F + + IQ +P L+G D + +++G+GK++ +++ A+ + P +
Sbjct: 39 NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLE 98
Query: 91 ----PQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT----QVERPKRPVQIVV 142
P ++LAPTRE+A Q+ V L GG Q+ +R V+I +
Sbjct: 99 RGDGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERGVEICI 157
Query: 143 GSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATY 202
+PGR+ ++ N+ ++DEAD++++ GF I I Q+ P +Q L+ SAT+
Sbjct: 158 ATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATW 217
Query: 203 SHD--NLATLQKYMVDPLLI 220
+ LA + ++ D + I
Sbjct: 218 PKEVRQLA--EDFLKDYIHI 235
>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 = 131 bits (333), Expect = 3e-35
Identities = 44/128 (34%), Positives = 63/128 (49%), Gaps = 4/128 (3%)
Query: 249 YVDEEKK----LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKAR 304
D+ + LV LL Q + ++F + R + L A YL G Q R
Sbjct: 10 RADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKR 69
Query: 305 LASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGL 364
++ G+V +LV TD+AARGID +V V N ++P TYLHR+GR R G +G
Sbjct: 70 NEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGT 129
Query: 365 VITIVSAE 372
I++V A
Sbjct: 130 AISLVEAH 137
>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 = 134 bits (341), Expect = 4e-35
Identities = 53/218 (24%), Positives = 103/218 (47%), Gaps = 22/218 (10%)
Query: 22 FENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALN 81
F+ L IR + + + +PIQ A P +L D + +++G+GK+ F++ +N
Sbjct: 25 FDELKLDP-TIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83
Query: 82 KLIKLPVQQ--------PQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGT---- 129
L+ + Q P+ +ILAPTRE+A+QI + + L GG
Sbjct: 84 HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHS 142
Query: 130 QVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQL 189
Q+ + ++V +PGR+ I+ ++++ + ++DEAD++++ GF I I +
Sbjct: 143 QIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEES 202
Query: 190 PPMK----QMLVVSATYSHD--NLATLQKYMVDPLLIR 221
Q L+ SAT+ + LA ++ + + +
Sbjct: 203 NMPSGINRQTLMFSATFPKEIQKLA--ADFLYNYIFMT 238
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 131 bits (331), Expect = 6e-35
Identities = 46/126 (36%), Positives = 70/126 (55%), Gaps = 3/126 (2%)
Query: 250 VDEEKK---LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLA 306
V EE K L +L + C+IF + + + L + + + + G Q+ R
Sbjct: 17 VREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFD 76
Query: 307 SLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVI 366
++ FKRG+ R LV TD+AARGID N+ LVIN ++P + +Y+HR GR GR G +G I
Sbjct: 77 VMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAI 136
Query: 367 TIVSAE 372
+ V+A
Sbjct: 137 SFVTAF 142
>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 = 127 bits (321), Expect = 2e-33
Identities = 38/133 (28%), Positives = 64/133 (48%), Gaps = 9/133 (6%)
Query: 251 DEEKK---LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLAS 307
+ K L + Q +IF + + + + LSG + R +
Sbjct: 17 HRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASI 76
Query: 308 LDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIP------HDAATYLHRMGRAGRYGT 361
+ F+ GK ++L+TT++ ARGID V +V+N ++P D TYLHR+GR GR+G
Sbjct: 77 IQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGK 136
Query: 362 RGLVITIVSAESL 374
+GL ++ + L
Sbjct: 137 KGLAFNMIEVDEL 149
>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 = 111 bits (281), Expect = 1e-27
Identities = 50/195 (25%), Positives = 84/195 (43%), Gaps = 14/195 (7%)
Query: 250 VDEEKK---LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLA 306
+ L LL ++ ++F+ + E I + L A+ L G Q R
Sbjct: 13 APVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERER 72
Query: 307 SLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVI 366
L +F++G+VR+LV TD+AARG+D VDLV++ +P A Y HR GR GR G G V+
Sbjct: 73 VLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVV 132
Query: 367 TIVSAESLVKFHSLMGEINLDHAFNVGLVPDNLTGDQINWTQRVQTLLAKPLDQAQE--- 423
+ +L + F P T +++ + + LLA+ ++
Sbjct: 133 LLYGPRERRDVEALERAVGRR--FKRVNPP---TPEEVL-EAKWRHLLARLARVPEKDYR 186
Query: 424 --REDVEQTAEESSK 436
++ + E
Sbjct: 187 LYQDFAGRLFAEGRV 201
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 108 bits (271), Expect = 1e-26
Identities = 47/168 (27%), Positives = 79/168 (47%), Gaps = 22/168 (13%)
Query: 210 LQKYMVDPL--LIRPEDATRPLLG-----VKQLVALIPECKNPSLRYVDEEKK---LVQL 259
+ + + E+ +G V Q V YV EE K L++
Sbjct: 1 MHHHHHHSSGVDLGTENLYFQSMGAASLDVIQEV-----------EYVKEEAKMVYLLEC 49
Query: 260 LSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRIL 319
L +TP +IF+ + + I E L A + G +DQ+ R ++++F+ GK +L
Sbjct: 50 LQKTP-PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVL 108
Query: 320 VTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVIT 367
V TD+A++G+D + VIN ++P + Y+HR+GR G G G+ T
Sbjct: 109 VATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATT 156
>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 = 108 bits (272), Expect = 1e-25
Identities = 41/115 (35%), Positives = 62/115 (53%)
Query: 256 LVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGK 315
L LL ++ ++F+ + E I + L A+ L G Q R + +F++G+
Sbjct: 19 LSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGE 78
Query: 316 VRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVS 370
VR+LV TD+AARG+D VDLV++ +P A Y HR GR GR G G V+ +
Sbjct: 79 VRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYG 133
>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 = 104 bits (262), Expect = 2e-25
Identities = 42/123 (34%), Positives = 68/123 (55%), Gaps = 4/123 (3%)
Query: 249 YVDEEKK---LVQLLSQT-PFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKAR 304
+V+E K L+ LL+ T + ++F + + + + L + + + G + Q+ R
Sbjct: 26 WVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDR 85
Query: 305 LASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGL 364
+L F+ GK ILV T +AARG+D +NV VIN ++P D Y+HR+GR GR G GL
Sbjct: 86 EEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGL 145
Query: 365 VIT 367
+
Sbjct: 146 ATS 148
>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 = 80.2 bits (197), Expect = 3e-15
Identities = 42/193 (21%), Positives = 77/193 (39%), Gaps = 15/193 (7%)
Query: 192 MKQMLVVSATYSHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVD 251
+ + + T L K + + A++ + K++ I +D
Sbjct: 282 LHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLD 341
