RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16913
(81 letters)
>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 = 102 bits (256), Expect = 2e-30
Identities = 49/79 (62%), Positives = 58/79 (73%), Gaps = 14/79 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF+PFGNV+S+KVFID+ TN SKCFG FVS+DNP SA AIQ+MNGF
Sbjct: 45 MFMPFGNVVSAKVFIDKQTNLSKCFG--------------FVSYDNPVSAQAAIQSMNGF 90
Query: 61 QIGMKRLKVQLKRPKDAAR 79
QIGMKRLKVQLKR K+ ++
Sbjct: 91 QIGMKRLKVQLKRSKNDSK 109
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 97.4 bits (243), Expect = 2e-28
Identities = 46/73 (63%), Positives = 52/73 (71%), Gaps = 14/73 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
FLPFGNVIS+KVFID+ T+ SKCFG FVSFDNP SA AI+AMNGF
Sbjct: 60 TFLPFGNVISAKVFIDKQTSLSKCFG--------------FVSFDNPDSAQVAIKAMNGF 105
Query: 61 QIGMKRLKVQLKR 73
Q+G KRLKVQLK+
Sbjct: 106 QVGTKRLKVQLKK 118
>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 = 95.6 bits (238), Expect = 2e-27
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 14/76 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + S K+ DR T QS+ +G FV F + +SA AI +NGF
Sbjct: 62 LFERYGPIESVKIVCDRETRQSRGYG--------------FVKFQSGSSAQQAIAGLNGF 107
Query: 61 QIGMKRLKVQLKRPKD 76
I KRLKV L
Sbjct: 108 NILNKRLKVALAASGH 123
>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 = 86.4 bits (215), Expect = 2e-24
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 14/73 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ P+G ++S+K +D+ TN+ K +G FV FD+P++A A+ A+
Sbjct: 25 LCQPYGKIVSTKAILDKTTNKCKGYG--------------FVDFDSPSAAQKAVTALKAS 70
Query: 61 QIGMKRLKVQLKR 73
+ + K
Sbjct: 71 GVQAQMAKQSGPS 83
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 74.6 bits (184), Expect = 1e-19
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 20/80 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F PFGN+I + + FV+++ SA A+ +NG
Sbjct: 33 AFSPFGNIIDLSMDPP--------------------RNCAFVTYEKMESADQAVAELNGT 72
Query: 61 QIGMKRLKVQLKRPKDAARP 80
Q+ +LKV + R +
Sbjct: 73 QVESVQLKVNIARKQPMLDS 92
>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 = 74.2 bits (183), Expect = 2e-19
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FGN++S KV D + K +GFV F+ +A AI+ MNG
Sbjct: 25 TFSAFGNILSCKVVCDENGS----------------KGYGFVHFETQEAAERAIEKMNGM 68
Query: 61 QIGMKRLKVQLKRPKD 76
+ +++ V + +
Sbjct: 69 LLNDRKVFVGRFKSRK 84
>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 = 73.8 bits (182), Expect = 4e-19
Identities = 16/76 (21%), Positives = 23/76 (30%), Gaps = 15/76 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
M PFG VIS+++ D + S+ G F ++ I NG
Sbjct: 45 MLKPFGQVISTRILRDS-SGTSRGVG--------------FARMESTEKCEAVIGHFNGK 89
Query: 61 QIGMKRLKVQLKRPKD 76
I P
Sbjct: 90 FIKTPPGVSAPTEPLL 105
>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 = 68.8 bits (169), Expect = 3e-17
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 16/76 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F PFG + S+KV ++ +SK FG FV F +P A A+ MNG
Sbjct: 35 AFSPFGTITSAKVMME--GGRSKGFG--------------FVCFSSPEEATKAVTEMNGR 78
Query: 61 QIGMKRLKVQLKRPKD 76
+ K L V L + K+
Sbjct: 79 IVATKPLYVALAQRKE 94
>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 = 66.5 bits (163), Expect = 2e-16
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG++ + D+ T QSK F F+SF A AI ++GF
Sbjct: 35 LFRPFGSISRIYLAKDKTTGQSKGFA--------------FISFHRREDAARAIAGVSGF 80
Query: 61 QIGMKRLKVQLKRPKDAARP 80
L V+ +P + P
Sbjct: 81 GYDHLILNVEWAKPSTNSGP 100
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 64.4 bits (158), Expect = 7e-16
Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 14/75 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F F + +S V D T S+ +G FVSF + A A+ +M G
Sbjct: 22 FKDFPSYLSGHVMWDMQTGSSRGYG--------------FVSFTSQDDAQNAMDSMQGQD 67
Query: 62 IGMKRLKVQLKRPKD 76
+ + L++ +
Sbjct: 68 LNGRPLRINWAAKLE 82
>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 = 66.4 bits (163), Expect = 9e-16
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + + ++ D T S + FV F + + AI+ +NG
Sbjct: 23 LFRAIGPINTCRIMRDYKTGYSYGYA--------------FVDFTSEMDSQRAIKVLNGI 68
Query: 61 QIGMKRLKVQLKRPK 75
+ KRLKV RP
Sbjct: 69 TVRNKRLKVSYARPG 83
Score = 61.4 bits (150), Expect = 7e-14
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 16/73 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G+++ + D+ T + + FV ++ A AI A+N
Sbjct: 109 IFGKYGSIVQKNILRDKLTGRPRGVA--------------FVRYNKREEAQEAISALNNV 154
Query: 61 QI--GMKRLKVQL 71
G + L V+L
Sbjct: 155 IPEGGSQPLSVRL 167
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 67.0 bits (164), Expect = 1e-15
Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 16/82 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + S+ + D T + K +G F+ ++ S+ A+ +MN F
Sbjct: 145 VFEAFGKIKSATLARDPTTGKHKGYG--------------FIEYEKAQSSQDAVSSMNLF 190
Query: 61 QIGMKRLKVQL--KRPKDAARP 80
+G + L+V P P
Sbjct: 191 DLGGQYLRVGKAVTPPMPLLTP 212
Score = 62.3 bits (152), Expect = 9e-14
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F PFG + S + D T + K F FV ++ P +A A++ MN
Sbjct: 48 AFAPFGPIKSIDMSWDSVTMKHKGFA--------------FVEYEVPEAAQLALEQMNSV 93
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+G + +KV A+P
Sbjct: 94 MLGGRNIKVGRPSNIGQAQP 113
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 64.1 bits (157), Expect = 2e-15
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 16/79 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F G+V+ + + ++ +SK G V F++P A A + MNG
Sbjct: 28 KFNECGHVLYADIKME--NGKSKGCG--------------VVKFESPEVAERACRMMNGM 71
Query: 61 QIGMKRLKVQLKRPKDAAR 79
++ + + V++ R
Sbjct: 72 KLSGREIDVRIDRNASGPS 90
>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 = 64.2 bits (157), Expect = 2e-15
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 14/79 (17%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + G F FV F+ A AI MN +
Sbjct: 33 FIPFGDITDIQIPLDYETEKHR--G------------FAFVEFELAEDAAAAIDNMNESE 78
Query: 62 IGMKRLKVQLKRPKDAARP 80
+ + ++V L +P
Sbjct: 79 LFGRTIRVNLAKPMRIKES 97
>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 = 64.2 bits (157), Expect = 2e-15
Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F F + T + + F++F N A A+ +NG+
Sbjct: 45 LFARFQEKKGPPIQFRMMTGRMRGQA--------------FITFPNKEIAWQALHLVNGY 90
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ K L ++ + K
Sbjct: 91 KLYGKILVIEFGKNKKQRSS 110
>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 = 64.3 bits (157), Expect = 2e-15
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 14/79 (17%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D AT +SK +G FVSF N A AIQ M G
Sbjct: 36 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 81
Query: 62 IGMKRLKVQLKRPKDAARP 80
+G ++++ K A
Sbjct: 82 LGGRQIRTNWATRKPPAPK 100
>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 = 63.0 bits (154), Expect = 3e-15
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 14/74 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D AT +SK +G FVSF N A AIQ M G
Sbjct: 27 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 72
Query: 62 IGMKRLKVQLKRPK 75
+G ++++ K
Sbjct: 73 LGGRQIRTNWATRK 86
>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 = 63.6 bits (155), Expect = 4e-15
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 20/74 (27%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFGN+I + + FV+++ SA A+ +NG Q
Sbjct: 58 FSPFGNIIDLSMDPP--------------------RNCAFVTYEKMESADQAVAELNGTQ 97
Query: 62 IGMKRLKVQLKRPK 75
+ +LKV + R +
Sbjct: 98 VESVQLKVNIARKQ 111
>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 = 62.7 bits (153), Expect = 7e-15
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 14/76 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG + S ++ +D T +SK G +GF++F + A A++ +NGF
Sbjct: 46 IFEPFGRIESIQLMMDSETGRSK--G------------YGFITFSDSECAKKALEQLNGF 91
Query: 61 QIGMKRLKVQLKRPKD 76
++ + +KV +
Sbjct: 92 ELAGRPMKVGHVTERT 107
>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 = 64.1 bits (157), Expect = 8e-15
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 14/76 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS +G FV++ +P A AI +NG
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYG--------------FVNYIDPKDAEKAINTLNGL 67
Query: 61 QIGMKRLKVQLKRPKD 76
++ K +KV RP
Sbjct: 68 RLQTKTIKVSYARPSS 83
Score = 61.4 bits (150), Expect = 7e-14
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 16/73 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG- 59
+F +G +I+S++ +D+ T S+ G F+ FD A AI+ +NG
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVG--------------FIRFDKRIEAEEAIKGLNGQ 153
Query: 60 -FQIGMKRLKVQL 71
+ + V+
Sbjct: 154 KPSGATEPITVKF 166
>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 = 62.7 bits (153), Expect = 8e-15
Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 15/81 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V+ + + D+ +S+ G V+F+ A AI NG
Sbjct: 35 VFSMAGVVVRADILEDK-DGKSRGIG--------------TVTFEQSIEAVQAISMFNGQ 79
Query: 61 QIGMKRLKVQLKRPKDAARPY 81
+ + + V++ +
Sbjct: 80 LLFDRPMHVKMDERALPKGDF 100
>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 = 61.9 bits (151), Expect = 1e-14
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 14/79 (17%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G + V DR T +S+ G FGFV+F+N A A+ AMNG
