RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11978
(91 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 = 78.1 bits (193), Expect = 1e-20
Identities = 31/76 (40%), Positives = 42/76 (55%), Gaps = 9/76 (11%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEA 75
S D D IK+F+GQIPR++DE DL +F E+G++Y + VL+D+ TG KG
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG----C 57
Query: 76 AFLKI-----ARAAIE 86
AFL A A
Sbjct: 58 AFLTYCERESALKAQS 73
>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 = 65.0 bits (159), Expect = 1e-15
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 10/76 (13%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEA 75
S E K+FVG + + E D+ ++F +G + VLR G SKG
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKG----C 58
Query: 76 AFLKI-----ARAAIE 86
AF+K A+AAI
Sbjct: 59 AFVKFSSHTEAQAAIH 74
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 64.6 bits (158), Expect = 8e-15
Identities = 28/66 (42%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLK-----I 80
D IKMFVGQ+PR+ E DL ++F +YG VY INVLRD+ + K F+
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC--CFVTFYTRKA 59
Query: 81 ARAAIE 86
A A
Sbjct: 60 ALEAQN 65
Score = 56.1 bits (136), Expect = 1e-11
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 13 YVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKI 72
++ + + K+F+G I + E D+ MFS +G++ +LR G S+G
Sbjct: 81 QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRG-- 137
Query: 73 FEAAFLK-----IARAAIE 86
AF+ +A+ AI+
Sbjct: 138 --CAFVTFTTRAMAQTAIK 154
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA
complex, AU-rich element, transcription/RNA complex;
1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB:
1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 64.1 bits (157), Expect = 9e-15
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ V +P++M + + +F G + + ++RDK+TGQS G
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG 45
Score = 59.5 bits (145), Expect = 6e-13
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
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 = 63.0 bits (154), Expect = 3e-14
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ V +P+ M + +L +F G + ++RD TG S G
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG 46
Score = 60.7 bits (148), Expect = 3e-13
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
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 = 21/76 (27%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEA 75
S + P ++V +P S+ DL ++FS+YG+V + +++DK T +SKG
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG--V-- 60
Query: 76 AFLKI-----ARAAIE 86
AF+ A+
Sbjct: 61 AFILFLDKDSAQNCTR 76
>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: 24 DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+++ + + DL K+ YG++ + + DK T + KG
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG 48
>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 = 57.2 bits (139), Expect = 1e-12
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKI-----ARA 83
+++G IP E + + S G V N+ ++ D TG+SKG + AF++ + +
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG--Y--AFIEFRDLESSAS 59
Query: 84 AIE 86
A+
Sbjct: 60 AVR 62
>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 = 56.8 bits (138), Expect = 2e-12
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFL 78
P + D + V + E DL ++F +G + I + +DK TGQSKG F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 79 KIARAAIE 86
+ A AI
Sbjct: 68 EDAARAIA 75
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 56.5 bits (137), Expect = 3e-12
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKI 80
Q + +FV + E D+ F+EYG + NI++ D+ TG KG E K
Sbjct: 18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77
Query: 81 ARAAIE 86
A+AA+E
Sbjct: 78 AQAAME 83
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition
motif, C-terminal helix, N-terminal helix, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 55.7 bits (135), Expect = 4e-12
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 23 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
D +FVG IP E L +FSE G V + ++ D+ TG+ KG
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG 51
>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 = 55.8 bits (135), Expect = 6e-12
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + D +F Q+ + DL FS G+V ++ ++ D+ + +SKG
Sbjct: 13 EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
>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 = 6e-12
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARA 83
++VG + ++ E L +F +G++ NI +++D TG+SKG F + + AR
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 84 AIE 86
A+E
Sbjct: 63 ALE 65
>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 = 56.3 bits (136), Expect = 7e-12
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + V IP ++DE L ++F YG + ++ ++ D+ T QS+G
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 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 = 55.4 bits (134), Expect = 8e-12
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ ++ P+ +F+ +P+ + DL +MF +G V + V DK T SK
Sbjct: 14 GAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68
>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 = 8e-12
Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAA 76
+ ++ ++++VG + ++ E L +F +GR+ +I ++ D TG+SKG F +
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 77 FLKIARAAIE 86
+ A+ A+E
Sbjct: 77 DSECAKKALE 86
>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 = 55.3 bits (134), Expect = 9e-12
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 17 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ +Q + D +++ +P SMDE +L M +G+V + +LRD +G S+G
Sbjct: 15 AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRG 67
>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 = 55.4 bits (134), Expect = 9e-12
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKI 80
Q + +FV I E ++ + F +YG + NI++ D+ TG SKG E K
Sbjct: 21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80
Query: 81 ARAAIE 86
A AA E
Sbjct: 81 ALAAKE 86
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 56.9 bits (138), Expect = 1e-11
