RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6962
(88 letters)
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dgq_A
Length = 106
Score = 78.5 bits (194), Expect = 6e-21
Identities = 26/55 (47%), Positives = 37/55 (67%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S D D IK+F+GQIPR++DE DL +F E+G++Y + VL+D+ TG KG
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG 56
>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 = 64.2 bits (157), Expect = 2e-15
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S E K+FVG + + E D+ ++F +G + VLR G SKG
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKG 57
>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 = 65.3 bits (160), Expect = 4e-15
Identities = 28/47 (59%), Positives = 34/47 (72%), Gaps = 2/47 (4%)
Query: 27 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG--QSKG 71
D IKMFVGQ+PR+ E DL ++F +YG VY INVLRD+ QSKG
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG 48
Score = 56.5 bits (137), Expect = 8e-12
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 1 MNN-RINPLMFSLVCFRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNIN 59
++N ++ P M + + + + K+F+G I + E D+ MFS +G++
Sbjct: 67 LHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECR 126
Query: 60 VLRDKVTGQSKG 71
+LR G S+G
Sbjct: 127 ILRGP-DGLSRG 137
>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 = 63.4 bits (155), Expect = 2e-14
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ V +P++M + + +F G + + ++RDK+TGQS G
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG 45
Score = 58.7 bits (143), Expect = 1e-12
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + P ++V +P++M + +L ++FS+YGR+ +L D+VTG S+G
Sbjct: 77 SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG 131
>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 = 62.6 bits (153), Expect = 3e-14
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ V +P+ M + +L +F G + ++RD TG S G
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG 46
Score = 59.9 bits (146), Expect = 3e-13
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P ++V +PR++ + L +F +YG + N+LRDK+TG+ +G
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG 132
>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 = 60.7 bits (148), Expect = 4e-14
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + P ++V +P S+ DL ++FS+YG+V + +++DK T +SKG
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59
>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 = 58.3 bits (142), Expect = 3e-13
Identities = 10/47 (21%), Positives = 21/47 (44%)
Query: 25 DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+++ + + DL K+ YG++ + + DK T + KG
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG 48
>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 = 59.3 bits (144), Expect = 3e-13
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + D +F Q+ + DL FS G+V ++ ++ D+ + +SKG
Sbjct: 13 EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
>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 = 59.0 bits (143), Expect = 4e-13
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 1 MNNRINPLMFSLVCFRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINV 60
++++ ++ + +S E+ + D ++VG + DL FS G + I +
Sbjct: 9 THSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITI 68
Query: 61 LRDKVTGQSKG 71
L DK +G KG
Sbjct: 69 LCDKFSGHPKG 79
>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 = 58.0 bits (141), Expect = 6e-13
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 24 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
D +FVG IP E L +FSE G V + ++ D+ TG+ KG
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG 51
>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 = 57.6 bits (140), Expect = 9e-13
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ +Q + D +++ +P SMDE +L M +G+V + +LRD +G S+G
Sbjct: 12 GVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRG 67
>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 = 57.2 bits (139), Expect = 1e-12
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P + D + V + E DL ++F +G + I + +DK TGQSKG
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG 58
>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 = 56.9 bits (138), Expect = 1e-12
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+++G IP E + + S G V N+ ++ D TG+SKG
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG 45
>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 = 56.5 bits (137), Expect = 2e-12
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S S D + V + L ++F +YGRV ++ + R+ T +G
Sbjct: 2 SSGSSGPDVDGMI-TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG 56
>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 = 56.7 bits (137), Expect = 4e-12
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + V IP ++DE L ++F YG + ++ ++ D+ T QS+G
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85
>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 = 55.8 bits (135), Expect = 5e-12
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q + +FV I E ++ + F +YG + NI++ D+ TG SKG
Sbjct: 21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 69
>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 = 55.8 bits (135), Expect = 5e-12
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S LP +F+ + +E L ++ ++G + + V+ T SKG
Sbjct: 5 SSGLPSDVTEGK-TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG 58
>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 = 55.3 bits (134), Expect = 5e-12
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 26 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++VG + ++ E L +F +G++ NI +++D TG+SKG
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKG 48
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 57.7 bits (140), Expect = 5e-12
Identities = 12/51 (23%), Positives = 26/51 (50%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ +++VG I + E + + F+ +G + +I++ D VT + KG
Sbjct: 21 RQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG 71
Score = 51.5 bits (124), Expect = 9e-10
Identities = 11/51 (21%), Positives = 27/51 (52%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ F +++V + + + + D+ +F +G++ + + RD TG+ KG
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG 168
>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 = 55.4 bits (134), Expect = 6e-12
Identities = 14/53 (26%), Positives = 31/53 (58%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ ++ ++++VG + ++ E L +F +GR+ +I ++ D TG+SKG
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG 69
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 55.3 bits (134), Expect = 6e-12
