RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13319
(117 letters)
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 121 bits (306), Expect = 2e-37
Identities = 40/104 (38%), Positives = 57/104 (54%), Gaps = 3/104 (2%)
Query: 10 RFSPLTGDLL--ASSILPANTMNG-SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
SPL L A++ + G G +F+Y+L E ++ L F PFG V S KV
Sbjct: 14 STSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVF 73
Query: 67 RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK 110
D QT+ K FGFV+ N D A VAI+++NG+ +G + L+V K
Sbjct: 74 IDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
>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 = 120 bits (303), Expect = 5e-37
Identities = 37/83 (44%), Positives = 49/83 (59%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
G +F+Y+L E + L Q+F PFG V S KV D QTN K FGFV+ N A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 92 IQSLNGYALGNRILQVSFKTNKG 114
IQS+NG+ +G + L+V K +K
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKN 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 = 116 bits (292), Expect = 2e-35
Identities = 29/89 (32%), Positives = 49/89 (55%), Gaps = 3/89 (3%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
I V NL+ +T E+ L +LF PFG++ + + +D T + KGF F++ ++A A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 92 IQSLNGYALGNRILQVSF---KTNKGKTS 117
I ++G+ + IL V + TN G +S
Sbjct: 74 IAGVSGFGYDHLILNVEWAKPSTNSGPSS 102
>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 = 109 bits (276), Expect = 3e-33
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
+ + +++ L P T + L +L P+G + S K I D TNKCKG+GFV +
Sbjct: 2 SSGSSG-----LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 56
Query: 85 YDEAVVAIQSLNGYALGNRILQVS 108
A A+ +L + ++ + S
Sbjct: 57 PSAAQKAVTALKASGVQAQMAKQS 80
>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 = 101 bits (255), Expect = 6e-30
Identities = 31/83 (37%), Positives = 50/83 (60%)
Query: 31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
GS + +FV +L+PE + + F PFG + +V++D+ T K KG+GFV+ N +A
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 91 AIQSLNGYALGNRILQVSFKTNK 113
AIQ + G LG R ++ ++ T K
Sbjct: 64 AIQQMGGQWLGGRQIRTNWATRK 86
>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 = 103 bits (259), Expect = 9e-30
Identities = 22/83 (26%), Positives = 45/83 (54%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
GW +FV ++ E +E + + F +G ++++ + D +T KG+ V + +A+ A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 92 IQSLNGYALGNRILQVSFKTNKG 114
++LNG + + +QV + KG
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKG 153
>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 = 102 bits (257), Expect = 1e-29
Identities = 25/80 (31%), Positives = 45/80 (56%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V + +E L QLF +G ++SVK++ D +T + +G+GFV + A AI L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 96 NGYALGNRILQVSFKTNKGK 115
NG+ + N+ L+V+ + +
Sbjct: 105 NGFNILNKRLKVALAASGHQ 124
>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 = 100 bits (251), Expect = 6e-29
Identities = 23/86 (26%), Positives = 40/86 (46%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
GW +FV + E E + F +G ++++ + D +T KG+ V Y EA A
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 92 IQSLNGYALGNRILQVSFKTNKGKTS 117
++ LNG L + + V + +G
Sbjct: 81 MEGLNGQDLMGQPISVDWCFVRGPPK 106
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 99.3 bits (248), Expect = 9e-29
Identities = 24/90 (26%), Positives = 42/90 (46%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
P + GW +FV + E E + F +G ++++ + D +T KG+ V
Sbjct: 15 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
Y EA A++ LNG L + + V + +G
Sbjct: 75 YKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104
>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 = 98.5 bits (246), Expect = 3e-28
Identities = 24/79 (30%), Positives = 39/79 (49%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+++ NL+P E L LF F + + + T + +G F+T N + A A+
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 95 LNGYALGNRILQVSFKTNK 113
+NGY L +IL + F NK
Sbjct: 87 VNGYKLYGKILVIEFGKNK 105
>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 = 98.1 bits (245), Expect = 3e-28
Identities = 22/83 (26%), Positives = 45/83 (54%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
GW +FV ++ E +E + + F +G ++++ + D +T KG+ V + +A+ A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 92 IQSLNGYALGNRILQVSFKTNKG 114
++LNG + + +QV + KG
Sbjct: 85 KEALNGAEIMGQTIQVDWCFVKG 107
>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 = 96.8 bits (242), Expect = 5e-28
Identities = 24/78 (30%), Positives = 42/78 (53%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV +L ++ L F F + S V+ D+QT +G+GFV+ T+ D+A A+ S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 96 NGYALGNRILQVSFKTNK 113
G L R L++++
Sbjct: 64 QGQDLNGRPLRINWAAKL 81
>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 = 97.4 bits (243), Expect = 7e-28
Identities = 29/78 (37%), Positives = 46/78 (58%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV +L+PE + F PFG + +V++D+ T K KG+GFV+ N +A AIQ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 96 NGYALGNRILQVSFKTNK 113
G LG R ++ ++ T K
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 97.9 bits (244), Expect = 8e-28
Identities = 23/75 (30%), Positives = 37/75 (49%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ V NL T L ++F +G V V + RD T + +GF FV + +A A+ +
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 95 LNGYALGNRILQVSF 109
++G L R L+V
Sbjct: 109 MDGAVLDGRELRVQM 123
>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 = 96.7 bits (241), Expect = 2e-27
Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
C+ V+ L+ T E L ++F +G + V ++ D Q+ + +GF FV N D+A A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 95 LNGYALGNRILQVSF 109
NG L R ++V F
Sbjct: 108 ANGMELDGRRIRVDF 122
>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 = 95.8 bits (239), Expect = 2e-27
Identities = 21/82 (25%), Positives = 46/82 (56%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+++ ++ + E + L G V ++K++ D QT + KG+ F+ + + + A+++L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
NGY LG+R L+ + +N +
Sbjct: 65 NGYQLGSRFLKCGYSSNSDISG 86
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 96.4 bits (240), Expect = 4e-27
Identities = 24/74 (32%), Positives = 41/74 (55%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V LA E ++ VL F PFG + +++ D +T K +GF FV ++A AI ++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 96 NGYALGNRILQVSF 109
N L R ++V+
Sbjct: 126 NESELFGRTIRVNL 139
>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 = 94.1 bits (235), Expect = 6e-27
Identities = 25/81 (30%), Positives = 44/81 (54%)
Query: 28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
+M + ++V LA E ++ VL F PFG + +++ D +T K +GF FV ++
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 88 AVVAIQSLNGYALGNRILQVS 108
A AI ++N L R ++V+
Sbjct: 62 AAAAIDNMNESELFGRTIRVN 82
>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 = 94.2 bits (235), Expect = 9e-27
Identities = 28/82 (34%), Positives = 40/82 (48%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV NL+ + E L +LF +G + + D T K KGF FVT + AV A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+G R+L V T K + S
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEAS 92
>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 = 96.1 bits (240), Expect = 1e-26
Identities = 23/82 (28%), Positives = 44/82 (53%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V L + + L+ LF G + + +++RD +T G+ FV T+ ++ AI+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
NG + N+ L+VS+ G++
Sbjct: 66 NGITVRNKRLKVSYARPGGESI 87
Score = 84.9 bits (211), Expect = 2e-22
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V NL + L +FG +G++ ++RD T + +G FV +EA AI +L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 96 NGYAL--GNRILQVSF 109
N G++ L V
Sbjct: 152 NNVIPEGGSQPLSVRL 167
>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 = 94.3 bits (235), Expect = 1e-26
Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 5/89 (5%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
A M ++V +L E +L +F PFG ++S++++ D +T + KG+GF+T ++
Sbjct: 23 SAGPMR-----LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
+ A A++ LNG+ L R ++V T +
Sbjct: 78 SECAKKALEQLNGFELAGRPMKVGHVTER 106
>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 = 95.7 bits (238), Expect = 1e-26
Identities = 23/75 (30%), Positives = 37/75 (49%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ V NL T L ++F +G V V + RD T + +GF FV + +A A+ +
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 95 LNGYALGNRILQVSF 109
++G L R L+V
Sbjct: 132 MDGAVLDGRELRVQM 146
>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 = 93.4 bits (233), Expect = 2e-26
Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
C+ V+ L+ T E L ++F +G + V ++ D Q+ + +GF FV N D+A A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 95 LNGYALGNRILQVSF 109
NG L R ++VS
Sbjct: 77 ANGMELDGRRIRVSG 91
>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 = 93.4 bits (233), Expect = 2e-26
Identities = 24/74 (32%), Positives = 41/74 (55%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V LA E ++ VL F PFG + +++ D +T K +GF FV ++A AI ++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 96 NGYALGNRILQVSF 109
N L R ++V+
Sbjct: 75 NESELFGRTIRVNL 88
>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 = 93.4 bits (233), Expect = 2e-26
Identities = 23/74 (31%), Positives = 45/74 (60%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V +L E +L +F PFG + ++ +++D T + KG+GF+T ++ + A A++ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 96 NGYALGNRILQVSF 109
NG+ L R ++V
Sbjct: 68 NGFELAGRPMRVGH 81
