RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4698
(258 letters)
>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 = 404 bits (1040), Expect = e-145
Identities = 143/224 (63%), Positives = 175/224 (78%), Gaps = 1/224 (0%)
Query: 35 DGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSG 94
+ I+TN+D V FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSG
Sbjct: 2 ESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSG 61
Query: 95 TGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTI 154
TGKT TFSI+ LQ++D ++K QAL+LAPTRELA QIQKVV+AL M + HACIGGT
Sbjct: 62 TGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTS 121
Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
+D L AQ+VVGTPGRVFD I R T +I+MF+LDEADEMLS GFK+QIY +F
Sbjct: 122 FVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF 180
Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
L QV+LLSATMP DVL+V+ KFMR+P++ILVKK+ELTLE
Sbjct: 181 TLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224
>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 = 410 bits (1055), Expect = e-144
Identities = 170/250 (68%), Positives = 210/250 (84%), Gaps = 1/250 (0%)
Query: 10 EDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEK 69
+ ++ + NGP GM +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEK
Sbjct: 3 LGSPEFMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEK 62
Query: 70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ 129
PSAIQQRAI+PC++G DVIAQAQSGTGKTATF+ISILQQ++ ++K QAL+LAPTRELAQ
Sbjct: 63 PSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQ 122
Query: 130 QIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRGALSTK 188
QIQKVV+ALGD+M SCHACIGGT VR +++KL+ ++VGTPGRVFDM++R LS K
Sbjct: 123 QIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPK 182
Query: 189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKI 248
I+MFVLDEADEMLSRGFKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+I
Sbjct: 183 YIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRI 242
Query: 249 LVKKEELTLE 258
LVKKEELTLE
Sbjct: 243 LVKKEELTLE 252
>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 = 395 bits (1016), Expect = e-141
Identities = 161/236 (68%), Positives = 195/236 (82%), Gaps = 1/236 (0%)
Query: 19 NEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAI 78
+ + G+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAI
Sbjct: 2 HHHHHHSSGRENLYFQGGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAI 61
Query: 79 IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL 138
IPC++G DVIAQAQSGTGKTATF+ISILQQ++ KE QAL+LAPTRELAQQIQKV++AL
Sbjct: 62 IPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILAL 121
Query: 139 GDFMSVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDE 197
GD+M +CHACIGGT VR++++KL+A +VVGTPGRVFDM++R LS K I+MFVLDE
Sbjct: 122 GDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDE 181
Query: 198 ADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
ADEMLSRGFKDQIY++F+ LN +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKE
Sbjct: 182 ADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237
>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 = 397 bits (1022), Expect = e-140
Identities = 143/224 (63%), Positives = 175/224 (78%), Gaps = 1/224 (0%)
Query: 35 DGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSG 94
+ I+TN+D V FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSG
Sbjct: 9 ESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSG 68
Query: 95 TGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTI 154
TGKT TFSI+ LQ++D ++K QAL+LAPTRELA QIQKVV+AL M + HACIGGT
Sbjct: 69 TGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTS 128
Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
+D L AQ+VVGTPGRVFD I R T +I+MF+LDEADEMLS GFK+QIY +F
Sbjct: 129 FVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF 187
Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
L QV+LLSATMP DVL+V+ KFMR+P++ILVKK+ELTLE
Sbjct: 188 TLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 231
>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 = 396 bits (1021), Expect = e-139
Identities = 147/242 (60%), Positives = 185/242 (76%)
Query: 17 AENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQR 76
A + + + M + V FD M L E+LLRGIYAYGFEKPSAIQQR
Sbjct: 7 ATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQR 66
Query: 77 AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI 136
AI ++G DVIAQ+QSGTGKTATFSIS+LQ +D ++E QALILAPTRELA QIQK ++
Sbjct: 67 AIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLL 126
Query: 137 ALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLD 196
ALGD+M+V CHACIGGT V +DIRKL+ G VV GTPGRVFDMI R +L T+ I+M VLD
Sbjct: 127 ALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLD 186
Query: 197 EADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
EADEML++GFK+QIYDV+++L QV+L+SAT+P ++L+++ KFM DPI+ILVK++ELT
Sbjct: 187 EADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELT 246
Query: 257 LE 258
LE
Sbjct: 247 LE 248
>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 = 374 bits (963), Expect = e-130
Identities = 96/232 (41%), Positives = 132/232 (56%), Gaps = 2/232 (0%)
Query: 28 GP-PGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
GP + + F+D L ELL GI+ GFEKPS IQ+ AI + G D
Sbjct: 1 GPLGSKDTRPQTDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRD 60
Query: 87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
++A+A++GTGKTA F I L++V + + QALI+ PTRELA Q +VV LG +SC
Sbjct: 61 ILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISC 120
Query: 147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF 206
GGT +RDDI +L ++VGTPGRV D+ SR +F++DEAD+MLSR F
Sbjct: 121 MVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDF 180
Query: 207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
K I + L Q +L SAT P V + +K + P +I + + ELTL+
Sbjct: 181 KTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLK 231
>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 = 354 bits (910), Expect = e-122
Identities = 83/217 (38%), Positives = 135/217 (62%), Gaps = 7/217 (3%)
Query: 45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFS 102
+A++FD++ L+ ELL+GIYA F+KPS IQ+RA+ + ++IAQ+QSGTGKTA FS
Sbjct: 3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 103 ISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL 162
+++L +V+ QA+ LAP+RELA+Q +VV +G F ++ + + ++
Sbjct: 63 LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK---- 118
Query: 163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNNDV 221
+ AQV+VGTPG V D++ R + ++I++FVLDEAD ML +G DQ V + L D
Sbjct: 119 QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDT 178
Query: 222 QVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
Q++L SAT V + K + + + ++ E+ ++
Sbjct: 179 QLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVD 215
>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 = 352 bits (906), Expect = e-122
Identities = 82/220 (37%), Positives = 130/220 (59%), Gaps = 8/220 (3%)
Query: 44 HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATF 101
+ ++F+++ L +LL+G+YA GF +PS IQ+ A+ + ++IAQ+QSGTGKTA F
Sbjct: 22 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF 81
Query: 102 SISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIR 160
+++L QV+ K Q L L+PT ELA Q KV+ +G F + + G + +
Sbjct: 82 VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 141