Identities = 16/49 (32%), Positives = 25/49 (51%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q + +FV + E D+ F+EYG + NI++ D+ TG KG
Sbjct: 18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66
>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 = 54.4 bits (132), Expect = 9e-12
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 24 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ D ++VG + +L F G V + +L DK +G KG
Sbjct: 2 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG 49
>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 = 54.5 bits (132), Expect = 1e-11
Identities = 12/56 (21%), Positives = 27/56 (48%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + V + E DL ++FS+YG + +++++ D+ + +S+G
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 58
>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 = 55.5 bits (134), Expect = 1e-11
Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
R + PDP+ + V + E DL ++FS+YG + +++++ D+ + +S+G
Sbjct: 35 RHVGNRANPDPNC-CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 89
>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 = 56.0 bits (135), Expect = 1e-11
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q + +FV I E ++ + F +YG + NI++ D+ TG SKG
Sbjct: 67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 115
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 54.6 bits (132), Expect = 1e-11
Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + K+F+ +P S + +L ++ +G V ++ ++ ++ G+ KG
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59
>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 = 54.6 bits (132), Expect = 2e-11
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ ++ P+ +F+ +P+ + DL +MF +G V + V DK T SK
Sbjct: 14 GAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 54.7 bits (132), Expect = 2e-11
Identities = 14/57 (24%), Positives = 25/57 (43%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + + P+ +F+ +P+ + DL F +G V + V DK T SK
Sbjct: 27 AAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 54.7 bits (132), Expect = 2e-11
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P + + V + L ++F +YGRV ++ + RD+ T +S+G
Sbjct: 35 MSYGRPPPDVEGMT-SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 90
>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 = 54.3 bits (131), Expect = 2e-11
Identities = 16/49 (32%), Positives = 25/49 (51%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q + +FV + E D+ F+EYG + NI++ D+ TG KG
Sbjct: 17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65
>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 = 54.3 bits (131), Expect = 2e-11
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + F +FVG + + D+ F+ +GR+ + V++D TG+SKG
Sbjct: 5 SSGQKKDTSNHF-HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG 58
>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 = 53.8 bits (130), Expect = 3e-11
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 22 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++FV + + E DL K+FS YG + ++ D +T + KG
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG 51
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 54.8 bits (133), Expect = 3e-11
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
R++ EQ K+FVG I + + + FS++G + + ++ DK TGQS+G
Sbjct: 77 RAIPRDEQDKTG--KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRG 130
Score = 53.7 bits (130), Expect = 9e-11
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
KMF+G + E +L + F +YG V ++ +++D TG+S+G
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRG 46
>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 = 53.4 bits (129), Expect = 4e-11
Identities = 15/42 (35%), Positives = 29/42 (69%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
K+FVG + +E L ++FS+YG++ + V++D+ T +S+G
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG 55
>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 = 53.4 bits (129), Expect = 4e-11
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S P ++VG + + E L ++F + G V N ++ +D+VTGQ +G
Sbjct: 6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG 58
>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 = 52.9 bits (128), Expect = 4e-11
Identities = 12/42 (28%), Positives = 27/42 (64%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++VG + S + ++FS++G+V+N+ ++ D+ T + KG
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG 44
>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 = 52.6 bits (127), Expect = 5e-11
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 24 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
F +FVG + + A + F+ +GR+ + V++D TG+SKG
Sbjct: 3 LGSHF-HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG 49
>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 = 54.1 bits (130), Expect = 6e-11
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + V + L ++F +YGRV ++ + RD+ T +S+G
Sbjct: 59 HHHHHHMDVEGMT-SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 113
>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 = 55.4 bits (134), Expect = 7e-11
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 26 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P + V +P S+ + ++ +G + ++ + TGQSKG
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138
Score = 39.6 bits (93), Expect = 3e-05
Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 32 FVGQIPRSMDEAD-LTKMFSEYGRVYNINVLRDKVTGQSKG 71
V ++P ++ D L + S + + GQ KG
Sbjct: 188 CVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKG 227
Score = 36.9 bits (86), Expect = 2e-04
Identities = 8/57 (14%), Positives = 20/57 (35%), Gaps = 8/57 (14%)
Query: 16 RSMSLPEQPDP-DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
R + + K+ + +P + ++ + S+Y L+ + KG
Sbjct: 9 RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKG 58
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 52.8 bits (127), Expect = 8e-11
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++ ++ E L M +YG V + +L T + G
Sbjct: 10 TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG 49
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 53.2 bits (128), Expect = 9e-11
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++VG + +D+ L F +G + +I + D T + +G
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 106
>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 = 52.3 bits (126), Expect = 1e-10
Identities = 20/56 (35%), Positives = 29/56 (51%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S Q D F K+FVG +P +A L K F +G + V+ D+ TG+S+G
Sbjct: 5 SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
>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 = 51.4 bits (124), Expect = 1e-10
