RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9277
(178 letters)
>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 = 278 bits (714), Expect = 3e-94
Identities = 132/173 (76%), Positives = 150/173 (86%), Gaps = 4/173 (2%)
Query: 1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
MA GS + + ED++ VEFETSE+V+V TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 6 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 65
Query: 61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 66 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 125
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR RR+
Sbjct: 126 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR----RRS 174
>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 = 266 bits (682), Expect = 2e-89
Identities = 100/174 (57%), Positives = 124/174 (71%), Gaps = 5/174 (2%)
Query: 1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
M+A ++ P+ + S E+V +FD+M L E LLRGIYAYGFEKPSAIQQ
Sbjct: 9 MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQ 68
Query: 61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
R+I P +KG DVIAQAQSGTGKTATF+ISILQ ++ L+ TQ L L+PTRELA QIQKVV
Sbjct: 69 RAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVV 128
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRSSQGRRT 173
+ALGD+M CHACIGGTN+ +++KL H++ GTPGRVFDM+ RR
Sbjct: 129 MALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLN----RRY 178
>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 = 259 bits (664), Expect = 4e-89
Identities = 99/150 (66%), Positives = 117/150 (78%), Gaps = 5/150 (3%)
Query: 25 SEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTA 84
S E+V FD+M L+E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTA
Sbjct: 23 SNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTA 82
Query: 85 TFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL 144
TF+ISILQ L+ + +ETQ L L+PTRELA QIQKV+LALGD+M CHACIGGTN+ ++
Sbjct: 83 TFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEM 142
Query: 145 RKLDY-GQHVVSGTPGRVFDMIRSSQGRRT 173
+KL H+V GTPGRVFDM+ RR
Sbjct: 143 QKLQAEAPHIVVGTPGRVFDMLN----RRY 168
>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 = 258 bits (662), Expect = 6e-89
Identities = 88/153 (57%), Positives = 114/153 (74%), Gaps = 6/153 (3%)
Query: 21 EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
+ +T+ D +VV FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGT
Sbjct: 4 QIQTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGT 62
Query: 81 GKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNL 140
GKT TFSI+ LQ +DT ++ Q L L+PTRELA+QIQKVV+AL M+++ HACIGGT+
Sbjct: 63 GKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSF 122
Query: 141 SEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
ED L +V GTPGRVFD I+ RR
Sbjct: 123 VEDAEGLR-DAQIVVGTPGRVFDNIQ----RRR 150
>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 = 260 bits (667), Expect = 2e-87
Identities = 89/159 (55%), Positives = 116/159 (72%), Gaps = 6/159 (3%)
Query: 15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
D+ + +T+ D +VV FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+A
Sbjct: 5 TDIEESQIQTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLA 63
Query: 75 QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
QAQSGTGKT TFSI+ LQ +DT ++ Q L L+PTRELA+QIQKVV+AL M+++ HAC
Sbjct: 64 QAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHAC 123
Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
IGGT+ ED L +V GTPGRVFD I+ RR
Sbjct: 124 IGGTSFVEDAEGLRDA-QIVVGTPGRVFDNIQ----RRR 157
>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 = 247 bits (633), Expect = 4e-82
Identities = 63/151 (41%), Positives = 95/151 (62%), Gaps = 6/151 (3%)
Query: 25 SEDV--EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGK 82
++DV +TF++ L+ +LL GI+ GFEKPS IQ+ +I + GRD++A+A++GTGK
Sbjct: 12 TDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGK 71
Query: 83 TATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE 142
TA F I L+ + +L + Q L + PTRELA+Q +VV LG + C GGTNL +
Sbjct: 72 TAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRD 131
Query: 143 DLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
D+ +L+ H++ GTPGRV D+ R+
Sbjct: 132 DILRLNETVHILVGTPGRVLDLAS----RKV 158
>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 = 240 bits (615), Expect = 1e-81
Identities = 64/154 (41%), Positives = 94/154 (61%), Gaps = 3/154 (1%)
