RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4080
(403 letters)
>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 = 133 bits (337), Expect = 2e-38
Identities = 60/140 (42%), Positives = 77/140 (55%), Gaps = 12/140 (8%)
Query: 123 GYRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCL 182
G + SG RG + R NP P+ CL
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASM------------TGGQQMGRGSRHVGNRANPDPNCCL 49
Query: 183 GVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT 242
GVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE+ DDA AK+
Sbjct: 50 GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 109
Query: 243 GMEIDGRQIRVDFSVTQRAH 262
GME+DGR+IRVDFS+T+R H
Sbjct: 110 GMELDGRRIRVDFSITKRPH 129
>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 = 129 bits (326), Expect = 4e-37
Identities = 49/87 (56%), Positives = 63/87 (72%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ R NP P+ CLGVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE
Sbjct: 6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ DDA AK+ GME+DGR+IRV
Sbjct: 66 NVDDAKEAKERANGMELDGRRIRVSGP 92
>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 = 118 bits (299), Expect = 6e-33
Identities = 20/95 (21%), Positives = 45/95 (47%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+P++ L + LS TE+ + +F+++ + + TGR RG F+ F +++
Sbjct: 19 YNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE 78
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A A G ++ G+ + ++F ++ + P
Sbjct: 79 IAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPS 113
>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 = 112 bits (283), Expect = 8e-31
Identities = 31/98 (31%), Positives = 43/98 (43%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ L V L+ T+ + +F KYG V V + + T RGF FV F
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
R DA A+ A G E+DGR++RV + R P
Sbjct: 64 DRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101
>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 = 114 bits (287), Expect = 1e-30
Identities = 33/103 (32%), Positives = 49/103 (47%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + + S L V LS YTTE+QI +FSK G ++++ + +D + GFCFV +
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGR 272
SR DA A G +D R IR D+ + G
Sbjct: 90 SRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGG 132
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 112 bits (283), Expect = 2e-30
Identities = 38/167 (22%), Positives = 52/167 (31%), Gaps = 34/167 (20%)
Query: 103 SRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEA 162
S+ G R G S G
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGR---------------------- 39
Query: 163 TAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRG 222
+ + L V L+ T+ + +F KYG V V + D T SRG
Sbjct: 40 ---------PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 90
Query: 223 FCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIY 269
F FV F + DA A DA G +DGR++RV + R P +
Sbjct: 91 FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR---PPDSHH 134
>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 = 109 bits (275), Expect = 1e-29
Identities = 26/96 (27%), Positives = 44/96 (45%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
+ + V LS T E + +F +G + R+ + D TG+S+GF F+ F R
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
+DAA A +G D + V+++ P+ G
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103
>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 = 109 bits (274), Expect = 2e-29
Identities = 42/98 (42%), Positives = 51/98 (52%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ L V GLS T EQ + +FSKYG + V VV D +T RSRGF FV FE
Sbjct: 3 SGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE 62
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
+ DDA A A G +DGRQIRVD + + P
Sbjct: 63 NIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100
>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 = 108 bits (273), Expect = 3e-29
Identities = 31/114 (27%), Positives = 49/114 (42%), Gaps = 7/114 (6%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R P+ +R L + L T +++ IF KYGP+ ++ V T +RG +V +E
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIF 58
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQSELG 286
DA A D +G + R + V + RA EQL + + G
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKK----EEQLKLLKEKYG 108
>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 = 107 bits (270), Expect = 5e-29
Identities = 27/100 (27%), Positives = 46/100 (46%), Gaps = 6/100 (6%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ S+ L + LS TE+ + +F K + V + G+S+G+ F+ F
Sbjct: 6 SGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFA 61
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSV--TQRAHTPTPG 267
S +DA A ++C EI+GR IR++ P+ G
Sbjct: 62 SFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSSG 101
>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 = 109 bits (273), Expect = 1e-28
Identities = 35/143 (24%), Positives = 56/143 (39%), Gaps = 8/143 (5%)
Query: 125 RKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGV 184
K + +R G G DS E +E G + L V
Sbjct: 26 LKEKAKHRKGRGFGSDSNTRE--------AIHSYERVRNEDDDELEPGPQRSVEGWILFV 77
Query: 185 FGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM 244
+ E +I F YG ++ + + +D +TG S+G+ V +E+ A AAK+A G
Sbjct: 78 TSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA 137
Query: 245 EIDGRQIRVDFSVTQRAHTPTPG 267
EI G+ I+VD+ +
Sbjct: 138 EIMGQTIQVDWCFVKGPKRVKKS 160
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 105 bits (263), Expect = 5e-28
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 6/91 (6%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYG--PVERVEVVIDAKTGRSRGFCFVYFE 229
G + + + ++ +T I S Y V + ++ D +T ++RGF FV
Sbjct: 2 GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61
Query: 230 SRDDAAAAKDACTGME----IDGRQIRVDFS 256
S DA+ + IDG+ I VDF+
Sbjct: 62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 106 bits (265), Expect = 1e-27
Identities = 31/106 (29%), Positives = 44/106 (41%)
Query: 157 EEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAK 216
+ + + L V L+ T+ + +F KYG V V + D
Sbjct: 48 ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107
Query: 217 TGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAH 262
T SRGF FV F + DA A DA G +DGR++RV + R
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 106 bits (266), Expect = 1e-27
Identities = 30/142 (21%), Positives = 57/142 (40%), Gaps = 1/142 (0%)
Query: 119 SRSPGYRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQP 178
+ R+ + + GGR + + + + + G E +
Sbjct: 28 KLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVET 87
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
L V L ++ I +F+++G +++ V D ++GRS G V+FE R DA A
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAM 146
Query: 239 DACTGMEIDGRQIRVDFSVTQR 260
G+ +DGR + + +Q
Sbjct: 147 KQYKGVPLDGRPMDIQLVASQI 168
>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 = 101 bits (255), Expect = 8e-27
Identities = 36/97 (37%), Positives = 51/97 (52%), Gaps = 3/97 (3%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ QPS+ L V GLS TTE+ + F R +V D +TG S+GF FV F
Sbjct: 6 SGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFN 62
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTP 266
S +DA AAK+A EIDG ++ +D++ + P
Sbjct: 63 SEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGP 99
>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 = 101 bits (253), Expect = 2e-26
Identities = 26/103 (25%), Positives = 51/103 (49%), Gaps = 8/103 (7%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ + + + LS + E+ + + ++G ++ V VV+ T S+G F F +++
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68
Query: 233 DAAAAKDA------CTGMEIDGRQIRVDFSVT--QRAHTPTPG 267
A A G+++DGRQ++VD +VT + A P+ G
Sbjct: 69 AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 98.2 bits (245), Expect = 2e-25
Identities = 18/81 (22%), Positives = 29/81 (35%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
P + + L+ E + + KYG VE VE+++ +T + G V F S A
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 236 AAKDACTGMEIDGRQIRVDFS 256
+ G I
Sbjct: 63 ETVKNLHLTSVMGNIIHAQLD 83
>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 = 96.9 bits (242), Expect = 5e-25
Identities = 24/79 (30%), Positives = 45/79 (56%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
PSR + + + TE+QI + S GPV ++++ D +TGRS+G+ F+ F + +A+A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 238 KDACTGMEIDGRQIRVDFS 256
G ++ R ++ +S
Sbjct: 61 VRNLNGYQLGSRFLKCGYS 79
>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 = 96.9 bits (242), Expect = 6e-25
Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 8/93 (8%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G P+ L V GL T+ + F ++G + ++ V + F ++ +ES
Sbjct: 10 GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESL 63
Query: 232 DDAAAAKDACTGMEIDG--RQIRVDFSVTQRAH 262
D A AA G + G R++RVDF+ + +
Sbjct: 64 DAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96
>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 = 96.2 bits (240), Expect = 1e-24
Identities = 29/100 (29%), Positives = 47/100 (47%)
Query: 157 EEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAK 216
E +E G + L V + E +I F YG ++ + + +D +
Sbjct: 4 SYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 63
Query: 217 TGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
TG S+G+ V +E+ A AAK+A G EI G+ I+VD+
Sbjct: 64 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103
>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 = 95.4 bits (238), Expect = 2e-24
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 8/97 (8%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ + L V L + T+E+ I F+ P V + R + FV+F +R+
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNRE 62
Query: 233 DAAAAKDACTGMEIDGRQIRVDFS--VTQRAHTPTPG 267
DA A A G +DG I V + V + + P+ G
Sbjct: 63 DAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99
>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 = 95.4 bits (238), Expect = 2e-24
Identities = 23/82 (28%), Positives = 37/82 (45%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
+ V L T + IFSKYG V +V ++ D T +S+G F+ F +D A
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 236 AAKDACTGMEIDGRQIRVDFSV 257
A ++ GR I+ ++
Sbjct: 73 NCTRAINNKQLFGRVIKASIAI 94
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 95.4 bits (238), Expect = 3e-24
Identities = 24/85 (28%), Positives = 46/85 (54%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G + L V G+ TE+ I+ F++YG ++ + + +D +TG +G+ V +E+
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFS 256
+A AA + G ++ G+ I VD+
Sbjct: 76 KEAQAAMEGLNGQDLMGQPISVDWC 100
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 93.9 bits (234), Expect = 9e-24
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
EN + L V + + + +F ++G + VE++ + S+GF FV FE+
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENS 79
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFS 256
DA A++ G ++GR+I V+ +
Sbjct: 80 ADADRAREKLHGTVVEGRKIEVNNA 104
>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 = 93.1 bits (232), Expect = 1e-23
Identities = 28/98 (28%), Positives = 50/98 (51%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
+ R + V + TE+Q+ IFS+ GPV +V D +TG+ +G+ F ++ ++ A
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 236 AAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRP 273
+A G E GR +RVD + +++ + G P
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102
>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 = 92.7 bits (231), Expect = 2e-23
Identities = 23/98 (23%), Positives = 46/98 (46%), Gaps = 2/98 (2%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ E+ + L V + + + +F ++G + VE++ + S+GF FV FE
Sbjct: 6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFE 63
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