>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 = 92.7 bits (231), Expect = 3e-26
Identities = 21/78 (26%), Positives = 39/78 (50%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
S ++V NL + L+++F +G V V +++D T K KG F+ + D A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 92 IQSLNGYALGNRILQVSF 109
+++N L R+++ S
Sbjct: 75 TRAINNKQLFGRVIKASI 92
>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 = 97.4 bits (243), Expect = 4e-26
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 2/80 (2%)
Query: 35 CIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
C+ V L P + L + + ++ Q + KGF + + A A Q
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQ 244
Query: 94 SLNGYALGNRILQVSFKTNK 113
+G +LG L+VSF
Sbjct: 245 QADGLSLGGSHLRVSFCAPG 264
Score = 96.2 bits (240), Expect = 1e-25
Identities = 24/82 (29%), Positives = 36/82 (43%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V NL P + +L PFG+++ ++ +T + KG+GF D A A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
G LG R L V + T
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTP 179
Score = 75.0 bits (185), Expect = 1e-17
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 7/78 (8%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
I + L + + L + ++ V + KG FVT+ N ++A AI +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY------KGTAFVTLLNGEQAEAAINAF 77
Query: 96 NGYALGNRILQVSFKTNK 113
+ L R L V +
Sbjct: 78 HQSRLRERELSVQLQPTD 95
>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 = 92.7 bits (231), Expect = 4e-26
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ V NL T L ++F +G V V + R+ T +GF FV + +A A +
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 95 LNGYALGNRILQVSF 109
++G L R L+V
Sbjct: 75 MDGAELDGRELRVQV 89
>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 = 92.3 bits (230), Expect = 5e-26
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V NL ++ L + F PFG + S KV+ + + KGFGFV ++ +EA A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 96 NGYALGNRILQVSFKTNK 113
NG + + L V+ K
Sbjct: 76 NGRIVATKPLYVALAQRK 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 = 92.3 bits (230), Expect = 7e-26
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IF+ NL + L+ F FG + S KV+ D N KG+GFV + A AI+ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 96 NGYALGNRILQVSFKTNK 113
NG L +R + V ++
Sbjct: 66 NGMLLNDRKVFVGRFKSR 83
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 94.7 bits (236), Expect = 8e-26
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ L + + +L FG +++ +++D T KG+ F + + AI L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
NG LG++ L V + K +
Sbjct: 177 NGMQLGDKKLLVQRASVGAKNA 198
Score = 74.3 bits (183), Expect = 7e-18
Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 6/85 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVK-----VIRDLQTNKCKGFGFVTMTNYDEAVV 90
++V N+ E + F + + + +Q N+ K F F+ + DE
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 91 AIQSLNGYALGNRILQVSFKTNKGK 115
A+ +G + L++ +
Sbjct: 67 AMA-FDGIIFQGQSLKIRRPHDYQP 90
>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 = 93.3 bits (232), Expect = 1e-25
Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
++V NL+ T E +++LF G ++ + + D GF FV + +A A++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 95 LNGYALGNRILQVSF 109
+NG L +RI++ +
Sbjct: 101 INGTRLDDRIIRTDW 115
>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 = 91.6 bits (228), Expect = 1e-25
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTN 84
++ +G +++ +L P +E+ + + F G V SVK+IR+ T G+ FV +
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTN 112
A + +NG L FK N
Sbjct: 62 LATAEKCLHKINGKPLPGATPAKRFKLN 89
>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 = 93.0 bits (232), Expect = 1e-25
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V L + LFG G ++S K++RD T + G+GFV + +A AI +L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 96 NGYALGNRILQVSF 109
NG L + ++VS+
Sbjct: 65 NGLRLQTKTIKVSY 78
Score = 81.5 bits (202), Expect = 5e-21
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 2/76 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V L + L QLF +G + + +++ D T +G GF+ EA AI+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 96 NGYAL--GNRILQVSF 109
NG + V F
Sbjct: 151 NGQKPSGATEPITVKF 166
>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 = 90.8 bits (226), Expect = 2e-25
Identities = 27/75 (36%), Positives = 46/75 (61%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+FV L+ +T E L Q+F +G + V V++D +T + +GFGFVT N D+A A+ +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 95 LNGYALGNRILQVSF 109
+NG ++ R ++V
Sbjct: 74 MNGKSVDGRQIRVDQ 88
>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 = 90.8 bits (226), Expect = 2e-25
Identities = 20/73 (27%), Positives = 40/73 (54%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
++V L + E +LW+LF G V + + +D T + +G+GFV + ++A AI+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 95 LNGYALGNRILQV 107
++ L + ++V
Sbjct: 77 MDMIKLYGKPIRV 89
>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 = 91.2 bits (227), Expect = 2e-25
Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ L ET E +L +FG G + V +I+D +T+K +GF F+T N +A A + +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 96 NGYALGNRILQV 107
NG +L + ++V
Sbjct: 69 NGKSLHGKAIKV 80
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 90.9 bits (226), Expect = 3e-25
Identities = 14/74 (18%), Positives = 31/74 (41%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ L E+ L + +G V+ V+++ +T K G V T+ A +++L
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 96 NGYALGNRILQVSF 109
+ ++ I+
Sbjct: 69 HLTSVMGNIIHAQL 82
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 93.5 bits (233), Expect = 3e-25
Identities = 21/82 (25%), Positives = 39/82 (47%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
I+V ++ + + + +F FG ++S + RD T K KG+GF+ + A+ S+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
N + LG + L+V
Sbjct: 188 NLFDLGGQYLRVGKAVTPPMPL 209
Score = 91.2 bits (227), Expect = 3e-24
Identities = 26/80 (32%), Positives = 44/80 (55%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V ++ E E + Q F PFG ++S+ + D T K KGF FV + A +A++ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 96 NGYALGNRILQVSFKTNKGK 115
N LG R ++V +N G+
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQ 110
>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 = 89.6 bits (223), Expect = 7e-25
Identities = 25/78 (32%), Positives = 42/78 (53%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV N+ E E L +F G V S +++ D +T K KG+GF + + A+ A+++L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 96 NGYALGNRILQVSFKTNK 113
NG R L+V ++
Sbjct: 71 NGREFSGRALRVDNAASE 88
>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 = 89.2 bits (222), Expect = 7e-25
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 3/93 (3%)
Query: 20 ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGF 79
+S + PA +FV NL E +L++LF G + V + +D + K K FGF
Sbjct: 5 SSGMFPAQEEADR--TVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGF 61
Query: 80 VTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN 112
V + + AI LNG L R + VS ++
Sbjct: 62 VCFKHPESVSYAIALLNGIRLYGRPINVSGPSS 94
>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 = 89.2 bits (222), Expect = 7e-25
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV NL P+ E + +LF +G V + +D KGFGF+ + A +A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+ L + L+V F + +
Sbjct: 72 DNMPLRGKQLRVRFACHSASLT 93
>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 = 89.2 bits (222), Expect = 1e-24
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+++ NL +E L + PFG V S +++RD + +G GF M + ++ I
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 96 NGYALGNRILQVS 108
NG + +
Sbjct: 87 NGKFIKTPPGVSA 99
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 88.9 bits (221), Expect = 2e-24
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 20 ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGF 79
SS LP++ G +F+ NL+ ++EE L ++ FG ++ V+V+ T KG F
Sbjct: 4 GSSGLPSDVTEGK--TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 80 VTMTNYDEAVVAIQSLN------GYALGNRILQVSF 109
+ A + + + G L R L+V
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>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 = 89.9 bits (224), Expect = 2e-24
Identities = 24/74 (32%), Positives = 42/74 (56%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV +L ++ L F F + S V+ D+QT +G+GFV+ T+ D+A A+ S+
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 96 NGYALGNRILQVSF 109
G L R L++++
Sbjct: 150 QGQDLNGRPLRINW 163
Score = 81.0 bits (201), Expect = 6e-21
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V NL E +L Q F G + ++K++ D + NK + FV +A +A+Q+L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
NG + N I+++++ ++S
Sbjct: 62 NGKQIENNIVKINWAFQSQQSS 83
>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 = 90.0 bits (224), Expect = 2e-24
Identities = 19/73 (26%), Positives = 35/73 (47%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ L + + +L FG +++ +++D T KG+ F + + AI L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 96 NGYALGNRILQVS 108
NG LG++ L V
Sbjct: 157 NGMQLGDKKLLVQ 169
Score = 72.6 bits (179), Expect = 1e-17
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVK-----VIRDLQTNKCKGFGFVTMTNYDEAVV 90
++V N+ E + F + + + +Q N+ K F F+ + DE
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 91 AIQSLNGYALGNRILQV 107
A+ +G + L++
Sbjct: 67 AMA-FDGIIFQGQSLKI 82
>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 = 87.6 bits (218), Expect = 3e-24
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
I+V NL + +LF FG V +VK+I D +T K KGFGFV M + AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 96 NGYALGNRILQVS 108
+ R ++V+
