RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13227
(247 letters)
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 112 bits (282), Expect = 5e-32
Identities = 45/84 (53%), Positives = 64/84 (76%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
RR DD IR++NLS +T E DL++L + FG S++YL++DKT G KGFA+I F + D
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
AA+AI ++G+GYDHLIL+V+W+K
Sbjct: 70 AARAIAGVSGFGYDHLILNVEWAK 93
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 85.9 bits (213), Expect = 1e-21
Identities = 27/126 (21%), Positives = 53/126 (42%), Gaps = 1/126 (0%)
Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
M +S G + + G G + T++++ NL+ T
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDV-EGMTSLKVDNLTYRT 59
Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL 237
S + L + +++G +Y+ RD+ +GFA++ F +K DA A+ ++G D L
Sbjct: 60 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
Query: 238 SVDWSK 243
V ++
Sbjct: 120 RVQMAR 125
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 85.6 bits (212), Expect = 4e-21
Identities = 26/104 (25%), Positives = 46/104 (44%)
Query: 140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR 199
YV S + + + + + NLS T+E + +L + G K+ +
Sbjct: 14 YVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL 73
Query: 200 DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
DK GF ++ + ++ADA A++Y+NG D I+ DW
Sbjct: 74 DKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 74.6 bits (184), Expect = 1e-17
Identities = 21/88 (23%), Positives = 43/88 (48%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + D +++ NL+ TS + L + +++G +Y+ R+ +GFA++ F
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
++ DA A ++G D L V ++
Sbjct: 64 DRRDAQDAEAAMDGAELDGRELRVQVAR 91
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 75.3 bits (185), Expect = 3e-17
Identities = 31/145 (21%), Positives = 57/145 (39%), Gaps = 1/145 (0%)
Query: 99 LFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYN 158
L L K T + A K+ G G G +
Sbjct: 5 LILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHH-H 63
Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
+ T++++ NL+ TS + L + +++G +Y+ RD+ +GFA++ F +K
Sbjct: 64 HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123
Query: 219 DAAKAIQYLNGYGYDHLILSVDWSK 243
DA A+ ++G D L V ++
Sbjct: 124 DAEDAMDAMDGAVLDGRELRVQMAR 148
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 73.3 bits (180), Expect = 6e-17
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 6/86 (6%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + T I NL T ++++ +FG ++ L A + F
Sbjct: 1 GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFL 54
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDW 241
+A KA ++L + H+ L ++W
Sbjct: 55 EPLEARKAFRHLAYSKFHHVPLYLEW 80
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 74.1 bits (182), Expect = 1e-16
Identities = 28/122 (22%), Positives = 49/122 (40%), Gaps = 3/122 (2%)
Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTA--IRISNLSVNTSENDL 182
+ + GG P L + + T + +SNL S+ D+
Sbjct: 46 RPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADI 105
Query: 183 EDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
++L +FG K + D++ G G A +HF+ +ADA KA++ G D + +
Sbjct: 106 QELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 164
Query: 243 KS 244
S
Sbjct: 165 AS 166
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 71.6 bits (176), Expect = 1e-16
Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 6/90 (6%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+ I + N++ +T + + + + + + L +DK +GFA++ + D
Sbjct: 6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65
Query: 220 AAKAIQYLNGYGYDHLI----LSVDWSKST 245
A++ +Q L I + VD++KS
Sbjct: 66 ASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 72.5 bits (178), Expect = 2e-16
Identities = 27/112 (24%), Positives = 52/112 (46%)
Query: 132 GAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP 191
G + + + G N D + + LS+ T+E DL ++ ++GP
Sbjct: 13 GLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGP 72
Query: 192 TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
+ + + D+ + +GFA+++F+N DA +A + NG D + VD+S
Sbjct: 73 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 71.7 bits (176), Expect = 2e-16
Identities = 12/77 (15%), Positives = 30/77 (38%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + L+ N E L+D+ +++G ++ + G A + F + A + ++ L
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 228 NGYGYDHLILSVDWSKS 244
+ I+
Sbjct: 69 HLTSVMGNIIHAQLDIK 85
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 70.4 bits (173), Expect = 7e-16
Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 3/97 (3%)
Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
G ++ I + NL + D+ED+ ++G + L K
Sbjct: 5 SSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGP 61
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
FA++ F++ DA A+ +GY YD L V++ +S
Sbjct: 62 PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 98
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 69.2 bits (170), Expect = 1e-15
Identities = 25/94 (26%), Positives = 46/94 (48%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
G N D + + LS+ T+E DL ++ ++GP + + + D+ + +GFA
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
+++F+N DA +A + NG D + V S
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 72.4 bits (177), Expect = 1e-15
Identities = 23/141 (16%), Positives = 45/141 (31%), Gaps = 2/141 (1%)
Query: 109 FNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAI 168
+ ++ + G +PP++ + G A+
Sbjct: 12 YGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIAL 71
Query: 169 RISNLSVNTSENDLEDLVKQFGPTS--KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
I NL+ T++ DL + V G ++ ++ NG KGFA + ++A + K +
Sbjct: 72 YIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 131
Query: 227 LNGYGYDHLILSVDWSKSTNQ 247
L V
Sbjct: 132 LPKRELHGQNPVVTPVNKQFL 152
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 73.1 bits (180), Expect = 2e-15
Identities = 20/82 (24%), Positives = 37/82 (45%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+ ++NL + ++ E+LV+ FG + +L + G KG+ + + K AA+A
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
L G L V W+ +
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQL 177
Score = 60.8 bits (148), Expect = 4e-11
Identities = 18/110 (16%), Positives = 35/110 (31%), Gaps = 11/110 (10%)
Query: 135 GGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSEND-LEDLVKQFGPTS 193
G +YV + + + + L ++ D L + +
Sbjct: 163 GPRTLYVHWTDAGQLTPALLHSRC---------LCVDRLPPGFNDVDALCRALSAVHSPT 213
Query: 194 KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
L+ + G KGFA + ++ A +A Q +G L V +
Sbjct: 214 FCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCA 262
Score = 55.0 bits (133), Expect = 3e-09
Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 7/88 (7%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
+ R+ + I I L + + ++ DL+ + ++ + K G A++ N
Sbjct: 14 HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKY-CFVDKYK------GTAFVTLLN 66
Query: 217 KADAAKAIQYLNGYGYDHLILSVDWSKS 244
A AI + LSV +
Sbjct: 67 GEQAEAAINAFHQSRLRERELSVQLQPT 94
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 69.5 bits (170), Expect = 5e-15
Identities = 20/125 (16%), Positives = 47/125 (37%)
Query: 120 ASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSE 179
+ G G+ + R +R+ + + ++++ E
Sbjct: 27 KEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQE 86
Query: 180 NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV 239
+++++ +G ++L+ D+ G KG+A + ++ A A + LNG + V
Sbjct: 87 DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
Query: 240 DWSKS 244
DW
Sbjct: 147 DWCFV 151
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 69.5 bits (171), Expect = 6e-15
Identities = 19/78 (24%), Positives = 41/78 (52%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++ L + ++ +L L + GP + + RD G G+A++ F ++ D+ +AI+ LNG
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
Query: 230 YGYDHLILSVDWSKSTNQ 247
+ L V +++ +
Sbjct: 68 ITVRNKRLKVSYARPGGE 85
Score = 59.1 bits (144), Expect = 4e-11
Identities = 16/71 (22%), Positives = 36/71 (50%)
Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
+ T + ++NL +++ L+ + ++G + + RDK G +G A++ + +
Sbjct: 83 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142
Query: 219 DAAKAIQYLNG 229
+A +AI LN
Sbjct: 143 EAQEAISALNN 153
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 67.5 bits (165), Expect = 6e-15
Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 3/84 (3%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ + ++I N+ + L+ L+ Q+G + + + +K
Sbjct: 8 SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSK 64
Query: 218 ADAAKAIQYLNGYGYDHLILSVDW 241
A +A+ LNG+ ++ L V +
Sbjct: 65 DQARQALDKLNGFQLENFTLKVAY 88
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 66.8 bits (164), Expect = 7e-15
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
+ ++ + I L T++ DL L + +G DKT CKG+ ++ F + + A
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 222 KAIQYLNGYGYD 233
KA+ L G
Sbjct: 62 KAVTALKASGVQ 73
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 67.8 bits (166), Expect = 8e-15
Identities = 19/93 (20%), Positives = 44/93 (47%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
+ + +R+ + + ++ + +E D+ D ++G ++L+ D+ G KG+
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67
Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
+ ++ +A A++ LNG +SVDW
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 66.5 bits (163), Expect = 2e-14
Identities = 17/93 (18%), Positives = 41/93 (44%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
+R+ + + ++++ E+++++ +G ++L+ D+ G KG+A
Sbjct: 12 DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71
Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
+ ++ A A + LNG + VDW
Sbjct: 72 LVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 104
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 66.1 bits (162), Expect = 2e-14
Identities = 25/84 (29%), Positives = 40/84 (47%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+ + + + NLS +SE DLE L +GP S+++ D KGFA++ F
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
A KA ++G + +L V S
Sbjct: 63 AVKAYAEVDGQVFQGRMLHVLPST 86
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 66.1 bits (162), Expect = 2e-14
Identities = 19/98 (19%), Positives = 44/98 (44%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
+ + +R+ + + ++ + +E D+ D ++G ++L+ D+ G
Sbjct: 4 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63
Query: 206 CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
KG+ + ++ +A A++ LNG +SVDW
Sbjct: 64 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 66.2 bits (162), Expect = 2e-14
Identities = 23/87 (26%), Positives = 39/87 (44%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ + + + NLS +E DL L +F + G +G A+I F NK
Sbjct: 18 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 77