+ DA A++ G ++GR+I V+ + + P
Sbjct: 64 NSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 91.6 bits (228), Expect = 5e-23
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 1/87 (1%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
L + GL T++++ I +G V+ + +V + + G+ +G +V +E
Sbjct: 8 VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYE 66
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ A+ A GM I I+V S
Sbjct: 67 NESQASQAVMKMDGMTIKENIIKVAIS 93
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 91.8 bits (228), Expect = 1e-22
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 1/109 (0%)
Query: 149 IIAVVTEVE-EEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVE 207
T V E + R L V GL+ ++ ++ F +G +
Sbjct: 32 ESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT 91
Query: 208 RVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
+++ +D +T + RGF FV FE +DAAAA D E+ GR IRV+ +
Sbjct: 92 DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 89.6 bits (223), Expect = 3e-22
Identities = 27/85 (31%), Positives = 39/85 (45%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G S L V LS ++E+ + +FS YGP+ + ID+ T + +GF FV F
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFS 256
+ A A G GR + V S
Sbjct: 61 EHAVKAYAEVDGQVFQGRMLHVLPS 85
>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 = 90.5 bits (225), Expect = 3e-22
Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 3/96 (3%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
L V G+ TE+ I+ F++YG ++ + + +D +TG +G+ V +E+ +A AA
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 238 KDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRP 273
+ G ++ G+ I VD+ P G G
Sbjct: 81 MEGLNGQDLMGQPISVDWC---FVRGPPKGKRRGGR 113
Score = 27.0 bits (60), Expect = 6.6
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 108 PRGRRGGYRSRSRSPGYRKR 127
P+G+R G R RSRSP R+R
Sbjct: 105 PKGKRRGGRRRSRSPDRRRR 124
>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 = 88.8 bits (221), Expect = 4e-22
Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVID-AKTGRSRGFCFVYFESRDDA 234
+P++ + + L+ T+ I IFS YG ++ +++ ++ S+G+ +V FE+ D+A
Sbjct: 2 MKPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 235 AAAKDACTGMEIDGRQIRVDF 255
A G +IDG++I
Sbjct: 61 EKALKHMDGGQIDGQEITATA 81
>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 = 89.7 bits (223), Expect = 6e-22
Identities = 26/105 (24%), Positives = 48/105 (45%), Gaps = 1/105 (0%)
Query: 156 VEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDA 215
+ + + + G E + L V L ++ I +F+++G +++ V D
Sbjct: 12 RDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD- 70
Query: 216 KTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQR 260
++GRS G V+FE R DA A G+ +DGR + + +Q
Sbjct: 71 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 115
>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 = 93.9 bits (234), Expect = 6e-22
Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 155 EVEEEAEATAMVEEFADGRE--------NPQPSRC-LGVFGLSIYTTEQQINHIFSKYGP 205
+ +A A + F QP+ L V L T+QQ + +G
Sbjct: 63 TLLNGEQAEAAINAF-HQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGS 121
Query: 206 VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ER +V +TG+S+G+ F + +D AA AK G + R + V ++
Sbjct: 122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT 172
Score = 79.3 bits (196), Expect = 7e-17
Identities = 21/112 (18%), Positives = 37/112 (33%), Gaps = 7/112 (6%)
Query: 173 RENPQPSRCLGVFGLSIYTTE-QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
SRCL V L + + S ++ + G+ +GF + +E+
Sbjct: 178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETA 236
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQS 283
+ A A+ G+ + G +RV F PG M +
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSF-----CAPGPPGRSMLAALIAAQATALN 283
Score = 69.6 bits (171), Expect = 1e-13
Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 7/90 (7%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
+ R + + GL T Q+++ + S Y + + +G FV
Sbjct: 12 LEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTL 64
Query: 229 ESRDDAAAAKDACTGMEIDGRQIRVDFSVT 258
+ + A AA +A + R++ V T
Sbjct: 65 LNGEQAEAAINAFHQSRLRERELSVQLQPT 94
>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 = 88.0 bits (219), Expect = 8e-22
Identities = 25/69 (36%), Positives = 41/69 (59%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D E
Sbjct: 14 GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 73
Query: 246 IDGRQIRVD 254
+ GR IRV+
Sbjct: 74 LFGRTIRVN 82
>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 = 88.0 bits (219), Expect = 1e-21
Identities = 25/79 (31%), Positives = 40/79 (50%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
S L V L TE + IF +G ++ + ++ D+ TGRS+G+ F+ F + A A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 238 KDACTGMEIDGRQIRVDFS 256
+ G E+ GR +RV
Sbjct: 64 LEQLNGFELAGRPMRVGHV 82
>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 = 88.5 bits (220), Expect = 1e-21
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ GL+ T E+ + +F K+GP+ V ++ D +T +SRGF F+ FE+ DA A G
Sbjct: 12 IGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDMNG 70
Query: 244 MEIDGRQIRVDFS 256
+ G+ I+V+ +
Sbjct: 71 KSLHGKAIKVEQA 83
>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 = 87.4 bits (217), Expect = 2e-21
Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 3/103 (2%)
Query: 154 TEVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVI 213
A AM ++ L V L TE + IF +G +E +++++
Sbjct: 4 HHHHHSHMAAAMANNL---QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60
Query: 214 DAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
D++TGRS+G+ F+ F + A A + G E+ GR ++V
Sbjct: 61 DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103
>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 = 87.3 bits (217), Expect = 2e-21
Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 1/94 (1%)
Query: 165 MVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFC 224
+ + G + L V L ++ I +F+++G +++ V D ++GRS G
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTA 73
Query: 225 FVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVT 258
V+FE + DA A G+ +DGR + + +
Sbjct: 74 DVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS 107
>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 = 86.5 bits (215), Expect = 3e-21
Identities = 27/82 (32%), Positives = 44/82 (53%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D E
Sbjct: 19 GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 78
Query: 246 IDGRQIRVDFSVTQRAHTPTPG 267
+ GR IRV+ + R P
Sbjct: 79 LFGRTIRVNLAKPMRIKESGPS 100
>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 = 86.6 bits (215), Expect = 3e-21
Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
+ + +R L LS TE ++ +F E+ + ++ G+S+G ++ F+S
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSE 63
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFS 256
DA + G EIDGR + + ++
Sbjct: 64 ADAEKNLEEKQGAEIDGRSVSLYYT 88
>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 = 86.2 bits (214), Expect = 6e-21
Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 2/97 (2%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDA-KTGRSRGFCFVYFESR 231
Q + + V + +++I +FS +G ++ V + TG RGF FV F ++
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 232 DDAAAAKDA-CTGMEIDGRQIRVDFSVTQRAHTPTPG 267
DA A +A C + GR++ ++++ ++ P
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPS 105
>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 = 85.0 bits (211), Expect = 1e-20
Identities = 23/83 (27%), Positives = 39/83 (46%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ V GL +E + +F + GPV + D TG+ +G+ FV F S +D
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 234 AAAAKDACTGMEIDGRQIRVDFS 256
A A +++ G+ IRV+ +
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKA 92
>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 = 84.5 bits (210), Expect = 1e-20
Identities = 22/71 (30%), Positives = 42/71 (59%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L++ ++ + + F + V+ D +TG SRG+ FV F S+DDA A D+ G +
Sbjct: 8 DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67
Query: 246 IDGRQIRVDFS 256
++GR +R++++
Sbjct: 68 LNGRPLRINWA 78
>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 = 86.1 bits (214), Expect = 3e-20
Identities = 18/82 (21%), Positives = 39/82 (47%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ + L + GL Y + Q+ + + +GP++ +V D+ TG S+G+ F + +
Sbjct: 88 YQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 147
Query: 233 DAAAAKDACTGMEIDGRQIRVD 254
A GM++ +++ V
Sbjct: 148 VTDQAIAGLNGMQLGDKKLLVQ 169
Score = 73.0 bits (180), Expect = 1e-15
Identities = 22/121 (18%), Positives = 48/121 (39%), Gaps = 10/121 (8%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERV-----EVVIDAKTGRSRGFCFVYFESRDD 233
+R L V + TE+ + F+ + + V+ + + + F F+ F S D+
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGR-PTY---EQLNNTQSELGSLL 289
A A G+ G+ +++ + +++G P Y +Q+ + G L
Sbjct: 64 TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLK 122
Query: 290 S 290
+
Sbjct: 123 A 123
>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 = 83.0 bits (206), Expect = 4e-20
Identities = 25/71 (35%), Positives = 37/71 (52%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
LS T I F+ +G + VV D TG+S+G+ FV F ++ DA A G
Sbjct: 13 DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72
Query: 246 IDGRQIRVDFS 256
+ GRQIR +++
Sbjct: 73 LGGRQIRTNWA 83
>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 = 86.2 bits (214), Expect = 6e-20
Identities = 20/102 (19%), Positives = 45/102 (44%)
Query: 155 EVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVID 214
+ +E ++ P + L + GL Y + Q+ + + +GP++ +V D
Sbjct: 90 PLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD 149
Query: 215 AKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ TG S+G+ F + + A GM++ +++ V +
Sbjct: 150 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
Score = 68.9 bits (169), Expect = 8e-14
Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 6/84 (7%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERV-----EVVIDAKTGRSRGFCFVYFESRD 232
+R L V + TE+ + F+ + + V+ + + + F F+ F S D
Sbjct: 3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 233 DAAAAKDACTGMEIDGRQIRVDFS 256
+ A A G+ G+ +++
Sbjct: 63 ETTQAM-AFDGIIFQGQSLKIRRP 85
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 85.0 bits (210), Expect = 7e-20
Identities = 22/144 (15%), Positives = 47/144 (32%), Gaps = 3/144 (2%)
Query: 133 SGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTT 192
SG ++ + V + + V S +TT
Sbjct: 9 SGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTT 68
Query: 193 EQQINHIFSKYGPVERVEVVI--DAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
+QQ+ + G + VE+ + G+S+G+ V S + + G ++G +
Sbjct: 69 DQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK 128
Query: 251 IRVDFSVTQRAHTPTPGIYMGRPT 274
+ V + T++ + R
Sbjct: 129 VDVRPA-TRQNLSQFEAQARKREC 151
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 86.2 bits (214), Expect = 7e-20
Identities = 17/82 (20%), Positives = 37/82 (45%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
+ ++ I +F +G ++ + D TG+ +G+ F+ +E + A + +
Sbjct: 132 SVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFD 191
Query: 246 IDGRQIRVDFSVTQRAHTPTPG 267
+ G+ +RV +VT TP
Sbjct: 192 LGGQYLRVGKAVTPPMPLLTPA 213
Score = 80.4 bits (199), Expect = 1e-17
Identities = 19/81 (23%), Positives = 36/81 (44%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
+ E I F+ +GP++ +++ D+ T + +GF FV +E + A A + +
Sbjct: 35 SIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVM 94
Query: 246 IDGRQIRVDFSVTQRAHTPTP 266
+ GR I+V P
Sbjct: 95 LGGRNIKVGRPSNIGQAQPII 115
>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 = 82.6 bits (205), Expect = 8e-20
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 2/73 (2%)
Query: 186 GLSIYTTEQQINHIFSKYGP--VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
L+ +TT++ + G + ++ + G+S+GF V S + D
