RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8615
(128 letters)
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 95.5 bits (238), Expect = 7e-27
Identities = 48/79 (60%), Positives = 58/79 (73%)
Query: 10 MTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGT 69
A +S + L+ +A S AA ++GKQ+ GPEG NLFIYHLP EF+D DLAS F PFG
Sbjct: 7 FGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGN 66
Query: 70 VLSAKVFIDKQNNRSKCFG 88
V+SAKVFIDKQ + SKCFG
Sbjct: 67 VISAKVFIDKQTSLSKCFG 85
>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 = 93.5 bits (233), Expect = 4e-26
Identities = 42/64 (65%), Positives = 48/64 (75%)
Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
+ ++G++G Q GPEGANLFIYHLP EF D DL MF PFG V+SAKVFIDKQ N S
Sbjct: 7 GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 85 KCFG 88
KCFG
Sbjct: 67 KCFG 70
>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 = 79.8 bits (197), Expect = 2e-20
Identities = 11/73 (15%), Positives = 27/73 (36%)
Query: 16 MSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
+ + + NL + ++P + L +F +G + S K+
Sbjct: 15 QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74
Query: 76 FIDKQNNRSKCFG 88
D++ +S+ +G
Sbjct: 75 VCDRETRQSRGYG 87
>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 = 77.2 bits (191), Expect = 4e-20
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
+ L+I L P +D DL + P+G ++S K +DK N+ K +G + F
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFD 55
>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 = 69.3 bits (170), Expect = 1e-16
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG G G+ +F+ +L + L +F G V+ A + DK + +S+ G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59
Query: 89 TIIF 92
T+ F
Sbjct: 60 TVTF 63
>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 = 67.7 bits (166), Expect = 4e-16
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ + + NL+I +LP + +L +M PFG V+S ++ D + S+ G
Sbjct: 15 AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVG 69
>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 = 67.2 bits (165), Expect = 6e-16
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG ++T + NL++ +L D L F PFGT+ SAKV ++ RSK FG
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58
>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 = 65.7 bits (161), Expect = 3e-15
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 40 GPEG-ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GP G N+FI +L + L F FG +LS KV D+ N SK +G
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYG 48
>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 = 63.1 bits (154), Expect = 2e-14
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG + G LF+ L + S+ D+ +F PFG + V + SK +
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVK 62
Query: 92 F 92
F
Sbjct: 63 F 63
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 61.1 bits (149), Expect = 1e-13
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG +F+ +LP +F+ L F G VL A + ++ N +SK G +
Sbjct: 1 GSSGS----SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVK 54
Query: 92 F 92
F
Sbjct: 55 F 55
>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 = 62.2 bits (152), Expect = 2e-13
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 31 VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
V + + NL++ +LP +D L ++FG +G+++ + DK R +
Sbjct: 77 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVA 134
Score = 58.4 bits (142), Expect = 6e-12
Identities = 10/47 (21%), Positives = 23/47 (48%)
Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
NL + +LP + +D +L ++F G + + ++ D + S +
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYA 48
>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 = 60.0 bits (146), Expect = 4e-13
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG + L + ++P F D DL MFG FG +L ++ ++ SK FG
Sbjct: 1 GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFG 58
>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 = 61.4 bits (150), Expect = 4e-13
Identities = 12/58 (20%), Positives = 28/58 (48%)
Query: 31 VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
V + ANL++ LP + +L +F +G ++++++ +D+ S+ G
Sbjct: 76 VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVG 133
Score = 56.0 bits (136), Expect = 4e-11
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
NL + +LP + + S+FG G + S K+ DK +S +G
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYG 47
>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 = 62.7 bits (153), Expect = 5e-13
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 35 GKQLT---GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
++L+ P A L + +LPP + + PFG++ + ++ +SK +G
Sbjct: 84 ERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAE 143
Query: 92 FMRK 95
+M+K
Sbjct: 144 YMKK 147
Score = 52.3 bits (126), Expect = 3e-09
Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 42 EGANLFIYHLPPEFSDAD-LASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
L + LPP F+D D L + ++ Q+ + K F + +
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEY 233
Score = 38.4 bits (90), Expect = 2e-04
Identities = 5/52 (9%), Positives = 17/52 (32%), Gaps = 7/52 (13%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ I LP + ++ ++ + + + V ++ K +
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTL 64
>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 = 59.7 bits (145), Expect = 6e-13
Identities = 19/60 (31%), Positives = 32/60 (53%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG++ ++F+ L PE + D+ + F PFG + A+V D +SK +G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
>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 = 58.9 bits (143), Expect = 1e-12
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 32 GSSG-KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTI 90
GSSG + + LFI +P + DL +F FG + V D+ K +
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 91 IF 92
+
Sbjct: 61 TY 62
>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 = 58.1 bits (141), Expect = 2e-12
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
G G L + +L SDAD+ +F FGT+ A V D+ + RS +
Sbjct: 18 SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76
Query: 92 FMRK 95
F RK
Sbjct: 77 FERK 80
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 58.5 bits (142), Expect = 2e-12
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
+S GS + L + ++P F D DL MFG FG +L ++ ++ S
Sbjct: 11 SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGS 68
Query: 85 KCFG 88
K FG
Sbjct: 69 KGFG 72
>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 = 57.6 bits (140), Expect = 3e-12
Identities = 17/60 (28%), Positives = 29/60 (48%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG + A + + +L + + DL +F PFG++ + DK +SK F
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
>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 = 56.0 bits (136), Expect = 8e-12
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 40 GPEG--ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GP G ++F+ L PE + A +A+ F PFG + A+V D +SK +G