Query: 161 KLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLN 218
Q+V+GTPG V D S+ + K+I++FVLDEAD M++ +G +DQ + + L
Sbjct: 142 I---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLP 198
Query: 219 NDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
+ Q++L SAT V + K + DP I +K+EE TL+
Sbjct: 199 RNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 238
>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 = 345 bits (887), Expect = e-122
Identities = 83/206 (40%), Positives = 122/206 (59%), Gaps = 3/206 (1%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
+F+ + LS +L G+ A GFE+PS +Q +AI G D+I QA+SGTGKT FS L
Sbjct: 25 DFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALD 84
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGA 166
+ Q LILAPTRE+A QI V+ A+G M + CH IGGT + D +L+
Sbjct: 85 SLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KC 143
Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNNDVQVIL 225
+ VG+PGR+ +I L+ IR+F+LDEAD++L G F++QI ++ L Q++
Sbjct: 144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLA 203
Query: 226 LSATMPADVLDVSMKFMRDPIKILVK 251
+SAT P + + K+MRDP + +
Sbjct: 204 VSATYPEFLANALTKYMRDPTFVRLN 229
>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 = 346 bits (889), Expect = e-119
Identities = 80/222 (36%), Positives = 124/222 (55%), Gaps = 4/222 (1%)
Query: 41 NWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTAT 100
+ H++ F D L ELLR I GFE PS +Q I + G DV+ QA+SG GKTA
Sbjct: 2 SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 61
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDI 159
F ++ LQQ++ + L++ TRELA QI K +M V GG ++ D
Sbjct: 62 FVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121
Query: 160 RKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHL 217
L+ +VVGTPGR+ + +L+ K I+ F+LDE D+ML + + + ++F+
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT 181
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILVK-KEELTLE 258
++ QV++ SAT+ ++ V KFM+DP++I V + +LTL
Sbjct: 182 PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLH 223
>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 = 348 bits (895), Expect = e-119
Identities = 89/274 (32%), Positives = 141/274 (51%), Gaps = 23/274 (8%)
Query: 2 AEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWD------------HVAENF 49
+ N E E+ A Q N L++ + ++F
Sbjct: 38 VVKTNANAEKTDEEEKEDRAAQSLLNKLIR---SNLVDNTNQVEVLQRDPNSPLYSVKSF 94
Query: 50 DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQ 107
+++ L +LL+G+YA GF +PS IQ+ A+ + ++IAQ+QSGTGKTA F +++L
Sbjct: 95 EELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLS 154
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGA 166
QV+ K Q L L+PT ELA Q KV+ +G F + + G + +
Sbjct: 155 QVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SE 211
Query: 167 QVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVI 224
Q+V+GTPG V D S+ + K+I++FVLDEAD M++ +G +DQ + + L + Q++
Sbjct: 212 QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQML 271
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
L SAT V + K + DP I +K+EE TL+
Sbjct: 272 LFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 305
>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 = 335 bits (860), Expect = e-116
Identities = 83/262 (31%), Positives = 134/262 (51%), Gaps = 13/262 (4%)
Query: 2 AEQRGDNWEDPKNGPAENE-----AEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSE 56
E+ K A + + V + + ++F+++ L
Sbjct: 42 NANAEKTDEEEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKP 101
Query: 57 ELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIK 114
+LL+G+YA GF +PS IQ+ A+ + ++IAQ+QSGTGKTA F +++L QV+ K
Sbjct: 102 QLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK 161
Query: 115 ECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
Q L L+PT ELA Q KV+ +G F + + G + + Q+V+GTP
Sbjct: 162 YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SEQIVIGTP 218
Query: 174 GRVFDMISR-GALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVILLSATMP 231
G V D S+ + K+I++FVLDEAD M++ +G +DQ + + L + Q++L SAT
Sbjct: 219 GTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFE 278
Query: 232 ADVLDVSMKFMRDPIKILVKKE 253
V + K + DP I +K+E
Sbjct: 279 DSVWKFAQKVVPDPNVIKLKRE 300
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 335 bits (862), Expect = e-114
Identities = 71/189 (37%), Positives = 114/189 (60%), Gaps = 7/189 (3%)
Query: 73 IQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ 130
IQ++A+ + ++I Q+QSGTGKTA F++++L +VD ++ + QA+ LAP+RELA+Q
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQ 204
Query: 131 IQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQI 190
I VV +G + V I ++ + + AQ+V+GTPG V D++ R L + I
Sbjct: 205 IMDVVTEMGKYTEVKTAFGIKDSV----PKGAKIDAQIVIGTPGTVMDLMKRRQLDARDI 260
Query: 191 RMFVLDEADEML-SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKIL 249
++FVLDEAD ML +G DQ + L + Q++L SAT V + +F + +I
Sbjct: 261 KVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSERVEKYAERFAPNANEIR 320
Query: 250 VKKEELTLE 258
+K EEL++E
Sbjct: 321 LKTEELSVE 329
>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 = 321 bits (824), Expect = e-112
Identities = 77/202 (38%), Positives = 120/202 (59%), Gaps = 1/202 (0%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
F+D L ELL GI+ G+EKPS IQ+ +I + G D++A+A++GTGK+ + I +L+
Sbjct: 4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGA 166
++D QA+++ PTRELA Q+ ++ I + M A GGT +RDDI +L+
Sbjct: 64 RLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123
Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
VV+ TPGR+ D+I +G ++M VLDEAD++LS+ F + D+ L + Q++L
Sbjct: 124 HVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLY 183
Query: 227 SATMPADVLDVSMKFMRDPIKI 248
SAT P V + P +I
Sbjct: 184 SATFPLSVQKFMNSHLEKPYEI 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 = 315 bits (809), Expect = e-110
Identities = 76/217 (35%), Positives = 121/217 (55%), Gaps = 4/217 (1%)
Query: 38 IETNWDHVAE-NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTG 96
++ ++ + F D L ELLR I GFE PS +Q I + G DV+ QA+SG G
Sbjct: 4 VKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMG 63
Query: 97 KTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIV 155
KTA F ++ LQQ++ + L++ TRELA QI K +M +V GG +
Sbjct: 64 KTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSI 123
Query: 156 RDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDV 213
+ D L+ +VVGTPGR+ + +L+ K I+ F+LDE D+ML + + + ++
Sbjct: 124 KKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEI 183
Query: 214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
F+ ++ QV++ SAT+ ++ V KFM+DP++I V
Sbjct: 184 FRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 250 bits (640), Expect = 2e-84
Identities = 68/210 (32%), Positives = 107/210 (50%), Gaps = 4/210 (1%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
F ++ I F KP+ IQ+R I +RG ++ Q+Q+GTGKT + + I++
Sbjct: 5 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS----VSCHACIGGTIVRDDIRKLE 163
++ E QA+I APTRELA QI + + F + IGGT + + KL
Sbjct: 65 KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 124
Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
+V+GTPGR+ D I AL + V+DEAD ML GF + + + D+Q+
Sbjct: 125 VQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQM 184
Query: 224 ILLSATMPADVLDVSMKFMRDPIKILVKKE 253
++ SAT+P + K+M +P + V +
Sbjct: 185 LVFSATIPEKLKPFLKKYMENPTFVHVLEH 214
>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 = 238 bits (609), Expect = 1e-77
