RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15152
(192 letters)
>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 = 166 bits (423), Expect = 2e-53
Identities = 95/142 (66%), Positives = 119/142 (83%), Gaps = 1/142 (0%)
Query: 8 KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDE-EPGPQRSVEGWILFVTGV 66
+GI RLKEKA+ +KGRGFG++++TR I YE + + DE EPGPQRSVEGWILFVT +
Sbjct: 21 QGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI 80
Query: 67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
HEEAQED++ EKF +YGEIKN+HLNLDRRTGF KGYALVEY+++K+A AA++ALNG I+
Sbjct: 81 HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM 140
Query: 127 GQTVTVDWCFVKGPKKVAGEQK 148
GQT+ VDWCFVKGPK+V +K
Sbjct: 141 GQTIQVDWCFVKGPKRVKKSEK 162
>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 = 154 bits (391), Expect = 4e-49
Identities = 77/109 (70%), Positives = 93/109 (85%), Gaps = 1/109 (0%)
Query: 35 IREYESMETDVGDE-EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLD 93
I YE + + DE EPGPQRSVEGWILFVT +HEEAQED++ EKF +YGEIKN+HLNLD
Sbjct: 2 IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61
Query: 94 RRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
RRTGF KGYALVEY+++K+A AA++ALNG I+GQT+ VDWCFVKGPK+
Sbjct: 62 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 153 bits (388), Expect = 1e-48
Identities = 74/105 (70%), Positives = 92/105 (87%), Gaps = 2/105 (1%)
Query: 36 REYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR 95
+Y+S+E D +EPGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRR
Sbjct: 3 EDYDSVEQD--GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60
Query: 96 TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
TG+LKGY LVEY++YKEA AA + LNG ++GQ ++VDWCFV+GP
Sbjct: 61 TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105
>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 = 149 bits (377), Expect = 8e-47
Identities = 75/106 (70%), Positives = 93/106 (87%), Gaps = 2/106 (1%)
Query: 37 EYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT 96
+Y+S+E D +EPGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRT
Sbjct: 3 DYDSVEQD--GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 97 GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
G+LKGY LVEY++YKEA AA + LNG ++GQ ++VDWCFV+GP K
Sbjct: 61 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK 106
>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 = 93.1 bits (232), Expect = 3e-25
Identities = 22/84 (26%), Positives = 44/84 (52%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
+R+ + + VT + E+ +E D+ E F +G I ++L D+ TG KG+A + +
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 111 KEASAARDALNGTTILGQTVTVDW 134
++A+ A ++G + V+W
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEW 91
>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 = 84.9 bits (210), Expect = 2e-21
Identities = 26/89 (29%), Positives = 44/89 (49%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
GD E + + L+V + E+ ++E FS+ G+IK + + LD+ G+ V
Sbjct: 27 GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
EY S +A A +NGT + + + DW
Sbjct: 87 EYYSRADAENAMRYINGTRLDDRIIRTDW 115
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 82.5 bits (204), Expect = 1e-20
Identities = 23/116 (19%), Positives = 43/116 (37%)
Query: 19 KKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEK 78
G S + + M P L V + D +
Sbjct: 8 HHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRV 67
Query: 79 FSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
F +YG + ++++ DR T +G+A V + ++A A DA++G + G+ + V
Sbjct: 68 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123
>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 = 81.7 bits (202), Expect = 1e-20
Identities = 26/104 (25%), Positives = 43/104 (41%), Gaps = 8/104 (7%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGF 98
P + ++V G+++ DD+ + F + G +K +H+ LD+ TG
Sbjct: 4 GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63
Query: 99 LKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
KG A V Y+ A AA + +G G + V K P
Sbjct: 64 PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107
>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 = 78.8 bits (195), Expect = 1e-19
Identities = 22/74 (29%), Positives = 40/74 (54%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V G+ E+ E + E F + G + N H+ DR TG +GY VE+ S ++A A +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 121 NGTTILGQTVTVDW 134
+ + G+ + V+
Sbjct: 78 DMIKLYGKPIRVNK 91
>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 = 78.4 bits (194), Expect = 1e-19
Identities = 19/88 (21%), Positives = 41/88 (46%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+++ + + E+ + + S G + NL + D +TG KGYA +E+ + +++A L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
NG + + + + V+ E
Sbjct: 65 NGYQLGSRFLKCGYSSNSDISGVSLEHH 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 = 79.9 bits (197), Expect = 1e-19
Identities = 24/120 (20%), Positives = 46/120 (38%)
Query: 15 EKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDD 74
EK K+ G + + T+ L V + D
Sbjct: 27 EKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDT 86
Query: 75 MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
+ F +YG + ++++ DR T +G+A V + ++A A DA++G + G+ + V
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 78.6 bits (194), Expect = 2e-19
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 50 PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
P + V +++ +E + + +YGE++ + + L RT G A V + S
Sbjct: 3 QIPLKEV-----TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTS 57
Query: 110 YKEASAARDALNGTTILGQTVTVD 133
+ A L+ T+++G +
Sbjct: 58 TRGAKETVKNLHLTSVMGNIIHAQ 81
>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 = 77.3 bits (191), Expect = 4e-19
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V + + E + + FS+ G K+ + + + Y VE+ +++A+AA A+
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 75
Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
NG ILG+ V V+W +K
Sbjct: 76 NGRKILGKEVKVNWATTPSSQK 97
>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 = 76.5 bits (189), Expect = 8e-19
Identities = 24/83 (28%), Positives = 38/83 (45%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
G S LFV + + E+D+ + FS YG + LH +D T KG+A V +
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 111 KEASAARDALNGTTILGQTVTVD 133
+ A A ++G G+ + V
Sbjct: 61 EHAVKAYAEVDGQVFQGRMLHVL 83
>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 = 76.6 bits (189), Expect = 8e-19
Identities = 20/85 (23%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSY 110
+ + V + +A + ++ E FS +GE+K + L TG +G+ V++ +
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 111 KEASAARDAL-NGTTILGQTVTVDW 134
++A A +AL + T + G+ + ++W
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEW 93
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 77.5 bits (191), Expect = 9e-19
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 5/108 (4%)
Query: 27 TETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK 86
T + + S + +R L+V G+ EE + +H F +G+I
Sbjct: 37 TCVNCTERHVDGGSGGSGGSGGSATTKRV-----LYVGGLAEEVDDKVLHAAFIPFGDIT 91
Query: 87 NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
++ + LD T +G+A VE++ ++A+AA D +N + + G+T+ V+
Sbjct: 92 DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
>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 = 76.1 bits (188), Expect = 1e-18
Identities = 16/74 (21%), Positives = 35/74 (47%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V + D + F +YG + ++++ + T +G+A V + ++A A A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 121 NGTTILGQTVTVDW 134
+G + G+ + V
Sbjct: 76 DGAELDGRELRVQV 89
>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 = 75.8 bits (187), Expect = 2e-18
Identities = 27/74 (36%), Positives = 38/74 (51%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV + EA E+ + + FSE G + + L DR TG KGY EY + A +A L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 121 NGTTILGQTVTVDW 134
NG G+ + VD
Sbjct: 71 NGREFSGRALRVDN 84
>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 = 76.3 bits (188), Expect = 2e-18
Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 5/106 (4%)
Query: 29 TSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNL 88
S + P P L V G+ E D+ E FS+YG I ++
Sbjct: 22 ASMTGGQQMGRGSRHVGNRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADV 76
Query: 89 HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
+ D+++ +G+A V +++ +A A++ NG + G+ + VD+
Sbjct: 77 SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>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 = 75.3 bits (186), Expect = 2e-18
Identities = 24/74 (32%), Positives = 46/74 (62%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V G+ EE + +H F +G+I ++ + LD T +G+A VE++ ++A+AA D +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 121 NGTTILGQTVTVDW 134
N + + G+T+ V+
Sbjct: 75 NESELFGRTIRVNL 88
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 75.4 bits (186), Expect = 2e-18
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
S+E LF++G+ ++++ E +G +K+L L +R G KG A VEY++
Sbjct: 10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENE 68
Query: 111 KEASAARDALNGTTILGQTVTVD 133
+AS A ++G TI + V
Sbjct: 69 SQASQAVMKMDGMTIKENIIKVA 91
>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 = 74.5 bits (184), Expect = 3e-18
Identities = 24/74 (32%), Positives = 46/74 (62%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V G+ EE + +H F +G+I ++ + LD T +G+A VE++ ++A+AA D +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 121 NGTTILGQTVTVDW 134
N + + G+T+ V+
Sbjct: 70 NESELFGRTIRVNL 83
>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 = 74.3 bits (183), Expect = 5e-18
Identities = 29/97 (29%), Positives = 40/97 (41%), Gaps = 9/97 (9%)
Query: 45 VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRT 96
+G S I FV G+ E + + + F + G IK ++L DR T
Sbjct: 1 MGHHHHHHSHSDNNTI-FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59
Query: 97 GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
G LKG A V +D A AA D +G G + V
Sbjct: 60 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96
>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 = 73.8 bits (182), Expect = 7e-18
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 40 SMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL 99
S + P P L V G+ E D+ E FS+YG I ++ + D+++
Sbjct: 2 SSGSSGNRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 56