Sbjct: 1 GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYG 51
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 58.1 bits (141), Expect = 1e-11
Identities = 14/68 (20%), Positives = 26/68 (38%)
Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
A +++ + + SD D+ S+F FG + SA + D +
Sbjct: 107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKH 166
Query: 85 KCFGTIIF 92
K +G I +
Sbjct: 167 KGYGFIEY 174
Score = 53.1 bits (128), Expect = 1e-09
Identities = 10/56 (17%), Positives = 23/56 (41%)
Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
++ +Q + +++ + E + + F PFG + S + D + K F
Sbjct: 18 AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 54.8 bits (133), Expect = 2e-11
Identities = 15/45 (33%), Positives = 20/45 (44%)
Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
NLF+ L D L + F F + LS V D Q S+ +G
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYG 46
>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 = 55.5 bits (134), Expect = 3e-11
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
G GA L + +L SDAD+ +F FGT+ A V D+ + RS +
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVH 82
Query: 92 FMRK 95
F R+
Sbjct: 83 FERR 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 = 56.1 bits (136), Expect = 4e-11
Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ ++ E LFI + + ++ D+ MF FG + ++ + S+
Sbjct: 85 ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCA 139
Score = 52.2 bits (126), Expect = 1e-09
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN--RSKCFGTIIF 92
+F+ +P +S+ DL +F +G V V D+ N +SK + F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>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 = 54.2 bits (131), Expect = 4e-11
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG++ +G L++Y + + L F PFG ++ + +
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCA 52
Query: 89 TIIF 92
+ +
Sbjct: 53 FVTY 56
>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 = 55.6 bits (135), Expect = 5e-11
Identities = 16/56 (28%), Positives = 24/56 (42%)
Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+Q + + NLF+ L D L + F F + LS V D Q S+ +G
Sbjct: 77 FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYG 132
Score = 40.2 bits (95), Expect = 3e-05
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
L++ +L ++ L F G + + K+ IDK NN++ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYA 44
>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 = 54.2 bits (131), Expect = 7e-11
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG + LF+ L + ++ L +F +G + V D++ RS+ FG
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57
>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 = 56.2 bits (136), Expect = 8e-11
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
GA L + +L P S+ L F FG V A V +D R+ G + F
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEF 144
Score = 47.4 bits (113), Expect = 1e-07
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ T + LF+ +LP + ++ D +F +G + NR + FG
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFG 61
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 55.2 bits (133), Expect = 9e-11
Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 1/83 (1%)
Query: 13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
A P L + G GA L + +L SDAD+ +F FGT+
Sbjct: 58 APYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK 117
Query: 73 AKVFIDKQNNRSKCFGTIIFMRK 95
A V D+ + RS + F R+
Sbjct: 118 AAVDYDR-SGRSLGTADVHFERR 139
>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 = 56.8 bits (136), Expect = 1e-10
Identities = 7/50 (14%), Positives = 23/50 (46%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
LF+ + + +++ L F +G + + K++ + + + I + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
>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 = 53.0 bits (128), Expect = 1e-10
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG + L ++ L ++ DL +F +G + + D+Q+ RS+ F
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
>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 = 53.4 bits (129), Expect = 2e-10
Identities = 12/53 (22%), Positives = 20/53 (37%)
Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
G L++ +L P ++ DL S+F F + R + I F
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITF 74
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 53.2 bits (128), Expect = 2e-10
Identities = 6/52 (11%), Positives = 16/52 (30%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ L + L M +G V ++ + + + ++F
Sbjct: 4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLF 55
>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 = 53.0 bits (128), Expect = 2e-10
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG L++ L E D L + F PFG + ++ +D + + + F
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 57
>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 = 54.7 bits (131), Expect = 3e-10
Identities = 16/87 (18%), Positives = 27/87 (31%), Gaps = 2/87 (2%)
Query: 8 AAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPF 67
A M + + + L+I +L +D DL
Sbjct: 33 DAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSL 92
Query: 68 GT--VLSAKVFIDKQNNRSKCFGTIIF 92
G +L K F ++ N +SK F +
Sbjct: 93 GVNDILEIKFFENRANGQSKGFALVGV 119
>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 = 53.8 bits (130), Expect = 6e-10
Identities = 21/76 (27%), Positives = 28/76 (36%), Gaps = 13/76 (17%)
Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
L N+FI +L + L F FG +LS KV D N SK +G F
Sbjct: 93 QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYG---F 147
Query: 93 MRKFFILTIRFDTAND 108
+ F+T
Sbjct: 148 --------VHFETQEA 155
Score = 50.0 bits (120), Expect = 1e-08
Identities = 17/60 (28%), Positives = 27/60 (45%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+GS A+L++ L P+ ++A L F P G +LS +V D RS +
Sbjct: 1 GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60
>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 = 53.0 bits (128), Expect = 7e-10
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
NLFI +L P S A+L V +D + ++ FG + F
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDF 61
Score = 44.5 bits (106), Expect = 1e-06
Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 5/57 (8%)
Query: 36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
L +L ++ +L +F + Q+ +SK I F
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEF 143
>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 = 51.5 bits (124), Expect = 8e-10
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 26 SSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSK 85
S AA ++ Q L++ L ++ L +F PFG + S ++ +D + RSK
Sbjct: 9 SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68
Query: 86 CFG 88
+G
Sbjct: 69 GYG 71
>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 = 50.7 bits (122), Expect = 1e-09
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 27 SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
