RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5350
(377 letters)
>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure,
transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1
Length = 179
Score = 113 bits (285), Expect = 2e-30
Identities = 30/170 (17%), Positives = 60/170 (35%), Gaps = 10/170 (5%)
Query: 69 MRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSG 128
M + + + ++G KY+ + G ++ F +++ + G G
Sbjct: 6 MAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGRE---FPEGEG 62
Query: 129 KSKKEAKHNAAKSVLDQL----IGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPP 184
+SKKEAK+ AAK ++ L L + N +G + ++
Sbjct: 63 RSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTVN 122
Query: 185 VYETEETTGLPHERMFTVCAYVNVYK-EEGMGKSKKIAKREAALNMLKFL 233
+ G+ F + + G G +K+ AK+ AA +
Sbjct: 123 YEQCAS--GVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQI 170
Score = 64.5 bits (157), Expect = 1e-12
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 2/80 (2%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREA 225
+ +L + Y+ +G PH+R FT ++ EG G+SKK AK A
Sbjct: 14 FFMEELNTYRQKQGVVLK-YQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAA 72
Query: 226 ALNMLKFLETVPIEIPEKKQ 245
A ++ L +
Sbjct: 73 AKLAVEILNKEKKAVSPLLL 92
Score = 54.5 bits (131), Expect = 5e-09
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
+ L+ + ++ YE G F Y+ + + +IG+G +K+EAK
Sbjct: 106 YIGLINRIAQKKRLTVNYEQCA-SGVHGPEGFHYKCKMGQKE---YSIGTGSTKQEAKQL 161
Query: 138 AAKSVLDQLIG 148
AAK Q++
Sbjct: 162 AAKLAYLQILS 172
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein;
2.60A {Homo sapiens}
Length = 232
Score = 107 bits (269), Expect = 1e-27
Identities = 32/186 (17%), Positives = 63/186 (33%), Gaps = 29/186 (15%)
Query: 71 LNTGDRTPVSLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGK 129
+N ++ V ++ E + R P Y + E F +++ + G+
Sbjct: 17 INPNGKSEVCILHEYMQRVLKVRPVYNFFECENP--SEPFGASVTIDGVT---YGSGTAS 71
Query: 130 SKKEAKHNAAKSVLDQLIGRDDEKLMCQKEN----------------------LFKVEPN 167
SKK AK+ AA++ L+ LI ++ +K +
Sbjct: 72 SKKLAKNKAARATLEILIPDFVKQTSEEKPKDSEELEYFNHISIEDSRVYELTSKAGLLS 131
Query: 168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAAL 227
P L E C+ R + + + G K+K++ K+ A+
Sbjct: 132 PYQILHE-CLKRNHGMGDTSIKFEVVPGKNQKSEYVMACGKHTVRGWCKNKRVGKQLASQ 190
Query: 228 NMLKFL 233
+L+ L
Sbjct: 191 KILQLL 196
Score = 57.1 bits (137), Expect = 1e-09
Identities = 22/100 (22%), Positives = 36/100 (36%), Gaps = 1/100 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
+ V L E PVY E +V Y G SKK+AK +AA
Sbjct: 23 SEVCILHEYMQRVLKVRPVYNFFECENPSEPFGASVTIDGVTY-GSGTASSKKLAKNKAA 81
Query: 227 LNMLKFLETVPIEIPEKKQGEDVDEKGESNGLKHTHDSTF 266
L+ L ++ +++ +D +E N + +
Sbjct: 82 RATLEILIPDFVKQTSEEKPKDSEELEYFNHISIEDSRVY 121
Score = 50.9 bits (121), Expect = 1e-07
Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 4/76 (5%)
Query: 73 TGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKK 132
G +P ++ E L R + +Y ++ + G K+K+
Sbjct: 127 AGLLSPYQILHECLKRNHGMGDTSIKFEVVPGKNQKSEYVMAC----GKHTVRGWCKNKR 182
Query: 133 EAKHNAAKSVLDQLIG 148
K A++ +L L
Sbjct: 183 VGKQLASQKILQLLHP 198
>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.50.1.1
Length = 89
Score = 95.1 bits (237), Expect = 1e-24
Identities = 23/82 (28%), Positives = 31/82 (37%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
P+ +L + RK P Y G+P R F + V G G +KKIAK+ AA
Sbjct: 7 GPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAA 66
Query: 227 LNMLKFLETVPIEIPEKKQGED 248
ML L +
Sbjct: 67 EAMLLQLGYKASTSLQDSGPSS 88
Score = 66.6 bits (163), Expect = 4e-14
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 78 PVSLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKH 136
P+S + ++ +R+ P Y L+ G F ++ + + VA G+G +KK AK
Sbjct: 8 PISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGN----EVATGTGPNKKIAKK 63
Query: 137 NAAKSVLDQL 146
NAA+++L QL
Sbjct: 64 NAAEAMLLQL 73
>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene
regulation-RNA complex; 2.20A {Homo sapiens}
Length = 88
Score = 93.9 bits (234), Expect = 3e-24
Identities = 30/81 (37%), Positives = 42/81 (51%)
Query: 159 ENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSK 218
L + VG LQE + + W P Y + +G H + FT+ V + E G G SK
Sbjct: 8 SGLVPRGSHEVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSK 67
Query: 219 KIAKREAALNMLKFLETVPIE 239
K+AKR AA ML + TVP++
Sbjct: 68 KLAKRNAAAKMLLRVHTVPLD 88
Score = 63.9 bits (156), Expect = 3e-13
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 78 PVSLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKH 136
V +QEL+ + P+Y + Q G + F + ++ IGSG SKK AK
Sbjct: 17 EVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVER----FIEIGSGTSKKLAKR 72
Query: 137 NAAKSVLDQL 146
NAA +L ++
Sbjct: 73 NAAAKMLLRV 82
>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex,
protein-RNA interactions, RNA-bining protein; 1.90A
{Xenopus laevis} SCOP: d.50.1.1
Length = 69
Score = 90.3 bits (225), Expect = 5e-23