Identities = 80/210 (38%), Positives = 130/210 (61%), Gaps = 3/210 (1%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISIL 106
NF+++ LS+ +L I GFEKP+ IQ + I + +++AQA++G+GKTA+F+I ++
Sbjct: 7 NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
+ V++N +A+IL PTRELA Q+ + +L ++ GG + I+ L+ A
Sbjct: 67 ELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124
Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
+VVGTPGR+ D I+RG L+ K ++ F+LDEADEML+ GF + + N D +++L
Sbjct: 125 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLF 184
Query: 227 SATMPADVLDVSMKFMRDPIKILVKKEELT 256
SATMP ++L+++ K+M D I K
Sbjct: 185 SATMPREILNLAKKYMGDYSFIKAKINANI 214
>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 = 224 bits (573), Expect = 2e-74
Identities = 73/208 (35%), Positives = 116/208 (55%), Gaps = 5/208 (2%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
F D L E+L ++ G P+ IQ A+ + G D+I QA++GTGKT F++ I +
Sbjct: 2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 108 QVDQN---IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
++ + ++ +AL+L PTRELA Q+ + A+ + V A GGT L
Sbjct: 62 RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLR 119
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
GA VV TPGR D + +G L ++ + VLDEADEMLS GF++++ + Q +
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKK 252
L SAT+P+ ++ ++M++P+ I V K
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINVIK 207
>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 = 218 bits (558), Expect = 3e-70
Identities = 57/198 (28%), Positives = 105/198 (53%), Gaps = 7/198 (3%)
Query: 54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI 113
++E++ + I GF+ + +Q + I ++G +V+ +A++G+GKTA ++I IL+
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54
Query: 114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
++L++ PTREL +Q+ + +G +M GG + I ++ A +VV TP
Sbjct: 55 LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113
Query: 174 GRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPAD 233
GR+ D+ S+G + + ++DEAD M GF D I + +N L SAT+P +
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173
Query: 234 VLDVSMKFMRDPIKILVK 251
+ V F+ + +I
Sbjct: 174 IRKVVKDFITNYEEIEAC 191
>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 = 211 bits (538), Expect = 1e-68
Identities = 65/252 (25%), Positives = 115/252 (45%), Gaps = 5/252 (1%)
Query: 1 MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLR 60
M + ++ P + + E + F D+ +++ L
Sbjct: 1 MHHHHHHSSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEE----TKTFKDLGVTDVLCE 56
Query: 61 GIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALI 120
G+ KP+ IQ AI ++G D+I A++G+GKT F++ IL + + + AL+
Sbjct: 57 ACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALV 116
Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
L PTRELA QI + ALG + V +GG L +++ TPGR+ D +
Sbjct: 117 LTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHL 176
Query: 181 SRG-ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
+ + ++ V+DEAD +L+ F+ ++ + K + D + L SATM V +
Sbjct: 177 ENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQR 236
Query: 240 KFMRDPIKILVK 251
+++P+K V
Sbjct: 237 AALKNPVKCAVS 248
>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 = 219 bits (559), Expect = 5e-68
Identities = 67/237 (28%), Positives = 115/237 (48%), Gaps = 23/237 (9%)
Query: 45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP--CVRGNDVIAQAQSGTGKTATFS 102
+ ++ L +E+ + I F + +QQ+ I P +DVIA+A++GTGKT F
Sbjct: 19 LDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL 78
Query: 103 ISILQQVDQNIKE----CQALILAPTRELAQQIQKVVIALGDFM----SVSCHACIGGTI 154
I I Q + + +A+I+APTR+LA QI+ V + D +C + +GGT
Sbjct: 79 IPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTD 138
Query: 155 VRDDIRKLE-AGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIYD 212
R + K+ +V+ TPGR+ D++ + + + + VLDEAD +L GF+D +
Sbjct: 139 FRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLET 198
Query: 213 VFKHLNN-------DVQVILLSATMPADVLDVSMKFMRDPIKILV----KKEELTLE 258
+ LN +++ +L SAT+ V ++ M + + K E E
Sbjct: 199 ISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE 255
>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 = 218 bits (557), Expect = 8e-68
Identities = 70/279 (25%), Positives = 126/279 (45%), Gaps = 23/279 (8%)
Query: 3 EQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGI 62
R ++ ++ ++E + V + + ++ L +E+ + I
Sbjct: 28 NSRFNSRPRTRSREDDDEVHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAI 87
Query: 63 YAYGFEKPSAIQQRAIIPC--VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKE----C 116
F + +QQ+ I P +DVIA+A++GTGKT F I I Q + +
Sbjct: 88 TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV 147
Query: 117 QALILAPTRELAQQIQKVVIALGDF----MSVSCHACIGGTIVRDDIRKLE-AGAQVVVG 171
+A+I+APTR+LA QI+ V + D +C + +GGT R + K+ +V+
Sbjct: 148 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIA 207
Query: 172 TPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-------DVQV 223
TPGR+ D++ + + + + VLDEAD +L GF+D + + LN +++
Sbjct: 208 TPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKT 267
Query: 224 ILLSATMPADVLDVSMKFMRDPIKILV----KKEELTLE 258
+L SAT+ V ++ M + + K E E
Sbjct: 268 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE 306
>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 = 195 bits (499), Expect = 7e-63
Identities = 61/213 (28%), Positives = 109/213 (51%), Gaps = 6/213 (2%)
Query: 46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISI 105
F D LS++ L+G+ + + IQ++ I ++G DV+ A++G+GKT F + +
Sbjct: 24 ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV 83
Query: 106 LQQVDQNIKE----CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
L+ + + LI++PTRELA Q +V+ +G S IGG ++ + +
Sbjct: 84 LEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAER 143
Query: 162 LEAGAQVVVGTPGRVFDMISRGA-LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
+ ++V TPGR+ + ++M VLDEAD +L GF D + V ++L
Sbjct: 144 I-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKK 202
Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
Q +L SAT V D++ +++P + V ++
Sbjct: 203 RQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK 235
>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 = 191 bits (488), Expect = 5e-61
Identities = 70/215 (32%), Positives = 108/215 (50%), Gaps = 7/215 (3%)
Query: 47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISI 105
NF + ++ I F +P+AIQ + P G D++ AQ+G+GKT ++ +
Sbjct: 29 LNFYEANFPANVMDVIARQNFTEPTAIQAQGW-PVALSGLDMVGVAQTGSGKTLSYLLPA 87
Query: 106 LQQV-DQNIKECQ----ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
+ + Q E L+LAPTRELAQQ+Q+V + GG IR
Sbjct: 88 IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147
Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
LE G ++ + TPGR+ D + G + ++ VLDEAD ML GF+ QI + + D
Sbjct: 148 DLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPD 207
Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL 255
Q ++ SAT P +V ++ F++D I I + EL
Sbjct: 208 RQTLMWSATWPKEVRQLAEDFLKDYIHINIGALEL 242
>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 = 191 bits (487), Expect = 9e-61
Identities = 69/217 (31%), Positives = 110/217 (50%), Gaps = 13/217 (5%)
Query: 47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISIL 106
ENFD+++L + I +++P+ IQ+ AI + D++A AQ+G+GKTA F I I+
Sbjct: 23 ENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII 82