S+ + G SG P + +++ +LP ++ DL +F +G V+ + DK +SK
Sbjct: 2 SSGSSGMSGGL--APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59
Query: 87 FG 88
Sbjct: 60 VA 61
>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 = 53.1 bits (128), Expect = 1e-09
Identities = 8/49 (16%), Positives = 19/49 (38%)
Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
L++ + PP ++ ++ + V + + N S+ F I
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDV 166
Score = 50.8 bits (122), Expect = 9e-09
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 42 EGANLFIYHLPPEFSDAD-LASMFGPFGTVLSAKVFID-KQNNRSKCFGTIIF 92
EG + I +L E D + L F FG++ + K+++ + C ++F
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261
Score = 46.9 bits (112), Expect = 2e-07
Identities = 7/47 (14%), Positives = 16/47 (34%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
E + + +LP ++ + F G ++ V + N
Sbjct: 39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFAR 85
>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 = 50.4 bits (121), Expect = 2e-09
Identities = 15/57 (26%), Positives = 23/57 (40%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG EG +FI +L + + L + FG + +V + SK
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60
>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 = 50.4 bits (121), Expect = 2e-09
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
LFI L E ++ L ++FG G + + D+ ++S+ F I F
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITF 55
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 50.9 bits (122), Expect = 2e-09
Identities = 14/72 (19%), Positives = 28/72 (38%)
Query: 17 SPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVF 76
+ + + GS G + L++ L E D L + F PFG + ++
Sbjct: 37 TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP 96
Query: 77 IDKQNNRSKCFG 88
+D + + + F
Sbjct: 97 LDYETEKHRGFA 108
>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 = 50.5 bits (121), Expect = 3e-09
Identities = 13/73 (17%), Positives = 28/73 (38%)
Query: 16 MSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
+++G G + L ++ L ++ DL +F +G + +
Sbjct: 19 SHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 78
Query: 76 FIDKQNNRSKCFG 88
D+Q+ RS+ F
Sbjct: 79 VYDQQSRRSRGFA 91
>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 = 49.1 bits (118), Expect = 4e-09
Identities = 11/44 (25%), Positives = 23/44 (52%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
N+++ +L + + +F FG V + K+ D++ + K FG
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFG 46
>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 = 50.6 bits (121), Expect = 5e-09
Identities = 10/48 (20%), Positives = 23/48 (47%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
EG LF+ + E + ++ F +G + + + +D++ SK +
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 117
>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 = 48.7 bits (117), Expect = 7e-09
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG +G + +F+ +P + +L F FG V + D + R + FG I
Sbjct: 1 GSSGS--SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFIT 58
Query: 92 F 92
F
Sbjct: 59 F 59
>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 = 50.4 bits (121), Expect = 7e-09
Identities = 12/64 (18%), Positives = 22/64 (34%)
Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
+ + V + LFI LP +D + + FG + + + D S
Sbjct: 96 ENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS 155
Query: 85 KCFG 88
K +
Sbjct: 156 KGYA 159
Score = 40.8 bits (96), Expect = 3e-05
Identities = 7/48 (14%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLS-----AKVFIDKQNNRSKCFG 88
L++ ++P ++ + F + + Q N+ K F
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFA 54
>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 = 50.3 bits (121), Expect = 7e-09
Identities = 12/48 (25%), Positives = 19/48 (39%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
P LFI LP +D + + FG + + + D SK +
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 139
Score = 38.7 bits (91), Expect = 1e-04
Identities = 7/53 (13%), Positives = 17/53 (32%), Gaps = 5/53 (9%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLS-----AKVFIDKQNNRSKCFG 88
L++ ++P ++ + F + + Q N+ K F
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFA 54
>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 = 48.3 bits (116), Expect = 8e-09
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ L++ L ++ L +F PFG + + + D RSK +G
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYG 50
>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 = 48.8 bits (117), Expect = 8e-09
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 23 GLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN 82
G + S+ GS +F+ LP +DA L F FG + A V D+Q
Sbjct: 1 GSSGSSGMHGSQK----DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTG 56
Query: 83 RSKCFGTIIF 92
+S+ +G +
Sbjct: 57 KSRGYGFVTM 66
>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 = 48.6 bits (116), Expect = 1e-08
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 8/75 (10%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--------AKVFIDKQ 80
+ GSSG + + +++ L + DLA F G V +++DK+
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 81 NNRSKCFGTIIFMRK 95
+ K T+ +
Sbjct: 61 TGKPKGDATVSYEDP 75
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 48.4 bits (116), Expect = 1e-08
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 35 GKQLTGPEGANLFIYHLPPEFSDADLASMFG-PFGTVLSAKVFIDKQNNRSKCFG 88
G + +LF+ L P+ D L F + + KV +D Q SK +G
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYG 54
>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 = 48.0 bits (115), Expect = 1e-08
Identities = 9/45 (20%), Positives = 22/45 (48%)
Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+++ +P + ++ + + G V++ K+ D Q RSK +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYA 47
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 48.6 bits (116), Expect = 2e-08
Identities = 13/85 (15%), Positives = 28/85 (32%)
Query: 8 AAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPF 67
+ + G+ + G ++ +L + +L S L +F +
Sbjct: 12 SGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY 71
Query: 68 GTVLSAKVFIDKQNNRSKCFGTIIF 92
G V + D+ S+ F + F
Sbjct: 72 GRVGDVYIPRDRYTKESRGFAFVRF 96
>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 = 47.6 bits (114), Expect = 2e-08
Identities = 13/60 (21%), Positives = 28/60 (46%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG + A +++ L + S+ L +F G V++ + D+ + + +G
Sbjct: 1 GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 47.4 bits (113), Expect = 2e-08
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 3/57 (5%)
Query: 32 GSSGKQLTGPE---GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSK 85
GSSG + P+ L I ++PP L S+ +G V S +
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVV 57
>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 = 47.6 bits (114), Expect = 2e-08
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 39 TGPEGA----NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ PEG +F+ + + ++ S F +G+V K+ D+ SK +G + F