Query: 15 EDLSNVEFETSEDVEV-VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVI 73
+DLS+ T + + + F+++ L +L G+ A GFE+PS +Q ++I G D+I
Sbjct: 6 QDLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLI 65
Query: 74 AQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCH 132
QA+SGTGKT FS L SL + TQ+L L+PTRE+AVQI V+ A+G M ++CH
Sbjct: 66 VQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECH 125
Query: 133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
IGGT LS+D +L H+ G+PGR+ +I
Sbjct: 126 VFIGGTPLSQDKTRLKKC-HIAVGSPGRIKQLIE 158
>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 = 240 bits (616), Expect = 2e-79
Identities = 51/155 (32%), Positives = 88/155 (56%), Gaps = 6/155 (3%)
Query: 15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDV 72
+ ++ + + + V +F+ + L+ LL+G+YA GF +PS IQ+ ++ ++ +++
Sbjct: 8 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 67
Query: 73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQC 131
IAQ+QSGTGKTA F +++L ++ + Q LCLSPT ELA+Q KV+ +G F ++
Sbjct: 68 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 127
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
+ G L + + +V GTPG V D
Sbjct: 128 AYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCS 159
>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 = 236 bits (603), Expect = 5e-79
Identities = 51/155 (32%), Positives = 88/155 (56%), Gaps = 6/155 (3%)
Query: 15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDV 72
+ ++ + + + V +F+ + L+ LL+G+YA GF +PS IQ+ ++ ++ +++
Sbjct: 75 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 134
Query: 73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQC 131
IAQ+QSGTGKTA F +++L ++ + Q LCLSPT ELA+Q KV+ +G F ++
Sbjct: 135 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 194
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
+ G L + + +V GTPG V D
Sbjct: 195 AYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCS 226
>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 = 238 bits (609), Expect = 1e-77
Identities = 51/155 (32%), Positives = 88/155 (56%), Gaps = 6/155 (3%)
Query: 15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDV 72
+ ++ + + + V +F+ + L+ LL+G+YA GF +PS IQ+ ++ ++ +++
Sbjct: 75 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 134
Query: 73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQC 131
IAQ+QSGTGKTA F +++L ++ + Q LCLSPT ELA+Q KV+ +G F ++
Sbjct: 135 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 194
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
+ G L + + +V GTPG V D
Sbjct: 195 AYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCS 226
>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 = 227 bits (581), Expect = 2e-74
Identities = 54/146 (36%), Positives = 87/146 (59%), Gaps = 10/146 (6%)
Query: 30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS 87
+ +FD +GL +LL+GIYA F+KPS IQ+R++ ++ R++IAQ+QSGTGKTA FS
Sbjct: 3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
+++L ++ + Q +CL+P+RELA Q +VV +G F + + + +
Sbjct: 63 LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSF----EKNK 118
Query: 148 DYGQHVVSGTPGRVFDMIRSSQGRRT 173
V+ GTPG V D++R R+
Sbjct: 119 QINAQVIVGTPGTVLDLMR----RKL 140
>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 = 224 bits (572), Expect = 5e-73
Identities = 54/140 (38%), Positives = 75/140 (53%), Gaps = 2/140 (1%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
+ S F + L+ +LLR I GFE PS +Q I + G DV+ QA+SG GKTA F +
Sbjct: 5 HMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL 64
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
+ LQ L+ + VL + TRELA QI K +M NV+ GG ++ +D L
Sbjct: 65 ATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL 124
Query: 148 DYG-QHVVSGTPGRVFDMIR 166
H+V GTPGR+ + R
Sbjct: 125 KKNCPHIVVGTPGRILALAR 144
>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 = 217 bits (556), Expect = 5e-73
Identities = 55/143 (38%), Positives = 90/143 (62%), Gaps = 5/143 (3%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
+ F++ L+ +LL GI+ G+EKPS IQ+ SI + GRD++A+A++GTGK+ + I +L
Sbjct: 3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
+ LD + Q + + PTRELA+Q+ ++ + + M + A GGTNL +D+ +LD
Sbjct: 63 ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122
Query: 151 QHVVSGTPGRVFDMIRSSQGRRT 173
HVV TPGR+ D+I+ +
Sbjct: 123 VHVVIATPGRILDLIK----KGV 141