Query: 100 KGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
+G+A V +++ +A A++ NG + G+ + V
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG 91
>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 = 76.2 bits (188), Expect = 9e-18
Identities = 23/79 (29%), Positives = 34/79 (43%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ G+ +D + E + +G +K +L D TG KGYA EY A L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 121 NGTTILGQTVTVDWCFVKG 139
NG + + + V V
Sbjct: 177 NGMQLGDKKLLVQRASVGA 195
Score = 61.2 bits (149), Expect = 4e-12
Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 6/100 (6%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
L+V + E+ M + F+ + L L + K +A +E+ S E +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 116 ARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGV 155
A A +G GQ++ + P E GV
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGV 105
>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 = 73.9 bits (182), Expect = 1e-17
Identities = 23/109 (21%), Positives = 46/109 (42%), Gaps = 8/109 (7%)
Query: 26 GTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEI 85
G+ S+ EIR+ PG V L++ + E D+ F+ + E
Sbjct: 1 GSSGSSGEEIRKIPMF----SSYNPGEPNKV----LYLKNLSPRVTERDLVSLFARFQEK 52
Query: 86 KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
K + TG ++G A + + + + A A +NG + G+ + +++
Sbjct: 53 KGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF 101
>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 = 73.0 bits (180), Expect = 1e-17
Identities = 23/73 (31%), Positives = 36/73 (49%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V +H ED + F +G+I N+ L D TG KGY + + + A A + L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 121 NGTTILGQTVTVD 133
NG + G+ + V
Sbjct: 68 NGFELAGRPMRVG 80
>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 = 73.0 bits (180), Expect = 2e-17
Identities = 15/73 (20%), Positives = 34/73 (46%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V+ + +D++ FS+YG++ + + D+ T KG A + + A A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 121 NGTTILGQTVTVD 133
N + G+ +
Sbjct: 79 NNKQLFGRVIKAS 91
>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 = 74.1 bits (183), Expect = 3e-17
Identities = 19/74 (25%), Positives = 37/74 (50%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V + ++ + +++ F G I + D +TG+ GYA V++ S ++ A L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 121 NGTTILGQTVTVDW 134
NG T+ + + V +
Sbjct: 66 NGITVRNKRLKVSY 79
Score = 61.8 bits (151), Expect = 1e-12
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+VT + +D + F +YG I ++ D+ TG +G A V Y+ +EA A AL
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 121 NGTTILGQT--VTVDW 134
N G + ++V
Sbjct: 152 NNVIPEGGSQPLSVRL 167
>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 = 73.8 bits (182), Expect = 5e-17
Identities = 22/74 (29%), Positives = 33/74 (44%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ G+ +D + E + +G +K +L D TG KGYA EY A L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 121 NGTTILGQTVTVDW 134
NG + + + V
Sbjct: 157 NGMQLGDKKLLVQR 170
Score = 56.5 bits (137), Expect = 2e-10
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
L+V + E+ M + F+ + L L + K +A +E+ S E +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 116 ARDALNGTTILGQTVTVDW 134
A A +G GQ++ +
Sbjct: 67 AM-AFDGIIFQGQSLKIRR 84
>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 = 71.4 bits (176), Expect = 5e-17
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAARDA 119
+ + + +D + E FS YG+IK + + ++R KGYA VE+++ EA A
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 120 LNGTTILGQTVTVD 133
++G I GQ +T
Sbjct: 67 MDGGQIDGQEITAT 80
>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 = 73.4 bits (181), Expect = 6e-17
Identities = 22/74 (29%), Positives = 36/74 (48%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V + + +++ F GEI++ L D+ TG GY V Y K+A A + L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 121 NGTTILGQTVTVDW 134
NG + +T+ V +
Sbjct: 65 NGLRLQTKTIKVSY 78
Score = 60.3 bits (147), Expect = 5e-12
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V+G+ + + ++ + FS+YG I + +D+ TG +G + +D EA A L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 121 NGTTILGQT--VTVDW 134
NG G T +TV +
Sbjct: 151 NGQKPSGATEPITVKF 166
>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 = 71.2 bits (175), Expect = 1e-16
Identities = 22/74 (29%), Positives = 37/74 (50%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V +H ED + F +G I+++ L +D TG KGY + + + A A + L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 121 NGTTILGQTVTVDW 134
NG + G+ + V
Sbjct: 89 NGFELAGRPMKVGH 102
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 70.8 bits (174), Expect = 1e-16
Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 6/96 (6%)
Query: 39 ESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGF 98
+ E+ Q S + ++ G+ + M + FS +G+I + + +
Sbjct: 6 SGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----- 60
Query: 99 LKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
KGY+ V + +++ A+ A ++NGTTI G V W
Sbjct: 61 -KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 95
>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 = 70.0 bits (172), Expect = 3e-16
Identities = 25/108 (23%), Positives = 40/108 (37%), Gaps = 5/108 (4%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G + + LF+ + E D+ F E+G+I L + DR TG KG A +
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 106 EYDSYKEASAARDALNGTTIL---GQTVTVDWCFVKGPKKVAGEQKVG 150
Y + A A+ AL+ L + + V + G
Sbjct: 61 TYCERESALKAQSALHEQKTLPGMNRPIQVK--PADSESRGGSGPSSG 106
>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 = 69.5 bits (171), Expect = 3e-16
Identities = 20/72 (27%), Positives = 33/72 (45%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L++ G+ + D+ + YG+I + LD+ T KGY V++DS A A AL
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 121 NGTTILGQTVTV 132
+ + Q
Sbjct: 68 KASGVQAQMAKQ 79
>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 = 70.9 bits (174), Expect = 3e-16
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V + E + + F YG I+++ + DR T +GY V++ S A A L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 121 NGTTILGQTVTVDW 134
NG IL + + V
Sbjct: 105 NGFNILNKRLKVAL 118
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 73.5 bits (181), Expect = 3e-16
Identities = 21/82 (25%), Positives = 32/82 (39%)
Query: 53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
Q +L V + + E +G ++ L RTG KGY EY
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149
Query: 113 ASAARDALNGTTILGQTVTVDW 134
A+ A+ L G + +T+ V W
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHW 171
Score = 67.7 bits (166), Expect = 5e-14
Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 61 LFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
L V + D + S L + G LKG+A++EY++ + A A+
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQ 245
Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
+G ++ G + V +C P +
Sbjct: 246 ADGLSLGGSHLRVSFCAPGPPGR 268
Score = 58.1 bits (141), Expect = 1e-10
Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+ + G+ + ++H+ S+Y +K ++ KG A V + ++A AA +A
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY------KGTAFVTLLNGEQAEAAINAF 77
Query: 121 NGTTILGQTVTVDW 134
+ + + + ++V
Sbjct: 78 HQSRLRERELSVQL 91
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 70.1 bits (172), Expect = 4e-16
Identities = 29/106 (27%), Positives = 44/106 (41%), Gaps = 8/106 (7%)
Query: 53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYAL 104
Q + + +FV G+ E + + + F + G IK ++L DR TG LKG A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVG 150
V +D A AA D +G G + V + + G G
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRG 107
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 69.3 bits (170), Expect = 4e-16
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++ + A E D+ F +G I + + KG ++YD++++A+ AL
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVAL 83
Query: 121 NGTTILGQTVTVDW 134
G+ + W
Sbjct: 84 ANFPFQGRNLRTGW 97
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 68.9 bits (169), Expect = 6e-16
Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 6/91 (6%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYD 108
G + + + D + S Y + N+ L D++T +G+A V+
Sbjct: 2 GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61
Query: 109 SYKEASAARDALNGT----TILGQTVTVDWC 135
S +AS L I G+T+ VD+
Sbjct: 62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 69.2 bits (170), Expect = 6e-16
Identities = 23/74 (31%), Positives = 42/74 (56%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV G+ + E + + FS+YG+I + + DR T +G+ V +++ +A A A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 121 NGTTILGQTVTVDW 134
NG ++ G+ + VD
Sbjct: 75 NGKSVDGRQIRVDQ 88
>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 = 70.7 bits (174), Expect = 8e-16
Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 6/96 (6%)
Query: 45 VGDEEPGPQRSVEGWI-LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYA 103
+ + + V L + ED++ E F + EI+ L + G KG A
Sbjct: 85 LEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIA 139
Query: 104 LVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG 139
+E+ S +A + G I G++V++ + KG
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175
Score = 62.2 bits (152), Expect = 1e-12
Identities = 19/97 (19%), Positives = 43/97 (44%), Gaps = 2/97 (2%)
Query: 53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
S + LF+ ++ ++ SE +L + +D RTG + + V+++S ++
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAED 66
Query: 113 ASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKV 149
A + L G + G + ++ + KKV + +
Sbjct: 67 LEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTL 102
>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 = 68.5 bits (168), Expect = 9e-16
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G ++ L ++ + A E+ + E F + IK + G KGYA +
Sbjct: 8 NSTWSGESKT-----LVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFI 58
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
E+ S+++A A ++ N I G+ + ++
Sbjct: 59 EFASFEDAKEALNSCNKREIEGRAIRLEL 87
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 71.2 bits (175), Expect = 1e-15
Identities = 23/80 (28%), Positives = 40/80 (50%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V VH++ +DD+ F +G+IK+ L D TG KGY +EY+ + + A ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 121 NGTTILGQTVTVDWCFVKGP 140
N + GQ + V
