RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11948
(167 letters)
>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 = 78.4 bits (194), Expect = 1e-18
Identities = 23/56 (41%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
F + + ++ L + ++ T+IQ + AL KD++GAA+TGSGKTLAF +P+L
Sbjct: 30 FPLSKKTLKGLQEAQYRLVTEIQKQTIGLAL-QGKDVLGAAKTGSGKTLAFLVPVL 84
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 78.0 bits (193), Expect = 2e-18
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F II A+ F PT+IQ ++P L + +VG ++TG+GKT A+ +PI+ I
Sbjct: 9 FPFQPFIIEAIKTLRFYKPTEIQERIIP-GALRGESMVGQSQTGTGKTHAYLLPIMEKIK 67
Query: 67 NKLENP 72
+
Sbjct: 68 PERAEV 73
>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 = 79.5 bits (196), Expect = 4e-18
Identities = 30/161 (18%), Positives = 51/161 (31%), Gaps = 76/161 (47%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ + I +A+ + F T +Q + PIL+
Sbjct: 26 GVLDKEIHKAITRMEFPGLTPVQQKTIK-------------------------PILSS-- 58
Query: 67 NKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEE 126
D++ A+TG+GKT AF IPI ++N +
Sbjct: 59 --------------EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS------------ 92
Query: 127 EAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
+ + A+I+APTR+LA+Q
Sbjct: 93 -----------------------QYMVKAVIVAPTRDLALQ 110
>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 = 78.7 bits (195), Expect = 4e-18
Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
N+ + I+ A+ KGF+ PT IQ V+P L +IV A TGSGKT +F IP++ +
Sbjct: 11 LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELV 69
>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 = 78.7 bits (194), Expect = 9e-18
Identities = 29/161 (18%), Positives = 50/161 (31%), Gaps = 76/161 (47%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ + I +A+ + F T +Q + L S +
Sbjct: 77 GVLDKEIHKAITRMEFPGLTPVQQKTIKPIL-------------SSE------------- 110
Query: 67 NKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEE 126
D++ A+TG+GKT AF IPI ++N +
Sbjct: 111 ---------------DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS------------ 143
Query: 127 EAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
+ + A+I+APTR+LA+Q
Sbjct: 144 -----------------------QYMVKAVIVAPTRDLALQ 161
>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 = 75.0 bits (185), Expect = 3e-17
Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ + + A Q G+ PTKIQ +P AL +DI+G AETGSGKT AF +PIL
Sbjct: 48 LGVTDVLCEACDQLGWTKPTKIQIEAIPLAL-QGRDIIGLAETGSGKTGAFALPIL 102
>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 = 72.9 bits (180), Expect = 9e-17
Identities = 18/66 (27%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ + ++ +++ G++ P+ IQ +P L+ +DI+ A+ G+GK+ A+ IP+L +
Sbjct: 8 YCLKRELLMGIFEMGWEKPSPIQEESIP-IALSGRDILARAKNGTGKSGAYLIPLLERLD 66
Query: 67 NKLENP 72
K +N
Sbjct: 67 LKKDNI 72
>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 = 73.9 bits (182), Expect = 1e-16
Identities = 23/55 (41%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ E ++A+ + GF T+IQ + LL +D++ AA+TGSGKTLAF IP +
Sbjct: 60 LVNENTLKAIKEMGFTNMTEIQHKSIR-PLLEGRDLLAAAKTGSGKTLAFLIPAV 113
>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 = 72.2 bits (178), Expect = 2e-16
Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
F + I+ AL+ +G TPT IQ+ +P L KD++G A TG+GKTLAF +PI +
Sbjct: 6 FPLKPEILEALHGRGLTTPTPIQAAALP-LALEGKDLIGQARTGTGKTLAFALPIAERL 63
>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 = 72.6 bits (179), Expect = 3e-16