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>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 = 47.6 bits (114), Expect = 2e-08
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFG 88
GSSG + +FI +L PE + L F FG +L K+ D SK +
Sbjct: 1 GSSGS-------SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYA 51
>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 = 47.6 bits (114), Expect = 2e-08
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK---QNNRSKCFG 88
+ LFI +L ++ L +F G + S + K S FG
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFG 53
>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 = 47.6 bits (114), Expect = 2e-08
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
NLFI +L P S A+L V +D + ++ FG
Sbjct: 15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFG 61
>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 = 47.2 bits (113), Expect = 3e-08
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 5/61 (8%)
Query: 32 GSSGKQLTGP----EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
GSSG P +F+ +L + L +F G + + D+ + K F
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSF 59
Query: 88 G 88
G
Sbjct: 60 G 60
>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 = 46.8 bits (112), Expect = 3e-08
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
LF+ +L S+ DL +F +G + ID + K F + FM
Sbjct: 6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM 58
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 48.0 bits (114), Expect = 3e-08
Identities = 9/69 (13%), Positives = 23/69 (33%), Gaps = 2/69 (2%)
Query: 26 SSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGT--VLSAKVFIDKQNNR 83
++ A +++ +D L + G V+ K ++ N +
Sbjct: 38 NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ 97
Query: 84 SKCFGTIIF 92
SK + ++
Sbjct: 98 SKGYAEVVV 106
>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 = 48.3 bits (116), Expect = 4e-08
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
E +FI L + ++ +L FG +GTV K+ D RS+ FG + F
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF 52
Score = 46.8 bits (112), Expect = 1e-07
Identities = 11/52 (21%), Positives = 27/52 (51%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ +F+ + P+ + F +GT++ A++ +DK +S+ FG + +
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
>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 = 46.4 bits (111), Expect = 4e-08
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGT--VLSAKVFIDKQNNRSKCFG 88
L+I +L +D DL G +L K F ++ N +SK F
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 48
>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 = 47.4 bits (113), Expect = 4e-08
Identities = 10/48 (20%), Positives = 23/48 (47%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
EG LF+ + E ++ D+ F +G + + + +D++ K +
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67
>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 = 46.8 bits (112), Expect = 5e-08
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 32 GSSGKQLTGPEGAN----LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
GSSG GA+ LF+ L + L S F +G V+ + DK N+S+ F
Sbjct: 1 GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60
Query: 88 GTIIF 92
G + F
Sbjct: 61 GFVKF 65
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 46.5 bits (111), Expect = 5e-08
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 29 AAVGSSG--KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
+ GSSG + T E LFI LP + +L + GTV ++ ++ + K
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59
Query: 87 FG 88
Sbjct: 60 LA 61
>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 = 46.5 bits (111), Expect = 5e-08
Identities = 21/61 (34%), Positives = 32/61 (52%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG + + ++L + LP + ++ DL F FG VL +V D + SK FG +
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 92 F 92
F
Sbjct: 64 F 64
>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 = 46.5 bits (111), Expect = 6e-08
Identities = 10/48 (20%), Positives = 23/48 (47%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
EG LF+ + E + ++ F +G + + + +D++ SK +
Sbjct: 24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 46.5 bits (111), Expect = 6e-08
Identities = 10/48 (20%), Positives = 23/48 (47%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
EG LF+ + E ++ D+ F +G + + + +D++ K +
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68
>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 = 48.1 bits (115), Expect = 6e-08
Identities = 17/52 (32%), Positives = 24/52 (46%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ LFI L E +D L S F +GT+ V D RS+ FG + +
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Score = 44.2 bits (105), Expect = 1e-06
Identities = 7/47 (14%), Positives = 21/47 (44%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+F+ + + + L F +G + ++ D+ + + + F + F
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 45.6 bits (109), Expect = 8e-08
Identities = 11/48 (22%), Positives = 21/48 (43%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
L++ L E D L + F PFG + ++ +D + + + F
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 52
>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 = 46.1 bits (110), Expect = 8e-08
Identities = 14/48 (29%), Positives = 27/48 (56%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
GSSG + T + + LF+ +LPP+ ++ ++ +F +G + DK
Sbjct: 4 GSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51
>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 = 46.1 bits (110), Expect = 9e-08
Identities = 10/61 (16%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK-QNNRSKCF 87
+ GSSG+ + + + ++P + + ++ +F FG + + ++ + F
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 88 G 88
G
Sbjct: 61 G 61
>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 = 47.1 bits (112), Expect = 9e-08
Identities = 10/47 (21%), Positives = 18/47 (38%)
Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+L + +L S L +F +G V + D+ S+ F
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 115
>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 = 45.7 bits (109), Expect = 1e-07
Identities = 16/47 (34%), Positives = 21/47 (44%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+FI L + + L FG FG V V D RS+ FG + F
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 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 = 47.4 bits (112), Expect = 1e-07
Identities = 7/61 (11%), Positives = 18/61 (29%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
+ K L ++ P E ++ + + G V + + G +
Sbjct: 112 EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLE 171
Query: 92 F 92
+
Sbjct: 172 W 172
Score = 41.2 bits (96), Expect = 2e-05
Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 1/52 (1%)
Query: 40 GPEGANLFIYHLPPEFSDAD-LASMFGPFGTVLSAKVFIDKQNNRSKCFGTI 90
G + L +Y L + D + ++F +G V K K
Sbjct: 1 GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADG 52
>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 = 45.7 bits (109), Expect = 1e-07