>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 = 209 bits (533), Expect = 2e-69
Identities = 55/148 (37%), Positives = 77/148 (52%), Gaps = 2/148 (1%)
Query: 21 EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
+ + S S F + L+ +LLR I GFE PS +Q I + G DV+ QA+SG
Sbjct: 3 DVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGM 62
Query: 81 GKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTN 139
GKTA F ++ LQ L+ + VL + TRELA QI K +M NV+ GG +
Sbjct: 63 GKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS 122
Query: 140 LSEDLRKLDYG-QHVVSGTPGRVFDMIR 166
+ +D L H+V GTPGR+ + R
Sbjct: 123 IKKDEEVLKKNCPHIVVGTPGRILALAR 150
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 199 bits (509), Expect = 2e-62
Identities = 40/118 (33%), Positives = 68/118 (57%), Gaps = 10/118 (8%)
Query: 58 IQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ 115
IQ++++ ++ R++I Q+QSGTGKTA F++++L +D + + Q +CL+P+RELA Q
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQ 204
Query: 116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
I VV +G + V+ I + + +V GTPG V D+++ RR
Sbjct: 205 IMDVVTEMGKYTEVKTAFGIKDSV----PKGAKIDAQIVIGTPGTVMDLMK----RRQ 254
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 158 bits (402), Expect = 1e-49
Identities = 47/139 (33%), Positives = 74/139 (53%), Gaps = 4/139 (2%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
+ F + ++ I F KP+ IQ+R I ++G ++ Q+Q+GTGKT + + I+
Sbjct: 4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 63
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDLRKL 147
+ + + E Q + +PTRELA QI L + F + IGGT+ + L KL
Sbjct: 64 EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 123
Query: 148 DYGQHVVSGTPGRVFDMIR 166
+ H+V GTPGR+ D IR
Sbjct: 124 NVQPHIVIGTPGRINDFIR 142
>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 = 157 bits (398), Expect = 1e-48
Identities = 50/156 (32%), Positives = 81/156 (51%)
Query: 15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
D + + E TF ++G+ + L G+ KP+ IQ +I ++GRD+I
Sbjct: 26 HDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIG 85
Query: 75 QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
A++G+GKT F++ IL +L + L L+PTRELA QI + ALG + VQ
Sbjct: 86 LAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVI 145
Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG 170
+GG + L H++ TPGR+ D + +++G
Sbjct: 146 VGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKG 181
>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 = 146 bits (371), Expect = 5e-45
Identities = 45/137 (32%), Positives = 74/137 (54%), Gaps = 5/137 (3%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
F + L+ ++L ++ G P+ IQ ++ ++G+D+I QA++GTGKT F++ I +
Sbjct: 2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 93 SLDT---QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY 149
L + R+ + L L+PTRELA+Q+ + A+ + V A GGT + L
Sbjct: 62 RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLR 119
Query: 150 GQHVVSGTPGRVFDMIR 166
G V TPGR D +R
Sbjct: 120 GADAVVATPGRALDYLR 136
>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 = 151 bits (384), Expect = 9e-44
Identities = 47/164 (28%), Positives = 85/164 (51%), Gaps = 11/164 (6%)
Query: 23 ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPI--VKGRDVIAQAQSGT 80
+ S++V + S + L +++ + I F + +QQ++IKPI + DVIA+A++GT
Sbjct: 12 DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71
Query: 81 GKTATFSISILQSLDTQLRE----TQVLCLSPTRELAVQIQKVVLALGDFM----NVQCH 132
GKT F I I Q L + + + ++PTR+LA+QI+ V + D C
Sbjct: 72 GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACV 131
Query: 133 ACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRRTTN 175
+ +GGT+ + K++ ++V TPGR+ D++ +
Sbjct: 132 SLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRF 175
>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 = 150 bits (381), Expect = 2e-43
Identities = 48/181 (26%), Positives = 89/181 (49%), Gaps = 11/181 (6%)
Query: 6 SRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP 65
K + + + + S++V + S + L +++ + I F + +QQ++IKP
Sbjct: 46 VHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKP 105
Query: 66 I--VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE----TQVLCLSPTRELAVQIQKV 119
I + DVIA+A++GTGKT F I I Q L + + + ++PTR+LA+QI+
Sbjct: 106 ILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAE 165
Query: 120 VLALGDF----MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRRTT 174
