RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1539
(175 letters)
>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 = 167 bits (426), Expect = 3e-53
Identities = 81/105 (77%), Positives = 87/105 (82%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE V VLVMCHTRE
Sbjct: 34 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 93
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 94 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 138
>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 = 166 bits (422), Expect = 1e-50
Identities = 81/105 (77%), Positives = 87/105 (82%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE V VLVMCHTRE
Sbjct: 28 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 87
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 132
>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 = 140 bits (354), Expect = 3e-42
Identities = 35/105 (33%), Positives = 51/105 (48%), Gaps = 2/105 (1%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + Q + IP G+D++ QAKSG GKT VF L L + + +L++ TRE
Sbjct: 44 FERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTRE 103
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
+A QI M ++ VF GG P+ +D+ LK I
Sbjct: 104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KCHIA 146
>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 = 138 bits (349), Expect = 7e-40
Identities = 38/105 (36%), Positives = 56/105 (53%), Gaps = 2/105 (1%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + + Q E IP A+ G DIL +AK+G GKTA FV+ TL++++ + + L+M TRE
Sbjct: 41 FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE 100
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA Q S+ K+ I V GG ++ D L I+
Sbjct: 101 LALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLN-ETVHIL 143
>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 = 112 bits (282), Expect = 2e-31
Identities = 37/105 (35%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + ++ Q I + G D++ QA+SG GKTA F ++ LQQLE LV+ TRE
Sbjct: 50 FEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRE 109
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA QI K YM GG ++ + + L+ P IV
Sbjct: 110 LAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIV 153
>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 = 113 bits (286), Expect = 1e-30
Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + ++ Q I + G D++ QA+SG GKTA F ++ LQQ+E LV+ TRE
Sbjct: 60 FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRE 119
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA QI K YM GG ++ + + L+ P I+
Sbjct: 120 LAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHII 163
>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 = 108 bits (272), Expect = 3e-30
Identities = 35/105 (33%), Positives = 58/105 (55%), Gaps = 1/105 (0%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
+ + + Q E IP A+ G DIL +AK+G GK+ +++ L++L+ N+ +V+ TRE
Sbjct: 23 WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE 82
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA Q+S+ + SK+M KV GG ++ D L +V
Sbjct: 83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-DTVHVV 126
>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 = 106 bits (268), Expect = 2e-29
Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F E ++ Q I + G D+L QA+SG GKT F +A LQ+++T+ L++ TRE
Sbjct: 34 FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 93
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA QI K + +M +IKV GG +D E L+ + QIV
Sbjct: 94 LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 135
>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 = 109 bits (276), Expect = 3e-29
Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F E ++ Q I + G D+L QA+SG GKT F +A LQ+++T+ L++ TRE
Sbjct: 41 FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 100
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA QI K + +M +IKV GG +D E L+ + QIV
Sbjct: 101 LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 142
>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 = 108 bits (271), Expect = 2e-28
Identities = 34/105 (32%), Positives = 53/105 (50%), Gaps = 2/105 (1%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + ++ Q I Q + G D++ Q++SG GKTA F ++ LQ L+ L++ TRE
Sbjct: 57 FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE 116
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA QI K YM N++ GG + +D L + +V
Sbjct: 117 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLD-YGQHVV 159