Identities = 12/51 (23%), Positives = 26/51 (50%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ +++VG I + E + + F+ +G + +I++ D VT + KG
Sbjct: 21 RQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG 71
Score = 51.2 bits (123), Expect = 2e-09
Identities = 11/51 (21%), Positives = 27/51 (52%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ F +++V + + + + D+ +F +G++ + + RD TG+ KG
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG 168
>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 = 54.2 bits (131), Expect = 2e-11
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S S D + V + L ++F +YGRV ++ + R+ T +G
Sbjct: 2 SSGSSGPDVDGMI-TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG 56
>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 = 54.7 bits (132), Expect = 2e-11
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ +S E+ + D ++VG + DL FS G + I +L DK +G KG
Sbjct: 24 QPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79
>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 = 53.7 bits (130), Expect = 2e-11
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFE 74
S + V + E DL ++FS+YG + +++++ D+ + +S+G F
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG--F- 59
Query: 75 AAFLKI-----ARAAIE 86
AF+ A+ A E
Sbjct: 60 -AFVYFENVDDAKEAKE 75
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 54.3 bits (131), Expect = 3e-11
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 16 SMSLPEQPD-PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + +Q + P+ +F+ +P+ + DL F +G V + V DK T SK
Sbjct: 28 AAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83
>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 = 53.9 bits (130), Expect = 3e-11
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S LP +F+ + +E L ++ ++G + + V+ T SKG
Sbjct: 5 SSGLPSDVTEGK-TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG 58
>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 = 53.3 bits (129), Expect = 4e-11
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 23 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ D ++VG + +L F G V + +L DK +G KG
Sbjct: 2 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG 49
>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 = 53.9 bits (130), Expect = 4e-11
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S + F +FVG + + D+ F+ +GR+ + V++D TG+SKG
Sbjct: 5 SSGQKKDTSNHF-HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG 58
>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 = 53.9 bits (130), Expect = 4e-11
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKI 80
Q + +FV + E D+ F+EYG + NI++ D+ TG KG E K
Sbjct: 17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76
Query: 81 ARAAIE 86
A+AA+E
Sbjct: 77 AQAAME 82
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 54.0 bits (130), Expect = 5e-11
Identities = 10/69 (14%), Positives = 21/69 (30%)
Query: 2 GREKRRECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR 61
++VG + +D+ L F +G + +I +
Sbjct: 38 CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97
Query: 62 DKVTGQSKG 70
D T + +G
Sbjct: 98 DYETEKHRG 106
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 52.7 bits (127), Expect = 6e-11
Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF- 73
S + K+F+ +P S + +L ++ +G V ++ ++ ++ G+ KG +
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63
Query: 74 EAAFLKIARAAIE 86
E A A+
Sbjct: 64 EYENESQASQAVM 76
>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 = 52.2 bits (126), Expect = 7e-11
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 23 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
F +FVG + + A + F+ +GR+ + V++D TG+SKG
Sbjct: 3 LGSHF-HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG 49
>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 = 53.2 bits (128), Expect = 8e-11
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 1 MGREKRRECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVL 60
M + R + PDP+ + V + E DL ++FS+YG + +++++
Sbjct: 21 MASMTGGQQMGRGSRHVGNRANPDPNC-CLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79
Query: 61 RDKVTGQSKG 70
D+ + +S+G
Sbjct: 80 YDQQSRRSRG 89
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 53.7 bits (130), Expect = 9e-11
Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 15/89 (16%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG---- 70
R++ EQ K+FVG I + + + FS++G + + ++ DK TGQS+G
Sbjct: 77 RAIPRDEQDKTG--KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV 134
Query: 71 ---------KIFEAAFLKIARAAIEPQKA 90
++ + F+ IE ++A
Sbjct: 135 TYDSADAVDRVCQNKFIDFKDRKIEIKRA 163
Score = 52.1 bits (126), Expect = 3e-10
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
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 = 52.2 bits (126), Expect = 1e-10
Identities = 15/42 (35%), Positives = 29/42 (69%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+FVG + +E L ++FS+YG++ + V++D+ T +S+G
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG 55
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 53.2 bits (128), Expect = 1e-10
Identities = 15/70 (21%), Positives = 27/70 (38%)
Query: 1 MGREKRRECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVL 60
M + S P + V + L ++F +YGRV ++ +
Sbjct: 21 MASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIP 80
Query: 61 RDKVTGQSKG 70
RD+ T +S+G
Sbjct: 81 RDRYTKESRG 90
>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 = 51.8 bits (125), Expect = 2e-10
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 21 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++FV + + E DL K+FS YG + ++ D +T + KG
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG 51
>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 = 51.9 bits (125), Expect = 2e-10
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S P ++VG + + E L ++F + G V N ++ +D+VTGQ +G
Sbjct: 6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG 58
>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: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
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: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNI-----NVLRDKVTGQSKG 70