Sbjct: 188 NLFDLGGQYLRVGKAVTPPM 207
Score = 70.4 bits (173), Expect = 2e-15
Identities = 23/99 (23%), Positives = 47/99 (47%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V ++ E ED + + F+ +G IK++ ++ D T KG+A VEY+ + A A + +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLF 159
N + G+ + V G + +Q ++
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY 129
>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 = 71.3 bits (174), Expect = 1e-15
Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 2/96 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
L++ + ++D+ E G +I + +R G KG+ALV S + D
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 119 ALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
L + GQ V + + + + + G
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSG 166
>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 = 68.6 bits (168), Expect = 1e-15
Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
IL++ + + ++M++ F +YG I+ + + T +G A V Y+ +A A D
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVD 65
Query: 119 ALNGTTILGQTVTVDW 134
L+G + + + V +
Sbjct: 66 HLSGFNVSNRYLVVLY 81
>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 = 68.1 bits (167), Expect = 1e-15
Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 5/91 (5%)
Query: 43 TDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGY 102
+ + ++ ++ L + ED++ E F + EI+ L + G KG
Sbjct: 1 SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGI 55
Query: 103 ALVEYDSYKEASAARDALNGTTILGQTVTVD 133
A +E+ S +A + G I G++V++
Sbjct: 56 AYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 86
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 67.4 bits (165), Expect = 4e-15
Identities = 19/78 (24%), Positives = 38/78 (48%)
Query: 57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
EG LF+ + +E + D+ F +G + + + +D++T K + V +D+ A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 117 RDALNGTTILGQTVTVDW 134
A+NG + + + V
Sbjct: 99 IKAMNGFQVGTKRLKVQL 116
>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 = 67.4 bits (165), Expect = 4e-15
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ G++ E E + F ++G I + L DR T +G+A + +++ +A A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 121 NGTTILGQTVTVDW 134
NG ++ G+ + V+
Sbjct: 69 NGKSLHGKAIKVEQ 82
>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 = 66.9 bits (164), Expect = 5e-15
Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V+ + ++ D+ + F ++G+I ++ + + R KG+ V +++ +A AR+ L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 75
Query: 121 NGTTILGQTVTVDW 134
+GT + G+ + V+
Sbjct: 76 HGTVVEGRKIEVNN 89
>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 = 67.0 bits (164), Expect = 5e-15
Identities = 21/76 (27%), Positives = 40/76 (52%)
Query: 57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
EG LF+ + +E + D+ + F +G + + + +D++T K + V YD+ A AA
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 117 RDALNGTTILGQTVTV 132
++NG I + + V
Sbjct: 84 IQSMNGFQIGMKRLKV 99
>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 = 66.5 bits (163), Expect = 5e-15
Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 50 PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
G + + LFV + + E++M + F +YG+ + ++ D KG+ + ++
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLET 60
Query: 110 YKEASAARDALNGTTILGQTVTVDW 134
A A+ L+ + G+ + V +
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRF 85
>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 = 69.2 bits (170), Expect = 5e-15
Identities = 24/74 (32%), Positives = 37/74 (50%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V +H + E ++EKFS G I ++ + D T GYA V + +A A D +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 121 NGTTILGQTVTVDW 134
N I G+ V + W
Sbjct: 78 NFDVIKGKPVRIMW 91
Score = 65.4 bits (160), Expect = 1e-13
Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+F+ + + +++ FS +G I + + D KGY V +++ + A A + +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
NG + + V V + ++ +
Sbjct: 164 NGMLLNDRKVFVGRFKSRKEREAELGAR 191
>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 = 66.1 bits (162), Expect = 6e-15
Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 12/98 (12%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G L++ + DD+ + F + L + GYA V
Sbjct: 1 GSSGSSGMNK-----LYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFV 49
Query: 106 EYDSYKEASAARDALNGTTIL-GQTVTVDWCFVKGPKK 142
+Y A A + L+G L G+ + VD+ K +
Sbjct: 50 DYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRS 87
>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 = 66.6 bits (163), Expect = 6e-15
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV + E +D+ F+ +G I + + D TG KGY V + + +A A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 121 NGTTILGQTVTVDW 134
G + G+ + +W
Sbjct: 78 GGQWLGGRQIRTNW 91
>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 = 66.1 bits (162), Expect = 7e-15
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV + +E+ ++E F + G + + + DR G K + V + + S A L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALL 77
Query: 121 NGTTILGQTVTVDW 134
NG + G+ + V
Sbjct: 78 NGIRLYGRPINVSG 91
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 66.2 bits (162), Expect = 8e-15
Identities = 18/86 (20%), Positives = 44/86 (51%), Gaps = 2/86 (2%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
+ + L V+ + ++ D+ + F ++G+I ++ + + R KG+ V +
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTF 76
Query: 108 DSYKEASAARDALNGTTILGQTVTVD 133
++ +A AR+ L+GT + G+ + V+
Sbjct: 77 ENSADADRAREKLHGTVVEGRKIEVN 102
>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 = 66.7 bits (163), Expect = 9e-15
Identities = 23/104 (22%), Positives = 45/104 (43%), Gaps = 1/104 (0%)
Query: 30 STRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLH 89
+T +++ E ++ ++ ++V V + D+ FS G I +
Sbjct: 8 TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67
Query: 90 LNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
+ D+ +G KGYA +E+ AA A++ T G+T+ V
Sbjct: 68 ILCDKFSGHPKGYAYIEFAERNSVDAA-VAMDETVFRGRTIKVL 110
>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 = 65.3 bits (160), Expect = 1e-14
Identities = 18/74 (24%), Positives = 33/74 (44%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV + E + F+ +G I + + D TG KGY V + + +A A +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 121 NGTTILGQTVTVDW 134
G + G+ + +W
Sbjct: 69 GGQWLGGRQIRTNW 82
>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 = 64.8 bits (159), Expect = 1e-14
Identities = 18/74 (24%), Positives = 38/74 (51%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV ++ ++ + F ++ + H+ D +TG +GY V + S +A A D++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 121 NGTTILGQTVTVDW 134
G + G+ + ++W
Sbjct: 64 QGQDLNGRPLRINW 77
>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 = 65.4 bits (160), Expect = 2e-14
Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V + + + D+ + F +YG I+++ L R +A VE++ ++A A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAVYGR 81
Query: 121 NGTTILGQTVTVDW 134
+G G + V++
Sbjct: 82 DGYDYDGYRLRVEF 95
>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 = 64.9 bits (159), Expect = 2e-14
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V + A + + E FS++G++ N+ L DR T KG+ VE + S A L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 121 NGTTILGQTVTVD 133
+ T +G+T+ V
Sbjct: 63 DNTDFMGRTIRVT 75
>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 = 65.4 bits (160), Expect = 2e-14
Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
P EG +F+ + +++E+ + E ++G++K + + L T KG A ++ + +
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68
Query: 112 EASAARDALN------GTTILGQTVTVDW 134
A A + G + G+ + VD
Sbjct: 69 AAQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>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 = 65.0 bits (159), Expect = 2e-14
Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
+ +G L+V G E+ + FS +G I +L ++ + A V
Sbjct: 4 GSSGERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVT 55
Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW 134
Y+ + A A LNGT + + V+
Sbjct: 56 YEKMESADQAVAELNGTQVESVQLKVNI 83
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 65.5 bits (160), Expect = 2e-14
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 8/88 (9%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
D P + +G L+V G E+ + FS +G I +L ++ + A V
Sbjct: 28 DSFPERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVT 79
Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW 134
Y+ + A A LNGT + + V+
Sbjct: 80 YEKMESADQAVAELNGTQVESVQLKVNI 107
>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 = 64.6 bits (158), Expect = 3e-14
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
RS LFV G+ E+ E+ + E F + + DR TG KG+ V++
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---IVTDRETGSSKGFGFVDF 61
Query: 108 DSYKEASAARDALNGTTILGQTVTVDW 134
+S ++A AA++A+ I G VT+DW
Sbjct: 62 NSEEDAKAAKEAMEDGEIDGNKVTLDW 88
>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 = 64.2 bits (157), Expect = 4e-14
Identities = 21/107 (19%), Positives = 37/107 (34%), Gaps = 12/107 (11%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
IL+V + E+ + ++F+ R ++ YA V +
Sbjct: 5 SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHF 58
Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
+ ++A A ALNG + G + V K + GP G
Sbjct: 59 SNREDAVEAMKALNGKVLDGSPIEVTL------AKPVDKDSSGPSSG 99
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 63.6 bits (155), Expect = 6e-14
Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 4/89 (4%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G P+R L + + Q + + +YG +++ V
Sbjct: 4 GSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNV 59
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
Y S +A A D LNG + T+ V +
Sbjct: 60 TYSSKDQARQALDKLNGFQLENFTLKVAY 88
>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 = 63.3 bits (155), Expect = 6e-14
Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V V A +++ F G + + + D+ +G KG+A +E+ + + AL
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67
Query: 121 NGTTILGQTVTVD 133
+ + G+ + V
Sbjct: 68 DESLFRGRQIKVI 80
>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 = 64.0 bits (156), Expect = 6e-14
Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDRR-TGFLKGYALVEYD 108
G S LF+ G+ + + +++ E+ ++ E + ++ + +G+A VEY+
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60
Query: 109 SYKEASAARDALN--GTTILGQTVTVDW 134
S++ A+ AR L + G + VDW