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 100 bits (252), Expect = 4e-27
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 4/108 (3%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + T Q IP A+ G ++ Q+++G GKT ++L +++++ + V ++ TRE
Sbjct: 24 FYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE 83
Query: 94 LAFQISKEYERFSKYMSN---IKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA QI E + +K+ I GG QK E L P IV
Sbjct: 84 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN-VQPHIV 130
>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 = 99.0 bits (247), Expect = 1e-25
Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 6/107 (5%)
Query: 34 FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
F + Q +P + +++ Q++SG GKTA FVLA L Q+E + L + T
Sbjct: 112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 171
Query: 92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
ELA Q K E+ K+ +K+ G +++ ++ + QIV
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK----ISEQIV 214
>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 = 97.2 bits (243), Expect = 2e-24
Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 6/107 (5%)
Query: 34 FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
F + Q +P + +++ Q++SG GKTA FVLA L Q+E + L + T
Sbjct: 45 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 104
Query: 92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
ELA Q K E+ K+ +K+ G +++ ++ + QIV
Sbjct: 105 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK----ISEQIV 147
>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 = 97.4 bits (243), Expect = 2e-24
Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 6/107 (5%)
Query: 34 FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
F + Q +P + +++ Q++SG GKTA FVLA L Q+E + L + T
Sbjct: 112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 171
Query: 92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
ELA Q K E+ K+ +K+ G +++ ++ + QIV
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK----ISEQIV 214
>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 = 93.9 bits (234), Expect = 3e-24
Identities = 37/109 (33%), Positives = 55/109 (50%), Gaps = 2/109 (1%)
Query: 30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC 89
+ + + T Q E IP A+ G DI+ A++G GKT F L L L T ++ LV+
Sbjct: 59 DQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLT 118
Query: 90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
TRELAFQIS+++E + ++ V GG+ L P I+
Sbjct: 119 PTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKK-PHII 165
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 92.6 bits (231), Expect = 1e-22
Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 8/100 (8%)
Query: 41 QHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI 98
Q + +P + +++ Q++SG GKTA F L L +++ + + + +RELA QI
Sbjct: 146 QEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQI 205
Query: 99 SKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
KY +V FG K + QIV
Sbjct: 206 MDVVTEMGKYT---EVKTAFGIKDSVPKG--AK-IDAQIV 239
>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 = 88.1 bits (219), Expect = 4e-22
Identities = 33/109 (30%), Positives = 54/109 (49%), Gaps = 7/109 (6%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE----TTDSNVYVLVMC 89
+R T Q + I A+ G D+L AK+G GKT F++ L+ L T+ + VL++
Sbjct: 45 YRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIIS 104
Query: 90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
TRELA+Q + + K G+ GG ++ + E + N I+
Sbjct: 105 PTRELAYQTFEVLRKVGKNHD-FSAGLIIGGKDLKHEAERIN--NINIL 150
>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 = 86.1 bits (214), Expect = 1e-21
Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 7/108 (6%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---VYVLVMCH 90
T Q +P A+ G D++ QA++G GKT F L ++L + LV+
Sbjct: 21 LTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTP 80
Query: 91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
TRELA Q++ E + ++ KV +GG K +E L V
Sbjct: 81 TRELALQVASELTAVAPHL---KVVAVYGGTGYGKQKEALL-RGADAV 124
>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 = 88.7 bits (220), Expect = 3e-21
Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 9/114 (7%)
Query: 34 FREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLV 87
F T Q + I + D++ +AK+G GKT F++ Q L T V ++
Sbjct: 41 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVI 100
Query: 88 MCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