Identities = 28/68 (41%), Positives = 39/68 (57%)
Query: 168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAAL 227
PVG LQE + + W P Y + +G PH+R FT+ V + E G G SK++AKR AA
Sbjct: 2 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAE 61
Query: 228 NMLKFLET 235
+L +T
Sbjct: 62 KLLTKFKT 69
Score = 65.7 bits (161), Expect = 4e-14
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 78 PVSLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKH 136
PV +QEL + P+Y + Q G ++ F + + +V GSG SK+ AK
Sbjct: 2 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVET----FVETGSGTSKQVAKR 57
Query: 137 NAAKSVLDQL 146
AA+ +L +
Sbjct: 58 VAAEKLLTKF 67
>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain,
DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.50.1.1
Length = 89
Score = 88.5 bits (220), Expect = 5e-22
Identities = 28/67 (41%), Positives = 37/67 (55%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
NPVG LQE + + W P Y + +G H + FT+ V + E G G SKK+AKR AA
Sbjct: 17 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAA 76
Query: 227 LNMLKFL 233
ML +
Sbjct: 77 AKMLLRV 83
Score = 62.7 bits (153), Expect = 9e-13
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 78 PVSLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKH 136
PV +QEL+ + P+Y + Q G + F + ++ IGSG SKK AK
Sbjct: 18 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVER----FIEIGSGTSKKLAKR 73
Query: 137 NAAKSVLDQL 146
NAA +L ++
Sbjct: 74 NAAAKMLLRV 83
>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase
activator A; structure genomics, DSRM domain,
hypothetical protein PRKRA; NMR {Homo sapiens} SCOP:
d.50.1.1
Length = 84
Score = 83.1 bits (206), Expect = 3e-20
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 75 DRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEA 134
+TP+ ++ E + P YE + + I+ P F +R+++ G G SKK A
Sbjct: 7 GKTPIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRVTVGD----ITCTGEGTSKKLA 62
Query: 135 KHNAAKSVLDQLIG 148
KH AA++ ++ L
Sbjct: 63 KHRAAEAAINILKA 76
Score = 76.2 bits (188), Expect = 1e-17
Identities = 24/69 (34%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
P+ L E M K PVYE E + H FT V G G SKK+AK AA
Sbjct: 9 TPIQVLHEYGMKTK-NIPVYECERSDVQIHVPTFTFRVTVGDITCTGEGTSKKLAKHRAA 67
Query: 227 LNMLKFLET 235
+ L+
Sbjct: 68 EAAINILKA 76
>1ekz_A DSRBDIII, maternal effect protein (staufen); structure,
protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila
melanogaster} SCOP: d.50.1.1 PDB: 1stu_A
Length = 76
Score = 82.8 bits (205), Expect = 4e-20
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
+P+ Q+ E + R ++ G H + F V EG G KK++K+ AA
Sbjct: 8 SPISQVHEIGIKRNMTVH-FKVLREEGPAHMKNFITACIVGSIVTEGEGNGKKVSKKRAA 66
Query: 227 LNMLKFLETV 236
ML L+ +
Sbjct: 67 EKMLVELQKL 76
Score = 72.0 bits (177), Expect = 3e-16
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 72 NTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSK 131
++P+S + E+ +R +++++ EG + F + S V G G K
Sbjct: 3 EGDKKSPISQVHEIGIKRNMTVHFKVLREEGPAHMKNFITACIVGS----IVTEGEGNGK 58
Query: 132 KEAKHNAAKSVLDQL 146
K +K AA+ +L +L
Sbjct: 59 KVSKKRAAEKMLVEL 73
>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition,
DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus}
Length = 236
Score = 85.4 bits (210), Expect = 2e-19
Identities = 38/230 (16%), Positives = 69/230 (30%), Gaps = 75/230 (32%)
Query: 76 RTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAK 135
+ + + E+ + G +Y L+ G ++ P+F + + + V GSG +KK+AK
Sbjct: 7 KNALMQLNEI--KPG--LQYMLLSQTGPVHAPLFVMSVEVNGQ----VFEGSGPTKKKAK 58
Query: 136 HNAAKSVLDQLIGRDDEKLMCQKEN----------------------------------- 160
+AA+ L + +
Sbjct: 59 LHAAEKALRSFVQFPNASEAHLAMGRTLSVNTDFTSDQADFPDTLFNGFETPDKSEPPFY 118
Query: 161 ---------------LFKVEPNPVGQLQEACMTRKWPPP-----------------VYET 188
P P Q PP Y+
Sbjct: 119 VGSNGDDSFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSGKNPVMILNELRPGLKYDF 178
Query: 189 EETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLETVPI 238
+G H + F + V+ EG G++KK+AK AA + L + + +
Sbjct: 179 LSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAAQSALATVFNLHL 228
Score = 57.2 bits (137), Expect = 1e-09
Identities = 45/230 (19%), Positives = 75/230 (32%), Gaps = 30/230 (13%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
N + QL E P Y TG H +F + VN EG G +KK AK AA
Sbjct: 8 NALMQLNE-----IKPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGSGPTKKKAKLHAA 62
Query: 227 LNMLKFL-----ETVPIEIPEKKQGEDVDEKGESNGLKHTHDSTFLTPQILKKIQQYHTV 281
L+ + + + D + T + F TP + +
Sbjct: 63 EKALRSFVQFPNASEAHLAMGRTLSVNTDFTSDQADFPDTLFNGFETPDKSEPPFYVGSN 122
Query: 282 FSQKTKGPLLEKLLSTRNLIDEV---------------EDPILYLEDLSDELKYRVSFVD 326
L ++ ++P++ L +L LKY
Sbjct: 123 GDDSFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSGKNPVMILNELRPGLKYDFLSES 182
Query: 327 IEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMN 376
E +K+ F + + F G+G + ++AK A AL + ++
Sbjct: 183 GESHAKS--FVMSVVVDG---QFFEGSGRNKKLAKARAAQSALATVFNLH 227