Query: 107 QQVDQN---------IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
+ + LILAPTRELA QI + GG
Sbjct: 83 NHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHS 142
Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
IR+++ G ++V TPGR+ D I + +S + + VLDEAD ML GF+ QI + +
Sbjct: 143 QIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEES 202
Query: 218 N----NDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
N + Q ++ SAT P ++ ++ F+ + I + V
Sbjct: 203 NMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 239
>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 = 188 bits (479), Expect = 1e-59
Identities = 59/216 (27%), Positives = 105/216 (48%), Gaps = 12/216 (5%)
Query: 47 ENFDDME----LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFS 102
F ++ ++ LL+ I GF+ P+ IQ +AI + G +++A A +G+GKT FS
Sbjct: 25 ATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFS 84
Query: 103 ISILQQVDQNIKE-CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI-R 160
I IL Q+ Q + +ALI++PTRELA QI + +I + + H +
Sbjct: 85 IPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGP 144
Query: 161 KLEAGAQVVVGTPGRVFDMISRG--ALSTKQIRMFVLDEADEML---SRGFKDQIYDVFK 215
K ++V TP R+ ++ + + + V+DE+D++ GF+DQ+ +F
Sbjct: 145 KSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFL 204
Query: 216 HLNND-VQVILLSATMPADVLDVSMKFMRDPIKILV 250
+ V+ + SAT DV + + I + +
Sbjct: 205 ACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSI 240
>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 = 185 bits (471), Expect = 1e-58
Identities = 63/229 (27%), Positives = 108/229 (47%), Gaps = 11/229 (4%)
Query: 32 MAVDGLIETNWDHV---AENFDD-MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDV 87
M D L + F D + +LL+ I G KP+ IQ +A ++G D+
Sbjct: 1 MTCDDLKSGEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDL 60
Query: 88 IAQAQSGTGKTATFSISILQQVDQNIKECQ------ALILAPTRELAQQIQKVVIALGDF 141
I AQ+GTGKT ++ + +D + L+L PTRELA ++ +
Sbjct: 61 IVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-Y 119
Query: 142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM 201
+ GG I + G +++ TPGR+ D+ +++ + I V+DEAD+M
Sbjct: 120 KGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKM 179
Query: 202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
L F+ QI + + D Q ++ SAT P V +++ +++DP+ + V
Sbjct: 180 LDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228
>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 = 188 bits (481), Expect = 8e-58
Identities = 62/212 (29%), Positives = 111/212 (52%), Gaps = 9/212 (4%)
Query: 47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISI 105
++F +L + ++ + G++ P+ IQ+ +I P + G D++A AQ+G+GKTA F + I
Sbjct: 56 QHFTSADLRDIIIDNVNKSGYKIPTPIQKCSI-PVISSGRDLMACAQTGSGKTAAFLLPI 114
Query: 106 L-----QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
L + + Q +I++PTRELA QI + GGT R
Sbjct: 115 LSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNE 174
Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN- 219
+ G VV+ TPGR+ D + R ++ + R VLDEAD ML GF + + + H+
Sbjct: 175 CITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMR 234
Query: 220 -DVQVILLSATMPADVLDVSMKFMRDPIKILV 250
+ Q ++ SAT P ++ ++ +F+++ + + +
Sbjct: 235 PEHQTLMFSATFPEEIQRMAGEFLKNYVFVAI 266
>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 = 182 bits (464), Expect = 4e-57
Identities = 67/250 (26%), Positives = 116/250 (46%), Gaps = 8/250 (3%)
Query: 7 DNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDM--ELSEELLRGIYA 64
D + + N E+P + + +F + ++E L+ I
Sbjct: 12 DLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKE 71
Query: 65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----IKECQALI 120
GF + IQ ++I P + G D++A A++G+GKT F I ++ + + LI
Sbjct: 72 MGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLI 131
Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFD-M 179
L+PTRELA Q V+ L + +GG+ + +KL G ++V TPGR+ D M
Sbjct: 132 LSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHM 191
Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLD-VS 238
+ K ++ V+DEAD +L GF++++ + K L Q +L SAT V D
Sbjct: 192 QNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLAR 251
Query: 239 MKFMRDPIKI 248
+ ++P+ +
Sbjct: 252 ISLKKEPLYV 261
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 185 bits (473), Expect = 9e-57
Identities = 71/227 (31%), Positives = 111/227 (48%), Gaps = 24/227 (10%)
Query: 47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISI 105
E+F D+E+ E ++ I + +P+ +Q+ AI P + D++A AQ+G+GKTA F + I
Sbjct: 15 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAI-PIIKEKRDLMACAQTGSGKTAAFLLPI 73
Query: 106 LQQVDQNIK------------------ECQALILAPTRELAQQIQKVVIALGDFMSVSCH 147
L Q+ + +L+LAPTRELA QI + V
Sbjct: 74 LSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPC 133
Query: 148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK 207
GG + IR LE G ++V TPGR+ DM+ RG + + VLDEAD ML GF+
Sbjct: 134 VVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFE 193
Query: 208 DQIYDVFKHLN----NDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
QI + + ++ SAT P ++ ++ F+ + I + V
Sbjct: 194 PQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAV 240
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 174 bits (442), Expect = 3e-52
Identities = 28/200 (14%), Positives = 63/200 (31%), Gaps = 10/200 (5%)
Query: 53 ELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN 112
E+ + + Q+ V+G A +G GKT ++ L +
Sbjct: 5 NEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG 64
Query: 113 IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA----GAQV 168
K + ++ PT L +Q + + L D V + + ++ +
Sbjct: 65 KK---SALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHI 120
Query: 169 VVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA 228
+V + V +R LS K+ +D+ D +L + + ++ S
Sbjct: 121 LVFSTQFVSK--NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFST 178
Query: 229 TMPADVLDVSMKFMRDPIKI 248
+ + + +
Sbjct: 179 IKQGKIYERPKNLKPGILVV 198
>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 = 78.3 bits (192), Expect = 9e-17
Identities = 34/163 (20%), Positives = 66/163 (40%), Gaps = 3/163 (1%)
Query: 75 QRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV 134
Q I + + + +G GKT + ++ + + L+LAPT+ L Q +
Sbjct: 14 QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG--KVLMLAPTKPLVLQHAES 71
Query: 135 VIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV 194
L + + G ++ K A A+V+V TP + + + G +S + + + V
Sbjct: 72 FRRLFNLPPEKI-VALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIV 130
Query: 195 LDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDV 237
DEA + I +K + VI L+A+ + +
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKI 173
>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 = 65.6 bits (160), Expect = 2e-12
Identities = 34/191 (17%), Positives = 71/191 (37%), Gaps = 30/191 (15%)
Query: 54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI 113
+S + + G E+ Q A+ G +++ + GKT ++++++ +
Sbjct: 10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG 69
Query: 114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
K +L + P R LA + + + G + + ++V T
Sbjct: 70 K---SLYVVPLRALAGEKYESFKKWEKI-GLRIGISTGDY---ESRDEHLGDCDIIVTTS 122
Query: 174 GRVFDMISR-GALSTKQIRMFVLDE----ADE--------MLSRGFKDQIYDVFKHLNND 220
+ D + R A K + V+DE E ++++ + +N
Sbjct: 123 EK-ADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK---------MRRMNKA 172
Query: 221 VQVILLSATMP 231