Sbjct: 8 NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67
Query: 244 MEIDGRQIRVDFS 256
E+ G+ V S
Sbjct: 68 RELHGQNPVVTPS 80
>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 = 82.7 bits (205), Expect = 8e-20
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 175 NPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
+ R + V L E+ + +F + GP+ +V + D + G+ + F FV F+ +
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESV 70
Query: 235 AAAKDACTGMEIDGRQIRVDFS 256
+ A G+ + GR I V
Sbjct: 71 SYAIALLNGIRLYGRPINVSGP 92
>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 = 83.6 bits (207), Expect = 1e-19
Identities = 27/86 (31%), Positives = 42/86 (48%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
P R L V + E Q+ +F +YGP+E V++V D +T +SRG+ FV F+
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDF 255
S A A G I ++++V
Sbjct: 93 SGSSAQQAIAGLNGFNILNKRLKVAL 118
>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 = 83.0 bits (206), Expect = 4e-19
Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 4/111 (3%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L T++++ +F GP+ ++ D KTG S G+ FV F S D+ A G+
Sbjct: 10 YLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGIT 69
Query: 246 IDGRQIRVDFSVTQRAHTPTPGIYMGR--PTY--EQLNNTQSELGSLLSEK 292
+ ++++V ++ +Y+ T +QL+ + GS++ +
Sbjct: 70 VRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Score = 73.0 bits (180), Expect = 1e-15
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 2/89 (2%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
+A L V L T+ Q++ IF KYG + + ++ D TGR RG FV +
Sbjct: 79 YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 138
Query: 229 ESRDDAAAAKDACTGMEIDG--RQIRVDF 255
R++A A A + +G + + V
Sbjct: 139 NKREEAQEAISALNNVIPEGGSQPLSVRL 167
>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 = 83.0 bits (206), Expect = 5e-19
Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 7/91 (7%)
Query: 168 EFADGRENPQPSRCLGVF--GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCF 225
E GR++ + + LS TE ++ +F E+ + ++ G+S+G +
Sbjct: 86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAY 140
Query: 226 VYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ F+S DA + G EIDGR + + ++
Sbjct: 141 IEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171
Score = 78.8 bits (195), Expect = 2e-17
Identities = 19/104 (18%), Positives = 42/104 (40%), Gaps = 4/104 (3%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
L + L+ + ++ S+ + V +D +TG +R F +V FE
Sbjct: 4 MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFE 62
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG--IYMG 271
S +D A + TG+++ G +I+++ + + +
Sbjct: 63 SAEDLEKALEL-TGLKVFGNEIKLEKPKGRDSKKVRAARTLLAK 105
>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 = 80.9 bits (200), Expect = 5e-19
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
LS T + I F+ +G + VV D TG+S+G+ FV F ++ DA A G
Sbjct: 22 DLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 81
Query: 246 IDGRQIRVDFSVTQRAHTPTPG 267
+ GRQIR +++ T++ P
Sbjct: 82 LGGRQIRTNWA-TRKPPAPKST 102
>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 = 80.4 bits (199), Expect = 6e-19
Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
E+ R L V LS TE I +FS+ GP + +++ + + +CFV F
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHR 66
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSV--TQRAHTPTPG 267
DAAAA A G +I G++++V+++ + + P+ G
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSSG 103
>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 = 80.4 bits (199), Expect = 6e-19
Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 8/94 (8%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPV--------ERVEVVIDAKTGRSR 221
+ + + V GL T + + F + G + + + D +TG+ +
Sbjct: 4 HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63
Query: 222 GFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
G V F+ A AA D G E G I+V F
Sbjct: 64 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>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 = 80.4 bits (199), Expect = 7e-19
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 6/96 (6%)
Query: 171 DGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
G + L V L TE+++ +F KYG V + + +GF F+ E+
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLET 60
Query: 231 RDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTP 266
R A AK M + G+Q+RV F+ + T P
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGP 96
>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 = 79.9 bits (198), Expect = 7e-19
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 6/91 (6%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
+R + V + T +++ F G V RV ++ D +G +GF ++ F ++ +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 238 KDACTGMEIDGRQIRVDFSVTQRAHTPTPGI 268
A GRQI+V T PGI
Sbjct: 65 -LALDESLFRGRQIKVI-----PKRTNRPGI 89
>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 = 80.0 bits (198), Expect = 7e-19
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 2/89 (2%)
Query: 168 EFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVY 227
E L + L+ + ++ S+ + V+D +TG +R F +V
Sbjct: 6 EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVD 64
Query: 228 FESRDDAAAAKDACTGMEIDGRQIRVDFS 256
FES +D A + TG+++ G +I+++
Sbjct: 65 FESAEDLEKALEL-TGLKVFGNEIKLEKP 92
>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 = 81.9 bits (203), Expect = 9e-19
Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 4/111 (3%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L T+++ +F G +E ++V D TG+S G+ FV + DA A + G+
Sbjct: 9 YLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLR 68
Query: 246 IDGRQIRVDFSVTQRAHTPTPGIYMGR--PTY--EQLNNTQSELGSLLSEK 292
+ + I+V ++ A +Y+ T ++L S+ G +++ +
Sbjct: 69 LQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSR 119
Score = 72.6 bits (179), Expect = 2e-15
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GL T++++ +FS+YG + +++D TG SRG F+ F+ R +A A G +
Sbjct: 95 GLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
Query: 246 IDG--RQIRVDF 255
G I V F
Sbjct: 155 PSGATEPITVKF 166
>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 = 79.5 bits (197), Expect = 1e-18
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L T +Q+ +FS++G V V+++ D +T + +GF FV + + + A
Sbjct: 6 VGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDN 64
Query: 244 MEIDGRQIRVDFS 256
+ GR IRV +
Sbjct: 65 TDFMGRTIRVTEA 77
>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 = 79.1 bits (196), Expect = 1e-18
Identities = 17/70 (24%), Positives = 32/70 (45%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ GL TT+Q + + YG + + ++D T + +G+ FV F+S A A A
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69
Query: 244 MEIDGRQIRV 253
+ + +
Sbjct: 70 SGVQAQMAKQ 79
>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 = 79.7 bits (197), Expect = 2e-18
Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 1/94 (1%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ +R + L+ + + FS G V V ++ D + RS+G +V F
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A TG + G I V S ++ P
Sbjct: 80 VPLA-IGLTGQRLLGVPIIVQASQAEKNRLSGPS 112
>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 = 79.8 bits (197), Expect = 2e-18
Identities = 25/115 (21%), Positives = 46/115 (40%), Gaps = 6/115 (5%)
Query: 154 TEVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVI 213
+++ A + + + R + V + +T Q + FS G + R+ ++
Sbjct: 11 SKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70
Query: 214 DAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGI 268
D +G +G+ ++ F R+ AA A GR I+V T PGI
Sbjct: 71 DKFSGHPKGYAYIEFAERNSVDAA-VAMDETVFRGRTIKVL-----PKRTNMPGI 119
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 77.9 bits (193), Expect = 2e-18
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GLS+ TT + + H F ++G V+ ++ D T R RGF FV FES D + E
Sbjct: 6 GLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHE 64
Query: 246 IDGRQIRVD 254
I+ + +
Sbjct: 65 INNKMVECK 73
>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 = 80.3 bits (198), Expect = 2e-18
Identities = 24/88 (27%), Positives = 37/88 (42%), Gaps = 5/88 (5%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R++ + V L + ++ F YGP+ V V GF FV FE
Sbjct: 67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPGFAFVEFEDPR 121
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQR 260
DAA A G + G ++RV+ S ++
Sbjct: 122 DAADAVRELDGRTLCGCRVRVELSNGEK 149
>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 = 83.5 bits (207), Expect = 2e-18
Identities = 19/130 (14%), Positives = 39/130 (30%), Gaps = 15/130 (11%)
Query: 132 RSGGGSRGDSYGGRGKIIIAVVT-EVEEEAE-ATAMVEEFADGRE---NPQPSRCLGVFG 186
S + A + + A A + E + L +
Sbjct: 75 DSLKKNFR----------FARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTN 124
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
T++ I + V + + SR F ++ S++DA + G++I
Sbjct: 125 FPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI 184
Query: 247 DGRQIRVDFS 256
+G + S
Sbjct: 185 EGYTLVTKVS 194
Score = 74.6 bits (184), Expect = 3e-15
Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 10/98 (10%)
Query: 168 EFADGRENPQPSRCLGVFGLSIY--------TTEQQINHIFSKYGPVERVEVVIDAK-TG 218
+ ++ E + + + G I E + F +G +E++ + K
Sbjct: 192 KVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHS 251
Query: 219 RSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ F+ FE++D A A + R+I V +
Sbjct: 252 FNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLA 288
Score = 60.8 bits (148), Expect = 1e-10
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 3/70 (4%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L + ++ F GP+ V+V ++ F + F D A AA
Sbjct: 46 VKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKTHK 103
Query: 244 MEIDGRQIRV 253
+ + +I V
Sbjct: 104 V-VGQNEIIV 112
>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 = 78.8 bits (195), Expect = 3e-18
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
G+ E ++ F K+G V V ++ DA+ R RGF F+ FE A + +
Sbjct: 17 GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM-HFHD 75
Query: 246 IDGRQIRVDFSVTQRAHTPTPG 267
I G+++ V + + + + P
Sbjct: 76 IMGKKVEVKRAEPRDSKSSGPS 97
>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 = 80.7 bits (200), Expect = 3e-18
Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
A R+ + + V G+ ++ FS++G + ++++D TG+SRGF FV ++
Sbjct: 78 AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSV 257
S D ++ R+I + +
Sbjct: 138 SADAVDRVC-QNKFIDFKDRKIEIKRAE 164
Score = 77.6 bits (192), Expect = 4e-17
Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 2/89 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ GL+ TTE + F KYG V ++++ D TGRSRGF F+ FE
Sbjct: 8 IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--Q 65
Query: 244 MEIDGRQIRVDFSVTQRAHTPTPGIYMGR 272
+DG+ I ++ + T I++G
Sbjct: 66 HILDGKVIDPKRAIPRDEQDKTGKIFVGG 94
>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 = 78.9 bits (195), Expect = 3e-18
Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 4/90 (4%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ G ++ + L + + E+ + +F ++G + + V+ D TG +G F+ +
Sbjct: 5 SSGMKDHDAIK-LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 230 SRDDAAAAKDACTGMEI---DGRQIRVDFS 256
R+ A A+ A + R I+V +
Sbjct: 64 ERESALKAQSALHEQKTLPGMNRPIQVKPA 93
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 78.6 bits (194), Expect = 3e-18
Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 8/90 (8%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
S + + GL E + ++GP+ V V+ + V FE
Sbjct: 15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVL 68
Query: 233 DAAAAKDACTGM--EIDGRQIRVDFSVTQR 260
A A + I G V++S +Q+
Sbjct: 69 GACNAVNYAADNQIYIAGHPAFVNYSTSQK 98
>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 = 78.4 bits (194), Expect = 3e-18
Identities = 18/68 (26%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
G+ + E +I F++YG V+ V+++ D +TG S+G+ FV F + D ++ +