Query: 252 EEK--KLVQLLSQ----TPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGA------- 298
K KL +++ + ++ ++F+NY+ + I L A+ G
Sbjct: 342 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDR 401
Query: 299 -QDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAG 357
Q+ + LD F RG+ +LV T + G+D VDLV+ E A + R GR G
Sbjct: 402 GLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTG 461
Query: 358 RYGTRGLVITIVS 370
R+ G VI +++
Sbjct: 462 RHMP-GRVIILMA 473
Score = 68.7 bits (167), Expect = 1e-11
Identities = 26/169 (15%), Positives = 70/169 (41%), Gaps = 8/169 (4%)
Query: 46 PIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQ 105
Q + + ++ +G GK+++ ++ A +L K + ++LAPT+ + +Q
Sbjct: 12 IYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKYGGK---VLMLAPTKPLVLQ 67
Query: 106 ITDVVRSVGAHVKNLHVDYFIGGTQVERPKRPV---QIVVGSPGRIKQMIKLKYLNMDSV 162
+ R + ++ + G E + +++V +P I+ + ++++ V
Sbjct: 68 HAESFRRL-FNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDV 126
Query: 163 RLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYSHDNLATLQ 211
L + DEA + + I Y + ++ ++A+ ++
Sbjct: 127 SLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIME 175
>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 = 67.3 bits (164), Expect = 4e-11
Identities = 66/431 (15%), Positives = 116/431 (26%), Gaps = 93/431 (21%)
Query: 20 VLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGY-DAIVQSKSGTGKSIVFVVA 78
V + E ++ P V + A + + +G+GKS A
Sbjct: 193 VCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAA 252
Query: 79 ALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHV-KNLHVDYFIGGTQVERPKRP 137
+ K ++L P+ GA++ K +D I T V
Sbjct: 253 YAAQGYK-------VLVLNPSVAAT-------LGFGAYMSKAHGIDPNI-RTGVRTITTG 297
Query: 138 VQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLV 197
+ + G+ + + + + I DE ++ + I + Q LV
Sbjct: 298 APVTYSTYGK---FLADGGCSGGAYDIIICDECHST-DSTTILGIGTVLDQAETAGARLV 353
Query: 198 VSATYSHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKN----PSLRYVDEE 253
V AT + T+ ++ + P G + I ++ S + DE
Sbjct: 354 VLATATPPGSVTVPHPNIEE-VALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKKCDE- 411
Query: 254 KKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKR 313
+ L+ A D
Sbjct: 412 ---------------------------LAAKLSGLGINAVAYYRGLDVSV-------IPT 437
Query: 314 GKVRILVTTDLAARG--IDAANVDLVI---------------------NLEIPHDAATYL 350
++V TD G D D VI +P DA +
Sbjct: 438 IGDVVVVATDALMTGYTGD---FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRS 494
Query: 351 HRMGRAGRYGTRGLVITIVSAESLVKFHSLMGEINLDHAFNVGLVPDNLTGDQINWTQRV 410
R GR GR G+ + E + + L ++ G LT + R+
Sbjct: 495 QRRGRTGRGRR-GIYRFVTPGE---RPSGMFDSSVLCECYDAGCAWYELT--PAETSVRL 548
Query: 411 QTLLAKPLDQA 421
+ L P
Sbjct: 549 RAYLNTPGLPV 559
>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 = 66.4 bits (162), Expect = 1e-10
Identities = 74/465 (15%), Positives = 161/465 (34%), Gaps = 79/465 (16%)
Query: 32 IRQGLQENGFVKESPIQMAAFPYVLN-GYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQ 90
I+ L+E G P Q A + G +A++ + +GK+++ +A +++++ Q
Sbjct: 12 IKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILT---QG 68
Query: 91 PQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERPKRP-VQIVVGSPGRIK 149
+ + + P + +A + + L V G + I++ + +
Sbjct: 69 GKAVYIVPLKALAEEKFQEFQDWEKI--GLRVAMATGDYDSKDEWLGKYDIIIATAEKFD 126
Query: 150 QMIKLKYLNMDSVRLFIMDE----ADKLINTGFV-EDITWIYSQLPPMKQMLVVSATYS- 203
+++ + V++ + DE + + G E I + + Q++ +SAT
Sbjct: 127 SLLRHGSSWIKDVKILVADEIHLIGSR--DRGATLEVIL---AHMLGKAQIIGLSATIGN 181
Query: 204 HDNLAT---------------LQKYMVDPLLIRPEDATRPLL-GVKQLVALIPECKNPSL 247
+ LA L++ + + ED + ++LV K +L
Sbjct: 182 PEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGAL 241
Query: 248 ------RYVDEE-----KKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANA-NFGAEYL 295
R + KK+ LL++ ++ L E LA A G +
Sbjct: 242 IFVNMRRKAERVALELSKKVKSLLTKPEIRALNELAD-SLEENPTNEKLAKAIRGGVAFH 300
Query: 296 SGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVI--NLEI-------PHDA 346
+ R+ ++F++G ++ +V T + GI+ VI ++
Sbjct: 301 HAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTP-AFRVIIRDIWRYSDFGMERIPI 359
Query: 347 ATYLHRMGRAGR--YGTRGLVITIVSAESLVKFH-------------SLMGEINLDHAFN 391
+GRAGR Y G I + +++ + L E NL
Sbjct: 360 IEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSNESNLRSQVL 419
Query: 392 VGLVPDNLT--GDQINWTQRVQTLLAKPLDQAQEREDVEQTAEES 434
+ + + + + T A Q ++ +E+
Sbjct: 420 ALIATFGYSTVEEILKFISN--TFYAY---QRKDTYSLEEKIRNI 459
>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-10
Identities = 68/391 (17%), Positives = 138/391 (35%), Gaps = 52/391 (13%)
Query: 30 KPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQ 89
L+E G + P Q A V +G + ++ + GK+++ +A + + IK
Sbjct: 12 SYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---- 67
Query: 90 QPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERPK-RPVQIVVGSPGRI 148
+++ + P R +A + + + L + G + I+V + +
Sbjct: 68 GGKSLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYESRDEHLGDCDIIVTTSEKA 125
Query: 149 KQMIKLKYLNMDSVRLFIMDE----ADKLINTGFV-EDITWIYSQLPPMKQMLVVSATYS 203
+I+ + + +V ++DE + G E + ++ +++ +SAT
Sbjct: 126 DSLIRNRASWIKAVSCLVVDEIHLLDSE--KRGATLEILVTKMRRMNKALRVIGLSATAP 183
Query: 204 -HDNLAT---------------LQKYMVDPLLIRPEDATRPLLGVKQLVALIPEC---KN 244
+A L + ++ + D + L+ EC
Sbjct: 184 NVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENG 243
Query: 245 PSL------RYVDEE-KKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANA-NFGAEYLS 296
L R ++ KL + ++ N+ + + + + LA GA +
Sbjct: 244 GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHH 303
Query: 297 GAQDQKARLASLDSFKRGKVRILVTTDLAARGID--AANVDLVINLEI------PHDAAT 348
R D+F+RG ++++V T A G++ A V +V +L +
Sbjct: 304 AGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRV-IVRSLYRFDGYSKRIKVSE 362
Query: 349 YLHRMGRAGR--YGTRGLVITIVSAESLVKF 377
Y GRAGR RG I IV
Sbjct: 363 YKQMAGRAGRPGMDERGEAIIIVGKRDREIA 393
>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 = 66.0 bits (160), Expect = 1e-10
Identities = 64/441 (14%), Positives = 121/441 (27%), Gaps = 150/441 (34%)
Query: 11 TKDVLSNIDVLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTG 70
K +LS ++ + +++ K G L + ++
Sbjct: 42 PKSILSKEEI---DHIIMSKDAVSGT-----------------LRL--FWTLLSK----Q 75
Query: 71 KSIV--FVVAALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGG 128
+ +V FV L K + +T P+ + I R + + Y
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ--RDRLYNDNQVFAKYN--- 130
Query: 129 TQVERPK------------RPVQIVV--GSPGRIKQMIKLKYLNMDSVRLFIMDEADKLI 174