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
A +A+ +NGY IL +++ K+
Sbjct: 78 EIAWQALHLVNGYKLYGKILVIEFGKN 104
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 65.7 bits (161), Expect = 3e-14
Identities = 26/100 (26%), Positives = 41/100 (41%), Gaps = 11/100 (11%)
Query: 148 GPGGKRVE-GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC 206
G G + GY + + TT + + L NTS L +FG + +
Sbjct: 1 GSSGSSGKIGYG--KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD----- 53
Query: 207 KGFAYIHFKNKADAAKAIQYLNGY--GYDHLILSVDWSKS 244
FAYI +++ A A + G+ G L VD++KS
Sbjct: 54 -SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS 92
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 65.8 bits (161), Expect = 3e-14
Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
+ + + + IS L + ++ +LE++ K G + L ++ G KG AY+ ++N
Sbjct: 9 FRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYEN 67
Query: 217 KADAAKAIQYLNGYGYDHLILSVDWSKS 244
++ A++A+ ++G I+ V S S
Sbjct: 68 ESQASQAVMKMDGMTIKENIIKVAISNS 95
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 66.8 bits (163), Expect = 4e-14
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ + + NL N ++ +LE +GP ++++R+ GFA++ F++
Sbjct: 66 HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDP 120
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSK 243
DAA A++ L+G + V+ S
Sbjct: 121 RDAADAVRELDGRTLCGCRVRVELSN 146
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 65.4 bits (160), Expect = 4e-14
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + NL + +LE +GP ++++R+ GFA++ F++ DA A++ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 228 NGYGYDHLILSVDWSKS 244
+G + V+ S
Sbjct: 58 DGKVICGSRVRVELSTG 74
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 65.5 bits (160), Expect = 5e-14
Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 8/117 (6%)
Query: 128 GGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVK 187
G P + G GG + + +SNL S+ D+++L
Sbjct: 5 TGGQQMGRDPDKWQHDLFDSGCGG-------GEGVETGAKLLVSNLDFGVSDADIQELFA 57
Query: 188 QFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
+FG K + D++ G G A +HF+ +ADA KA++ G D + + S
Sbjct: 58 EFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 113
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 65.0 bits (159), Expect = 6e-14
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G G + RN D T + + L SE L +L Q GP ++ +D+ G +G+
Sbjct: 1 GSSGSSGPISERNQDAT-VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59
Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
++ F ++ DA AI+ ++ + V+ +
Sbjct: 60 GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS 93
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 64.6 bits (158), Expect = 6e-14
Identities = 20/93 (21%), Positives = 39/93 (41%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G G + + + +SNL + + NDL + ++G K+ + +DK KG
Sbjct: 1 GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV 60
Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
A+I F +K A + +N ++ +
Sbjct: 61 AFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 66.1 bits (162), Expect = 9e-14
Identities = 19/78 (24%), Positives = 36/78 (46%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++ L N ++ + L G L RDK G G+ ++++ + DA KAI LNG
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66
Query: 230 YGYDHLILSVDWSKSTNQ 247
+ V +++ ++
Sbjct: 67 LRLQTKTIKVSYARPSSA 84
Score = 61.0 bits (149), Expect = 6e-12
Identities = 18/74 (24%), Positives = 35/74 (47%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
+ + + +S L ++ +LE L Q+G + D+ G+ +G +I F
Sbjct: 80 RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139
Query: 217 KADAAKAIQYLNGY 230
+ +A +AI+ LNG
Sbjct: 140 RIEAEEAIKGLNGQ 153
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 63.9 bits (156), Expect = 1e-13
Identities = 24/110 (21%), Positives = 35/110 (31%), Gaps = 10/110 (9%)
Query: 135 GGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK 194
G I +PP + V+ T I N+ +E DL L + FG
Sbjct: 1 GSQTIGLPPQVNPQA----VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILD 56
Query: 195 MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
+K G +I + AA I L + + L W K
Sbjct: 57 FKHYPEK------GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE 100
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 63.3 bits (155), Expect = 2e-13
Identities = 16/67 (23%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQY 226
+ I L+ N +++ + ++ +G + + ++ + L KG+AY+ F+N +A KA+++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 227 LNGYGYD 233
++G D
Sbjct: 67 MDGGQID 73
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 63.8 bits (156), Expect = 2e-13
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 3/93 (3%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
G R+ + + + LS +T+E L++ F + + + D+ G KGF
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFG 57
Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
++ F ++ DA A + + D +++DW+K
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 63.5 bits (155), Expect = 2e-13
Identities = 14/82 (17%), Positives = 31/82 (37%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
T I++ N+ S +++ D + + G+ G A + F+++ +A
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
A+ LN + + S
Sbjct: 73 AVIDLNDRPIGSRKVKLSGPSS 94
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 64.0 bits (156), Expect = 2e-13
Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 12/103 (11%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFG----------PTSKMYLSRD 200
G + + D +AI + L+ + + +DL D KQ G P +Y D
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY--LD 58
Query: 201 KTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
K G KG A + +++ A A+++ +G + L V ++
Sbjct: 59 KETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 65.4 bits (160), Expect = 3e-13
Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 3/92 (3%)
Query: 159 ARRNDDTTAIR---ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
A+R + + ++ E+ + FGP + +S D KGFA++ ++
Sbjct: 19 AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
A A++ +N + V + Q
Sbjct: 79 VPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110
Score = 60.8 bits (148), Expect = 2e-11
Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 1/95 (1%)
Query: 135 GGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK 194
GG I V G ++ I ++++ + S++D++ + + FG
Sbjct: 96 GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKS 154
Query: 195 MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
L+RD T G KG+ +I ++ + A+ +N
Sbjct: 155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL 189
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 63.1 bits (154), Expect = 4e-13
Identities = 20/84 (23%), Positives = 37/84 (44%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+ + + + +L N +E+ L + + FG + L D G KG+ +I F +
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
A KA++ LNG+ + V
Sbjct: 81 AKKALEQLNGFELAGRPMKVGHVT 104
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 62.7 bits (153), Expect = 4e-13
Identities = 19/75 (25%), Positives = 38/75 (50%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + ++ D + I + N E DL+ L ++FG ++ + +D+ G+ KG A++ +
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 216 NKADAAKAIQYLNGY 230
+ A KA L+
Sbjct: 64 ERESALKAQSALHEQ 78
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 62.7 bits (153), Expect = 4e-13
Identities = 15/87 (17%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ + + + NL + +E ++ L +++G ++++ +DK GF +I + +
Sbjct: 8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETR 61
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
A A L+ L V ++
Sbjct: 62 TLAEIAKVELDNMPLRGKQLRVRFACH 88
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 62.3 bits (152), Expect = 5e-13
Identities = 14/94 (14%), Positives = 32/94 (34%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
G + T I++ N+ S +++ D + + G+ G A
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
+ F+++ +A A+ LN + +
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 63.6 bits (155), Expect = 5e-13
Identities = 19/84 (22%), Positives = 32/84 (38%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
R GG G + + + L+ + L FG + + + D
Sbjct: 44 RHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK 103
Query: 206 CKGFAYIHFKNKADAAKAIQYLNG 229
+GFA++ F+ DAA AI +N
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNE 127
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 62.3 bits (152), Expect = 7e-13
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 155 EGYNARRNDDTTA-IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIH 213
G+ +T + +SNL S+ D+++L +FG K + D++ G G A +H
Sbjct: 18 SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVH 76
Query: 214 FKNKADAAKAIQYLNGYGYD 233
F+ KADA KA++ NG D
Sbjct: 77 FERKADALKAMKQYNGVPLD 96
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 63.8 bits (156), Expect = 7e-13
Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 5/98 (5%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G VEG + + I NL+ N S +L+ + + + + + +T G + F
Sbjct: 1 GSHMVEG--SESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKF 56
Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
Y+ F++ D KA++ L G + ++ K +
Sbjct: 57 GYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDS 93
Score = 58.8 bits (143), Expect = 5e-11
Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 5/86 (5%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
++++ + NLS N +E++L+++ + + +G KG AYI FK++
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSE 146
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSK 243
ADA K ++ G D +S+ ++
Sbjct: 147 ADAEKNLEEKQGAEIDGRSVSLYYTG 172
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 61.6 bits (150), Expect = 1e-12
Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 12/96 (12%)
Query: 155 EGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFG----------PTSKMYLSRDKTNG 204
++ + D I + L N + + D KQ G P +Y D+ G
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY--TDRETG 60
Query: 205 LCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD 240
KG A + F + A AI + +G + + V
Sbjct: 61 KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 61.1 bits (149), Expect = 1e-12
Identities = 20/74 (27%), Positives = 36/74 (48%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ ++ + +E + DL GP + + D G KG+A+I F++ +A A++ LNG
Sbjct: 7 LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66
Query: 230 YGYDHLILSVDWSK 243
Y L +S
Sbjct: 67 YQLGSRFLKCGYSS 80
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 62.6 bits (152), Expect = 1e-12
Identities = 21/131 (16%), Positives = 46/131 (35%), Gaps = 3/131 (2%)
Query: 119 AASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTS 178
+ P P P + Y+ RN A+ + + S T+
Sbjct: 10 GVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNR-RAAVYVGSFSWWTT 68
Query: 179 ENDLEDLVKQFGPT--SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI 236