+ TR+LA QI E ++ + GG + + P IV
Sbjct: 101 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 154
>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 = 88.7 bits (220), Expect = 3e-21
Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 9/114 (7%)
Query: 34 FREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLV 87
F T Q + I + D++ +AK+G GKT F++ Q L T V ++
Sbjct: 92 FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVI 151
Query: 88 MCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
+ TR+LA QI E ++ + GG + + P IV
Sbjct: 152 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 205
>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 = 87.6 bits (218), Expect = 4e-21
Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 8/107 (7%)
Query: 34 FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
F++ + Q +P + +++ Q++SG GKTA F L L ++ D++ + + +
Sbjct: 25 FQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS 84
Query: 92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
RELA Q + + K+ + K N Q++
Sbjct: 85 RELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQ------INAQVI 125
>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 = 84.9 bits (211), Expect = 2e-20
Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 9/105 (8%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F+ T Q + IP + G +++ +AK+G GKTA + + L+ + LV+ TRE
Sbjct: 14 FKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRE 67
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
L Q++ +YM + KV +GG+P + ++ N IV
Sbjct: 68 LTRQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVR--NADIV 109
>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 = 83.3 bits (207), Expect = 1e-19
Identities = 32/106 (30%), Positives = 55/106 (51%), Gaps = 5/106 (4%)
Query: 34 FREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR 92
F + T Q + IP + +I+ QA++G GKTA F + ++ + ++ + +++ TR
Sbjct: 26 FEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-NNGIEAIILTPTR 84
Query: 93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
ELA Q++ E E N+K+ +GG I + LK N IV
Sbjct: 85 ELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK--NANIV 127
>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 = 80.8 bits (200), Expect = 3e-19
Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 6/113 (5%)
Query: 30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN----VYV 85
+ F T QH+ I + G D+L AK+G GKT F++ ++ + V
Sbjct: 70 KEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGV 129
Query: 86 LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
L++ TRELA Q + + G+ GG + + L + I+
Sbjct: 130 LILSPTRELAMQTFGVLKELMTHHV-HTYGLIMGGSNRSAEAQKLG-NGINII 180
>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 = 79.9 bits (198), Expect = 6e-19
Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 2/94 (2%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN-VYVLVMCHTR 92
F+ T Q + IP + G ++L A +G GKT F + L QL+ + L++ TR
Sbjct: 49 FQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTR 108
Query: 93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
ELA QI +E + S+ + ++ + K
Sbjct: 109 ELASQIHRELIKISEG-TGFRIHMIHKAAVAAKK 141
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 80.5 bits (199), Expect = 2e-18
Identities = 17/98 (17%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
++ T +Q + V G A +G+GKT ++ L ++ T
Sbjct: 19 GKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVT 75
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
L Q + ++ + +K+ F+ + ++ E++ K
Sbjct: 76 LVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEK 111
>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 = 71.0 bits (175), Expect = 1e-15
Identities = 31/138 (22%), Positives = 56/138 (40%), Gaps = 18/138 (13%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE------TTDSNVYVLV 87
+ T Q + P + G+D++ A++G GKT +++ L+ + +LV
Sbjct: 40 ILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLV 99
Query: 88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV----G---- 139
+ TRELA + E ++S +K +GG E + I+ G
Sbjct: 100 LTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDIS-KGVDIIIATPGRLND 156
Query: 140 -LVNYETNLSGVVVNVMD 156
+N NL + V+D
Sbjct: 157 LQMNNSVNLRSITYLVID 174
>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 = 68.7 bits (169), Expect = 9e-15
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 10/99 (10%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV---------Y 84
++ T Q IP + DI+ A++G GKTA F++ + L D N