V R + RP + V+ G G K + +D +
Sbjct: 131 --VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-----VALDVCL-------SYKV 176
Query: 175 NTGFVEDITWIYSQLPPMKQMLVVSATYSHDN-----LATLQK--YMVDPLLIRPEDATR 227
I W+ + N L LQK Y +DP D +
Sbjct: 177 QCKMDFKIFWL---------------NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS- 220
Query: 228 PLLGVKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLAN 287
N LR + +L +LL P+ C++ + N+ N
Sbjct: 221 ---------------SNIKLRIHSIQAELRRLLKSKPYENCLL----------VLLNVQN 255
Query: 288 ANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAA 347
A + ++F +IL+TT R D + AA
Sbjct: 256 AK-----------------AWNAFN-LSCKILLTT----R--FKQVTDFL-------SAA 284
Query: 348 TYLHRMGRAGRYG-----TRGLVITIVSAESLVKFHSLMGEINLDHAFNVGLVPDNLTGD 402
T H + L++ + + L E+ + + ++ +++
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLD----CRPQDLPREVLTTNPRRLSIIAESIRDG 340
Query: 403 QINWTQRVQTLLAKPLDQAQE 423
W + + L E
Sbjct: 341 LATW-DNWKHVNCDKLTTIIE 360
Score = 58.3 bits (140), Expect = 3e-08
Identities = 63/494 (12%), Positives = 123/494 (24%), Gaps = 125/494 (25%)
Query: 693 DTIPNDETSNDNKLTPV-------DFD--YINDFVNQ--TPSETGDRPLVHGPNSVPKID 741
D + + V +FD + D + E ++ ++V
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH--IIMSKDAVSGTL 65
Query: 742 TPSDDYLVANMKACLTNDSVRVQVLMEKLDHVDASVLADWILNKHNNVAALFRSEDQSNS 801
L + + + VQ +E++ ++ L I + + + R +
Sbjct: 66 -----RLFWTL--LSKQEEM-VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117
Query: 802 VRIGDNDGTGNRSITRSKQNSQSGDHTDLKD---SNRPNANT----DPSTGKNV---KDI 851
DN +++R + + L+ RP N +GK
Sbjct: 118 RLYNDNQVFAKYNVSRLQP------YLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171
Query: 852 QSREIKSYASLSMF----SPCQTTLNKFDTQYNSSDYQSDSKPYGDRTKRRSRPRKNKEN 907
S +++ +F C + + YQ D + R+ S + +
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL-YQID-PNWTSRSDHSSNIKLRIHS 229
Query: 908 T-DILNTLGQDKTSAHGRTPSGGHRTPERRRS----DGVRN-------D--------TRD 947
L L + K V+N + TR
Sbjct: 230 IQAELRRLLKSK---------------PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRF 274
Query: 948 ERNGAYTGDKGGRNRGHSVNSRKDHSFAGETPR-SKGGFDSYLDQSMDSFLDKSCREESF 1006
++ T H DH TP K YLD +
Sbjct: 275 KQV---TDFLSAATTTH---ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 1007 L------KRSHMPKR----DLVVYDDAFDMFSPAANNLDEYEI-DYVEQ----PVDEK-- 1049
V D + + N L+ E ++ P
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP 388
Query: 1050 ----------KSRRELSQKMDSDRYRPDSDGDPNRRPSSQESLHHNDSLDIKLRKKLKPG 1099
+ ++ ++ + P S S+ + ++L+ KL
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE---STISIPS---IYLELKVKL--- 439
Query: 1100 HRLQRNSKKRHSKI 1113
N H I
Sbjct: 440 ----ENEYALHRSI 449
Score = 45.2 bits (106), Expect = 3e-04
Identities = 51/271 (18%), Positives = 86/271 (31%), Gaps = 71/271 (26%)
Query: 1278 SYHDEHAVFLPNSSSEDDCDGLSHGDEANG-LASEDADEY--SGSSLNSS--CIDLNCDH 1332
Y D +VF DC + D L+ E+ D S +++ +
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQ--DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74
Query: 1333 LEN---DFSEEE------------AEEYLEETYVTDEYHECDDERCSHDDCGDLDY---- 1373
E F EE E + + +T Y E D R +D+ Y
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD-RLYNDNQVFAKYNVSR 133
Query: 1374 -QQYEKLR-GRQANTPTKTIGDTQGKRG-GRVNTRSNHVNSEDKS-------RVHTSEDR 1423
Q Y KLR P K + G G G K+ + + +
Sbjct: 134 LQPYLKLRQALLELRPAKNVL-IDGVLGSG-------------KTWVALDVCLSYKVQCK 179
Query: 1424 LNFKG-WIREMELYNVSTNVNVSDDDGLDESYNMIKTPTPRKRNGASGESSVEREDVGGG 1482
++FK W+ N+ N N S + L+ ++ P + + S+++
Sbjct: 180 MDFKIFWL------NLK-NCN-SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231
Query: 1483 KSLRNLL----LRRALMNKQNEV--NLWHRE 1507
LR LL L+ V N+ + +
Sbjct: 232 AELRRLLKSKPYENCLL-----VLLNVQNAK 257
Score = 42.5 bits (99), Expect = 0.002
Identities = 78/547 (14%), Positives = 152/547 (27%), Gaps = 167/547 (30%)
Query: 424 REDVEQTAEESSKVENTK----PLRGAPSKEVTK--KGASKEGTKWNLTDGQSEEESDSE 477
+E+++ V T L + V K + + K+ L E+
Sbjct: 48 KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF-LMSPIKTEQRQPS 106
Query: 478 NDGK-------PDENGSQRGSK----RSKEFKTQEKCVKGAGEDENGDRKASKDEQKI-- 524
+ N +Q +K R + + + + + + +
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL-----------RPAKNVLI 155
Query: 525 DG---------ANSA--EKSLEDKHGKKI-------TNSFEAVGEIVQN-----DTETTK 561
DG A ++ K KI NS E V E++Q D T
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS 215
Query: 562 ENNQTDEVPEE------------------NGL-----VGNPNKAEVGDLNEC-------- 590
++ + + N L V N +L+ C
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS-CKILLTTRF 274
Query: 591 ESCTDSFHMNEHS----DENDLGNNTKESQ----KQKGHKSKKKKDRKRKGNGDKRDPQG 642
+ TD + D + + E + K + + N P+
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN-----PRR 329
Query: 643 NNANQREIRDNSATLD-----------KTEKESVNNVESKDERP--------PSTANNPD 683
+ IRD AT D + S+N +E + R P +A+ P
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389
Query: 684 GT---EWEDIPSDTIPNDETSNDNKLTPVDFD------YINDFVNQTPSETGDRPLVH-- 732
W D+ + +K + V+ I + + + +H
Sbjct: 390 ILLSLIWFDVIKSD-VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS 448
Query: 733 ------GPNSVPKID--TPSDD-----YLVANMKACLTNDSVRVQVLMEKLDHVDASVLA 779
P + D P D ++ ++K + + L + +D
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMT---LFRMV-FLD----F 500
Query: 780 DWILNK--HNNVAALFRSE--DQSNSVR-----IGDNDGTGNRSIT-------RSKQNSQ 823
++ K H++ A + ++ I DND R + + ++N
Sbjct: 501 RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLI 560
Query: 824 SGDHTDL 830
+TDL
Sbjct: 561 CSKYTDL 567
Score = 38.3 bits (88), Expect = 0.042
Identities = 91/615 (14%), Positives = 176/615 (28%), Gaps = 200/615 (32%)
Query: 1015 RDLV-VYDDAF----------DMFSPAANNLDEYEIDY-VEQPVDEKKSRR-----ELSQ 1057
+D++ V++DAF DM L + EID+ + + R Q
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSI---LSKEEIDHIIMSKDAVSGTLRLFWTLLSKQ 75
Query: 1058 KMDSDRYRPDSDGDPN------------RRPSSQESLHHNDSLDIKLRKKLKPGHRLQRN 1105
+ ++ + N R+PS ++ I+ R +L N
Sbjct: 76 EEMVQKFVEEVL-RINYKFLMSPIKTEQRQPSMMTRMY------IEQRDRL-------YN 121
Query: 1106 SKKRHSKISTERSNSNSAPREKSSDAKQAANE---EENIT----GGNDENKTPVASEVRN 1158
+ +K + R + +QA E +N+ G+ KT VA +V
Sbjct: 122 DNQVFAKYNVSR-------LQPYLKLRQALLELRPAKNVLIDGVLGS--GKTWVALDVCL 172
Query: 1159 KNKKVKGVKEKNPSIVGDEKRRYWWRSPPGGGPNAARHKVCDDTDFQISWNDPHPPKLTH 1218
K V+ K + +W ++ +T ++ L +
Sbjct: 173 SYK----VQCKMDFKI------FWLN---------LKNCNSPETVLEMLQK------LLY 207
Query: 1219 GTGKS-RSKSSHSKQSKRSAENPSCRRMRGQDAFAPGGVATPSFGMNRAYEENFSKLDLS 1277