>3llh_A RISC-loading complex subunit tarbp2; DSRBD, DSRM, microrna, RNA
binding protein; 2.14A {Homo sapiens}
Length = 90
Score = 77.7 bits (192), Expect = 3e-18
Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 4/80 (5%)
Query: 69 MRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSG 128
M +TP+SL+QE +R G P Y+L++ EG ++P F +R+++ G G
Sbjct: 7 MLAANPGKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDT----SCTGQG 62
Query: 129 KSKKEAKHNAAKSVLDQLIG 148
SKK AKH AA+ L L G
Sbjct: 63 PSKKAAKHKAAEVALKHLKG 82
Score = 74.7 bits (184), Expect = 4e-17
Identities = 27/76 (35%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
P+ LQE TR PVY+ + G H+ FT V G G SKK AK +AA
Sbjct: 15 TPISLLQE-YGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDTSCTGQGPSKKAAKHKAA 73
Query: 227 LNMLKFLETVPIEIPE 242
LK L+ + P
Sbjct: 74 EVALKHLKGGSMLEPA 89
>2l33_A Interleukin enhancer-binding factor 3; structural genomics,
northeast structural genomics consortiu PSI-biology,
protein structure initiative, DRBM; NMR {Homo sapiens}
Length = 91
Score = 70.5 bits (173), Expect = 1e-15
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
NPV +L E K YE TG H++ F + V+ K +G G +KK+AK AA
Sbjct: 18 NPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAA 72
Query: 227 LNMLKFLETVPIEIPEKKQ 245
L L+ L + +
Sbjct: 73 LAALEKLFPDTPLALDANK 91
Score = 62.5 bits (152), Expect = 1e-12
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 71 LNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKS 130
L + PV + E RRG KYELI G ++ F + + + G+G +
Sbjct: 12 LTKHGKNPVMELNEK--RRG--LKYELISETGGSHDKRFVMEVEVDGQ----KFQGAGSN 63
Query: 131 KKEAKHNAAKSVLDQL 146
KK AK AA + L++L
Sbjct: 64 KKVAKAYAALAALEKL 79
>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding
protein, hydrolase; NMR {Rattus norvegicus} SCOP:
d.50.1.1 PDB: 2l2k_B
Length = 71
Score = 68.5 bits (168), Expect = 4e-15
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
NPV L E P Y+ +G H + F + V+ EG G++KK+AK AA
Sbjct: 5 NPVMILNELR-----PGLKYDFLSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAA 59
Query: 227 LNMLKFLETVPI 238
+ L + + +
Sbjct: 60 QSALATVFNLHL 71
Score = 62.7 bits (153), Expect = 6e-13
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 74 GDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKE 133
+ PV ++ EL R G KY+ + G + F + + + GSG++KK
Sbjct: 2 SGKNPVMILNEL--RPG--LKYDFLSESGESHAKSFVMSVVVDGQ----FFEGSGRNKKL 53
Query: 134 AKHNAAKSVLDQLIG 148
AK AA+S L +
Sbjct: 54 AKARAAQSALATVFN 68
>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene
regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A
Length = 76
Score = 66.5 bits (163), Expect = 3e-14
Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 1/65 (1%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREAALNM 229
LQE + P+Y+ ++ L FT + + ++KK A+ A
Sbjct: 9 LLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAATRTKKDAEISAGRTA 68
Query: 230 LKFLE 234
L ++
Sbjct: 69 LLAIQ 73
Score = 58.5 bits (142), Expect = 2e-11
Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 80 SLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
+L+QE + P Y+ ++E F + + + ++KK+A+ +A
Sbjct: 8 NLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIK---YTGAATRTKKDAEISA 64
Query: 139 AKSVLDQL 146
++ L +
Sbjct: 65 GRTALLAI 72
>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase;
structure genomics, DSRM domain, structural genomics,
NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1
Length = 97
Score = 66.6 bits (163), Expect = 4e-14
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREA 225
+ +L + Y+ T+G PH+R FT ++ E G+SK+ A+ A
Sbjct: 15 FYMDKLNKYRQMHGVAIT-YKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNAA 73
Query: 226 ALNMLKFLE 234
A + L+
Sbjct: 74 AKLAVDILD 82
Score = 65.9 bits (161), Expect = 8e-14
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
+ + + G A Y+ + G ++ F +++ + + G+SK+EA++
Sbjct: 16 YMDKLNKYRQMHGVAITYKELSTSGPPHDRRFTFQVLIDEKE---FPEAKGRSKQEARNA 72
Query: 138 AAKSVLDQLIGRDDEKL 154
AAK +D L +
Sbjct: 73 AAKLAVDILDNENKVDC 89
>3p1x_A Interleukin enhancer-binding factor 3; structural genomics,
PSI-biology, protein structure initiati northeast
structural genomics consortium, NESG; 1.90A {Homo
sapiens}
Length = 75
Score = 65.7 bits (161), Expect = 4e-14
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
NPV +L E K YE TG H++ F + V+ K +G G +KK+AK AA
Sbjct: 8 NPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAA 62
Query: 227 LNMLKFL 233
L L+ L
Sbjct: 63 LAALEKL 69
Score = 61.9 bits (151), Expect = 1e-12
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 71 LNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKS 130
L + PV + E RRG KYELI G ++ F + + + G+G +
Sbjct: 2 LTKHGKNPVMELNEK--RRG--LKYELISETGGSHDKRFVMEVEVDGQ----KFQGAGSN 53
Query: 131 KKEAKHNAAKSVLDQL 146
KK AK AA + L++L
Sbjct: 54 KKVAKAYAALAALEKL 69
>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference,
endonucleolytic cleavage, hydrolase/RNA complex; 1.70A
{Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A
2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A
1jfz_A 1rc5_A
Length = 221
Score = 68.7 bits (169), Expect = 1e-13
Identities = 24/64 (37%), Positives = 32/64 (50%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNML 230
LQE R P Y G H++ F V A + Y+ G GKSKK A++ AA ++
Sbjct: 155 ILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELI 214
Query: 231 KFLE 234
K LE
Sbjct: 215 KLLE 218
Score = 54.1 bits (131), Expect = 1e-08
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 80 SLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
+++QE+ R P+Y LI +EG ++ F + Y +G GKSKKEA+ A
Sbjct: 154 TILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKE----YRTLGEGKSKKEAEQRA 209
Query: 139 AKSVLDQL 146
A+ ++ L
Sbjct: 210 AEELIKLL 217
>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding
protein, hydrolase; NMR {Rattus norvegicus} SCOP:
d.50.1.1 PDB: 2l3c_A
Length = 73
Score = 63.8 bits (156), Expect = 2e-13
Identities = 23/71 (32%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
N + QL E P Y TG H +F + VN EG G +KK AK AA
Sbjct: 8 NALMQLNE-----IKPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGSGPTKKKAKLHAA 62
Query: 227 LNMLKFLETVP 237
L+ P
Sbjct: 63 EKALRSFVQFP 73
Score = 60.4 bits (147), Expect = 3e-12
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 76 RTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAK 135
+ + + E+ + G +Y L+ G ++ P+F + + + V GSG +KK+AK
Sbjct: 7 KNALMQLNEI--KPG--LQYMLLSQTGPVHAPLFVMSVEVNGQ----VFEGSGPTKKKAK 58
Query: 136 HNAAKSVLDQLI 147
+AA+ L +
Sbjct: 59 LHAAEKALRSFV 70
>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding
protein, gene regulation; 1.70A {Arabidopsis thaliana}
PDB: 3adi_A
Length = 73
Score = 62.3 bits (152), Expect = 7e-13
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN--VYKEEGMGKSKKIAKREAALN 228
+LQE K P PVYE + G H+ +F ++ Y ++K A++ AA
Sbjct: 8 RLQEYAQKYKLPTPVYEIVK-EGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAAEV 66
Query: 229 MLKFLE 234
L+ L
Sbjct: 67 ALRELA 72
Score = 53.0 bits (128), Expect = 2e-09
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 80 SLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
S +QE + P YE+++ EG ++ +F+ + L Y ++ ++K A+ +A
Sbjct: 7 SRLQEYAQKYKLPTPVYEIVK-EGPSHKSLFQSTVILDGVR--YNSLPGFFNRKAAEQSA 63
Query: 139 AKSVLDQL 146
A+ L +L
Sbjct: 64 AEVALREL 71
>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA
binding domain, DSRBD, DSRM, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.50.1.1
Length = 128
Score = 63.4 bits (154), Expect = 1e-12
Identities = 31/109 (28%), Positives = 44/109 (40%), Gaps = 13/109 (11%)
Query: 159 ENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN--VYKEEGMGK 216
+ + P L E C K P PVYET + +RMF V Y+ K
Sbjct: 19 RRAYPPQITPKMCLLEWCRREKLPQPVYETVQR---TIDRMFCSVVTVAEQKYQSTLWDK 75
Query: 217 SKKIAKREAALNMLKFL--------ETVPIEIPEKKQGEDVDEKGESNG 257
SKK+A++ AA+ L+ E P K++ D D G +G
Sbjct: 76 SKKLAEQTAAIVCLRSQGLPEGRLGEESPSLNKRKREAPDQDPGGPRSG 124
Score = 49.5 bits (118), Expect = 8e-08
Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 6/94 (6%)
Query: 62 EAARLEVMRLNTGDRTPVSLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESR 120
+ A R TP + E R P YE +Q + +F +++ +
Sbjct: 12 KMAIRFDRRAYPPQITPKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTV--AEQ 66
Query: 121 LYVAIGSGKSKKEAKHNAAKSVLDQLIGRDDEKL 154
Y + KSKK A+ AA L +
Sbjct: 67 KYQSTLWDKSKKLAEQTAAIVCLRSQGLPEGRLG 100
>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.50.1.1
Length = 97
Score = 62.2 bits (151), Expect = 1e-12
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 13/83 (15%)
Query: 151 DEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYK 210
D K + N + +L + P Y+ +G H +FT+ V+
Sbjct: 12 DSKAIDLM--------NALMRLNQI-----RPGLQYKLLSQSGPVHAPVFTMSVDVDGTT 58
Query: 211 EEGMGKSKKIAKREAALNMLKFL 233
E G SKK AK A+ +L+ +
Sbjct: 59 YEASGPSKKTAKLHVAVKVLQAM 81
Score = 58.3 bits (141), Expect = 4e-11
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 75 DRTPVSLMQEL--LSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKK 132
D + LM L L++ +Y+L+ G ++ P+F + + SG SKK
Sbjct: 12 DSKAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGT----TYEASGPSKK 67
Query: 133 EAKHNAAKSVLDQL 146
AK + A VL +
Sbjct: 68 TAKLHVAVKVLQAM 81
>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Mus musculus} SCOP: d.50.1.1
PDB: 2rs6_A
Length = 99
Score = 62.2 bits (151), Expect = 2e-12
Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 72 NTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSK 131
++G + + +R P YE+ G N F + + + Y +G+ +K
Sbjct: 2 SSGSSGIKNFLYAWCGKRKMTPAYEIRA-VGNKNRQKFMCEVRVEGFN--YAGMGNSTNK 58
Query: 132 KEAKHNAAKSVLDQLI 147
K+A+ NAA+ ++ L+
Sbjct: 59 KDAQSNAARDFVNYLV 74
Score = 52.6 bits (126), Expect = 4e-09
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 170 GQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN--VYKEEGMGKSKKIAKREAAL 227