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++VG + +D+ L F +G + +I + D T + +G
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 50
>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 = 51.8 bits (125), Expect = 1e-10
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++VG + +D+ L F +G + +I + D T + +G
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 55
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 53.5 bits (129), Expect = 1e-10
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 18 MSLPEQP--DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
MS E P K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Score = 52.7 bits (127), Expect = 4e-10
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 16 RSMSLPEQPDPDFI----KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
R++S + P K+FVG I +E L F +YG++ I ++ D+ +G+ +G
Sbjct: 88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147
>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 = 53.0 bits (128), Expect = 2e-10
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
QP P K+F+G +P +++ + ++ + +G + N+++D TG SKG
Sbjct: 87 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG 137
Score = 43.0 bits (102), Expect = 1e-06
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNI-----NVLRDKVTGQSKG 71
+++VG IP + E + F+ R+ + N + Q K
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN 52
>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 = 51.1 bits (123), Expect = 2e-10
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
SLPE +FVG I MDE ++ F+ YG V + ++ D+ TG SKG
Sbjct: 1 SLPEGK-IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKG 51
>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 = 50.7 bits (122), Expect = 4e-10
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
K+FVG IP + E +L + F ++G V + ++ D + +G
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRG 53
>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 = 52.2 bits (126), Expect = 4e-10
Identities = 9/51 (17%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+F+G + + A+L SE ++ V+ + TG ++
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRK 55
Score = 45.7 bits (109), Expect = 1e-07
Identities = 7/51 (13%), Positives = 18/51 (35%), Gaps = 5/51 (9%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + + ++ E +L ++F + + G+SKG
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKG 137
>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 = 49.8 bits (120), Expect = 4e-10
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
K+FVG + E + + F +G V +I + D T + +G
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG 42
>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 = 50.3 bits (121), Expect = 4e-10
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + + +FVG + + E L ++F + G + + + +D+ G+ K
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKS 58
>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 = 49.8 bits (120), Expect = 5e-10
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+FVG + ++D+ L F ++ + +V+ D TG S+G
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 44
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 49.8 bits (120), Expect = 5e-10
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
K+FVG + + D+ F ++G+V + ++ DK T + +G
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG 42
>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 = 49.8 bits (120), Expect = 5e-10
Identities = 11/47 (23%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 26 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV-TGQSKG 71
K+ +G++ R++ + + ++FS YG++ I++ +++ SKG
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG 48
>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 = 52.3 bits (126), Expect = 6e-10
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P P ++VG + + EA L + FS G + +I V RD +T +S G
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG 58
Score = 43.8 bits (104), Expect = 7e-07
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P +F+ + +S+D L FS +G + + V+ D SKG
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKG 144
>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 = 50.4 bits (121), Expect = 6e-10
Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 22 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK-VTGQSKG 71
K+ V IP ++ ++ ++FS +G + + + + TG +G
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59
>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 = 51.3 bits (123), Expect = 6e-10
Identities = 11/51 (21%), Positives = 23/51 (45%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
E+ ++VG + E + ++FS+ G + I + DK+ + G
Sbjct: 32 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 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 = 50.3 bits (121), Expect = 7e-10
Identities = 17/55 (30%), Positives = 25/55 (45%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S ++ + V +P E DL + FS +G V + V +D TG SKG
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG 58
>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 = 49.9 bits (120), Expect = 7e-10
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ F +F+G + + A+L SE N + D TG ++
Sbjct: 9 VEGSESTTPF-NLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRK 59
>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 = 50.0 bits (120), Expect = 9e-10
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 22 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
KMF+G + + L + F ++G V V+RD +T +S+G
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 68
>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 = 49.1 bits (118), Expect = 1e-09
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + D KMFVG + + DL F+++G V + + D TG+S+G
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRG 54
>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 = 49.6 bits (119), Expect = 1e-09
Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + + + + S E L ++F + + + G+SKG
Sbjct: 3 SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKG 54
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 49.2 bits (118), Expect = 1e-09
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGR--VYNINVLRDKVTGQSKG 71
+ + I + S Y V NI +++DK T Q++G
Sbjct: 4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG 54
>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 = 48.7 bits (117), Expect = 1e-09
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 29 IKMFVGQIPRSMDEADLTKMFSEYG--RVYNINVLRDKVTGQSKG 71
I +++G + + DLT+ G + I ++ GQSKG
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 46
>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 = 2e-09
Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ PD K+F+G +P +++ + ++ + +G + N+++D TG SKG
Sbjct: 103 PGVVSTVVPDSAH-KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG 157
Score = 44.3 bits (105), Expect = 4e-07
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNI-----NVLRDKVTGQSKG 71
+++VG IP + E + F+ R+ + N + Q K
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN 52
>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 = 49.2 bits (118), Expect = 2e-09
Identities = 12/46 (26%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 26 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
K+F+G + R +E L +F ++G + + +++D+ T +S+G
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRG 49
>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 = 50.8 bits (122), Expect = 3e-09
Identities = 12/49 (24%), Positives = 23/49 (46%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ E+ ++FVG +P + E D ++F YG + + RD+
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR 58
Score = 47.0 bits (112), Expect = 6e-08
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ V + + L + FS++G V V+ D G++ G
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATG 138
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 48.5 bits (116), Expect = 3e-09
Identities = 12/56 (21%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
R + + ++ V IP + DL +MF ++G++ ++ ++ ++ SKG
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKG 70
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 49.5 bits (118), Expect = 3e-09
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYG--RVYNINVLRDKVTGQSKG 71
++VG + L ++ G V + ++ GQSKG
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKG 100
>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 = 48.4 bits (116), Expect = 3e-09
Identities = 13/46 (28%), Positives = 26/46 (56%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
S E+ ++FVG +P + E ++ K+F +YG+ + + +DK
Sbjct: 6 SGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51
>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 = 48.4 bits (116), Expect = 4e-09
Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 16 RSMSLPEQP--DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++ L + F K+F+G + E L + ++G++ + V+RD + +S+G
Sbjct: 13 ETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 47.5 bits (114), Expect = 4e-09
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
KMF+G + + L + F ++G V V+RD +T +S+G
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 43
>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 = 48.0 bits (115), Expect = 4e-09
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
F S K+ V + + +AD+ ++F+E+G + V D+ +G+S G
Sbjct: 16 FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLG 71
>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 = 48.0 bits (115), Expect = 4e-09
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 16 RSMSLPEQPD-PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S S ++ + ++V + +D+ L K FS +G + + V+ + G+SKG
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKG 56
>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 = 48.0 bits (115), Expect = 4e-09
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + + K+FVG + S + L FS+YG V + +++DK T QS+G
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG 59
>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 = 48.0 bits (115), Expect = 5e-09
Identities = 9/51 (17%), Positives = 23/51 (45%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQS 69
S + D ++VG + R + E + ++FS+ G + ++ + +
Sbjct: 6 SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP 56
>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 = 47.6 bits (114), Expect = 5e-09
Identities = 7/51 (13%), Positives = 18/51 (35%), Gaps = 5/51 (9%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + + ++ E +L ++F + + G+SKG
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKG 54
>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 = 47.7 bits (114), Expect = 5e-09
Identities = 11/43 (25%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYG-RVYNINVLRDKVTGQSKG 71
+++G + MDE +++ F+ G V ++ ++R+++TG G
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAG 53
>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 = 47.7 bits (114), Expect = 6e-09
Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S + ++ V IP + DL +MF ++G++ ++ ++ ++ SKG
Sbjct: 6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKG 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 = 48.7 bits (117), Expect = 7e-09
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ D +FVG + ++D+ L F ++ + +V+ D TG S+G
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 130
Score = 47.5 bits (114), Expect = 2e-08
Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+VG + +++ E L + F G + NI ++ DK ++
Sbjct: 4 YVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVN 42
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 46.4 bits (111), Expect = 1e-08
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++FV +P L F+E G V ++ + G+SKG
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKG 49
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 46.5 bits (111), Expect = 2e-08
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S E P +VG +P + + D+ +F + + ++ ++RDK T + KG
Sbjct: 3 SGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKG 57
>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 = 46.1 bits (110), Expect = 2e-08
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 3/56 (5%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S P +FV + E L + F R ++ D+ TG SKG
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKG 55
>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 = 46.6 bits (111), Expect = 2e-08
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
F S + K+ V + + +AD+ ++F+E+G + V D+ +G+S G
Sbjct: 22 FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLG 77
>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 = 48.1 bits (115), Expect = 3e-08
Identities = 7/56 (12%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + + + + V +P+S ++ + K F G + +++V ++
Sbjct: 29 KKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFR 82
Score = 44.2 bits (105), Expect = 6e-07
Identities = 5/40 (12%), Positives = 13/40 (32%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++ P S + ++ + + V L S+
Sbjct: 121 WMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 160
Score = 40.0 bits (94), Expect = 2e-05
Identities = 8/44 (18%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 30 KMFVGQIPRSM-DEADLTKMFSEYGRVYNINVLRD-KVTGQSKG 71
++ + + + DE L + F +G + IN+ K +