+ L +++ G ++ + ++ NG KG+A + ++ K ++ L G +
Sbjct: 69 DQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK 128
Query: 237 LSVDWSKSTNQ 247
+ V + N
Sbjct: 129 VDVRPATRQNL 139
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 61.1 bits (149), Expect = 2e-12
Identities = 20/82 (24%), Positives = 39/82 (47%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
++ + N+ +E L+D+ + GP L D+ G KG+ + ++++ A
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
A++ LNG + L VD + S
Sbjct: 66 AMRNLNGREFSGRALRVDNAAS 87
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 60.8 bits (148), Expect = 2e-12
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
+ + NL ++TSE +E P + + + +A++HF N+ DA +
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVE 66
Query: 223 AIQYLNGYGYDHLILSVDWSKSTNQ 247
A++ LNG D + V +K ++
Sbjct: 67 AMKALNGKVLDGSPIEVTLAKPVDK 91
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 61.2 bits (149), Expect = 2e-12
Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 2/96 (2%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGF 209
G + T+ I + N+ ++ ++ +L FG + L + T G +GF
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 210 AYIHFKNKADAAKAIQYL-NGYGYDHLILSVDWSKS 244
++ F K DA KA L + L ++W+ S
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 64.6 bits (158), Expect = 2e-12
Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 6/99 (6%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP-TSKMYLSRDKTNGLCKG 208
G + + T + ++N + ++ ++ DL++ + L + +
Sbjct: 106 GQNEII---VSHLTECT-LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRR 160
Query: 209 FAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
FAYI +K DA ++ LNG + L S +
Sbjct: 161 FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK 199
Score = 61.2 bits (149), Expect = 3e-11
Identities = 20/101 (19%), Positives = 33/101 (32%), Gaps = 4/101 (3%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
G K+ R + TT + + NL + ++N + K GP + ++
Sbjct: 23 AAGLTSKKANEALTRNRELTT-VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KK 79
Query: 206 CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN 246
FA I F A AI + + I V
Sbjct: 80 NFRFARIEFARYDGALAAITKTHKVVGQNEI-IVSHLTECT 119
Score = 57.3 bits (139), Expect = 5e-10
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 168 IRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRD-KTNGLCKGFAYIHFKNKADAAKAIQ 225
I I NLS EN L + + FG K+ + K + A++ F+NK A +A+Q
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272
Query: 226 YLNGYGYDHLILSVDWSKS 244
+N + +SV +
Sbjct: 273 -MNRSLLGNREISVSLADK 290
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 60.7 bits (148), Expect = 2e-12
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
NLS + +E + L Q GP + + T+ + ++ F DAA A+ +NG
Sbjct: 22 NLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRK 79
Query: 232 YDHLILSVDWSKS 244
+ V+W+ +
Sbjct: 80 ILGKEVKVNWATT 92
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 61.2 bits (149), Expect = 2e-12
Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + I L+ T+E L+ + + GP S++ L +D+T +GFA+I F+N ADA
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKN 63
Query: 223 AIQYLNGYGYDHLILSVDWSK 243
A + +NG + V+ +K
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAK 84
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 60.9 bits (148), Expect = 2e-12
Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 8/92 (8%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFG--------PTSKMYLSRDKTNGLCKGFAY 211
+ N D I + L N + + D KQ G + L D+ G KG A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 212 IHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
+ F + A AI + +G + + V ++
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 59.9 bits (146), Expect = 3e-12
Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 1/85 (1%)
Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
+ + + L+ + L FG + + + D +GFA++ F+
Sbjct: 2 SMATTKRV-LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 219 DAAKAIQYLNGYGYDHLILSVDWSK 243
DAA AI +N + V+ +K
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLAK 85
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 60.8 bits (148), Expect = 3e-12
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 2/98 (2%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
R N + +SN+ + DL + QFG + + ++
Sbjct: 10 HSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS- 68
Query: 206 CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
KGF ++ F+N ADA +A + L+G + + V+ +
Sbjct: 69 -KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 60.3 bits (147), Expect = 3e-12
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 1/88 (1%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + + + L+ + L FG + + + D +GFA++ F+
Sbjct: 4 GSSGMATTKRV-LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
DAA AI +N + V+ +K
Sbjct: 63 LAEDAAAAIDNMNESELFGRTIRVNLAK 90
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 60.1 bits (146), Expect = 3e-12
Identities = 17/64 (26%), Positives = 26/64 (40%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I + V + L L + G M D+ G KGF ++ + DA K I+ +G
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
Query: 230 YGYD 233
D
Sbjct: 77 KRLD 80
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 60.3 bits (146), Expect = 4e-12
Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 168 IRISNLSVNTSENDL---EDLVKQFGPTSKMYLSRDKTNGLCK---GFAYIHFKNKADAA 221
+ + LS ++ ++ + +FG K+ ++ + + AY+ + DA
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 222 KAIQYLNGYGYDHLILSVDWS 242
+AIQ +N D L
Sbjct: 78 RAIQCVNNVVVDGRTLKASLG 98
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 60.0 bits (146), Expect = 4e-12
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 2/87 (2%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
A+ D T + + NL E L +L Q GP +K+ + +D+ G K F ++ FK+
Sbjct: 10 PAQEEADRT-VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHP 67
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
+ AI LNG ++V S
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVSGPSS 94
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 59.9 bits (146), Expect = 4e-12
Identities = 19/82 (23%), Positives = 39/82 (47%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
+ ++ + + +L N +E+ L + + FG + L +D G KG+ +I F + A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 222 KAIQYLNGYGYDHLILSVDWSK 243
+A++ LNG+ + V
Sbjct: 62 RALEQLNGFELAGRPMRVGHVT 83
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 60.1 bits (146), Expect = 6e-12
Identities = 16/108 (14%), Positives = 35/108 (32%), Gaps = 8/108 (7%)
Query: 140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR 199
VP GP + R + + + + L FG + +
Sbjct: 14 LVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDP 71
Query: 200 DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
+ A++ ++ A +A+ LNG + + L V+ ++
Sbjct: 72 PR------NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 113
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 60.1 bits (146), Expect = 6e-12
Identities = 24/117 (20%), Positives = 37/117 (31%)
Query: 127 SGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLV 186
+G P P + + + I +L ++ DL
Sbjct: 2 AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61
Query: 187 KQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
FG + DK L K F ++ F N A AI+ +NG+ L V K
Sbjct: 62 LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 59.6 bits (145), Expect = 6e-12
Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
G N+ + ++ + +SNLS + +E L+++ ++ K+ NG KG+A
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI-KVP---QNQNGKSKGYA 56
Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
+I F + DA +A+ N + + ++
Sbjct: 57 FIEFASFEDAKEALNSCNKREIEGRAIRLELQG 89
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 60.5 bits (147), Expect = 6e-12
Identities = 20/112 (17%), Positives = 45/112 (40%), Gaps = 1/112 (0%)
Query: 133 APGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPT 192
P G + ++ N + + ++ + E L L +++GP
Sbjct: 11 DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLM-VNYIPTTVDEVQLRQLFERYGPI 69
Query: 193 SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
+ + D+ +G+ ++ F++ + A +AI LNG+ + L V + S
Sbjct: 70 ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 59.2 bits (144), Expect = 7e-12
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+++ + NLS N +E++L+++ + + +G KG AYI FK++
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSE 63
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
ADA K ++ G D +S+ ++
Sbjct: 64 ADAEKNLEEKQGAEIDGRSVSLYYTGE 90
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 61.6 bits (150), Expect = 7e-12
Identities = 22/88 (25%), Positives = 38/88 (43%)
Query: 142 PPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDK 201
P + E P + D + I L +++ +++L+ FGP L +D
Sbjct: 91 LPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150
Query: 202 TNGLCKGFAYIHFKNKADAAKAIQYLNG 229
GL KG+A+ + + +AI LNG
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Score = 53.5 bits (129), Expect = 5e-09
Identities = 10/79 (12%), Positives = 26/79 (32%), Gaps = 6/79 (7%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYIHFKNKADAAKAI 224
+ N+ +E + D + + K FA++ F++ + +A+
Sbjct: 9 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68
Query: 225 QYLNGYGYDHLILSVDWSK 243
+G + L +
Sbjct: 69 A-FDGIIFQGQSLKIRRPH 86
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 58.7 bits (143), Expect = 8e-12
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 2/80 (2%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPT--SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I NL+ T++ DL + V G ++ ++ NG KGFA + ++A + K + L
Sbjct: 6 IGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLL 65
Query: 228 NGYGYDHLILSVDWSKSTNQ 247
V S
Sbjct: 66 PKRELHGQNPVVTPSNKLEH 85
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 59.2 bits (144), Expect = 9e-12
Identities = 22/82 (26%), Positives = 42/82 (51%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + + LS +T+E LE + ++G S++ + +D+ +GF ++ F+N DA
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
A+ +NG D + VD +
Sbjct: 70 AMMAMNGKSVDGRQIRVDQAGK 91
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 58.8 bits (143), Expect = 9e-12
Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 8/89 (8%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + +T + + N+S + +L +++GP + + + +A++H +
Sbjct: 1 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHME 52
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSKS 244
DA +AI+ L+ + + V S S
Sbjct: 53 RAEDAVEAIRGLDNTEFQGKRMHVQLSTS 81
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 59.3 bits (144), Expect = 1e-11
Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 7/101 (6%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G G + + T + I NLS ++ E L ++++QFG + + KG
Sbjct: 1 GSSGSSGLPSDVTEGKT-VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGC 59