V + D C + +GGT+ + K++ ++V TPGR+ D++ +
Sbjct: 166 VKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFR 225
Query: 175 N 175
Sbjct: 226 F 226
>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 = 143 bits (362), Expect = 3e-43
Identities = 40/154 (25%), Positives = 80/154 (51%), Gaps = 5/154 (3%)
Query: 21 EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
+ +V ++ F + L + L+G+ + + IQ+++I ++G+DV+ A++G+
Sbjct: 14 QNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGS 73
Query: 81 GKTATFSISILQSLD----TQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG 136
GKT F + +L++L T VL +SPTRELA Q +V+ +G + IG
Sbjct: 74 GKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIG 133
Query: 137 GTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG 170
G +L + +++ +++ TPGR+ + +
Sbjct: 134 GKDLKHEAERIN-NINILVCTPGRLLQHMDETVS 166
>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 = 145 bits (368), Expect = 7e-43
Identities = 45/142 (31%), Positives = 81/142 (57%), Gaps = 7/142 (4%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISIL 91
F+ + L +++L I GFEKP+ IQ + I + +++AQA++G+GKTA+F+I ++
Sbjct: 7 NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
+ ++ + + L+PTRELA+Q+ + +L N++ GG + ++ L
Sbjct: 67 ELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124
Query: 152 HVVSGTPGRVFDMIRSSQGRRT 173
++V GTPGR+ D I R T
Sbjct: 125 NIVVGTPGRILDHIN----RGT 142
>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 = 137 bits (347), Expect = 7e-41
Identities = 50/162 (30%), Positives = 85/162 (52%), Gaps = 6/162 (3%)
Query: 15 EDLSNVEFETSEDVEVVSTFDNMG--LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDV 72
E ++F ++ + E+ L+ I GF + IQ +SI+P+++GRD+
Sbjct: 35 ESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDL 94
Query: 73 IAQAQSGTGKTATFSISILQSL----DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN 128
+A A++G+GKT F I ++ + T VL LSPTRELA+Q V+ L
Sbjct: 95 LAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHV 154
Query: 129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG 170
+GG+N S + +KL G +++ TPGR+ D ++++ G
Sbjct: 155 HTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPG 196
>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA,
N project on protein structural and functional analyses;
2.40A {Dugesia japonica} SCOP: c.37.1.19
Length = 253
Score = 130 bits (330), Expect = 2e-38
Identities = 47/164 (28%), Positives = 77/164 (46%), Gaps = 16/164 (9%)
Query: 24 TSEDVEV---VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
T D + FD + L + I +++P+ IQ+ +I I++ RD++A AQ+G+
Sbjct: 12 TGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGS 71
Query: 81 GKTATFSISILQSLDTQ---------LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC 131
GKTA F I I+ L Q + L L+PTRELA+QI ++
Sbjct: 72 GKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRS 131
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
GG + +R++ G H++ TPGR+ D I + +
Sbjct: 132 CVVYGGADTHSQIREVQMGCHLLVATPGRLVDFI----EKNKIS 171
>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 = 131 bits (333), Expect = 7e-38
Identities = 34/128 (26%), Positives = 70/128 (54%), Gaps = 7/128 (5%)
Query: 39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
+ E + + I GF+ + +Q ++I +++G++V+ +A++G+GKTA ++I IL+
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54
Query: 99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP 158
+ L ++PTREL Q+ + +G +M+ + GG + ++ +V TP
Sbjct: 55 LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113
Query: 159 GRVFDMIR 166
GR+ D+
Sbjct: 114 GRLLDLWS 121
>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 = 132 bits (334), Expect = 2e-37
Identities = 52/174 (29%), Positives = 81/174 (46%), Gaps = 21/174 (12%)
Query: 18 SNVEFETSEDVEV----------VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV 67
S + F ++ V + F + LR+ ++ + G++ P+ IQ+ SI P++
Sbjct: 32 SGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSI-PVI 90
Query: 68 -KGRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQ---VLCLSPTRELAVQIQKVVL 121
GRD++A AQ+G+GKTA F + IL L E V+ +SPTRELA+QI
Sbjct: 91 SSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEAR 150
Query: 122 ALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
++ GGT+ + G HVV TPGR+ D + R
Sbjct: 151 KFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFV----DRTFIT 200
>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 = 126 bits (318), Expect = 1e-36