Identities = 23/60 (38%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 6 KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
++ I +++ + GF+ PT IQ +P +L ++++ +A TGSGKTLAF IPIL +
Sbjct: 33 EYKINSRLLQNILDAGFQMPTPIQMQAIP-VMLHGRELLASAPTGSGKTLAFSIPILMQL 91
>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 = 71.8 bits (177), Expect = 4e-16
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ + N P ++ + ++ F PT IQ+ P AL D+VG A+TGSGKTL++ +P +
Sbjct: 30 NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGL-DMVGVAQTGSGKTLSYLLPAI 88
Query: 63 TGI 65
I
Sbjct: 89 VHI 91
>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 = 72.9 bits (180), Expect = 4e-16
Identities = 25/54 (46%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ E I +A+ + GFK T++QS +P +L K++V A+TGSGKT A+ IPIL
Sbjct: 1 MNEKIEQAIREMGFKNFTEVQSKTIP-LMLQGKNVVVRAKTGSGKTAAYAIPIL 53
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 72.6 bits (179), Expect = 7e-16
Identities = 35/168 (20%), Positives = 52/168 (30%), Gaps = 70/168 (41%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI- 61
+ + E I+ + + PT +Q IPI
Sbjct: 16 SFSDVEMGEIIMGNIELTRYTRPTPVQ--------------------------KHAIPII 49
Query: 62 LTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVN--KLENPTEEDE 119
+D++ A+TGSGKT AF +PIL+ I + E E
Sbjct: 50 KEK------------------RDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKE 91
Query: 120 NDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
N + +L+LAPTRELA+Q
Sbjct: 92 NGRYGRRKQYP-----------------------ISLVLAPTRELAVQ 116
>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 = 71.4 bits (176), Expect = 2e-15
Identities = 17/67 (25%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGI 65
+ +++ +Y F+ P+KIQ +P L ++++ +++G+GKT AF + +LT +
Sbjct: 10 LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69
Query: 66 VNKLENP 72
+ +P
Sbjct: 70 NPEDASP 76
>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 = 71.0 bits (175), Expect = 3e-15
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ E ++R ++ GF+ P+ IQ + ++ D++ A++G+GKT F I L I
Sbjct: 26 MELDENLLRGVFGYGFEEPSAIQQRAIM-PIIEGHDVLAQAQSGTGKTGTFSIAALQRID 84
Query: 67 NKLENP 72
++ P
Sbjct: 85 TSVKAP 90
>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 = 70.7 bits (174), Expect = 3e-15
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
N+ E+++R +Y GF+ P+ IQ + + D++ A++G+GKT F I IL I
Sbjct: 45 MNLSESLLRGIYAYGFEKPSAIQQRAIL-PCIKGYDVIAQAQSGTGKTATFAISILQQIE 103
Query: 67 NKLENP 72
L+
Sbjct: 104 LDLKAT 109
>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 = 68.7 bits (169), Expect = 5e-15
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
F +++++ + G PT IQS P L D++ A+TG+GKTL++ +P +
Sbjct: 25 FQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGI-DLIVVAQTGTGKTLSYLMPGFIHL 82
>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 = 70.3 bits (173), Expect = 5e-15
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ E ++R +Y GF+ P+ IQ + ++ +D++ +++G+GKT F I +L +
Sbjct: 42 MGLREDLLRGIYAYGFEKPSAIQQRAIK-QIIKGRDVIAQSQSGTGKTATFSISVLQCLD 100
Query: 67 NKLENP 72
++
Sbjct: 101 IQVRET 106
>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 = 68.7 bits (169), Expect = 5e-15
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
+ ++ + E ++R ++ GF+ P+ IQ + ++ D++ A++G+GKT F I
Sbjct: 13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIM-PIIEGHDVLAQAQSGTGKTGTFSIA 71
Query: 61 ILTGIVNKLENP 72
L I ++ P
Sbjct: 72 ALQRIDTSVKAP 83