Query: 210 AYIHFKNKADAAKAIQYLN------GYGYDHLILSVDWSKS 244
A+ F + A K + + G D L VD + +
Sbjct: 60 AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 61.1 bits (149), Expect = 1e-11
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
GP G A + + + +L + +E L + GP + + RD
Sbjct: 1 GPLGSMNPS--APSYPMAS-LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSL 57
Query: 208 GFAYIHFKNKADAAKAIQYLNGY 230
G+AY++F+ ADA +A+ +N
Sbjct: 58 GYAYVNFQQPADAERALDTMNFD 80
Score = 48.4 bits (116), Expect = 3e-07
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 2/90 (2%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ R I I NL + L D FG + D KG+ ++HF+ +
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQ 153
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
A +AI+ +NG + + V KS +
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFVGRFKSRKE 183
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 58.8 bits (143), Expect = 1e-11
Identities = 22/101 (21%), Positives = 45/101 (44%), Gaps = 10/101 (9%)
Query: 146 REGPGGKRVEGYNARRNDD--TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN 203
R + R+ + T + + ++ E++L ++ FGP ++ +
Sbjct: 10 HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----- 64
Query: 204 GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
GFA++ F+ AAKAI+ ++G + + L V +SK
Sbjct: 65 ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL 102
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 58.5 bits (142), Expect = 1e-11
Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+ ++ ++ + FG ++ + +K G++++ F AA AI
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIV 79
Query: 226 YLNGYGYDHLILSVDWSKSTN 246
+NG + ++ W K +
Sbjct: 80 SVNGTTIEGHVVKCYWGKESP 100
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 61.6 bits (150), Expect = 2e-11
Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 151 GKRVEGYNARRN--DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKG 208
G ++ R A+ + NLS S LE QFGP K + D G G
Sbjct: 80 GTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR-GRATG 138
Query: 209 FAYIHFKNKADAAKAIQYLNG 229
++ F K A KA++
Sbjct: 139 KGFVEFAAKPPARKALERCGD 159
Score = 60.9 bits (148), Expect = 3e-11
Identities = 21/111 (18%), Positives = 44/111 (39%), Gaps = 16/111 (14%)
Query: 136 GPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM 195
G I + L+ G + NL + +E D + L +++G S++
Sbjct: 3 GFTIDIKSFLKPG---------EKTYTQRCRLF-VGNLPTDITEEDFKRLFERYGEPSEV 52
Query: 196 YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN 246
+++RD+ GF +I +++ A A L+G L + ++
Sbjct: 53 FINRDR------GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA 97
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 58.0 bits (141), Expect = 2e-11
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NLS + +DL L L L G+A++ + ++ A +AI+ L+G
Sbjct: 13 IGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSG 66
Query: 230 YGYDH-LILSVDWSKSTNQ 247
H I+ VD+S S
Sbjct: 67 KVELHGKIMEVDYSVSKKL 85
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 59.5 bits (145), Expect = 2e-11
Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
NL +E+ L+ + GP + + + DK +A++ + DA A+Q LNG
Sbjct: 7 NLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQ 65
Query: 232 YDHLILSVDWSKSTNQ 247
++ I+ ++W+ + Q
Sbjct: 66 IENNIVKINWAFQSQQ 81
Score = 54.1 bits (131), Expect = 2e-09
Identities = 17/72 (23%), Positives = 34/72 (47%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+DDT + + +L+VN + L + K F ++ D G +G+ ++ F ++
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 218 ADAAKAIQYLNG 229
DA A+ + G
Sbjct: 140 DDAQNAMDSMQG 151
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 57.5 bits (140), Expect = 2e-11
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
D +I + N+ + +LE G +++ + DK +G KGFAYI F +K +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 224 IQYLNGY 230
+ L+
Sbjct: 65 LA-LDES 70
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 58.2 bits (141), Expect = 2e-11
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NL + ++ D+ ++GP ++ R +G AY+ +++ DA A+ +L+G
Sbjct: 13 IRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69
Query: 230 YGYDHLILSVDWSKS 244
+ + L V + +
Sbjct: 70 FNVSNRYLVVLYYNA 84
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 59.5 bits (145), Expect = 3e-11
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I +S +END+ + FG + + R GL +G A++ F +A A AI+ ++
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQ 158
Score = 59.2 bits (144), Expect = 3e-11
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL--CKGFAYIHFKNKADAA 221
D + + + SE DL +L +Q+G ++ + RD++ KG ++ F + A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 222 KAIQYLNG 229
+A L+
Sbjct: 62 EAQNALHN 69
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 59.6 bits (145), Expect = 3e-11
Identities = 18/73 (24%), Positives = 35/73 (47%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
++ + + I L +++ +++L+ FGP L +D GL KG+A+ + +
Sbjct: 86 HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145
Query: 217 KADAAKAIQYLNG 229
+AI LNG
Sbjct: 146 INVTDQAIAGLNG 158
Score = 51.8 bits (125), Expect = 2e-08
Identities = 10/83 (12%), Positives = 26/83 (31%), Gaps = 6/83 (7%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYIHFKNKADAAKAI 224
+ N+ +E + D + + K FA++ F++ + +A+
Sbjct: 9 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68
Query: 225 QYLNGYGYDHLILSVDWSKSTNQ 247
+G + L +
Sbjct: 69 A-FDGIIFQGQSLKIRRPHDYQP 90
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 57.7 bits (140), Expect = 3e-11
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 2/87 (2%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
N+ + +SN+ + DL + QFG + + ++ KGF ++ F+N
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 65
Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
ADA +A + L+G + + V+ + +
Sbjct: 66 ADADRAREKLHGTVVEGRKIEVNNATA 92
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 58.2 bits (141), Expect = 3e-11
Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
++ D ++ + N+ ++ DLE G +++ + DK +G KG+AYI F +
Sbjct: 31 KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS 90
Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
A+ ++ + + V ++
Sbjct: 91 VDAAVA-MDETVFRGRTIKVLPKRT 114
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 57.5 bits (139), Expect = 3e-11
Identities = 17/97 (17%), Positives = 34/97 (35%), Gaps = 5/97 (5%)
Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
G + + NL + +DL+ +++ G R G +
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQGP-R 56
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
A++H+ + A A +A+ L G L V ++
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 57.2 bits (139), Expect = 4e-11
Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+ + I NL +E ++ L +Q+G + + K + ++H ++K
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54
Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
A AI+ L+ Y + ++V+ SK+
Sbjct: 55 AEDAIRNLHHYKLHGVNINVEASKN 79
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 57.4 bits (139), Expect = 4e-11
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 2/88 (2%)
Query: 158 NARRNDDTTAIRI--SNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
+ ++ D + + +LS + D++ FG S + +D G KG+ ++ F
Sbjct: 6 SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFF 65
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
NK DA AIQ + G + +W+
Sbjct: 66 NKWDAENAIQQMGGQWLGGRQIRTNWAT 93
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 56.8 bits (138), Expect = 4e-11
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+ +T I + N+S + +L L ++ G + + K +A++H + +AD
Sbjct: 4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEAD 55
Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
A AI LNG ++V+ S
Sbjct: 56 AKAAIAQLNGKEVKGKRINVELSTK 80
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 57.3 bits (139), Expect = 5e-11
Identities = 24/99 (24%), Positives = 37/99 (37%), Gaps = 9/99 (9%)
Query: 132 GAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP 191
G+ G + G + EG N + I +L + DL + FG
Sbjct: 1 GSSGSSGLTQQSIGAAGSQKEGPEGAN---------LFIYHLPQEFGDQDLLQMFMPFGN 51
Query: 192 TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY 230
+ DK L K F ++ + N A AIQ +NG+
Sbjct: 52 VVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF 90
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 57.6 bits (139), Expect = 5e-11
Identities = 14/108 (12%), Positives = 31/108 (28%), Gaps = 6/108 (5%)
Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
M +S G + + G G + + + +R+ L
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSAD------SANDGFVRLRGLPFGC 54
Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
++ ++ G G A++ F ++ A KA+
Sbjct: 55 TKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 56.9 bits (138), Expect = 5e-11
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPT-SKMYLSRDKTNGLCKGFAYIHFKN 216
++ + ++ + +L EN + G T + + R++ G+ G+ ++ F +
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61
Query: 217 KADAAKAIQYLNG 229
A A K + +NG
Sbjct: 62 LATAEKCLHKING 74
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 56.9 bits (138), Expect = 7e-11
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ R + + L+ SE D+ L + FG + + R +G KG A++ F +
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSH 66
Query: 218 ADAAKAIQYLNG 229
+A AI L+G
Sbjct: 67 TEAQAAIHALHG 78
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 55.9 bits (135), Expect = 1e-10
Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 7/83 (8%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
+ ++ I + NL +++ ++ DL+K + + K A++ N A
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQ 54
Query: 222 KAIQYLNGYGYDHLILSVDWSKS 244
AIQ + Y + L V +
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPT 77
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 57.8 bits (139), Expect = 2e-10
Identities = 14/126 (11%), Positives = 34/126 (26%)
Query: 105 NKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDD 164
N ++ G G + R + R
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ + N + +E + ++ + G + + + +K+DA + +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182
Query: 225 QYLNGY 230
+LN Y
Sbjct: 183 GFLNHY 188
Score = 50.5 bits (120), Expect = 6e-08
Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 6/84 (7%)
Query: 164 DTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D+ + + L + + + ++ +G K+ + K G A + + +
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57
Query: 223 AIQYLNGYGYDHLILSVDWSKSTN 246
AI +LN ++V SK
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPA 81
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 55.3 bits (134), Expect = 2e-10
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL + + L+D + G + + NG KG + F++ A +A + +NG
Sbjct: 13 VRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 230 Y 230
Sbjct: 71 M 71