Sbjct: 63 DNTDFMGRTIRVT 75
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 87.7 bits (218), Expect = 3e-24
Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ L + L ++ G V+ ++++ + + K KG +V N +A A+ +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMKM 78
Query: 96 NGYALGNRILQVSF---KTNKG 114
+G + I++V+ + G
Sbjct: 79 DGMTIKENIIKVAISNSGPSSG 100
>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 = 87.3 bits (217), Expect = 5e-24
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V N+ + L Q+FG FG + V++I + KGFGFVT N +A A + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKL 75
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+G + R ++V+ T + T+
Sbjct: 76 HGTVVEGRKIEVNNATARVMTN 97
>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 = 87.3 bits (217), Expect = 5e-24
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSV-KVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
IF+ NL PE +E +L+ F FG + K++RD T KG+ F+ ++D + AI++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 95 LNGYALGNRILQVSFKTNK 113
+NG L NR + VS+ K
Sbjct: 68 MNGQYLCNRPITVSYAFKK 86
>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 = 86.4 bits (215), Expect = 7e-24
Identities = 12/75 (16%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRD-LQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ + L + + ++F +G ++ + + + + + KG+ +V N DEA A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 95 LNGYALGNRILQVSF 109
++G + + + +
Sbjct: 67 MDGGQIDGQEITATA 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 = 86.5 bits (215), Expect = 9e-24
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
++V NL+ + E ++ QLF G +S K+I + +N + FV + +A A+ +
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74
Query: 95 LNGYALGNRILQVSFKTNKGKTS 117
+NG + + ++V++ T
Sbjct: 75 MNGRKILGKEVKVNWATTPSSQK 97
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 86.6 bits (215), Expect = 1e-23
Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVV 90
+ I V N+ + + + +LF FG +++V++ + + T +GFGFV +A
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 91 AIQSL-NGYALGNRILQVSFKTNKGKTS 117
A +L + L R L + + ++
Sbjct: 74 AFNALCHSTHLYGRRLVLEWADSEVTVQ 101
>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 = 86.6 bits (215), Expect = 1e-23
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ + +E L LF FG + + V++D T KG F+T + A+ A +L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 96 NGYAL---GNRILQVSFKTNKGK 115
+ NR +QV ++ +
Sbjct: 76 HEQKTLPGMNRPIQVKPADSESR 98
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 86.2 bits (214), Expect = 2e-23
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ V N+ + L Q+FG FG + V++I + KGFGFVT N +A A +
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREK 88
Query: 95 LNGYALGNRILQVSF 109
L+G + R ++V+
Sbjct: 89 LHGTVVEGRKIEVNN 103
>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 = 85.4 bits (212), Expect = 3e-23
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKC---KGFGFVTMTNYDEAVVAI 92
+F+ NL T E L +F GA++S + + GFGFV ++A A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 93 QSLNGYALGNRILQVSFKTNKGK 115
+ L G+ + L+V K
Sbjct: 68 KQLQGHTVDGHKLEVRISERATK 90
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 85.1 bits (211), Expect = 3e-23
Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 12/99 (12%)
Query: 11 FSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQ 70
+P D + S P T ++ N+ E+ L LF FG + K +
Sbjct: 11 VNPQAVDHIIRSAPPRVTT------AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-- 62
Query: 71 TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
KG F+ +++A V I +L + R L+ +
Sbjct: 63 ----KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW 97
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 84.7 bits (210), Expect = 4e-23
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
I + N+AP T + P+ + V ++++I+D QT + +GF FV +++ +A +Q
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 94 SLNG----YALGNRILQVSF 109
L + + + V F
Sbjct: 72 ILQSLHPPLKIDGKTIGVDF 91
>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 = 85.1 bits (211), Expect = 5e-23
Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 1/78 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV NL + L ++F G V ++ D + K +G G VT EAV AI
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 96 NGYALGNRILQVSFKTNK 113
NG L +R + V
Sbjct: 77 NGQLLFDRPMHVKMDERA 94
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 84.5 bits (210), Expect = 5e-23
Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 2/90 (2%)
Query: 26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY 85
++ + IFV NL + +L F G V + + K KG G V +
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 86 DEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
+ A A + +NG L R + V N
Sbjct: 59 EVAERACRMMNGMKLSGREIDVRIDRNASG 88
>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 = 84.3 bits (209), Expect = 1e-22
Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
+G + V NL ++ + +LF FG ++ V D ++ + G V +A+ A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKA 92
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
++ G L R + + ++
Sbjct: 93 MKQYKGVPLDGRPMDIQLVASQ 114
>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 = 83.8 bits (208), Expect = 1e-22
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+FV L+ +T E L + F +++ D +T KGFGFV + ++A A ++
Sbjct: 17 TLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 95 LNGYALGNRILQVSFKTNKGK 115
+ + + + + KG+
Sbjct: 74 MEDGEIDGNKVTLDWAKPKGE 94
>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 = 86.6 bits (215), Expect = 1e-22
Identities = 18/81 (22%), Positives = 43/81 (53%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V +L P+ E++L++ F P G + S++V RD+ T + G+ +V +A A+ ++
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 96 NGYALGNRILQVSFKTNKGKT 116
N + + +++ +
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSL 98
Score = 81.2 bits (201), Expect = 2e-20
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IF+ NL + L+ F FG + S KV+ D N KG+GFV + A AI+ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 96 NGYALGNRILQVSFKTNK 113
NG L +R + V ++
Sbjct: 164 NGMLLNDRKVFVGRFKSR 181
>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 = 83.1 bits (206), Expect = 2e-22
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
+G + V NL ++ + +LF FG ++ V D ++ + G V +A+ A
Sbjct: 28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKA 86
Query: 92 IQSLNGYALGNRILQVSF 109
++ NG L R + +
Sbjct: 87 MKQYNGVPLDGRPMNIQL 104
>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 = 82.6 bits (205), Expect = 3e-22
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
I+V N+ L F G+V V ++ D + KGF ++ ++ E+V +L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLAL 67
Query: 96 NGYALGNRILQVSFK-TNK 113
+ R ++V K TN+
Sbjct: 68 DESLFRGRQIKVIPKRTNR 86
>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 = 86.3 bits (213), Expect = 3e-22
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 2/85 (2%)
Query: 27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTN 84
T G +++ NL T + L + G + +K + + KGF V + +
Sbjct: 62 YTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS 121
Query: 85 YDEAVVAIQSLNGYALGNRILQVSF 109
+ + L L + V+
Sbjct: 122 EASSKKLMDLLPKRELHGQNPVVTP 146
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 84.9 bits (210), Expect = 3e-22
Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
+G + V NL ++ + +LF FG ++ V D ++ + G V +A+ A
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKA 145
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
++ G L R + + ++
Sbjct: 146 MKQYKGVPLDGRPMDIQLVASQ 167
>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 = 82.8 bits (205), Expect = 4e-22
Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++ +A + ++ Q F PFG + ++V + KG+ FV + ++ A AI S+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 96 NGYALGNRILQVSF 109
NG + +++ +
Sbjct: 82 NGTTIEGHVVKCYW 95
>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 = 83.2 bits (206), Expect = 4e-22
Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 1/75 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V N+ + L F G++ + ++ D + KG+ ++ +V A ++
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVAM 97
Query: 96 NGYALGNRILQVSFK 110
+ R ++V K
Sbjct: 98 DETVFRGRTIKVLPK 112
>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 = 85.9 bits (213), Expect = 7e-22
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV NL + E +LF +G V + RD +GFGF+ + + A +A L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 96 NGYALGNRILQVSFKTNKGK 115
+G L +R L++ F T+
Sbjct: 79 DGTILKSRPLRIRFATHGAA 98
Score = 77.8 bits (192), Expect = 9e-19
Identities = 21/83 (25%), Positives = 30/83 (36%), Gaps = 5/83 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V NL+P +L Q F FG V+ V+ D + G GFV A A++
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157
Query: 96 NGYAL----GNRILQVSFKTNKG 114
A R + V
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFD 180
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 81.7 bits (202), Expect = 8e-22
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ + N+ P + VL L +G V+S + + VT ++ D+A A+ L
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKL 74
Query: 96 NGYALGNRILQVSFKTNK 113
NG+ L N L+V++ ++
Sbjct: 75 NGFQLENFTLKVAYIPDE 92
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 83.0 bits (205), Expect = 1e-21
Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 2/103 (1%)
Query: 9 QRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGA--VQSVKVI 66
Q SP + + + + + ++V + + T + L Q+ G V +K
Sbjct: 31 QEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFA 90
Query: 67 RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
+ + KG+ V + + + ++ L G L + V