Sbjct: 212 EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 45.5 bits (108), Expect = 4e-08
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
S S+P++ K+ + IP + L + +YG V + +
Sbjct: 6 SGSVPKRQRI--RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN 58
>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 = 47.5 bits (112), Expect = 4e-08
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q D F +FV ++ E+ L + F YG + I+++ K +G+ +G
Sbjct: 98 QGDA-FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
>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 = 45.4 bits (108), Expect = 5e-08
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV--------YNINVLRDKVTGQSKG 71
D +FV + ++ + F + G + IN+ D+ TG+ KG
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 64
>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 = 47.0 bits (111), Expect = 5e-08
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYG--RVYNINVLRDKVTGQSKG 71
+ ++ I +++G + + DLT+ G + I ++ GQSKG
Sbjct: 56 AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 45.0 bits (107), Expect = 7e-08
Identities = 9/49 (18%), Positives = 23/49 (46%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
M ++ + ++FV P + E++L ++F +G + + +L
Sbjct: 18 GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 66
>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 = 45.0 bits (107), Expect = 9e-08
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q +FV + + L ++FS G V ++L DK G+S+G
Sbjct: 8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRG 57
>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 = 43.7 bits (104), Expect = 1e-07
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
K+FVG + + +L +F GRV +V++D
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 43.9 bits (104), Expect = 2e-07
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+FV PR +D A L++ F +G V ++ + +DK
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK 44
>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 = 44.0 bits (104), Expect = 2e-07
Identities = 7/44 (15%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGR-VYNINVLRD-KVTGQSKG 71
++F+G IP+ ++ + ++ V ++ V +++G
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRG 53
>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 = 43.4 bits (103), Expect = 2e-07
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 26 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ---SKG 71
+F+ + S E L +FS+ G + + + + K S G
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMG 51
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 43.5 bits (103), Expect = 3e-07
Identities = 11/45 (24%), Positives = 19/45 (42%)
Query: 20 LPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ P ++G IP EADL +F +G + + +K
Sbjct: 19 IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 43.2 bits (102), Expect = 4e-07
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 22 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV--------YNINVLRDKVTGQSKG 71
EQ + D +FV + ++ + F + G + IN+ D+ TG+ KG
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 58
>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 = 11/46 (23%), Positives = 22/46 (47%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
S D ++VG + ++ E DL F ++G + I V++ +
Sbjct: 3 SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48
>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 = 42.6 bits (101), Expect = 4e-07
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
K+ VG I + +L F EYG V ++++D
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>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 = 43.2 bits (102), Expect = 5e-07
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV--------YNINVLRDKVTGQSKG 71
D D ++V + S+ DL F + G V I++ DK TG+ KG
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 66
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 43.0 bits (101), Expect = 5e-07
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSK 70
K+FVG +P +DE ++T F +G + + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFP 50
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 42.4 bits (100), Expect = 7e-07
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + + LT +FS+ G+V N+ D+ TG++KG
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKG 55
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 43.3 bits (102), Expect = 8e-07
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
F S + K+ V + + +AD+ ++F+E+G + V D+ +G+S G
Sbjct: 75 FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLG 130
>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 = 42.3 bits (100), Expect = 8e-07
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
Q P ++ G I + + + + FS +G++ I V +K
Sbjct: 18 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43
inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA;
1.65A {Mus musculus}
Length = 89
Score = 41.8 bits (99), Expect = 9e-07
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 18 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
M K+FVG+ M +L + F +YG V ++ + +
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47
>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 = 41.8 bits (99), Expect = 1e-06
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR 62
K+F+G +PR E ++ +F +YG+V ++++
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42
>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 = 42.3 bits (100), Expect = 1e-06
Identities = 9/55 (16%), Positives = 21/55 (38%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
M P +++ + + E DL +F+ + + +TG+ +G
Sbjct: 14 PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG 68
>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 = 41.4 bits (98), Expect = 1e-06
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+FVG+ M E +L + FS+YG V ++ + +
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF 41
>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 = 41.9 bits (99), Expect = 1e-06
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+F+ + +S+D L FS +G + + V+ D SKG
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKG 46
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 41.1 bits (97), Expect = 2e-06
Identities = 9/35 (25%), Positives = 20/35 (57%)
Query: 29 IKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
+K++VG + + +L + FS YG + + + R+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN 35
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 41.3 bits (97), Expect = 2e-06
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+++ P D+ + + G+V NI + R KG
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKG 53
>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 = 41.0 bits (97), Expect = 2e-06