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 55.4 bits (134), Expect = 2e-10
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
NL+ +E LE QFG ++ +D +A+IHF + A KA++ +NG
Sbjct: 18 NLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNGKD 69
Query: 232 YDHLILSVDWSKSTNQ 247
+ + + ++K +Q
Sbjct: 70 LEGENIEIVFAKPPDQ 85
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 54.9 bits (133), Expect = 2e-10
Identities = 19/72 (26%), Positives = 31/72 (43%)
Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
+LS + + FG S + +D G KG+ ++ F NK DA AIQ + G
Sbjct: 13 DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72
Query: 232 YDHLILSVDWSK 243
+ +W+
Sbjct: 73 LGGRQIRTNWAT 84
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 54.8 bits (133), Expect = 2e-10
Identities = 17/83 (20%), Positives = 37/83 (44%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
T + + +L+VN + L + K F ++ D G +G+ ++ F ++ DA A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 225 QYLNGYGYDHLILSVDWSKSTNQ 247
+ G + L ++W+
Sbjct: 61 DSMQGQDLNGRPLRINWAAKLEH 83
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 55.0 bits (133), Expect = 2e-10
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC---KGFAYIHFKNKADA 220
++ + I NL+ +T+E L+ + + G +S+ K GF ++ +K A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 221 AKAIQYLNGYGYDHLILSVDWSK 243
KA++ L G+ D L V S+
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISE 86
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 55.0 bits (133), Expect = 3e-10
Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 9/88 (10%)
Query: 160 RRNDDTTAIRISNLSVNT-SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
R + + + I NL + S+ DL + +G ++ + F +I F N
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQ 68
Query: 219 DAAKAIQYLNGYGYDHLILSVDWSKSTN 246
AI+ + L ++ S S
Sbjct: 69 SVRDAIEXESQEMNFGKKLILEVSSSNA 96
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 56.0 bits (135), Expect = 3e-10
Identities = 17/106 (16%), Positives = 34/106 (32%), Gaps = 3/106 (2%)
Query: 120 ASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSE 179
SS G P G + ++ G + + + + L +E
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHC-VHMRGLPYKATE 60
Query: 180 NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
ND+ + P +++ +G G A + F +A A+
Sbjct: 61 NDIYNFFSPLNPVR-VHIEIGP-DGRVTGEADVEFATHEEAVAAMS 104
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 55.0 bits (133), Expect = 4e-10
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
++ D T + ISNL ++ E +LE+++K FG + RD + G +G + ++
Sbjct: 17 MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGVGFARMES 75
Query: 217 KADAAKAIQYLNGY 230
I + NG
Sbjct: 76 TEKCEAVIGHFNGK 89
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 54.4 bits (131), Expect = 7e-10
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 4/82 (4%)
Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
G G EG N I+N+ + ++ D+ ++ NG
Sbjct: 1 GSSGSSGEG---DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGL 57
Query: 208 GFAYIHFKNKADAAKAIQYLNG 229
G A + FKN+ DA K+ + L+
Sbjct: 58 GQALVQFKNEDDARKSER-LHR 78
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 54.2 bits (131), Expect = 7e-10
Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 1/86 (1%)
Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
+ D + L+ DLED G + + D+ + KG AY+ F
Sbjct: 19 SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
Query: 219 DAAKAIQYLNGYGYDHLILSVDWSKS 244
AI L G + + V S++
Sbjct: 79 SVPLAIG-LTGQRLLGVPIIVQASQA 103
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 53.9 bits (130), Expect = 7e-10
Identities = 22/119 (18%), Positives = 42/119 (35%), Gaps = 23/119 (19%)
Query: 127 SGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVN-TSENDLEDL 185
SG G + A V RV + I NL+ ++D+E +
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRV--F------------IGNLNTALVKKSDVETI 48
Query: 186 VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
++G + + KG+A++ + N+ A A+ NG L ++ +
Sbjct: 49 FSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 54.2 bits (131), Expect = 8e-10
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NL + L D FG + D+ KG+ ++HF+ + A +AI+ +NG
Sbjct: 10 IKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNG 67
Query: 230 YGYDHLILSVDWSKS 244
+ + V KS
Sbjct: 68 MLLNDRKVFVGRFKS 82
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 56.2 bits (135), Expect = 8e-10
Identities = 27/137 (19%), Positives = 47/137 (34%), Gaps = 6/137 (4%)
Query: 111 TVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARR-NDDTTAIR 169
+ G I S + P + K+ N + + +
Sbjct: 96 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 155
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+SN+ + SE DL+ L G K + K + A I + +A +A+ L+
Sbjct: 156 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHN 211
Query: 230 YGYDH-LILSVDWSKST 245
+ L V +SKST
Sbjct: 212 HDLGENHHLRVSFSKST 228
Score = 49.2 bits (117), Expect = 2e-07
Identities = 21/121 (17%), Positives = 38/121 (31%), Gaps = 21/121 (17%)
Query: 127 SGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV-NTSENDLEDL 185
S G P L + + +SNL+ + L L
Sbjct: 11 SSGLVPRGSHMGRIAIPGLAGAGN---------------SVLLVSNLNPERVTPQSLFIL 55
Query: 186 VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST 245
+G ++ + +K K A + + A A+ +LNG+ + + SK
Sbjct: 56 FGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ 110
Query: 246 N 246
N
Sbjct: 111 N 111
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 53.9 bits (130), Expect = 9e-10
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++NL L+++ G + + DK +G +G + F+ +A +AI NG
Sbjct: 20 VANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNG 78
Query: 230 Y 230
Sbjct: 79 Q 79
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 55.7 bits (134), Expect = 1e-09
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 5/88 (5%)
Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
+ + +SN+ + SE DL+ L G K + K + A I +
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVE 169
Query: 219 DAAKAIQYLNGYGYDH-LILSVDWSKST 245
+A +A+ L+ + L V +SKST
Sbjct: 170 EAVQALIDLHNHDLGENHHLRVSFSKST 197
Score = 49.5 bits (118), Expect = 1e-07
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 170 ISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
+SNL+ + L L +G ++ + +K K A + + A A+ +LN
Sbjct: 8 VSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLN 62
Query: 229 GYGYDHLILSVDWSKSTNQ 247
G+ + + SK N
Sbjct: 63 GHKLHGKPIRITLSKHQNV 81
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 57.2 bits (137), Expect = 1e-09
Identities = 16/75 (21%), Positives = 42/75 (56%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++ ++ +T+E+ L + +GP ++++ K +G +G+A+I ++++ D A ++ +G
Sbjct: 107 VARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG 166
Query: 230 YGYDHLILSVDWSKS 244
D + VD +
Sbjct: 167 KKIDGRRVLVDVERG 181
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 53.4 bits (129), Expect = 1e-09
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGP-TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
I NL E L D FG + RD G KG+A+I+F + + AI+ +N
Sbjct: 10 IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69
Query: 229 G 229
G
Sbjct: 70 G 70
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 52.7 bits (127), Expect = 1e-09
Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
T + + L +E DL + QFG + + + + A+I F + A A
Sbjct: 12 ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAA 65
Query: 225 QY-LNGYGYDHLILSVDWSK 243
+ N + L+V W +
Sbjct: 66 EKSFNKLIVNGRRLNVKWGR 85
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 52.8 bits (127), Expect = 2e-09
Identities = 12/75 (16%), Positives = 25/75 (33%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
G N+ + +R+ L S+ ++ G G A
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 211 YIHFKNKADAAKAIQ 225
++ F ++ A KA++
Sbjct: 61 FVQFASQEIAEKALK 75
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 53.3 bits (128), Expect = 2e-09
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 7/81 (8%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
GG Y + +S L + S DL+D +++ G + RD G
Sbjct: 1 GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GT 53
Query: 210 AYIHFKNKADAAKAIQYLNGY 230
+ F K D A++ L+
Sbjct: 54 GVVEFVRKEDMTYAVRKLDNT 74
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 52.5 bits (126), Expect = 2e-09
Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + L + E DL + +++FG + + K A + F+N A + + +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71
Query: 228 NGYGY--DHLILSVDWSKS 244
++S S
Sbjct: 72 ADVPVYIAGQQAFFNYSTS 90
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 52.5 bits (126), Expect = 2e-09
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 8/77 (10%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I L E DL + +++FGP S + + K A + F++ A A+ Y
Sbjct: 26 IRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAAD 79
Query: 230 YGY--DHLILSVDWSKS 244
V++S S
Sbjct: 80 NQIYIAGHPAFVNYSTS 96
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 52.2 bits (126), Expect = 3e-09
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 1/63 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ NL + +E +++ + ++ KGF Y F++ A+ L
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 80
Query: 228 NGY 230
N
Sbjct: 81 NEE 83
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 51.8 bits (125), Expect = 3e-09
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 1/76 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I + NL + + +++L QFG + L D+ KGF ++ + ++AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 228 NGYGYDHLILSVDWSK 243
+ + + V +
Sbjct: 63 DNTDFMGRTIRVTEAN 78
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 52.5 bits (126), Expect = 3e-09
Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G G R + + +S L + S DL+D +++ G + RD G
Sbjct: 1 GSSGSSGGPPSRRSENR-VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GT 52
Query: 210 AYIHFKNKADAAKAIQYLNGY 230
+ F K D A++ L+
Sbjct: 53 GVVEFVRKEDMTYAVRKLDNT 73
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 52.5 bits (126), Expect = 3e-09
Identities = 15/97 (15%), Positives = 31/97 (31%), Gaps = 4/97 (4%)
Query: 143 PSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKT 202
R + I + NL S DL+DL ++ +
Sbjct: 7 HHHHSSGLVPRGSHMSKLPAKRYR-ITMKNLPEGCSWQDLKDLARENSLETTF---SSVN 62
Query: 203 NGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV 239
G + F ++ +A++ LN + +++V
Sbjct: 63 TRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 51.8 bits (125), Expect = 3e-09
Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 9/76 (11%)
Query: 170 ISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
I NL + N S+ DL + +G ++ + F +I F N AI+ +
Sbjct: 15 IGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIECES 66
Query: 229 GYGYDHLILSVDWSKS 244
L ++ S S
Sbjct: 67 QEMNFGKKLILEVSSS 82
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 51.7 bits (124), Expect = 4e-09