Sbjct: 91 ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP 133
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 81.6 bits (202), Expect = 1e-21
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV + +ES L ++FGPFG ++ VK++ GF FV + A AI+ +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85
Query: 96 NGYALGNRILQVSF 109
+G + N+ L+V +
Sbjct: 86 HGKSFANQPLEVVY 99
>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 = 81.2 bits (201), Expect = 1e-21
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ + NL+ E L ++F + + Q K KG+ F+ ++++A A+ S
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 95 LNGYALGNRILQVSFKTNKGK 115
N + R +++ + +G
Sbjct: 73 CNKREIEGRAIRLELQGPRGS 93
>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 = 81.6 bits (202), Expect = 1e-21
Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 2/83 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F LA L F G V+ V++I D + + KG +V +AI L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 96 NGYALGNRILQVSFK-TNKGKTS 117
G L + V K + S
Sbjct: 87 TGQRLLGVPIIVQASQAEKNRLS 109
>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 = 84.3 bits (208), Expect = 2e-21
Identities = 27/110 (24%), Positives = 41/110 (37%), Gaps = 12/110 (10%)
Query: 5 NKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVK 64
N L RF + P+ T + + N+ P E L LF G V
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSAT-------LHLSNIPPSVSEEDLKVLFSSNGGVVKGF 182
Query: 65 VIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-RILQVSFKTNK 113
K + + M + +EAV A+ L+ + LG L+VSF +
Sbjct: 183 KFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
Score = 71.6 bits (175), Expect = 1e-16
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 36 IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ V NL PE L+ LFG +G VQ VK++ K V M + ++A +A+
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAMSH 91
Query: 95 LNGYALGNRILQVSFKTNKGKTS 117
LNG+ L + ++++ ++
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQL 114
>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 = 84.7 bits (210), Expect = 3e-21
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 36 IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQ 93
I + NL+ E +E++L + F FG+++ + + + + F+ N D A A+Q
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272
Query: 94 SLNGYALGNRILQVSFKTNK 113
+N LGNR + VS K
Sbjct: 273 -MNRSLLGNREISVSLADKK 291
Score = 80.8 bits (200), Expect = 1e-19
Identities = 13/75 (17%), Positives = 30/75 (40%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+++ N P + + L V + L+ N + F ++ +T+ ++A ++ L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 96 NGYALGNRILQVSFK 110
NG + L
Sbjct: 180 NGLKIEGYTLVTKVS 194
Score = 75.4 bits (186), Expect = 7e-18
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 2/69 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V NL ++ +++ F G + V V K F + YD A+ AI
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101
Query: 96 NGYALGNRI 104
+ N I
Sbjct: 102 HKVVGQNEI 110
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 80.5 bits (199), Expect = 3e-21
Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 8/88 (9%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYDE 87
IFV L + F G +++ + + D +T K KG V+ +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 88 AVVAIQSLNGYALGNRILQVSFKTNKGK 115
A AI +G ++VSF T +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>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 = 80.4 bits (199), Expect = 3e-21
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV NLA E +L + F FG ++ VK ++D + F+ D AV A++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 96 NGYALGNRILQVSF 109
NG L +++ F
Sbjct: 66 NGKDLEGENIEIVF 79
>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 = 80.5 bits (199), Expect = 3e-21
Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+++ NL + ++ +FG +G ++ ++V +T +G +V + +A A+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVD 65
Query: 94 SLNGYALGNRILQVSFKTNK 113
L+G+ + NR L V +
Sbjct: 66 HLSGFNVSNRYLVVLYYNAN 85
>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 = 82.8 bits (204), Expect = 3e-21
Identities = 12/85 (14%), Positives = 28/85 (32%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
N + + +N E E +++ G + V ++ G + +
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDS 174
Query: 85 YDEAVVAIQSLNGYALGNRILQVSF 109
+A+ + LN Y + N +
Sbjct: 175 KSDALETLGFLNHYQMKNPNGPYPY 199
Score = 65.9 bits (160), Expect = 1e-14
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 6/75 (8%)
Query: 36 IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ VY L ++ +F +G V+ VK ++ G V M + AI
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61
Query: 95 LNGYALGNRILQVSF 109
LN + + + V
Sbjct: 62 LNNNFMFGQKMNVCV 76
>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 = 80.1 bits (198), Expect = 5e-21
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 8/92 (8%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMT 83
I+V L L F G V+ + + D +T K KG V+
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 84 NYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
+ A A++ +G L+VS K
Sbjct: 74 DPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>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 = 81.5 bits (202), Expect = 5e-21
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTN--KCKGFGFVTMTNYDEAVVAIQ 93
+FV + E L +LF +GAV + V+RD N + KG FVT A+ A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 94 SLNGYALGNRILQVSF 109
+L+ + +
Sbjct: 66 ALHNMKVLPGMHHPIQ 81
Score = 76.5 bits (189), Expect = 4e-19
Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ ++ + E+ + +F FG ++ +++R +G FVT T A AI+++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 96 NGY---ALGNRILQVSF 109
+ + + V F
Sbjct: 157 HQAQTMEGCSSPMVVKF 173
>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 = 79.6 bits (197), Expect = 5e-21
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV + +E+ + F +G+V+ VK+I D +T KG+GFV+ N + ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE-- 68
Query: 96 NGYALGNRILQV 107
+ + L++
Sbjct: 69 SQINFHGKKLKL 80
>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 = 79.6 bits (197), Expect = 5e-21
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV L + E + +LF PFG + V+R KG FV +++ EA AI +L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 96 NG---YALGNRILQVSFKTNKGK 115
+G + L V F +
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKE 99
>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 = 79.2 bits (196), Expect = 5e-21
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 2/76 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+++ NL T + L + G + +K + + KGF V + + + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 94 SLNGYALGNRILQVSF 109
L L + V+
Sbjct: 64 LLPKRELHGQNPVVTP 79
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 79.6 bits (197), Expect = 6e-21
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 36 IFVYNLAPETEESVLWQLFG-PFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+FV +L P+ ++ +L++ F + + + KV+ D QT KG+GFV T+ E A+
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALTE 70
Query: 95 LNG-YALGNRILQVSFKTNK 113
G LG++ +++S K
Sbjct: 71 CQGAVGLGSKPVRLSVAIPK 90
>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 = 79.2 bits (196), Expect = 6e-21
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V N++P L F +G V +++ + FV M ++AV AI+ L
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGL 64
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+ + + V T++ +T+
Sbjct: 65 DNTEFQGKRMHVQLSTSRLRTA 86
>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 = 78.9 bits (195), Expect = 9e-21
Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 8/85 (9%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYD 86
IFV L + F G +++ + + D +T K KG V+ +
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 87 EAVVAIQSLNGYALGNRILQVSFKT 111
A AI +G ++VSF T
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKVSFAT 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 = 78.0 bits (193), Expect = 1e-20
Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 8/88 (9%)
Query: 30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
+G+ W IFV N++ L LF G V V+ K + FV M +A
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAK 57
Query: 90 VAIQSLNGYALGNRILQVSFKTNKGKTS 117
AI LNG + + + V T K S
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKKS 85
>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 = 80.7 bits (199), Expect = 2e-20
Identities = 27/110 (24%), Positives = 41/110 (37%), Gaps = 12/110 (10%)
Query: 5 NKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVK 64
N L RF + P+ T + + N+ P E L LF G V
Sbjct: 99 NSPLHRFKKPGSKNFQNIFPPSAT-------LHLSNIPPSVSEEDLKVLFSSNGGVVKGF 151
Query: 65 VIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-RILQVSFKTNK 113
K + + M + +EAV A+ L+ + LG L+VSF +
Sbjct: 152 KFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197
Score = 71.5 bits (175), Expect = 8e-17
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 36 IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ V NL PE L+ LFG +G VQ VK++ + K V M + ++A +A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60
Query: 95 LNGYALGNRILQVSFKTNKGKTS 117
LNG+ L + ++++ ++
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQL 83
>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 = 78.4 bits (193), Expect = 2e-20
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 36 IFVYNLAPE-TEESVL--WQLFGPFGAVQSVKVIRDLQTNKCK---GFGFVTMTNYDEAV 89
+FV L+ + VL + FG FG + V + + +VT ++A+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 90 VAIQSLNGYALGNRILQVSFKTNK 113
AIQ +N + R L+ S T K
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
>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 = 77.7 bits (192), Expect = 2e-20