Sbjct: 61 SHRAAAMARRKLMPGRIQLWGHQIAVDW 88
>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 = 66.9 bits (164), Expect = 9e-14
Identities = 12/74 (16%), Positives = 28/74 (37%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L++T + ++ + + + R + +A ++ S ++A + L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 121 NGTTILGQTVTVDW 134
NG I G T+
Sbjct: 180 NGLKIEGYTLVTKV 193
Score = 62.3 bits (152), Expect = 3e-12
Identities = 17/137 (12%), Positives = 41/137 (29%), Gaps = 20/137 (14%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
R+ E + V + + ++ +++ F G I ++ + +A +E
Sbjct: 30 KANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIE 87
Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW-----CFVKG-PKKVAGEQ------KVGPEGG 154
+ Y A AA + + + V ++ P +
Sbjct: 88 FARYDGALAAITKTHK-VVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINV--- 143
Query: 155 VKVLFPVIMYSTETSMS 171
V + + S + S
Sbjct: 144 --VALSIRLPSLRFNTS 158
Score = 58.1 bits (141), Expect = 1e-10
Identities = 14/89 (15%), Positives = 39/89 (43%), Gaps = 3/89 (3%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALV 105
+ ++EG + + + E E+ + E F +G I+ +++ ++ F A +
Sbjct: 200 SKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFM 259
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
+++ A A +N + + + ++V
Sbjct: 260 VFENKDSAERAL-QMNRSLLGNREISVSL 287
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 63.1 bits (154), Expect = 1e-13
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV + QE +++E F +G +K + + L G+A VE++ + A+ A + +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85
Query: 121 NGTTILGQTVTVDW 134
+G + Q + V +
Sbjct: 86 HGKSFANQPLEVVY 99
>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 = 63.0 bits (154), Expect = 1e-13
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEI-KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
+F+ + E E +++ FS +G I + + D TG KGYA + + S+ + AA +A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 120 LNGTTILGQTVTVDWCFVKGPK 141
+NG + + +TV + F K K
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
>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 = 63.1 bits (154), Expect = 1e-13
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 1/87 (1%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
G G L V+ + + D+ E F+E+G +K ++ DR +G G A V
Sbjct: 18 SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76
Query: 107 YDSYKEASAARDALNGTTILGQTVTVD 133
++ +A A NG + G+ + +
Sbjct: 77 FERKADALKAMKQYNGVPLDGRPMNIQ 103
>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 = 64.6 bits (158), Expect = 1e-13
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL--KGYALVEYDSYKEASAARD 118
+FV V E D+ E F +YG + +++ DR KG V + + K A A++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 119 ALNGTTILGQTVTVDW 134
AL+ +L
Sbjct: 66 ALHNMKVLPGMHHPIQ 81
Score = 58.8 bits (143), Expect = 2e-11
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 4/77 (5%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ + ++ E+D+ FS +G+I+ + G +G A V + + A A A+
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 121 NGTTIL---GQTVTVDW 134
+ + + V +
Sbjct: 157 HQAQTMEGCSSPMVVKF 173
>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 = 64.5 bits (158), Expect = 1e-13
Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 1/89 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V + + ED + + F G I N+ + +D+ YA VEY +A+ A L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKV 149
NG I V ++W F +
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNL 90
Score = 64.1 bits (157), Expect = 2e-13
Identities = 18/74 (24%), Positives = 38/74 (51%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV ++ ++ + F ++ + H+ D +TG +GY V + S +A A D++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 121 NGTTILGQTVTVDW 134
G + G+ + ++W
Sbjct: 150 QGQDLNGRPLRINW 163
>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 = 65.1 bits (158), Expect = 1e-13
Identities = 17/127 (13%), Positives = 36/127 (28%), Gaps = 4/127 (3%)
Query: 14 KEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQED 73
+ + G + + + E + ++ + +L E E+
Sbjct: 79 QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEE 138
Query: 74 DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
+ E E G + + + L+E+DS +A LN +
Sbjct: 139 NFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198
Query: 134 ----WCF 136
CF
Sbjct: 199 YTLKLCF 205
Score = 51.2 bits (122), Expect = 2e-08
Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 8/96 (8%)
Query: 60 ILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
+L V G+ + D + F YG ++ + + G A+VE A
Sbjct: 6 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAIT 60
Query: 119 ALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
LN + GQ + V K P + G+ +G
Sbjct: 61 HLNNNFMFGQKMNVCVS--KQPAIMPGQSYGLEDGS 94
>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 = 63.2 bits (154), Expect = 2e-13
Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 2/99 (2%)
Query: 36 REYESMETDVGDEEPGPQRSVE-GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDR 94
R+ + + D+ D G VE G L V+ + + D+ E F+E+G +K ++ DR
Sbjct: 12 RDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR 71
Query: 95 RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
+G G A V ++ +A A G + G+ + +
Sbjct: 72 -SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 109
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 64.2 bits (156), Expect = 2e-13
Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 2/77 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
++V + + + G ++ L +R G KGYA V S +
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 119 ALNGTTILGQTVTVDWC 135
L G + G+ V V
Sbjct: 118 LLPGKVLNGEKVDVRPA 134
>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 = 61.8 bits (151), Expect = 2e-13
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
L++ + ++D+ E G +I + +R G KG+ALV S + D
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 119 ALNGTTILGQTVTVD 133
L + GQ V
Sbjct: 64 LLPKRELHGQNPVVT 78
>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 = 65.5 bits (160), Expect = 2e-13
Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 12/98 (12%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
+PG + + LFV + + E+D F YGE + +N DR G+ +
Sbjct: 12 LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRL 65
Query: 108 DSYKEASAARDALNGTTILGQTVTVDW------CFVKG 139
+S A A+ L+GT + + + + + VK
Sbjct: 66 ESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKN 103
Score = 52.4 bits (126), Expect = 1e-08
Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V + + + + FS++G ++ + +D G G VE+ + A A +
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERC 157
Query: 121 NGTTILGQT 129
L T
Sbjct: 158 GDGAFLLTT 166
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 63.3 bits (154), Expect = 4e-13
Identities = 23/120 (19%), Positives = 46/120 (38%), Gaps = 3/120 (2%)
Query: 16 KARKKKGRGFGTETSTRNEIREYESMETDVGDEEP--GPQRSVEGWILFVTGVHEEAQED 73
+ R RG + + + + G + G L V+ + +
Sbjct: 44 RNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDA 103
Query: 74 DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
D+ E F+E+G +K ++ D R+G G A V ++ +A A G + G+ + +
Sbjct: 104 DIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 162
>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 = 61.5 bits (150), Expect = 4e-13
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV ++++ E+D+ F +G I + G KG A V++ S+ EA AA AL
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 121 NGTTIL---GQTVTVDW 134
+G+ + ++ V +
Sbjct: 77 HGSQTMPGASSSLVVKF 93
>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 = 61.9 bits (151), Expect = 5e-13
Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+F+ + + +++ FS +G I + + D KGY V +++ + A A + +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEKM 65
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
NG + + V V + ++ +
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGAR 93
>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 = 61.1 bits (149), Expect = 5e-13
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV + E+ + + FS++G+++ + LK YA + +D A A + +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAMEEM 65
Query: 121 NGTTILGQTVTVDW 134
NG + G+ + + +
Sbjct: 66 NGKDLEGENIEIVF 79
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 61.1 bits (149), Expect = 6e-13
Identities = 19/106 (17%), Positives = 39/106 (36%), Gaps = 11/106 (10%)
Query: 49 EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYD 108
+ + +V + + D+ F + I+++ L D+ T KG+ VE+D
Sbjct: 6 SGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFD 64
Query: 109 SYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
A +G + +++ VD +A +K G
Sbjct: 65 EVDSLKEAL-TYDGALLGDRSLRVD---------IAEGRKQDKSGP 100
>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 = 60.7 bits (148), Expect = 6e-13
Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA-SAARDA 119
L+V G+ + E D+ F ++GEI+ + + + A +++ + + A AA +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 120 LNGTTILGQTVTVDW 134
N + G+ + V W
Sbjct: 69 FNKLIVNGRRLNVKW 83
>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 = 60.7 bits (148), Expect = 6e-13
Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 6/84 (7%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V G+ + +F +G I+ + D G +A ++Y+S A AA +
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTI----DHVKG--DSFAYIQYESLDAAQAACAKM 73
Query: 121 NGTTILGQTVTVDWCFVKGPKKVA 144
G + G + F K
Sbjct: 74 RGFPLGGPDRRLRVDFAKSGPSSG 97
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 60.7 bits (148), Expect = 7e-13
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV + + + +KF+E G + L+ ++ G KG +V+++S + A A +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 121 NGTTILGQTVTV 132
NG + G+ + V
Sbjct: 69 NGMKLSGREIDV 80
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 60.5 bits (147), Expect = 9e-13
Identities = 14/69 (20%), Positives = 28/69 (40%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
+ + + FS+ G++ N+ +D TG KG+ VE S +A +
Sbjct: 14 APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
Query: 120 LNGTTILGQ 128
+G + +
Sbjct: 74 FHGKRLDLK 82
>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 = 60.8 bits (148), Expect = 9e-13
Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
E R+V F + + D+ + FS G+++++ + DR + KG A VE+
Sbjct: 20 PEERDARTV-----FCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
Query: 108 DSYKEASAARDALNGTTILGQTVTVD 133