+ S+S HS K + R ++ YE L L
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRR--------------LLKSKPYEN--CLLVLL 251
Query: 1278 SYHDEHAV--FLPNSSSEDDCDGLSHGDEANGLASED---ADEYSGSSLNSSCIDLNCDH 1332
+ + A F + C L L + D S ++ +D H
Sbjct: 252 NVQNAKAWNAFNLS------CKIL--------LTTRFKQVTDFLSAATTTHISLD----H 293
Query: 1333 LENDFSEEEAEEYLEETYVTDEYHECDDERCSHDDCGDLDYQQYEKLRGRQANT--P--T 1388
+ +E + L + DL R+ T P
Sbjct: 294 HSMTLTPDEVKSLL--------------LKYLDCRPQDLP---------REVLTTNPRRL 330
Query: 1389 KTIGDTQGKRGGRVNTRSNHVNSEDKSRVHTSEDRLNFKGWIREMELYNVSTNVNVSDDD 1448
I ++ + HVN + + + + +++NV +
Sbjct: 331 SIIAESIRDGLATWD-NWKHVNCDKLTTI--------------------IESSLNVLEPA 369
Query: 1449 GLDESYNMI-----KTPTPRKRNG---ASGESSVEREDVGGGKSLRNLLLRRALMNKQNE 1500
+ ++ + P S V N L + +L+ KQ +
Sbjct: 370 EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV-------NKLHKYSLVEKQPK 422
Query: 1501 VNLWHRENQGWNQKAQGWNE---HTEVQTGLNQGWHQKTQGWNEHSELQNGID-YGRLPI 1556
+ + K + NE H + ++ + + ++ + +D Y I
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSI---VDH--YNIPKTFDSDDLIPPYLDQYFYSHI 477
Query: 1557 GHQHNHDHRHKHRFN 1571
GH H + H R
Sbjct: 478 GH-HLKNIEHPERMT 491
Score = 35.6 bits (81), Expect = 0.26
Identities = 17/106 (16%), Positives = 34/106 (32%), Gaps = 24/106 (22%)
Query: 2266 DRLSSDYDSTFSCGDFFLDSSYED---GPAHESEGCSYEH-VLRAHPAYYPSLDVPRLKA 2321
+ L +Y FL S + P+ + + L + +V RL+
Sbjct: 85 EVLRINYK--------FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136
Query: 2322 VLERQREFME-SYASQMSVY-----------LNVARNIAGNSYFDF 2355
L+ ++ +E A + + L+V + DF
Sbjct: 137 YLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Score = 32.9 bits (74), Expect = 1.8
Identities = 25/140 (17%), Positives = 41/140 (29%), Gaps = 58/140 (41%)
Query: 2216 ENTNSFR--YLDNRVCGHKDAKSRYQG-------------NQIR---GHIKDAKPCFHGN 2257
E FR +LD R + K R+ Q++ +I D P
Sbjct: 488 ERMTLFRMVFLDFRFL---EQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDP----- 539
Query: 2258 LNETDLTYDRLSSDYDSTFSCGDFFLDSSYEDGPAHESEGCSYEHVLRAHPAYYPSLDVP 2317
Y+RL + DF P E E+++ D+
Sbjct: 540 ------KYERLVNAI------LDFL--------PKIE------ENLIC-----SKYTDLL 568
Query: 2318 RLKAVLERQREFMESYASQM 2337
R+ A++ E Q+
Sbjct: 569 RI-ALMAEDEAIFEEAHKQV 587
>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 = 57.9 bits (140), Expect = 2e-08
Identities = 54/395 (13%), Positives = 122/395 (30%), Gaps = 90/395 (22%)
Query: 46 PIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQ 105
Q A L + +G+GK+ V + A + P T+I+ PT +A Q
Sbjct: 96 DYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI--NELSTP-----TLIVVPTLALAEQ 148
Query: 106 ITDVVRSVGAHVKNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLF 165
+ + G +V F G + +P + V + + L
Sbjct: 149 WKERLGIFG----EEYVGEFSGRIKELKP-----LTVSTYDSAYVNAEKLGNRFM---LL 196
Query: 166 IMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSAT-------------------YSHDN 206
I DE L +V+ + L ++AT +
Sbjct: 197 IFDEVHHLPAESYVQIAQ-----MSIAPFRLGLTATFEREDGRHEILKEVVGGKVFELFP 251
Query: 207 LATLQKYMVDPLLIR-----PEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLVQ--- 258
+ K++ + R ED +++ + +LR ++ K+V
Sbjct: 252 DSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASG 311
Query: 259 -----------------LLSQTPFNQCVIFSNYQLRPE----VICENLANAN-----FGA 292
+ + + + + + + F
Sbjct: 312 YDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFLI 371
Query: 293 EYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDAAT---- 348
++ ++ R L+ F+ G+ R +V++ + GID + ++ + + + +
Sbjct: 372 PAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIM-----SGSGSAR 426
Query: 349 -YLHRMGRAGRY---GTRGLVITIVSAESLVKFHS 379
Y+ R+GR R ++ ++S + +
Sbjct: 427 EYIQRLGRILRPSKGKKEAVLYELISRGTGEVNTA 461
>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 = 57.4 bits (138), Expect = 7e-08
Identities = 84/478 (17%), Positives = 145/478 (30%), Gaps = 181/478 (37%)
Query: 1 MAHDIQKCARTKDVLSNIDVLFEN--DVL--IEKPIRQGLQENGFVKESPI--------Q 48
A + + RT + + +F ++L +E P ++ ++ PI Q
Sbjct: 191 SAETLSELIRTT---LDAEKVFTQGLNILEWLENPSNTPDKD--YLLSIPISCPLIGVIQ 245
Query: 49 MAAFPYVLN--GYD-----AIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTRE 101
+A + G+ + ++ +G + +V A I + E
Sbjct: 246 LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV--TAVA-------------IAETDSWE 290
Query: 102 IAVQITDVVRSVGAHVKNLHVDYFIG--GTQV----ERPKRPVQIVV----GSPGRIKQM 151
K + V +FIG + P ++ + G P M
Sbjct: 291 SFFVSV---------RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSP---M 338
Query: 152 IKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQMLVVSATYSHDNLATLQ 211
+ + L + V+ ++ N+ LP KQ + +S N
Sbjct: 339 LSISNLTQEQVQDYV-----NKTNS-----------HLPAGKQ-VEISLVNGAKN----- 376
Query: 212 KYMV--DPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQ-C 268
+V P P+ L L N +LR L Q S+ PF++
Sbjct: 377 --LVVSGP----PQS----------LYGL-----NLTLRKAKAPSGLDQ--SRIPFSERK 413
Query: 269 VIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARG 328
+ FSN L P + + F + L A D L+ DL
Sbjct: 414 LKFSNRFL-P--V-----ASPFHSHLLVPASD------------------LINKDLVKNN 447
Query: 329 IDAANVDLVINLEIP-HDAATYLHRMGRAGRYGTRGLVITIVSA--------ESLVKF-- 377
+ D ++IP +D G R + + IV E+ +F
Sbjct: 448 VSFNAKD----IQIPVYDTFD-----GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKA 498
Query: 378 -HSLMGEINLDHAFNVG-------LVPDNL--TGDQINWTQRVQTLLAKPLDQAQERE 425
H I LD F G L N TG V+ ++A LD + +
Sbjct: 499 TH-----I-LD--FGPGGASGLGVLTHRNKDGTG--------VRVIVAGTLDINPDDD 540
Score = 52.4 bits (125), Expect = 2e-06
Identities = 66/349 (18%), Positives = 109/349 (31%), Gaps = 117/349 (33%)
Query: 143 GS--PGRIKQMIKLKYLNMDSVR-LFIMDEADK-LINT-GFVEDITWIYSQLPPMKQMLV 197
GS G M Y + + ++ + AD +T GF I I P + +
Sbjct: 1625 GSQEQG----MGMDLYKTSKAAQDVW--NRADNHFKDTYGF--SILDIVINNP--VNLTI 1674
Query: 198 VSATYSHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLV 257
+ + Y +I E L +++ I E + S + E+
Sbjct: 1675 HFGGEKGKRIR--ENYSA---MIF-ETIVDGKLKTEKIFKEINE-HSTSYTFRSEKG--- 1724
Query: 258 QLLSQTPFNQCVIF----SNYQ-LRPEVICENLANANF-----GAEYLSGAQDQKARLA- 306
LLS T F Q + + ++ L+ + + A+A F G EY A LA
Sbjct: 1725 -LLSATQFTQPALTLMEKAAFEDLKSKGLIP--ADATFAGHSLG-EY--AA------LAS 1772
Query: 307 -----SLDS-----FKRGK-VRILVTTDLAAR---GIDAANVDLVINLEIPHDAATYLHR 352
S++S F RG +++ V D R G+ A N V +A Y
Sbjct: 1773 LADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA-ASFSQEALQY--- 1828
Query: 353 MGRAGRYGTRGLVITIVSAES--LVKFHSLMGEI-NLDHAFNVGLVPDNLTGDQINWTQR 409
V+ V + LV EI N N+ Q
Sbjct: 1829 ------------VVERVGKRTGWLV-------EIVN-----------YNVENQQY----- 1853