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYN-INVLRDKVTGQSKG 71
+F+G + +DE L FS +G + ++RD TG SKG
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKG 49
>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 = 41.8 bits (98), Expect = 3e-06
Identities = 10/41 (24%), Positives = 22/41 (53%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
P K++VG + + ++ +L + F YG + ++ V R+
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN 108
>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 = 40.3 bits (95), Expect = 3e-06
Identities = 6/42 (14%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
K+++G + ++ DL ++F + G
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSG 45
>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 = 40.0 bits (94), Expect = 6e-06
Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
++ +P + ++ +F +YG + I R T +++G
Sbjct: 12 YIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRG 48
>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 = 39.5 bits (93), Expect = 7e-06
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+VG + + A L + F +G + I+ ++
Sbjct: 21 WVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
>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 = 39.6 bits (93), Expect = 9e-06
Identities = 8/35 (22%), Positives = 21/35 (60%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+++VG +P + D+ +F +YG + +I++ +
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR 58
>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 = 39.2 bits (92), Expect = 1e-05
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
+FV + ++ E L K FS++G++ + L+D
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 39.0 bits (91), Expect = 1e-05
Identities = 12/47 (25%), Positives = 19/47 (40%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR 62
S P + P ++VG +PR +DL + E G V +
Sbjct: 7 GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ 53
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 38.4 bits (90), Expect = 2e-05
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 22 EQPDPDFIKMFVGQIPRSMDEADLTKMFSE-YGRVYNINVLRDKVTGQSKG 71
P++ +FVG + +D+ L + F + Y V+ D+ TG SKG
Sbjct: 4 GSSGPEY-SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKG 52
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 38.2 bits (89), Expect = 3e-05
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ + + EADL + E+G + + V+ K
Sbjct: 25 HIRGLIDGVVEADLVEALQEFGPISYVVVMPKK 57
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 38.3 bits (89), Expect = 3e-05
Identities = 7/33 (21%), Positives = 19/33 (57%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ ++P + E ++ + +G+V N+ +L+ K
Sbjct: 20 HIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 52
>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 = 37.6 bits (88), Expect = 4e-05
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 19 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVT-GQSKG 71
LP+ P P F+G +P + E + + F + + + R+ + KG
Sbjct: 13 RLPKSP-PY--TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG 62
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 37.2 bits (87), Expect = 6e-05
Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 26 PDFIKMFVGQIP-RSMDEADLTKMFSEYGRVYNINVLR 62
P ++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 45
>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 = 37.3 bits (87), Expect = 6e-05
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 24 PDPDFIKMFVGQIP-RSMDEADLTKMFSEYGRVYNINVLR 62
++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>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 = 37.2 bits (87), Expect = 6e-05
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 20 LPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV-TGQSKG 71
LP+ P P F+G +P + E + + F + + + R+ + KG
Sbjct: 10 LPKSP-PY--TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG 58
>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 = 37.6 bits (87), Expect = 7e-05
Identities = 7/33 (21%), Positives = 19/33 (57%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ ++P + E ++ + +G+V N+ +L+ K
Sbjct: 35 HIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 67
>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 = 36.7 bits (85), Expect = 9e-05
Identities = 8/33 (24%), Positives = 19/33 (57%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ ++P + E ++ + +G+V NI +L+ K
Sbjct: 19 HIRKLPGEVTETEVIALGLPFGKVTNILMLKGK 51
>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 = 37.0 bits (86), Expect = 9e-05
Identities = 11/40 (27%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 24 PDPDFIKMFVGQIPRS-MDEADLTKMFSEYGRVYNINVLR 62
P ++F+G + + + ++D+ +FS+YGRV +V +
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK 62
>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 = 36.7 bits (85), Expect = 1e-04
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 67
V + S+ EADL + ++G + + ++ K
Sbjct: 19 HVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQA 54
>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 = 36.7 bits (85), Expect = 1e-04
Identities = 6/36 (16%), Positives = 15/36 (41%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 67
+P A++ + FS +G + + + +T
Sbjct: 14 LAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITA 49
>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 = 37.4 bits (86), Expect = 1e-04
Identities = 5/41 (12%), Positives = 12/41 (29%)
Query: 31 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ P + E + ++ E G +V +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSS 166
Score = 32.4 bits (73), Expect = 0.010
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 32 FVGQI-PRSMDEADLTKMFSEYGRVYNINVLRDK 64
V + M+ + +F YG V + ++ K
Sbjct: 8 MVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK 41
>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 = 36.3 bits (84), Expect = 2e-04
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 16 RSMSLPEQPDPDFI-KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
RS S PE+ P ++V M L FS +G + ++++ +
Sbjct: 26 RSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR 73
>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 = 35.1 bits (81), Expect = 3e-04
Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 67
+ V +P+ + ++ + +Y Y V R+K T
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYDLKY-CYVDRNKRTA 43
>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 = 34.8 bits (80), Expect = 6e-04
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
++ V +P S DL E G V +V RD
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 50
>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 = 33.8 bits (78), Expect = 0.001
Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 2/51 (3%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+P P I V +P ++ ++ F Y + L+ G G
Sbjct: 10 SGKPGPTVI--KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58
>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 = 33.9 bits (78), Expect = 0.001
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 18 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV-YNINVLRDKVTGQSKG 71
S + + + IP S+ + D+ + ++VL D GQ G
Sbjct: 5 SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLG 58
>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 = 33.4 bits (77), Expect = 0.002
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 2/49 (4%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+P P I V +P ++ ++ F Y + L+ G G
Sbjct: 12 KPGPTII--KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58
>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 = 33.6 bits (77), Expect = 0.002
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 63
++ V +P S DL E G V +V RD
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 51
>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 = 33.4 bits (77), Expect = 0.002
Identities = 7/43 (16%), Positives = 14/43 (32%)
Query: 22 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
E ++V + S E + K F+ V + +
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR 51
>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 = 33.0 bits (76), Expect = 0.002
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 17 SMSLPEQPDPDFIK-MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
S S E+ P ++V M L FS +G + ++++ +
Sbjct: 3 SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR 49
>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 = 33.4 bits (76), Expect = 0.002
Identities = 5/33 (15%), Positives = 12/33 (36%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
G + + L + + G V + + +K
Sbjct: 31 ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK 63
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 33.6 bits (76), Expect = 0.004
Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 9/57 (15%)
Query: 17 SMSLPEQPDPDFIKMFVGQIPRSMD---------EADLTKMFSEYGRVYNINVLRDK 64
M ++VG I +++ E+ + +FS G + I + K
Sbjct: 123 DMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK 179
>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 = 32.9 bits (75), Expect = 0.004
Identities = 8/51 (15%), Positives = 17/51 (33%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + + +P + ++ + FS V N L G+ G
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITG 85
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 32.4 bits (74), Expect = 0.005
Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 11/61 (18%)
Query: 20 LPEQPDPDFI---KMFVGQIPRSMDE------ADLTKMFSEYGRVYNINVLRDKVTGQSK 70
L ++P + V +P+ + + K+FS++G++ N + G++K
Sbjct: 4 LKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTK 61
Query: 71 G 71
G
Sbjct: 62 G 62
>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 = 32.9 bits (74), Expect = 0.005
Identities = 10/71 (14%), Positives = 23/71 (32%), Gaps = 1/71 (1%)
Query: 1 MNNRINPLMFSLVCFRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINV 60
++ ++ + D +++ P D+ + + G+V NI +
Sbjct: 82 SEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM 141
Query: 61 LRDKVTGQSKG 71
R KG
Sbjct: 142 RRTL-HKAFKG 151
>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 = 32.1 bits (73), Expect = 0.006
Identities = 7/43 (16%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 32 FVGQIPRSMDEADLTK---MFSEYGRVYNINVLRDKVTGQSKG 71
FV + + + + ++ K F ++G+++ + + S+G
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQG 61
>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 = 32.0 bits (73), Expect = 0.007
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
LP PD ++ V +P S E D+ F RV +++L+D G++ G
Sbjct: 6 SGKPLPINPDDLYV--SVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNG 57
>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 = 32.5 bits (73), Expect = 0.009
Identities = 13/58 (22%), Positives = 32/58 (55%), Gaps = 9/58 (15%)
Query: 18 MSLPEQPDPDFIKMFVGQIPRSMDEADLTK----MFSEYGRVYNINVLRDKVTGQSKG 71
M++PE P+ +++ + + + +L K +FS++G++ +I V R + + +G
Sbjct: 1 MAVPETR-PNHT-IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRG 53
Score = 28.7 bits (63), Expect = 0.21
Identities = 8/64 (12%), Positives = 25/64 (39%)
Query: 1 MNNRINPLMFSLVCFRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINV 60
+ P + + P +P +F+ +P +E L+ +F+++ + +
Sbjct: 180 IPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 239
Query: 61 LRDK 64
+ +
Sbjct: 240 VPGR 243
>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 = 31.3 bits (71), Expect = 0.013
Identities = 6/51 (11%), Positives = 17/51 (33%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
P +++ +P + + F + V + + G++ G
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 68
>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 = 31.8 bits (72), Expect = 0.016
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 31 MFVGQI-PRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ V + P + L +F YG V + +L +K
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 40
Score = 31.0 bits (70), Expect = 0.022
Identities = 12/48 (25%), Positives = 17/48 (35%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ 68
+ P + + IP S+ E DL +FS G V K
Sbjct: 113 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM 160
>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 = 30.5 bits (69), Expect = 0.019
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINV 60
+VG IP + E + F+ R+ +
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQ 38
>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 = 31.5 bits (71), Expect = 0.022
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 18 MSLPEQPDPDFIKMFVGQI-PRSMDEADLTKMFSEYGRVYNINVLRDK 64
+++P + V + P + L +F YG V + +L +K
Sbjct: 24 IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 71
Score = 31.1 bits (70), Expect = 0.027
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 64
+ IP S+ E DL +FS G V K
Sbjct: 155 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187
>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 = 30.7 bits (69), Expect = 0.022
Identities = 8/34 (23%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 32 FVGQIPRS-MDEADLTKMFSEYGRVYNINVLRDK 64
+ +P S ++ + K+ YG++ N ++R K
Sbjct: 29 HLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
>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 = 30.6 bits (69), Expect = 0.032
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 30 KMFVGQIPRSMDEADLTKMFSEYGRV--YNINVLRDKV---TGQSKG 71