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+++ NL+P L QLFG + Q G+ FV + + A+ AI++L
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 64
Query: 96 NGYA-LGNRILQVSFKTNKGKTS 117
+G L +I++V + +K S
Sbjct: 65 SGKVELHGKIMEVDYSVSKKLRS 87
>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 = 78.6 bits (194), Expect = 2e-20
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
G ++VY + ++L F PFG + + + + FVT + A A
Sbjct: 38 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA 89
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
+ LNG + + L+V+ +
Sbjct: 90 VAELNGTQVESVQLKVNIARKQ 111
>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 = 77.7 bits (192), Expect = 3e-20
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
++V NL T E ++ + F +V K + + FV +N ++AV A+++
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70
Query: 95 LNGYALGNRILQVSF 109
LNG L ++V+
Sbjct: 71 LNGKVLDGSPIEVTL 85
>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 = 77.7 bits (192), Expect = 3e-20
Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ NL P + L A + + D++T + FG+V + ++ A++ L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-L 77
Query: 96 NGYALGNRILQVSFKTNKGKT 116
G + +++ + T
Sbjct: 78 TGLKVFGNEIKLEKPKGRDGT 98
>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 = 76.9 bits (190), Expect = 6e-20
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
G ++VY + ++L F PFG + + + + FVT + A A
Sbjct: 14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA 65
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
+ LNG + + L+V+ +
Sbjct: 66 VAELNGTQVESVQLKVNIARKQ 87
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 76.9 bits (190), Expect = 6e-20
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+V NL T + + +F ++SV+++RD T+K KGF +V D A+ +
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75
Query: 96 NGYALGNRILQVSFKTNK 113
+G LG+R L+V +
Sbjct: 76 DGALLGDRSLRVDIAEGR 93
>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 = 78.8 bits (195), Expect = 6e-20
Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 2/80 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ NL P + L A + V+ +T + FG+V + ++ A++ L
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 96 NGYALGNRILQVSFKTNKGK 115
G + +++ +
Sbjct: 74 TGLKVFGNEIKLEKPKGRDS 93
Score = 78.8 bits (195), Expect = 8e-20
Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 5/79 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ NL+ E L ++F ++ Q K KG ++ + +A ++
Sbjct: 102 LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 96 NGYALGNRILQVSFKTNKG 114
G + R + + + KG
Sbjct: 157 QGAEIDGRSVSLYYTGEKG 175
>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 = 76.2 bits (188), Expect = 9e-20
Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 5/82 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ NL+ E L ++F ++ Q K KG ++ + +A ++
Sbjct: 19 LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
G + R + + + KG T
Sbjct: 74 QGAEIDGRSVSLYYTGEKGGTR 95
>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 = 75.7 bits (187), Expect = 1e-19
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ NL E E + LF +G V +I K +GFV + + A AI++L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+ Y L + V NK K S
Sbjct: 63 HHYKLHGVNINVEASKNKSKAS 84
>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 = 75.7 bits (187), Expect = 2e-19
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQT-NKCKGFGFVTMTNYDEAVVAIQS 94
F+ NL + E + + F + +V++ R+ + KGFG+ + D + A+
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79
Query: 95 LNGYALGNRILQVSF 109
LN +LGNR ++V
Sbjct: 80 LNEESLGNRRIRVDV 94
>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 = 75.6 bits (186), Expect = 5e-19
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKV-----IRDLQTNKCKGFGFVTMTNYDEAVV 90
I+V NLA +E L +FG + S IR ++ + KG F+ + N A
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 91 AIQSLNGYALGNRILQVSFKTNK 113
A++ NGY L + + V F +
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSA 130
>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 = 74.2 bits (183), Expect = 6e-19
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
++V L P T + L + F FG+++++ ++ F ++ + D A A
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72
Query: 95 LNGYALGN--RILQVSF 109
+ G+ LG R L+V F
Sbjct: 73 MRGFPLGGPDRRLRVDF 89
>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 = 74.2 bits (183), Expect = 7e-19
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IFV + E+ L + F FG V V +I D + + +GFGF+T + +++V ++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED-EQSVDQAVNM 71
Query: 96 NGYALGNRILQV 107
+ + + + ++V
Sbjct: 72 HFHDIMGKKVEV 83
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 74.3 bits (183), Expect = 8e-19
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
+ I+V NL P+ + +F +GA++ + + F FV + +A A
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDA 77
Query: 92 IQSLNGYALGNRILQVSFKTNKGKTS 117
+ +GY L+V F + T
Sbjct: 78 VYGRDGYDYDGYRLRVEFPRSGRGTG 103
>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 = 74.2 bits (183), Expect = 8e-19
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQS 94
F+ NL + E + + F + +V++ R+ + KGFG+ + D + A+ S
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75
Query: 95 LNGYALGNRILQVSF 109
LN +LGN+ ++V
Sbjct: 76 LNEESLGNKRIRVDV 90
>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 = 78.4 bits (192), Expect = 2e-18
Identities = 20/120 (16%), Positives = 46/120 (38%), Gaps = 19/120 (15%)
Query: 3 AINKGLQRFSP-----LTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
+ L+ + P GD T +FV + +T ES L + F +
Sbjct: 81 EVETELKMWDPHNDPNAQGD-------AFKT-------LFVARVNYDTTESKLRREFEVY 126
Query: 58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
G ++ + ++ ++ K +G+ F+ + + A + +G + R + V + +
Sbjct: 127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKG 186
>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 = 73.1 bits (180), Expect = 3e-18
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IFV L T ++ L + F FG ++ VI D QT K +G+GFVTM + A A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 96 NGYALGNRILQV 107
N + R V
Sbjct: 80 NPI-IDGRKANV 90
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 72.1 bits (177), Expect = 4e-18
Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 7/84 (8%)
Query: 31 GSGWCIFVYNL------APETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
GS I V + L LF G V +++ D T K KGF FV +
Sbjct: 4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGS 63
Query: 85 YDEAVVAIQSLNGYAL-GNRILQV 107
++A I+S +G L L +
Sbjct: 64 MNDAKKIIKSFHGKRLDLKHRLFL 87
>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 = 72.9 bits (180), Expect = 1e-17
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IFV + P+ + F +G + +++ D T + +GFGFVT + D Q
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-N 148
Query: 96 NGYALGNRILQVSF 109
+R +++
Sbjct: 149 KFIDFKDRKIEIKR 162
Score = 71.4 bits (176), Expect = 5e-17
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ L +T E L + FG +G V +K+++D T + +GFGF++ ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-- 63
Query: 96 NGYALGNRILQV 107
+ L +++
Sbjct: 64 TQHILDGKVIDP 75
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 71.2 bits (175), Expect = 1e-17
Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V NL + L + F +G +++V + R+ GF FV + +A A++ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+G + ++V T + S
Sbjct: 58 DGKVICGSRVRVELSTGMPRRS 79
>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 = 70.5 bits (173), Expect = 1e-17
Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 7/82 (8%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
I V NL ++ + L + ++ ++ K FVT+ N ++A AIQ
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+ Y+ + L V +
Sbjct: 61 HQYSFRGKDLIVQLQPTDALLC 82
>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 = 70.8 bits (174), Expect = 1e-17
Identities = 15/77 (19%), Positives = 30/77 (38%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
I V N+ + F + + ++ + G V + DEA A+
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 95 LNGYALGNRILQVSFKT 111
LN +G+R +++S +
Sbjct: 77 LNDRPIGSRKVKLSGPS 93
>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 = 71.0 bits (174), Expect = 1e-17
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 6/78 (7%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
S I NL T + + + F FG++ V + + V EA A
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKA 62
Query: 92 IQSLNGYALGNRILQVSF 109
+ L + L + +
Sbjct: 63 FRHLAYSKFHHVPLYLEW 80
>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 = 71.8 bits (176), Expect = 2e-17
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
++V NL ++ L + FG +G ++SV V R+ GF FV + +A A++ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 130
Query: 96 NGYALGNRILQVSFKTNKGK 115
+G L ++V + +
Sbjct: 131 DGRTLCGCRVRVELSNGEKR 150
>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 = 70.6 bits (173), Expect = 2e-17
Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
S + V L P L G V V RD G G V ++ A
Sbjct: 14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66
Query: 92 IQSLNGYALGNRILQVSF 109
++ L+ + + ++
Sbjct: 67 VRKLDNTKFRSHEGETAY 84
>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 = 69.6 bits (171), Expect = 4e-17
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 36 IFVYNLAPETEESVL----WQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
I++ NL + ++ L +F FG + + V R L+ +G FV A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 67
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
++S+ G+ ++ +++ +
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTD 89
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 69.9 bits (171), Expect = 5e-17
Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)