+ A L G +LG + V
Sbjct: 75 CEIQSVPLAI-GLTGQRLLGVPIIVQ 99
>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 = 59.9 bits (146), Expect = 1e-12
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 8/74 (10%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV V ++ F G + + +K YA V + +A AA L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIAQL 63
Query: 121 NGTTILGQTVTVDW 134
NG + G+ + V+
Sbjct: 64 NGKEVKGKRINVEL 77
>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 = 64.5 bits (156), Expect = 1e-12
Identities = 25/76 (32%), Positives = 41/76 (53%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LFV V+ + E + +F YG IK +H+ +R+G +GYA +EY+ ++ +A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 121 NGTTILGQTVTVDWCF 136
+G I G+ V VD
Sbjct: 165 DGKKIDGRRVLVDVER 180
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 60.0 bits (146), Expect = 2e-12
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V + A + ++ FS YG ++ + + + G+A VE++ ++A A L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGL 57
Query: 121 NGTTILGQTVTVDW 134
+G I G V V+
Sbjct: 58 DGKVICGSRVRVEL 71
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 58.8 bits (143), Expect = 4e-12
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 8/74 (10%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V + ++ KF EYG + + +K YA V + ++A A L
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDAVEAIRGL 64
Query: 121 NGTTILGQTVTVDW 134
+ T G+ + V
Sbjct: 65 DNTEFQGKRMHVQL 78
>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 = 58.7 bits (143), Expect = 4e-12
Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
G S LF+ + EA E ++ F +YG++ + +K Y V +
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDK 52
Query: 111 KEASAARDALNGTTILGQTVTVDW 134
A A L+ + G + V+
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVEA 76
>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 = 59.6 bits (144), Expect = 4e-12
Identities = 19/108 (17%), Positives = 40/108 (37%), Gaps = 13/108 (12%)
Query: 36 REYESMETDVGDEE-PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDR 94
++ G E +S+ + G+ + + + G + L + +
Sbjct: 7 GAKHTLLRHEGIETVSYATQSL--VV-ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN- 62
Query: 95 RTGFLKGYALVEYDSYKEASAARDALNGTTIL---GQTVTVDWCFVKG 139
K Y+ Y + +E+ A LNG ++ GQ +T+ FV+
Sbjct: 63 -----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105
>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 = 58.9 bits (143), Expect = 4e-12
Identities = 31/130 (23%), Positives = 55/130 (42%), Gaps = 21/130 (16%)
Query: 26 GTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGV-HEEAQEDDMHEKFSEYGE 84
G+ S+ ++ S T+ D + R +F+ + ++ D+ FS+YG
Sbjct: 1 GSSGSSGMSLKLQASNVTNKNDPKSINSR------VFIGNLNTALVKKSDVETIFSKYGR 54
Query: 85 IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVA 144
+ ++ KGYA V+Y + + A AA NG + GQT+ ++ PK
Sbjct: 55 VAGCSVH--------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA--GEPKP-- 102
Query: 145 GEQKVGPEGG 154
+ GP G
Sbjct: 103 --DRSGPSSG 110
>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 = 58.5 bits (142), Expect = 6e-12
Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 5/87 (5%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
L++ + E+ + F+ GE + ++ + +R TG GY VE+ A
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 120 LNGTTILGQTVT----VDWCFVKGPKK 142
+NG + G T +++ GP
Sbjct: 72 INGKPLPGATPAKRFKLNYATYSGPSS 98
>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 = 61.2 bits (148), Expect = 7e-12
Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 5/78 (6%)
Query: 58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
L ++ + E+D+ FS G + + + AL++ S +EA A
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQAL 206
Query: 118 DALNGTTIL-GQTVTVDW 134
L+ + + V +
Sbjct: 207 IDLHNHDLGENHHLRVSF 224
Score = 59.6 bits (144), Expect = 2e-11
Identities = 23/142 (16%), Positives = 49/142 (34%), Gaps = 8/142 (5%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL 104
G +L V+ ++ E + F YG+++ + + ++ K AL
Sbjct: 22 GRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENAL 76
Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMY 164
V+ +A A LNG + G+ + + + + Q+ P+ +
Sbjct: 77 VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRF 136
Query: 165 STETSMSTTLYNAPWIFKTMHI 186
S + P T+H+
Sbjct: 137 KKPGSKNFQNIFPP--SATLHL 156
>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 = 58.3 bits (141), Expect = 9e-12
Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 12/109 (11%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
RS ++ + ++ E FS +G + + L A+VE+
Sbjct: 2 SSGSSGRS--KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEF 53
Query: 108 DSYKEASAARDALNGTTILGQTVTVDW----CFVKGPKKVAGEQKVGPE 152
EA A L + + ++W F P+K + + E
Sbjct: 54 LEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102
>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 = 57.7 bits (140), Expect = 1e-11
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL---KGYALVEYDSYKEASAAR 117
LF+ ++ E+ + FS+ G IK+ ++ + + G+ VEY ++A A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 118 DALNGTTILGQTVTVD 133
L G T+ G + V
Sbjct: 68 KQLQGHTVDGHKLEVR 83
>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 = 59.9 bits (145), Expect = 1e-11
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 5/77 (6%)
Query: 59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
L ++ + E+D+ FS G + + + AL++ S +EA A
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALI 176
Query: 119 ALNGTTIL-GQTVTVDW 134
L+ + + V +
Sbjct: 177 DLHNHDLGENHHLRVSF 193
Score = 54.1 bits (130), Expect = 2e-09
Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 6/89 (6%)
Query: 61 LFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
L V+ ++ E + F YG+++ + + ++ K ALV+ +A A
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60
Query: 120 LNGTTILGQTVTVDWCFVKGPKKVAGEQK 148
LNG + G+ + + + + Q+
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQE 89
>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 = 58.1 bits (141), Expect = 1e-11
Identities = 24/111 (21%), Positives = 38/111 (34%), Gaps = 5/111 (4%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
Q G +FV + + + E FS G + + D+ G +G V +
Sbjct: 5 SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTF 63
Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGE----QKVGPEGG 154
+ EA A NG + + + V PK Q+ GP G
Sbjct: 64 EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114
>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 = 57.7 bits (140), Expect = 1e-11
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ ++ ++ SE +L + +D RTG + + V+++S ++ A + L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKALE-L 77
Query: 121 NGTTILGQTVTVDW 134
G + G + ++
Sbjct: 78 TGLKVFGNEIKLEK 91
>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 = 57.2 bits (139), Expect = 2e-11
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+V + + ++ + + FS +G I + + ++ G KG+ V + S +EA+ A +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
NG + + + V K ++
Sbjct: 76 NGRIVATKPLYVALAQRKEERQ 97
>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 = 58.0 bits (140), Expect = 3e-11
Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
++V + + ++ F YG ++++ + + G+A VE++ ++A+ A L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVREL 130
Query: 121 NGTTILGQTVTVDW 134
+G T+ G V V+
Sbjct: 131 DGRTLCGCRVRVEL 144
>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 = 56.5 bits (137), Expect = 5e-11
Identities = 11/72 (15%), Positives = 27/72 (37%), Gaps = 1/72 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L+++ + E ++ +G++ + + D +G +G +S ++ A
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 121 NGTTILGQTVTV 132
NG I
Sbjct: 87 NGKFIKTPPGVS 98
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 56.1 bits (136), Expect = 5e-11
Identities = 11/83 (13%), Positives = 33/83 (39%), Gaps = 11/83 (13%)
Query: 61 LFVTGVH-EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
LF+ + + ++D+ FS YG I +++ + +++D+ + A +
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEC 64
Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
+ G+ + ++ +
Sbjct: 65 ESQEMNFGKKLILE--VSSSNAR 85
>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 = 59.1 bits (142), Expect = 6e-11
Identities = 13/78 (16%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 61 LFVTGVHEEAQEDDM----HEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
+++ ++E+ ++D++ + FS++G+I ++ + R+ ++G A V + A+ A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68
Query: 117 RDALNGTTILGQTVTVDW 134
++ G + + + +
Sbjct: 69 LRSMQGFPFYDKPMRIQY 86
Score = 54.5 bits (130), Expect = 2e-09
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
ILF+T + EE E + F+++ K + L R A VE+D+ +A AARD
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262
Query: 119 ALNGTTIL-GQTVTVDW 134
AL G I + + +
Sbjct: 263 ALQGFKITQNNAMKISF 279
>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 = 56.0 bits (135), Expect = 7e-11
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 8/91 (8%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
++ V G+ E E D+ E ++G I + + K ALVE+++ A
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF 70
Query: 120 L--NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
I GQ ++ K +
Sbjct: 71 AADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101
>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 = 55.4 bits (134), Expect = 7e-11
Identities = 18/76 (23%), Positives = 30/76 (39%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
++ V + D++ + F Y I G G A+V ++S EA+AA
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 120 LNGTTILGQTVTVDWC 135
LN I + V +
Sbjct: 77 LNDRPIGSRKVKLSGP 92
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 55.4 bits (134), Expect = 8e-11
Identities = 11/83 (13%), Positives = 33/83 (39%), Gaps = 11/83 (13%)
Query: 61 LFVTGV-HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
LF+ + + ++D+ FS YG I +++ + +++D+ + A +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76
Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
+ G+ + ++ +
Sbjct: 77 ESQEMNFGKKLILE--VSSSNAR 97
>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 = 54.9 bits (133), Expect = 1e-10
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ E ++ F+ YG +K + + D RTG KGY V + + + +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE-- 68
Query: 121 NGTTILGQTVTV 132
+ G+ + +
Sbjct: 69 SQINFHGKKLKL 80