+++V + + + E DL +F Y ++ D G+ KG
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKG 93
>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 = 29.9 bits (68), Expect = 0.042
Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 32 FVGQIPRSMDEADLTK----MFSEYGRVYNINVLRDKVTGQSKG 71
++ + + + +L K +FS +G++ +I V R + + +G
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRG 52
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 28.9 bits (65), Expect = 0.061
Identities = 8/30 (26%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 42 EADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + K+FS++G++ N + G++KG
Sbjct: 21 KNVIHKIFSKFGKITNDFYPEE--DGKTKG 48
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 28.6 bits (64), Expect = 0.15
Identities = 8/56 (14%), Positives = 16/56 (28%), Gaps = 4/56 (7%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
R + + P + ++ + +P DL + E T G
Sbjct: 17 RGSHMSKLPAKRY-RITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDG 68
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 27.9 bits (62), Expect = 0.29
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 7/44 (15%)
Query: 32 FVGQIPRSMDEADLTK----MFSEYGRVYNINVLRDKVTGQSKG 71
+ I + + L + S G + +I V + + G
Sbjct: 33 LITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSG 73
>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 = 27.1 bits (60), Expect = 0.37
Identities = 5/34 (14%), Positives = 11/34 (32%), Gaps = 1/34 (2%)
Query: 32 FVGQIPRSM-DEADLTKMFSEYGRVYNINVLRDK 64
+ R L ++ +G + N +L
Sbjct: 19 HIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI 52
>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 = 27.0 bits (59), Expect = 0.70
Identities = 8/54 (14%), Positives = 18/54 (33%)
Query: 15 FRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ 68
+ +++ V + + L ++FS++G V I Q
Sbjct: 33 AVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ 86
>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 = 27.1 bits (59), Expect = 0.81
Identities = 11/75 (14%), Positives = 21/75 (28%), Gaps = 26/75 (34%)
Query: 4 RINPLMFSLVCFRSMSLPEQPD-PDF------------IKMFVGQIPRSMDEADLTKMFS 50
NP S++ + S+ + D I+ + ++ A+ KMF
Sbjct: 324 TTNPRRLSII---AESIRDGLATWDNWKHVNCDKLTTIIESSL----NVLEPAEYRKMFD 376
Query: 51 EYGRVYNINVLRDKV 65
V
Sbjct: 377 RLS------VFPPSA 385
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 26.5 bits (58), Expect = 0.88
Identities = 8/36 (22%), Positives = 14/36 (38%)
Query: 33 VGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ 68
V + + L ++FS++G V I Q
Sbjct: 33 VENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ 68
>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 = 26.3 bits (58), Expect = 1.1
Identities = 7/51 (13%), Positives = 15/51 (29%), Gaps = 2/51 (3%)
Query: 21 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ + +P E D+ FS +++ G+ G
Sbjct: 39 FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTG 87
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 25.9 bits (56), Expect = 1.1
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 40 MDEADLTKMFSEYGRVYNINVLRDK 64
+ L ++ +YG V N+ + K
Sbjct: 29 YSKDVLLRLLQKYGEVLNLVLSSKK 53
>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 = 26.1 bits (57), Expect = 1.4
Identities = 7/58 (12%), Positives = 16/58 (27%), Gaps = 2/58 (3%)
Query: 16 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR--DKVTGQSKG 71
R + + + + +P S D+ S+ + G+ G
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSG 89
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 25.7 bits (56), Expect = 1.5
Identities = 6/40 (15%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 29 IKMFVGQIPRSMDEAD----LTKMFSEYGRVYNINVLRDK 64
+ V I + + L + F+ +G+V ++ +
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT 49
>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 = 25.0 bits (55), Expect = 2.1
Identities = 6/40 (15%), Positives = 16/40 (40%), Gaps = 2/40 (5%)
Query: 32 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
+ P ++ E ++ + + I ++R+ G G
Sbjct: 14 KLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTG 51
>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 = 24.7 bits (54), Expect = 3.4
Identities = 8/49 (16%), Positives = 16/49 (32%), Gaps = 3/49 (6%)
Query: 23 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 71
Q + + +P E D+ FS +++ G+ G
Sbjct: 11 QSTTGHC-VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTG 56
>2hyv_A Annexin A2; calcium-binding protein, membrane-binding protein,
helix BUN heparin, hexasaccharide, metal binding
protein; HET: UAP SGN IDS; 1.42A {Homo sapiens} PDB:
2hyu_A* 2hyw_A 1w7b_A 1xjl_A
Length = 308
Score = 24.9 bits (54), Expect = 4.0
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 7 PLMFSLVCFRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVT 66
PL F+ + SM D I++ V S E D+ K+ SE+ R Y + L +
Sbjct: 236 PLYFADRLYDSMKGKGTRDKVLIRIMV-----SRSEVDMLKIRSEFKRKYGKS-LYYYIQ 289
Query: 67 GQSKG 71
+KG
Sbjct: 290 QDTKG 294
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 24.1 bits (52), Expect = 6.8
Identities = 5/52 (9%), Positives = 18/52 (34%), Gaps = 5/52 (9%)
Query: 24 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYN----INVLRDKVTGQSKG 71
+ + + + +P + ++ F ++ + I + G+ G
Sbjct: 19 SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTG 69
>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium
pasteurianum} SCOP: c.37.1.10
Length = 269
Score = 24.2 bits (53), Expect = 7.7
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 34 GQIPRSMDEADLTKMFSEYG 53
IP+ M + L ++ +YG
Sbjct: 250 FVIPKPMTQERLEEILMQYG 269
>1m2o_A SEC23, protein transport protein SEC23, SEC23P; zinc-finger, beta
barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A
{Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1
c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1m2v_A 2qtv_A*
Length = 768
Score = 24.2 bits (51), Expect = 9.1
Identities = 4/31 (12%), Positives = 11/31 (35%)
Query: 18 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKM 48
M D + ++ P + +A+ +
Sbjct: 1 MDFETNEDINGVRFTWNVFPSTRSDANSNVV 31
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
0.320 0.135 0.388
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: 1,276,449
Number of extensions: 63390
Number of successful extensions: 364
Number of sequences better than 10.0: 1
Number of HSP's gapped: 350
Number of HSP's successfully gapped: 197
Length of query: 88
Length of database: 6,701,793
Length adjustment: 56
Effective length of query: 32
Effective length of database: 5,138,217
Effective search space: 164422944
Effective search space used: 164422944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)