Query: 36 IFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
+ + N+ PE + L L G + + V ++ G ++ + A
Sbjct: 32 VLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAF 88
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
+++ GY L ++F
Sbjct: 89 VEAFQGYPFQGNPLVITFSETP 110
>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 = 68.9 bits (169), Expect = 8e-17
Identities = 14/75 (18%), Positives = 28/75 (37%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
I V N+ + F + + ++ + G V + DEA A+
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 95 LNGYALGNRILQVSF 109
LN +G+R +++
Sbjct: 77 LNDRPIGSRKVKLVL 91
>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 = 71.2 bits (175), Expect = 8e-17
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+F+ L+ ET + L F +G + V+RD T + +GFGFVT +E A+ +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74
Query: 96 NGYALGNRILQV 107
+ + R+++
Sbjct: 75 RPHKVDGRVVEP 86
Score = 70.0 bits (172), Expect = 2e-16
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IFV + +TEE L F +G ++ ++++ D + K +GF FVT ++D +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ- 165
Query: 96 NGYALGNRILQVSFKTNKGKTS 117
+ + +V +K + +
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMA 187
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 69.0 bits (169), Expect = 9e-17
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 30 NGSGWCIFVYNLAPETEE------SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMT 83
+G I V N+ + +V+ ++F FG + + + K KG+ F+
Sbjct: 12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYA 69
Query: 84 NYDEAVVAIQSLNGYAL-GNRILQV 107
+ AV A+++ +GY L +V
Sbjct: 70 SPAHAVDAVKNADGYKLDKQHTFRV 94
>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 = 68.1 bits (167), Expect = 1e-16
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 7/75 (9%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-S 94
++V L E+ L F FG ++++ V++ + F+ A VA + S
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 95 LNGYALGNRILQVSF 109
N + R L V +
Sbjct: 69 FNKLIVNGRRLNVKW 83
>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 = 70.7 bits (172), Expect = 4e-16
Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 36 IFVYNLAPETEE----SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
I++ NL + ++ L+ +F FG + + V R + K +G FV A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68
Query: 92 IQSLNGYALGNRILQVSFKTNK 113
++S+ G+ ++ +++ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTD 90
Score = 70.3 bits (171), Expect = 8e-16
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+F+ NL ET E +L LF F + V+++ FV N +A A
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARD 262
Query: 94 SLNGYAL-GNRILQVSF 109
+L G+ + N +++SF
Sbjct: 263 ALQGFKITQNNAMKISF 279
>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 = 66.0 bits (162), Expect = 6e-16
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI--- 92
IFV L+P+T E + + FG FG V+S+++ D +TNK +GF F+T + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 93 -QSLNG 97
++
Sbjct: 62 YHNVGL 67
>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 = 66.8 bits (163), Expect = 9e-16
Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
S + V L P L G V V RD G G V ++ A
Sbjct: 15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 67
Query: 92 IQSLNGYALGNRILQVSF 109
++ L+ + + ++
Sbjct: 68 VRKLDNTKFRSHEGETAY 85
>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 = 65.7 bits (161), Expect = 2e-15
Identities = 23/61 (37%), Positives = 32/61 (52%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ V L +T E L + F FG V V+V +DL+T KGFGFV T Y+ V +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 96 N 96
+
Sbjct: 78 H 78
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 64.4 bits (158), Expect = 2e-15
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
IFV L+ T + F FG V ++ D TN+ +GFGFVT + ++ V + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 96 NGYALGNRILQV 107
+ + + N++++
Sbjct: 61 HFHEINNKMVEC 72
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 64.7 bits (158), Expect = 2e-15
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 35 CIFVYNLAPETEES-------VLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
I V N+ P+ V+ ++F FG + + + K KG+ F+ +
Sbjct: 3 VIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 59
Query: 88 AVVAIQSLNGYAL-GNRILQV 107
AV A+++ +GY L +V
Sbjct: 60 AVDAVKNADGYKLDKQHTFRV 80
>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 = 64.7 bits (158), Expect = 4e-15
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 9/82 (10%)
Query: 36 IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+F+ NL ++S + +F +G V V KG+ FV +N A A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLG 81
Query: 95 LNGYALGNRILQVSFKTNKGKT 116
NG L + L ++
Sbjct: 82 ENGRVLAGQTLDINMAGEPKPD 103
>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 = 64.6 bits (157), Expect = 7e-15
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
I + L + E + L PFG V ++ +++ K F+ M + A +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 87
Query: 94 SLNGYALGNRILQVSFKTNK 113
+ L + + + F +K
Sbjct: 88 TSVTPVLRGQPIYIQFSNHK 107
>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 = 63.5 bits (155), Expect = 1e-14
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+F+ L+ ET E L + +G + V+RD + + +GFGFVT ++ E A+ +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 62.1 bits (152), Expect = 2e-14
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+F+ L+ +T + L + FG FG V+ V+RD T + +GFGFVT + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>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 = 62.7 bits (153), Expect = 3e-14
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI--- 92
+F+ L+ +T + L + FG FG V+ V+RD T + +GFGFVT + +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 93 -QSLNG 97
L+
Sbjct: 88 RHELDS 93
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 62.2 bits (151), Expect = 3e-14
Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 5/85 (5%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
P ++V NL + S L + G+V + + F+ +
Sbjct: 11 PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ-----GPRRRAFLHYPD 65
Query: 85 YDEAVVAIQSLNGYALGNRILQVSF 109
A A+ L G LG L+V+
Sbjct: 66 SAAAQQAVSCLQGLRLGTDTLRVAL 90
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 62.5 bits (152), Expect = 4e-14
Identities = 14/81 (17%), Positives = 24/81 (29%), Gaps = 3/81 (3%)
Query: 32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
+ I + NL L L + T G G + + + V A
Sbjct: 27 KRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEA 83
Query: 92 IQSLNGYALGNRILQVSFKTN 112
++ LN ++ V N
Sbjct: 84 LERLNNIEFRGSVITVERDDN 104
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 62.2 bits (151), Expect = 4e-14
Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
I + L + E + L PFG V ++ +++ K F+ M + A +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72
Query: 94 SLNGYALGNRILQVSFKTNKGKTS 117
+ L + + + F +K +
Sbjct: 73 TSVTPVLRGQPIYIQFSNHKELKT 96
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 62.1 bits (151), Expect = 4e-14
Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 8/81 (9%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ + L E+ L + FG + V V+ K V + A A+
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNY 76
Query: 95 LNGYA--LGNRILQVSFKTNK 113
+ V++ T++
Sbjct: 77 AADNQIYIAGHPAFVNYSTSQ 97
>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 = 61.7 bits (150), Expect = 6e-14
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGA-VQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQ 93
+F+ + + + + V V V K +GF FV ++ A +A +
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 94 SLN--GYALGNRILQVSF 109
L L + V +
Sbjct: 71 KLMPGRIQLWGHQIAVDW 88
>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 = 61.0 bits (149), Expect = 7e-14
Identities = 17/69 (24%), Positives = 27/69 (39%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV L+ +T + L F FG V + D T + +GFGF+ + +
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 96 NGYALGNRI 104
G I
Sbjct: 74 EHRLDGRVI 82
>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 = 61.1 bits (149), Expect = 1e-13
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+FV L T + L F +G V +++D TN+ +GFGFV + + + S
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
>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 = 60.5 bits (147), Expect = 1e-13
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKV-----IRDLQTNKCKGFGFVTMTNYDEAVV 90
++V N+ E + F + + + +Q N+ K F F+ + DE
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 91 AIQSLNGYALGNRILQV 107
A+ +G + L++
Sbjct: 69 AMA-FDGIIFQGQSLKI 84
>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 = 60.0 bits (146), Expect = 2e-13
Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 11/97 (11%)
Query: 20 ASSILPANTMNGSGWCIFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFG 78
+S ++P + S +F+ NL + + L+++F P+G + + + FG
Sbjct: 11 SSGLVPRGSHMKS--RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFG 60
Query: 79 FVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
F+ N AI+ + + L + ++ +
Sbjct: 61 FIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 60.1 bits (146), Expect = 2e-13
Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 2/75 (2%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+++ + + + G V ++++ R KG FV + + A ++
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-T 71
Query: 96 NGYALGNRILQVSFK 110
G L + FK
Sbjct: 72 PGQKYKETDLLILFK 86
>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 = 59.0 bits (143), Expect = 5e-13
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 8/81 (9%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ- 93