Sbjct: 43 YQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK 102
Query: 85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
L++ TRELA QI E ++FS + ++ V +GG
Sbjct: 103 CLILAPTRELAIQILSESQKFSLN-TPLRSCVVYGGADT 140
>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 = 67.2 bits (165), Expect = 3e-14
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 6/99 (6%)
Query: 30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----Y 84
Q F E T+ Q + P A+ G+D++ A++G GKT ++L + +
Sbjct: 45 ARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI 104
Query: 85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
LV+ TRELA Q+ + + +K +GG P
Sbjct: 105 CLVLAPTRELAQQVQQVAAEYC-RACRLKSTCIYGGAPK 142
>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 = 67.6 bits (166), Expect = 6e-14
Identities = 31/95 (32%), Positives = 50/95 (52%), Gaps = 6/95 (6%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----YVLVM 88
++ T Q IP G D++ A++G GKTA F+L L +L + V+++
Sbjct: 76 YKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIV 135
Query: 89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
TRELA QI E +F+ + S +K+G+ +GG
Sbjct: 136 SPTRELAIQIFNEARKFA-FESYLKIGIVYGGTSF 169
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 61.4 bits (150), Expect = 7e-12
Identities = 33/108 (30%), Positives = 46/108 (42%), Gaps = 19/108 (17%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVL---------ATLQQLETTDSNV- 83
+ T Q IP D++ A++G GKTA F+L + L N
Sbjct: 35 YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94
Query: 84 --------YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
LV+ TRELA QI +E +FS Y S ++ V +GG I
Sbjct: 95 YGRRKQYPISLVLAPTRELAVQIYEEARKFS-YRSRVRPCVVYGGADI 141
>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 = 47.2 bits (111), Expect = 8e-07
Identities = 37/191 (19%), Positives = 67/191 (35%), Gaps = 57/191 (29%)
Query: 10 GVTVKVLSSRNRREKEDRIGESQPF------REQTSFQ-HECIPQ-------AVLGMDIL 55
+T + R+R ++Q F R Q + + + + + G+
Sbjct: 107 MMTRMYIEQRDRLY-----NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV--- 158
Query: 56 CQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVM--CHTRE--------LAFQISKEY 102
G GKT L + D ++ L + C++ E L +QI +
Sbjct: 159 ----LGSGKT-WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW 213
Query: 103 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGW 162
S + SNIK L I + L+ ++ YE L +V+ +V++
Sbjct: 214 TSRSDHSSNIK-------LRIHSIQAELRR----LLKSKPYENCL--LVLL--NVQNAKA 258
Query: 163 W--LDLEALIL 171
W +L IL
Sbjct: 259 WNAFNLSCKIL 269
>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 = 42.5 bits (100), Expect = 3e-05
Identities = 17/91 (18%), Positives = 43/91 (47%), Gaps = 5/91 (5%)
Query: 30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC 89
+ + E Q E + + G ++L + GKT + +A +++ ++YV+ +
Sbjct: 19 KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPL- 77
Query: 90 HTRELAFQISKEYERFSKYMSNIKVGVFFGG 120
R LA + + ++++ K +++G+ G
Sbjct: 78 --RALAGEKYESFKKWEKI--GLRIGISTGD 104
>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 = 39.4 bits (92), Expect = 2e-04
Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 12/110 (10%)
Query: 39 SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY---VLVMCHTRELA 95
+Q E A+ G +I+ +G GKT V V L+ V+V+ + L
Sbjct: 36 PYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLV 95
Query: 96 FQ-ISKEYERFSKYMSNIKVGVFFGGLPIQKD-EEYLKTHN-----PQIV 138
Q KE++ F K +V G ++ E +K+ + QI+
Sbjct: 96 EQLFRKEFQPFLKKW--YRVIGLSGDTQLKISFPEVVKSCDIIISTAQIL 143
>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 = 39.8 bits (92), Expect = 2e-04
Identities = 18/108 (16%), Positives = 38/108 (35%), Gaps = 9/108 (8%)
Query: 36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA 95
+ +Q I + L +G+GKT + ++ +L VL++ T+ L
Sbjct: 9 QPRIYQEV-IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGK--VLMLAPTKPLV 65
Query: 96 FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-----NPQIV 138
Q ++ + R K+ G ++ + PQ +
Sbjct: 66 LQHAESFRRLFNL-PPEKIVALTGEKSPEERSKAWARAKVIVATPQTI 112
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 39.1 bits (90), Expect = 3e-04
Identities = 19/108 (17%), Positives = 41/108 (37%), Gaps = 9/108 (8%)
Query: 39 SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY--VLVMCHTRELAF 96
++Q E A G + + A +G GKT V +L L+ V+ + +
Sbjct: 7 NYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYE 66
Query: 97 QISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYLKTHN-----PQIV 138