Sbjct: 16 GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES--QIN 72
Query: 246 IDGRQIRV 253
G+++++
Sbjct: 73 FHGKKLKL 80
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 78.0 bits (193), Expect = 3e-18
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 4/96 (4%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G + + V L T + + F++ G V ++ ++ G+S+G V FES
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
+ A A GM++ GR+I V + A P+ G
Sbjct: 59 EVAERACRMMNGMKLSGREIDVRID--RNASGPSSG 92
>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 = 79.9 bits (198), Expect = 5e-18
Identities = 24/115 (20%), Positives = 48/115 (41%), Gaps = 7/115 (6%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TE + F GP+ ++++ID K ++ + FV + DA A G
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTLNG 63
Query: 244 MEIDGRQIRVDFSVTQRAHTPTPG--IYMG----RPTYEQLNNTQSELGSLLSEK 292
+I+ ++++++ + + +++G E L N + S LS
Sbjct: 64 KQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Score = 78.7 bits (195), Expect = 1e-17
Identities = 25/88 (28%), Positives = 48/88 (54%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
F + + + L V L++ ++ + + F + V+ D +TG SRG+ FV F
Sbjct: 77 FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136
Query: 229 ESRDDAAAAKDACTGMEIDGRQIRVDFS 256
S+DDA A D+ G +++GR +R++++
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 78.0 bits (193), Expect = 5e-18
Identities = 30/99 (30%), Positives = 43/99 (43%), Gaps = 4/99 (4%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + Q + L V GL TTEQ + FS +G V V+V D KTG S+GF FV F
Sbjct: 6 SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF- 64
Query: 230 SRDDAAAAKDACTGM-EIDGRQIRVDFSVTQRAHTPTPG 267
+ + IDGR ++++ P
Sbjct: 65 --TEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDSGPS 101
>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 = 77.3 bits (191), Expect = 5e-18
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 8/98 (8%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + S L V +S T Q++ F +YGPV ++V + + FV+ E
Sbjct: 1 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHME 52
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
+DA A E G+++ V S ++ P
Sbjct: 53 RAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASGPS 90
>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 = 77.7 bits (192), Expect = 6e-18
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 5/89 (5%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTG---RSRGFCFVYFESRDDAAAAKDA 240
+ L+ TTE+ + +FSK G ++ + S GF FV ++ + A A
Sbjct: 10 IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 69
Query: 241 CTGMEIDGRQIRVDFS--VTQRAHTPTPG 267
G +DG ++ V S T+ A P+ G
Sbjct: 70 LQGHTVDGHKLEVRISERATKPASGPSSG 98
>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 = 76.4 bits (189), Expect = 7e-18
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM- 244
GLS T E++I F +G VE +E+ +D KT + RGFCF+ F + K
Sbjct: 6 GLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF---KEEEPVKKIMEKKY 62
Query: 245 -EIDGRQIRVD 254
+ + +
Sbjct: 63 HNVGLSKCEIK 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 = 77.3 bits (191), Expect = 1e-17
Identities = 32/109 (29%), Positives = 49/109 (44%), Gaps = 8/109 (7%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
G + + V GL +TT+ + F +G +E V+ D +TG+SRG+ FV
Sbjct: 8 MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 67
Query: 230 SRDDAAAAKDACTGM--EIDGRQIRVDFSV---TQRAHTPTPGIYMGRP 273
D AAA+ AC IDGR+ V+ + R+ I + P
Sbjct: 68 ---DRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
>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 = 76.2 bits (188), Expect = 2e-17
Identities = 17/83 (20%), Positives = 29/83 (34%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ V + + +I F Y + + + G G V FESRD+
Sbjct: 10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69
Query: 234 AAAAKDACTGMEIDGRQIRVDFS 256
A AA I R++++
Sbjct: 70 ATAAVIDLNDRPIGSRKVKLSGP 92
>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 = 75.7 bits (187), Expect = 2e-17
Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 9/96 (9%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ + + V +S T Q++ +F + G V +VV + + FV+ E
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHT-PTPG 267
DA AA G E+ G++I V+ S + + P+ G
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSSG 90
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 75.9 bits (187), Expect = 3e-17
Identities = 23/96 (23%), Positives = 41/96 (42%)
Query: 160 AEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGR 219
+A A + L ++ L T+ + F +G V +V ID +T
Sbjct: 21 VALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL 80
Query: 220 SRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
S+ F FV F++ D A A A G ++ ++++V
Sbjct: 81 SKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116
>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 = 75.2 bits (185), Expect = 4e-17
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 8/95 (8%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
S + V GL E + K+G + V ++ + V FE+ D
Sbjct: 9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVEFENID 62
Query: 233 DAAAAKDACT--GMEIDGRQIRVDFSVTQRAHTPT 265
A + I G+Q ++S ++R P
Sbjct: 63 SAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 75.9 bits (187), Expect = 4e-17
Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 8/90 (8%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVE--------RVEVVIDAKTGRSRGFCFVY 227
+ + V GL T + + F + G ++ + + D +TG+ +G V
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 228 FESRDDAAAAKDACTGMEIDGRQIRVDFSV 257
F+ A AA D G E G I+V F+
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93
>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 = 74.6 bits (184), Expect = 6e-17
Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 1/90 (1%)
Query: 168 EFADGRENPQPS-RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV 226
+ G + +P + V + + +I F Y + + + G G V
Sbjct: 3 SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
FESRD+A AA I R++++
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLG 92
>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 = 77.7 bits (192), Expect = 6e-17
Identities = 26/109 (23%), Positives = 45/109 (41%), Gaps = 7/109 (6%)
Query: 170 ADGRENPQPSRCLG----VF--GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGF 223
A RE+ Q +F G+ T E + F +YG +E +E++ D +G+ RGF
Sbjct: 89 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 148
Query: 224 CFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGR 272
FV F+ D ++G V +++++ GR
Sbjct: 149 AFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196
Score = 76.2 bits (188), Expect = 2e-16
Identities = 31/109 (28%), Positives = 54/109 (49%), Gaps = 7/109 (6%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
++ + P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV +
Sbjct: 4 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSV------TQRAHTPTPGIYMGR 272
+ ++ AA +A ++DGR + +V AH I++G
Sbjct: 64 TVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGG 111
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 74.6 bits (184), Expect = 7e-17
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
+P V L T + I+ IF + V +V D T + +GFC+V F+ D
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 237 AKDACTGMEIDGRQIRVDFS 256
A G + R +RVD +
Sbjct: 72 A-LTYDGALLGDRSLRVDIA 90
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 75.3 bits (185), Expect = 8e-17
Identities = 16/97 (16%), Positives = 44/97 (45%), Gaps = 7/97 (7%)
Query: 167 EEFADGRENPQPSRCLGVFGLSIYTTEQQINH----IFSKYGPVERVEVVIDAKTGRSRG 222
+ + +PS+ + + ++ ++++ + S G + +++V+D + + G
Sbjct: 17 PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVD-LSDDNSG 73
Query: 223 FCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQ 259
++ F +++ A A +A G G + + FS T
Sbjct: 74 KAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110
>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 = 74.7 bits (184), Expect = 8e-17
Identities = 24/106 (22%), Positives = 38/106 (35%), Gaps = 3/106 (2%)
Query: 162 ATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSR 221
++ M + V L + I +F KYG + +++
Sbjct: 5 SSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGP 61
Query: 222 GFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
F FV FE DA A G + DG ++RV+F + R P
Sbjct: 62 PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPS 107
>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 = 74.2 bits (183), Expect = 1e-16
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 8/95 (8%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R P+ L V+G + T + FS +G + ID R FV +E +
Sbjct: 9 RRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKME 60
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A A G +++ Q++V+ + Q P
Sbjct: 61 SADQAVAELNGTQVESVQLKVNIARKQPMLDSGPS 95
>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 = 77.8 bits (191), Expect = 1e-16
Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 2/89 (2%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVI--DAKTGRSRGFCFVY 227
L + L+ +TT++ + G + +E+ + G+S+GF V
Sbjct: 59 NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 118
Query: 228 FESRDDAAAAKDACTGMEIDGRQIRVDFS 256
S + D E+ G+ V
Sbjct: 119 VGSEASSKKLMDLLPKRELHGQNPVVTPV 147
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 74.3 bits (183), Expect = 1e-16
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 6/83 (7%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R P + + + TE + +F +G + K +G CF+ +++ +
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDF------KHYPEKGCCFIKYDTHE 74
Query: 233 DAAAAKDACTGMEIDGRQIRVDF 255
AA A GR +R +
Sbjct: 75 QAAVCIVALANFPFQGRNLRTGW 97
>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 = 73.8 bits (182), Expect = 1e-16
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKT-GRSRGFCFVYFESRDDAA 235
P + L TE+ I F + V + + R +GF + FE D
Sbjct: 17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 75
Query: 236 AAKDACTGMEIDGRQIRVDFS 256
+A + + R+IRVD +
Sbjct: 76 SA-LSLNEESLGNRRIRVDVA 95
>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 = 76.9 bits (190), Expect = 1e-16
Identities = 26/88 (29%), Positives = 37/88 (42%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
+ P L V L TE + FS GP+ + V D T RS G+ +V F
Sbjct: 5 SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF 64
Query: 229 ESRDDAAAAKDACTGMEIDGRQIRVDFS 256
+ DA A D I G+ +R+ +S
Sbjct: 65 QQPADAERALDTMNFDVIKGKPVRIMWS 92
Score = 73.9 bits (182), Expect = 2e-15
Identities = 21/106 (19%), Positives = 46/106 (43%), Gaps = 2/106 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L + + FS +G + +VV D S+G+ FV+FE+++ A A + GM
Sbjct: 110 NLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGML 167
Query: 246 IDGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQSELGSLLSE 291
++ R++ V +++ G + + G ++++
Sbjct: 168 LNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGRIVTD 213
>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 = 73.4 bits (181), Expect = 2e-16
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVI-DAKTGRSRGFCFVYFESRDDAAAAKDACTGM 244
L E+ + FS +G + + ++ D TG S+G+ F+ F S D + AA +A G
Sbjct: 12 NLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ 71
Query: 245 EIDGRQIRVDFSV--TQRAHTPTPG 267
+ R I V ++ + P+ G
Sbjct: 72 YLCNRPITVSYAFKKDSKGSGPSSG 96
>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 = 72.7 bits (179), Expect = 3e-16
Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 9/99 (9%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G L + LS T + +F + + + G+ FV + +
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQ 54
Query: 232 DDAAAAKDACTG-MEIDGRQIRVDFSV--TQRAHTPTPG 267
+ A A + +G +E+ G+ + VD+SV R+ P+ G
Sbjct: 55 NWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPSSG 93
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 71.4 bits (176), Expect = 5e-16
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ GLS TT++ + F ++G V+ V+ D T RSRGF FV F + +