>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 = 54.9 bits (133), Expect = 1e-10
Identities = 13/79 (16%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 60 ILFVTGVHEEAQEDDMHEK----FSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASA 115
+++ ++E+ ++D++ + FS +G+I ++ + R+ ++G A V + A+
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 66
Query: 116 ARDALNGTTILGQTVTVDW 134
A ++ G + + + +
Sbjct: 67 ALRSMQGFPFYDKPMRIQY 85
>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 = 54.6 bits (132), Expect = 2e-10
Identities = 19/76 (25%), Positives = 30/76 (39%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
I+ V + D++ + F Y I G G A+V ++S EA+AA
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 120 LNGTTILGQTVTVDWC 135
LN I + V +
Sbjct: 77 LNDRPIGSRKVKLVLG 92
>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 = 54.9 bits (132), Expect = 2e-10
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 11/99 (11%)
Query: 53 QRSVEGWILFVTGVHEEAQEDDM---HEKFSEYGEIKNLHLNLDRRTGFLK---GYALVE 106
R V+ ++FV G+ + + ++ E F ++G+I + +N + A V
Sbjct: 10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVT 69
Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW-----CFVKGP 140
Y ++A A +N + G+T+ C GP
Sbjct: 70 YIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSGP 108
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 54.9 bits (132), Expect = 2e-10
Identities = 15/112 (13%), Positives = 43/112 (38%), Gaps = 12/112 (10%)
Query: 27 TETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDM----HEKFSEY 82
+ + E + +S + P + ++ +T ++ E ++ + + S
Sbjct: 3 ETAAAKFERQHMDSPDLGSTPPHTEPSQ-----VVLITNINPEVPKEKLQALLYALASSQ 57
Query: 83 GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
G+I ++ + + G A + + + + A A +A G G + + +
Sbjct: 58 GDILDIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 54.4 bits (131), Expect = 2e-10
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
P ++ ++ + G+ + E D+ E E+G I + + K ALVE++
Sbjct: 15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVL 68
Query: 112 EASAARDALNGT--TILGQTVTVDW 134
A A + I G V++
Sbjct: 69 GACNAVNYAADNQIYIAGHPAFVNY 93
>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 = 54.0 bits (130), Expect = 3e-10
Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 7/92 (7%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
GP + V+G+ D+ + E G++ + D G +VE
Sbjct: 4 GSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVE 56
Query: 107 YDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
+ ++ + A L+ T + VK
Sbjct: 57 FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 88
>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 = 53.8 bits (129), Expect = 5e-10
Identities = 10/77 (12%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD- 118
++ + + + E ++ +G++ NL + K A +E ++ + A+ +
Sbjct: 33 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 86
Query: 119 -ALNGTTILGQTVTVDW 134
+ GQ + + +
Sbjct: 87 YTSVTPVLRGQPIYIQF 103
>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 = 54.4 bits (131), Expect = 6e-10
Identities = 26/122 (21%), Positives = 45/122 (36%), Gaps = 13/122 (10%)
Query: 32 RNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN 91
R E+ EPG ++V + + QE D+ F Y + +
Sbjct: 27 REEMETLSVFR----SYEPGEPNCR----IYVKNLAKHVQEKDLKYIFGRYVDFSSETQR 78
Query: 92 L-----DRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGE 146
+ + G +KG A + + K A+ A NG + G+ + V + PK+ E
Sbjct: 79 IMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKE 138
Query: 147 QK 148
K
Sbjct: 139 GK 140
>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 = 53.0 bits (128), Expect = 7e-10
Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 5/88 (5%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT-GFLKGYALV 105
P+ + F+ + + E+ + E F I + L + LKG+
Sbjct: 10 HRSRLPKSP--PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 66
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVD 133
E++ +A +LN ++ + + VD
Sbjct: 67 EFEDLDSLLSAL-SLNEESLGNRRIRVD 93
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 53.2 bits (128), Expect = 7e-10
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 60 ILFVTGV------HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
++ V V E ++ +H+ FS++G+I N G KGY +EY S A
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHA 74
Query: 114 SAARDALNGTTILGQ 128
A +G + Q
Sbjct: 75 VDAVKNADGYKLDKQ 89
>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 = 54.1 bits (131), Expect = 9e-10
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ + + + E FS++G I + L LD+ TG +G+ V YDS
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QN 148
Query: 121 NGTTILGQTVTVD 133
+ + +
Sbjct: 149 KFIDFKDRKIEIK 161
Score = 42.9 bits (102), Expect = 1e-05
Identities = 15/87 (17%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+F+ G++ + ED++ E F +YG + +L + D TG +G+ + ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 121 NGTTILGQTVTVDWCFVKG----PKKV 143
+ + G+ + + K+
Sbjct: 66 H--ILDGKVIDPKRAIPRDEQDKTGKI 90
>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 = 51.7 bits (124), Expect = 2e-09
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
L+V + E+ M + F+ + L L + K +A +E+ S E +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 116 ARDALNGTTILGQTVTV 132
A A +G GQ++ +
Sbjct: 69 AM-AFDGIIFQGQSLKI 84
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 50.9 bits (122), Expect = 2e-09
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 8/72 (11%)
Query: 60 ILFVTGV------HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
++ V V E ++ +H+ FS++G+I N G KGY +EY S A
Sbjct: 3 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHA 60
Query: 114 SAARDALNGTTI 125
A +G +
Sbjct: 61 VDAVKNADGYKL 72
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 51.5 bits (124), Expect = 3e-09
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAAR 117
+ F+ + + E+ + E F I + L + LKG+ E++ +A
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
Query: 118 DALNGTTILGQTVTVDW 134
+LN ++ + + VD
Sbjct: 75 -SLNEESLGNKRIRVDV 90
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 53.5 bits (129), Expect = 3e-09
Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 47 DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
++ P + +FV G+ E+ +E + + F +YG+I+ + + DR +G +G+A V
Sbjct: 93 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152
Query: 107 YDSYKEASAARDALNGTTILGQTVTVD 133
+D + T+ G V
Sbjct: 153 FDDHDSVDKIV-IQKYHTVNGHNCEVR 178
Score = 43.4 bits (103), Expect = 8e-06
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ G+ E ++ + F ++G + + + D T +G+ V Y + +E AA +A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74
Query: 121 NGTTILGQTVTVD 133
+ G+ V
Sbjct: 75 RPHKVDGRVVEPK 87
>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 = 51.0 bits (122), Expect = 4e-09
Identities = 10/77 (12%), Positives = 29/77 (37%), Gaps = 8/77 (10%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD- 118
+L + + E E ++ +G++ N+ + K A +E + + A +
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNY 70
Query: 119 -ALNGTTILGQTVTVDW 134
+ + Q + + +
Sbjct: 71 YSAVTPHLRNQPIYIQY 87
>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 = 50.5 bits (121), Expect = 5e-09
Identities = 13/94 (13%), Positives = 30/94 (31%), Gaps = 13/94 (13%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+ V + +++ ++H+ +Y K A V + ++A A
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
+ + G+ + V + GP G
Sbjct: 61 HQYSFRGKDLIVQL------QPTDALLCSGPSSG 88
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 50.6 bits (121), Expect = 6e-09
Identities = 10/77 (12%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
++ + + + E ++ +G++ NL + K A +E ++ + A+ +
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 71
Query: 120 L--NGTTILGQTVTVDW 134
+ GQ + + +
Sbjct: 72 YTSVTPVLRGQPIYIQF 88
>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 = 49.9 bits (120), Expect = 9e-09
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ E ++ E F ++G + + + D +G+ + ++ + A +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 121 NGTTILGQTVTVD 133
+ I+G+ V V
Sbjct: 72 HFHDIMGKKVEVK 84
>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 = 50.2 bits (120), Expect = 1e-08
Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 9/93 (9%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G P +RS + V+G+ D+ + E G++ + D G +V
Sbjct: 6 GRYGPPSRRS--ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 56
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
E+ ++ + A L+ T + VK
Sbjct: 57 EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 89
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 50.1 bits (120), Expect = 1e-08
Identities = 23/109 (21%), Positives = 40/109 (36%), Gaps = 3/109 (2%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G + + + V G+ A E+D+ + F + +HL D G G LV
Sbjct: 4 GSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLV 61
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
++ S ++ A N ++ + V V + G GP G
Sbjct: 62 KFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 51.3 bits (122), Expect = 2e-08
Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 15/88 (17%)
Query: 61 LFVTGVHE---------EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
L+V G+ E + FS G+I + K V++
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQA 190
Query: 112 EASAARDALNGTTILGQTVTVDWCFVKG 139
A A++A++ T+L + +G
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREG 218
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 49.0 bits (117), Expect = 2e-08
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+++ G +A DD+ E + G++ N+ + F KG V +DS + A
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFV-ET 71
Query: 121 NGTTILGQTVTVDW 134
G + + +
Sbjct: 72 PGQKYKETDLLILF 85
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 47.5 bits (113), Expect = 6e-08
Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 5/90 (5%)
Query: 45 VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL 104
G P + + ++V + +A+ D+ E G + L + A
Sbjct: 6 SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAF 60
Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDW 134
+ Y A A L G + T+ V
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTDTLRVAL 90
>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 = 47.2 bits (113), Expect = 9e-08
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 2/85 (2%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
L V G+ + E D+ E FS +GE+ + + D +TG KG+ V + Y+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAG 145