Q + + R+ + + + G + ++ ++ PQI+
Sbjct: 67 QQATVFSRYFERLG-YNIASISGATSDSVSVQHIIEDNDIIILTPQIL 113
>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 = 38.1 bits (88), Expect = 9e-04
Identities = 35/163 (21%), Positives = 55/163 (33%), Gaps = 47/163 (28%)
Query: 37 QTSF-QHECIPQAVLGMDILC----QAKSGMGKTAVFV---------LATLQQLETTDSN 82
T F Q P A+ M+ ++K + A F LA+L + + +S
Sbjct: 1728 ATQFTQ----P-ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESL 1782
Query: 83 VYVLVMCHTRELAFQISKEYERFSKYMSNI--------KVGVFFGGLPIQKDEEYLKTHN 134
V V+ R + Q R SN +V F +Q E +
Sbjct: 1783 VEVV---FYRGMTMQ--VAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRT 1837
Query: 135 PQIVGLVNYETNLSG--VVVNVMDVRSGGWWLDLEAL-ILSKC 174
+V +VNY N+ V +G DL AL ++
Sbjct: 1838 GWLVEIVNY--NVENQQYVA------AG----DLRALDTVTNV 1868
Score = 37.3 bits (86), Expect = 0.002
Identities = 32/173 (18%), Positives = 56/173 (32%), Gaps = 48/173 (27%)
Query: 31 SQPFREQTSFQHECIPQAVLGM------DILCQAKSGMGK---TAVFVLA--TLQQLETT 79
S P H + +LG L + +G + TAV + + + +
Sbjct: 237 SCPLIGVIQLAHYVVTAKLLGFTPGELRSYL-KGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 80 DSNVYVL-----VMCH----TRELAFQISKEYERFSK----YMSNIKVGVFFGGLPIQKD 126
+ V C+ L I ++ ++ M +I L ++
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS------NLTQEQV 349
Query: 127 EEYLKTHN---P---QI-VGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILS 172
++Y+ N P Q+ + LVN NL VV G L L L+
Sbjct: 350 QDYVNKTNSHLPAGKQVEISLVNGAKNL--VV--------SGPPQSLYGLNLT 392
Score = 26.6 bits (58), Expect = 6.5
Identities = 18/101 (17%), Positives = 32/101 (31%), Gaps = 30/101 (29%)
Query: 57 QAKSGMGKT--AVFVLATLQQL-ETTDSNVYVLVMCHTRE-LAFQISKEYERFSKYMSNI 112
Q + GMG A Q + D+ H ++ F I ++
Sbjct: 1627 QEQ-GMGMDLYKTSKAA--QDVWNRADN--------HFKDTYGFSILDIVINNPVNLT-- 1673
Query: 113 KVGVFFGGLPIQK-DEEYLKTHNPQIVGLVNYETNLSGVVV 152
+ FGG ++ E Y + +ET + G +
Sbjct: 1674 ---IHFGGEKGKRIRENYSA---------MIFETIVDGKLK 1702
>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 = 36.9 bits (84), Expect = 0.002
Identities = 20/107 (18%), Positives = 38/107 (35%), Gaps = 7/107 (6%)
Query: 39 SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAF 96
S+Q E A+ G + L A +G GKT V +L + V+ + +
Sbjct: 251 SYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYE 310
Query: 97 QISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN-----PQIV 138
Q ++ + G+ E+ ++ + PQI+
Sbjct: 311 QQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQIL 357
>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 = 36.5 bits (83), Expect = 0.003
Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 6/83 (7%)
Query: 39 SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAF 96
S+Q E A+ G + L A +G GKT V +L + V+ + +
Sbjct: 251 SYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYE 310
Query: 97 QISKEYERFSKYMSNIKVGVFFG 119
Q F + + G
Sbjct: 311 QQ---KNVFKHHF-ERQGYSVQG 329
>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 = 35.2 bits (81), Expect = 0.007
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 14/68 (20%)
Query: 61 GMGKT--AVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 118
G GKT A+ + L L++ T LA Q + F VG F
Sbjct: 118 GSGKTHVAMAAINELSTP--------TLIVVPTLALAEQWKERLGIF----GEEYVGEFS 165
Query: 119 GGLPIQKD 126
G + K
Sbjct: 166 GRIKELKP 173
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 34.6 bits (78), Expect = 0.013
Identities = 20/108 (18%), Positives = 42/108 (38%), Gaps = 9/108 (8%)
Query: 39 SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT--DSNVYVLVMCHTRELAF 96
++Q E A+ G + + A +G GKT V +L L+ V+ + +
Sbjct: 16 NYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYE 75
Query: 97 QISKEYERFSKYMSNIKVGVFFGGLPIQKD-EEYLKTHN-----PQIV 138
Q + ++ + +V G E+ ++ ++ PQI+
Sbjct: 76 QNKSVFSKYFE-RHGYRVTGISGATAENVPVEQIVENNDIIILTPQIL 122
>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 = 34.1 bits (77), Expect = 0.018
Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 6/83 (7%)
Query: 39 SFQHECIPQAVLGMDILCQAKSGMGKT--AVFVLATLQQLETTDSNVYVLVMCHTRELAF 96
S+Q E A+ G + L A +G GKT ++ + Q V+ + +
Sbjct: 10 SYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYE 69
Query: 97 QISKEYERFSKYMSNIKVGVFFG 119
Q + F + + G
Sbjct: 70 Q---QKNVFKHHF-ERQGYSVQG 88
>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 = 30.4 bits (69), Expect = 0.20
Identities = 17/62 (27%), Positives = 22/62 (35%), Gaps = 14/62 (22%)
Query: 61 GMGKT--AVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 118
G GKT A+ + L L++ T LA Q ER + VG F