Sbjct: 33 FSKYGQISEVVVVKDRETQRSR--G------------FGFVTFENIDDAKDAMMAMNGKS 78
Query: 62 IGMKRLKVQLKRPKDAARP 80
+ ++++V R
Sbjct: 79 VDGRQIRVDQAGKSSDNRS 97
>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 = 60.6 bits (148), Expect = 2e-14
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + G F FV F+ A AI MN +
Sbjct: 28 FIPFGDITDIQIPLDYETEKHR--G------------FAFVEFELAEDAAAAIDNMNESE 73
Query: 62 IGMKRLKV 69
+ + ++V
Sbjct: 74 LFGRTIRV 81
>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 = 61.0 bits (149), Expect = 3e-14
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 14/76 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG + + + D T +SK G +GF++F + A A++ +NGF
Sbjct: 25 IFEPFGKIDNIVLMKDSDTGRSK--G------------YGFITFSDSECARRALEQLNGF 70
Query: 61 QIGMKRLKVQLKRPKD 76
++ + ++V +
Sbjct: 71 ELAGRPMRVGHVTERL 86
>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 = 62.6 bits (153), Expect = 3e-14
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 12/79 (15%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V V DR+ N + K FV+F +A A A++
Sbjct: 23 LFEQYGAVYEINVLRDRSQNPPQS------------KGCCFVTFYTRKAALEAQNALHNM 70
Query: 61 QIGMKRLKVQLKRPKDAAR 79
++ +P D+ +
Sbjct: 71 KVLPGMHHPIQMKPADSEK 89
Score = 52.6 bits (127), Expect = 2e-10
Identities = 17/74 (22%), Positives = 26/74 (35%), Gaps = 18/74 (24%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF FG + ++ S+ FV+F A A TAI+AM+
Sbjct: 115 MFSSFGQIEECRILRG-PDGLSRGCA--------------FVTFTTRAMAQTAIKAMHQA 159
Query: 61 QI---GMKRLKVQL 71
Q + V+
Sbjct: 160 QTMEGCSSPMVVKF 173
>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 = 60.7 bits (148), Expect = 3e-14
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ G VI+ K+ D T +SK G + F+ F + S+ +A++ +NG+
Sbjct: 22 LCSNVGPVINLKMMFDPQTGRSK--G------------YAFIEFRDLESSASAVRNLNGY 67
Query: 61 QIGMKRLKVQLKRPKDAARP 80
Q+G + LK D +
Sbjct: 68 QLGSRFLKCGYSSNSDISGV 87
>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 = 60.8 bits (148), Expect = 3e-14
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 16/75 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF FG ++ ++ + + K FGFV+F+N A A A + ++G
Sbjct: 35 MFGQFGKILDVEIIFNERGS----------------KGFGFVTFENSADADRAREKLHGT 78
Query: 61 QIGMKRLKVQLKRPK 75
+ ++++V +
Sbjct: 79 VVEGRKIEVNNATAR 93
>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 = 62.2 bits (152), Expect = 4e-14
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 14/69 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
FG + + + D AT SK + F + + AI +NG Q
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYA--------------FCEYVDINVTDQAIAGLNGMQ 160
Query: 62 IGMKRLKVQ 70
+G K+L VQ
Sbjct: 161 LGDKKLLVQ 169
Score = 39.9 bits (94), Expect = 1e-05
Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 22/80 (27%)
Query: 2 FLPFGNVIS-----SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
F + + NQ K F F+ F + A+ A
Sbjct: 25 FNAQMRLGGLTQAPGNPVLAVQINQDKNFA--------------FLEFRSVDETTQAM-A 69
Query: 57 MNGFQIGMKRLKVQLKRPKD 76
+G + LK+ +RP D
Sbjct: 70 FDGIIFQGQSLKI--RRPHD 87
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 60.9 bits (148), Expect = 4e-14
Identities = 10/79 (12%), Positives = 22/79 (27%), Gaps = 14/79 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
M +G V ++ + T + G V F + A ++ ++
Sbjct: 26 MCRKYGEVEEVEILLHPRTRKHL--G------------LARVLFTSTRGAKETVKNLHLT 71
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+ + QL
Sbjct: 72 SVMGNIIHAQLDIKGQQRM 90
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 62.4 bits (152), Expect = 5e-14
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 16/78 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
FG + + + D AT SK + F + + AI +NG Q
Sbjct: 135 LTSFGPLKAFNLVKDSATGLSKGYA--------------FCEYVDINVTDQAIAGLNGMQ 180
Query: 62 IGMKRLKVQL--KRPKDA 77
+G K+L VQ K+A
Sbjct: 181 LGDKKLLVQRASVGAKNA 198
Score = 41.6 bits (98), Expect = 4e-06
Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 22/81 (27%)
Query: 1 MFLPFGNVIS-----SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQ 55
F + + NQ K F F+ F + A+
Sbjct: 24 FFNAQMRLGGLTQAPGNPVLAVQINQDKNFA--------------FLEFRSVDETTQAM- 68
Query: 56 AMNGFQIGMKRLKVQLKRPKD 76
A +G + LK++ RP D
Sbjct: 69 AFDGIIFQGQSLKIR--RPHD 87
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 61.3 bits (149), Expect = 6e-14
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F+PFG++ ++ +D T + + G F FV F+ A AI MN
Sbjct: 83 AFIPFGDITDIQIPLDYETEKHR--G------------FAFVEFELAEDAAAAIDNMNES 128
Query: 61 QIGMKRLKV 69
++ + ++V
Sbjct: 129 ELFGRTIRV 137
>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 = 63.5 bits (155), Expect = 6e-14
Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 14/78 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ PFG++ + T QSK +G F + SA A + G
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYG--------------FAEYMKKDSAARAKSDLLGK 160
Query: 61 QIGMKRLKVQLKRPKDAA 78
+G + L V
Sbjct: 161 PLGPRTLYVHWTDAGQLT 178
Score = 60.4 bits (147), Expect = 8e-13
Identities = 12/79 (15%), Positives = 22/79 (27%), Gaps = 15/79 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ ++ + Q K F + ++ A A Q +G
Sbjct: 205 ALSAVHSPTFCQLACGQ-DGQLKGFA--------------VLEYETAEMAEEAQQQADGL 249
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+G L+V P R
Sbjct: 250 SLGGSHLRVSFCAPGPPGR 268
Score = 46.5 bits (111), Expect = 8e-08
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
+ V K FV+ N A AI A + ++ + L VQL+
Sbjct: 46 YELKYCFVDKY-KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95
>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 = 59.9 bits (146), Expect = 7e-14
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 15/76 (19%)
Query: 2 FLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FG ++ + K+ D T SK + F++F + ++ AI+AMNG
Sbjct: 26 FSAFGVILQTPKIMRDPDTGNSKGYA--------------FINFASFDASDAAIEAMNGQ 71
Query: 61 QIGMKRLKVQLKRPKD 76
+ + + V KD
Sbjct: 72 YLCNRPITVSYAFKKD 87
>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 = 59.1 bits (144), Expect = 1e-13
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 15/75 (20%)
Query: 2 FLPFGNVISSKVFIDRA-TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F +G + + ++R + SK + +V F+NP A A++ M+G
Sbjct: 25 FSTYGKIKMIDMPVERMHPHLSKGYA--------------YVEFENPDEAEKALKHMDGG 70
Query: 61 QIGMKRLKVQLKRPK 75
QI + +
Sbjct: 71 QIDGQEITATAVLAP 85
>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 = 59.6 bits (145), Expect = 1e-13
Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 11/80 (13%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S + + FGFV + P A A++ + G
Sbjct: 25 VFSKVGAIKSCTISKKKNKAGVLLS-----------MGFGFVEYKKPEQAQKALKQLQGH 73
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ +L+V++
Sbjct: 74 TVDGHKLEVRISERATKPAS 93
>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 = 59.1 bits (144), Expect = 1e-13
Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 16/83 (19%)
Query: 1 MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
G +++ K F +RA QSK G F V + AS+ + +
Sbjct: 21 AVHSLGVNDILEIKFFENRANGQSK--G------------FALVGVGSEASSKKLMDLLP 66
Query: 59 GFQIGMKRLKVQLKRPKDAARPY 81
++ + V + +
Sbjct: 67 KRELHGQNPVVTPSNKLEHHHHH 89
>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 = 62.3 bits (152), Expect = 1e-13
Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ V S N S+ F ++ + A ++ +NG
Sbjct: 137 LLQDINVVALSIRLPSLRFNTSRRFA--------------YIDVTSKEDARYCVEKLNGL 182
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+I L ++ P + ++
Sbjct: 183 KIEGYTLVTKVSNPLEKSKR 202
Score = 53.1 bits (128), Expect = 3e-10
Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FG++ + + + C F+ F+N SA A+Q MN
Sbjct: 231 SFEGFGSIEKINIPAGQKEHS-------------FNNCCAFMVFENKDSAERALQ-MNRS 276
Query: 61 QIGMKRLKVQLKRPK 75
+G + + V L K
Sbjct: 277 LLGNREISVSLADKK 291
Score = 41.1 bits (97), Expect = 5e-06
Identities = 12/69 (17%), Positives = 17/69 (24%), Gaps = 17/69 (24%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F G +I V N F + F A AI +
Sbjct: 61 YFKHCGPIIHVDVADSLKKN----------------FRFARIEFARYDGALAAITKTHKV 104
Query: 61 QIGMKRLKV 69
+G + V
Sbjct: 105 -VGQNEIIV 112
>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 = 59.2 bits (144), Expect = 2e-13
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 14/76 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+FL G V+++ + DR T Q + G +GFV F + A AI+ M+
Sbjct: 35 LFLQAGPVVNTHMPKDRVTGQHQ--G------------YGFVEFLSEEDADYAIKIMDMI 80
Query: 61 QIGMKRLKVQLKRPKD 76
++ K ++V +
Sbjct: 81 KLYGKPIRVNKASAHN 96
>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 = 60.6 bits (148), Expect = 2e-13
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 14/71 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F F + +S V D T S+ +G FVSF + A A+ +M G
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYG--------------FVSFTSQDDAQNAMDSMQGQ 152
Query: 61 QIGMKRLKVQL 71
+ + L++
Sbjct: 153 DLNGRPLRINW 163
Score = 49.8 bits (120), Expect = 2e-09
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 15/69 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F G + + K+ ID+ N++ + FV + A+ A+Q +NG
Sbjct: 20 YFQVGGPIANIKIMIDK-NNKNVNYA--------------FVEYHQSHDANIALQTLNGK 64
Query: 61 QIGMKRLKV 69
QI +K+
Sbjct: 65 QIENNIVKI 73
>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 = 59.3 bits (144), Expect = 2e-13