>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 = 68.8 bits (169), Expect = 5e-15
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
+ + N+ E+++R +Y GF+ P+ IQ + + D++ A++G+GKT F I
Sbjct: 29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAII-PCIKGYDVIAQAQSGTGKTATFAIS 87
Query: 61 ILTGIVNKLENP 72
IL + + +
Sbjct: 88 ILQQLEIEFKET 99
>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 = 69.1 bits (170), Expect = 6e-15
Identities = 37/162 (22%), Positives = 48/162 (29%), Gaps = 75/162 (46%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI-LTGI 65
+ TI + ++ PT IQ IP L
Sbjct: 28 LKLDPTIRNNILLASYQRPTPIQ--------------------------KNAIPAILEH- 60
Query: 66 VNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLE 125
+DI+ A+TGSGKT AF IPI+ +V + N +
Sbjct: 61 -----------------RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK- 102
Query: 126 EEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
LILAPTRELAIQ
Sbjct: 103 -----------------------------CLILAPTRELAIQ 115
>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 = 69.5 bits (171), Expect = 1e-14
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGI 65
+ +++ +Y GF P+KIQ +P L ++++ +++G+GKT AF + +L+ +
Sbjct: 30 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89
Query: 66 VNKLENP 72
+ P
Sbjct: 90 EPANKYP 96
>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 = 68.8 bits (169), Expect = 1e-14
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F + ++ +++ GF+ P+ IQ +P A+ R DI+ A+ G+GKT AF IP L +
Sbjct: 26 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGR-DILARAKNGTGKTAAFVIPTLEKVK 84
Query: 67 NKLENP 72
KL
Sbjct: 85 PKLNKI 90
>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 = 67.6 bits (166), Expect = 2e-14
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ ++ L GF+ P+ +Q +P D++ A++G+GKT F L +V
Sbjct: 29 LLLSRPVLEGLRAAGFERPSPVQLKAIP-LGRCGLDLIVQAKSGTGKTCVFSTIALDSLV 87
Query: 67 NKLENP 72
+ +
Sbjct: 88 LENLST 93
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F + ++RA+ GF+ P+++Q +P A+L D++ A++G GKT F + L +
Sbjct: 19 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGM-DVLCQAKSGMGKTAVFVLATLQQLE 77
Query: 67 NKLENP 72
Sbjct: 78 PVTGQV 83
>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 = 67.7 bits (166), Expect = 4e-14
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGI 65
+ +++ +Y GF P+KIQ +P L ++++ +++G+GKT AF + +L+ +
Sbjct: 97 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156
Query: 66 VNKLENP 72
+ P
Sbjct: 157 EPANKYP 163
>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 = 5e-14
Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ ++ + II + + G+K PT IQ +P + + +D++ A+TGSGKT AF +PIL
Sbjct: 57 HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIP-VISSGRDLMACAQTGSGKTAAFLLPIL 115
Query: 63 TGIVNK 68
+ ++
Sbjct: 116 SKLLED 121
>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 = 65.7 bits (161), Expect = 2e-13
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F + ++RA+ GF+ P+++Q +P A+L D++ A++G GKT F + L +
Sbjct: 13 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGM-DVLCQAKSGMGKTAVFVLATLQQLE 71
Query: 67 NKLENP 72
Sbjct: 72 PVTGQV 77
>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 = 64.7 bits (158), Expect = 3e-13
Identities = 17/73 (23%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGI 59
+ + + + +++ +Y GF P+KIQ +P L ++++ +++G+GKT AF +
Sbjct: 91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 60 PILTGIVNKLENP 72
+L+ + + P
Sbjct: 151 AMLSQVEPANKYP 163