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SR 63
Query: 244 MEIDGRQIRVD 254
E+D + I
Sbjct: 64 HELDSKTIDPK 74
>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 = 71.4 bits (176), Expect = 6e-16
Identities = 27/86 (31%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 171 DGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
+ +N + + + V GLS T+++ + F+K+G V + +D TGRSRGF F+ F+
Sbjct: 3 NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK- 61
Query: 231 RDDAAAAKDACTGM--EIDGRQIRVD 254
DAA+ + +DGR I
Sbjct: 62 --DAASVEKVLDQKEHRLDGRVIDPK 85
>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 = 71.9 bits (177), Expect = 7e-16
Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAK-TGRSRGFCFVYFESRDDAA 235
P + L TE+ I F + V + + R +GF + FE D
Sbjct: 13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71
Query: 236 AAKDACTGMEIDGRQIRVDFS 256
+A + + ++IRVD +
Sbjct: 72 SAL-SLNEESLGNKRIRVDVA 91
>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 = 71.5 bits (176), Expect = 7e-16
Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 8/96 (8%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G L + L TEQ+I +F +YG V +++ + + FV+ E +
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDK 52
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A A ++ G I V+ S + + P
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPS 88
>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 = 72.4 bits (178), Expect = 7e-16
Identities = 21/87 (24%), Positives = 41/87 (47%)
Query: 167 EEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV 226
A ++ L ++ L +Q + +F +G V +V ID +T S+ F FV
Sbjct: 13 IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 72
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIRV 253
+++ A AA + G +I ++++V
Sbjct: 73 SYDNPVSAQAAIQSMNGFQIGMKRLKV 99
>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 = 72.1 bits (177), Expect = 8e-16
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 186 GLSIYTTEQQINHIFSKYGP-VERVEVVIDAK-TGRSRGFCFVYFESRDDAAAAKDAC-- 241
G+ ++I +K V V V A ++RGF FV +ES AA A+
Sbjct: 15 GIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMP 74
Query: 242 TGMEIDGRQIRVDFSVTQR 260
+++ G QI VD++ +
Sbjct: 75 GRIQLWGHQIAVDWAEPEI 93
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 71.3 bits (175), Expect = 1e-15
Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 3/86 (3%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
Q R L + + + + ++ + +YG VE E V T V + S+D A
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQAR 68
Query: 236 AAKDACTGMEIDGRQIRVDFSVTQRA 261
A D G +++ ++V + + A
Sbjct: 69 QALDKLNGFQLENFTLKVAYIPDEMA 94
>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 = 74.0 bits (181), Expect = 1e-15
Identities = 14/90 (15%), Positives = 28/90 (31%)
Query: 168 EFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVY 227
E A PS L F + TE+ I + G V + + +
Sbjct: 112 EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLE 171
Query: 228 FESRDDAAAAKDACTGMEIDGRQIRVDFSV 257
++S+ DA ++ +++
Sbjct: 172 WDSKSDALETLGFLNHYQMKNPNGPYPYTL 201
Score = 58.6 bits (141), Expect = 3e-10
Identities = 20/108 (18%), Positives = 39/108 (36%), Gaps = 7/108 (6%)
Query: 178 PSRCLGVFGLSI-YTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
S L V+GL ++ ++F YG VE+V+ + G V
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57
Query: 237 AKDACTGMEIDGRQIRVDFSVTQRAHTPTP-GIYMGRPTYEQLNNTQS 283
A + G+++ V S G+ G +Y+ + +++
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRN 105
>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 = 76.8 bits (188), Expect = 2e-15
Identities = 30/121 (24%), Positives = 53/121 (43%)
Query: 157 EEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAK 216
+E M + D + L V ++ TTE ++ F YGP++R+ +V +
Sbjct: 80 QEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR 139
Query: 217 TGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRPTYE 276
+G+ RG+ F+ +E D +A G +IDGR++ VD + P G
Sbjct: 140 SGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199
Query: 277 Q 277
+
Sbjct: 200 R 200
Score = 37.5 bits (86), Expect = 0.006
Identities = 20/104 (19%), Positives = 29/104 (27%)
Query: 44 SSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRS 103
L + ++ + + R R R + + RD RSR
Sbjct: 220 DERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRE 279
Query: 104 RSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGK 147
RS R SRSR R+R GG +
Sbjct: 280 RSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323
Score = 36.7 bits (84), Expect = 0.010
Identities = 26/147 (17%), Positives = 41/147 (27%), Gaps = 10/147 (6%)
Query: 1 MWTIFLKVLGLCGLSEPDGKVPVWYLCRSHVSGRLLPKEPAQTSSDQCYYRLSPARSGSA 60
+ + G S R P D+ R RS
Sbjct: 189 PRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRER 248
Query: 61 GSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSR 120
+++ +S R R + +R +R RS+ +R RSR R
Sbjct: 249 DKERERRRSRSRDRRRRSRSRDKEERR----------RSRERSKDKDRDRKRRSSRSRER 298
Query: 121 SPGYRKRSSSYRSGGGSRGDSYGGRGK 147
+ R+R R GGG +
Sbjct: 299 ARRERERKEELRGGGGDMAEPSEAGDA 325
Score = 34.8 bits (79), Expect = 0.042
Identities = 16/122 (13%), Positives = 26/122 (21%)
Query: 24 WYLCRSHVSGRLLPKEPAQTSSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRR 83
LP ++ S R + + RR
Sbjct: 216 TSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERR 275
Query: 84 SKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYG 143
R + + SRSR + R R R + S + +
Sbjct: 276 RSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGEL 335
Query: 144 GR 145
G
Sbjct: 336 GP 337
Score = 34.4 bits (78), Expect = 0.053
Identities = 16/102 (15%), Positives = 21/102 (20%)
Query: 44 SSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRS 103
+ G G + + R R S R + RD R
Sbjct: 325 APPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERG 384
Query: 104 RSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGR 145
RGG + S GD Y
Sbjct: 385 SERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAP 426
Score = 34.1 bits (77), Expect = 0.089
Identities = 13/92 (14%), Positives = 21/92 (22%)
Query: 56 RSGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGY 115
R G + + + + R RS RR
Sbjct: 310 RGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRD 369
Query: 116 RSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGK 147
R R R +++ G GG+
Sbjct: 370 RDRDRDREHKRGERGSERGRDEARGGGGGQDN 401
Score = 29.8 bits (66), Expect = 1.5
Identities = 15/100 (15%), Positives = 21/100 (21%), Gaps = 8/100 (8%)
Query: 56 RSGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPR------ 109
R + + + P G D G + R
Sbjct: 300 RRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHR 359
Query: 110 --GRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGK 147
R R R R + S G GG G+
Sbjct: 360 SERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQ 399
>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 = 70.8 bits (174), Expect = 2e-15
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G + L V L+ TE+ + FS++G +ERV+ + + + F++F+ R
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDER 55
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFS 256
D A A + G +++G I + F+
Sbjct: 56 DGAVKAMEEMNGKDLEGENIEIVFA 80
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 70.8 bits (174), Expect = 2e-15
Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 8/100 (8%)
Query: 157 EEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAK 216
+ +E + L V + E ++N IF +GP++ V+++
Sbjct: 9 HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---- 64
Query: 217 TGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
GF FV FE + AA A + G + + V +S
Sbjct: 65 ----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
>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 = 70.3 bits (173), Expect = 3e-15
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 1/98 (1%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
L V GL TT++ + FS+YG V ++ D T +SRGF FV F+
Sbjct: 7 GMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
+ + +DGR I + P
Sbjct: 67 DPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPSGPS 103
>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 = 70.4 bits (173), Expect = 4e-15
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 1/84 (1%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + + + V L +++ +FS G V R +++ D K G+SRG V FE
Sbjct: 6 SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFE 64
Query: 230 SRDDAAAAKDACTGMEIDGRQIRV 253
+A A G + R + V
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMHV 88
>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 = 70.0 bits (172), Expect = 4e-15
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 1/98 (1%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + R L + GLS TTE+ + + + ++G + V+ D + RSRGF FV F
Sbjct: 18 ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
S + AA A IDGR + +V + P
Sbjct: 78 SMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGSGPS 114
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 69.6 bits (171), Expect = 4e-15
Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L + ++ FS YGP+ V + GF FV FE DA A G
Sbjct: 7 NLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 246 IDGRQIRVDFS 256
I G ++RV+ S
Sbjct: 62 ICGSRVRVELS 72
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 69.4 bits (170), Expect = 5e-15
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ + ++ + +FSK G V +E ID TG+++GF FV S +DA + G
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
Query: 244 MEIDGR-QIRV 253
+D + ++ +
Sbjct: 77 KRLDLKHRLFL 87
>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 = 68.9 bits (169), Expect = 9e-15
Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 6/95 (6%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
++ + + G++ T+Q + FS +G + + V + +G+ FV F + +
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHE 72
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
AA A + G I+G ++ + T P
Sbjct: 73 SAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107
>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 = 68.9 bits (169), Expect = 9e-15
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 1/84 (1%)
Query: 175 NPQPSRCLGVFGLSIYTTEQQINHIFSKYG-PVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ + L + L Y E I+ F+ G V V+++ + TG G+CFV F
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 234 AAAAKDACTGMEIDGRQIRVDFSV 257
A G + G F +
Sbjct: 65 AEKCLHKINGKPLPGATPAKRFKL 88
>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 = 69.2 bits (170), Expect = 9e-15
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ L + + FS +G + +VV D S+G+ FV+FE+++ A A + G
Sbjct: 10 IKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 244 MEIDGRQIRVDF 255
M ++ R++ V
Sbjct: 68 MLLNDRKVFVGR 79
>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 = 69.2 bits (170), Expect = 9e-15
Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 1/97 (1%)
Query: 157 EEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAK 216
+ A + ++ Q L + L + EQ++ ++ +G V ++ D
Sbjct: 3 SGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-S 61
Query: 217 TGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+G SRG F ES + A G I
Sbjct: 62 SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS 98
>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 = 69.1 bits (169), Expect = 9e-15
Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 184 VFGLSIYTTEQQI---NHIFSKYGPVERVEVVIDAKTGRSR---GFCFVYFESRDDAAAA 237
V GLS + ++ F K+G + +V + S+ +V + +DA A
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79
Query: 238 KDACTGMEIDGRQIRVDFSVT 258
+ +DGR ++ T
Sbjct: 80 IQCVNNVVVDGRTLKASLGTT 100
>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 = 68.8 bits (169), Expect = 1e-14
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+ GLS TT++ + F ++G V+ V+ D T RSRGF FV F + +
Sbjct: 30 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SR 88
Query: 244 MEIDGRQIRVD 254
E+D + I