L C RK P YE G + + F V Y G +KK A+ AA
Sbjct: 10 NFLYAWCGKRKMTP-AYEIRAV-GNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAAR 67
Query: 228 NMLKFL 233
+ + +L
Sbjct: 68 DFVNYL 73
>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG,
PSI, protein structure initiative, joint center for
structural genomics; 2.00A {Thermotoga maritima} SCOP:
a.149.1.1 d.50.1.1
Length = 252
Score = 65.3 bits (160), Expect = 3e-12
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREAALNM 229
LQE + PP Y T +R+F V VN G G++KK A++EAA
Sbjct: 184 ALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIA 243
Query: 230 LKFLE 234
+ L
Sbjct: 244 YEKLL 248
Score = 56.1 bits (136), Expect = 3e-09
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 80 SLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
+ +QE++ S P+Y L++ E + IF + + ++ +A G G++KKEA+ A
Sbjct: 183 TALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKT---IATGKGRTKKEAEKEA 239
Query: 139 AKSVLDQL 146
A+ ++L
Sbjct: 240 ARIAYEKL 247
>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing,
hydrolase; NMR {Drosophila melanogaster}
Length = 114
Score = 61.9 bits (150), Expect = 3e-12
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 157 QKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGK 216
+K+ + P P + + +Y+ E TG H +FT+ V+ K G G+
Sbjct: 25 KKKMCKERIPQPKNTVAM--LNELRHGLIYKLESQTGPVHAPLFTISVEVDGQKYLGQGR 82
Query: 217 SKKIAKREAALNMLKFLETVP 237
SKK+A+ EAA L+
Sbjct: 83 SKKVARIEAAATALRSFIQFK 103
Score = 54.2 bits (130), Expect = 2e-09
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
P + + L R Y+L G ++ P+F + + + +G G+SKK A+
Sbjct: 36 PKNTVAMLNELRHG-LIYKLESQTGPVHAPLFTISVEVDGQ----KYLGQGRSKKVARIE 90
Query: 138 AAKSVLDQLI 147
AA + L I
Sbjct: 91 AAATALRSFI 100
>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.50.1.1
Length = 98
Score = 61.4 bits (149), Expect = 3e-12
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 6/91 (6%)
Query: 71 LNTGDRTPVSLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGK 129
+N ++ V ++ E + R P Y + E F +++ + G+
Sbjct: 11 INPNGKSEVCILHEYMQRVLKVRPVYNFFECENP--SEPFGASVTIDGVT---YGSGTAS 65
Query: 130 SKKEAKHNAAKSVLDQLIGRDDEKLMCQKEN 160
SKK AK+ AA++ L+ LI ++ +
Sbjct: 66 SKKLAKNKAARATLEILIPDFVKQTSESGPS 96
Score = 59.1 bits (143), Expect = 2e-11
Identities = 25/92 (27%), Positives = 34/92 (36%), Gaps = 11/92 (11%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREA 225
+ V L E PVY E F ++ V G SKK+AK +A
Sbjct: 17 SEVCILHEYMQRVLKVRPVYNFFECENPSEP--FGASVTIDGVTYGSGTASSKKLAKNKA 74
Query: 226 ALNMLKFLETVPIEIPEKKQGEDVDEKGESNG 257
A L+ L IP+ + E G S+G
Sbjct: 75 ARATLEIL------IPDFV--KQTSESGPSSG 98
>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant
protein; NMR {Arabidopsis thaliana}
Length = 103
Score = 60.6 bits (147), Expect = 6e-12
Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 5/85 (5%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN--VYKEEGMGKSKKIAKREAALN 228
+LQE K P PVYE + G H+ +F ++ Y ++K A++ AA
Sbjct: 22 RLQEYAQKYKLPTPVYEIVKE-GPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAAEV 80
Query: 229 MLKFLETVPIEIPEKKQGEDVDEKG 253
L+ L + + V E G
Sbjct: 81 ALRELAKSS--ELSQCVSQPVHETG 103
Score = 51.7 bits (124), Expect = 1e-08
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 80 SLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
S +QE + P YE+++ EG ++ +F+ + L + Y ++ ++K A+ +A
Sbjct: 21 SRLQEYAQKYKLPTPVYEIVK-EGPSHKSLFQSTVIL--DGVRYNSLPGFFNRKAAEQSA 77
Query: 139 AKSVLDQLIGRDDEK 153
A+ L +L +
Sbjct: 78 AEVALRELAKSSELS 92
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic
protein structure initiative; 2.10A {Mycobacterium
tuberculosis}
Length = 242
Score = 63.4 bits (155), Expect = 9e-12
Identities = 25/77 (32%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREAALNM 229
LQE R P Y T G H++ FT V G+G+SKK A+++AA
Sbjct: 167 SLQELTAARGLGAPSYLVTST-GPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKAAAAA 225
Query: 230 LKFLETVPIEIPEKKQG 246
K LE + +P K
Sbjct: 226 WKALEVLDNAMPGKTSA 242
Score = 50.3 bits (121), Expect = 2e-07
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 80 SLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
+ +QEL +R AP Y L+ G ++ F + + G G+SKKEA+ A
Sbjct: 166 TSLQELTAARGLGAPSY-LVTSTGPDHDKEFTAVVVVMDSE---YGSGVGRSKKEAEQKA 221
Query: 139 AKSVLDQLIGRDD 151
A + L D+
Sbjct: 222 AAAAWKALEVLDN 234
>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862,
csgid, structura genomics; 2.21A {Campylobacter jejuni
subsp}
Length = 248
Score = 62.2 bits (152), Expect = 2e-11
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 1/67 (1%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYV-NVYKEEGMGKSKKIAKREAALNM 229
+LQE + P YET G H + F + + + SKK A++ AA
Sbjct: 182 KLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAIAGSKKEAQQMAAKIA 241
Query: 230 LKFLETV 236
L+ L +
Sbjct: 242 LEKLGAL 248
Score = 56.4 bits (137), Expect = 2e-09
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 80 SLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