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 64.7 bits (158), Expect = 5e-13
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 1/56 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+N E +K K T Q + ++ K A TG GKT + L
Sbjct: 4 WNEYEDFRSFFKKKFGKDLTGYQRLWAK-RIVQGKSFTMVAPTGVGKTTFGMMTAL 58
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 61.0 bits (149), Expect = 8e-12
Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
++++G +++G+GKT AF + +L+ + + P
Sbjct: 159 RNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQ--------------------------- 191
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
A+ LAP+RELA Q
Sbjct: 192 ------------AICLAPSRELARQ 204
Score = 53.3 bits (129), Expect = 4e-09
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 27 KIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENP 72
KIQ +P L ++++G +++G+GKT AF + +L+ + + P
Sbjct: 144 KIQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKP 190
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 49.0 bits (117), Expect = 1e-07
Identities = 15/56 (26%), Positives = 27/56 (48%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+P +I + ++G K Q+ + LL ++ + TGSGKTL + I+
Sbjct: 13 LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGII 68
>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 = 44.8 bits (106), Expect = 3e-06
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ E I L ++G ++ Q+ + S +L K+ + + T SGKTL I ++
Sbjct: 6 LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMV 61
Score = 27.9 bits (62), Expect = 1.6
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSM 31
+ RALY GF++ I
Sbjct: 653 LVGRRRARALYNSGFRSIEDISQA 676
>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 = 37.9 bits (88), Expect = 0.001
Identities = 11/61 (18%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
+I + L ++G + Q+ + + + K+++ A T +GKTL + ++ +
Sbjct: 9 SISSYAVGILKEEGIEELFPPQAEAVE-KVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK 67
Query: 68 K 68
Sbjct: 68 G 68
Score = 25.5 bits (56), Expect = 9.7
Identities = 6/24 (25%), Positives = 8/24 (33%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSM 31
+I R LY G + I
Sbjct: 639 HIGRVRARKLYNAGIRNAEDIVRH 662
>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 = 36.4 bits (83), Expect = 0.003
Identities = 42/271 (15%), Positives = 75/271 (27%), Gaps = 126/271 (46%)
Query: 5 VKFNIP-----ETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKT-LA-- 56
K+N+ + +AL + + P+ + I G GSGKT +A
Sbjct: 127 AKYNVSRLQPYLKLRQALLE------------LRPAKNVL---IDGVL--GSGKTWVALD 169
Query: 57 ------------FGIPILT--------GIVNKLEN-PTEEDENDSARKDI-------VGA 88
F I L ++ L+ + D N ++R D + +
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229
Query: 89 AETG---------------------SGKTL-AFGI--PIL-----TGIVNKLENPTEE-- 117
+ + K AF + IL + + L T
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 118 --DENDSGL-EEEAEEVL--------EELEEES------------------ANTTEFVKK 148
D + L +E + +L ++L E T + K
Sbjct: 290 SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH 349
Query: 149 -TRNKLYALI------LAPT------RELAI 166
+KL +I L P L++
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Score = 28.3 bits (62), Expect = 1.5
Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 32/82 (39%)
Query: 103 ILTGIVNKLENPTE------------EDEN----------DSGLEEEAEEVLEELEEESA 140
I+ +N LE P E + ++ + V+ +L + S
Sbjct: 358 IIESSLNVLE-PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL 416
Query: 141 NTTEFVKKTRNK----LYALIL 158