Identities = 11/82 (13%), Positives = 31/82 (37%), Gaps = 4/82 (4%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPT-SKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQYL 227
I + ++ + + + + + + +GFA++ +++ AA A + L
Sbjct: 13 IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL 72
Query: 228 NGYGY--DHLILSVDWSKSTNQ 247
++VDW++
Sbjct: 73 MPGRIQLWGHQIAVDWAEPEID 94
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 52.2 bits (125), Expect = 5e-09
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 7/79 (8%)
Query: 170 ISNLSVNTSENDL----EDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I+N++ + L L G + + + G AYI F + A ++
Sbjct: 34 ITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVE 90
Query: 226 YLNGYGYDHLILSVDWSKS 244
GY + L + +S++
Sbjct: 91 AFQGYPFQGNPLVITFSET 109
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 51.5 bits (124), Expect = 5e-09
Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NL+ N S +L+ + + + + + +T G + F Y+ F++ D KA++ L G
Sbjct: 22 IGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYVDFESAEDLEKALE-LTG 79
Query: 230 YGYDHLILSVDWSKS 244
+ ++ K
Sbjct: 80 LKVFGNEIKLEKPKG 94
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 51.8 bits (124), Expect = 7e-09
Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 1/80 (1%)
Query: 147 EGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC 206
+ P G++ + + + L + D K+ NG
Sbjct: 8 KSPSGQKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA 66
Query: 207 KGFAYIHFKNKADAAKAIQY 226
G ++ F+N+AD A+
Sbjct: 67 TGEGFVEFRNEADYKAALCR 86
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 51.1 bits (123), Expect = 8e-09
Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 1/80 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ NL + +E +++ + ++ KGF Y F++ A+ L
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 76
Query: 228 NGYGYDHLILSVDWSKSTNQ 247
N + + VD +
Sbjct: 77 NEESLGNKRIRVDVADQAQD 96
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 50.5 bits (121), Expect = 1e-08
Identities = 9/69 (13%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
+ + + ++ I + + +D+++ ++ G + + R + KG ++ F +
Sbjct: 3 WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDS 61
Query: 217 KADAAKAIQ 225
A K ++
Sbjct: 62 IESAKKFVE 70
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 50.5 bits (121), Expect = 1e-08
Identities = 12/55 (21%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD 233
+N + + +FG + + + +G KG+ ++ + + A A A++ +GY D
Sbjct: 35 KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 50.0 bits (120), Expect = 2e-08
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ NL NT + D++ + K S + L RDK KGF Y+ F +A+
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLSIRS-VRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-Y 75
Query: 228 NGYGYDHLILSVDWSK 243
+G L VD ++
Sbjct: 76 DGALLGDRSLRVDIAE 91
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 51.0 bits (122), Expect = 2e-08
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTS-----KMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ NL+ + E DL+ + ++ S M+ R G KG A+I N+ AAKA+
Sbjct: 50 VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
Query: 225 QYLNGYGYDHLILSVDWSKS 244
+ NGY + V +++S
Sbjct: 110 KEANGYVLFGKPMVVQFARS 129
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 49.3 bits (118), Expect = 2e-08
Identities = 12/55 (21%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD 233
+N + + +FG + + + +G KG+ ++ + + A A A++ +GY D
Sbjct: 21 KNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 49.2 bits (118), Expect = 3e-08
Identities = 12/56 (21%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+ + V E ++ ++G ++ + D+T G+ KG+ ++ F N D K ++
Sbjct: 14 VGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 49.5 bits (119), Expect = 3e-08
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL + L FG + + + G KGF ++ F + +A KA+ +NG
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 230 YGYDHLILSVDWSK 243
L V ++
Sbjct: 78 RIVATKPLYVALAQ 91
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 49.3 bits (118), Expect = 3e-08
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 3/76 (3%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G G + + + + L +END+ + P +++ +G G
Sbjct: 1 GSSGSSGSSFQSTTGHC-VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGP-DGRVTGE 57
Query: 210 AYIHFKNKADAAKAIQ 225
A + F DA A+
Sbjct: 58 ADVEFATHEDAVAAMA 73
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 49.5 bits (118), Expect = 3e-08
Identities = 10/66 (15%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ + L S N L ++++ G + + +K +++ ++ ++ +A
Sbjct: 27 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAY 80
Query: 225 QYLNGY 230
LNG
Sbjct: 81 VTLNGK 86
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 48.8 bits (117), Expect = 4e-08
Identities = 16/79 (20%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 170 ISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I+NL+ +++L+ + +FG + +SR +G A++ FK + A A++
Sbjct: 13 INNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNALR 69
Query: 226 YLNGYGYDHLILSVDWSKS 244
+ G+ + + + ++K+
Sbjct: 70 SMQGFPFYDKPMRIQYAKT 88
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 48.8 bits (117), Expect = 4e-08
Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 8/82 (9%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+ + + + L FG + + + A++ ++ A +A+
Sbjct: 16 NTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVA 67
Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
LNG + + L V+ ++
Sbjct: 68 ELNGTQVESVQLKVNIARKQPM 89
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 49.4 bits (118), Expect = 4e-08
Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
G G N D + + + + END+ D + ++L +D G G
Sbjct: 1 GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDA-VHLLKDH-VGRNNGN 58
Query: 210 AYIHFKNKADAAKAIQ 225
+ F + D +A++
Sbjct: 59 GLVKFLSPQDTFEALK 74
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 48.5 bits (116), Expect = 5e-08
Identities = 10/70 (14%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + +++ N +E ++ + + P + + + R+ +G G+ ++ F
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNA-HGNKTGYIFVDFS 58
Query: 216 NKADAAKAIQ 225
N+ + +A++
Sbjct: 59 NEEEVKQALK 68
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 49.1 bits (117), Expect = 5e-08
Identities = 13/84 (15%), Positives = 27/84 (32%), Gaps = 3/84 (3%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS---RDKT 202
GG E ++ +R+ L + ++ Q P +
Sbjct: 4 GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63
Query: 203 NGLCKGFAYIHFKNKADAAKAIQY 226
+G G A++ F + A A++
Sbjct: 64 DGRPTGDAFVLFACEEYAQNALRK 87
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 51.4 bits (122), Expect = 6e-08
Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 170 ISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I+NL+ +++L+ + QFG + +SR +G A++ FK + A A++
Sbjct: 14 INNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKEVSSATNALR 70
Query: 226 YLNGYGYDHLILSVDWSKS 244
+ G+ + + + ++K+
Sbjct: 71 SMQGFPFYDKPMRIQYAKT 89
Score = 48.3 bits (114), Expect = 6e-07
Identities = 28/199 (14%), Positives = 50/199 (25%), Gaps = 18/199 (9%)
Query: 45 NTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADA 104
+ + IQ+ ++ + + + + T
Sbjct: 74 GFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPV 133
Query: 105 NKKPFNTVPGTNIMAASSDDKKSGG---PGGAPGGPAIYVPPSLREGPGGKRVEGYNARR 161
VPG M + P P G + + P G
Sbjct: 134 VGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPG 193
Query: 162 NDDTTAIR----------ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAY 211
++NL T+E L L QF ++ L + A+
Sbjct: 194 QMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAF 248
Query: 212 IHFKNKADAAKAIQYLNGY 230
+ F N+ A A L G+
Sbjct: 249 VEFDNEVQAGAARDALQGF 267
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 48.5 bits (115), Expect = 1e-07
Identities = 14/115 (12%), Positives = 31/115 (26%), Gaps = 6/115 (5%)
Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
M +S G S+ G R + +++ L +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSH----MASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSC 56
Query: 178 SENDLEDLVKQFGPTSKMYLSR--DKTNGLCKGFAYIHFKNKADAAKAIQYLNGY 230
S D+++ + G G A++ ++ D A++
Sbjct: 57 SVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRES 111
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 47.2 bits (112), Expect = 2e-07
Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 8/77 (10%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I L ++ +E ++ L FG + + + + K A+I + A + Y
Sbjct: 21 IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS 74
Query: 230 YGYDHL--ILSVDWSKS 244
+ + +S
Sbjct: 75 VTPVLRGQPIYIQFSNH 91
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 47.9 bits (113), Expect = 5e-07
Identities = 20/160 (12%), Positives = 51/160 (31%), Gaps = 14/160 (8%)
Query: 69 EENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSG 128
+ NL + KF+ + + P + F + N++ + K+
Sbjct: 26 DFNLPRDKFLKEQIKLDEGW---VPLEIMIKF-----NRLNRLTTDFNVIVEALSKSKAE 77
Query: 129 GPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQ 188
+ I PS + + ++ I + + +D+++ ++
Sbjct: 78 LMEISEDKTKIRRSPSKP-----LPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLED 132
Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
G + + R KG ++ F + A K ++
Sbjct: 133 KGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVETPG 171
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 46.8 bits (112), Expect = 7e-07
Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 7/86 (8%)
Query: 151 GKRVEGYNA---RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
GK ++ A D T I + + + + E+ Q+G L DK G +
Sbjct: 70 GKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSR 129
Query: 208 GFAYIHFKNKADAAKAI----QYLNG 229
GF ++ + + +
Sbjct: 130 GFGFVTYDSADAVDRVCQNKFIDFKD 155
Score = 46.4 bits (111), Expect = 1e-06
Identities = 11/56 (19%), Positives = 31/56 (55%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I L+ +T+E++L + ++G + + + +D G +GF ++ F+ + + ++
Sbjct: 8 IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 45.7 bits (108), Expect = 8e-07
Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 8/77 (10%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I L ++ +E ++ L FG + + + + K A+I + A + Y
Sbjct: 36 IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS 89
Query: 230 YGYDHL--ILSVDWSKS 244
+ + +S
Sbjct: 90 VTPVLRGQPIYIQFSNH 106
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 45.2 bits (107), Expect = 1e-06
Identities = 11/77 (14%), Positives = 26/77 (33%), Gaps = 8/77 (10%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I L +E ++ L FG + + + + K A++ + A + Y +
Sbjct: 20 IRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSA 73
Query: 230 YGYDHL--ILSVDWSKS 244
+ + +S
Sbjct: 74 VTPHLRNQPIYIQYSNH 90
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 46.9 bits (112), Expect = 1e-06