++VI LSAT P
Sbjct: 173 LRVIGLSATAP 183
>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 = 63.3 bits (154), Expect = 1e-11
Identities = 37/204 (18%), Positives = 78/204 (38%), Gaps = 32/204 (15%)
Query: 50 DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND-VIAQAQSGTGKTATFSISILQQ 108
D++ + E + + G E Q A+ + + + +GKT I+++ +
Sbjct: 4 DELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHR 63
Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDF-----MSVSCHACIGGTIVRDDIRKLE 163
+ +A+ + P + LA++ +F + + G +D+
Sbjct: 64 ILTQGG--KAVYIVPLKALAEEK------FQEFQDWEKIGLRVAMATGDYDSKDEWLG-- 113
Query: 164 AGAQVVVGTPGRVFDMISRGALS-TKQIRMFVLDE----ADEMLSRGFKDQIYDVFKHLN 218
+++ T + FD + R S K +++ V DE RG + + H+
Sbjct: 114 -KYDIIIATAEK-FDSLLRHGSSWIKDVKILVADEIHLIGSR--DRG--ATLEVILAHML 167
Query: 219 NDVQVILLSATMP-----ADVLDV 237
Q+I LSAT+ A+ L+
Sbjct: 168 GKAQIIGLSATIGNPEELAEWLNA 191
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 54.8 bits (132), Expect = 2e-09
Identities = 25/180 (13%), Positives = 57/180 (31%), Gaps = 25/180 (13%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKT--ATFSI-SILQQVDQNIKECQALILAPTRELA-Q 129
Q P + G ++I +G+GKT A + L + + + + ++L L Q
Sbjct: 38 QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQ 97
Query: 130 QIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI------SRG 183
+K G T ++ ++ +++ T + + +
Sbjct: 98 LFRKEFQPFLKKWYRVIGLS-GDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDA 156
Query: 184 ALSTKQIRMFVLDEA-------------DEMLSRGFKDQIYDVFKHLNNDVQVIL-LSAT 229
+ + ++DE L + K+ + IL L+A+
Sbjct: 157 GVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS 216
>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 = 55.8 bits (133), Expect = 4e-09
Identities = 31/213 (14%), Positives = 72/213 (33%), Gaps = 3/213 (1%)
Query: 7 DNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYG 66
+ W+ ++ + ++E + A E + + +E + + Y
Sbjct: 186 ELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYE 245
Query: 67 FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALILAPT 124
+K + Q P + G + + A +G+GKT + Q ++ + + LA
Sbjct: 246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATK 305
Query: 125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA 184
+ +Q + V + S G + K+ + ++V TP + + G
Sbjct: 306 VPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGT 365
Query: 185 L-STKQIRMFVLDEADEMLSRGFKDQIYDVFKH 216
L S + + DE + + +
Sbjct: 366 LTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE 398
>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 = 55.2 bits (132), Expect = 7e-09
Identities = 49/321 (15%), Positives = 102/321 (31%), Gaps = 110/321 (34%)
Query: 32 MAVDGLIETNWDHVAENFDDMELSEELLRGIYAYG----------FEK-----PSAIQQ- 75
V+ ++ N+ + + ++ +Y F K +
Sbjct: 81 KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL 140
Query: 76 -RAIIPCVRGNDVIAQAQSGTGKT-----ATFSISILQQVDQNI-----KECQ--ALILA 122
+A++ +V+ G+GKT S + ++D I K C +L
Sbjct: 141 RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200
Query: 123 PTRELAQQIQKVVIALGDFMS---VSCHA----------------CIGGTIVRDDI---R 160
++L QI + D S + H+ C+ +V ++ +
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLLNVQNAK 257
Query: 161 KLEA---GAQVVVGTPGR---VFDMISRGALSTKQIRM------FVLDEADEMLSR---- 204
A ++++ T R V D +S A +T I + DE +L +
Sbjct: 258 AWNAFNLSCKILLTT--RFKQVTDFLS--AATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313
Query: 205 ----------------------GFKDQI--YDVFKHLNNDVQVILLSATM----PADV-- 234
+D + +D +KH+N D ++ +++ PA+
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
Query: 235 --LDVSMKFMRD---PIKILV 250
+S+ F P +L
Sbjct: 374 MFDRLSV-FPPSAHIPTILLS 393
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 52.7 bits (125), Expect = 4e-08
Identities = 23/151 (15%), Positives = 54/151 (35%), Gaps = 3/151 (1%)
Query: 69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKEC--QALILAPTRE 126
KP Q +P ++G + I A +G GKT + + + + + + A
Sbjct: 13 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72
Query: 127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL- 185
+ +Q + V + G T + ++ +++ TP + + + +G +
Sbjct: 73 VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIP 132
Query: 186 STKQIRMFVLDEADEMLSRGFKDQIYDVFKH 216
S + + DE + + I +
Sbjct: 133 SLSIFTLMIFDECHNTSKQHPYNMIMFNYLD 163
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 52.4 bits (126), Expect = 5e-08
Identities = 35/190 (18%), Positives = 73/190 (38%), Gaps = 22/190 (11%)
Query: 50 DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND-VIAQAQSGTGKTATFSISILQQ 108
+D++L ++ I G +K + Q A+ + + ++ + +G+GKT + I+
Sbjct: 11 EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISF 70
Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDF--MSVSCHACIGGTIVRDDIRKLEAGA 166
+ +N +A+ + P R L + + D+ + G D
Sbjct: 71 LLKNGG--KAIYVTPLRALTNE---KYLTFKDWELIGFKVAMTSGDY---DTDDAWLKNY 122
Query: 167 QVVVGTPGRVFDMISRGALS-TKQIRMFVLDE----ADEMLSRGFKDQIYDVFKHLNNDV 221
+++ T + D + R ++ FVLDE D RG + +
Sbjct: 123 DIIITTYEK-LDSLWRHRPEWLNEVNYFVLDELHYLNDP--ERG---PVVESVTIRAKRR 176
Query: 222 QVILLSATMP 231
++ LSAT+
Sbjct: 177 NLLALSATIS 186
>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 = 52.2 bits (124), Expect = 5e-08
Identities = 28/189 (14%), Positives = 63/189 (33%), Gaps = 8/189 (4%)
Query: 69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL--APTRE 126
K + Q P + G + + A +G+GKT + +A ++ A
Sbjct: 7 KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66
Query: 127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL- 185
+ +Q + V + S G + K+ + ++V TP + + G L
Sbjct: 67 VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 126
Query: 186 STKQIRMFVLDEA-----DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK 240
S + + DE + + + F + Q++ L+A++ +
Sbjct: 127 SLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEE 186
Query: 241 FMRDPIKIL 249
+ +
Sbjct: 187 TIEHICSLC 195
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 51.8 bits (123), Expect = 7e-08
Identities = 29/185 (15%), Positives = 68/185 (36%), Gaps = 9/185 (4%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQ--ALILAPTRELAQQI 131
Q +P +G + I A +G GKT + + + + + A + +Q
Sbjct: 9 QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68
Query: 132 QKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQI 190
V + + + + G T ++ + +++ TP + + ++ GA+ S
Sbjct: 69 ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF 128
Query: 191 RMFVLDEADEMLSRGFKDQIYDVFKHL------NNDVQVILLSATMPADVLDVSMKFMRD 244
+ + DE +QI + + QV+ L+A++ + + M+
Sbjct: 129 TLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAMQH 188
Query: 245 PIKIL 249
K+
Sbjct: 189 ICKLC 193
>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 = 7e-08
Identities = 34/232 (14%), Positives = 79/232 (34%), Gaps = 8/232 (3%)
Query: 7 DNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYG 66
+ W+ ++ + ++E + A E + + +E + + Y
Sbjct: 186 ELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYE 245
Query: 67 FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL--APT 124
+K + Q P + G + + A +G+GKT + +A ++ A
Sbjct: 246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATK 305
Query: 125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA 184
+ +Q + V + S G + K+ + ++V TP + + G
Sbjct: 306 VPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGT 365
Query: 185 L-STKQIRMFVLDEADEM-----LSRGFKDQIYDVFKHLNNDVQVILLSATM 230
L S + + DE + + F + Q++ L+A++