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 15/75 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + + DR T++S+ F F++F+NPA A A + MNG
Sbjct: 27 VFGKHGPISEVLLIKDR-TSKSRGFA--------------FITFENPADAKNAAKDMNGK 71
Query: 61 QIGMKRLKVQLKRPK 75
+ K +KV+ +
Sbjct: 72 SLHGKAIKVEQAKKP 86
>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 = 58.8 bits (143), Expect = 2e-13
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 14/76 (18%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
F + +++ DR T SK G FGFV F++ A A +AM +I
Sbjct: 36 FDGSVRARIVTDRETGSSK--G------------FGFVDFNSEEDAKAAKEAMEDGEIDG 81
Query: 65 KRLKVQLKRPKDAARP 80
++ + +PK
Sbjct: 82 NKVTLDWAKPKGEGGS 97
>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 = 58.8 bits (143), Expect = 2e-13
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V + + T + G F FV F + A A AM+G
Sbjct: 33 VFEKYGRVGDVYIPREPHTKAPR--G------------FAFVRFHDRRDAQDAEAAMDGA 78
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ + L+VQ+ R
Sbjct: 79 ELDGRELRVQVARYGRRDLS 98
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 58.4 bits (142), Expect = 3e-13
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 14/70 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + + D+ + +S+ F FV F+N A A + NG
Sbjct: 35 VFSKYGPIADVSIVYDQQSRRSRGFA--------------FVYFENVDDAKEAKERANGM 80
Query: 61 QIGMKRLKVQ 70
++ +R++V
Sbjct: 81 ELDGRRIRVS 90
>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 = 58.0 bits (141), Expect = 4e-13
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V+ + D+ T +SK G F+ F + SA +A+N
Sbjct: 36 IFSKYGKVVKVTIMKDKDTRKSK--G------------VAFILFLDKDSAQNCTRAINNK 81
Query: 61 QIGMKRLKV 69
Q+ + +K
Sbjct: 82 QLFGRVIKA 90
>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 = 60.0 bits (146), Expect = 5e-13
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 16/80 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FGN++S KV D N SK +G FV F+ +A AI+ MNG
Sbjct: 123 TFSAFGNILSCKVVCD--ENGSKGYG--------------FVHFETQEAAERAIEKMNGM 166
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ +++ V + +
Sbjct: 167 LLNDRKVFVGRFKSRKEREA 186
Score = 55.4 bits (134), Expect = 3e-11
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F P G ++S +V D T +S + +V+F PA A A+ MN
Sbjct: 35 KFSPAGPILSIRVCRDMITRRSLGYA--------------YVNFQQPADAERALDTMNFD 80
Query: 61 QIGMKRLKV 69
I K +++
Sbjct: 81 VIKGKPVRI 89
>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 = 58.6 bits (142), Expect = 6e-13
Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 17/80 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + + D+ + +S+ F FV F+N A A + NG
Sbjct: 66 VFSKYGPIADVSIVYDQQSRRSRGFA--------------FVYFENVDDAKEAKERANGM 111
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ +R++V K RP
Sbjct: 112 ELDGRRIRVDFSITK---RP 128
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 57.7 bits (140), Expect = 7e-13
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 16/75 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF FG ++ ++ + SK FG FV+F+N A A A + ++G
Sbjct: 49 MFGQFGKILDVEIIFNE--RGSKGFG--------------FVTFENSADADRAREKLHGT 92
Query: 61 QIGMKRLKVQLKRPK 75
+ ++++V +
Sbjct: 93 VVEGRKIEVNNATAR 107
>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 = 57.7 bits (140), Expect = 7e-13
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 15/71 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + + V DR + +S V F+ A A A++ NG
Sbjct: 49 LFAEFGTLKKAAVHYDR-SGRSLGTA--------------DVHFERKADALKAMKQYNGV 93
Query: 61 QIGMKRLKVQL 71
+ + + +QL
Sbjct: 94 PLDGRPMNIQL 104
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 57.8 bits (140), Expect = 9e-13
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V + DR T +S+ G F FV F + A A+ AM+G
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESR--G------------FAFVRFHDKRDAEDAMDAMDGA 112
Query: 61 QIGMKRLKVQLKRPKDAARPY 81
+ + L+VQ+ R +
Sbjct: 113 VLDGRELRVQMARYGRPPDSH 133
>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 = 57.2 bits (139), Expect = 9e-13
Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 14/79 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + ID T + K F FV+F P A A ++G
Sbjct: 28 LFSAYGPLSELHYPIDSLTKKPKGFA--------------FVTFMFPEHAVKAYAEVDGQ 73
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+ L V K A
Sbjct: 74 VFQGRMLHVLPSTIKKEAS 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 = 57.6 bits (139), Expect = 2e-12
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 16/81 (19%)
Query: 1 MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
+ G +V+ K +RA QSK G + V + S H ++ +
Sbjct: 75 VIRSIGVYDVVELKFAENRANGQSK--G------------YAEVVVASENSVHKLLELLP 120
Query: 59 GFQIGMKRLKVQLKRPKDAAR 79
G + +++ V+ ++ ++
Sbjct: 121 GKVLNGEKVDVRPATRQNLSQ 141
>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 = 59.0 bits (142), Expect = 2e-12
Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 16/81 (19%)
Query: 1 MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
G +++ K F +RA QSK F V + AS+ + +
Sbjct: 88 AVHSLGVNDILEIKFFENRANGQSKGFA--------------LVGVGSEASSKKLMDLLP 133
Query: 59 GFQIGMKRLKVQLKRPKDAAR 79
++ + V + ++
Sbjct: 134 KRELHGQNPVVTPVNKQFLSQ 154
>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 = 56.1 bits (136), Expect = 2e-12
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 15/69 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+FL G + + DR + K FG FV F +P S AI +NG
Sbjct: 36 LFLQAGPLTKVTICKDR-EGKPKSFG--------------FVCFKHPESVSYAIALLNGI 80
Query: 61 QIGMKRLKV 69
++ + + V
Sbjct: 81 RLYGRPINV 89
>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 = 56.6 bits (137), Expect = 2e-12
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 15/81 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + + V DR + +S G V F+ A A A++ G
Sbjct: 55 LFAEFGTLKKAAVDYDR-SGRSL--G------------TADVHFERRADALKAMKQYKGV 99
Query: 61 QIGMKRLKVQLKRPKDAARPY 81
+ + + +QL + +
Sbjct: 100 PLDGRPMDIQLVASQIDLEHH 120
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 55.7 bits (135), Expect = 3e-12
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F +G + + + +DR T K G + V ++ A A++ +NG
Sbjct: 43 KFAEYGEIKNIHLNLDRRTGYLK--G------------YTLVEYETYKEAQAAMEGLNGQ 88
Query: 61 QIGMKRLKVQLKRPK 75
+ + + V +
Sbjct: 89 DLMGQPISVDWCFVR 103
>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 = 55.7 bits (135), Expect = 4e-12
Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 16/79 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G S K+ + +N + FV F A A+ AMNG
Sbjct: 35 LFSQIGPCKSCKMITEHTSNDP----------------YCFVEFYEHRDAAAALAAMNGR 78
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+I K +KV + +
Sbjct: 79 KILGKEVKVNWATTPSSQK 97
>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 = 55.3 bits (134), Expect = 5e-12
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V+S ++ DR T + K G +GF + + +A +A++ +NG
Sbjct: 28 IFSEVGPVVSFRLVYDRETGKPK--G------------YGFCEYQDQETALSAMRNLNGR 73
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ + L+V +
Sbjct: 74 EFSGRALRVDNAASEKNKEE 93
>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 = 56.4 bits (136), Expect = 5e-12
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V + DR T +S+ G F FV F + A A+ AM+G
Sbjct: 90 VFEKYGRVGDVYIPRDRYTKESR--G------------FAFVRFHDKRDAEDAMDAMDGA 135
Query: 61 QIGMKRLKVQLKRPKDAARPY 81
+ + L+VQ+ R +
Sbjct: 136 VLDGRELRVQMARYGRPPDSH 156
>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 = 54.5 bits (132), Expect = 7e-12
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 15/81 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG V + K+ DR T + K FGFV S AI ++
Sbjct: 21 LFSQFGKVFNVKLIYDRETKKP--------------KGFGFVEMQE-ESVSEAIAKLDNT 65
Query: 61 QIGMKRLKVQLKRPKDAARPY 81
+ ++V PK + +
Sbjct: 66 DFMGRTIRVTEANPKKSLEHH 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 = 56.4 bits (136), Expect = 8e-12
Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F +G + + + +DR T SK + V ++ A A +A+NG
Sbjct: 92 KFCDYGEIKNIHLNLDRRTGFSKGYA--------------LVEYETHKQALAAKEALNGA 137
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+I + ++V K R
Sbjct: 138 EIMGQTIQVDWCFVKGPKRV 157
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 54.9 bits (132), Expect = 1e-11
Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 11/75 (14%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FG + + + S+ +V++ A AIQ +N
Sbjct: 38 YFGKFGKIHKVVINNSTSYAGSQ-----------GPSASAYVTYIRSEDALRAIQCVNNV 86
Query: 61 QIGMKRLKVQLKRPK 75
+ + LK L K
Sbjct: 87 VVDGRTLKASLGTTK 101
>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 = 54.6 bits (132), Expect = 1e-11
Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F +G + + + +DR T SK + V ++ A A +A+NG
Sbjct: 46 KFCDYGEIKNIHLNLDRRTGFSKGYA--------------LVEYETHKQALAAKEALNGA 91
Query: 61 QIGMKRLKVQLKRPK 75
+I + ++V K
Sbjct: 92 EIMGQTIQVDWCFVK 106
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 53.8 bits (130), Expect = 2e-11
Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 15/78 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ G V ++ +R + K G +V ++N + A A+ M+G
Sbjct: 37 ICKAHGTVKDLRLVTNR-AGKPK--G------------LAYVEYENESQASQAVMKMDGM 81
Query: 61 QIGMKRLKVQLKRPKDAA 78
I +KV + ++
Sbjct: 82 TIKENIIKVAISNSGPSS 99
>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 = 53.9 bits (130), Expect = 2e-11