+ +QE+ + G P+YE ++ G + F+ + L + +A SKKEA+ A
Sbjct: 181 TKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKE---LARAIAGSKKEAQQMA 237
Query: 139 AKSVLDQL 146
AK L++L
Sbjct: 238 AKIALEKL 245
>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene
regulation, NUCL protein, gene regulation,nuclear
protein; NMR {Homo sapiens}
Length = 85
Score = 57.7 bits (140), Expect = 4e-11
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 171 QLQEACMT-----RKWPPPVYETEETTGLPHERMFTVCAYVNVYKE-EGMGKSKKIAKRE 224
QLQ+ C+T ++ P+Y+T +T G H R +TV Y + G G S + A+
Sbjct: 6 QLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMG 65
Query: 225 AALNMLKFL 233
AA++ L+
Sbjct: 66 AAMDALEKY 74
Score = 50.8 bits (122), Expect = 1e-08
Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 3/67 (4%)
Query: 80 SLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAA 139
L + P Y+ +Q G + + + E + G G S ++A+ AA
Sbjct: 11 CLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGER---IGCGKGPSIQQAEMGAA 67
Query: 140 KSVLDQL 146
L++
Sbjct: 68 MDALEKY 74
>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 = 60.6 bits (146), Expect = 4e-10
Identities = 45/354 (12%), Positives = 97/354 (27%), Gaps = 109/354 (30%)
Query: 12 EDKADINMPSTVS-LDCNEVKVEENSPSRVLFDNNEIKQIPKVSTNNLPLEEAARLEVMR 70
+D + + V DC +V ++ P +L EI I + RL
Sbjct: 19 KDILSVFEDAFVDNFDCKDV---QDMPKSIL-SKEEIDHIIMSKD---AVSGTLRLFWTL 71
Query: 71 LNTGDRTPVSLMQELLSRRGTAPKYELI--QIEGAINEPIFKYRISLTSESRLYVAIGSG 128
L+ + ++E+L Y+ + I+ +P R+ + RLY
Sbjct: 72 LSKQEEMVQKFVEEVL-----RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY-----N 121
Query: 129 KSKKEAKHNAAKSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYET 188
++ AK+N + R + + ++ L ++ P
Sbjct: 122 DNQVFAKYN---------VSRL-QPYLKLRQALLELRPAK-------------------- 151
Query: 189 EETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLETVP-----IEIPEK 243
V + G GK+ K + + +
Sbjct: 152 ----------------NVLIDGVLGSGKTWVAL---DVCLSYKVQCKMDFKIFWLNL--- 189
Query: 244 KQGEDVDEKGESNGLKHTHDSTFLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNLIDE 303
++ ++ +L+ +Q+ + + N+
Sbjct: 190 -------------KNCNSPET------VLEMLQKLLYQIDP----NWTSRSDHSSNIKLR 226
Query: 304 VEDPILYLEDLSDELKYRVSFV---DIEEKSKADGF----QSLLQLTTTPVTVF 350
+ L L Y + +++ + F + L LTT V
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL--LTTRFKQVT 278
>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding,
endonuclease, HEL hydrolase, nucleotide-binding,
phosphoprotein, RN binding; HET: MSE; 1.68A {Mus
musculus} PDB: 3c4t_A 2eb1_A
Length = 265
Score = 54.4 bits (131), Expect = 1e-08
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 6/69 (8%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
P S ++ELL P+ + + + + + G G+S + AK
Sbjct: 199 PRSPVRELLEME---PETAKFSPAERTYDGKVRVTVEVVGKG---KFKGVGRSYRIAKSA 252
Query: 138 AAKSVLDQL 146
AA+ L L
Sbjct: 253 AARRALRSL 261
Score = 53.2 bits (128), Expect = 3e-08
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 5/68 (7%)
Query: 168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKE-EGMGKSKKIAKREAA 226
P ++E P ++ V V + +G+G+S +IAK AA
Sbjct: 199 PRSPVRELLEME----PETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAA 254
Query: 227 LNMLKFLE 234
L+ L+
Sbjct: 255 RRALRSLK 262
>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 = 52.7 bits (126), Expect = 1e-07
Identities = 76/513 (14%), Positives = 133/513 (25%), Gaps = 212/513 (41%)
Query: 36 SPSRVLFDNNEIKQIPK--------VSTNNLPLEEAARLEVMR----------LNTGDRT 77
P+ ++E + VS+ P + +V+ L D
Sbjct: 43 EPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND-- 100
Query: 78 PV-SLMQELLSRRGTAP--KYELIQI----EGAINEPIFKYRISLTSESRLYVAIGSGKS 130
+ +L +LL T ELI+ P K S S L+ A+G G +
Sbjct: 101 -IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK-----KSNSALFRAVGEGNA 154
Query: 131 K---------------KEAK--HNAAKSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQ 173
+ +E + + ++ LI E L L + +
Sbjct: 155 QLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETL----SELIRTTLDAEKVFT 210
Query: 174 EACMTRKW-------PP-------PV------------YE-TEETTGLPHERMF------ 200
+ +W P P+ Y T + G +
Sbjct: 211 QGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA 270
Query: 201 TVCAYVNVYKEEGMGKSKKIAK-------REAALNMLKFL--------ETVPIEIPEKKQ 245
T + +G+ + IA+ + + L E P
Sbjct: 271 TGHS-------QGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSI 323
Query: 246 GEDVDEKGE-----------------------SN-----------GLKHTHDSTFLT--P 269
ED E E +N L + + ++ P
Sbjct: 324 LEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPP 383
Query: 270 Q-------ILKKIQ------QYHTVFSQKTKGPLLEKL-LSTRNLIDEVEDPI------L 309
Q L+K + Q FS++ KL S R L P+
Sbjct: 384 QSLYGLNLTLRKAKAPSGLDQSRIPFSER-------KLKFSNRFL------PVASPFHSH 430
Query: 310 YLEDLSDELKYRVSFVDIEEKSKA---------DG--FQSL-------L--QLTTTPV-- 347
L SD + + ++ +K DG + L + + PV
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKW 490
Query: 348 ---TVF-------CGTGASIEVAKIEAVYRALD 370