Sbjct: 366 LTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASV 417
>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 = 48.9 bits (116), Expect = 8e-07
Identities = 36/197 (18%), Positives = 60/197 (30%), Gaps = 42/197 (21%)
Query: 58 LLRGIYAYGFEKPSAIQQRAIIPCV------------RGNDVIAQAQSGTGKTATFSISI 105
RG+ P + + V A +G+GK+ +
Sbjct: 194 CTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKST----KV 249
Query: 106 LQQ-VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
Q K L+L P+ + G +MS + +R +R +
Sbjct: 250 PAAYAAQGYK---VLVLNPSVAAT-------LGFGAYMSKAHG---IDPNIRTGVRTITT 296
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM-----LSRGFKDQIYDVFKHLNN 219
GA V T G+ ++ G S + + DE L G + D +
Sbjct: 297 GAPVTYSTYGK---FLADGGCSGGAYDIIICDECHSTDSTTILGIGT---VLDQAETA-G 349
Query: 220 DVQVILLSATMPADVLD 236
V+L +AT P V
Sbjct: 350 ARLVVLATATPPGSVTV 366
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 43.7 bits (102), Expect = 4e-05
Identities = 47/209 (22%), Positives = 86/209 (41%), Gaps = 25/209 (11%)
Query: 28 GPPGMAVDGLIETNWDHVAE-NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
GP M ++ W HV + N E + ++ FE Q+ A+ +G+
Sbjct: 1 GPDSMVP---VKKEWAHVVDLNHKIENFDELIPNPARSWPFE-LDTFQKEAVYHLEQGDS 56
Query: 87 VIAQAQSGTGKT--ATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV 144
V A + GKT A ++I++ + + + +P + L+ Q + D +++
Sbjct: 57 VFVAAHTSAGKTVVAEYAIAMAHRNMT-----KTIYTSPIKALSNQKFRDFKETFDDVNI 111
Query: 145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-- 202
G I D ++ A ++ T + M+ RGA + + + DE +
Sbjct: 112 -------GLITGDV--QINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQ 162
Query: 203 SRGFKDQIYDVFKHLNNDVQVILLSATMP 231
RG + +V L V+ ILLSAT+P
Sbjct: 163 DRGVVWE--EVIIMLPQHVKFILLSATVP 189
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 43.2 bits (101), Expect = 5e-05
Identities = 37/171 (21%), Positives = 69/171 (40%), Gaps = 19/171 (11%)
Query: 63 YAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALI 120
Y F Q AI RG V+ A + GKT A ++I+ + Q + +
Sbjct: 81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ-----RVIY 134
Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
+P + L+ Q + ++ +G ++ DI + A +V T + M+
Sbjct: 135 TSPIKALSNQK------YREL--LAEFGDVG--LMTGDI-TINPDAGCLVMTTEILRSML 183
Query: 181 SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP 231
RG+ +++ + DE M + + L + V+ + LSAT+P
Sbjct: 184 YRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 234
>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 = 42.5 bits (100), Expect = 7e-05
Identities = 26/156 (16%), Positives = 53/156 (33%), Gaps = 14/156 (8%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM 142
+G + G GKT F IL + + + L+LAPTR + ++++ A +
Sbjct: 7 KGMTTVLDFHPGAGKTRRFLPQILAE--CARRRLRTLVLAPTRVVLSEMKE---AFHG-L 60
Query: 143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML 202
V H + + + + + ++DEA +
Sbjct: 61 DVKFH-------TQAFSAHGSGREVIDAMCHATLTYRMLEPTRV-VNWEVIIMDEAHFLD 112
Query: 203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS 238
+ + + N+ IL++AT P +
Sbjct: 113 PASIAARGWAAHRARANESATILMTATPPGTSDEFP 148
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 41.4 bits (96), Expect = 2e-04
Identities = 37/171 (21%), Positives = 69/171 (40%), Gaps = 19/171 (11%)
Query: 63 YAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALI 120
Y F Q AI RG V+ A + GKT A ++I+ + Q + +
Sbjct: 179 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ-----RVIY 232
Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
+P + L+ Q + ++ +G ++ DI + A +V T + M+
Sbjct: 233 TSPIKALSNQK------YREL--LAEFGDVG--LMTGDI-TINPDAGCLVMTTEILRSML 281
Query: 181 SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP 231
RG+ +++ + DE M + + L + V+ + LSAT+P
Sbjct: 282 YRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 332
>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 = 36.3 bits (84), Expect = 0.007
Identities = 27/183 (14%), Positives = 65/183 (35%), Gaps = 27/183 (14%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK 133
Q++A+ + +G+GKT +++ + ++ LI+ PT LA+Q ++
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKTHV-AMAAINELSTPT-----LIVVPTLALAEQWKE 151
Query: 134 VVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF 193
+ G+ G +++ + V T + + + +
Sbjct: 152 RLGIFGE----EYVGEFSGR--IKELKP------LTVSTYDSAYVNAEK---LGNRFMLL 196
Query: 194 VLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP-ADVLDVSMKFMRDPIKILVKK 252
+ DE + + + QI ++ + L+AT D +K + +
Sbjct: 197 IFDEVHHLPAESYV-QIAQ----MSIAPFRLGLTATFEREDGRHEILKEVVGGKVFELFP 251
Query: 253 EEL 255
+ L
Sbjct: 252 DSL 254
>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3
catalytic subunit; nucleotide-binding, capsid protein;
2.75A {Murray valley encephalitis virus}
Length = 673
Score = 36.1 bits (83), Expect = 0.009
Identities = 28/152 (18%), Positives = 49/152 (32%), Gaps = 18/152 (11%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQ-VDQNIKECQA-LILAPTRELAQQIQKVVIALGD 140
+ + G GKT IL Q + I++ +LAPTR +A +
Sbjct: 240 KRQLTVLDLHPGAGKT-R---RILPQIIKDAIQKRLRTAVLAPTRVVAAE---------- 285
Query: 141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE 200
M+ + + R+ V V + + +FV+DEA
Sbjct: 286 -MAEALRGLPVRYLTPAVQREHSGNEIVDVMCHATLTHRLMSPL-RVPNYNLFVMDEAHF 343
Query: 201 MLSRGFKDQIYDVFKHLNNDVQVILLSATMPA 232
+ Y + + I ++AT P
Sbjct: 344 TDPASIAARGYIATRVEAGEAAAIFMTATPPG 375
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 35.3 bits (81), Expect = 0.020
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 50 DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQV 109
+D+ + +L + A G + Q A+ ++ + Q GTGKT T + +
Sbjct: 337 EDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLA 396
Query: 110 DQNIKECQALILAPTR 125
Q L+ AP+
Sbjct: 397 RQG--NGPVLVCAPSN 410
>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding,
viral nucleoprotein, endoplasmic reticulum, helicase,
hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A*
2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A
2bhr_A
Length = 451
Score = 34.8 bits (80), Expect = 0.021
Identities = 27/163 (16%), Positives = 51/163 (31%), Gaps = 28/163 (17%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQA-LILAPTRELAQQIQKVVIAL-GD 140
+ I G GKT + V + + LILAPTR +A ++++ + L
Sbjct: 18 KKRLTIMDLHPGAGKTKRI---LPSIVREALLRRLRTLILAPTRVVAAEMEEALRGLPIR 74
Query: 141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEA-- 198
+ + + + G V + + + V+DEA
Sbjct: 75 YQTPAVKSDHTG------------REIVDLMCHATFTTRLLSSTRV-PNYNLIVMDEAHF 121
Query: 199 ---DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS 238
+ +RG+ + I ++AT P
Sbjct: 122 TDPCSVAARGYISTR-----VEMGEAAAIFMTATPPGSTDPFP 159
>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 = 34.2 bits (78), Expect = 0.041
Identities = 27/163 (16%), Positives = 45/163 (27%), Gaps = 28/163 (17%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQA-LILAPTRELAQQIQKVVIALGDF 141
+ I G GKT + V + +K LILAPTR +A +
Sbjct: 185 KKRLTIMDLHPGAGKTKRI---LPSIVREALKRRLRTLILAPTRVVAAE----------- 230
Query: 142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI-SRGALSTKQIRMFVLDE--- 197
M + V + + S + + V+DE
Sbjct: 231 MEEALRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVP--NYNLIVMDEAHF 288
Query: 198 --ADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS 238
+ +RG+ + I ++AT P
Sbjct: 289 TDPCSVAARGYISTR-----VEMGEAAAIFMTATPPGSTDPFP 326
>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication,
viral replication, nucleotide-binding; 2.10A {Kokobera