Identities = 40/147 (27%), Positives = 73/147 (49%), Gaps = 6/147 (4%)
Query: 31 VSTFDNM----GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF 86
++TF + + LL+ I GF+ P+ IQ ++I ++ GR+++A A +G+GKT F
Sbjct: 24 IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAF 83
Query: 87 SISILQSLDTQLRET-QVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL- 144
SI IL L + + L +SPTRELA QI + ++ + + + H ++
Sbjct: 84 SIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFG 143
Query: 145 RKLDYGQHVVSGTPGRVFDMIRSSQGR 171
K ++ TP R+ +++
Sbjct: 144 PKSSKKFDILVTTPNRLIYLLKQDPPG 170
>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 = 124 bits (314), Expect = 4e-36
Identities = 39/140 (27%), Positives = 66/140 (47%), Gaps = 5/140 (3%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
V F +++ I F +P+AIQ + + G D++ AQ+G+GKT ++ +
Sbjct: 28 VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPA 87
Query: 91 LQSLDTQ--LRETQ---VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
+ ++ Q L L L+PTRELA Q+Q+V ++ GG +R
Sbjct: 88 IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147
Query: 146 KLDYGQHVVSGTPGRVFDMI 165
L+ G + TPGR+ D +
Sbjct: 148 DLERGVEICIATPGRLIDFL 167
>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 = 121 bits (306), Expect = 5e-35
Identities = 43/152 (28%), Positives = 72/152 (47%), Gaps = 12/152 (7%)
Query: 31 VSTF-DNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSIS 89
F D DLL+ I G KP+ IQ ++ I++G D+I AQ+GTGKT ++ +
Sbjct: 18 TCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMP 77
Query: 90 ILQSLDTQLRETQ------VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSED 143
LD+Q + +L L+PTRELA+ ++ + ++ GG N +
Sbjct: 78 GFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQ 136
Query: 144 LRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
+ + G ++ TPGR+ D+ + N
Sbjct: 137 IEDISKGVDIIIATPGRLNDLQ----MNNSVN 164
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 125 bits (316), Expect = 7e-35
Identities = 48/164 (29%), Positives = 82/164 (50%), Gaps = 24/164 (14%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV-KGRDVIAQAQSGTGKTATFSIS 89
+ +F ++ + E ++ I + +P+ +Q+ +I PI+ + RD++A AQ+G+GKTA F +
Sbjct: 14 IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAI-PIIKEKRDLMACAQTGSGKTAAFLLP 72
Query: 90 ILQSLDTQ---------------LRETQ---VLCLSPTRELAVQIQKVVLALGDFMNVQC 131
IL + + R Q L L+PTRELAVQI + V+
Sbjct: 73 ILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRP 132
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
GG ++ + +R L+ G H++ TPGR+ DM+ R
Sbjct: 133 CVVYGGADIGQQIRDLERGCHLLVATPGRLVDMM----ERGKIG 172
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 111 bits (279), Expect = 1e-29
Identities = 23/129 (17%), Positives = 41/129 (31%), Gaps = 8/129 (6%)
Query: 39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
ED + + Q+ K IV+G+ A +G GKT ++ L
Sbjct: 6 EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR--- 62
Query: 99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVV 154
+ + + PT L Q + + L D V+ E + H++
Sbjct: 63 KGKKSALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHIL 121
Query: 155 SGTPGRVFD 163
+ V
Sbjct: 122 VFSTQFVSK 130
>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 = 41.1 bits (95), Expect = 1e-04
Identities = 19/121 (15%), Positives = 43/121 (35%), Gaps = 2/121 (1%)
Query: 50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLS 107
Y +K + Q +P + G++ + A +G+GKT + R+ +V+ L+
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLA 303
Query: 108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS 167
+ Q + V + G + + K+ ++ TP + +
Sbjct: 304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED 363
Query: 168 S 168
Sbjct: 364 G 364
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 40.3 bits (93), Expect = 2e-04
Identities = 20/117 (17%), Positives = 44/117 (37%), Gaps = 2/117 (1%)
Query: 54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLSPTRE 111
KP Q P +KG++ I A +G GKT + Q ++ +V+ +
Sbjct: 13 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72
Query: 112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
+ Q + V + + G T + + ++ ++ TP + + ++
Sbjct: 73 VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKG 129
>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 = 39.2 bits (90), Expect = 4e-04
Identities = 18/117 (15%), Positives = 41/117 (35%), Gaps = 2/117 (1%)