T F G G + + + +R D
Sbjct: 491 ETTTQFKATHILDFGPGGASGLGVL--THRNKD 521
Score = 50.0 bits (119), Expect = 9e-07
Identities = 52/303 (17%), Positives = 93/303 (30%), Gaps = 90/303 (29%)
Query: 1 MAR----VSNVSDEVEDKADINMPSTVSLDCNEVKVEENSPSR--VLFDNNEIKQI---- 50
M S + +V ++AD + T ++ V N P + F + K+I
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDI-VINN-PVNLTIHFGGEKGKRIRENY 1688
Query: 51 PKVSTNNLPLEEAARLEVMRLNTGDRTPVSLM----QELLSRRGTA---P--------KY 95
+ + + ++ + S + LLS T P +
Sbjct: 1689 SAMIFETIVDGKLKTEKI--FKEINEHSTSYTFRSEKGLLSA--TQFTQPALTLMEKAAF 1744
Query: 96 ELIQIEGAINEPIF-------KY--------RISLTSESRLYVAI-GSGKSKKEAKHNAA 139
E ++ +G I +Y +S+ S + V G A
Sbjct: 1745 EDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEV-VFYRG------MTMQVAV 1797
Query: 140 KSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQL--QEACMTRKWPPPVYETEETTGLPHE 197
D+L GR + M + P V QEA + V + TG
Sbjct: 1798 PR--DEL-GRSNYG-MI------AINPGRVAASFSQEAL--QYV---VERVGKRTGW--- 1839
Query: 198 RMFTVCAYVNVYKEEGM-----GKSKKIAKREAALNMLKFLETVPIEI---PEKKQGEDV 249
+ VN Y E G + + + N+L F++ I+I + E+V
Sbjct: 1840 ----LVEIVN-YNVENQQYVAAGDLRAL---DTVTNVLNFIKLQKIDIIELQKSLSLEEV 1891
Query: 250 DEK 252
+
Sbjct: 1892 EGH 1894
Score = 37.7 bits (87), Expect = 0.007
Identities = 40/257 (15%), Positives = 77/257 (29%), Gaps = 99/257 (38%)
Query: 211 EEGMGK----SKKIAKR--EAA----LNMLKF--LETV---PIEI---PEKKQGEDVDEK 252
E+GMG + K A+ A + F L+ V P+ + ++G+ + E
Sbjct: 1628 EQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIREN 1687
Query: 253 GESNGLKHTHDSTFLTPQILKKIQQ--------------YHTVFSQKTKGP---LLE--- 292
+ + D T +I K+I + T F+Q P L+E
Sbjct: 1688 YSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ----PALTLMEKAA 1743
Query: 293 -KLLSTRNLIDEV---------EDPILY-----------LEDLSDELKYRVSFVD--IEE 329
+ L ++ LI E Y +E L + + YR + +
Sbjct: 1744 FEDLKSKGLIPADATFAGHSLGE----YAALASLADVMSIESLVEVVFYRGMTMQVAVPR 1799
Query: 330 KSKADGFQSLLQLTTTPVTVFCG--------------TGASIEVA-------------KI 362
++ + V TG +E+ +
Sbjct: 1800 DELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDL 1859
Query: 363 EAVYRA---LDFLQIMN 376
A+ L+F+++
Sbjct: 1860 RALDTVTNVLNFIKLQK 1876
>1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken
structural genomics/proteomics initiative, RSGI RNA
binding protein; NMR {Mus musculus} SCOP: d.50.1.1 PDB:
2rs7_A
Length = 113
Score = 43.9 bits (103), Expect = 7e-06
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 8/73 (10%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEE------GMGKSKKI 220
N +L + K T+ G H R F + + + G +KK+
Sbjct: 27 NAKARLNQYFQKEKIQGEYKYTQ--VGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKL 84
Query: 221 AKREAALNMLKFL 233
A + AL++++ L
Sbjct: 85 AAQSCALSLVRQL 97
Score = 35.4 bits (81), Expect = 0.006
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 83 QELLSRRGTAPKYELIQIEGAINEPIF--KYRISLTSESRLYVAIGSGKSKKEAKHNAAK 140
+ + +Y+ G + F + I + R A G +KK A + A
Sbjct: 33 NQYFQKEKIQGEYK-YTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCAL 91
Query: 141 SVLDQL 146
S++ QL
Sbjct: 92 SLVRQL 97
>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A
{Vanderwaltozyma polyspora}
Length = 341
Score = 45.1 bits (107), Expect = 2e-05
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYV-NVYKEEGMGKSKKIAKREAALNM 229
+L E K ++ L F V + ++ +E G S + A+ AA+ +
Sbjct: 259 ELAELLQINKLGHKLHYR----KLTEMPPFRVEVKIGDILLDEAEGNSIREAEHRAAMKV 314
Query: 230 LKFLE 234
L+ E
Sbjct: 315 LENDE 319
Score = 42.8 bits (101), Expect = 1e-04
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 10/66 (15%)
Query: 83 QELLSRRGTA--PKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAK 140
ELL Y + P F+ + + + G S +EA+H AA
Sbjct: 261 AELLQINKLGHKLHYRKLT-----EMPPFRVEVKIGDIL---LDEAEGNSIREAEHRAAM 312
Query: 141 SVLDQL 146
VL+
Sbjct: 313 KVLEND 318
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase;
3.00A {Giardia intestinalis} PDB: 2ffl_A
Length = 756
Score = 43.8 bits (103), Expect = 8e-05
Identities = 5/90 (5%), Positives = 23/90 (25%), Gaps = 8/90 (8%)
Query: 137 NAAKSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPH 196
+ L + + + + + P+ V + + + + +
Sbjct: 423 YGCEEFLAKTLMSPEHS-----KTVGSACPDAVTKASKRVCMGEAGAHEFRSLVDYACEQ 477
Query: 197 ERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
+ V+ + + + I +
Sbjct: 478 GISVFCSSRVS---TMFLERLRDIPAEDML 504
>1x48_A Interferon-induced, double-stranded RNA- activated protein kinase;
structure genomics, DSRM domain, structural genomics,
NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1
Length = 88
Score = 38.9 bits (90), Expect = 2e-04
Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
+ L+ ++ + YE + + F + + GSG +K+EAK
Sbjct: 8 YIGLVNSFAQKKKLSVNYEQCE-PNSELPQRFICKCKIGQT---MYGTGSGVTKQEAKQL 63
Query: 138 AAKSVLDQL 146
AAK +L
Sbjct: 64 AAKEAYQKL 72
Score = 36.9 bits (85), Expect = 0.001
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 1/67 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
+G + +K + E + LP +R C G G +K+ AK+ AA