+ I G+ K +
Sbjct: 78 H--MIDGRWCDCKLPNSKQSQDSGP 100
>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 = 46.3 bits (111), Expect = 1e-07
Identities = 12/73 (16%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ + E+ + E F +GE++++ L +D +T +G+ + + + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60
Query: 121 NGTTILGQTVTVD 133
+ +
Sbjct: 61 KYHNVGLSKCEIK 73
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 46.5 bits (111), Expect = 1e-07
Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 9/93 (9%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV+G + E F +G + ++ +D+ G +A+VE A +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDKDKG---VFAIVEMGDVGAREAVL-SQ 64
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEG 153
+ ++ G + V + K+ P+G
Sbjct: 65 SQHSLGGHRLRVR---PREQKEFQSPASKSPKG 94
>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 = 48.2 bits (114), Expect = 1e-07
Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 9/93 (9%)
Query: 44 DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYA 103
D G G + V + D +H+ FS++G + + A
Sbjct: 35 DAGMAMAGQSPV---LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QA 87
Query: 104 LVEYDSYKEASAARDALNGTTIL--GQTVTVDW 134
L++Y A A+ +L+G I T+ +D+
Sbjct: 88 LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 47.3 bits (112), Expect = 2e-07
Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 7/95 (7%)
Query: 44 DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYA 103
D G G + + V + D +H+ FS++G + + A
Sbjct: 17 DAGMAMAGQSPVL---RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QA 69
Query: 104 LVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
L++Y A A+ +L+G I T+ F K
Sbjct: 70 LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104
>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 = 46.7 bits (111), Expect = 2e-07
Identities = 18/108 (16%), Positives = 42/108 (38%), Gaps = 7/108 (6%)
Query: 52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN-LHLNLDRRTGFLKGYALVEYDSY 110
+ +T + + D+ + +N +H+ +D G G ALV++ +
Sbjct: 9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNE 67
Query: 111 KEASAARDALNGTTILGQTVTVDWCFVKGPKKVA----GEQKVGPEGG 154
+A + L+ + G+ V ++ +++ + K GP G
Sbjct: 68 DDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 45.5 bits (109), Expect = 2e-07
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ +D+ F ++G++ + L D+ T +G+ V ++S +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60
Query: 121 NGTTILGQTVTVD 133
+ I + V
Sbjct: 61 HFHEINNKMVECK 73
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 46.6 bits (110), Expect = 2e-07
Identities = 20/115 (17%), Positives = 43/115 (37%), Gaps = 17/115 (14%)
Query: 26 GTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVT--GVHEEAQEDDMHEKFSEYG 83
G+ S+ I + D+ G + +L ++ D ++ + G
Sbjct: 1 GSSGSSGKRITRPGN-----TDDPSGGNK-----VLLLSIQNPLYPITVDVLYTVCNPVG 50
Query: 84 EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
+++ + + A+VE++S A A+ ALNG I T+ + +
Sbjct: 51 KVQRIVIFKRNGI-----QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR 100
>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 = 46.8 bits (111), Expect = 3e-07
Identities = 25/133 (18%), Positives = 51/133 (38%), Gaps = 4/133 (3%)
Query: 22 GRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSE 81
G S + + M + +S G + + G+ +A E+D++ FS
Sbjct: 11 SSGLVPRGSHMASMTGGQQMGRG-SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSP 69
Query: 82 YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK 141
+H+ + G + G A VE+ +++EA AA + + + + + + G
Sbjct: 70 LN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS 126
Query: 142 KVAGEQKVGPEGG 154
A +V G
Sbjct: 127 NGAYSSQVMQGMG 139
>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 = 45.4 bits (108), Expect = 6e-07
Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 1/95 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ + + + F +G+I+ + DR+TG +GY V A A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGV 155
N I G+ V+ ++ + G
Sbjct: 80 NP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 45.2 bits (107), Expect = 6e-07
Identities = 15/101 (14%), Positives = 28/101 (27%), Gaps = 5/101 (4%)
Query: 32 RNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN 91
+ + S G + + + + E D+ + E
Sbjct: 4 SHHHHHHSSGLVPRGSHMSKLPAK--RYRITMKNLPEGCSWQDLKDLARENSLE---TTF 58
Query: 92 LDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV 132
T G +E+ S + A + LN G +TV
Sbjct: 59 SSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
>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 = 44.1 bits (105), Expect = 1e-06
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV + ED++ E FS+YG++ ++ + R +A V + + A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFAD--DQIAQSLCG 60
Query: 121 NGTTILGQTVTVD 133
I G +V +
Sbjct: 61 EDLIIKGISVHIS 73
>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 = 44.4 bits (105), Expect = 1e-06
Identities = 17/111 (15%), Positives = 38/111 (34%), Gaps = 5/111 (4%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
G+ +++ G+ EA+ + + F + +++ G G VE+
Sbjct: 15 RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 74
Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAG----EQKVGPEGG 154
+ + AA + + + + V KG + + GP G
Sbjct: 75 RNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 43.9 bits (103), Expect = 2e-06
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
W+L + + + + ++G + + H L+ +G AL +Y + +EA+ A+
Sbjct: 9 WLL-LKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN------QGIALCKYTTREEANKAQM 61
Query: 119 ALNGTTILGQTVTVD 133
ALN + T+ +
Sbjct: 62 ALNNCVLANTTIFAE 76
>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 = 42.6 bits (101), Expect = 3e-06
Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV G+ + + D+ + F+++GE+ + + +D TG +G+ + + D
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 121 NGTTILGQTVTVD 133
+ G+ +
Sbjct: 74 EH-RLDGRVIDPK 85
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 42.1 bits (100), Expect = 4e-06
Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+F+ G+ + ++ + E F ++GE+K + D T +G+ V +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61
Query: 121 NGTTILGQTVTVD 133
+ + +T+
Sbjct: 62 SRHELDSKTIDPK 74
>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 = 43.3 bits (102), Expect = 5e-06
Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 1/87 (1%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
S + + G+ ++++ + FS + N G + G A V
Sbjct: 30 MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89
Query: 106 EYDSYKEASAARDALNGTTILGQTVTV 132
++ S + A A + I + + V
Sbjct: 90 QFASQELAEKALG-KHKERIGHRYIEV 115
>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 = 42.5 bits (100), Expect = 6e-06
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 68 EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG 127
+E E+ E +YGE++ +++ D L G V++ ++A A LN G
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG 95
Query: 128 QTVTVDWC 135
Q + +
Sbjct: 96 QPIHAELS 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 = 41.8 bits (99), Expect = 8e-06
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+FV E+ +++ + F +YGE+ ++ + R +A V + + A
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFAD--DKVAQSLCG 66
Query: 121 NGTTILGQTVTVD 133
I G +V +
Sbjct: 67 EDLIIKGISVHIS 79
>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 = 41.8 bits (99), Expect = 8e-06
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 1/88 (1%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
G + E LFV G+ ++ + FS+YGE+ + + D+ T +G+ V
Sbjct: 4 GSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVD 133
++ + T+ G+ +
Sbjct: 64 KFKDPNCVGTVLAS-RPHTLDGRNIDPK 90
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
LF+ G+ E E+ + + ++G++ + + D + +G+ V + S E AA A
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88
Query: 121 NGTTILGQTVTVD 133
+I G+ V
Sbjct: 89 RPHSIDGRVVEPK 101
>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 = 41.6 bits (98), Expect = 1e-05
Identities = 24/107 (22%), Positives = 44/107 (41%), Gaps = 9/107 (8%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
+S G + + G+ A E+D++ FS +H+ + G + G A VE+
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEF 62
Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
++++A AA A + + + V + AG GP G
Sbjct: 63 ATHEDAVAAM-AKDKANMQHRYVELF------LNSTAGTSGSGPSSG 102
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 41.1 bits (97), Expect = 2e-05
Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
G G +F+ G+ + ++ + E F ++GE+K + D T +G+ V +
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 111 KEASAARDALNGTTILGQTVTVD 133
+ + +T+
Sbjct: 78 AGVDKVLAQ-SRHELDSKTIDPK 99
>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 = 42.5 bits (99), Expect = 2e-05
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
+++ G +A DD+ E + G++ N+ + F KG V +DS + A +
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVETP 170
Query: 121 NGT 123
Sbjct: 171 GQK 173
>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 = 42.5 bits (99), Expect = 3e-05
Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 11/98 (11%)
Query: 61 LFV--TGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
L V G+ + + + G + L + + K Y+ Y + +E+ A
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYV 74
Query: 119 ALNGTTI---LGQTVTVDWCFVKGPKKVAGEQKVGPEG 153
LNG + LGQ +T+ FV+ + + P G
Sbjct: 75 TLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPG 112
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 19/121 (15%), Positives = 36/121 (29%), Gaps = 8/121 (6%)
Query: 15 EKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDD 74
G S + + M P EG+++ + G+ +D
Sbjct: 4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGG---EGFVVKLRGLPWSCSVED 60
Query: 75 MHEKFSEY---GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
+ S+ +H R G G A VE S + A + ++ + +
Sbjct: 61 VQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE 118
Query: 132 V 132
V
Sbjct: 119 V 119
>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 = 40.4 bits (95), Expect = 4e-05
Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 72 EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
+DD+ E+ +++G + +H+ +D+ + +G V+ S A AA +AL+G
Sbjct: 31 KDDVIEECNKHGGV--IHIYVDKNSA--QGNVYVKCPSIAAAIAAVNALHG 77
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 39.6 bits (93), Expect = 6e-05
Identities = 24/96 (25%), Positives = 38/96 (39%), Gaps = 5/96 (5%)
Query: 61 LFVTGVHEEAQEDDMHEKFSE-YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