Identities = 13/56 (23%), Positives = 25/56 (44%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
GSSG + L++ +L + ++ + +F G S K+ + +N CF
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF 59
>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 = 45.4 bits (108), Expect = 1e-07
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 35 GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIF 92
G + A+L++ L P + ++ F G TV+S K+ ++ + + F
Sbjct: 1 GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF 59
>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 = 45.2 bits (108), Expect = 1e-07
Identities = 7/53 (13%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN-NRSKCFGTIIF 92
+ + I L + + +F +G + + +++ + + SK + + F
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF 54
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 45.2 bits (107), Expect = 2e-07
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
+ GSSG ++ G L I LP E ++ ++ ++ PFG V + + K
Sbjct: 1 GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK 51
>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 = 44.9 bits (107), Expect = 3e-07
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 32 GSSGKQLTGPE---GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG +GP+ L + +L S L +F +G V + + + F
Sbjct: 1 GSSGS--SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58
Query: 89 TIIF 92
+ F
Sbjct: 59 FVRF 62
>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 = 44.6 bits (106), Expect = 3e-07
Identities = 11/45 (24%), Positives = 26/45 (57%)
Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
++F+ ++P E ++ L +F G V+S ++ D++ + K +G
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYG 53
>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 = 44.1 bits (105), Expect = 3e-07
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+F+ L + S DL F FG V+ + +D RS+ FG I+F
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60
>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 = 43.6 bits (104), Expect = 4e-07
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+F+ L P+ + + FG FG V S ++ +D + N+ + F I F
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
>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 = 44.2 bits (105), Expect = 4e-07
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG LF+ L + ++ L F + A++ D++ SK FG
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57
>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 = 44.2 bits (105), Expect = 5e-07
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 26 SSNAAVGSSGKQLTGPEGAN---LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN 82
SS ++ S G + GP G N +++ +LPP+ D+ +F +G + + K
Sbjct: 2 SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRR 58
Query: 83 RSKCFGTIIF 92
F + F
Sbjct: 59 GGPPFAFVEF 68
>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 = 44.1 bits (104), Expect = 5e-07
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 7/69 (10%)
Query: 16 MSPTA-----LSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTV 70
M + SGL + +G S + G + I LP + ++ ++ S+ PFG V
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMGDS--RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV 58
Query: 71 LSAKVFIDK 79
+ + K
Sbjct: 59 TNLLMLKGK 67
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 43.1 bits (102), Expect = 8e-07
Identities = 6/50 (12%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFI--DKQNNRSKCFG 88
+ + ++ P + + P+ ++ + + DKQ +++ F
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFA 56
>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 = 43.6 bits (103), Expect = 8e-07
Identities = 12/49 (24%), Positives = 18/49 (36%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ 80
GSSG + + L +ADL FGT+ + K+
Sbjct: 4 GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR 52
>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 = 43.5 bits (103), Expect = 8e-07
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
+ P+ ++ + +D + F PFG ++ +VF +K
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61
>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 = 43.5 bits (103), Expect = 1e-06
Identities = 8/48 (16%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
L+I +LP + + ++ +FG +G + +V ++ +++
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVY 54
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 42.5 bits (101), Expect = 1e-06
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+F+ L + D+ F FG V A + DK NR + FG + F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>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 = 43.0 bits (102), Expect = 1e-06
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
LFI L E ++ L + + +G + V D + RS+ FG + F
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
>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 = 1e-06
Identities = 13/49 (26%), Positives = 21/49 (42%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ 80
GSSG L++ L ++ DL + F FG + + V +Q
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ 49
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 42.7 bits (101), Expect = 1e-06
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
+ P +I ++P ++ADL +F FG +L K + +K
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 42.1 bits (100), Expect = 2e-06
Identities = 16/47 (34%), Positives = 21/47 (44%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+FI L + + L FG FG V V D RS+ FG + F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 42.7 bits (101), Expect = 2e-06
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
LF+ P + +++L +FGPFG + K+
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63
>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 = 43.3 bits (102), Expect = 2e-06
Identities = 7/52 (13%), Positives = 21/52 (40%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ L++ +L ++ + +F G + + +DK + F + +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
>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 = 42.3 bits (100), Expect = 2e-06
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG E L + +L ++ L +F + QN +SK +
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYA 56
>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 = 42.3 bits (100), Expect = 2e-06
Identities = 10/73 (13%), Positives = 25/73 (34%), Gaps = 8/73 (10%)
Query: 31 VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSA--------KVFIDKQNN 82
+G + + +F+ L + +A F G + + ++ D++
Sbjct: 1 MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60
Query: 83 RSKCFGTIIFMRK 95
+ K T+ F
Sbjct: 61 KLKGEATVSFDDP 73
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 42.4 bits (100), Expect = 2e-06
Identities = 9/67 (13%), Positives = 23/67 (34%), Gaps = 8/67 (11%)
Query: 37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSA--------KVFIDKQNNRSKCFG 88
+ + +F+ L + +A F G + + ++ D++ + K
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 89 TIIFMRK 95
T+ F
Sbjct: 61 TVSFDDP 67