Query: 410 VQTLLAKPLDQAQEREDVEQTAE--ESSKVENTK--PLRGAPSKEVTKK 454
V A + ++ K++ L+ + S E +
Sbjct: 1854 V---------AAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 50.4 bits (120), Expect = 8e-06
Identities = 88/555 (15%), Positives = 170/555 (30%), Gaps = 175/555 (31%)
Query: 44 ESPIQMAA-FPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREI 102
+P ++ F L GY + + S G ++++ L + + + L +I
Sbjct: 55 TTPAELVGKF---L-GYVSSLVEPSKVG--------QFDQVLNLCLTEFENCYLE-GNDI 101
Query: 103 ---AVQITDVVRSVGAHVKNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYLNM 159
A ++ + K L +Y +RP S + + +
Sbjct: 102 HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK-----KSNSAL-----FRAVGE 151
Query: 160 DSVRLFIM-----------DEADKLINT--GFVED-ITWIYSQLPPM-KQMLVVSATYSH 204
+ +L + +E L T V D I + L + + L ++
Sbjct: 152 GNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ 211
Query: 205 --DNLATLQKYMVDPLLIRPEDATR------PLLGVKQLVALIPECK----NPS-LR--- 248
+ L L+ +P +D PL+GV QL + K P LR
Sbjct: 212 GLNILEWLE----NPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYL 267
Query: 249 ------------------------YVDEEKKLVQLL------SQTPFNQCVIFSNYQLRP 278
+ +K + +L + + N L P
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCY----EA--YPNTSLPP 321
Query: 279 EVICENLANANFGA----------------EYL-----SGAQDQKARLASLDSFKR---- 313
++ ++L N N G +Y+ ++ ++ ++ K
Sbjct: 322 SILEDSLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVS 380
Query: 314 GKVRILVTTDLAARGIDA-ANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSAE 372
G + L +L R A + +D IP R ++ R L +
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGLD---QSRIPFS--------ERKLKFSNRFLPVA----- 424
Query: 373 SLVKFHS-LMGE----INLD-HAFNVGLVPDNL------TGDQINWTQRVQTLLAKPLDQ 420
FHS L+ IN D NV ++ T D + + + +++ +
Sbjct: 425 --SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL-RVLSGSISERIVD 481
Query: 421 AQEREDV--EQTAEESSKVENTKPL---RGAPSK--EVTKKGASKEGTKWNLTDGQSEEE 473
R V E T + + T L G S +T + +K+GT G
Sbjct: 482 CIIRLPVKWETTTQFKA----THILDFGPGGASGLGVLTHR--NKDGT------GVRVIV 529
Query: 474 SDSENDGKPDENGSQ 488
+ + + D+ G +
Sbjct: 530 AGTLDINPDDDYGFK 544
Score = 47.4 bits (112), Expect = 8e-05
Identities = 30/175 (17%), Positives = 48/175 (27%), Gaps = 69/175 (39%)
Query: 2030 RSGSSGLNNRTEG------NSVSHTWENHFATGTDR----------RSHQYPAYGSMSRH 2073
RS G ++G + + +WE+ F + R ++ AY + S
Sbjct: 264 RSYLKGATGHSQGLVTAVAIAETDSWES-FFVSVRKAITVLFFIGVRCYE--AYPNTS-- 318
Query: 2074 DLYFDESQLLGNEALGRGE------IRG--------------SGGGFASRVS-SV--GPA 2110
S L + G I S +V S+ G
Sbjct: 319 ---LPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK 375
Query: 2111 NESGLVVAGWNRCDREGHDPARGL-PMRSHFHGVKRSNHCD--------RKPRGG 2156
N LVV+G P + L + K + D RK +
Sbjct: 376 N---LVVSG----------PPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFS 417
Score = 38.5 bits (89), Expect = 0.038
Identities = 65/370 (17%), Positives = 91/370 (24%), Gaps = 139/370 (37%)
Query: 1861 QSSSAQSEDGTSYKSISWDAYSVIDEPE---------SYDVSW------------RTCSS 1899
+ D + + ++ P S +S T
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTA-- 253
Query: 1900 ESAAREKNSGQ-----RSRGSGDKAARKSASLPASQ-IALRDGKGDF-KSPRKASHSL-K 1951
K G RS G A S L + IA D F S RKA L
Sbjct: 254 ------KLLGFTPGELRSYLKG--ATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF 305
Query: 1952 DGKR----YGNA-------QSFEAARNSNPYEAPM---PGAWQPVLEGTSVFDDAEKSSK 1997
G R Y N + P +PM Q ++ D K++
Sbjct: 306 IGVRCYEAYPNTSLPPSILEDSLENNEGVP--SPMLSISNLTQEQVQ-----DYVNKTNS 358
Query: 1998 SGPKSSK--------------AGPKSS-------------KPGPKSSK-PG----PKSSK 2025
P + +GP S G S+ P K S
Sbjct: 359 HLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN 418
Query: 2026 RY-----P--S---RSGSSGLNNRTEGNSVSHTWEN--------HFATGTDRRSH----- 2062
R+ P S S +N N+VS + G+D R
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVS--FNAKDIQIPVYDTFDGSDLRVLSGSIS 476
Query: 2063 --------QYPAY-----GSMSRHDLYFDESQLLGNEALGRGEIRGSGGGFASRVSSVG- 2108
+ P + H L F G L G+G RV G
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTG----VRVIVAGT 532
Query: 2109 ----PANESG 2114
P ++ G
Sbjct: 533 LDINPDDDYG 542
Score = 33.5 bits (76), Expect = 1.3
Identities = 27/147 (18%), Positives = 42/147 (28%), Gaps = 52/147 (35%)
Query: 688 EDIPSDTIPNDETSNDNKL-TPVDFDYINDFVNQTPSETG-D-RPLVHGPNSVPKIDTPS 744
+ I D + N+ + N + PV +D + G D R L
Sbjct: 437 DLINKDLVKNNVSFNAKDIQIPV-YD----------TFDGSDLRVL-------------- 471
Query: 745 DDYLVANMKACLTNDSVRVQVLMEKLDHVDASVLADWILNKHNNVAALFRSEDQSNSVRI 804
+ + C+ R+ V E A+ IL F + +
Sbjct: 472 SGSISERIVDCII----RLPVKWETTTQFKAT----HIL--------DF---GPGGASGL 512
Query: 805 GD-----NDGTGNRSITRSKQNSQSGD 826
G DGTG R I + D
Sbjct: 513 GVLTHRNKDGTGVRVIVAGTLDINPDD 539
Score = 33.1 bits (75), Expect = 1.6
Identities = 15/98 (15%), Positives = 31/98 (31%), Gaps = 16/98 (16%)
Query: 1311 EDADEYSGSSLNSSCIDL---NCDHLENDFSEEEAEEYLEETYVTDEYHECDDERCSHDD 1367
AD + + S +D+ N +L F E+ + + E Y + D + +
Sbjct: 1647 NRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKG-KRIRENYSAMIFETIVDGKLKTEK 1705
Query: 1368 -CGDLDYQQYEKLRGRQANTPTKTIGDTQGKRGGRVNT 1404
+++ E + + TQ T
Sbjct: 1706 IFKEIN----EHSTSYTFRSEKGLLSATQ-------FT 1732
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 54.1 bits (129), Expect = 4e-07
Identities = 53/325 (16%), Positives = 109/325 (33%), Gaps = 30/325 (9%)
Query: 72 SIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQV 131
S++ V ++ V +PQ I + ++ + + L D
Sbjct: 199 SVIATVRDNVAELEQVVYKPQKISRKVASRTSNTFKCIISQLMKETEKLAKDVS------ 252
Query: 132 ERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPP 191
E + QI G K + ++ + ADK + + + S L
Sbjct: 253 EELGKLFQIQNREFGTQKYEQWIVGVHK---ACSVFQMADKEEESRVCKALFLYTSHLRK 309
Query: 192 MKQMLVVSAT-YSHDNLATLQKYMVDPLLIRPEDATRPLL-----GVKQLVALIPECKNP 245
L++S D L L+ + D ++ R L +++L + + N
Sbjct: 310 YNDALIISEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNE 369
Query: 246 SLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLAN----ANFGAEYLSG---- 297
+ + D L + P + ++F + + + + + + L+G
Sbjct: 370 NPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRT 429
Query: 298 ----AQDQKARLASLDSFK-RGKVRILVTTDLAARGIDAANVDLVINLEIPHDAATYLHR 352
A+ L++F+ G IL+ T +A GID A +LVI E + +
Sbjct: 430 NRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQT 489
Query: 353 MGRAGRYGTRGLVITIVSAESLVKF 377
GR + S+ +++
Sbjct: 490 RGRGRA--RDSKCFLLTSSADVIEK 512
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 54.2 bits (129), Expect = 5e-07