+ V L E+ L + FG + V ++ K V N D A +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF 70
Query: 94 -SLNGYALGNRILQVSFKTNK 113
+ + + ++ T+K
Sbjct: 71 AADVPVYIAGQQAFFNYSTSK 91
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 58.5 bits (142), Expect = 9e-13
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+FV + + L + F FG V SV + +D F V M + A A+ S
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD--KGV---FAIVEMGDVG-AREAVLSQ 64
Query: 96 NGYALGNRILQVSFKTNK 113
+ ++LG L+V + K
Sbjct: 65 SQHSLGGHRLRVRPREQK 82
>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 = 58.7 bits (142), Expect = 9e-13
Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 8/80 (10%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
+ + L E E+ + L PFG V ++ +++ K F+ + + A+ +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY 71
Query: 94 SLNGYALGNRILQVSFKTNK 113
S L N+ + + + +K
Sbjct: 72 SAVTPHLRNQPIYIQYSNHK 91
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 58.0 bits (141), Expect = 1e-12
Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 9/82 (10%)
Query: 36 IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+F+ NL + + L+++F P+G + + + FGF+ N AI+
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIEC 64
Query: 95 LNGYALGNRILQVSFKTNKGKT 116
+ + L + ++ +
Sbjct: 65 ESQEMNFGKKLILEVSSSNARP 86
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 61.0 bits (147), Expect = 1e-12
Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 6/77 (7%)
Query: 40 NLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA 99
+L P ES + +F G + ++ + K GFV A A ++++
Sbjct: 150 HLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT 203
Query: 100 LGNRILQVSFKTNKGKT 116
L + +G
Sbjct: 204 LLLPSDKEWDDRREGTG 220
>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 = 57.1 bits (138), Expect = 5e-12
Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 3/89 (3%)
Query: 26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTN 84
+N + C + N+ + + Q +V V+ D + G V N
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKN 66
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
D+A + + L+ L R V T +
Sbjct: 67 EDDARKSER-LHRKKLNGREAFVHVVTLE 94
>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 = 57.2 bits (138), Expect = 6e-12
Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
+ +G C+ + L + E+ ++ F P V V + + G V
Sbjct: 38 EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIG-PDGRVTGEADVEFAT 95
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
++EAV A+ S + + +R +++ + G
Sbjct: 96 HEEAVAAM-SKDRANMQHRYIELFLNSTTG 124
>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 = 56.8 bits (137), Expect = 8e-12
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 1/89 (1%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
+ + + +G+C+++ L E E + F V+ I K G GFV N
Sbjct: 17 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
+ A+ + +GNR +QV T K
Sbjct: 77 EADYKAALC-RHKQYMGNRFIQVHPITKK 104
>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 = 55.9 bits (135), Expect = 1e-11
Identities = 15/95 (15%), Positives = 39/95 (41%), Gaps = 3/95 (3%)
Query: 20 ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGF 79
+S ++ + +G C+ + L E+ ++ F P V + + G
Sbjct: 2 SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEAD 59
Query: 80 VTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
V +++AV A+ + + + +R +++ + G
Sbjct: 60 VEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAG 93
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 54.6 bits (131), Expect = 3e-11
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 7/96 (7%)
Query: 26 ANTMNGSGWCIFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVT 81
++ +G+G + V N+ L Q F G V+SV++ + V
Sbjct: 2 SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQ 58
Query: 82 MTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
M N +A+ A+ SL+ Y +G++ + VS T S
Sbjct: 59 MENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPS 94
>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 = 54.2 bits (131), Expect = 3e-11
Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 4/88 (4%)
Query: 30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
+ + + E + + P +++++R+ G+ FV +N +E
Sbjct: 7 GTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRN-AHGNKTGYIFVDFSNEEEVK 64
Query: 90 VAIQSLNGYALGNRILQVSFKTNKGKTS 117
A++ N +G R ++V F+ G +S
Sbjct: 65 QALK-CNREYMGGRYIEV-FREKSGPSS 90
>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 = 53.8 bits (130), Expect = 5e-11
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+FV + E L + F +G V V + + + F FVT + A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG 60
>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 = 53.6 bits (129), Expect = 1e-10
Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 3/89 (3%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
+N + V+ + E+ + F V +V +++D + G G V +
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKD-HVGRNNGNGLVKFLS 65
Query: 85 YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
+ A++ N + R ++VS T +
Sbjct: 66 PQDTFEALK-RNRMLMIQRYVEVSPATER 93
>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 = 53.7 bits (129), Expect = 1e-10
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 1/74 (1%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ + L + + Q F V + + K G FV + + A A+
Sbjct: 44 FVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG- 102
Query: 95 LNGYALGNRILQVS 108
+ +G+R ++V
Sbjct: 103 KHKERIGHRYIEVF 116
>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 = 53.4 bits (128), Expect = 1e-10
Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 8/74 (10%)
Query: 35 CIFVYN--LAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
+ V N L + L + G V ++ + + K + F +E+ A
Sbjct: 27 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80
Query: 93 QSLNGYALGNRILQ 106
+LNG + + + Q
Sbjct: 81 VTLNGKEVVDDLGQ 94
>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 = 51.8 bits (125), Expect = 3e-10
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 5/58 (8%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+FV + L Q F +G V V + + + F FVT + A
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG 66
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 52.4 bits (126), Expect = 3e-10
Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 1/73 (1%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ + L + + Q F V + + + G FV + + A A++
Sbjct: 17 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK- 75
Query: 95 LNGYALGNRILQV 107
+ +G+R +++
Sbjct: 76 KHKERIGHRYIEI 88
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 51.9 bits (124), Expect = 5e-10
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKC--KGFGFVTMTNYDEAVVAIQ 93
+FV L P+ +E + F FG + + + KG+ F+ + +V A+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLF-QEESSVQALI 69
Query: 94 SLNGYALGNRILQVSFKTNKGK 115
G L VS T K K
Sbjct: 70 DACLEEDGKLYLCVSSPTIKDK 91
>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 = 50.0 bits (119), Expect = 4e-09
Identities = 11/91 (12%), Positives = 31/91 (34%), Gaps = 3/91 (3%)
Query: 25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL--QTNKCKGFGFVTM 82
G G+ + + L + + + + + G FV +
Sbjct: 36 MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVEL 95
Query: 83 TNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
+ D+ +A++ + ++G+R ++V
Sbjct: 96 GSEDDVKMALK-KDRESMGHRYIEVFKSHRT 125
>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 = 49.1 bits (117), Expect = 6e-09
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 5/81 (6%)
Query: 30 NGSGWCIFVYNLAPETEESVLWQLFGPF---GAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
G G+ + + L + V V I + + G FV + + D
Sbjct: 14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT-REGRQSGEAFVELESED 72
Query: 87 EAVVAIQSLNGYALGNRILQV 107
+ +A++ + ++G+R ++V
Sbjct: 73 DVKLALK-KDRESMGHRYIEV 92
>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 = 48.3 bits (115), Expect = 1e-08
Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 3/83 (3%)
Query: 33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIR--DLQTNKCKGFGFVTMTNYDEAVV 90
+ I L + F I + K +G + M + +
Sbjct: 11 VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQK 70
Query: 91 AIQSLNGYALGNRILQVSFKTNK 113
A++ + +G R ++V N+
Sbjct: 71 ALE-KHRMYMGQRYVEVYEINNE 92
>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 = 49.3 bits (117), Expect = 1e-08
Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGF-GFVTMTNYDEAVVAI 92
I V NL VL Q+F FG V + + K F + + A A
Sbjct: 47 LRIIVENLFYPVTLDVLHQIFSKFGTVL-----KIITFTKNNQFQALLQYADPVSAQHAK 101
Query: 93 QSLNGYAL--GNRILQVSF 109
SL+G + L++ F
Sbjct: 102 LSLDGQNIYNACCTLRIDF 120
>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 = 47.2 bits (112), Expect = 3e-08
Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 1/66 (1%)
Query: 44 ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR 103
E E V ++ +G V+ + V + + G +V ++A A+ LN +
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 104 ILQVSF 109
+
Sbjct: 97 PIHAEL 102
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 46.9 bits (111), Expect = 6e-08
Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 6/77 (7%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
I V NL VL Q+F FG V + + + + A A S
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLS 85
Query: 95 LNGYAL--GNRILQVSF 109
L+G + L++ F
Sbjct: 86 LDGQNIYNACCTLRIDF 102
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 45.3 bits (107), Expect = 2e-07
Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 7/83 (8%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFG----AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
+ + L + FG + + + + G FV + A
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQN 83
Query: 91 AIQSLNGYALGNRILQVSFKTNK 113
A++ + LG R +++ F++