>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 = 42.4 bits (100), Expect = 3e-06
Identities = 11/72 (15%), Positives = 29/72 (40%)
Query: 22 SGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN 81
+G + S ++ + ++++ ++ + DL + F G++ + DK +
Sbjct: 15 AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74
Query: 82 NRSKCFGTIIFM 93
K + I F
Sbjct: 75 GHPKGYAYIEFA 86
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 41.8 bits (98), Expect = 4e-06
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
+G + I LP + ++ ++ S+ PFG V + + K
Sbjct: 12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 52
>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 = 43.1 bits (101), Expect = 4e-06
Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 7/83 (8%)
Query: 12 GAGTMSPTALSGLASSNAAVGSSGKQ-LTGPEGANLFIYHLPPE-FSDADLASMFGPFGT 69
G+ SGL + +G L G + L + +L PE + L +FG +G
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61
Query: 70 VLSAKVFIDKQNNRSKCFGTIIF 92
V K+ +K K +
Sbjct: 62 VQRVKILFNK-----KENALVQM 79
Score = 41.5 bits (97), Expect = 2e-05
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
GS Q P A L + ++PP S+ DL +F G V+ F Q +R
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF--FQKDRKMAL 193
>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 = 41.7 bits (98), Expect = 6e-06
Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV-----FIDKQNNRSKCFGTIIF 92
G +++ +L + DL +FG + S + R K I
Sbjct: 42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99
>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 = 40.7 bits (96), Expect = 8e-06
Identities = 9/61 (14%), Positives = 20/61 (32%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG P + + ++P S ++ F + + + + +
Sbjct: 4 GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
Query: 92 F 92
F
Sbjct: 64 F 64
>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 = 40.2 bits (95), Expect = 9e-06
Identities = 8/44 (18%), Positives = 20/44 (45%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
++++ ++ + +L + F G+V + DK + K F
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFA 51
>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 = 40.4 bits (95), Expect = 9e-06
Identities = 9/64 (14%), Positives = 21/64 (32%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSG P + + ++P S ++ F + + + +
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 89 TIIF 92
+ F
Sbjct: 61 MVAF 64
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 40.1 bits (94), Expect = 1e-05
Identities = 8/48 (16%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+++I P + + D+ G VL+ ++ + K ++F
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVF 59
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 39.7 bits (93), Expect = 2e-05
Identities = 10/40 (25%), Positives = 13/40 (32%)
Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
P + I L +ADL FG + V K
Sbjct: 18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK 57
>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 = 39.6 bits (93), Expect = 2e-05
Identities = 11/43 (25%), Positives = 16/43 (37%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+F L DL F G V ++ D+ + RSK
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70
>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 = 40.3 bits (94), Expect = 4e-05
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GS Q P A L + ++PP S+ DL +F G V+ F K + I
Sbjct: 109 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQ 164
Query: 92 F 92
Sbjct: 165 M 165
Score = 37.2 bits (86), Expect = 4e-04
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 44 ANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+ L + +L PE + L +FG +G V K+ +K K +
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQM 48
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 38.8 bits (90), Expect = 6e-05
Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNR--SKCFGTIIFMR 94
+F+ LPP+ + ++ + F FG ++ + + K + ++F
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
>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 = 38.0 bits (89), Expect = 6e-05
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
GSSG +G L + ++ P ++ +L + F +G V+ +
Sbjct: 1 GSSGS--SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI 42
>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 = 38.0 bits (89), Expect = 8e-05
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
GSSG + LF+ +L ++ L F FG + K
Sbjct: 1 GSSGSS-GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK 43
>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 = 37.3 bits (87), Expect = 2e-04
Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG + T L++ +L S+ + F +V + + + +
Sbjct: 4 GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVH 57
Query: 92 F 92
F
Sbjct: 58 F 58
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
GSSG +F+ ++ + +L S+F G V+ V
Sbjct: 1 GSSGS---SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV 41
>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 = 37.4 bits (87), Expect = 2e-04
Identities = 10/61 (16%), Positives = 19/61 (31%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG+ I ++P + D+ +A + N + +
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63
Query: 92 F 92
F
Sbjct: 64 F 64
>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 = 37.4 bits (87), Expect = 2e-04
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 22 SGLASSNAAVGSSGKQLTGPE------GANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
SGL + +G + + PE G L++Y + + L F PFG ++ +
Sbjct: 12 SGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM 69
Query: 76 FIDK 79
+
Sbjct: 70 DPPR 73
>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 = 36.8 bits (86), Expect = 2e-04
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
GSSG LFI +LP E ++ ++ S+F +G VL +
Sbjct: 1 GSSG----SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI 40
>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 = 38.3 bits (88), Expect = 3e-04
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 7/56 (12%)
Query: 41 PEGANLFIYHLPPEFSDADLAS----MFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
++I +L + +L +F FG +L V ++ + + +IF
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIF 59
Score = 33.7 bits (76), Expect = 0.010
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN 81
LF+ +LP E ++ L+ +F F ++ + +
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD 245
>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 = 36.6 bits (85), Expect = 3e-04
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 3/64 (4%)
Query: 32 GSSGKQLTGPEGAN---LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG P+ AN + + LP S ++ F V + RS
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 89 TIIF 92
+ F
Sbjct: 61 FVQF 64
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 36.1 bits (84), Expect = 4e-04
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG ++F+ P A L+ F FG V A V +DK F +
Sbjct: 1 GSSGSSGLR----SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVE 51
Query: 92 F 92
Sbjct: 52 M 52