Query: 54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLSPTRE 111
K + Q +P + G++ + A +G+GKT + R+ +V+ L+
Sbjct: 7 KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66
Query: 112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
+ Q + V + G + + K+ ++ TP + +
Sbjct: 67 VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDG 123
>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 = 39.0 bits (90), Expect = 4e-04
Identities = 22/109 (20%), Positives = 42/109 (38%), Gaps = 3/109 (2%)
Query: 60 QRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV 119
Q I K + + +G GKT + L +VL L+PT+ L +Q +
Sbjct: 14 QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG--KVLMLAPTKPLVLQHAES 71
Query: 120 VLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
L + + A G + E + + +V+ TP + + + +
Sbjct: 72 FRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVA-TPQTIENDLLAG 119
>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 = 38.3 bits (89), Expect = 4e-04
Identities = 18/117 (15%), Positives = 43/117 (36%), Gaps = 3/117 (2%)
Query: 59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQ---VLCLSPTRELAVQ 115
Q +P ++G+++I +G+GKT LD + + ++ V+ L L Q
Sbjct: 38 QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQ 97
Query: 116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR 172
+ + + G T L ++ ++ T + + + + +
Sbjct: 98 LFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGE 154
>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 = 37.6 bits (86), Expect = 0.001
Identities = 19/121 (15%), Positives = 43/121 (35%), Gaps = 2/121 (1%)
Query: 50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLS 107
Y +K + Q +P + G++ + A +G+GKT + R+ +V+ L+
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLA 303
Query: 108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS 167
+ Q + V + G + + K+ ++ TP + +
Sbjct: 304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED 363
Query: 168 S 168
Sbjct: 364 G 364
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 37.2 bits (85), Expect = 0.002
Identities = 19/112 (16%), Positives = 40/112 (35%), Gaps = 2/112 (1%)
Query: 59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQ--VLCLSPTRELAVQI 116
Q P KG++ I A +G GKT + L + V+ + + Q
Sbjct: 9 QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68
Query: 117 QKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
V + + + G T+ S ++ + ++ TP + + + +
Sbjct: 69 ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNG 120
>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 = 36.7 bits (85), Expect = 0.002
Identities = 12/76 (15%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 38 GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ 97
+ + + G E+ Q +++ + G++++ + GKT +++++
Sbjct: 9 SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREA--- 65
Query: 98 LRETQVLCLSPTRELA 113
++ + L + P R LA
Sbjct: 66 IKGGKSLYVVPLRALA 81
>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 = 36.8 bits (84), Expect = 0.002
Identities = 37/226 (16%), Positives = 67/226 (29%), Gaps = 78/226 (34%)
Query: 8 ITKKVI------PEDLSNVE--FETSED--VEVVSTFDNMGLREDLLRGIYAYGF----- 52
++K+ I + +S F T E+V F LR + Y F
Sbjct: 46 LSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN-------YKFLMSPI 98
Query: 53 ----EKPSA-----IQQRS----------------IKPIVKGRDVIAQAQ---------- 77
+PS I+QR ++P +K R + + +
Sbjct: 99 KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV 158
Query: 78 SGTGKTATFSISILQSLDTQLR-------------ETQVLCLSPTRELAVQIQKVVLALG 124
G+GKT ++ + S Q + + L ++L QI +
Sbjct: 159 LGSGKT-WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS 217
Query: 125 DFM-NVQCHACIGGTNLSEDLRKLDYGQ------HVVSGTPGRVFD 163
D N++ L L+ Y +V + F+
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN 263
>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 = 35.4 bits (81), Expect = 0.008
Identities = 34/180 (18%), Positives = 54/180 (30%), Gaps = 57/180 (31%)
Query: 14 PEDLSNVEFETSEDVEVVSTF----------DNMGLREDLLRGIYAYGFEKPSAIQQRSI 63
P + + E + E+V F +G + +L FE
Sbjct: 44 PTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE-FE---------- 92
Query: 64 KPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL-- 121
++G D+ + +LQ DT L +T+ L + + +
Sbjct: 93 NCYLEGNDI-----------HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKS 141
Query: 122 --ALGDFMNVQ-----CHACIGG--TNLS--EDLRKL--DYGQHVVSGTPGRVFDMIRSS 168
AL F V A GG E+LR L Y V D+I+ S