Sbjct: 7 GYIGLVNSFAQKKKLSVNYEQCEPNSELP-QRFICKCKIGQTMYGTGSGVTKQEAKQLAA 65
Query: 227 LNMLKFL 233
+ L
Sbjct: 66 KEAYQKL 72
>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces
cerevisiae} SCOP: d.50.1.1
Length = 94
Score = 37.6 bits (87), Expect = 6e-04
Identities = 11/70 (15%), Positives = 23/70 (32%), Gaps = 3/70 (4%)
Query: 75 DRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEA 134
D + L+ Y ++ + +P + + G G++ K A
Sbjct: 5 DMNAKRQLYSLIGYASLRLHYVTVK-KPTAVDPNSI--VECRVGDGTVLGTGVGRNIKIA 61
Query: 135 KHNAAKSVLD 144
AA++ L
Sbjct: 62 GIRAAENALR 71
Score = 29.5 bits (66), Expect = 0.42
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 184 PVYETEETTGLPHERMFTVCAYVNVYK-EEGMGKSKKIAKREAALNMLK 231
Y T + C + G+G++ KIA AA N L+
Sbjct: 23 LHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALR 71
>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A
{Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B
2lbs_B
Length = 117
Score = 37.0 bits (85), Expect = 0.002
Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 3/70 (4%)
Query: 75 DRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEA 134
D + L+ Y ++ + +P + + L G G++ K A
Sbjct: 7 DMNAKRQLYSLIGYASLRLHYVTVK-KPTAVDPNSIVECRVGDGTVL--GTGVGRNIKIA 63
Query: 135 KHNAAKSVLD 144
AA++ L
Sbjct: 64 GIRAAENALR 73
Score = 27.7 bits (61), Expect = 2.6
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 184 PVYETEETTGLPHERMFTVCAYVNVYK-EEGMGKSKKIAKREAALNMLK 231
Y T + C + G+G++ KIA AA N L+
Sbjct: 25 LHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALR 73
>1zl0_A Hypothetical protein PA5198; structural genomics, PSI, PROT
structure initiative, midwest center for structural
genomic unknown function; HET: TLA PEG; 1.10A
{Pseudomonas aeruginosa} SCOP: c.8.10.1 c.23.16.7 PDB:
1zrs_A 2aum_A 2aun_A
Length = 311
Score = 31.2 bits (71), Expect = 0.46
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 290 LLEKLLSTRNLIDEVEDPILYLEDLSDELKYRV 322
L + T + IL LED E YR+
Sbjct: 197 ALACMAGTLGGLHAPAGSILVLED-VGEPYYRL 228
>3sn6_R Lysozyme, beta-2 adrenergic receptor; seven transmembrane receptor,
nanobody, G protein-coupled RE GPCR, signal
transduction, G protein signaling; HET: P0G; 3.20A
{Enterobacteria phage T4} PDB: 3kj6_A 2r4s_A 2r4r_A
Length = 514
Score = 30.7 bits (69), Expect = 0.89
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 95 YELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKS-KKEAKHNAAKSVLDQLIGRDDEK 153
+E+++I+ + I+K ++ Y IG G K NAAKS LD+ IGR+
Sbjct: 18 FEMLRIDEGLRLKIYK-------DTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNG 70
Query: 154 LMCQKE 159
++ + E
Sbjct: 71 VITKDE 76
>3sr3_A Microcin immunity protein MCCF; csgid, structural genomics, MCCF
protein, center for structu genomics of infectious
diseases, immune system; 1.50A {Bacillus anthracis} PDB:
3gjz_A 3t5m_A* 3u1b_A* 3tyx_A*
Length = 336
Score = 29.6 bits (67), Expect = 1.8
Identities = 14/106 (13%), Positives = 36/106 (33%), Gaps = 19/106 (17%)
Query: 224 EAALNMLKFLETVPIEIPEKKQGEDVDEKGESNGLKHTHDSTFLTPQILKKIQQYHTVFS 283
+ L L + +P I + D ++ T + + + +V +
Sbjct: 154 KYFLETLLHDQALPYNIKQPLFWSD-----------EFINAEEKTKEKELRPNNWISVTN 202
Query: 284 QKTKGPL-------LEKLLSTRNLIDEVEDPILYLEDLSDELKYRV 322
+ G + ++ + + + E IL++ED S + +
Sbjct: 203 GQATGRVIGGNLNTIQGIWGSPYMPCIQEGDILFIED-SSKDAATI 247
>3tla_A MCCF; serine protease, hydrolase; 1.20A {Escherichia coli} PDB:
3tle_A* 3tlg_A 3tlb_A* 3tlc_A* 3tlz_A* 3tly_A
Length = 371
Score = 29.4 bits (66), Expect = 2.0
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 290 LLEKLLSTRNLIDEVEDPILYLEDLSDELKYRV 322
L + + + + IL++ED S + V
Sbjct: 248 TLTGIWGSEWMPEIRNGDILFIED-SRKSIATV 279
>2kou_A Dicer-like protein 4; ATP-binding, endonuclease, helicase,
hydrolase, nuclease, nucleotide-binding, nucleus, RNA-
binding; NMR {Arabidopsis thaliana}
Length = 102
Score = 26.3 bits (58), Expect = 7.5
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 216 KSKKIAKREAALNMLKFL 233
S + AK++A L + L
Sbjct: 61 PSTEAAKKDACLKAVHEL 78
>4e5s_A MCCFLIKE protein (BA_5613); structural genomics, center for
structural genomi infectious diseases, csgid, serine
peptidase S66; 1.95A {Bacillus anthracis}
Length = 331
Score = 27.6 bits (62), Expect = 8.0
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 290 LLEKLLSTRNLIDEVEDPILYLED---LSDELKYRV 322
L L T + + ++D IL+LE+
Sbjct: 210 TLNLLQGTSYMPN-LKDKILFLEEDSLTGTSTLKTF 244
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
0.313 0.131 0.362
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,534,422
Number of extensions: 334377
Number of successful extensions: 623
Number of sequences better than 10.0: 1
Number of HSP's gapped: 559
Number of HSP's successfully gapped: 87
Length of query: 377
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 282
Effective length of database: 4,049,298
Effective search space: 1141902036
Effective search space used: 1141902036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.0 bits)