>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 = 36.4 bits (84), Expect = 5e-04
Identities = 7/81 (8%), Positives = 20/81 (24%)
Query: 12 GAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVL 71
+G + + + +G + + LP + ++ F V
Sbjct: 11 SSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP 70
Query: 72 SAKVFIDKQNNRSKCFGTIIF 92
+ + + F
Sbjct: 71 NGITLPVDPEGKITGEAFVQF 91
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 35.6 bits (82), Expect = 8e-04
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
SS ++ S P A++++ +LP + +DL G+V + + Q R
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV---PLRLTWQGPRR 57
Query: 85 KCF 87
+ F
Sbjct: 58 RAF 60
>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 = 34.7 bits (80), Expect = 0.001
Identities = 9/61 (14%), Positives = 23/61 (37%), Gaps = 14/61 (22%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG + + + +LP + + ++ + + ++D R+K +
Sbjct: 1 GSSGS-------SGILVKNLPQDSNCQEVHDLLKDYDLK---YCYVD----RNKRTAFVT 46
Query: 92 F 92
Sbjct: 47 L 47
>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 = 35.0 bits (81), Expect = 0.001
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 19 TALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEF-SDADLASMFGPFGTVLSAKV 75
+ SG++ A + K + +FI +L +D+ ++F +G V V
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60
>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 = 34.5 bits (80), Expect = 0.002
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 39 TGPEGAN-LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+G G N L+I +L P + DL +FG L+ +V +
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYA 47
>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 = 35.2 bits (81), Expect = 0.002
Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 2/73 (2%)
Query: 22 SGLASSNAAVGSSGKQLTGPEGAN--LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
S +S + G + P A +++ LP E + + F V +
Sbjct: 2 SSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG 61
Query: 80 QNNRSKCFGTIIF 92
N ++ G + F
Sbjct: 62 PNGKATGEGFVEF 74
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 34.3 bits (79), Expect = 0.002
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 8/61 (13%)
Query: 40 GPEGANLFIY--------HLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GP G++ +I L S+F G V++ + ID+ ++K F +
Sbjct: 1 GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60
Query: 92 F 92
Sbjct: 61 C 61
>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 = 34.4 bits (79), Expect = 0.002
Identities = 17/64 (26%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 32 GSSGKQLTGP---EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
GSSG P + + LPP S DL G V A V+ G
Sbjct: 1 GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTG 53
Query: 89 TIIF 92
+ F
Sbjct: 54 VVEF 57
>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 = 34.1 bits (79), Expect = 0.002
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
L++ L P S A LA F FG++ +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
>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 = 34.5 bits (79), Expect = 0.002
Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 6/56 (10%)
Query: 46 LFIYHLPPEFSDADL---ASMFGPFGTVLSAKVFIDKQNNRSK---CFGTIIFMRK 95
+F+ L +D ++ FG FG + + S+ + ++R
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 34.5 bits (79), Expect = 0.003
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
P +++ +L + +L FG +G + S V F + F
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPGFAFVEF 117
>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 = 34.0 bits (78), Expect = 0.004
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 7/50 (14%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
+ + LPP S DL G V A V+ G + F+RK
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRK 61
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 33.4 bits (77), Expect = 0.004
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
+ GSSGK+L ++ +LP D+ ++F + S ++ DK ++ K F
Sbjct: 1 GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59
>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 = 33.4 bits (77), Expect = 0.004
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 5/52 (9%)
Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
L +L ++ +L +F + + Q+ +SK I F
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEF 60
>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 = 33.0 bits (76), Expect = 0.005
Identities = 7/47 (14%), Positives = 18/47 (38%), Gaps = 5/47 (10%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+F+ + ++ +L F +G V+ + + F + F
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTF 49
>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 = 33.2 bits (76), Expect = 0.006
Identities = 7/49 (14%), Positives = 16/49 (32%), Gaps = 6/49 (12%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMR 94
+ +LP A++ F FG++ + + F+
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLE 55
>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 = 32.6 bits (75), Expect = 0.008
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+F+ + + +L F +G V+ VFI K + F + F
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVD--VFIPK---PFRAFAFVTF 55
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 32.7 bits (75), Expect = 0.010
Identities = 6/48 (12%), Positives = 16/48 (33%), Gaps = 5/48 (10%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+++ +L +L F +G + + + F + F
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEF 44
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 32.5 bits (74), Expect = 0.011
Identities = 11/67 (16%), Positives = 17/67 (25%), Gaps = 3/67 (4%)
Query: 26 SSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSK 85
SS S + + + +LP S DL + F
Sbjct: 11 SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFD 67
Query: 86 CFGTIIF 92
G + F
Sbjct: 68 GTGALEF 74
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 32.6 bits (74), Expect = 0.012
Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 8/82 (9%)
Query: 16 MSPTALSGLASSNAAVGSSGKQ-LTGPEGANLFIYHLPPEFSDADLA----SMFGPFGTV 70
M TA + + G + I ++ PE L ++ G +
Sbjct: 1 MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60
Query: 71 LSAKVFIDKQNNRSKCFGTIIF 92
L V ++ + I+F
Sbjct: 61 LDIVV---DLSDDNSGKAYIVF 79
>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 = 31.8 bits (73), Expect = 0.014
Identities = 10/52 (19%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 45 NLFIYHLPPEFSDADL----ASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
++I +L + +L ++F FG +L V ++ + + +IF
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIF 58
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 102
Score = 31.8 bits (72), Expect = 0.018
Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 1/52 (1%)
Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDK 79
+ GSSG++ + I L + PFG + + +
Sbjct: 1 GSSGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI 52
>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 = 31.8 bits (72), Expect = 0.019