Sbjct: 142 NSAL--FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTY--------HVLVGDLIKFS 191
Score = 33.1 bits (75), Expect = 0.049
Identities = 22/112 (19%), Positives = 40/112 (35%), Gaps = 33/112 (29%)
Query: 9 TKKVIPEDL--SNVEFETSE-DVEVVSTFDNMGLR-------EDLLRGIYAYGFEKP--- 55
+I +DL +NV F + + V TFD LR E ++ I P
Sbjct: 435 ASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCI----IRLPVKW 490
Query: 56 -SAIQQRSIKPIVKGR-------DVIAQAQSGTGKTATFSISILQ--SLDTQ 97
+ Q ++ + G + + + GTG + ++ +LD
Sbjct: 491 ETTTQFKATHILDFGPGGASGLGVLTHRNKDGTG------VRVIVAGTLDIN 536
Score = 32.7 bits (74), Expect = 0.058
Identities = 30/190 (15%), Positives = 49/190 (25%), Gaps = 72/190 (37%)
Query: 4 GGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPS------A 57
GG + K I E+ S + FET D ++ + + E Y F
Sbjct: 1677 GGEK--GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTS----YTFRSEKGLLSATQ 1730
Query: 58 IQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ 117
Q ++ + + L + +
Sbjct: 1731 FTQPAL--------------------TLMEKAAFEDL---------------KSKGLIPA 1755
Query: 118 KVVLALGDFMNVQCH--------ACIGGTNLS-EDLRKL-----DYGQHVVS-GTPGR-V 161
A G H A + +S E L ++ Q V GR
Sbjct: 1756 DATFA-G-------HSLGEYAALASLADV-MSIESLVEVVFYRGMTMQVAVPRDELGRSN 1806
Query: 162 FDMIRSSQGR 171
+ MI + GR
Sbjct: 1807 YGMIAINPGR 1816
Score = 32.3 bits (73), Expect = 0.085
Identities = 21/114 (18%), Positives = 36/114 (31%), Gaps = 26/114 (22%)
Query: 74 AQAQSGTGKTATFSISILQ-SLDTQLRETQVLCLSPTRELAV------QIQKVVLALGDF 126
+ T+ SIL+ SL+ E P+ L++ Q+Q V
Sbjct: 308 VRCYEAYPNTS-LPPSILEDSLENN--EGV-----PSPMLSISNLTQEQVQDYVNKTNSH 359
Query: 127 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPG---RVFDMIRSSQGRRTTNQA 177
+ I N VVSG P + +R ++ +Q+
Sbjct: 360 LPAGKQVEISLVN-GAK-------NLVVSGPPQSLYGLNLTLRKAKAPSGLDQS 405
>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 = 33.5 bits (77), Expect = 0.029
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELA 113
+P AIQ+ K I++ A A +G GKT +F +++ SL L+ + + PT L
Sbjct: 56 EPRAIQKMWAKRILRKESFAATAPTGVGKT-SFGLAM--SLFLALKGKRCYVIFPTSLLV 112
Query: 114 VQIQKVVLALGDFMNV 129
+Q + + + V
Sbjct: 113 IQAAETIRKYAEKAGV 128
>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 = 32.5 bits (74), Expect = 0.070
Identities = 15/80 (18%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 35 DNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV-KGRDVIAQAQSGTGKTATFSISILQS 93
D + + E + + G E Q ++K + +G++ + + +GKT I+++
Sbjct: 4 DELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHR 63
Query: 94 LDTQLRETQVLCLSPTRELA 113
+ T + + + + P + LA
Sbjct: 64 ILT--QGGKAVYIVPLKALA 81
>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 = 32.5 bits (73), Expect = 0.073
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS 107
Y F Q +I I +G V+ A + GKT +I QSL + R V+ S
Sbjct: 81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR---VIYTS 136
Query: 108 PTRELAVQ 115
P + L+ Q
Sbjct: 137 PIKALSNQ 144
>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 = 31.8 bits (72), Expect = 0.11
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR 110
Q ++K +++ + Q GTGKT T + + VL +P+
Sbjct: 361 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQG--NGPVLVCAPSN 410
>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 = 31.7 bits (72), Expect = 0.11
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
+ KG + G GKT F IL + R + L L+PTR + ++++
Sbjct: 5 LKKGMTTVLDFHPGAGKTRRFLPQIL--AECARRRLRTLVLAPTRVVLSEMKEAF 57
>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 = 31.7 bits (71), Expect = 0.11
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS 107
Y F Q +I I +G V+ A + GKT +I QSL + R V+ S
Sbjct: 179 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR---VIYTS 234
Query: 108 PTRELAVQ 115
P + L+ Q
Sbjct: 235 PIKALSNQ 242
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 30.7 bits (69), Expect = 0.25
Identities = 10/51 (19%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT 109
Q ++ +++ + Q GTGKT T + + +++ + ++L +P+
Sbjct: 365 QSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHL--SKIHKDRILVCAPS 413
>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 = 30.6 bits (69), Expect = 0.27
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE 111
Q ++K +++ + Q GTGKT T + + + VL +P+
Sbjct: 185 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLA--RQGNGPVLVCAPSNI 235
>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 = 30.2 bits (68), Expect = 0.30