Sbjct: 89 HELDSKTIDPK 99
>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 = 69.1 bits (169), Expect = 1e-14
Identities = 21/112 (18%), Positives = 35/112 (31%), Gaps = 3/112 (2%)
Query: 145 RGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYG 204
++ + + M + + + GL T+++I FS
Sbjct: 10 HSSGLVPRGSHMASMTGGQQM--GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLE 67
Query: 205 PVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
V + G+ G FV F S++ A A I R I V S
Sbjct: 68 IVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS 118
>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 = 71.1 bits (174), Expect = 1e-14
Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 5/88 (5%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + PS L + + +E+ + +FS G V + + R +
Sbjct: 111 KNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMG 166
Query: 230 SRDDAAAAKDACTGMEI-DGRQIRVDFS 256
S ++A A ++ + +RV FS
Sbjct: 167 SVEEAVQALIDLHNHDLGENHHLRVSFS 194
Score = 63.4 bits (154), Expect = 6e-12
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T Q + +F YG V+RV+++ + + V + A A G ++ G+ I
Sbjct: 17 TPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPI 71
Query: 252 RVDFSVTQRAHTPTPG 267
R+ S Q P G
Sbjct: 72 RITLSKHQNVQLPREG 87
>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 = 68.2 bits (167), Expect = 2e-14
Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 8/93 (8%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVER--------VEVVIDAKTGRSR 221
+ + + + V GL+ T + F + G V+ + + +D +TG+ +
Sbjct: 6 SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65
Query: 222 GFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
G V +E A AA + G + G +++V
Sbjct: 66 GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVS 98
>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 = 67.7 bits (166), Expect = 2e-14
Identities = 26/101 (25%), Positives = 42/101 (41%), Gaps = 4/101 (3%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ R L V L+ +E+ + +F +G ++ V+ G S+G FV F
Sbjct: 6 SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFS 64
Query: 230 SRDDAAAAKDACTG---MEIDGRQIRVDFSVTQRAHTPTPG 267
S +A AA A G M + V F+ T + P+ G
Sbjct: 65 SHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSSG 105
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 14/66 (21%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+ ++ IFS++G + +++++ ++ + RG FV F+ A A + G + +R+
Sbjct: 27 KSLHAIFSRFGQI--LDILVS-RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Query: 254 DFSVTQ 259
++ T
Sbjct: 84 QYAKTD 89
>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 = 67.8 bits (166), Expect = 2e-14
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 10/97 (10%)
Query: 173 RENPQPSRC-LGVFGLSI-YTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
+ +P+ + + L+ + + IFSKYG V V +G+ FV + +
Sbjct: 20 KNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSN 71
Query: 231 RDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A AA G + G+ + ++ + + P
Sbjct: 72 ERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPS 108
>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 = 70.9 bits (174), Expect = 3e-14
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 13/107 (12%)
Query: 166 VEEFADGRENPQPSRC-LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFC 224
++ F E RC L V L TE+ +F +YG V + R RGF
Sbjct: 8 IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFG 61
Query: 225 FVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMG 271
F+ ESR A AK G + R +R+ F+ T + +
Sbjct: 62 FIRLESRTLAEIAKAELDGTILKSRPLRIRFA------THGAALTVK 102
Score = 68.9 bits (169), Expect = 2e-13
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
L V LS + + + FS++GPVE+ VV+D GR+ G FV F ++ A
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARK 152
Query: 237 AKDACT-GMEIDGRQIRV 253
A + C G + R
Sbjct: 153 ALERCGDGAFLLTTTPRP 170
>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 = 67.5 bits (165), Expect = 4e-14
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 8/95 (8%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R P+ L V+G + T + FS +G + ID R FV +E +
Sbjct: 33 RRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKME 84
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A A G +++ Q++V+ + Q G
Sbjct: 85 SADQAVAELNGTQVESVQLKVNIARKQPMLDAATG 119
>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 = 67.6 bits (165), Expect = 5e-14
Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 1/90 (1%)
Query: 167 EEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV 226
++ + R + C+ + GL + + F K VE + G++ G FV
Sbjct: 13 QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 72
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
F + D AA + R I+V
Sbjct: 73 EFRNEADYKAAL-CRHKQYMGNRFIQVHPI 101
>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 = 67.9 bits (166), Expect = 5e-14
Identities = 27/114 (23%), Positives = 43/114 (37%), Gaps = 6/114 (5%)
Query: 160 AEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGR 219
+ ++ C+ + GL TE I + FS PV RV + I GR
Sbjct: 27 GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPD-GR 84
Query: 220 SRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRP 273
G V F + ++A AA + + R I + + T A + G Y +
Sbjct: 85 VTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA---SNGAYSSQV 134
>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 = 70.0 bits (171), Expect = 5e-14
Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 5/88 (5%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + PS L + + +E+ + +FS G V + + R +
Sbjct: 142 KNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMG 197
Query: 230 SRDDAAAAKDACTGMEI-DGRQIRVDFS 256
S ++A A ++ + +RV FS
Sbjct: 198 SVEEAVQALIDLHNHDLGENHHLRVSFS 225
Score = 61.6 bits (149), Expect = 4e-11
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 6/94 (6%)
Query: 175 NPQPSRCLGVFGLSIYT-TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ L V L+ T Q + +F YG V+RV+++ + + V +
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQ 84
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A A G ++ G+ IR+ S Q P G
Sbjct: 85 AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREG 118
>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 = 66.9 bits (164), Expect = 5e-14
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L ++++ FS +G + +V+++ GRS+GF FV F S ++A A G
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 244 MEIDGRQIRVDF 255
+ + + V
Sbjct: 78 RIVATKPLYVAL 89
>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 = 68.4 bits (168), Expect = 6e-14
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTG--RSRGFCFVYFESRDDAAAAKDAC 241
V + +E+ + +F +YG V + V+ D +S+G CFV F +R A A++A
Sbjct: 8 VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67
Query: 242 TGMEIDGRQIRV 253
M++
Sbjct: 68 HNMKVLPGMHHP 79
Score = 68.0 bits (167), Expect = 1e-13
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 4/86 (4%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ N R L + +S TE I +FS +G +E ++ G SRG FV F +R
Sbjct: 89 KNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRA 147
Query: 233 DAAAAKDACTG---MEIDGRQIRVDF 255
A A A ME + V F
Sbjct: 148 MAQTAIKAMHQAQTMEGCSSPMVVKF 173
>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 = 66.5 bits (162), Expect = 8e-14
Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
D R PSR + + L I TE ++ + +G V + ++ + + F+
Sbjct: 21 MGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEM 74
Query: 229 ESRDDAAAAKDACT--GMEIDGRQIRVDFS 256
+ + A + T + G+ I + FS
Sbjct: 75 NTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 65.7 bits (161), Expect = 9e-14
Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
+++ + IFS YG + ++ + F F+ F++ A + + G++
Sbjct: 23 VSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECESQEMNFGKK 74
Query: 251 IRVDFSVTQRAHTPTPG 267
+ ++ S + G
Sbjct: 75 LILEVSSSNARPQFDHG 91
>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 = 65.9 bits (161), Expect = 1e-13
Identities = 22/97 (22%), Positives = 34/97 (35%), Gaps = 1/97 (1%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
+ + + + GL ++++I FS V + GRS G FV F
Sbjct: 6 SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFA 65
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTP 266
S++ A A I R I + S T P
Sbjct: 66 SQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGP 101
>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 = 65.5 bits (160), Expect = 2e-13
Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 1/84 (1%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ C + + T+ + E V+ G+ G V F++ D
Sbjct: 9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 68
Query: 233 DAAAAKDACTGMEIDGRQIRVDFS 256
DA ++ +++GR+ V
Sbjct: 69 DARKSERLH-RKKLNGREAFVHVV 91
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 64.9 bits (158), Expect = 3e-13
Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 8/98 (8%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
+ PSR + + L I TE ++ + +G V + ++ + + F+
Sbjct: 6 HHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEM 59
Query: 229 ESRDDAAAAKDACT--GMEIDGRQIRVDFSVTQRAHTP 264
+ + A + T + G+ I + FS + T
Sbjct: 60 NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 97
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 64.8 bits (158), Expect = 3e-13
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR-QI 251
+ I+ IFSK+G + + G+++G+ F+ + S A A G ++D +
Sbjct: 35 KNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
Query: 252 RVDF 255
RV+
Sbjct: 93 RVNL 96
>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 = 64.1 bits (156), Expect = 4e-13
Identities = 15/96 (15%), Positives = 38/96 (39%), Gaps = 8/96 (8%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ + PSR L + L TE ++ + +G V + ++ + + F+ + +
Sbjct: 9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEE 62
Query: 233 DAAAAKDACTGM--EIDGRQIRVDFSVTQRAHTPTP 266
A + + + + + I + +S + T P
Sbjct: 63 AAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGP 98
>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 = 68.0 bits (165), Expect = 5e-13
Identities = 16/87 (18%), Positives = 42/87 (48%), Gaps = 7/87 (8%)
Query: 177 QPSRCLGVFGLSIYTTE----QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+P+ + + L+ + + + IFS++G + +++++ ++ + RG FV F+
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVS-RSLKMRGQAFVIFKEVS 63
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQ 259
A A + G + +R+ ++ T
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYAKTD 90
Score = 56.0 bits (134), Expect = 5e-09
Identities = 29/192 (15%), Positives = 60/192 (31%), Gaps = 7/192 (3%)
Query: 66 KKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYR 125
K + + R+ K + + G + + +G G +++P
Sbjct: 95 AKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIM 154
Query: 126 KRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGVF 185
G G + + A P+ L +
Sbjct: 155 HHMPGQPPYMPPPG-MIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLT 213
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L T E ++ +F+++ + V +V FV F++ A AA+DA G +
Sbjct: 214 NLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFK 268
Query: 246 I-DGRQIRVDFS 256
I +++ F+
Sbjct: 269 ITQNNAMKISFA 280
>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 = 63.6 bits (155), Expect = 6e-13
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 3/81 (3%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
C+ + GL TE I + FS P+ RV + I GR G V F + +DA
Sbjct: 12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIG-PDGRVTGEADVEFATHEDAV 69
Query: 236 AAKDACTGMEIDGRQIRVDFS 256
AA A + R + + +
Sbjct: 70 AAM-AKDKANMQHRYVELFLN 89
>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 = 63.5 bits (155), Expect = 6e-13
Identities = 16/89 (17%), Positives = 38/89 (42%), Gaps = 10/89 (11%)
Query: 173 RENPQPSRCLGVFGLSIYT-TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
R + SR L + L + +++ + IFS YG + ++ + F F+ F++
Sbjct: 17 RGSHMKSR-LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQR 260