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 4/81 (4%)
Query: 153 RVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYI 212
R + + I + + +T E+ L D +Q+G + + D+ +G +GFA++
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 213 HFKNKADAAKAI----QYLNG 229
F + K + +NG
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNG 172
Score = 44.2 bits (105), Expect = 1e-05
Identities = 12/56 (21%), Positives = 24/56 (42%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I LS T++ L +Q+G + + RD +GF ++ + + A+
Sbjct: 18 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 45.3 bits (107), Expect = 1e-06
Identities = 8/76 (10%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQF---GPTSKMYLSRDKTNGLCKGFAYIHF 214
+ +++ L + S D+++ + + ++ + G G A++
Sbjct: 10 LGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVEL 68
Query: 215 KNKADAAKAIQYLNGY 230
+++ D A++
Sbjct: 69 ESEDDVKLALKKDRES 84
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 44.5 bits (106), Expect = 2e-06
Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + + I + + N E +L + K+FG +++ + D +GF +I F+
Sbjct: 1 GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
Query: 216 NKADAAKAI----QYLNG 229
++ +A+ + G
Sbjct: 61 DEQSVDQAVNMHFHDIMG 78
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 43.7 bits (103), Expect = 3e-06
Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR--DKTNGLCKGFAYIHFKNKADA 220
DD IR L + + D+ + + +G +G A I +++ D
Sbjct: 9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDV 68
Query: 221 AKAIQ 225
KA++
Sbjct: 69 QKALE 73
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 43.1 bits (102), Expect = 7e-06
Identities = 14/73 (19%), Positives = 35/73 (47%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
+ ++++ T I + L +T++ L + FG + + D+ G +G+ ++
Sbjct: 8 MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 67
Query: 216 NKADAAKAIQYLN 228
++A A +A + N
Sbjct: 68 DRAAAERACKDPN 80
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 41.7 bits (99), Expect = 9e-06
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 4/64 (6%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI----Q 225
+ LS +T E + + FG + L D +GF +I FK + K +
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 63
Query: 226 YLNG 229
+
Sbjct: 64 NVGL 67
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 41.9 bits (99), Expect = 1e-05
Identities = 9/56 (16%), Positives = 18/56 (32%), Gaps = 5/56 (8%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+S L + FGP + + + +DK FA + + +
Sbjct: 13 VSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLS 63
>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 = 40.9 bits (96), Expect = 2e-05
Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 12/78 (15%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYI 212
+ARR + + N+ +E + D + + K FA++
Sbjct: 5 SARR------LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 58
Query: 213 HFKNKADAAKAIQYLNGY 230
F++ + +A+ +G
Sbjct: 59 EFRSVDETTQAMA-FDGI 75
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 41.4 bits (97), Expect = 3e-05
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS 238
E ++ +++G +M + D G Y+ F+ + DA KA+ LN ++ +
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 239 VDWS 242
+ S
Sbjct: 100 AELS 103
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 42.4 bits (99), Expect = 3e-05
Identities = 20/110 (18%), Positives = 39/110 (35%), Gaps = 11/110 (10%)
Query: 139 IYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
+ + S G + G + I + NL + + L + +FG K+
Sbjct: 25 LALAASAAAVDAGMAMAGQSP-----VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 79
Query: 199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVDWSKSTN 246
+ A + + + A A L+G + L +D+SK T+
Sbjct: 80 TKNN----QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 125
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 41.1 bits (97), Expect = 3e-05
Identities = 15/75 (20%), Positives = 29/75 (38%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
+ + + I LS T++ L + QFG + + RD +GF
Sbjct: 11 SSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 211 YIHFKNKADAAKAIQ 225
++ F ++A K +
Sbjct: 71 FVTFMDQAGVDKVLA 85
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 41.2 bits (96), Expect = 4e-05
Identities = 20/109 (18%), Positives = 38/109 (34%), Gaps = 11/109 (10%)
Query: 140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR 199
+ S G + G + I + NL + + L + +FG K+
Sbjct: 8 ALAASAAAVDAGMAMAGQS-----PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT 62
Query: 200 DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVDWSKSTN 246
+ A + + + A A L+G + L +D+SK T+
Sbjct: 63 KNN----QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 40.3 bits (95), Expect = 4e-05
Identities = 8/64 (12%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
+ ++ + + + + +E++L + Q+G +++ + + FA++ F + A
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQ 56
Query: 222 KAIQ 225
Sbjct: 57 SLCG 60
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 39.4 bits (93), Expect = 5e-05
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 173 LSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI----QYLN 228
LSVNT+ D++ +QFG L DKT +GF ++ F+++ K +N
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEIN 66
Query: 229 G 229
Sbjct: 67 N 67
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 39.5 bits (93), Expect = 9e-05
Identities = 7/68 (10%), Positives = 26/68 (38%), Gaps = 5/68 (7%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ + + + + + + + +L+ Q+G +++ + + FA++ F +
Sbjct: 4 SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADD 58
Query: 218 ADAAKAIQ 225
A
Sbjct: 59 KVAQSLCG 66
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 39.1 bits (92), Expect = 1e-04
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 156 GYNARRND-DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
G NA +N+ D + + LS +TS+ DL+D +FG + D G +GF +I F
Sbjct: 1 GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60
Query: 215 KNKADAAKAIQ 225
K+ A K +
Sbjct: 61 KDAASVEKVLD 71
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 39.5 bits (93), Expect = 1e-04
Identities = 16/66 (24%), Positives = 28/66 (42%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
R T+ + + L T+E DL++ FG + + +D G KGF ++ F
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 220 AAKAIQ 225
K +
Sbjct: 70 QVKVMS 75
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 38.8 bits (91), Expect = 2e-04
Identities = 11/64 (17%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSK----MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+ +L+ + + L + + P+ + + D+T G+ KG+ ++ F ++ + +A+
Sbjct: 14 VGDLTPDVDDGMLYEFFVKVYPSCRGGKVV---LDQT-GVSKGYGFVKFTDELEQKRALT 69
Query: 226 YLNG 229
G
Sbjct: 70 ECQG 73
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 38.4 bits (89), Expect = 3e-04
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 168 IRISNL-SVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
I +SNL S++ + L + +G L R K A+I + + DA + +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH 81
Query: 227 LN 228
Sbjct: 82 CL 83
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 37.6 bits (88), Expect = 5e-04
Identities = 15/71 (21%), Positives = 29/71 (40%)
Query: 155 EGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
G N D+ + + L +T++ L Q+G + +DKT +GF ++ F
Sbjct: 6 SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Query: 215 KNKADAAKAIQ 225
K+ +
Sbjct: 66 KDPNCVGTVLA 76
>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 = 39.8 bits (92), Expect = 6e-04
Identities = 38/301 (12%), Positives = 68/301 (22%), Gaps = 144/301 (47%)
Query: 3 VESTKVVRTLKVE-KKLV---SKGIA------LRKH------------------LAKY-G 33
V++ K + K L+ K + H L KY
Sbjct: 253 VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLD 312
Query: 34 KSANDKPGPQSNTT------IIGEEV-----HIQFI--SNKEEVEKPEEENLEKLKFISC 80
D P + TT II E + N +++ E +L L+
Sbjct: 313 CRPQDLP-REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEY 371
Query: 81 RTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIY 140
R F ++F A+
Sbjct: 372 RKM----------FDRLSVFPPSAH----------------------------------- 386
Query: 141 VPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRD 200
+P L +S + + ++D+ +V + + +
Sbjct: 387 IPTIL------------------------LSLIWFDVIKSDVMVVVNKL--HKYSLVEKQ 420
Query: 201 KTNGLCKGFAYIH-----FKNKADAAKAI------QY---------------LNGYGYDH 234
I K K + A+ Y L+ Y Y H
Sbjct: 421 PKESTI----SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476
Query: 235 L 235
+
Sbjct: 477 I 477
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 36.7 bits (86), Expect = 6e-04
Identities = 15/56 (26%), Positives = 26/56 (46%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I LS T++ L + QFG + + RD +GF ++ F ++A K +
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 37.3 bits (87), Expect = 7e-04
Identities = 16/68 (23%), Positives = 31/68 (45%)
Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
R + + I LS T+E L + +Q+G + + RD + +GF ++ F +
Sbjct: 20 KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79
Query: 218 ADAAKAIQ 225
A+ A+
Sbjct: 80 AEVDAAMA 87
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 39.0 bits (90), Expect = 0.001
Identities = 12/67 (17%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 165 TTAIRISN--LSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
T ++ ++N L S N L ++++ G + + +K +++ ++ ++ +
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKR 71
Query: 223 AIQYLNG 229
A LNG
Sbjct: 72 AYVTLNG 78
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 36.9 bits (85), Expect = 0.001
Identities = 10/58 (17%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC--KGFAYIHFKNKADAAKAIQ 225
+ L + E+++ ++FGP + + ++ KG+A++ F+ ++ I
Sbjct: 13 VGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 35.9 bits (83), Expect = 0.002
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGL--CKGFAYIHFKNKADAAKAIQYLNG 229
D+ D ++G + + R G ++ F + D KA+Q L G
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 35.8 bits (82), Expect = 0.002
Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 6/66 (9%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
++ + + NL+ L L Q GP + L +G A + + +A KA
Sbjct: 7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY------LNQGIALCKYTTREEANKAQ 60
Query: 225 QYLNGY 230
LN
Sbjct: 61 MALNNC 66
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 35.6 bits (82), Expect = 0.002
Identities = 13/62 (20%), Positives = 19/62 (30%), Gaps = 7/62 (11%)
Query: 168 IRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
+ I + L LV+ FG S + A+I DA A+ Y
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDY 71
Query: 227 LN 228
Sbjct: 72 YT 73
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 35.1 bits (81), Expect = 0.004
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
DL +FG K+ L +G A + F++ +A IQ L+G
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDG----VASVSFRDPEEADYCIQTLDG 86