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 20/75 (26%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F PFG ++ +VF + K + FV F SA AI ++NG
Sbjct: 45 TFSPFGQIMEIRVFPE--------------------KGYSFVRFSTHESAAHAIVSVNGT 84
Query: 61 QIGMKRLKVQLKRPK 75
I +K +
Sbjct: 85 TIEGHVVKCYWGKES 99
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 53.1 bits (128), Expect = 3e-11
Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 20/75 (26%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG ++ K + + K F+ +D A I A+ F
Sbjct: 47 LFQNFGFILDFKHYPE--------------------KGCCFIKYDTHEQAAVCIVALANF 86
Query: 61 QIGMKRLKVQLKRPK 75
+ L+ + +
Sbjct: 87 PFQGRNLRTGWGKER 101
>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 = 53.6 bits (129), Expect = 3e-11
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 22/83 (26%)
Query: 1 MFLPFGNVISS--------KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHT 52
F G V + +++D+ T + K VS+++P +A
Sbjct: 35 FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA--------------TVSYEDPPTAKA 80
Query: 53 AIQAMNGFQIGMKRLKVQLKRPK 75
A++ +G +LKV L R K
Sbjct: 81 AVEWFDGKDFQGSKLKVSLARKK 103
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 52.8 bits (127), Expect = 5e-11
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 17/79 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ + +G V S + + V++ + A A+ +NGF
Sbjct: 35 LLVQYGVVESCEQVNTDSETAV-----------------VNVTYSSKDQARQALDKLNGF 77
Query: 61 QIGMKRLKVQLKRPKDAAR 79
Q+ LKV + AA+
Sbjct: 78 QLENFTLKVAYIPDEMAAQ 96
>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 = 52.6 bits (127), Expect = 5e-11
Identities = 11/80 (13%), Positives = 24/80 (30%), Gaps = 20/80 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + D+ FGF+ + A A ++
Sbjct: 35 LFEKYGKAGEVFIHKDKG--------------------FGFIRLETRTLAEIAKVELDNM 74
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ K+L+V+ +
Sbjct: 75 PLRGKQLRVRFACHSASLTS 94
>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 = 52.4 bits (126), Expect = 7e-11
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 8/80 (10%)
Query: 9 ISSKVFI-----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAIQAMNGF 60
I+S+VFI F + R + K + FV + N A A+ NG
Sbjct: 26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ + L + + R
Sbjct: 86 VLAGQTLDINMAGEPKPDRS 105
>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 = 51.9 bits (125), Expect = 9e-11
Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 19/79 (24%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F + + +SK G ++ F + A A ++ G
Sbjct: 36 VFEDALEIR-----LVSQDGKSK--G------------IAYIEFKSEADAEKNLEEKQGA 76
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+I + + + K R
Sbjct: 77 EIDGRSVSLYYTGEKGGTR 95
>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 = 52.3 bits (126), Expect = 9e-11
Identities = 19/83 (22%), Positives = 26/83 (31%), Gaps = 18/83 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG + V SK FV F + A AI A++G
Sbjct: 35 LFQPFGVIDECTVLRGP-DGSSKGCA--------------FVKFSSHTEAQAAIHALHGS 79
Query: 61 QI---GMKRLKVQLKRPKDAARP 80
Q L V+ + P
Sbjct: 80 QTMPGASSSLVVKFADTDKESGP 102
>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 = 51.7 bits (125), Expect = 9e-11
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 15/75 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F G+V + D+ + K G F ++ F + S T++ A++
Sbjct: 26 HFHGCGSVNRVTILCDKFSGHPK--G------------FAYIEFSDKESVRTSL-ALDES 70
Query: 61 QIGMKRLKVQLKRPK 75
+++KV KR
Sbjct: 71 LFRGRQIKVIPKRTN 85
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 52.4 bits (126), Expect = 1e-10
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F +G + + + +DR T K G + V ++ A A++ +NG
Sbjct: 42 KFAEYGEIKNIHLNLDRRTGYLK--G------------YTLVEYETYKEAQAAMEGLNGQ 87
Query: 61 QIGMKRLKVQLKRPK 75
+ + + V +
Sbjct: 88 DLMGQPISVDWCFVR 102
>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 = 52.0 bits (125), Expect = 1e-10
Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 20/86 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN-- 58
+ FG++ +V + T SK G F F +A + A +
Sbjct: 35 VLQQFGDLKYVRVVLHPDTEHSK--G------------CAFAQFMTQEAAQKCLAAASLE 80
Query: 59 ----GFQIGMKRLKVQLKRPKDAARP 80
G ++ ++LKV L +D A
Sbjct: 81 AEGGGLKLDGRQLKVDLAVTRDEAAS 106
>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 = 52.9 bits (127), Expect = 1e-10
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 14/80 (17%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F G++ + +D+ + G F FV + + A A A++ +NG +
Sbjct: 60 FSKSGDIKKIIMGLDKMKKTAC--G------------FCFVEYYSRADAENAMRYINGTR 105
Query: 62 IGMKRLKVQLKRPKDAARPY 81
+ + ++ R Y
Sbjct: 106 LDDRIIRTDWDAGFKEGRQY 125
>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 = 51.1 bits (123), Expect = 2e-10
Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 22/80 (27%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FG + K K + F+ FD A A++ MNG
Sbjct: 31 AFSQFGKLERVKKL----------------------KDYAFIHFDERDGAVKAMEEMNGK 68
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ + +++ +P D R
Sbjct: 69 DLEGENIEIVFAKPPDQKRK 88
>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 = 53.5 bits (129), Expect = 2e-10
Identities = 14/79 (17%), Positives = 23/79 (29%), Gaps = 19/79 (24%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V + V +D ++ G FV F A A++
Sbjct: 117 FSQFGPVEKAVVVVD-DRGRATGKG--------------FVEFAAKPPARKALERCGDGA 161
Query: 62 IGMKR----LKVQLKRPKD 76
+ + V+ D
Sbjct: 162 FLLTTTPRPVIVEPMEQFD 180
Score = 48.9 bits (117), Expect = 8e-09
Identities = 11/69 (15%), Positives = 23/69 (33%), Gaps = 20/69 (28%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + DR FGF+ ++ A A ++G
Sbjct: 42 LFERYGEPSEVFINRDR--------------------GFGFIRLESRTLAEIAKAELDGT 81
Query: 61 QIGMKRLKV 69
+ + L++
Sbjct: 82 ILKSRPLRI 90
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 51.1 bits (123), Expect = 2e-10
Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 16/78 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
V +D T ++ FG +V F++ A++ + G +
Sbjct: 38 ISELFAKNDLAV-VDVRTGTNRKFG--------------YVDFESAEDLEKALE-LTGLK 81
Query: 62 IGMKRLKVQLKRPKDAAR 79
+ +K++ + +D R
Sbjct: 82 VFGNEIKLEKPKGRDGTR 99
>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 = 52.6 bits (127), Expect = 2e-10
Identities = 11/80 (13%), Positives = 29/80 (36%), Gaps = 16/80 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
V +D T ++ FG +V F++ A++ + G
Sbjct: 33 AISELFAKNDLAV-VDVRTGTNRKFG--------------YVDFESAEDLEKALE-LTGL 76
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ +K++ + +D+ +
Sbjct: 77 KVFGNEIKLEKPKGRDSKKV 96
Score = 49.5 bits (119), Expect = 3e-09
Identities = 9/75 (12%), Positives = 21/75 (28%), Gaps = 19/75 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F + +SK ++ F + A A ++ G
Sbjct: 119 VFEDALEIRL-----VSQDGKSKGIA--------------YIEFKSEADAEKNLEEKQGA 159
Query: 61 QIGMKRLKVQLKRPK 75
+I + + + K
Sbjct: 160 EIDGRSVSLYYTGEK 174
>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 = 51.2 bits (123), Expect = 2e-10
Identities = 12/80 (15%), Positives = 27/80 (33%), Gaps = 17/80 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + +V T + +V +++ A A+ ++GF
Sbjct: 28 IFGKYGPIRQIRVGNTPET-----------------RGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 61 QIGMKRLKVQLKRPKDAARP 80
+ + L V A +
Sbjct: 71 NVSNRYLVVLYYNANRAFQK 90
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 52.2 bits (125), Expect = 4e-10
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 15/74 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG + + V DR + +S G V F+ A A A++ G
Sbjct: 109 FAEFGTLKKAAVDYDR-SGRSL--G------------TADVHFERRADALKAMKQYKGVP 153
Query: 62 IGMKRLKVQLKRPK 75
+ + + +QL +
Sbjct: 154 LDGRPMDIQLVASQ 167
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 50.4 bits (121), Expect = 4e-10
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 16/77 (20%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ-I 62
+ + KV +D+ T SK +G FV F + A+ G +
Sbjct: 33 VYPSCRGGKVVLDQ-TGVSKGYG--------------FVKFTDELEQKRALTECQGAVGL 77
Query: 63 GMKRLKVQLKRPKDAAR 79
G K +++ + PK +
Sbjct: 78 GSKPVRLSVAIPKASRV 94
>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 = 50.4 bits (121), Expect = 5e-10
Identities = 13/55 (23%), Positives = 22/55 (40%)
Query: 27 ECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY 81
+ + K F FV F++P A A+ +G+ RL+V+ R
Sbjct: 51 DIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSG 105
>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 = 50.0 bits (120), Expect = 5e-10
Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 15/73 (20%)
Query: 1 MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
F G V+S K+ +R T + FV F + A+A + +NG
Sbjct: 29 AFATMGETVMSVKIIRNRLTGIPAGYC--------------FVEFADLATAEKCLHKING 74
Query: 60 FQIGMKRLKVQLK 72
+ + K
Sbjct: 75 KPLPGATPAKRFK 87
>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 = 50.0 bits (120), Expect = 5e-10
Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 18/77 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F + +SK G + F+ F + A A+ + N
Sbjct: 35 VFEKATFI----KVPQNQNGKSK--G------------YAFIEFASFEDAKEALNSCNKR 76
Query: 61 QIGMKRLKVQLKRPKDA 77
+I + ++++L+ P+ +
Sbjct: 77 EIEGRAIRLELQGPRGS 93
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 50.0 bits (120), Expect = 6e-10
Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 22/76 (28%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG + K+ F FV F+ SA AI+ ++G
Sbjct: 51 IFGPFGPMKEVKI----------------------LNGFAFVEFEEAESAAKAIEEVHGK 88
Query: 61 QIGMKRLKVQLKRPKD 76
+ L+V +
Sbjct: 89 SFANQPLEVVYSKLPA 104
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 50.1 bits (120), Expect = 6e-10
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 22/82 (26%)
Query: 2 FLPFGNVISS--------KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTA 53
F G + ++ ++ DR T + K G VSFD+P SA A
Sbjct: 28 FKQIGIIKTNKKTGQPMINLYTDRETGKLK--G------------EATVSFDDPPSAKAA 73
Query: 54 IQAMNGFQIGMKRLKVQLKRPK 75
I +G + +KV +
Sbjct: 74 IDWFDGKEFSGNPIKVSFATRR 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 = 50.5 bits (121), Expect = 7e-10
Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 15/74 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F G++ + D+ + K G + ++ F S A+ AM+
Sbjct: 57 FSSCGSINRITILCDKFSGHPK--G------------YAYIEFAERNSVDAAV-AMDETV 101
Query: 62 IGMKRLKVQLKRPK 75
+ +KV KR
Sbjct: 102 FRGRTIKVLPKRTN 115
>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 = 49.6 bits (119), Expect = 9e-10
Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 16/68 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + V DR T K F+++ SA A A++
Sbjct: 33 LFEEFGKIYELTVLKDRFTGMHKGCA--------------FLTYCERESALKAQSALHEQ 78
Query: 61 QI--GMKR 66
+ GM R
Sbjct: 79 KTLPGMNR 86
>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 = 49.2 bits (118), Expect = 2e-09
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 15/74 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F G V ++ DR + +SK G +V F S AI + G +
Sbjct: 46 FSAVGKVRDVRIISDRNSRRSK--G------------IAYVEFCEIQSVPLAI-GLTGQR 90
Query: 62 IGMKRLKVQLKRPK 75
+ + VQ + +
Sbjct: 91 LLGVPIIVQASQAE 104
>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 = 48.4 bits (116), Expect = 2e-09
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 20/75 (26%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +V R + FV F N A A++A+NG
Sbjct: 36 FNNIKPGAVERVKKIR--------------------DYAFVHFSNREDAVEAMKALNGKV 75
Query: 62 IGMKRLKVQLKRPKD 76
+ ++V L +P D
Sbjct: 76 LDGSPIEVTLAKPVD 90
>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 = 48.0 bits (115), Expect = 2e-09
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
K +GFV ++ +A AI+ ++ +++ + V+ + K A
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 48.0 bits (115), Expect = 3e-09
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 10 SSKVFI-----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAIQAMNGFQ 61
S++FI + + + F + +N + FGF+ FDNP S AI+ +
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEM 69
Query: 62 IGMKRLKVQLKRPKDAARPY 81
K+L +++ +
Sbjct: 70 NFGKKLILEVSSSNARPQFD 89
>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 = 48.7 bits (116), Expect = 4e-09
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 9/79 (11%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F + + S I K K F+ N +A A++ NG+
Sbjct: 65 IFGRYVDFSSETQRIMFDIRLMK---------EGRMKGQAFIGLPNEKAAAKALKEANGY 115
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+ K + VQ R +
Sbjct: 116 VLFGKPMVVQFARSARPKQ 134
>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 = 47.6 bits (114), Expect = 4e-09
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 17/75 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG ++ V + FV F +SA A+++M GF
Sbjct: 32 IFSRFGQILDILVSRSL-----------------KMRGQAFVIFKEVSSATNALRSMQGF 74
Query: 61 QIGMKRLKVQLKRPK 75
K +++Q +
Sbjct: 75 PFYDKPMRIQYAKTD 89
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 47.8 bits (114), Expect = 4e-09
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 15/69 (21%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F G V++ + ID AT ++K F FV + A I++ +G +
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFL--------------FVECGSMNDAKKIIKSFHGKR 78
Query: 62 I-GMKRLKV 69
+ RL +
Sbjct: 79 LDLKHRLFL 87
>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 = 46.8 bits (112), Expect = 7e-09
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 10 SSKVFI----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAIQAMNGFQI 62
+ K+F+ T+Q F R + + K + FV + A A AI +NG ++
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV 68
Query: 63 GMKRLKVQLKRPKD 76
KR+ V+L
Sbjct: 69 KGKRINVELSTKGQ 82
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 47.1 bits (112), Expect = 7e-09
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 30 RKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
R + F+ + + A+A A+ + G ++G L+V L R +
Sbjct: 49 RLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94
>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 = 47.3 bits (113), Expect = 8e-09
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 15/79 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG++ + V DR T +S+ +G FV+ + A+A A + N
Sbjct: 38 FEGFGDIEEAVVITDRQTGKSRGYG--------------FVTMADRAAAERACKDPNP-I 82
Query: 62 IGMKRLKVQLKRPKDAARP 80
I ++ V L R
Sbjct: 83 IDGRKANVNLAYLGAKPRS 101
>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 = 46.9 bits (112), Expect = 9e-09
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 3 LPFGNVISSKVFI-----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAI 54
+P G+ + S++FI + + + F + +N + FGF+ FDNP S AI
Sbjct: 15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 74
Query: 55 QAMNGFQIGMKRLKVQLKRPK 75
+ + K+L +++
Sbjct: 75 EXESQEMNFGKKLILEVSSSN 95
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 46.9 bits (112), Expect = 1e-08
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 25 FGECNR-KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
+G ++ N F FV F++P A A++ ++G I R++V+L
Sbjct: 24 YGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM 75
>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 = 48.0 bits (114), Expect = 1e-08
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 31 KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
V+ N F FV F++P A A++ ++G + R++V+L +
Sbjct: 104 WVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148
>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 = 49.1 bits (116), Expect = 1e-08
Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 17/79 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG ++ V + FV F +SA A+++M GF
Sbjct: 33 IFSQFGQILDILVSRSL-----------------KMRGQAFVIFKEVSSATNALRSMQGF 75
Query: 61 QIGMKRLKVQLKRPKDAAR 79
K +++Q +
Sbjct: 76 PFYDKPMRIQYAKTDSDII 94
Score = 44.9 bits (105), Expect = 3e-07
Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 20/74 (27%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F F ++ R FV FDN A A A+ GF
Sbjct: 227 LFNQFPGFKEVRLVPGRHD-------------------IAFVEFDNEVQAGAARDALQGF 267
Query: 61 QI-GMKRLKVQLKR 73
+I +K+ +
Sbjct: 268 KITQNNAMKISFAK 281
>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 = 46.5 bits (111), Expect = 1e-08
Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 22/77 (28%)
Query: 2 FLPFGNVISS--------KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTA 53
F G + ++ ++ DR T + K G VSFD+P SA A
Sbjct: 34 FKQIGIIKTNKKTGQPMINLYTDRETGKLK--G------------EATVSFDDPPSAKAA 79
Query: 54 IQAMNGFQIGMKRLKVQ 70
I +G + +KV
Sbjct: 80 IDWFDGKEFSGNPIKVS 96
>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 = 46.5 bits (111), Expect = 1e-08
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 17/75 (22%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G+V K+ DR T SK +G FVSF N ++ +
Sbjct: 30 FARYGSVKEVKIITDR-TGVSKGYG--------------FVSFYNDVDVQKIVE--SQIN 72
Query: 62 IGMKRLKVQLKRPKD 76
K+LK+ K
Sbjct: 73 FHGKKLKLGPAIRKQ 87
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 45.8 bits (109), Expect = 2e-08
Identities = 12/80 (15%), Positives = 27/80 (33%), Gaps = 20/80 (25%)
Query: 1 MFLPFGNVISSKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
P+ ++ + + + D+ T Q++ F FV + A +Q +
Sbjct: 29 ALSPYASLAVNNIRLIKDKQTQQNRGFA--------------FVQLSSAMDASQLLQILQ 74
Query: 59 G----FQIGMKRLKVQLKRP 74
+I K + V +
Sbjct: 75 SLHPPLKIDGKTIGVDFAKS 94
>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 = 45.8 bits (109), Expect = 3e-08
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 16/78 (20%)
Query: 1 MFLPFGNVISSKVFIDR-ATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-N 58
+F FG + + ++ T + G FGFV F A A A+ +
Sbjct: 35 LFSTFGELKTVRLPKKMTGTGAHR--G------------FGFVDFITKQDAKKAFNALCH 80
Query: 59 GFQIGMKRLKVQLKRPKD 76
+ +RL ++ +
Sbjct: 81 STHLYGRRLVLEWADSEV 98
>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 = 45.3 bits (108), Expect = 3e-08
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
+ FV + A AI+ ++ + KR+ VQL +
Sbjct: 46 YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAS 87
>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 = 46.8 bits (111), Expect = 4e-08
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 19/80 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G+V K+ ++ K V + A A+ +NG
Sbjct: 24 LFGVYGDVQRVKILFNK-------------------KENALVQMADGNQAQLAMSHLNGH 64
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ K +++ L + ++ P
Sbjct: 65 KLHGKPIRITLSKHQNVQLP 84
Score = 40.7 bits (95), Expect = 7e-06
Identities = 9/76 (11%), Positives = 21/76 (27%), Gaps = 19/76 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V+ F + + + + A A+ ++