Identities = 32/145 (22%), Positives = 55/145 (37%), Gaps = 15/145 (10%)
Query: 236 VALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLAN----ANFG 291
V+ P +NP L + L + P ++F + + + + +
Sbjct: 371 VSRDPSNENPKLEDLCFI--LQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLK 428
Query: 292 AEYLSG--------AQDQKARLASLDSFK-RGKVRILVTTDLAARGIDAANVDLVINLEI 342
L+G A+ LD+FK G IL+ T +A GID A +LVI E
Sbjct: 429 PGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEY 488
Query: 343 PHDAATYLHRMGRAGRYGTRGLVIT 367
+ + GR G++ ++T
Sbjct: 489 VGNVIKMIQTRGRGRARGSKCFLLT 513
>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 = 52.6 bits (125), Expect = 1e-06
Identities = 28/149 (18%), Positives = 57/149 (38%), Gaps = 13/149 (8%)
Query: 232 VKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLAN---- 287
+L+AL + N + + + L P + ++F+ + + + +
Sbjct: 357 EPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPIL 416
Query: 288 ANFGAEYLSG--------AQDQKARLASLDSFKRGKV-RILVTTDLAARGIDAANVDLVI 338
L G ++ LD+FK K R+L+ T +A GID +LV+
Sbjct: 417 NYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV 476
Query: 339 NLEIPHDAATYLHRMGRAGRYGTRGLVIT 367
E + + GR G++ +++T
Sbjct: 477 LYEYSGNVTKMIQVRGRGRAAGSKCILVT 505
>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 = 52.4 bits (125), Expect = 2e-06
Identities = 19/143 (13%), Positives = 44/143 (30%), Gaps = 7/143 (4%)
Query: 221 RPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEV 280
R D P ++ N R + L+ L+ + ++
Sbjct: 463 RARDMLYPERIYQEFEGDNATWWNFDPRV----EWLMGYLTSHRSQKVLVICAKAATALQ 518
Query: 281 ICENL-ANANFGAEYLSGAQDQKARLASLDSFKR--GKVRILVTTDLAARGIDAANVDLV 337
+ + L A R + F ++L+ +++ + G + +
Sbjct: 519 LEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHM 578
Query: 338 INLEIPHDAATYLHRMGRAGRYG 360
+ ++P + R+GR R G
Sbjct: 579 VMFDLPFNPDLLEQRIGRLDRIG 601
>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 = 51.9 bits (123), Expect = 3e-06
Identities = 28/149 (18%), Positives = 57/149 (38%), Gaps = 13/149 (8%)
Query: 232 VKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLAN---- 287
+L+AL + N + + + L P + ++F+ + + + +
Sbjct: 598 EPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPIL 657
Query: 288 ANFGAEYLSG--------AQDQKARLASLDSFKRGKV-RILVTTDLAARGIDAANVDLVI 338
L G ++ LD+FK K R+L+ T +A GID +LV+
Sbjct: 658 NYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV 717
Query: 339 NLEIPHDAATYLHRMGRAGRYGTRGLVIT 367
E + + GR G++ +++T
Sbjct: 718 LYEYSGNVTKMIQVRGRGRAAGSKCILVT 746
Score = 43.0 bits (100), Expect = 0.001
Identities = 34/211 (16%), Positives = 75/211 (35%), Gaps = 18/211 (8%)
Query: 18 IDVLFENDVLIEKPIRQGLQENGFVKESPIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVV 77
D L EN + I + K Q+ +NG +A++ + +G+GK+ V ++
Sbjct: 223 DDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSIL 282
Query: 78 AALNKLIKLPVQQP-QTIILAPTREIAVQITDVVRSVGAHVKNLHVDYFIGGTQVERPKR 136
+ +P + + + LA + Q +V + G +
Sbjct: 283 ICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHF----ERQGYSVQGISGENFSNV 338
Query: 137 PV-------QIVVGSPGRIKQMIKLKYL-NMDSVRLFIMDEA-----DKLINTGFVEDIT 183
V I+V +P + + L ++ L I DE + N +
Sbjct: 339 SVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE 398
Query: 184 WIYSQLPPMKQMLVVSATYSHDNLATLQKYM 214
++ + Q+L ++A+ N +++ +
Sbjct: 399 QKFNSASQLPQILGLTASVGVGNAKNIEETI 429
>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 = 51.5 bits (122), Expect = 4e-06
Identities = 28/149 (18%), Positives = 57/149 (38%), Gaps = 13/149 (8%)
Query: 232 VKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLAN---- 287
+L+AL + N + + + L P + ++F+ + + + +
Sbjct: 598 EPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPIL 657
Query: 288 ANFGAEYLSG--------AQDQKARLASLDSFKRGKV-RILVTTDLAARGIDAANVDLVI 338
L G ++ LD+FK K R+L+ T +A GID +LV+
Sbjct: 658 NYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV 717
Query: 339 NLEIPHDAATYLHRMGRAGRYGTRGLVIT 367
E + + GR G++ +++T
Sbjct: 718 LYEYSGNVTKMIQVRGRGRAAGSKCILVT 746
Score = 44.2 bits (103), Expect = 6e-04
Identities = 30/180 (16%), Positives = 69/180 (38%), Gaps = 12/180 (6%)
Query: 46 PIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTII-LAPTREIAV 104
Q+ +NG +A++ + +G+GK+ V ++ + +P + ++ LA +
Sbjct: 251 SYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYE 310
Query: 105 QITDVVRSV----GAHVKNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYL-NM 159
Q +V + G V+ + + F VE+ I+V +P + + L ++
Sbjct: 311 QQKNVFKHHFERQGYSVQGISGENFS-NVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSL 369
Query: 160 DSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQ-----MLVVSATYSHDNLATLQKYM 214
L I DE + Y + +L ++A+ N +++ +
Sbjct: 370 SIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETI 429
>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 = 50.6 bits (121), Expect = 5e-06
Identities = 48/326 (14%), Positives = 92/326 (28%), Gaps = 66/326 (20%)
Query: 58 GYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHV 117
G ++ G GK+ F+ L + + ++ +T++LAPTR V+ +
Sbjct: 8 GMTTVLDFHPGAGKTRRFLPQILAECAR---RRLRTLVLAPTR-------VVLSEMKEAF 57
Query: 118 KNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDEADKLINTG 177
L V + R V + + + L+ + + + IMDEA L
Sbjct: 58 HGLDVKFHTQAFSAHGSGREVIDAMC-HATLTYRM-LEPTRVVNWEVIIMDEAHFLDPAS 115
Query: 178 FVEDITWIYSQLPPMKQMLVVSATYSHDNLATLQKYMVDPLLIRPEDATRPLLGVKQLVA 237
+ ++++AT P + +
Sbjct: 116 IAARGWAAHRARANESATILMTAT--------------------PPGTSDEFPHSNGEIE 155
Query: 238 LIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYLSG 297
+ E F V+ +L A L+
Sbjct: 156 DVQT------DIPSEPWNTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR 209
Query: 298 AQDQKARLASLDSFKRGKVRILVTTDLAARG--IDAANVDLVI----------------- 338
++ K+ K ++ TD+A G + V+ V+
Sbjct: 210 KTFEREYPT----IKQKKPDFILATDIAEMGANLC---VERVLDCRTAFKPVLVDEGRKV 262
Query: 339 --NLEIPHDAATYLHRMGRAGRYGTR 362
+ A++ R GR GR R
Sbjct: 263 AIKGPLRISASSAAQRRGRIGRNPNR 288
>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant
helicase, T4-bacteriophage, recombination, hydrolase;
2.70A {Enterobacteria phage T4}
Length = 510
Score = 49.5 bits (117), Expect = 1e-05
Identities = 51/343 (14%), Positives = 106/343 (30%), Gaps = 25/343 (7%)
Query: 46 PIQMAAFPYVLNGYDAIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQ 105
Q A L I+ + G+S++ + A L + + +I+ PT + Q
Sbjct: 116 WYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN---YEGKILIIVPTTALTTQ 172
Query: 106 ITDVVRSVGAHVKNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLF 165
+ D + G ++ ++ K +VVG+ + ++K +