A + + G+++ ++ S +
Sbjct: 68 QSVRDAIEXESQEMNFGKKLILEVSSSNA 96
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 63.3 bits (154), Expect = 7e-13
Identities = 14/88 (15%), Positives = 25/88 (28%), Gaps = 5/88 (5%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
E + + V L + + G V R F+++
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLT-----WQGPRRRAFLHYPDSA 67
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQR 260
A A G+ + +RV + QR
Sbjct: 68 AAQQAVSCLQGLRLGTDTLRVALARQQR 95
>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 = 64.5 bits (157), Expect = 8e-13
Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEV-----VIDAKTGRSRGFCFVYF 228
E +P+ + V L+ + E+ + +IF +Y + K GR +G F+
Sbjct: 40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99
Query: 229 ESRDDAAAAKDACTGMEIDGRQIRVDFSVTQR 260
+ AA A G + G+ + V F+ + R
Sbjct: 100 PNEKAAAKALKEANGYVLFGKPMVVQFARSAR 131
>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 = 63.4 bits (154), Expect = 1e-12
Identities = 14/101 (13%), Positives = 37/101 (36%), Gaps = 11/101 (10%)
Query: 171 DGRENPQPSRCL--GVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
++ L GL + Q+ + K G V+ + + + + + F +
Sbjct: 17 GIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARY 70
Query: 229 ESRDDAAAAKDACTGMEI---DGRQIRVDFSVTQRAHTPTP 266
+ +++ A G E+ G++I + + ++ P
Sbjct: 71 RTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSGP 111
>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 = 62.2 bits (152), Expect = 1e-12
Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 9/83 (10%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM- 244
+ TE ++ FS+YG V V + R F FV F D A+ C
Sbjct: 12 RCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFA---DDQIAQSLCGEDL 63
Query: 245 EIDGRQIRVDFSVTQRAHTPTPG 267
I G + + + + P
Sbjct: 64 IIKGISVHISNAEPKHNSNSGPS 86
>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 = 62.5 bits (152), Expect = 2e-12
Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 3/79 (3%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
+ V G+ E + F V+ V ++ D GR+ G V F S D A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKD-HVGRNNGNGLVKFLSPQDTFEA 72
Query: 238 KDACTGMEIDGRQIRVDFS 256
M + R + V +
Sbjct: 73 LK-RNRMLMIQRYVEVSPA 90
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC-T 242
V GL TE + + F ++G + + VV + + F+ F +R A A +
Sbjct: 17 VGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEKSFN 70
Query: 243 GMEIDGRQIRVDF 255
+ ++GR++ V +
Sbjct: 71 KLIVNGRRLNVKW 83
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 61.7 bits (150), Expect = 3e-12
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 2/80 (2%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+N +R + + G T I G V +++ +G FV F+S +
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIES 64
Query: 234 AAAAKDACTGMEIDGRQIRV 253
A + G + + +
Sbjct: 65 AKKFVET-PGQKYKETDLLI 83
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 60.5 bits (147), Expect = 5e-12
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR-Q 250
+ I+ IFSK+G + + G+++G+ F+ + S A A G ++D +
Sbjct: 20 LKNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 77
Query: 251 IRV 253
RV
Sbjct: 78 FRV 80
>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 = 60.5 bits (147), Expect = 6e-12
Identities = 14/89 (15%), Positives = 27/89 (30%), Gaps = 7/89 (7%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S + V L + Q+++ + Y + R++ FV + + A A
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57
Query: 239 DACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
G+ + V T P
Sbjct: 58 QMFHQYSFRGKDLIVQLQPTDALLCSGPS 86
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 61.6 bits (149), Expect = 6e-12
Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 8/90 (8%)
Query: 171 DGRENPQPSRCL--GVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
G S L V L T ++ IFSK+G V ++ ++ + +
Sbjct: 18 AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQY 73
Query: 229 ESRDDAAAAKDACTGMEI--DGRQIRVDFS 256
A AK + G I +R+DFS
Sbjct: 74 ADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103
>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 = 60.3 bits (147), Expect = 7e-12
Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 9/84 (10%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
+ + V + T +++ F +YG V V + R F FV F
Sbjct: 4 SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFA-- 56
Query: 232 DDAAAAKDACTGM-EIDGRQIRVD 254
D A+ C I G + +
Sbjct: 57 -DDKVAQSLCGEDLIIKGISVHIS 79
>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 = 60.0 bits (146), Expect = 9e-12
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 175 NPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
+ + + G TE+ + + PV + +V +A G G+ FV F + ++
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAH-GNKTGYIFVDFSNEEEV 63
Query: 235 AAAKDACTGMEIDGRQIRVDFS 256
A C + GR I V
Sbjct: 64 KQALK-CNREYMGGRYIEVFRE 84
>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 = 61.2 bits (148), Expect = 9e-12
Identities = 22/124 (17%), Positives = 36/124 (29%), Gaps = 5/124 (4%)
Query: 135 GGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQ 194
G S + G ++ + + M + + GL + +
Sbjct: 2 GSSHHHHHHSSG--LVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVE 59
Query: 195 QINHIFSKYGPVERVEVV--IDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+ + S + V I + GR G FV S DD A + R I
Sbjct: 60 DVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE 118
Query: 253 VDFS 256
V S
Sbjct: 119 VFKS 122
>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 = 59.8 bits (145), Expect = 2e-11
Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 6/77 (7%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
+ L T +I FS++G + RV V F +A A
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRV------LLPEGGITAIVEFLEPLEARKAF 63
Query: 239 DACTGMEIDGRQIRVDF 255
+ + +++
Sbjct: 64 RHLAYSKFHHVPLYLEW 80
>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 = 59.1 bits (143), Expect = 3e-11
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 3/85 (3%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVV--IDAKTGRSRGFCFVYFESR 231
E + GL T + + + FS + + + G+ RG + ES
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFS 256
D A M + R + V
Sbjct: 66 QDVQKAL-EKHRMYMGQRYVEVYEI 89
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 58.1 bits (141), Expect = 5e-11
Identities = 19/82 (23%), Positives = 29/82 (35%), Gaps = 6/82 (7%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G R + V G Q++ F +GPV VV+D G F V
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKGV---FAIVEMGDV 55
Query: 232 DDAAAAKDACTGMEIDGRQIRV 253
A + + + G ++RV
Sbjct: 56 GAREAVL-SQSQHSLGGHRLRV 76
>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 = 60.1 bits (145), Expect = 5e-11
Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 8/92 (8%)
Query: 169 FADGRENPQPSR--CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV 226
G S + V L T ++ IFSK+G V ++ ++ +
Sbjct: 34 VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALL 89
Query: 227 YFESRDDAAAAKDACTGMEI--DGRQIRVDFS 256
+ A AK + G I +R+DFS
Sbjct: 90 QYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 58.4 bits (141), Expect = 8e-11
Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 4/90 (4%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVI---DAKTGRSRGFCFV 226
+ + + + GL T +++ F ++ P+ + I GR G FV
Sbjct: 14 VAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFV 73
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
F + A A + R I + S
Sbjct: 74 LFACEEYAQNAL-RKHKDLLGKRYIELFRS 102
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 56.1 bits (136), Expect = 2e-10
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSK-YGPVERVEVVIDAKTGRSRGFCFVYFESR 231
+ P L V L+ + + F K Y +VV+D +TG S+G+ FV F
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDE 61
Query: 232 DDAAAAKDACTG-MEIDGRQIRV 253
+ A C G + + + +R+
Sbjct: 62 LEQKRALTECQGAVGLGSKPVRL 84
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 56.6 bits (136), Expect = 3e-10
Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 9/97 (9%)
Query: 170 ADGRENPQPSRCL--GVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVY 227
+ + ++ L + T + + + G V+R+ R+ V
Sbjct: 14 GNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRI-----VIFKRNGIQAMVE 68
Query: 228 FESRDDAAAAKDACTGMEI--DGRQIRVDFSVTQRAH 262
FES A AK A G +I ++++++ R +
Sbjct: 69 FESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLN 105
>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 = 55.7 bits (134), Expect = 5e-10
Identities = 20/83 (24%), Positives = 29/83 (34%), Gaps = 3/83 (3%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVV--IDAKTGRSRGFCFVYFESRDD 233
+ + GL + + + + S + V V I + GR G FV ES DD
Sbjct: 14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDD 73
Query: 234 AAAAKDACTGMEIDGRQIRVDFS 256
A + R I V S
Sbjct: 74 VKLAL-KKDRESMGHRYIEVFKS 95
>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 = 55.3 bits (133), Expect = 5e-10
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E+ + KYG VE + V D G +V F +DA A +G+ I
Sbjct: 41 EEVFTEMEEKYGEVEEM-NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 253 VDFS 256
+ S
Sbjct: 100 AELS 103
>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 = 56.0 bits (134), Expect = 2e-09
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 2/82 (2%)
Query: 175 NPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
N +R + + G T I G V +++ +G FV F+S + A
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 163
Query: 235 AAAKDACTGMEIDGRQIRVDFS 256
+ G + + + F
Sbjct: 164 KKFVET-PGQKYKETDLLILFK 184
>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 = 52.4 bits (126), Expect = 3e-09
Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEV-----VIDAKTGRSRGFCFVYFESRDD 233
+R L V + TE+ + F+ + + V+ + + + F F+ F S D+
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 234 AAAAKDACTGMEIDGRQIRV 253
A A G+ G+ +++
Sbjct: 66 TTQAM-AFDGIIFQGQSLKI 84
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 51.8 bits (124), Expect = 1e-08
Identities = 12/83 (14%), Positives = 23/83 (27%), Gaps = 3/83 (3%)
Query: 171 DGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
+ P + + L + Q + + + T G + F S
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPS 76
Query: 231 RDDAAAAKDACTGMEIDGRQIRV 253
+ A + +E G I V
Sbjct: 77 EEILVEALERLNNIEFRGSVITV 99
>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 = 51.3 bits (123), Expect = 2e-08
Identities = 12/72 (16%), Positives = 21/72 (29%), Gaps = 7/72 (9%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL + Q + + G V +V G V F ++D A
Sbjct: 20 VSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYAVRKLDN 72
Query: 244 MEIDGRQIRVDF 255
+ + +
Sbjct: 73 TKFRSHEGETAY 84
>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 = 50.7 bits (121), Expect = 2e-08
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 9/97 (9%)
Query: 173 RENPQPSRCLGVFGL-SIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
+ + R + + L ++ + + YG ++ ++ R + F+ E+R
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETR 72
Query: 232 DDAAAAKDACTGM--EIDGRQIRVDFSVTQRAHTPTP 266
+DA A D C GR ++VD S + P
Sbjct: 73 EDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGP 109
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 50.4 bits (120), Expect = 4e-08
Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 10/89 (11%)
Query: 175 NPQPSRCLGVF--GLSIYTTEQQINHIFSKYGPVERVEVVIDAK--TGRSRGFCFVYFES 230
+ S VF GL E +I F ++GP+ +G+ F+ F+
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
Query: 231 RDDAAAAKDACT------GMEIDGRQIRV 253
A DAC + + I+
Sbjct: 62 ESSVQALIDACLEEDGKLYLCVSSPTIKD 90
>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 = 48.1 bits (115), Expect = 2e-07
Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 14/97 (14%)
Query: 176 PQPSRCL---GVFGLSIYTTEQQINHI-------FSKYGPVERVEVVIDAKTGRSRGFCF 225
P ++C +F I +K+G V + +D + + G +