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 68 KGRDVIAQAQSGTGKTATFSISILQSLDTQL-RETQVLCLSPTRELA 113
K R I G GKT + + L R + L L+PTR +A
Sbjct: 18 KKRLTIMDLHPGAGKTKRI---LPSIVREALLRRLRTLILAPTRVVA 61
>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 = 30.4 bits (68), Expect = 0.33
Identities = 13/92 (14%), Positives = 29/92 (31%), Gaps = 30/92 (32%)
Query: 43 LLRGIYAYGFEKPSAIQQRSIKPIV------------KGRDVIAQAQSGTGKTATFSISI 90
RG+ P + +++ V + A +G+GK+
Sbjct: 194 CTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKS------- 246
Query: 91 LQSLDTQL------RETQVLCLSPTRELAVQI 116
T++ + +VL L+P+ +
Sbjct: 247 -----TKVPAAYAAQGYKVLVLNPSVAATLGF 273
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae}
PDB: 4a4k_A
Length = 997
Score = 30.2 bits (67), Expect = 0.37
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 14 PEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVI 73
P+ + V+ E + V++ +N E + ++ FE Q+ ++ + +G V
Sbjct: 2 PDSMVPVKKEWAHVVDLNHKIEN--FDELIPNPARSWPFE-LDTFQKEAVYHLEQGDSVF 58
Query: 74 AQAQSGTGKT--ATFSI 88
A + GKT A ++I
Sbjct: 59 VAAHTSAGKTVVAEYAI 75
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 29.0 bits (64), Expect = 0.82
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 79 GTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
G GKT IL ++ + + L L P R+ A I++
Sbjct: 171 GCGKTKE----ILSRVNFE----EDLILVPGRQAAEMIRRRA 204
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 28.9 bits (65), Expect = 0.92
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI 116
+ K V ++ +G+GKT S LQ + + +VL L T Q+
Sbjct: 19 LQKSYGVALESPTGSGKTIMALKSALQYSSER--KLKVLYLVRTNSQEEQV 67
>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication,
viral replication, nucleotide-binding; 2.10A {Kokobera
virus} PDB: 2v6j_A
Length = 431
Score = 28.3 bits (63), Expect = 1.4
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 68 KGRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQVLCLSPTRELAVQIQK 118
K + G GKT +L L + + + + L+PTR +A ++ +
Sbjct: 1 KRELTVLDLHPGAGKT-R---RVLPQLVREAVKKRLRTVILAPTRVVASEMYE 49
>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 = 27.1 bits (60), Expect = 3.2
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQVLCLSPTRELA 113
+ K + + G+GKT IL + + + L+PTR +A
Sbjct: 18 LRKRQMTVLDLHPGSGKT-R---KILPQIIKDAIQQRLRTAVLAPTRVVA 63
>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 = 26.8 bits (59), Expect = 4.4
Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 2/65 (3%)
Query: 49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP 108
+ K R I G GKT SI++ + + L L+P
Sbjct: 166 TQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRL--RTLILAP 223
Query: 109 TRELA 113
TR +A
Sbjct: 224 TRVVA 228
>2hqb_A Transcriptional activator of COMK gene; berkeley structure genomics
center target 1957B, structural genomics, PSI; 2.70A
{Bacillus halodurans}
Length = 296
Score = 26.5 bits (59), Expect = 4.5
Identities = 5/35 (14%), Positives = 9/35 (25%)
Query: 47 IYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTG 81
Y + + + + DV A G
Sbjct: 159 RYVGEWTDADKALELFQELQKEQVDVFYPAGDGYH 193
>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein,
transcription, chromatin REG; HET: GOL; 2.00A
{Saccharomyces cerevisiae} PDB: 3ted_A
Length = 270
Score = 26.0 bits (56), Expect = 7.0
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 38 GLRED--LLRGIYAYGFEKPSAIQ 59
ED LL G++ YG+ + I+
Sbjct: 172 TKEEDEKLLIGVFKYGYGSWTQIR 195
>3s99_A Basic membrane lipoprotein; ssgcid, structural genomics, SEA
structural genomics center for infectious disease,
adenine; HET: ADE; 2.05A {Brucella melitensis biovar
abortus}
Length = 356
Score = 25.9 bits (57), Expect = 9.2
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 47 IYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTG 81
I+ + P + I +G D+I Q T
Sbjct: 186 IWVNSWFDPGKEADAAKALIDQGVDIITQHTDSTA 220
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
0.317 0.133 0.368
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: 2,636,856
Number of extensions: 150780
Number of successful extensions: 518
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 87
Length of query: 178
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 91
Effective length of database: 4,272,666
Effective search space: 388812606
Effective search space used: 388812606
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.2 bits)