Sbjct: 140 LFSSNGGVVKGFKFFQK------------------DRKMALIQMGSVEEAVQALIDLHNH 181
Query: 61 QIGMKR-LKVQLKRPK 75
+G L+V +
Sbjct: 182 DLGENHHLRVSFSKST 197
>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 = 44.5 bits (106), Expect = 7e-08
Identities = 9/53 (16%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-FQIGMKRLKVQLKRPKD 76
+ + + FV + + A AI+ ++G ++ K ++V K
Sbjct: 32 RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK 84
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 44.9 bits (106), Expect = 1e-07
Identities = 8/76 (10%), Positives = 20/76 (26%), Gaps = 17/76 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ G+++ V + + ++ F SA ++A G+
Sbjct: 53 LASSQGDILDIVVDLSD-----------------DNSGKAYIVFATQESAQAFVEAFQGY 95
Query: 61 QIGMKRLKVQLKRPKD 76
L +
Sbjct: 96 PFQGNPLVITFSETPQ 111
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 43.9 bits (104), Expect = 1e-07
Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 17/70 (24%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + + F ++K + F+ + +PA A A++ +G+
Sbjct: 41 IFSKFGKITN--DFYPEEDGKTKGYI--------------FLEYASPAHAVDAVKNADGY 84
Query: 61 QIGMK-RLKV 69
++ + +V
Sbjct: 85 KLDKQHTFRV 94
>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 = 43.3 bits (103), Expect = 2e-07
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V + D + + FGF++F++ S A+ M+
Sbjct: 31 FKKFGVVTEVVMIYDAEKQRP--------------RGFGFITFEDEQSVDQAV-NMHFHD 75
Query: 62 IGMKRLKVQLKRPKDAARP 80
I K+++V+ P+D+
Sbjct: 76 IMGKKVEVKRAEPRDSKSS 94
>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 = 45.0 bits (106), Expect = 3e-07
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 19/80 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G+V K+ ++ K V + A A+ +NG
Sbjct: 55 LFGVYGDVQRVKILFNK-------------------KENALVQMADGNQAQLAMSHLNGH 95
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ K +++ L + ++ P
Sbjct: 96 KLHGKPIRITLSKHQNVQLP 115
Score = 40.4 bits (94), Expect = 9e-06
Identities = 9/76 (11%), Positives = 20/76 (26%), Gaps = 19/76 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V+ F + + + A A+ ++
Sbjct: 171 LFSSNGGVVKGFKFFQ------------------KDRKMALIQMGSVEEAVQALIDLHNH 212
Query: 61 QIGMKR-LKVQLKRPK 75
+G L+V +
Sbjct: 213 DLGENHHLRVSFSKST 228
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 42.8 bits (101), Expect = 3e-07
Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 17/70 (24%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + + F ++K + F+ + +PA A A++ +G+
Sbjct: 27 IFSKFGKITN--DFYPEEDGKTKGYI--------------FLEYASPAHAVDAVKNADGY 70
Query: 61 QIGMK-RLKV 69
++ + +V
Sbjct: 71 KLDKQHTFRV 80
>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 = 42.6 bits (101), Expect = 4e-07
Identities = 12/71 (16%), Positives = 21/71 (29%), Gaps = 21/71 (29%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NG 59
F FG + + V + F+ F +A A + N
Sbjct: 32 HFYQFGEIRTITVVQR--------------------QQCAFIQFATRQAAEVAAEKSFNK 71
Query: 60 FQIGMKRLKVQ 70
+ +RL V+
Sbjct: 72 LIVNGRRLNVK 82
>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 = 42.6 bits (101), Expect = 5e-07
Identities = 17/79 (21%), Positives = 25/79 (31%), Gaps = 16/79 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V+ +V D T S K FGFV F + + +
Sbjct: 36 FSTFGEVLMVQVKKDLKTGHS--------------KGFGFVRFTEYETQVKVMSQRH--M 79
Query: 62 IGMKRLKVQLKRPKDAARP 80
I + +L K +
Sbjct: 80 IDGRWCDCKLPNSKQSQDS 98
>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 = 42.2 bits (100), Expect = 6e-07
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG--MKRLKVQLKRPK 75
FG V F ++ +++ +A A M GF +G +RL+V +
Sbjct: 41 FGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93
>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 = 41.8 bits (99), Expect = 7e-07
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 14/57 (24%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
F FG V+ + +D T +S + FGF+ F + AS +
Sbjct: 32 FTKFGEVVDCTIKMDPNTGRS--------------RGFGFILFKDAASVEKVLDQKE 74
>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 = 43.5 bits (102), Expect = 7e-07
Identities = 7/69 (10%), Positives = 20/69 (28%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ G + V + ++ G + +D+ + A + +N +
Sbjct: 143 ICDELGVKRPTSVKVFSGKSERSSSG--------------LLEWDSKSDALETLGFLNHY 188
Query: 61 QIGMKRLKV 69
Q+
Sbjct: 189 QMKNPNGPY 197
Score = 41.2 bits (96), Expect = 4e-06
Identities = 10/71 (14%), Positives = 21/71 (29%), Gaps = 19/71 (26%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +GNV K + V + + AI +N
Sbjct: 25 VFCLYGNVEKVKFMKSK-------------------PGAAMVEMADGYAVDRAITHLNNN 65
Query: 61 QIGMKRLKVQL 71
+ +++ V +
Sbjct: 66 FMFGQKMNVCV 76
>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 = 42.9 bits (102), Expect = 8e-07
Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 15/74 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G +I +++ +D+ T QS + FGFV++D+ +
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQS--------------RGFGFVTYDSADAVDRVC-QNKFID 152
Query: 62 IGMKRLKVQLKRPK 75
++++++ P+
Sbjct: 153 FKDRKIEIKRAEPR 166
Score = 40.6 bits (96), Expect = 7e-06
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 16/79 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G V K+ D AT +S + FGF+SF+ P+S ++ +
Sbjct: 24 FGKYGTVTDLKIMKDPATGRS--------------RGFGFLSFEKPSSVDEVVKTQH--I 67
Query: 62 IGMKRLKVQLKRPKDAARP 80
+ K + + P+D
Sbjct: 68 LDGKVIDPKRAIPRDEQDK 86
>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 = 40.9 bits (96), Expect = 2e-06
Identities = 13/39 (33%), Positives = 17/39 (43%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
K FV+ N A AIQ + + K L VQL+
Sbjct: 40 KRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 40.6 bits (95), Expect = 3e-06
Identities = 8/56 (14%), Positives = 16/56 (28%), Gaps = 1/56 (1%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
G+ V + G V F A++ ++ + + R K
Sbjct: 39 AGDVCY-ADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR 93
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 40.4 bits (95), Expect = 3e-06
Identities = 11/77 (14%), Positives = 23/77 (29%), Gaps = 14/77 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F + + S V+F++ A A+ +N
Sbjct: 36 FYGYQVIPGSVCLKYNEKGMPTGEA--------------MVAFESRDEATAAVIDLNDRP 81
Query: 62 IGMKRLKVQLKRPKDAA 78
IG +++K+ L +
Sbjct: 82 IGSRKVKLVLGSGPSSG 98
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 39.9 bits (94), Expect = 5e-06
Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 15/73 (20%)
Query: 7 NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR 66
++ S ++ D+ T++ K G F +V FD S A+ +G +G +
Sbjct: 40 SIRSVRLVRDKDTDKFK--G------------FCYVEFDEVDSLKEAL-TYDGALLGDRS 84
Query: 67 LKVQLKRPKDAAR 79
L+V + + +
Sbjct: 85 LRVDIAEGRKQDK 97
>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 = 40.0 bits (94), Expect = 6e-06
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 18/69 (26%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
+ +G + V D A+ +S + FGFV+F + A A+ A +
Sbjct: 48 YEQWGKLTDCVVMRDPASKRS--------------RGFGFVTFSSMAEVDAAMAARPHSI 93
Query: 58 NGFQIGMKR 66
+G + KR
Sbjct: 94 DGRVVEPKR 102
>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 = 39.8 bits (93), Expect = 6e-06
Identities = 8/56 (14%), Positives = 16/56 (28%), Gaps = 1/56 (1%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
G+ V + G V F A++ ++ + + R K
Sbjct: 40 AGDVCY-ADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR 94
>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 = 39.9 bits (94), Expect = 6e-06
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 18/69 (26%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
F +G V+ + D+ TNQS + FGFV F +P T + + +
Sbjct: 37 FSQYGEVVDCVIMKDKTTNQS--------------RGFGFVKFKDPNCVGTVLASRPHTL 82
Query: 58 NGFQIGMKR 66
+G I K
Sbjct: 83 DGRNIDPKP 91
>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 = 39.4 bits (92), Expect = 8e-06
Identities = 9/46 (19%), Positives = 15/46 (32%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
FG R + V F P A A + + + L ++
Sbjct: 34 FGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE 79
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 38.6 bits (91), Expect = 9e-06
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 18/69 (26%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
F FG V + + D+ TN+ + FGFV+F++ + +
Sbjct: 20 FEQFGKVDDAMLMFDKTTNRH--------------RGFGFVTFESEDIVEKVCEIHFHEI 65
Query: 58 NGFQIGMKR 66
N + K+
Sbjct: 66 NNKMVECKK 74
>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 = 39.0 bits (91), Expect = 1e-05
Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 14/77 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN-- 58
+ + A ++ K + F FV +++ +A A + +
Sbjct: 28 EIAKVTEGVLDVIVYASAADKMK------------NRGFAFVEYESHRAAAMARRKLMPG 75
Query: 59 GFQIGMKRLKVQLKRPK 75
Q+ ++ V P+
Sbjct: 76 RIQLWGHQIAVDWAEPE 92
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 40.0 bits (94), Expect = 1e-05
Identities = 12/79 (15%), Positives = 25/79 (31%), Gaps = 15/79 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G + ++ DR + + + F FV+FD+ S +
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKK--------------RGFAFVTFDDHDSVDKIV-IQKYHT 169
Query: 62 IGMKRLKVQLKRPKDAARP 80
+ +V+ K
Sbjct: 170 VNGHNCEVRKALSKQEMAS 188
Score = 38.8 bits (91), Expect = 4e-05
Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 15/79 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G + V D T +S + FGFV++ A+ +
Sbjct: 34 FEQWGTLTDCVVMRDPNTKRS--------------RGFGFVTYATVEEVDAAM-NARPHK 78
Query: 62 IGMKRLKVQLKRPKDAARP 80
+ + ++ + ++ ++
Sbjct: 79 VDGRVVEPKRAVSREDSQR 97
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 37.9 bits (89), Expect = 2e-05
Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 14/55 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
F FG V V D T +S + FGFV+F + A +
Sbjct: 21 FGQFGEVKECLVMRDPLTKRS--------------RGFGFVTFMDQAGVDKVLAQ 61
>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 = 38.4 bits (90), Expect = 2e-05
Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 18/69 (26%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
F FG V V D T +S + FGFV+F + A + +
Sbjct: 46 FGQFGEVKECLVMRDPLTKRS--------------RGFGFVTFMDQAGVDKVLAQSRHEL 91
Query: 58 NGFQIGMKR 66
+ I K
Sbjct: 92 DSKTIDPKV 100
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 38.5 bits (89), Expect = 2e-05
Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 20/78 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG V+ F Q + + +P SA A +++G
Sbjct: 48 IFSKFGTVLKIITFTKNNQFQ------------------ALLQYADPVSAQHAKLSLDGQ 89
Query: 61 QI--GMKRLKVQLKRPKD 76
I L++ +
Sbjct: 90 NIYNACCTLRIDFSKLTS 107
>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 = 37.5 bits (88), Expect = 3e-05
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 18/69 (26%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
F FG V S ++ +D TN+ + F F++F ++ +
Sbjct: 20 FGGFGEVESIELPMDNKTNKR--------------RGFCFITFKEEEPVKKIMEKKYHNV 65
Query: 58 NGFQIGMKR 66
+ +K
Sbjct: 66 GLSKCEIKV 74
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 39.0 bits (90), Expect = 3e-05
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 20/76 (26%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G++ + V K GFV F A+A A +AM+
Sbjct: 163 VFSRLGDIDRIRY--------------------VESKNCGFVKFKYQANAEFAKEAMSNQ 202
Query: 61 QIGMKRLKVQLKRPKD 76
+ + K R +
Sbjct: 203 TLLLPSDKEWDDRREG 218
>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 = 38.5 bits (89), Expect = 3e-05
Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 20/78 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG V+ F Q + + +P SA A +++G
Sbjct: 66 IFSKFGTVLKIITFTKNNQFQ------------------ALLQYADPVSAQHAKLSLDGQ 107
Query: 61 QI--GMKRLKVQLKRPKD 76
I L++ +
Sbjct: 108 NIYNACCTLRIDFSKLTS 125
>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 = 37.7 bits (88), Expect = 3e-05
Identities = 10/68 (14%), Positives = 21/68 (30%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F + + S V+F++ A A+ +N
Sbjct: 36 FYGYQVIPGSVCLKYNEKGMPTGEA--------------MVAFESRDEATAAVIDLNDRP 81
Query: 62 IGMKRLKV 69
IG +++K+
Sbjct: 82 IGSRKVKL 89
>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 = 39.1 bits (90), Expect = 4e-05
Identities = 10/74 (13%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G + + + + + + + F+ +++ H+A + +G +
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYA--------------FIEYEHERDMHSAYKHADGKK 168
Query: 62 IGMKRLKVQLKRPK 75
I +R+ V ++R +
Sbjct: 169 IDGRRVLVDVERGR 182
>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 = 37.6 bits (87), Expect = 4e-05
Identities = 6/38 (15%), Positives = 14/38 (36%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
G + + K + F + + A +NG ++
Sbjct: 51 CGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 88
>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 = 37.1 bits (86), Expect = 6e-05
Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 2/58 (3%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKDAARP 80
FG + + K V F+N SA + I ++ K RP
Sbjct: 39 FGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRP 96
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 36.9 bits (86), Expect = 7e-05
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 20/79 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
FL FG V + V +D+ F V + + + + +
Sbjct: 29 FLAFGPV--ASVVMDKDKG-----------------VFAIVEMGDVGAREAVL-SQSQHS 68
Query: 62 IGMKRLKVQLKRPKDAARP 80
+G RL+V+ + K+ P
Sbjct: 69 LGGHRLRVRPREQKEFQSP 87
>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 = 37.2 bits (86), Expect = 8e-05
Identities = 8/58 (13%), Positives = 21/58 (36%), Gaps = 2/58 (3%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQ--AMNGFQIGMKRLKVQLKRPKDAARP 80
FG+ + + K F+ + +A+T + + + + +Q K+
Sbjct: 55 FGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 112
>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 = 35.9 bits (83), Expect = 2e-04
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 3/50 (6%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
K F F+ F + A+ +G + LK+ +RP
Sbjct: 41 GNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI--RRP 87
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 36.0 bits (83), Expect = 2e-04
Identities = 8/58 (13%), Positives = 21/58 (36%), Gaps = 2/58 (3%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQA--MNGFQIGMKRLKVQLKRPKDAARP 80
FG+ + + K F+ + +A+T + + + + +Q K+
Sbjct: 40 FGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 97
>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 = 35.2 bits (81), Expect = 3e-04
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 2/54 (3%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQ--AMNGFQIGMKRLKVQLKRPKD 76
FG+ + + K F+ +A T + + + + + +Q K+
Sbjct: 39 FGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92
>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 = 34.5 bits (80), Expect = 6e-04
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
FG+ F++ S +A+ ++N +G KR++V +
Sbjct: 59 FGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQ 95
>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 = 34.7 bits (80), Expect = 7e-04
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 10/55 (18%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
FG V +V I + + E K+ FV F + H AIQA+NG
Sbjct: 49 FGAVN--RVIIYQEKQGEEEDAEIIVKI--------FVEFSIASETHKAIQALNG 93
>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 = 34.1 bits (79), Expect = 7e-04
Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
FG+ F++ S +A+ ++N +G +R++V +
Sbjct: 63 FGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ 99
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 34.0 bits (78), Expect = 0.001
Identities = 6/45 (13%), Positives = 15/45 (33%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
+ G + F + A++ +N + + V+ R
Sbjct: 65 DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPIR 109
>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 = 33.6 bits (77), Expect = 0.001
Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+G V S + I R + V V FV F + A+Q + G
Sbjct: 39 YGLVKS--IEIPRPVDG----------VEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
>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 = 33.4 bits (76), Expect = 0.001
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
V +N A A+ +++ ++IG K++ V L
Sbjct: 54 KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGA 90
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 32.4 bits (74), Expect = 0.003
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQ 70
FG + V + +K V F++ A A+ QI + V
Sbjct: 45 FGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 32.4 bits (74), Expect = 0.004
Identities = 15/79 (18%), Positives = 24/79 (30%), Gaps = 16/79 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
G V++ ++ K F K FV FD+ SA + G
Sbjct: 31 WLEDKGQVLNIQM----RRTLHKAF-----------KGSIFVVFDSIESAKKFV-ETPGQ 74
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+ L + K A +
Sbjct: 75 KYKETDLLILFKDDYFAKK 93
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 32.3 bits (73), Expect = 0.006
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 25 FGECNRKVSVNQKCF-GFVSFDNPASAHTAIQAMNGFQI--GMKRLKVQLKRPKD 76
G+ R V + V F++ A A A+NG I G LK++ RP
Sbjct: 49 VGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 103
>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 = 31.4 bits (72), Expect = 0.008
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 2/44 (4%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
+ F FV+F + A + I + + PK +
Sbjct: 42 RAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNSNS 83
>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 = 31.4 bits (71), Expect = 0.009
Identities = 9/67 (13%), Positives = 18/67 (26%), Gaps = 15/67 (22%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
+G V V + + +V F A A+ +N
Sbjct: 51 YGEVEEMNVC---------------DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG 95
Query: 65 KRLKVQL 71
+ + +L
Sbjct: 96 QPIHAEL 102
>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 = 30.4 bits (69), Expect = 0.019
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
VSF +P A IQ ++G G +++ Q
Sbjct: 68 SVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 103
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 91
Score = 30.0 bits (67), Expect = 0.024
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+V+F +SA + +NG ++ + + + LK P
Sbjct: 53 WVTFLEGSSALNVLS-LNGKELLNRTITIALKSP 85
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 30.1 bits (67), Expect = 0.026