Sbjct: 4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHI--YVDKNSAQ--GNVY 59
Query: 226 VYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRAH 262
V S A AA +A G G+ I + H
Sbjct: 60 VKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYH 96
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 50.6 bits (120), Expect = 2e-07
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L E +I +FS+ G ++R+ V S+ FV F+ + +A AK+A +
Sbjct: 150 HLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQT 203
Query: 246 IDGRQIRVDFSVTQ 259
+ + +
Sbjct: 204 LLLPSDKEWDDRRE 217
>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 = 46.0 bits (109), Expect = 1e-06
Identities = 15/104 (14%), Positives = 29/104 (27%), Gaps = 7/104 (6%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G + + + V GL + Q + + G V +V G V F +
Sbjct: 9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRK 61
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRPTY 275
+D A + + + + +P R
Sbjct: 62 EDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRS 105
Score = 26.7 bits (59), Expect = 6.8
Identities = 9/26 (34%), Positives = 10/26 (38%)
Query: 108 PRGRRGGYRSRSRSPGYRKRSSSYRS 133
G R RSRS + S RS
Sbjct: 90 VDGPRSPSYGRSRSRSRSRSRSRSRS 115
>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 = 45.2 bits (107), Expect = 2e-06
Identities = 20/91 (21%), Positives = 32/91 (35%), Gaps = 12/91 (13%)
Query: 177 QPSRCL---GVFGLSIYTTEQQINHI-------FSKYGPVERVEV--VIDAKTGRSRGFC 224
P+ L + +++ I SKYG V+ +E+ +D G
Sbjct: 3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKI 62
Query: 225 FVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
FV F S D A TG + R + +
Sbjct: 63 FVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93
>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 = 43.7 bits (103), Expect = 6e-06
Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 9/97 (9%)
Query: 173 RENPQPSRCLGVFGLSI-YTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
+ + R + + Q+ + +G + ++ F+ +
Sbjct: 9 KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATT 62
Query: 232 DDAAAAKDACTGM--EIDGRQIRVDFSVTQRAHTPTP 266
+DA AA D T + G+ +RV S + P
Sbjct: 63 EDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKSGP 99
>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 = 43.9 bits (104), Expect = 6e-06
Identities = 15/97 (15%), Positives = 30/97 (30%), Gaps = 15/97 (15%)
Query: 170 ADGRENPQPSRCL---GVFGLSIYTTEQQINHIF--------SKYGPVERVEVVIDAKTG 218
+ G + R + +F + + + + SK+G + ++ +
Sbjct: 6 SGGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH--- 62
Query: 219 RSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
G V F ++A G GRQI
Sbjct: 63 -PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 42.1 bits (99), Expect = 2e-05
Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 1/65 (1%)
Query: 193 EQQINHIFSKYGPVERVEV-VIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E + KYG V + + I F+ FE + A A G GR +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 252 RVDFS 256
+ F
Sbjct: 87 KACFY 91
>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 = 45.8 bits (108), Expect = 2e-05
Identities = 48/273 (17%), Positives = 83/273 (30%), Gaps = 107/273 (39%)
Query: 164 AMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVER-VEV---------VI 213
+++E+ + E PS L + L+ + +N + + P + VE+ V+
Sbjct: 322 SILEDSLENNEG-VPSPMLSISNLTQEQVQDYVNK-TNSHLPAGKQVEISLVNGAKNLVV 379
Query: 214 DAKTG--RS-RGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQRA--------- 261
+G +S G R A + G++ Q R+ FS +R
Sbjct: 380 ---SGPPQSLYGLNLTL---RKAKAPS-----GLD----QSRIPFS--ERKLKFSNRFLP 422
Query: 262 -----HTPTPGIYMGRPTYEQLNNTQSELGSLLSEKHAIKGGKFEE-VFGEIATVVGVGA 315
H+ + P + + L+ + + V+ T G
Sbjct: 423 VASPFHSH----LL-VPASDLI------NKDLVKNNVSFNAKDIQIPVY---DTFDG--- 465
Query: 316 VTMTEMSGN--GRISPLQFSGGMENTDPICTQ----EKAKKMKKS-I-----GMNLSALP 363
+ +SG+ RI D I E + K + I G S L
Sbjct: 466 SDLRVLSGSISERI-----------VDCIIRLPVKWETTTQFKATHILDFGPG-GASGL- 512
Query: 364 QWGPLT----------------LDETIDCSHGF 380
G LT LD D +GF
Sbjct: 513 --GVLTHRNKDGTGVRVIVAGTLDINPDDDYGF 543
Score = 31.6 bits (71), Expect = 0.67
Identities = 47/263 (17%), Positives = 80/263 (30%), Gaps = 83/263 (31%)
Query: 143 GGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSK 202
G +GK I E + + E DG+ + +F E ++ F
Sbjct: 1678 GEKGKRI--------RENYSAMIFETIVDGKLKTEK-----IFK---EINEHSTSYTFR- 1720
Query: 203 YGPVER-------------VEVVIDAKTGRSRGFCFVYFESRDDAAA--------AKDAC 241
+E + +S+G D A A +
Sbjct: 1721 -SEKGLLSATQFTQPALTLMEKAA-FEDLKSKGL-----IPADATFAGHSLGEYAALASL 1773
Query: 242 TG-MEI-DGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQSELGSLLSEKHAIKGGK 299
M I + V V R G+ M Q+ + ELG AI G+
Sbjct: 1774 ADVMSIESL--VEV---VFYR------GMTM------QVAVPRDELGRSNYGMIAINPGR 1816
Query: 300 FEEVFGEIATVVGVGAVTMTEMSG--------NGRISPLQF--SGGMENTDPICTQEKAK 349
F + A V V + +G N + Q+ +G + D +
Sbjct: 1817 VAASFSQEALQYVVERVG--KRTGWLVEIVNYN--VENQQYVAAGDLRALDTVTNVLNFI 1872
Query: 350 KMKKSIGMNLSALPQWGPLTLDE 372
K++K I ++ L + L+L+E
Sbjct: 1873 KLQK-I--DIIELQK--SLSLEE 1890
>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 = 42.4 bits (100), Expect = 3e-05
Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 201 SKYGPVERVEVVIDAKTGRSR----GFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
K+G V RV + + + FV F + A A G GR++ +
Sbjct: 47 GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>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 = 40.9 bits (95), Expect = 5e-04
Identities = 16/105 (15%), Positives = 40/105 (38%), Gaps = 18/105 (17%)
Query: 177 QPSRCLGV--FGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
++ L V GL + Q+ + K G V+ + + ++ + F + + +++
Sbjct: 16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEES 69
Query: 235 AAAKDACTGMEI---DGRQIRVDFSVTQRAHTPT-------PGIY 269
A G E+ G++I + + ++ PG+
Sbjct: 70 KRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLM 114
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 36.9 bits (85), Expect = 0.002
Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 6/71 (8%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+ +F Y + +S + F + AA A+ E G+++++
Sbjct: 25 AKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL 78
Query: 254 DFSVTQRAHTP 264
F+ T +
Sbjct: 79 YFAQTLHIGSS 89
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 35.4 bits (81), Expect = 0.005
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+Q + F+++G V+ VE+ + V E+ DA A ++ +I ++I
Sbjct: 27 QQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL 83
Query: 253 VDFSVTQRAHTPTPG 267
V S+ A P+ G
Sbjct: 84 V--SLATGASGPSSG 96
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 32.1 bits (72), Expect = 0.077
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 5/52 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
++ + + KYG V + V+ K G + V F + A A G
Sbjct: 30 SKDVLLRLLQKYGEVLNL-VLSSKKPGTA----VVEFATVKAAELAVQNEVG 76
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 31.5 bits (71), Expect = 0.12
Identities = 16/87 (18%), Positives = 25/87 (28%), Gaps = 14/87 (16%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIF-----SKYGPVERVEVVIDAKTGRSRGFCFV 226
G + V GL ++ + F S GPV + R +
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVL 52
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIRV 253
F DA E+ G Q+ +
Sbjct: 53 TFREPADAERVLAQ-ADHELHGAQLSL 78
>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 = 32.9 bits (74), Expect = 0.23
Identities = 29/234 (12%), Positives = 57/234 (24%), Gaps = 76/234 (32%)
Query: 164 AMVEEFADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDA--KTGRSR 221
A V+ F D ++ + SI + E+ I+HI V +
Sbjct: 28 AFVDNF-DCKDVQDMPK-------SILSKEE-IDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 222 GFCFVYFESRDD----AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQ 277
FV R + + K + R + + R +
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL--QP 136
Query: 278 LNNTQSELGSLLSEKHAIKGGKFEEVFGEIATVVGVGAVTMTEMSGNGRISPLQFSGGME 337
+ L L K+ + + G + G+G
Sbjct: 137 YLKLRQALLELRPAKNVL-------IDG---------------VLGSG------------ 162
Query: 338 NTDPICTQEKAKKMKKSIGMNLSALPQWGPLTLDETIDCSHGFNSQMGWISGGN 391
K+ + L L + C + ++ W++ N
Sbjct: 163 ---------------KTW-VALDVC-------LSYKVQCK--MDFKIFWLNLKN 191
Score = 29.8 bits (66), Expect = 1.8
Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 21/87 (24%)
Query: 16 EPDGKVPVW---YLCRSHVSGRLLPKEPAQTSSD--QCY--YR--------LSPARSGSA 60
+ D +P + Y SH+ L E + + + +R S A + S
Sbjct: 460 DSDDLIPPYLDQYFY-SHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASG 518
Query: 61 GSIDD----KKYRKSITRSRSGSPHRR 83
++ K Y+ I + R
Sbjct: 519 SILNTLQQLKFYKPYICDN-DPKYERL 544
>2xzm_7 Plectin/S10 domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_7
Length = 162
Score = 30.0 bits (67), Expect = 0.78
Identities = 10/62 (16%), Positives = 16/62 (25%)
Query: 85 KRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGG 144
K V R ++ GR G R++ R G +
Sbjct: 93 KASNVNFISKEEDEEERPRRQFNKGGRTGERDGRNKRGVGRGTRREGEEAAKEEGAAETA 152
Query: 145 RG 146
+G
Sbjct: 153 QG 154
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 28.4 bits (63), Expect = 1.7
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T + ++ +FS +G ++ ++ V AK G + F+ + A A Q
Sbjct: 31 TCREDLHILFSNHGEIKWIDFVRGAKEG------IILFK--EKAKEALGKAKDANNGNLQ 82
Query: 251 IR 252
+R
Sbjct: 83 LR 84
>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I
2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I
3i8f_K 3i8i_K 3i9c_K 3i9e_K ...
Length = 148
Score = 28.7 bits (65), Expect = 2.0
Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 206 VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
+E + + I + G ++ + V ++D A A G+ ID +++ ++
Sbjct: 72 LENLTLTIPVRAGETKIYGSV--TAKDIAEALSRQ-HGVTIDPKRLALE 117
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 28.6 bits (64), Expect = 2.8
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 6/69 (8%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGF-----CFVYFESRDDAAAAKDACTGME 245
E ++ K+G V RV ++ K G FV F + A A G
Sbjct: 141 DLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW 199
Query: 246 IDGRQIRVD 254
GR++ +
Sbjct: 200 FAGRKVVAE 208
>4dim_A Phosphoribosylglycinamide synthetase; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG,
ligase; 2.61A {Anaerococcus prevotii}
Length = 403
Score = 28.8 bits (65), Expect = 3.6
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 8/43 (18%)
Query: 140 DSYGGRGKIII--------AVVTEVEEEAEATAMVEEFADGRE 174
D G +G I + +VEEF +G E
Sbjct: 153 DLQGSKGIYIAKKEEEAIDGFNETMNLTKRDYCIVEEFIEGYE 195
>1f7u_A Arginyl-tRNA synthetase; RNA-protein complex, aminoacylation; HET:
PSU 1MG 2MG H2U M2G 5MC 5MU 1MA ARG; 2.20A
{Saccharomyces cerevisiae} SCOP: a.27.1.1 c.26.1.1
d.67.2.1 PDB: 1bs2_A* 1f7v_A*
Length = 607
Score = 27.7 bits (62), Expect = 9.3
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 306 EIATVVGVGAVTMTEMSGNGRISPLQFS 333
E+A +VG+ AV + +M G RI+ +F
Sbjct: 448 EVADLVGISAVMIQDMQGK-RINNYEFK 474
>3ax6_A Phosphoribosylaminoimidazole carboxylase, ATPase; structural
genomics, riken structural genomics/proteomics in RSGI,
ATP grAsp, ATP binding; HET: ADP; 2.20A {Thermotoga
maritima}
Length = 380
Score = 27.5 bits (62), Expect = 9.6
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 132 RSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFAD 171
R GG Y GRG II ++E + +EEF +
Sbjct: 140 RKGG------YDGRGVFIIKNEKDLENAIKGETYLEEFVE 173
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
0.316 0.134 0.399
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: 6,221,848
Number of extensions: 380610
Number of successful extensions: 1340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1168
Number of HSP's successfully gapped: 238
Length of query: 403
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 307
Effective length of database: 4,021,377
Effective search space: 1234562739
Effective search space used: 1234562739
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.1 bits)