Sbjct: 173 MADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGT---WQTVVKQPKEWFSQFGMM 229
Query: 166 IMDEA------------DKLINTGFVEDITWIYS---QLPPMKQMLVVSATYSHDNLATL 210
+ DE L N F ++ + +
Sbjct: 230 MNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLM 289
Query: 211 QKYMVDPLLIRPEDATRPLLGVKQLVALIPECKNPSLRYVDEEKKLVQLLSQTPFNQ--- 267
+ V L I P +L + + + + + K + L+ +
Sbjct: 290 EDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQKDEN 349
Query: 268 CVIFSNYQLRPEVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTT-DLAA 326
+ + + I + + N Y+SG D + R + GK I+V + + +
Sbjct: 350 AFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS 409
Query: 327 RGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIV 369
GI N+ V+ L +GR R + T+
Sbjct: 410 TGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVW 452
>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 = 38.0 bits (88), Expect = 0.041
Identities = 49/325 (15%), Positives = 92/325 (28%), Gaps = 77/325 (23%)
Query: 61 AIVQSKSGTGKSIVFVVAALNKLIKLPVQQPQTIILAPTREIAVQITDVVRSVGAHVKNL 120
I+ G GK+ + + + + +K ++ T+ILAPTR +A + ++ L
Sbjct: 189 TIMDLHPGAGKTKRILPSIVREALKRRLR---TLILAPTRVVA-------AEMEEALRGL 238
Query: 121 HVDYFIGGTQVERPKRPVQIVVGSPGRIKQMIKLKYLNMDSVRLFIMDE-----ADKLIN 175
+ Y + + R + + + + L + + L +MDE +
Sbjct: 239 PIRYQTPAVKSDHTGREI-VDLMCHATFTTRL-LSSTRVPNYNLIVMDEAHFTDPCSVAA 296
Query: 176 TGFVEDITWIYSQLPPMKQMLVVSATYSHDNLATLQKYMVDPLLIRPEDATRPLLGVKQL 235
G++ + ++AT Q I + P
Sbjct: 297 RGYISTR-----VEMGEAAAIFMTATPPGSTDPFPQSNSP----IEDIEREIPERSWNTG 347
Query: 236 VALIPECKNPSLRYVDEEKKLVQLLSQTPFNQCVIFSNYQLRPEVICENLANANFGAEYL 295
I + + ++ +V K + L + L
Sbjct: 348 FDWITDYQGKTVWFVPSIKAGNDI----------------------ANCLRKSGKRVIQL 385
Query: 296 SGAQDQKARLASLDSFKRGKVRILVTTDLAARG--IDAANVDLVI--------------- 338
S + K +VTTD++ G VI
Sbjct: 386 SRKTFDTEYPKT----KLTDWDFVVTTDISEMGANFR---AGRVIDPRRCLKPVILTDGP 438
Query: 339 ----NLE-IPHDAATYLHRMGRAGR 358
IP A+ R GR GR
Sbjct: 439 ERVILAGPIPVTPASAAQRRGRIGR 463
>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 = 35.3 bits (80), Expect = 0.085
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 6/23 (26%)
Query: 1048 EKKSRREL--SQKMDSDRYRPDS 1068
EK++ ++L S K+ Y DS
Sbjct: 18 EKQALKKLQASLKL----YADDS 36
Score = 33.4 bits (75), Expect = 0.34
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 149 KQMIK-LKYLNMDSVRLFIMDEADKL-INTGFVE 180
KQ +K L+ S++L+ D A L I +E
Sbjct: 19 KQALKKLQ----ASLKLYADDSAPALAIKAT-ME 47
Score = 31.8 bits (71), Expect = 1.2
Identities = 5/26 (19%), Positives = 13/26 (50%), Gaps = 5/26 (19%)
Query: 661 EKESVNNVESK-----DERPPSTANN 681
EK+++ +++ D+ P+ A
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIK 43
Score = 31.8 bits (71), Expect = 1.4
Identities = 7/40 (17%), Positives = 13/40 (32%), Gaps = 20/40 (50%)
Query: 852 QSREIKSY-ASLSMFSPCQTTLNKFDTQYNSSDYQSDSKP 890
+ + +K ASL +++ DS P
Sbjct: 18 EKQALKKLQASLKLYAD-------------------DSAP 38
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.0 bits (77), Expect = 0.30
Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 12/89 (13%)
Query: 414 LAKPLDQAQEREDVEQTAEESSKVENTKPLRGAPSKEVTKKGASKEGTKWNLTDGQSEEE 473
+A+ QE E + + EE K ++ ++ A K+ +WN + E+
Sbjct: 74 IAQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEK 133
Query: 474 SDSENDGKPDENGSQRGSKRSKEFKTQEK 502
+ N R K F Q
Sbjct: 134 NKINN----------R--IADKAFYQQPD 150
Score = 33.6 bits (76), Expect = 0.42
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 6/68 (8%)
Query: 1002 REESFLKRSHMPKRDLVVYDDAFDMFSPAANNLDEYEIDYVEQPVDEKKSRRELSQKMDS 1061
REE +R + + D + A +L+E+ EQ K + R +
Sbjct: 91 REE---QRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQ 147
Query: 1062 DRYRPDSD 1069
D+D
Sbjct: 148 QP---DAD 152
Score = 30.1 bits (67), Expect = 5.7
Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 37/102 (36%)
Query: 476 SENDGKPDENGSQRGSKRSKEFKT--QEKCVKGAGEDENGDRKASKDEQKIDGANSAEKS 533
++ D E S R K +E + QE D + EQ+ A+K
Sbjct: 75 AQADRLTQEPESIR--KWREEQRKRLQEL-----------DAASKVMEQEW--REKAKKD 119
Query: 534 LED---KHGKKITNSFEAVGEIVQNDTETTKENNQTDEVPEE 572
LE+ + +++ E K NN+ + +
Sbjct: 120 LEEWNQRQSEQV---------------EKNKINNRIAD--KA 144
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 34.5 bits (79), Expect = 0.45
Identities = 22/151 (14%), Positives = 43/151 (28%), Gaps = 15/151 (9%)
Query: 991 QSMDSFLDKSCRE----ESFLKRSHMPKRDLVVY----------DDAFDMFSPAANNLDE 1036
+ F+ + E L + V + D+ F +F + E
Sbjct: 331 SVVSQFITVASFSFSDVEDLLAEAKDLFTKAVKHFGEEAGKIQPDEFFGIFDQFLQAVSE 390
Query: 1037 YEIDYVEQPVDEKKSRRELSQKMDSDRYRPDSDGDPNRRPSSQESLHHNDSLDIKLRKKL 1096
+ + +++ R + R + +S+ES D L LR
Sbjct: 391 AKQENENMRKKKEEEERRARMEAQLKEQRERERKMRKAKENSEESGEF-DDLVSALRSGE 449
Query: 1097 KPGHRLQRNSKKRHSKISTERSNSNSAPREK 1127
L + + R + +S P K
Sbjct: 450 VFDKDLSKLKRNRKRITNQMTDSSRERPITK 480
>4apc_A Serine/threonine-protein kinase NEK1; transferase; 2.10A {Homo
sapiens}
Length = 350
Score = 33.9 bits (78), Expect = 0.68
Identities = 25/129 (19%), Positives = 38/129 (29%), Gaps = 19/129 (14%)
Query: 1048 EKKSRRELSQKMDSDRYRPDSDG---------------DPNRRPSSQESLHHNDSLDIKL 1092
E S + L K+ S + P S +P RPS L + ++
Sbjct: 226 EAGSMKNLVLKIISGSFPPVSLHYSYDLRSLVSQLFKRNPRDRPSVNSILEK-GFIAKRI 284
Query: 1093 RKKLKPGHRLQRNSKKRHSKISTERSNSNSAPREKSSDAKQAANEEENITGGNDENKTPV 1152
K L P + S S A R S + + IT + P+
Sbjct: 285 EKFLSP---QLIAEEFCLKTFSKFGSQPIPAKRPASGQNSISVMPAQKITKPAAKYGIPL 341
Query: 1153 ASEVRNKNK 1161
A + K
Sbjct: 342 AYKKYGDKK 350
>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
signaling protein; NMR {Mus musculus} SCOP: a.4.5.47
Length = 84
Score = 30.9 bits (70), Expect = 0.83
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 2301 EHVLRAHPAYYPSLDVPRLKAVLERQREFMESYASQM 2337
EH L + Y ++ L A+LE E ASQM
Sbjct: 18 EHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQM 54
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 33.6 bits (77), Expect = 0.89
Identities = 25/145 (17%), Positives = 60/145 (41%), Gaps = 13/145 (8%)
Query: 30 KPIRQGLQENGFVKESPIQMAAFPYVLN-GYDAIVQSKSGTGKSIVFVVAALNKLIKLPV 88
+ + +++ G K +P Q A L G ++ S +G+GK+++ + ++ L+K
Sbjct: 17 SNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK--- 73
Query: 89 QQPQTII-LAPTREIAVQITD---VVRSVGAHVKNLHVDYFIGGTQVERPKRPVQIVVGS 144
I + P R + + +G V DY ++ I++ +
Sbjct: 74 -NGGKAIYVTPLRALTNEKYLTFKDWELIGFKVAMTSGDYDTDDAWLKN----YDIIITT 128
Query: 145 PGRIKQMIKLKYLNMDSVRLFIMDE 169
++ + + + ++ V F++DE
Sbjct: 129 YEKLDSLWRHRPEWLNEVNYFVLDE 153