Identities = 12/51 (23%), Positives = 16/51 (31%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
C KV C + F N SA A + M + R+ V
Sbjct: 34 SDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKN 84
>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 = 30.4 bits (69), Expect = 0.028
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 18/55 (32%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
G VI +++D+ + Q + V + A+A A+ A++G
Sbjct: 41 HGGVI--HIYVDKNSAQGNVY----------------VKCPSIAAAIAAVNALHG 77
>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 = 29.9 bits (68), Expect = 0.030
Identities = 8/40 (20%), Positives = 14/40 (35%), Gaps = 2/40 (5%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
+ F FV+F + A + I + + PK
Sbjct: 48 RAFAFVTFADDKVAQSLCG--EDLIIKGISVHISNAEPKH 85
>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 = 30.1 bits (67), Expect = 0.049
Identities = 6/38 (15%), Positives = 14/38 (36%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
G + + K + F + + A +NG ++
Sbjct: 44 CGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 81
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 29.3 bits (66), Expect = 0.054
Identities = 10/78 (12%), Positives = 22/78 (28%), Gaps = 15/78 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F V + +S FV F + A A++ + +
Sbjct: 36 FSGLEIVPNGMTLPVDFQGRSTGEA--------------FVQFASQEIAEKALK-KHKER 80
Query: 62 IGMKRLKVQLKRPKDAAR 79
IG + +++ +
Sbjct: 81 IGHRYIEIFKSSRAEVRT 98
>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 = 29.1 bits (65), Expect = 0.078
Identities = 6/48 (12%), Positives = 15/48 (31%), Gaps = 2/48 (4%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQ--AMNGFQIGMKRLKVQ 70
+G+ + + K F+ + A + + +KV
Sbjct: 50 YGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD 97
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.091
Identities = 7/19 (36%), Positives = 11/19 (57%), Gaps = 4/19 (21%)
Query: 64 MKRLKVQLK--RPKDAARP 80
+K+L+ LK D+A P
Sbjct: 22 LKKLQASLKLYAD-DSA-P 38
>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 = 28.6 bits (64), Expect = 0.11
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 1/43 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
G V F +P A++ N + + ++V +
Sbjct: 56 NGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVA 97
>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 95
Score = 28.5 bits (63), Expect = 0.12
Identities = 6/33 (18%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 42 VSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
V+F + SA + + ++G ++ + +K+
Sbjct: 63 VTFADSHSALSVLD-VDGMKVKGRAVKISGPSS 94
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 28.6 bits (64), Expect = 0.18
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
FV F + H AIQA+NG +++ ++
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVAEV 209
>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 = 28.3 bits (63), Expect = 0.18
Identities = 6/41 (14%), Positives = 14/41 (34%), Gaps = 1/41 (2%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
V F A A+ + + + +++ L A+
Sbjct: 88 EADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASN 127
>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 = 27.9 bits (62), Expect = 0.26
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
GFV F N A A+ + +G + ++V K
Sbjct: 67 TGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLE 108
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 27.5 bits (61), Expect = 0.28
Identities = 6/43 (13%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
FV F A A++ + +G + +++ + +
Sbjct: 68 TGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRSTAAEVQQ 109
>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 = 27.4 bits (61), Expect = 0.36
Identities = 6/40 (15%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
V F N A + + ++ ++ + V + +D
Sbjct: 57 LGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLED 95
>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 = 27.0 bits (60), Expect = 0.40
Identities = 5/43 (11%), Positives = 13/43 (30%), Gaps = 1/43 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
V F A A+ + + + +++ L +
Sbjct: 55 TGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSG 96
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 25.9 bits (57), Expect = 1.00
Identities = 9/48 (18%), Positives = 15/48 (31%), Gaps = 11/48 (22%)
Query: 12 KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
K I ++ F+ F+ SA A+ +NG
Sbjct: 42 KCVIFEIPGAPD-----------DEAVRIFLEFERVESAIKAVVDLNG 78
>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 = 26.0 bits (57), Expect = 1.3
Identities = 12/76 (15%), Positives = 23/76 (30%), Gaps = 15/76 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F V + + GE FV F + A A+ +
Sbjct: 62 FFSGLEIVPNGITLPVDPEGKIT--GEA------------FVQFASQELAEKALG-KHKE 106
Query: 61 QIGMKRLKVQLKRPKD 76
+IG + ++V ++
Sbjct: 107 RIGHRYIEVFKSSQEE 122
>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 = 25.7 bits (56), Expect = 1.3
Identities = 5/40 (12%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
FV ++ A++ + +G + ++V +
Sbjct: 61 SGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTE 99
>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure
initiative, NE structural genomix research consortium,
nysgxrc; 2.35A {Pichia guilliermondii}
Length = 132
Score = 25.5 bits (55), Expect = 1.7
Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG ++ + + + + + + +++DNPASA A+ NG
Sbjct: 27 FQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV 85
Query: 62 IG 63
Sbjct: 86 FN 87
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 24.9 bits (54), Expect = 2.3
Identities = 14/75 (18%), Positives = 22/75 (29%), Gaps = 13/75 (17%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG ++ + + K + F+ F +S I A +
Sbjct: 29 FRRFGPLVVDWPHKAESKSYFP------------PKGYAFLLFQEESSVQALIDACL-EE 75
Query: 62 IGMKRLKVQLKRPKD 76
G L V KD
Sbjct: 76 DGKLYLCVSSPTIKD 90
>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 = 25.0 bits (54), Expect = 2.4
Identities = 5/38 (13%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
FV + A++ + +G + ++V +
Sbjct: 90 EAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTE 126
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 24.9 bits (54), Expect = 2.4
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 11/59 (18%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQ----AMNGFQIGMKRLKVQLKRPKDAAR 79
G C G ++F PA A + ++G Q+ ++ P+ AR
Sbjct: 37 GGPV--LSWQRLGCGGVLTFREPADAERVLAQADHELHGAQLSLRPAP-----PRAPAR 88
>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 = 24.6 bits (54), Expect = 2.9
Identities = 8/42 (19%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA 78
+ FV F N A++ N +G + ++V ++ ++
Sbjct: 50 TGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGPSS 90
>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 = 24.8 bits (53), Expect = 3.1
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK 72
K FV FD+ SA ++ + L + K
Sbjct: 150 KGSIFVVFDSIESAKKFVETPGQ-KYKETDLLILFK 184
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI,
protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 24.3 bits (52), Expect = 4.0
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
+G + V N + + + + A A+ +G G
Sbjct: 47 YGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFG 84
>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 = 24.4 bits (53), Expect = 4.2
Identities = 4/41 (9%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA 77
+ + ++ A++ + +G + ++V +D
Sbjct: 55 RGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNEDV 94
>1wyu_B Glycine dehydrogenase subunit 2 (P-protein); alpha(2)beta(2)
tetramer, riken structural genomics/proteomi initiative,
RSGI; HET: PLP; 2.10A {Thermus thermophilus} SCOP:
c.67.1.7 PDB: 1wyt_B* 1wyv_B*
Length = 474
Score = 24.1 bits (53), Expect = 5.6
Identities = 7/17 (41%), Positives = 11/17 (64%), Gaps = 5/17 (29%)
Query: 46 NPASAHTAIQAMNGFQI 62
NPA+A +M G+Q+
Sbjct: 169 NPATA-----SMAGYQV 180
>3feo_A MBT domain-containing protein 1; MBTL1, structural genomics,
structural genomics consortium, metal-binding, nucleus,
zinc-finger; 2.50A {Homo sapiens}
Length = 437
Score = 23.8 bits (51), Expect = 8.1
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 47 PASAHTAIQAMNGFQIGMK 65
P +GF++GMK
Sbjct: 350 PVKLFNKDVPNHGFRVGMK 368
>1rli_A Trp repressor binding protein; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.80A {Bacillus subtilis} SCOP: c.23.5.6
Length = 184
Score = 23.6 bits (51), Expect = 8.6
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 12 KVFIDRATNQSKCFGECNRKVSVNQKCFGFVS---FDNPASAHTAIQAMNGF 60
K+FIDR + + + K ++ K ++ + IQ
Sbjct: 91 KLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHI 142
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
0.325 0.136 0.412
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: 1,127,614
Number of extensions: 49414
Number of successful extensions: 480
Number of sequences better than 10.0: 1
Number of HSP's gapped: 357
Number of HSP's successfully gapped: 209
Length of query: 81
Length of database: 6,701,793
Length adjustment: 50
Effective length of query: 31
Effective length of database: 5,305,743
Effective search space: 164478033
Effective search space used: 164478033
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)