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 33.9 bits (78), Expect = 0.011
Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++D+ + + G +Y+ ++ G Y+ + A A A+ L+G
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQG----NVYVKCPSIAAAIAAVNALHG 77
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 33.2 bits (76), Expect = 0.020
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 179 ENDLEDLVKQ----FGPTSKMYLSRDKTNGL----CKGFAYIHFKNKADAAKAIQYLNG 229
++DLE V + FG +++ + ++K ++ F ++ KAIQ LNG
Sbjct: 35 DDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 93
>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 = 33.5 bits (76), Expect = 0.073
Identities = 48/298 (16%), Positives = 81/298 (27%), Gaps = 108/298 (36%)
Query: 19 VS-KGIALRKHLAKY---GKSANDKPGPQSNTTIIGEEVHIQ------FIS---NKEEVE 65
+S I + + LA Y K PG + + + G H Q I+ + E
Sbjct: 236 ISCPLIGVIQ-LAHYVVTAKLLGFTPG-ELRSYLKGATGHSQGLVTAVAIAETDSWESFF 293
Query: 66 KPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDK 125
+ + L FI R C A+ P T++ + +D
Sbjct: 294 VSVRKAITVLFFIGVR-CYEAY-------------------------PNTSLPPSILEDS 327
Query: 126 KSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRND---DTTAIRISNLSVNTSEN-- 180
G P P + S+ ++V+ Y + N + IS VN ++N
Sbjct: 328 LENN-EGVPS-PML----SIS-NLTQEQVQDYVNKTNSHLPAGKQVEISL--VNGAKNLV 378
Query: 181 ------DLEDLVK---------------------------QFGPTSK----MYLSRDKTN 203
L L +F P + L ++
Sbjct: 379 VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLL-VPASD 437
Query: 204 GLCKGFAYIHFKNKADAAKAIQYLNGYGYD-------------HLILS--VDWSKSTN 246
+ K + A + Y G D I+ V W +T
Sbjct: 438 LINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQ 495
Score = 32.7 bits (74), Expect = 0.11
Identities = 31/216 (14%), Positives = 59/216 (27%), Gaps = 83/216 (38%)
Query: 18 LVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHI-------QFI------------ 58
L + ++ + Y N P ++V I +
Sbjct: 339 LSISNLT-QEQVQDYVNKTNSH-LPAG------KQVEISLVNGAKNLVVSGPPQSLYGLN 390
Query: 59 SNKEEVEKPEEENLEKLKFISCRTCKGAH-F-TNNCPFKDSALFLADANKK--------- 107
+ + P + ++ F S R K ++ F PF L A+
Sbjct: 391 LTLRKAKAPSGLDQSRIPF-SERKLKFSNRFLPVASPFHSH--LLVPASDLINKDLVKNN 447
Query: 108 ----------P-FNTVPGTNIMAASSDDKKSG-------------------------GPG 131
P ++T G+++ S + GPG
Sbjct: 448 VSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPG 507
Query: 132 GAPG-GPAIYVPPSLREGPGGKRVEG--YNARRNDD 164
GA G G + ++G G + + + +DD
Sbjct: 508 GASGLGVLTH---RNKDGTGVRVIVAGTLDINPDDD 540
>4a17_Q RPL17, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_Q 4a1c_Q 4a1e_Q
Length = 183
Score = 31.9 bits (72), Expect = 0.10
Identities = 10/66 (15%), Positives = 21/66 (31%), Gaps = 7/66 (10%)
Query: 9 VRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPE 68
L ++ V++ R+ + N + I +EV +V K
Sbjct: 111 TANLVIQHGQVNRAQKGRRRTYRAHGRINPYLNSGCHVEIFAQEV-------AAKVRKEA 163
Query: 69 EENLEK 74
++ K
Sbjct: 164 PKDAAK 169
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 32.1 bits (72), Expect = 0.14
Identities = 9/77 (11%), Positives = 24/77 (31%), Gaps = 6/77 (7%)
Query: 171 SNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY 230
+L E+ + + + G ++ K ++ FK +A+A A + ++
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKEAMSNQ 202
Query: 231 GYDHLILSVDWSKSTNQ 247
+
Sbjct: 203 TLLLPSDKEWDDRREGT 219
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 30.6 bits (69), Expect = 0.14
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNG-LCKGFAYIHFKNKADAAKAIQYLNGYGYD 233
E + ++ +++G K + ++ F+ A KA+ LNG +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG 82
>3u5e_P L20A, YL17, 60S ribosomal protein L17-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_I
2ww9_I 2wwb_I 3o5h_Q 3o58_Q 3u5i_P 1s1i_N 3izc_V 3izs_V
3jyw_N
Length = 184
Score = 30.7 bits (69), Expect = 0.26
Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 7/68 (10%)
Query: 9 VRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPE 68
L V V++ R+ + N S+ ++ E +E V K
Sbjct: 109 ATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTE-------KEEAVAKAA 161
Query: 69 EENLEKLK 76
E+ + +L
Sbjct: 162 EKKVVRLT 169
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 29.3 bits (65), Expect = 0.44
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 11/85 (12%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTS-----KMYLSRDKTNGLCKGFAYIHF 214
+ T I + LS S + + +++ + K+ L D NG A I F
Sbjct: 16 NSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-NG-----AIIIF 69
Query: 215 KNKADAAKAIQYLNGYGYDHLILSV 239
++ AAK + LNG + ++
Sbjct: 70 RDSKFAAKMLMILNGSQFQGKVIRS 94
>2zkr_r 60S ribosomal protein L17; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 184
Score = 29.5 bits (66), Expect = 0.75
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 9 VRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPE 68
V +L +E V+K +R+ + N + +I E ++ V KPE
Sbjct: 109 VDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEK-------EQIVPKPE 161
Query: 69 EENLEKLK 76
EE +K K
Sbjct: 162 EEVAQKKK 169
>3iz5_V 60S ribosomal protein L17 (L22P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_V
Length = 171
Score = 29.1 bits (65), Expect = 0.95
Identities = 14/68 (20%), Positives = 23/68 (33%), Gaps = 7/68 (10%)
Query: 9 VRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPE 68
V TL V V++ R+ + N + +I E +E V+K
Sbjct: 110 VDTLYVSHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELILSE-------KEEPVKKEP 162
Query: 69 EENLEKLK 76
E + K
Sbjct: 163 ESQIAARK 170
>3tv9_A Putative peptide maturation protein; structural genomics, center
for structural genomics of infec diseases, csgid,
alpha-beta, cytosol; 2.50A {Shigella flexneri}
Length = 457
Score = 28.8 bits (65), Expect = 1.8
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 157 YNARR-NDDTT--AIRISNLSVNTSENDLEDLVKQFG 190
Y+AR+ +T A I N + E ++K+ G
Sbjct: 342 YSARKLGLKSTGHAGGIHNWRIAGQGLSFEQMLKEMG 378
>3qtd_A PMBA protein; putative modulator of gyrase (PMBA), structural
genomics, PS biology, midwest center for structural
genomics, MCSG; 2.70A {Pseudomonas aeruginosa}
Length = 449
Score = 28.8 bits (65), Expect = 1.9
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 157 YNARR-NDDTT--AIRISNLSVNTSENDLEDLVKQFG 190
Y+ R+ +T A + NL V+ + D L+++
Sbjct: 331 YSGRKLGLPSTANAGGVHNLFVSHGDEDQAALIRRME 367
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 27.2 bits (60), Expect = 2.3
Identities = 9/69 (13%), Positives = 17/69 (24%), Gaps = 13/69 (18%)
Query: 162 NDDTTAIRISNLSVNTSENDLED-----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
+ A+ + L + L GP + F+
Sbjct: 5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFRE 56
Query: 217 KADAAKAIQ 225
ADA + +
Sbjct: 57 PADAERVLA 65
>3iz5_B 60S ribosomal protein L2 (L2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_B 2zkr_a
Length = 261
Score = 28.0 bits (63), Expect = 3.0
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 4/35 (11%)
Query: 128 GGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRN 162
GG G R+ P G++V ARR
Sbjct: 213 GGNHQHIGHA----STVRRDAPPGQKVGLIAARRT 243
>2wui_A MEXZ, transcriptional regulator; gene regulation, transcription
regulation, TETR, DNA-binding transcription; 2.90A
{Pseudomonas aeruginosa}
Length = 210
Score = 27.5 bits (61), Expect = 3.0
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 204 GLCKGFAYIHFKNKADAAKAI 224
G+ +G Y H+KNK + A+
Sbjct: 42 GVSRGAVYGHYKNKIEVCLAM 62
>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N
domain, MIF4G domain; 1.95A {Homo sapiens} SCOP:
d.58.7.4
Length = 91
Score = 26.3 bits (58), Expect = 3.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 210 AYIHFKNKADAAKAIQYLNGY 230
AYI+FKN+ D +GY
Sbjct: 48 AYINFKNQEDIILFRDRFDGY 68
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 28.0 bits (63), Expect = 3.7
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 6/84 (7%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
+ G +V R R++ S S D+++L+ Q+ ++M GL
Sbjct: 387 LDSTDGAKVFSKQPGR-----IQRVARGS-GVSTRDVQELLTQYTKFAQMVKKMGGIKGL 440
Query: 206 CKGFAYIHFKNKADAAKAIQYLNG 229
KG +++ AK Q +
Sbjct: 441 FKGGDMSKNVSQSQMAKLNQQMAK 464
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure initiative;
NMR {Homo sapiens}
Length = 97
Score = 26.3 bits (58), Expect = 3.7
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 210 AYIHFKNKADAAKAIQYLNGY 230
AYI+F+N D +GY
Sbjct: 56 AYINFRNPDDILLFRDRFDGY 76
>1vq8_A 50S ribosomal protein L2P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: b.34.5.3 b.40.4.5 PDB:
1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A*
1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A*
1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ...
Length = 240
Score = 26.7 bits (60), Expect = 5.9
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 128 GGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRND 163
GG PG P R P G++V ++R
Sbjct: 204 GGGRQHPGKP----KSISRNAPPGRKVGDIASKRTG 235
>1qb2_A SRP54, human signal recognition particle 54 KD protein;
alpha-helix, helix-turn-helix, signaling protein; 2.10A
{Homo sapiens} SCOP: a.36.1.1 PDB: 1ry1_W* 2go5_W
Length = 109
Score = 26.1 bits (58), Expect = 5.9
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM 195
+ G +V R R++ S S D+++L+ Q+ ++M
Sbjct: 62 LDSTDGAKVFSKQPGRI-----QRVARGS-GVSTRDVQELLTQYTKFAQM 105
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 26.6 bits (58), Expect = 6.7
Identities = 12/65 (18%), Positives = 19/65 (29%), Gaps = 19/65 (29%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC-------KGFAYI--HF 214
+ AI + + SEN+ D+ N C K + Y+ F
Sbjct: 172 ENIAIELPPNEILFSENN---------DMDNNNDGVDELNKKCTFWDAISKLY-YVQFFF 221
Query: 215 KNKAD 219
K
Sbjct: 222 KQAEQ 226
>1mfq_C SRP54, signal recognition particle 54KDA protein; RNA-protein
complex, A-minor motif, 3-helix junction, signaling
protein/RNA complex; HET: CCC; 3.10A {Homo sapiens}
SCOP: a.36.1.1
Length = 129
Score = 25.7 bits (57), Expect = 8.8
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM 195
+ G +V R R++ S S D+++L+ Q+ ++M
Sbjct: 75 LDSTDGAKVFSKQPGRI-----QRVARGS-GVSTRDVQELLTQYTKFAQM 118
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 25.7 bits (56), Expect = 10.0
Identities = 14/53 (26%), Positives = 16/53 (30%), Gaps = 6/53 (11%)
Query: 171 SNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
+L T DL L G + R G I FK KA A
Sbjct: 25 GDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEG------IILFKEKAKEALG 71
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
0.312 0.131 0.380
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,632,531
Number of extensions: 210558
Number of successful extensions: 765
Number of sequences better than 10.0: 1
Number of HSP's gapped: 658
Number of HSP's successfully gapped: 223
Length of query: 247
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 156
Effective length of database: 4,160,982
Effective search space: 649113192
Effective search space used: 649113192
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 (21.8 bits)
S2: 56 (25.3 bits)