Identities = 9/58 (15%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 25 ASSNAAVGSSGKQLTGPEGAN--LFIYHLP-PEFSDADLASMFGPFGTVLSAKVFIDK 79
+S G ++ + + + +LP +SD+ + + P+G + + + K
Sbjct: 5 SSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 32.1 bits (72), Expect = 0.043
Identities = 25/125 (20%), Positives = 40/125 (32%), Gaps = 37/125 (29%)
Query: 4 LVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLF-------IYHLPPEFS 56
L+T T ++ LS +++ ++ LT E +L LP E
Sbjct: 269 LLT----TRFKQVT-DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVL 323
Query: 57 DAD-LA-SMFGPFGTVLSAKVFID-----KQNNRSKCFGTII----------FMRKFFI- 98
+ S+ S + + K N K TII RK F
Sbjct: 324 TTNPRRLSIIA-----ESIRDGLATWDNWKHVNCDK-LTTIIESSLNVLEPAEYRKMFDR 377
Query: 99 LTIRF 103
L++ F
Sbjct: 378 LSV-F 381
>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 = 30.4 bits (69), Expect = 0.065
Identities = 12/61 (19%), Positives = 21/61 (34%), Gaps = 2/61 (3%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
GSSG G + + LP ++ D+ + F P + + R +
Sbjct: 4 GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGEADVE 61
Query: 92 F 92
F
Sbjct: 62 F 62
>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 = 30.1 bits (68), Expect = 0.074
Identities = 6/43 (13%), Positives = 13/43 (30%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
LFI +P ++ + + ++ K G
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRG 53
>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 = 29.3 bits (66), Expect = 0.11
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 40 GPEGAN--LFIYHLPPEFSDADLASMFGPFG-----TVLSAKVFIDKQNNRSKCFGTIIF 92
GP G+ L++ ++P ++ + F T + Q N+ K F + F
Sbjct: 1 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
Query: 93 M 93
Sbjct: 61 R 61
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 29.1 bits (66), Expect = 0.17
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 41 PEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKV 75
P + LFI +LP + S DL +F P+G ++ +
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 29.8 bits (66), Expect = 0.21
Identities = 7/36 (19%), Positives = 13/36 (36%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ 80
L HL P ++ + +F G + + K
Sbjct: 145 ALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKN 180
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 28.8 bits (64), Expect = 0.33
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 26 SSNAAVGSSGKQLTGPEGA-NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
+++AA +G + G + + +L + L +F FGTVL F +NN+
Sbjct: 10 AASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF--TKNNQF 67
Query: 85 KCF 87
+
Sbjct: 68 QAL 70
>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 = 28.5 bits (63), Expect = 0.39
Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 2/86 (2%)
Query: 2 QNLVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLA 61
+ + A A + LA+S AAV + + + +L + L
Sbjct: 5 HHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLH 64
Query: 62 SMFGPFGTVLSAKVFIDKQNNRSKCF 87
+F FGTVL F +NN+ +
Sbjct: 65 QIFSKFGTVLKIITF--TKNNQFQAL 88
>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 = 28.7 bits (64), Expect = 0.40
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 2/61 (3%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
G S + G + + LP + ++ D+ + F P V + R +
Sbjct: 35 GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV--RVHIEIGPDGRVTGEADVE 92
Query: 92 F 92
F
Sbjct: 93 F 93
>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 = 28.3 bits (62), Expect = 0.63
Identities = 8/48 (16%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
+++I P + + D+ G VL+ ++ + K ++F
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVF 157
>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 = 27.7 bits (61), Expect = 0.85
Identities = 13/68 (19%), Positives = 19/68 (27%), Gaps = 2/68 (2%)
Query: 27 SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV--FIDKQNNRS 84
GS G EG + + LP S D+ + A FI + R
Sbjct: 28 QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQ 87
Query: 85 KCFGTIIF 92
+
Sbjct: 88 SGEAFVEL 95
>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 = 27.2 bits (60), Expect = 1.1
Identities = 6/29 (20%), Positives = 10/29 (34%)
Query: 51 LPPEFSDADLASMFGPFGTVLSAKVFIDK 79
L S L + G V + + +K
Sbjct: 35 LGNGVSRNQLLPVLEKCGLVDALLMPPNK 63
>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, PARN, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*
Length = 100
Score = 27.0 bits (59), Expect = 1.1
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTV 70
S G L P+ ++ P E+ +DL +F FG +
Sbjct: 6 SGGPDLQ-PKRDHVLHVTFPKEWKTSDLYQLFSAFGNI 42
>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 = 26.8 bits (60), Expect = 1.2
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN-NRSKCFG 88
F+ +LP + ++ + F + + ++ + N R K FG
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 64
>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP,
M7GTP, RNA recognition motif, RRM, cytoplasm,
exonuclease, hydrolase, magnesium; HET: MGP; 2.10A
{Homo sapiens}
Length = 101
Score = 26.5 bits (58), Expect = 1.5
Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 48 IYHL--PPEFSDADLASMFGPFGTV 70
+ H+ P E+ +DL +F FG +
Sbjct: 8 VLHVTFPKEWKTSDLYQLFSAFGNI 32
>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 = 26.5 bits (59), Expect = 1.6
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 40 GPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKV 75
+ LFI +LP + S DL +F P+G ++ +
Sbjct: 19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>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 = 26.1 bits (58), Expect = 2.2
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN-NRSKCFG 88
F+ +LP + ++ + F + + ++ + N R K FG
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 60
>2vov_A MOPE, surface-associated protein; metal-binding protein, oxidized
tryptophan, methanotroph bacterium, kunurenine, copper
binding; HET: KYN; 1.35A {Methylococcus capsulatus} PDB:
2vox_A* 2vow_A
Length = 336
Score = 26.3 bits (57), Expect = 3.3
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 16 MSPTALSGLASSNAAVGSSGKQLTGPEGANLFIY 49
M PTA GLA ++ G+ K +T P+ +Y
Sbjct: 262 MHPTAFKGLALNDGTAGAFTKSITLPKTGYYMLY 295
>1ta9_A Glycerol dehydrogenase; oxidoredu; 1.90A {Schizosaccharomyces
pombe}
Length = 450
Score = 25.2 bits (55), Expect = 8.7
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 15 TMSPTALSGLASSNAAVGS 33
+ T +SGL N + +
Sbjct: 295 VEANTLMSGLGFENGGLAA 313
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
0.322 0.136 0.392
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: 1,854,324
Number of extensions: 100185
Number of successful extensions: 404
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 190
Length of query: 128
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 45
Effective length of database: 4,384,350
Effective search space: 197295750
Effective search space used: 197295750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.4 bits)