Sbjct: 118 GSGKTHVAMAAINELST--------PTLIVVPTLALAEQW---KERLGIF-GEEYVGEFS 165
Query: 119 GG 120
G
Sbjct: 166 GR 167
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 30.1 bits (68), Expect = 0.38
Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 3/83 (3%)
Query: 32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
+ + Q + ++ +G GKT + + + LQ V LV T
Sbjct: 3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLV--RT 60
Query: 92 RELAFQISKEYERFSKYMSNIKV 114
Q+ KE S M I+
Sbjct: 61 NSQEEQVIKELRSLSSTM-KIRA 82
>2egc_A SH3 and PX domain-containing protein 2A; SH3 domain, KIAA0418
protein, SH3MD1, SH3 multiple domains 1, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 26.3 bits (58), Expect = 2.1
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 138 VGLVNYETN---LS---GVVVNVMDVRSGGWWL 164
V + +YE + GV + V++ GWW
Sbjct: 14 VSIADYEGDEETAGFQEGVSMEVLERNPNGWWY 46
>3e5n_A D-alanine-D-alanine ligase A; bacterial blight; 2.00A {Xanthomonas
oryzae PV} PDB: 3r5f_A* 3rfc_A*
Length = 386
Score = 27.2 bits (61), Expect = 3.5
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 99 SKEYERFSKYMSNIKVGVFFGG 120
S E F +M I+VG+ FGG
Sbjct: 10 SSENLYFQGHMRKIRVGLIFGG 31
>3i12_A D-alanine-D-alanine ligase A; D-alanyl-alanine synthetase A, ADP
binding protein, csgid, A binding, cell shape; HET: ADP;
2.20A {Salmonella typhimurium} PDB: 3q1k_A*
Length = 364
Score = 26.8 bits (60), Expect = 4.2
Identities = 6/12 (50%), Positives = 10/12 (83%)
Query: 109 MSNIKVGVFFGG 120
M+ ++VG+ FGG
Sbjct: 1 MAKLRVGIVFGG 12
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 25.7 bits (56), Expect = 4.7
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 116 VFFGGLPIQKDEEYLKTH 133
VF GGLP DE+ +
Sbjct: 11 VFVGGLPPDIDEDEITAS 28
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 25.9 bits (57), Expect = 4.8
Identities = 4/28 (14%), Positives = 8/28 (28%)
Query: 116 VFFGGLPIQKDEEYLKTHNPQIVGLVNY 143
+ LP + LK + +
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTF 58
>1ehi_A LMDDL2, D-alanine:D-lactate ligase; ATP-binding. grAsp motif for
ATP.; HET: ADP PHY; 2.38A {Leuconostoc mesenteroides}
SCOP: c.30.1.2 d.142.1.1
Length = 377
Score = 26.5 bits (59), Expect = 5.3
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 109 MSNIKVGVFFGG 120
M+ +V + FGG
Sbjct: 1 MTKKRVALIFGG 12
>2i87_A D-alanine-D-alanine ligase; APO; 2.00A {Staphylococcus aureus
subsp} PDB: 2i8c_A* 3n8d_A* 2i80_A*
Length = 364
Score = 26.4 bits (59), Expect = 5.9
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 109 MSNIKVGVFFGG 120
M+ + + FGG
Sbjct: 1 MTKENICIVFGG 12
>3k3p_A D-alanine--D-alanine ligase; D-alanyl-alanine synthetase,
ATP-binding, cell shape, cell W biogenesis/degradation,
magnesium, manganese; 2.23A {Streptococcus mutans}
Length = 383
Score = 26.1 bits (58), Expect = 6.6
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 109 MSNIKVGVFFGG 120
MS + + +GG
Sbjct: 35 MSKETLVLLYGG 46
>1e4e_A Vancomycin/teicoplanin A-type resistance protein; ligase, cell
WALL, antibiotic resistance, membrane, peptidog
synthesis; HET: ADP PHY; 2.5A {Enterococcus faecium}
SCOP: c.30.1.2 d.142.1.1 PDB: 1e4e_B*
Length = 343
Score = 26.0 bits (58), Expect = 7.4
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 109 MSNIKVGVFFGG 120
M+ IKV + FGG
Sbjct: 1 MNRIKVAILFGG 12
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 24.7 bits (54), Expect = 8.9
Identities = 7/46 (15%), Positives = 14/46 (30%)
Query: 116 VFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGG 161
++ G +P EE + + L V+ V +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN 54
>2fb9_A D-alanine:D-alanine ligase; 1.90A {Thermus caldophilus} PDB:
2zdh_A* 2yzg_A 2yzn_A* 2yzm_A* 2zdg_A* 2zdq_A*
Length = 322
Score = 25.6 bits (57), Expect = 9.4
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 109 MSNIKVGVFFGG 120
M ++V + GG
Sbjct: 1 MEFMRVLLIAGG 12
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.135 0.399
Gapped
Lambda K H
0.267 0.0443 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,604,160
Number of extensions: 143890
Number of successful extensions: 380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 355
Number of HSP's successfully gapped: 59
Length of query: 175
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 88
Effective length of database: 4,272,666
Effective search space: 375994608
Effective search space used: 375994608
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 (21.9 bits)
S2: 54 (25.3 bits)