V+K + + ++ L
Sbjct: 417 -----VEKQPKESTISIPSIYL 433
>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 = 31.7 bits (71), Expect = 0.091
Identities = 8/45 (17%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 17 LYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
+ ++ P Q ++ + + TG GKTL +
Sbjct: 2 VLRRDLIQPRIYQEVIYAKCK--ETNCLIVLPTGLGKTLIAMMIA 44
Score = 27.1 bits (59), Expect = 2.9
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 82 RKDIVGAAETGSGKTLAFGIPI 103
+ + TG GKTL +
Sbjct: 23 ETNCLIVLPTGLGKTLIAMMIA 44
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.5 bits (68), Expect = 0.19
Identities = 10/45 (22%), Positives = 21/45 (46%)
Query: 108 VNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNK 152
+ + + T+E E+ EE + L+EL+ S + ++ K
Sbjct: 74 IAQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKK 118
>2j9i_A Glutamate-ammonia ligase domain-containing protein 1; 17.00A {Mus
musculus}
Length = 421
Score = 29.4 bits (67), Expect = 0.53
Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 9/51 (17%)
Query: 104 LTGIVNKLENPTEEDENDSGLEEEA-----EEVLEELEEESANTTEFVKKT 149
L GI + + + E+ L LE+++ E +K
Sbjct: 341 LDGIQSAGAAAGAAAADAAAAAPSEIPGKMEDALAALEQDA----ECLKAG 387
>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 = 29.4 bits (66), Expect = 0.61
Identities = 5/23 (21%), Positives = 9/23 (39%)
Query: 32 VMPSALLARKDIVGAAETGSGKT 54
V ++ + G+GKT
Sbjct: 11 VDEDIFRKKRLTIMDLHPGAGKT 33
Score = 26.7 bits (59), Expect = 3.8
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 72 PTEEDENDSARK--DIVGAAETGSGKT 96
P E + D RK + G+GKT
Sbjct: 7 PDYEVDEDIFRKKRLTIMDLHPGAGKT 33
>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A
{Brucella suis}
Length = 361
Score = 27.7 bits (62), Expect = 1.7
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 32 VMPSALLARKDIVGAAETGSGKT 54
+ A+ + IV A ETGSGKT
Sbjct: 167 FLRRAVQLERVIVVAGETGSGKT 189
Score = 26.1 bits (58), Expect = 5.6
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 81 ARKDIVGAAETGSGKT 96
+ IV A ETGSGKT
Sbjct: 174 LERVIVVAGETGSGKT 189
>1y4s_A Chaperone protein HTPG; HSP90, molecular chaperone, ATPase; HET:
ADP; 2.90A {Escherichia coli} PDB: 1y4u_A
Length = 559
Score = 27.9 bits (63), Expect = 1.9
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 110 KLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKT 149
++ ++ DE+ L +E +E +E E+ + VK
Sbjct: 479 PFQSVSKVDESLEKLADEVDESAKEAEKALTPFIDRVKAL 518
>2ioq_A Chaperone protein HTPG; heat shock protein, HSP90; 3.50A
{Escherichia coli} PDB: 2iop_A
Length = 624
Score = 27.6 bits (62), Expect = 2.2
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 110 KLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKT 149
++ ++ DE+ L +E +E +E E+ + VK
Sbjct: 479 PFQSVSKVDESLEKLADEVDESAKEAEKALTPFIDRVKAL 518
>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral
twinning, leucine-rich repeat protein, LRR, merohedral
twinning; 2.2A {Schizosaccharomyces pombe} SCOP:
c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A
Length = 386
Score = 27.4 bits (61), Expect = 2.7
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 109 NKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVK 147
E D+ + +EE E+ EE E +S +
Sbjct: 332 RGRGELDELDDMEELTDEEEEDEEEEAESQSPEPETSEE 370
>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N*
1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M*
2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M*
3gpw_M* 3hye_M* 3l5q_R 3mg0_M* 3mg4_M* ...