Sbjct: 84 ALR-KHKDLLGKRYIEL-FRSTA 104
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 44.3 bits (104), Expect = 2e-07
Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 7/86 (8%)
Query: 26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY 85
GS W + + NL + + L L G + S +G T
Sbjct: 1 GAMAWGSSW-LLLKNLTAQIDGPTLRTLCMQHGPLVS------FHPYLNQGIALCKYTTR 53
Query: 86 DEAVVAIQSLNGYALGNRILQVSFKT 111
+EA A +LN L N + +
Sbjct: 54 EEANKAQMALNNCVLANTTIFAESPS 79
>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 = 46.0 bits (108), Expect = 2e-07
Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 2/76 (2%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+++ + + + G V ++++ R KG FV + + A +++
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVET 169
Query: 95 LNGYALGNRILQVSFK 110
L + FK
Sbjct: 170 PGQKYKE-TDLLILFK 184
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 43.9 bits (103), Expect = 7e-07
Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 7/81 (8%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
+ + N VL+ + P G VQ R + + V + A A +
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKVQ-----RIVIFKRNGIQAMVEFESVLCAQKAKAA 81
Query: 95 LNGYAL--GNRILQVSFKTNK 113
LNG + G L++ +
Sbjct: 82 LNGADIYAGCCTLKIEYARPT 102
>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 = 43.0 bits (101), Expect = 1e-06
Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 36 IFVYNL-APETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ- 93
I + NL +S + +L P+G +++ ++R K F+ M ++A+ +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH 81
Query: 94 -SLNGYALGNRILQVSFKTNKGKTS 117
R ++V K
Sbjct: 82 CLKKALWFQGRCVKVDLSEKYKKLV 106
>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 = 39.8 bits (93), Expect = 1e-05
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 57 FGAVQSVKVIR--DLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
+G V+S+++ R D G FV T+ + A+Q L G NR++ +
Sbjct: 39 YGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93
>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 = 37.8 bits (88), Expect = 1e-04
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 57 FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
FG ++ + + G V+ + +EA IQ+L+G G R +
Sbjct: 50 FGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
>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 = 37.3 bits (87), Expect = 1e-04
Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 35 CIFVYNL-APETEESVLWQL---------FGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
C + N+ P+TEE V W G V + V + N +G +V +
Sbjct: 9 CFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDK----NSAQGNVYVKCPS 64
Query: 85 YDEAVVAIQSLNGYALGNRILQVSF 109
A+ A+ +L+G +++ ++
Sbjct: 65 IAAAIAAVNALHGRWFAGKMITAAY 89
>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 = 37.4 bits (87), Expect = 2e-04
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 57 FGAVQSVKVIRDLQTNKCKGFG----FVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
FGAV V + ++ Q + FV + E AIQ+LNG R +
Sbjct: 49 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 34.4 bits (79), Expect = 0.002
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 57 FGAVQSVKVIRDLQTNKC-KGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
+G V + F+ + A+ A+ LNG G R+++ F
Sbjct: 37 YGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>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 = 32.4 bits (73), Expect = 0.018
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 8/64 (12%)
Query: 36 IFVYNLAPETE--ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
+ V N + L + G V ++ + + K + F +E+ A
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYV 74
Query: 94 SLNG 97
+LNG
Sbjct: 75 TLNG 78
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 29.9 bits (67), Expect = 0.072
Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 14/87 (16%)
Query: 26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPF-----GAVQSVKVIRDLQTNKCKGFGFV 80
++ + G + V L P + +L F G V S + + G +
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVL 52
Query: 81 TMTNYDEAVVAIQSLNGYALGNRILQV 107
T +A + + + L L +
Sbjct: 53 TFREPADAERVLAQAD-HELHGAQLSL 78
>2gud_A Griffithsin, GRFT; lectins, domain swapping, mannose binding, HIV,
SARS, sugar binding protein; HET: MAN BMA; 0.94A
{Griffithsia} SCOP: b.77.3.1 PDB: 2guc_A* 2gty_A*
2gue_A* 2hyq_A* 2hyr_A* 2nu5_A* 2nuo_A* 3lky_A 3ll0_A
3ll2_A* 3ll1_A
Length = 122
Score = 27.4 bits (61), Expect = 0.75
Identities = 8/26 (30%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 92 IQSLNGYALGNRILQVSFKTNKGKTS 117
I ++ + G+ I +SF+TN G+
Sbjct: 59 ISNMTIRS-GDYIDNISFETNMGRRF 83
>2gux_A Griffithsin, GRFT; lectins, domain swapping, mannose binding, HIV,
sugar binding protein; 2.00A {Griffithsia} SCOP:
b.77.3.1
Length = 138
Score = 27.1 bits (60), Expect = 1.1
Identities = 8/26 (30%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 92 IQSLNGYALGNRILQVSFKTNKGKTS 117
I ++ + G+ I +SF+TN G+
Sbjct: 75 ISNMTIRS-GDYIDNISFETNMGRRF 99
>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP,
M7GTP, RNA recognition motif, RRM, cytoplasm,
exonuclease, hydrolase, magnesium; HET: MGP; 2.10A
{Homo sapiens}
Length = 101
Score = 26.1 bits (57), Expect = 1.5
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
+ E + S L+QLF FG +Q + I D FV+++ ++ +A+ +
Sbjct: 8 VLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDTSA-------FVSLSQPEQVKIAVNTS 59
Query: 96 N 96
Sbjct: 60 K 60
>4ddn_A Ipomoelin; beta prism, carbohydrate binding protein,
carbohydrate/sugar sugar binding protein; HET: AMG;
1.90A {Ipomoea batatas} PDB: 3r50_A* 3r52_A* 3r51_A*
Length = 160
Score = 26.4 bits (58), Expect = 1.8
Identities = 10/67 (14%), Positives = 20/67 (29%), Gaps = 9/67 (13%)
Query: 59 AVQSVKVIRDLQT--------NKCKGFGFVTMTNYDEAVVAIQ-SLNGYALGNRILQVSF 109
+ + + + + N D ++ I + Y N I + F
Sbjct: 52 TLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKF 111
Query: 110 KTNKGKT 116
TNK +
Sbjct: 112 TTNKKEY 118
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA
complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A
{Mus musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 26.1 bits (57), Expect = 2.7
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 72 NKCKGFGFVTMTN 84
N GFGF++MT
Sbjct: 18 NVRMGFGFLSMTA 30
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 25.9 bits (57), Expect = 3.4
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 55 GPFGAVQSVKVIRDLQTNKCKGFG----FVTMTNYDEAVVAIQSLNGYALGNRILQ 106
G FGAV V + ++ Q + FV + E AIQ+LNG R +
Sbjct: 151 GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVV 206
>1pgu_A Actin interacting protein 1; WD repeat, seven-bladed
beta-propeller, protein binding; 2.30A {Saccharomyces
cerevisiae} SCOP: b.69.4.1 b.69.4.1 PDB: 1pi6_A
Length = 615
Score = 26.0 bits (58), Expect = 3.7
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 11/54 (20%)
Query: 10 RFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSV 63
FSP +G+ + + GS I ++ ++ E L + VQ
Sbjct: 213 EFSPDSGEFVITV--------GSDRKISCFDG--KSGE-FLKYIEDDQEPVQGG 255
>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold
shock domain, ssDNA binding, DNA B protein; 2.80A {Homo
sapiens}
Length = 147
Score = 25.4 bits (55), Expect = 4.8
Identities = 9/45 (20%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 72 NKCKGFGFVTMTNYDEAV-VAIQSLNGYALGNRILQVSFKTNKGK 115
+ KG GF+T + + + I + G + +V++K
Sbjct: 71 CRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIP 115
>1o98_A 2,3-bisphosphoglycerate-independent phosphoglycerate mutase;
isomerase, alpha/beta-type structure; HET: 2PG; 1.4A
{Bacillus stearothermophilus} SCOP: c.105.1.1 c.76.1.3
PDB: 1ejj_A* 1eqj_A* 1o99_A* 2ify_A
Length = 511
Score = 25.2 bits (56), Expect = 7.0
Identities = 5/11 (45%), Positives = 8/11 (72%)
Query: 79 FVTMTNYDEAV 89
FV +T++ E V
Sbjct: 292 FVCLTHFSETV 302
>2kcm_A Cold shock domain family protein; nucleic acid binding protein,
beta barrel, structural genomi 2, protein structure
initiative; NMR {Shewanella oneidensis}
Length = 74
Score = 23.8 bits (52), Expect = 8.0
Identities = 3/30 (10%), Positives = 9/30 (30%), Gaps = 3/30 (10%)
Query: 72 NKCKGFGFVTMTNYDEAVV---AIQSLNGY 98
K +GF+ + + + +
Sbjct: 9 LAAKKYGFIQGDDGESYFLHFSELLDKKDE 38
>3igz_B Cofactor-independent phosphoglycerate mutase; glycolysis, cobalt,
isomerase; HET: 3PG 2PG; 1.90A {Leishmania mexicana}
PDB: 3igy_B* 3nvl_A
Length = 561
Score = 24.9 bits (55), Expect = 8.3
Identities = 3/9 (33%), Positives = 4/9 (44%)
Query: 79 FVTMTNYDE 87
+ M YD
Sbjct: 311 YAGMMRYDG 319
>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold,
structural genomics; NMR {Thermotoga maritima} SCOP:
b.40.4.5
Length = 66
Score = 23.7 bits (52), Expect = 9.0
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 72 NKCKGFGFVTMTNYDEAVV---AIQSLNGY 98
+ KG+GF+T + V AI+ G+
Sbjct: 9 DSKKGYGFITKDEGGDVFVHWSAIEM-EGF 37
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB
fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 23.8 bits (52), Expect = 9.1
Identities = 11/44 (25%), Positives = 17/44 (38%)
Query: 72 NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
K KGFGF+ N D + + L + V+F+
Sbjct: 11 FKDKGFGFIKDENGDNRYFHVIKVANPDLIKKDAAVTFEPTTNN 54
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
0.319 0.135 0.401
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: 1,673,767
Number of extensions: 84089
Number of successful extensions: 530
Number of sequences better than 10.0: 1
Number of HSP's gapped: 403
Number of HSP's successfully gapped: 222
Length of query: 117
Length of database: 6,701,793
Length adjustment: 80
Effective length of query: 37
Effective length of database: 4,468,113
Effective search space: 165320181
Effective search space used: 165320181
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)