virus} PDB: 2v6j_A
Length = 431
Score = 34.0 bits (78), Expect = 0.041
Identities = 29/162 (17%), Positives = 53/162 (32%), Gaps = 26/162 (16%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQA-LILAPTRELAQQIQKVVIALGDF 141
+ + G GKT + Q V + +K+ +ILAPTR +A ++ + AL
Sbjct: 1 KRELTVLDLHPGAGKTRRV---LPQLVREAVKKRLRTVILAPTRVVASEMYE---ALRG- 53
Query: 142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEA--- 198
I + V + +G ++++DEA
Sbjct: 54 ------EPIRYMTPAVQSER-TGNEIVDFMCHSTFTMKLLQGV-RVPNYNLYIMDEAHFL 105
Query: 199 --DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS 238
+ +RG+ + D I ++AT P
Sbjct: 106 DPASVAARGYIETR-----VSMGDAGAIFMTATPPGTTEAFP 142
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 34.0 bits (77), Expect = 0.044
Identities = 24/144 (16%), Positives = 46/144 (31%), Gaps = 34/144 (23%)
Query: 94 GTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGT 153
G GKT IL +V+ + LIL P R+ A+ I++ A G ++ + +
Sbjct: 171 GCGKTKE----ILSRVNFE----EDLILVPGRQAAEMIRRRANASGIIVATKDNVRTVDS 222
Query: 154 IVRDDIRKLEAGAQVVVGTPGRVFD---MISRGALS----------------TKQIRMFV 194
+ + + + + D M+ G ++ T+QI
Sbjct: 223 FLMNYGKGARCQFKRL------FIDEGLMLHTGCVNFLVEMSLCDIAYVYGDTQQIPYIN 276
Query: 195 LDEADEMLSRGFKDQIYDVFKHLN 218
+ F D +
Sbjct: 277 RVTGFPYPAH-FAKLEVDEVETRR 299
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 33.6 bits (77), Expect = 0.060
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE 126
Q A+ ++ + Q GTGKT T + + Q L+ AP+
Sbjct: 185 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQG--NGPVLVCAPSNI 235
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 33.4 bits (76), Expect = 0.072
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT 124
Q A+ ++ + Q GTGKT T + + + + + L+ AP+
Sbjct: 365 QSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIH--KDRILVCAPS 413
>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR
complex, HMR, HML, TELO AAA+ domain, structural,
nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}
Length = 318
Score = 33.0 bits (74), Expect = 0.090
Identities = 13/169 (7%), Positives = 45/169 (26%), Gaps = 22/169 (13%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM 142
+ + K + + EL + + + D++
Sbjct: 44 QNKLFYITNADDSTKFQL------------VNDV-------MDELITSSARKELPIFDYI 84
Query: 143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTP-GRVFDMISRGALSTKQIRMFVLDEADEM 201
+ G + + I + + + I+ + K+ + ++ + +
Sbjct: 85 HIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENL 144
Query: 202 LSRGFKDQIYDVFKHLNNDVQVILLSATM--PADVLDVSMKFMRDPIKI 248
LS N+ + +I + + +++ +I
Sbjct: 145 LSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEI 193
>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane,
nucleotide-binding, RNA replication, transmembrane,
viral protein; 1.80A {Japanese encephalitis virus} PDB:
2v8o_A 2qeq_A
Length = 459
Score = 32.1 bits (73), Expect = 0.15
Identities = 31/158 (19%), Positives = 53/158 (33%), Gaps = 18/158 (11%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQ-VDQNI-KECQALILAPTRELAQQIQKVVIALGD 140
+ + G+GKT IL Q + I + + +LAPTR +A ++ + AL
Sbjct: 20 KRQMTVLDLHPGSGKT-R---KILPQIIKDAIQQRLRTAVLAPTRVVAAEMAE---ALRG 72
Query: 141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE 200
+ V R+ + V V + + +FV+DEA
Sbjct: 73 -LPVRYQ-------TSAVQREHQGNEIVDVMCHATLTHRLMSPNRV-PNYNLFVMDEAHF 123
Query: 201 MLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS 238
+ Y K + I ++AT P
Sbjct: 124 TDPASIAARGYIATKVELGEAAAIFMTATPPGTTDPFP 161
>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 = 32.3 bits (73), Expect = 0.19
Identities = 29/262 (11%), Positives = 63/262 (24%), Gaps = 119/262 (45%)
Query: 27 NGPPGMAV--DGLIETNWDHVAENFDDM-------------ELSEELLRGIYAYGFEKPS 71
N P + + G + EN+ M ++ +E+ +Y F
Sbjct: 1667 NNPVNLTIHFGG---EKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK 1723
Query: 72 ------AIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKE---------- 115
Q A+ + + +K
Sbjct: 1724 GLLSATQFTQPAL--------------------TLMEKAAFED----LKSKGLIPADATF 1759
Query: 116 ------------CQALILAPTRELAQQIQKVVIALGDFMSVSCH------------ACIG 151
A ++ + + +VV G M V+ A
Sbjct: 1760 AGHSLGEYAALASLADVM----SIESLV-EVVFYRGMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 152 GTIV----RDDIRK------------LEA------GAQVVV-GTPGRVFDMISR--GALS 186
G + ++ ++ +E Q V G + D ++ +
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRAL-DTVTNVLNFIK 1873
Query: 187 TKQIRM------FVLDEADEML 202
++I + L+E + L
Sbjct: 1874 LQKIDIIELQKSLSLEEVEGHL 1895
>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition
domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus
fulgidus} SCOP: c.37.1.19
Length = 237
Score = 30.8 bits (70), Expect = 0.30
Identities = 21/126 (16%), Positives = 44/126 (34%), Gaps = 23/126 (18%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK 133
Q++A+ + +G+GKT +++ + ++ LI+ PT LA+Q ++
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKTHV-AMAAINELSTPT-----LIVVPTLALAEQWKE 151
Query: 134 VVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRM 192
+ G+ G I + V T +D + +
Sbjct: 152 RLGIFGE----EYVGEFSGRIKEL--------KPLTVST----YDSAYVNAEKLGNRFML 195
Query: 193 FVLDEA 198
+ DE
Sbjct: 196 LIFDEV 201
>2j1a_A Hyaluronidase, CBM32; protein-carbohydrate interaction, glycoside
hydrolase, GH84C, hydrolase; HET: GAL; 1.49A
{Clostridium perfringens} PDB: 2j1e_A* 2j7m_A*
Length = 150
Score = 30.3 bits (68), Expect = 0.34
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 7 DNWEDPKNGPAE-NEAEQPAYNGPPGMAVDGLIETNW 42
D + +P+ + E N P A DG + T W
Sbjct: 4 DPFTNPRTVKITASSEETSGENAPASFASDGDMNTFW 40
>1k12_A Lectin; beta barrel, protein carbohydrate complex, sugar binding
protein; HET: FUC; 1.90A {Anguilla anguilla} SCOP:
b.18.1.15
Length = 158
Score = 30.5 bits (68), Expect = 0.35
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 13 KNGPAE---NEAEQPAYNGPPGMAVDGLIETNWDH 44
G A + A N A+DG ++N+ H
Sbjct: 13 VRGKATQSAQLRGEHAANSEASNAIDGNRDSNFYH 47
>3cqo_A FBP32; F-lectin, fucolectin, sugar binding protein; HET: FUC;
2.32A {Morone saxatilis}
Length = 293
Score = 30.8 bits (68), Expect = 0.38
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 14 NGPAENEAEQPAYNGPPGMAVDGLIETNWDH 44
G A A +G A+DG ++++
Sbjct: 9 RGKATQSARYLHTHGAAYNAIDGNRNSDFEA 39
>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 386
Score = 30.4 bits (68), Expect = 0.63
Identities = 19/148 (12%), Positives = 44/148 (29%), Gaps = 34/148 (22%)
Query: 92 QSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIG 151
+GTGKTA + + ++ K + + ++
Sbjct: 53 LTGTGKTAV-----------------------VKFVLSKLHKKFLGKFKHVYINTRQI-- 87
Query: 152 GTIVRDDIRKLEAGAQVVVGTPG----RVFDMISRGALSTKQIRMFVLDEADEMLSRGFK 207
+ L V V G ++ + + + VLDE D + +
Sbjct: 88 -DTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYND 146
Query: 208 DQIYDVF----KHLNNDVQVILLSATMP 231
D +Y + + + + I ++ +
Sbjct: 147 DILYKLSRINSEVNKSKISFIGITNDVK 174
>2j22_A Fucolectin-related protein; carbohydrate-binding protein,
carbohydrate binding protein; 1.8A {Streptococcus
pneumoniae}
Length = 148
Score = 28.8 bits (64), Expect = 1.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 26 YNGPPGMAVDGLIETNWDH 44
YNG +AVDG ++ H
Sbjct: 28 YNGFSRLAVDGNKNGDYGH 46
>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase,
hypertherm protein, replication; HET: DNA BOG; 1.50A
{Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB:
1d2m_A*
Length = 664
Score = 29.8 bits (68), Expect = 1.1