Length = 233
Score = 26.9 bits (60), Expect = 2.8
Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 10/45 (22%)
Query: 91 TGSGKTLAFGIPILTGIVNKLENPTEEDENDSGL-EEEAEEVLEE 134
TG G +A + L + + + + AEE +
Sbjct: 144 TGFGAHMANPL---------LRKVVDRESDIPKTTVQVAEEAIVN 179
>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion,
hydrolas binding complex; 2.40A {Helicobacter pylori}
SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A
Length = 330
Score = 27.0 bits (60), Expect = 2.9
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 32 VMPSALLARKDIVGAAETGSGKT 54
+ + K+++ TGSGKT
Sbjct: 163 AIKDGIAIGKNVIVCGGTGSGKT 185
Score = 25.8 bits (57), Expect = 7.7
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 81 ARKDIVGAAETGSGKT 96
K+++ TGSGKT
Sbjct: 170 IGKNVIVCGGTGSGKT 185
>3cx5_F Cytochrome B-C1 complex subunit 6; complex III, electron transfer
complex, cytochrome BC1 complex,
mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ
HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces
cerevisiae} SCOP: f.28.1.1 PDB: 3cxh_F* 1ezv_H* 1kb9_F*
1p84_F* 2ibz_H* 1kyo_F*
Length = 146
Score = 26.4 bits (57), Expect = 3.2
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 112 ENPTEEDENDSGLEEEAEEVLEELEEESANTTE 144
E+ ++D+ D EEE + LE+L E NT E
Sbjct: 57 EDDDDDDDEDEEEEEEVTDQLEDLREHFKNTEE 89
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 26.5 bits (57), Expect = 5.7
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 11/54 (20%)
Query: 2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTL 55
+E N+ YQ + +P+ + K+ + A TG GKT
Sbjct: 1 SEVSDTNLYSPFKPRNYQ---------LELALPA--MKGKNTIICAPTGCGKTF 43
>1nvp_C Transcription initiation factor IIA beta chain; transcription
regulation, DNA, complex, transcription/DNA complex;
2.10A {Homo sapiens} SCOP: b.56.1.1
Length = 76
Score = 24.9 bits (54), Expect = 6.3
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 112 ENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNK 152
+ EE+ +S + EE E + E+ ++ K R+K
Sbjct: 6 DGQVEEEPLNSEDDVSDEEGQELFDTENVVVCQYDKIHRSK 46
>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 = 25.9 bits (57), Expect = 7.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 34 PSALLARKDIVGAAETGSGKT 54
P+ L R+ V GSGKT
Sbjct: 15 PNMLRKRQMTVLDLHPGSGKT 35
>3g9q_A Ferrichrome-binding protein; alpha-beta protein, structural
genomics, PSI-2, protein STRU initiative; 2.60A
{Bacillus subtilis subsp} PDB: 3hxp_A
Length = 279
Score = 25.8 bits (57), Expect = 8.0
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 123 GLEEEAEEVLEELEEESANTTEFVKKTRNKLYALIL 158
G E++AE+ L + +++ A +KK I+
Sbjct: 116 GTEDKAEKWLAKWDKKVAAAKTKIKKAVGDKTISIM 151
>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 = 25.9 bits (56), Expect = 8.9
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 36 ALLARKDIVGAAETGSGKTL 55
+ + ++ +A T +GKT+
Sbjct: 97 CIDRGESVLVSAHTSAGKTV 116
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 25.7 bits (57), Expect = 9.5
Identities = 10/42 (23%), Positives = 16/42 (38%)
Query: 101 IPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
IP TG + +EE +E +E E+E+
Sbjct: 1213 IPAGTGSDFVRFTQVVDQRTLKAIEEARKEAVEAKEKEAPRR 1254
>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein,
targeting factor, ATP-bindi TRC40, ARSA,
nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus
jannaschii} PDB: 3ug6_A*
Length = 349
Score = 25.7 bits (56), Expect = 10.0
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 98 AFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEE 138
+GIPI IVN+L + + E + LE ++E+
Sbjct: 263 KYGIPIDAVIVNQLIPEDVQCDFCRARRELQLKRLEMIKEK 303
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
0.309 0.130 0.347
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,563,365
Number of extensions: 156707
Number of successful extensions: 933
Number of sequences better than 10.0: 1
Number of HSP's gapped: 896
Number of HSP's successfully gapped: 176
Length of query: 167
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 80
Effective length of database: 4,272,666
Effective search space: 341813280
Effective search space used: 341813280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (24.7 bits)