Score = 31.2 bits (71), Expect = 5.4
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 15/82 (18%)
Query: 309 DSFKRGKVRILV-TTDLAA-----------RGIDAANVDLVINLEIPHDAATYLHRMGRA 356
+ F++ K++++V T LAA I N + + Y GRA
Sbjct: 332 EGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYD-EIPIMEYKQMSGRA 390
Query: 357 GR--YGTRGLVITIVSAESLVK 376
GR + G I +V + V
Sbjct: 391 GRPGFDQIGESIVVVRDKEDVD 412
>3mf7_A CIS-3-chloroacrylic acid dehalogenase; beta-alpha-beta motif,
tautomerase, CIS-3-CHLO acid dehalogenase, isomerase,
hydrolase; HET: PR4; 1.65A {Coryneform bacterium} PDB:
3mf8_A 2flt_A 2flz_A
Length = 149
Score = 31.2 bits (70), Expect = 1.7
Identities = 21/106 (19%), Positives = 34/106 (32%), Gaps = 19/106 (17%)
Query: 100 REIAVQITDVVRSVG------AHV---KNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQ 150
+A ITD R + A V + + F+GG Q V + GR
Sbjct: 18 HAVAKAITDAHRGLTGTQHFLAQVNFQEQPAGNVFLGGVQQGGDTIFVHGLHRE-GRSAD 76
Query: 151 MIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQML 196
+ + I+D+ W+Y P +QM+
Sbjct: 77 LK-------GQLAQRIVDDVSV--AAEIDRKHIWVYFGEMPAQQMV 113
>1tzz_A Hypothetical protein L1841; structural genomics, mandelate racemase
like fold, nysgxrc target T1523, PSI, protein structure
initiative; 1.86A {Bradyrhizobium japonicum} SCOP:
c.1.11.2 d.54.1.1 PDB: 2dw7_A* 2dw6_A*
Length = 392
Score = 31.6 bits (72), Expect = 3.5
Identities = 10/53 (18%), Positives = 16/53 (30%)
Query: 319 LVTTDLAARGIDAANVDLVINLEIPHDAATYLHRMGRAGRYGTRGLVITIVSA 371
L+ A+R ++A L+ D M + G G V
Sbjct: 66 LIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGT 118
>2pge_A MENC; OSBS, NYSGXRC, PSI-II, structural genomics, protein structure
initiative; 1.60A {Desulfotalea psychrophila LSV54}
Length = 377
Score = 31.6 bits (72), Expect = 3.7
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 1009 RSHMPKRDLVVYDDAFDMFSPA-----ANNLDEYEIDYVEQPV 1046
R + L + DA FSPA L ++ + +EQP+
Sbjct: 201 RESFSPQQLEIRVDANGAFSPANAPQRLKRLSQFHLHSIEQPI 243
>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 = 31.7 bits (72), Expect = 3.9
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 296 SGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVI 338
+ K L+ + IL T+ L G+DA V+
Sbjct: 480 EEGKIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVV 522
>2opj_A O-succinylbenzoate-COA synthase; TIM barrel, structural genomics,
protein structure initiative; 1.60A {Thermobifida fusca}
PDB: 2qvh_A*
Length = 327
Score = 31.2 bits (71), Expect = 3.9
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 1030 AANNLDEYEIDYVEQPVDEKKSRRELSQKMD 1060
LD +E++YVEQP E+ +++
Sbjct: 143 MIRLLDRFELEYVEQPCATVDELAEVRRRVS 173
>3aml_A OS06G0726400 protein; starch-branching, transferase; HET: EPE; 1.70A
{Oryza sativa japonica group} PDB: 3amk_A
Length = 755
Score = 31.6 bits (72), Expect = 4.6
Identities = 7/22 (31%), Positives = 8/22 (36%), Gaps = 2/22 (9%)
Query: 1261 FGMNRAYEENFSKLDLSSYHDE 1282
NR Y E S HD+
Sbjct: 450 TLTNRRYTEKCIAYAES--HDQ 469
>2x7f_A TRAF2 and NCK-interacting protein kinase; serine/threonine-protein
kinase, phosphoprotein; HET: 824; 2.80A {Homo sapiens}
Length = 326
Score = 30.8 bits (70), Expect = 5.0
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 1071 DPNRRPSSQESLHH----NDSLDIKLRKKLKPGHRLQRNSKKRHSKISTERSNS 1120
+ ++RP++++ + H + + ++R +LK + R KKR K TE S
Sbjct: 274 NHSQRPATEQLMKHPFIRDQPNERQVRIQLK--DHIDRTKKKRGEKDETEYEYS 325
>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 = 30.9 bits (71), Expect = 5.8
Identities = 22/80 (27%), Positives = 35/80 (43%)
Query: 279 EVICENLANANFGAEYLSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVI 338
E L + A + R + F+R ++I+V T GI+ NV V+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 339 NLEIPHDAATYLHRMGRAGR 358
+ +IP + +Y GRAGR
Sbjct: 310 HFDIPRNIESYYQETGRAGR 329
>1yco_A Branched-chain phosphotransacylase; structural genomics, protein
structure initiative, PSI, nysgxrc; 2.40A {Enterococcus
faecalis}
Length = 279
Score = 30.3 bits (69), Expect = 7.1
Identities = 13/90 (14%), Positives = 29/90 (32%), Gaps = 8/90 (8%)
Query: 295 LSGAQDQKARLASLDSFKRGKVRILVTTDLAARGIDAANVDLVINLEIPHDA---ATYLH 351
++G + + K + + +D N+ ++ A L
Sbjct: 6 IAGGSQPEILQLVKKALKEAEQPLQFIVFDTNENLDTENLWKYVHCSDEAAVAQEAVSLV 65
Query: 352 RMGRA-----GRYGTRGLVITIVSAESLVK 376
G+A G T L+ ++ +E +K
Sbjct: 66 ATGQAQILLKGIIQTHTLLKEMLKSEHQLK 95
>3n4h_A Putative tautomerase; CG10062, CIS-3-chloroacrylic acid
dehalogenase, tautomerase superfamily, beta-alpha-beta
motif, hydrolase; HET: PR7; 2.02A {Corynebacterium
glutamicum} PDB: 3n4d_A* 3n4g_A
Length = 148
Score = 29.3 bits (65), Expect = 7.5
Identities = 21/106 (19%), Positives = 29/106 (27%), Gaps = 19/106 (17%)
Query: 100 REIAVQITDV------VRSVGAHV---KNLHVDYFIGGTQVERPKRPVQIVVGSPGRIKQ 150
+ IA ITD V + YFI VQ + S KQ
Sbjct: 18 QRIAEAITDAHHELAHAPKYLVQVIFNEVEPDSYFIAAQSASENHIWVQATIRSGRTEKQ 77
Query: 151 MIKLKYLNMDSVRLFIMDEADKLINTGFVEDITWIYSQLPPMKQML 196
+L + + I G + W+Y P M
Sbjct: 78 KEEL----LLRLTQEIAL------ILGIPNEEVWVYITEIPGSNMT 113
>3fcp_A L-Ala-D/L-Glu epimerase, A muconate lactonizing enzyme; structural
genomics, nysgrc,target 9450E, PSI-2; 1.80A {Klebsiella
pneumoniae subsp}
Length = 381
Score = 30.3 bits (69), Expect = 8.3
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 1030 AANNLDEYEIDYVEQPV--DEKKSRRELSQKMD 1060
L +D +EQPV + + LSQ+++
Sbjct: 212 GCRELAAMGVDLIEQPVSAHDNAALVRLSQQIE 244
>3dgb_A Muconate cycloisomerase; muconate lactonizing enzyme, muconolactone
binding, isomeras structural genomics, PSI-2; HET: MUC;
1.70A {Pseudomonas fluorescens} PDB: 3ct2_A* 3fj4_A*
1muc_A 1bkh_A 3muc_A 2muc_A 1f9c_A
Length = 382
Score = 30.3 bits (69), Expect = 8.7
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 2/33 (6%)
Query: 1030 AANNLDEYEIDYVEQPV--DEKKSRRELSQKMD 1060
A L ID +EQP+ + + L+
Sbjct: 213 ACRILGGNGIDLIEQPISRNNRAGMVRLNASSP 245
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
0.310 0.128 0.373
Gapped
Lambda K H
0.267 0.0479 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 34,422,448
Number of extensions: 2064111
Number of successful extensions: 3528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3364
Number of HSP's successfully gapped: 119
Length of query: 2355
Length of database: 6,701,793
Length adjustment: 109
Effective length of query: 2246
Effective length of database: 3,658,404
Effective search space: 8216775384
Effective search space used: 8216775384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 65 (29.4 bits)