LFV + + + ++E F + Y + + LD+ TG KGY V++ E A
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 120 LNGTTILGQ-TVTVDWCFVKGPKKVAGEQKVGPEGG 154
G LG V + K + + GP G
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRV--KPVESGPSSG 104
>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 = 38.8 bits (91), Expect = 8e-05
Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 3/78 (3%)
Query: 55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
+ + G E ++ E + + + + G GY V++ + +E
Sbjct: 7 GTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVK 64
Query: 115 AARDALNGTTILGQTVTV 132
A N + G+ + V
Sbjct: 65 QALK-CNREYMGGRYIEV 81
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 4/87 (4%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
P + + G+ ++++ + FS + N G G A V
Sbjct: 6 SGNSPDTANDG---FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62
Query: 106 EYDSYKEASAARDALNGTTILGQTVTV 132
++ S + A A + I + + +
Sbjct: 63 QFASQEIAEKALK-KHKERIGHRYIEI 88
>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 = 38.4 bits (89), Expect = 2e-04
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 6/88 (6%)
Query: 48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEY---GEIKNLHLNLDRRTGFLKGYAL 104
GP+ EG+++ + G+ +D+ S+ + +H R G G A
Sbjct: 8 MMLGPE-GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAF 65
Query: 105 VEYDSYKEASAARDALNGTTILGQTVTV 132
VE +S + A + ++ + + V
Sbjct: 66 VELESEDDVKLAL-KKDRESMGHRYIEV 92
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 38.7 bits (90), Expect = 2e-04
Identities = 12/90 (13%), Positives = 29/90 (32%), Gaps = 4/90 (4%)
Query: 46 GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN---LDRRTGFLKGY 102
+E I+ + G+ A +++ F ++ I + G G
Sbjct: 11 SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70
Query: 103 ALVEYDSYKEASAARDALNGTTILGQTVTV 132
A V + + A A + + + + +
Sbjct: 71 AFVLFACEEYAQNAL-RKHKDLLGKRYIEL 99
>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 = 36.5 bits (84), Expect = 0.001
Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 14/107 (13%)
Query: 30 STRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGV-HEEAQEDDMHEKFSEYGEIKNL 88
S+ + ++ E D++ R ++ ++ + H + + + YG+IKN
Sbjct: 2 SSGSSGKKPEGKPDQKFDQKQELGR-----VIHLSNLPHSGYSDSAVLKLAEPYGKIKNY 56
Query: 89 HLNLDRRTGFLKGYALVEYDSYKEASAARD--ALNGTTILGQTVTVD 133
L K A +E ++ ++A A D G+ V VD
Sbjct: 57 ILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD 97
>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 = 36.2 bits (84), Expect = 0.001
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 72 EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
+D+ + S++G+I+ L L R G A V + +EA L+G G+ +T
Sbjct: 40 REDLRVECSKFGQIR--KLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95
Query: 132 V 132
Sbjct: 96 A 96
>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 = 35.9 bits (83), Expect = 0.001
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 68 EEAQEDDMHEKFSEYGEIKNLHL----NLDRRTGFLKGYALVEYDSYKEASAARDALNGT 123
++ E ++ E+ ++G + + + + + VE+ E A ALNG
Sbjct: 35 DDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR 94
Query: 124 TILGQTVTV 132
G+ V
Sbjct: 95 WFAGRKVVA 103
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 34.6 bits (79), Expect = 0.004
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 49 EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--LHLNLDRRTGFLKGYALVE 106
G S + +FV G+ + ED++ F +G + H + KGYA +
Sbjct: 2 SSGSSGSRK---VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLL 58
Query: 107 YDSYKEASAA 116
+ A
Sbjct: 59 FQEESSVQAL 68
>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 = 34.4 bits (79), Expect = 0.005
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 67 HEEAQEDDMHEKFSEYGEIKNL--HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT 124
E +D+ ++ S+YG +K++ +D G VE+ S + A L G
Sbjct: 24 EYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK 83
Query: 125 ILGQTVTV 132
+ V
Sbjct: 84 FANRVVVT 91
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 34.0 bits (77), Expect = 0.007
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 72 EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
+D + +YGE+ NL L+ + G A+VE+ + K A A G
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVG 76
>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 = 34.1 bits (78), Expect = 0.007
Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 57 EGWILFVTGVHEEAQEDDMHEKFSEY---GEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
+ +++ G+ +D+ FS+ +H L+R G +G AL+E +S ++
Sbjct: 10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDV 68
Query: 114 SAARDALNGTTILGQTVTV 132
A + + + V V
Sbjct: 69 QKAL-EKHRMYMGQRYVEV 86
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 32.9 bits (75), Expect = 0.015
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 68 EEAQEDDMHEKFSEYGEIKNLHL-NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
+E E + E+ +YG++ + + +E++ + A A LNG
Sbjct: 23 DEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG 82
Query: 127 GQTVTVD 133
G+ V
Sbjct: 83 GRVVKAC 89
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.4 bits (75), Expect = 0.023
Identities = 14/47 (29%), Positives = 16/47 (34%), Gaps = 19/47 (40%)
Query: 77 EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT 123
EK +K L LK YA DS A A A+ T
Sbjct: 18 EK----QALKKL-------QASLKLYAD---DS---APAL--AIKAT 45
>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 = 33.3 bits (75), Expect = 0.040
Identities = 23/139 (16%), Positives = 52/139 (37%), Gaps = 27/139 (19%)
Query: 67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL--VEYDSYKEASAAR---DALN 121
H + + E +Y +I L + D F+ + V+ D K + +
Sbjct: 3 HHHHMDFETGEHQYQYKDI--LSVFEDA---FVDNFDCKDVQ-DMPKSILSKEEIDHIIM 56
Query: 122 GTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIM--YSTET---SMSTTLY- 175
+ T+ + W + +++ ++ V E +++ + +M TE SM T +Y
Sbjct: 57 SKDAVSGTLRLFWTLLSKQEEMV-QKFV--EEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113
Query: 176 -------NAPWIFKTMHIT 187
N +F +++
Sbjct: 114 EQRDRLYNDNQVFAKYNVS 132
Score = 30.6 bits (68), Expect = 0.36
Identities = 19/115 (16%), Positives = 48/115 (41%), Gaps = 27/115 (23%)
Query: 1 MNARFRLKGIARLKEKARKKK--GRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEG 58
++ RF L++K R G+ +T +++ Y+ + D +P +R V
Sbjct: 498 LDFRF-------LEQKIRHDSTAWNASGSILNTLQQLKFYKPY---ICDNDPKYERLVNA 547
Query: 59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
+ F+ + E+++ S+Y ++ L + L + + +++K+
Sbjct: 548 ILDFLPKI-----EENLIC--SKYTDL--LRIALMAEDEAI--F----EEAHKQV 587
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 30.6 bits (68), Expect = 0.28
Identities = 18/111 (16%), Positives = 38/111 (34%), Gaps = 16/111 (14%)
Query: 9 GIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHE 68
+ R + G E R + M+ + ++ QR+V + E
Sbjct: 14 LVPRGSHMEQPSGSVETGFEDKIPK--RRFSEMQNERREQA---QRTV------LIHCPE 62
Query: 69 EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
+ E+ + S++G I N YA+VE+ + + ++
Sbjct: 63 KISENKFLKYLSQFGPINNHFFYESFGL-----YAVVEFCQKESIGSLQNG 108
>1sf9_A YFHH hypothetical protein; structural genomics, unknown function,
PSI, protein structure initiative, midwest center for
structural genomics; 1.71A {Bacillus subtilis} SCOP:
b.34.15.1
Length = 128
Score = 28.4 bits (63), Expect = 0.83
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 10 IARLKEKARKKKGRGFGTETS-TRNEIREYESMETDVGDEEPGPQRSVEG 58
IA L EKARK + G E + +I ++ + D PG VE
Sbjct: 41 IALLSEKARKAEQHGIINELAVLERKITMAKAYLLNPEDYSPGETYRVEN 90
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 27.6 bits (61), Expect = 1.5
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 5/81 (6%)
Query: 48 EEPGPQRSVEGWILFVTG-VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
G G +L +G + ++ +D+H FS +GEIK +D G +G L +
Sbjct: 8 HHHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIK----WIDFVRGAKEGIILFK 63
Query: 107 YDSYKEASAARDALNGTTILG 127
+ + A+DA NG L
Sbjct: 64 EKAKEALGKAKDANNGNLQLR 84
>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 = 28.1 bits (62), Expect = 2.3
Identities = 26/186 (13%), Positives = 55/186 (29%), Gaps = 49/186 (26%)
Query: 44 DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNL---DRR---T 96
+ + P P L ++ + +E +D + K + + K + ++L + +
Sbjct: 329 ENNEGVPSPM-------LSISNLTQEQVQDYV-NKTNSHLPAGKQVEISLVNGAKNLVVS 380
Query: 97 GFLKGYALVEYDSYKEASAARDALNGTTIL--GQTVTVDWCF--VKGP-----KKVAGEQ 147
G + +L + + A L+ + I + + F V P A +
Sbjct: 381 GPPQ--SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL 438
Query: 148 KVGPEGGVKVLF-------PVIMYSTET-----SMSTTLYN--APWIF-------KTMHI 186
V F PV Y T +S ++ I T
Sbjct: 439 INKDLVKNNVSFNAKDIQIPV--YDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQF 496
Query: 187 TILCVI 192
++
Sbjct: 497 KATHIL 502
Score = 26.2 bits (57), Expect = 9.1
Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 23/72 (31%)
Query: 108 DSYKEASAARDALN----------GTTILGQTVTVDWCFVKG-PKKVAGEQKVGPEGG-- 154
D YK + AA+D N G +IL V P + G E G
Sbjct: 1634 DLYKTSKAAQDVWNRADNHFKDTYGFSILD--------IVINNPVNLT--IHFGGEKGKR 1683
Query: 155 VKVLFPVIMYST 166
++ + +++ T
Sbjct: 1684 IRENYSAMIFET 1695
>2yxy_A Hypothetical conserved protein, GK0453; alpha and beta proteins
(A+B) class, structural GENO unknown function, NPPSFA;
2.20A {Geobacillus kaustophilus}
Length = 115
Score = 26.0 bits (57), Expect = 4.9
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 10 IARLKEKARKKKGRGFGTETST-RNEIREYESMETDVGDEEPGPQRSVEG 58
IA L EKARK + G E + +I ++ + D PG +EG
Sbjct: 23 IAMLTEKARKAEQMGMVNEYAVYERKIAMAKAYMLNPADFHPGEIYEIEG 72
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 25.9 bits (56), Expect = 7.1
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 6/71 (8%)
Query: 71 QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY--KEASAARDALNGTTILGQ 128
Q+ + F +YGEI + D + L++Y S K AA+ A + +
Sbjct: 19 QDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAV----R 74
Query: 129 TVTVDWCFVKG 139
CF+ G
Sbjct: 75 KHESSGCFIMG 85
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 0.395
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: 2,877,304
Number of extensions: 164103
Number of successful extensions: 559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 213
Length of query: 192
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 104
Effective length of database: 4,244,745
Effective search space: 441453480
Effective search space used: 441453480
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: 54 (24.5 bits)