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 15/69 (21%)
Query: 69 KPSAIQQRAIIPCVRGNDVIAQAQ-----SGTGKTATFSISILQQVDQNIKECQ--ALIL 121
P Q +AI V + +GTGKT T + + I+ AL+L
Sbjct: 8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA--------KVIEALGRPALVL 59
Query: 122 APTRELAQQ 130
AP + LA Q
Sbjct: 60 APNKILAAQ 68
>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex,
hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus
subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A*
1d9x_A 2d7d_B* 2nmv_B*
Length = 661
Score = 29.0 bits (66), Expect = 1.5
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 15/69 (21%)
Query: 69 KPSAIQQRAIIPCVRGNDVIAQAQ-----SGTGKTATFSISILQQVDQNIKECQ--ALIL 121
+P Q +AI V+G + Q +GTGKT T S IKE L++
Sbjct: 12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVS--------NLIKEVNKPTLVI 63
Query: 122 APTRELAQQ 130
A + LA Q
Sbjct: 64 AHNKTLAGQ 72
>3mj8_L Stimulatory hamster antibody HL4E10 FAB light CHA; hamster IGG,
immune system; 2.94A {Cricetulus migratorius} PDB:
3mj9_L*
Length = 213
Score = 28.5 bits (64), Expect = 1.5
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 93 SGTGKTATFSISILQQVDQNIKECQA 118
S +G AT +IS Q D+ CQ+
Sbjct: 64 SNSGNMATLTISKAQAGDEADYYCQS 89
>3lei_A Platelet aggregation factor SM-HPAF; lectin domain of
lectinolysin, fucose, blood clotting, nicke; HET: FUC;
1.90A {Streptococcus mitis} PDB: 3leg_A* 3le0_A*
3lek_A*
Length = 153
Score = 28.4 bits (63), Expect = 1.6
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 25 AYNGPPGMAVDGLIETNWDH 44
AY G AVDG +++++ H
Sbjct: 24 AYGGAATRAVDGNVDSDYGH 43
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 29.3 bits (66), Expect = 1.7
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA 128
+P AIQ+ +R A A +G GKT +F +++ + K C ++ PT L
Sbjct: 56 EPRAIQKMWAKRILRKESFAATAPTGVGKT-SFGLAMSLFLALKGKRC--YVIFPTSLLV 112
Query: 129 QQIQKVVIALGDFMSVS 145
Q + + + V
Sbjct: 113 IQAAETIRKYAEKAGVG 129
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 29.1 bits (66), Expect = 1.7
Identities = 22/87 (25%), Positives = 32/87 (36%), Gaps = 15/87 (17%)
Query: 94 GTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ----IQKVVIALGDFMSVSCHAC 149
G+GKT ++IL + Q + PT LA Q + +
Sbjct: 399 GSGKTVVAQLAILDNYEAG---FQTAFMVPTSILAIQHYRRTVESFSKFN----IHVALL 451
Query: 150 IGGTIV--RDDI-RKLEAG-AQVVVGT 172
IG T ++ I L G VV+GT
Sbjct: 452 IGATTPSEKEKIKSGLRNGQIDVVIGT 478
>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 = 28.0 bits (61), Expect = 1.9
Identities = 5/23 (21%), Positives = 9/23 (39%), Gaps = 4/23 (17%)
Query: 20 EAEQPAYNGP---PGMAVDGLIE 39
+A Y P +A+ +E
Sbjct: 26 QASLKLY-ADDSAPALAIKATME 47
Score = 27.6 bits (60), Expect = 3.0
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 8/33 (24%)
Query: 156 RDDIRKLEAGAQVVVGTPGRVFDMISRGALSTK 188
+ ++KL+A ++ S AL+ K
Sbjct: 19 KQALKKLQASLKLY--ADD------SAPALAIK 43
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 28.5 bits (64), Expect = 2.7
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 7/63 (11%)
Query: 74 QQRAIIPCV-----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA 128
Q I + + V ++ +G+GKT S LQ + + L L T
Sbjct: 7 YQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKV--LYLVRTNSQE 64
Query: 129 QQI 131
+Q+
Sbjct: 65 EQV 67
>2v1u_A Cell division control protein 6 homolog; DNA replication,
nucleotide-binding, replication, archaea; HET: ADP;
3.10A {Aeropyrum pernix}
Length = 387
Score = 27.9 bits (61), Expect = 3.3
Identities = 29/172 (16%), Positives = 57/172 (33%), Gaps = 34/172 (19%)
Query: 76 RAIIPCVRG---NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ 132
+ P +RG ++ + +GTGKTA R + ++++
Sbjct: 33 EVLAPALRGEKPSNALLYGLTGTGKTAV-----------------------ARLVLRRLE 69
Query: 133 KVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPG----RVFDMISRGALSTK 188
+LG + + V V G V++ + + +
Sbjct: 70 ARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLR 129
Query: 189 QIRMFVLDEADEMLSRGFKDQI-YDVFK---HLNNDVQVILLSATMPADVLD 236
I + VLDE D + R + Y + + L + V V L+ T ++
Sbjct: 130 GIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVE 181
>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC
transporter ATPase domain-like; HET: DNA ADP; 2.70A
{Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*
Length = 371
Score = 27.1 bits (60), Expect = 5.4
Identities = 9/44 (20%), Positives = 24/44 (54%)
Query: 184 ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS 227
AL ++ +LDE L + ++ ++F+ + + Q+I+++
Sbjct: 300 ALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIIT 343
>3gkq_A Terminal oxygenase component of carbazole 1,9A- dioxygenase; rieske
nonheme iron oxygenase, electron transfer,
putidaredoxin-type ferredoxin; 2.10A {Sphingomonas}
Length = 389
Score = 27.3 bits (60), Expect = 5.7
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 3/40 (7%)
Query: 16 PAENEAEQPAYNGPPGMAVDG---LIETNWDHVAENFDDM 52
P + + P +AV G +++ NW EN D
Sbjct: 145 PHDLAEDVPPGFLDADLAVHGQHRVVDANWRMGVENGFDA 184
>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A
{Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A
3n2e_A*
Length = 168
Score = 26.7 bits (60), Expect = 5.9
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 11/39 (28%)
Query: 124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL 162
EL VI+ G GG ++ ++++ L
Sbjct: 70 IDELKTLKTPHVISTG-----------GGIVMHENLKGL 97
>3khq_A B-cell antigen receptor complex-associated protei chain; CD79B,
CD79A, IG-beta, BCR, IG domain, V-SET, immunoglobulin
protein binding; HET: FLC GSH; 1.70A {Mus musculus} PDB:
3kho_A*
Length = 133
Score = 26.5 bits (59), Expect = 6.0
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 92 QSGTGKTATFSISILQQVDQNIKECQ 117
Q+ G T +I +Q D I C+
Sbjct: 70 QTQNGSVYTLTIQNIQYEDNGIYFCK 95
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 384
Score = 27.0 bits (59), Expect = 6.6
Identities = 20/145 (13%), Positives = 44/145 (30%), Gaps = 29/145 (20%)
Query: 92 QSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIG 151
+GTGKT ++ + +I++V ++ V
Sbjct: 53 LTGTGKTFV-----------------------SKYIFNEIEEVKKEDEEYKDVKQAYVNC 89
Query: 152 GTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF------VLDEADEMLSRG 205
+ L + A + G + + + LDE D ++ R
Sbjct: 90 REVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRR 149
Query: 206 FKDQIYDVFKHLNNDVQVILLSATM 230
D + + ++ VI++S +
Sbjct: 150 GGDIVLYQLLRSDANISVIMISNDI 174
>3gke_A DDMC; rieske cluster, non-heme mononuclear iron, oxygenase,
oxidoreductase; 1.75A {Stenotrophomonas maltophilia}
PDB: 3gb4_A 3gl0_A* 3gl2_A* 3gob_A* 3gte_A 3gts_A*
Length = 349
Score = 27.1 bits (60), Expect = 6.7
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 3/44 (6%)
Query: 9 WEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDM 52
DP P PAY G ++ N+ + +N D+
Sbjct: 118 LADPGAIPDFGCRVDPAYRTVGGYGH---VDCNYKLLVDNLMDL 158
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.135 0.388
Gapped
Lambda K H
0.267 0.0478 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,066,390
Number of extensions: 251479
Number of successful extensions: 907
Number of sequences better than 10.0: 1
Number of HSP's gapped: 795
Number of HSP's successfully gapped: 99
Length of query: 258
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 166
Effective length of database: 4,133,061
Effective search space: 686088126
Effective search space used: 686088126
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.0 bits)