+++VG IP + E + F+ R+ + N + Q K
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN 52
>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 = 52.9 bits (127), Expect = 2e-10
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKI 80
Q + +FV I E ++ + F +YG + NI++ D+ TG SKG E K
Sbjct: 67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 126
Query: 81 ARAAIE 86
A AA E
Sbjct: 127 ALAAKE 132
>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 = 51.9 bits (125), Expect = 2e-10
Identities = 20/56 (35%), Positives = 29/56 (51%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S Q D F K+FVG +P +A L K F +G + V+ D+ TG+S+G
Sbjct: 5 SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
>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 = 51.0 bits (123), Expect = 2e-10
Identities = 12/42 (28%), Positives = 27/42 (64%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++VG + S + ++FS++G+V+N+ ++ D+ T + KG
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG 44
>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 = 53.8 bits (130), Expect = 2e-10
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
P + V +P S+ + ++ +G + ++ + TGQSKG
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138
Score = 38.4 bits (90), Expect = 8e-05
Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 31 FVGQIPRSMDEAD-LTKMFSEYGRVYNINVLRDKVTGQSKG 70
V ++P ++ D L + S + + GQ KG
Sbjct: 188 CVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKG 227
Score = 36.5 bits (85), Expect = 4e-04
Identities = 8/58 (13%), Positives = 21/58 (36%), Gaps = 8/58 (13%)
Query: 14 VRSMSLPEQPDP-DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+R + + K+ + +P + ++ + S+Y L+ + KG
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------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 = 51.6 bits (124), Expect = 3e-10
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++ ++ E L M +YG V + +L T + G
Sbjct: 10 TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG 49
>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 = 50.6 bits (122), Expect = 3e-10
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++VG + +D+ L F +G + +I + D T + +G
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 50
>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 = 52.7 bits (127), Expect = 4e-10
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
P P ++VG + + EA L + FS G + +I V RD +T +S G
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG 58
Score = 44.2 bits (105), Expect = 5e-07
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
P +F+ + +S+D L FS +G + + V+ D SKG
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKG 144
>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 = 50.7 bits (122), Expect = 4e-10
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
++VG + +D+ L F +G + +I + D T + +G F E + A AAI+
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
>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 = 52.3 bits (126), Expect = 5e-10
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 3 REKRRECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
E YV + PD K+F+G +P +++ + ++ + +G + N+++D
Sbjct: 91 LPGMSENPSVYVPGVVSTVVPDSAH-KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD 149
Query: 63 KVTGQSKG 70
TG SKG
Sbjct: 150 SATGLSKG 157
Score = 43.9 bits (104), Expect = 7e-07
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNI-----NVLRDKVTGQSKG 70
+++VG IP + E + F+ R+ + N + Q K
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN 52
>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: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+FVG + ++D+ L F ++ + +V+ D TG S+G
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 44
>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 = 49.9 bits (120), Expect = 8e-10
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
SLPE +FVG I MDE ++ F+ YG V + ++ D+ TG SKG
Sbjct: 1 SLPEGK-IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKG 51
>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 = 49.9 bits (120), Expect = 9e-10
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S + + +FVG + + E L ++F + G + + + +D+ G+ K
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKS 58
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 99
Score = 49.9 bits (120), Expect = 1e-09
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+FVG IP + E +L + F ++G V + ++ D + +G
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRG 53
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 49.6 bits (119), Expect = 1e-09
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGR--VYNINVLRDKVTGQSKG 70
+ + I + S Y V NI +++DK T Q++G
Sbjct: 4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG 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 = 49.0 bits (118), Expect = 1e-09
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+FVG + + D+ F ++G+V + ++ DK T + +G
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG 42
>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 = 49.0 bits (118), Expect = 1e-09
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+FVG + E + + F +G V +I + D T + +G
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG 42
>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 = 51.1 bits (123), Expect = 1e-09
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 17 MSLPEQP--DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
MS E P K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Score = 50.4 bits (121), Expect = 3e-09
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 15 RSMSLPEQPDPDFI----KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
R++S + P K+FVG I +E L F +YG++ I ++ D+ +G+ +G
Sbjct: 88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147
>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 = 49.6 bits (119), Expect = 1e-09
Identities = 11/43 (25%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYG-RVYNINVLRDKVTGQSKG 70
+++G + MDE +++ F+ G V ++ ++R+++TG G
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAG 53
>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 = 49.5 bits (119), Expect = 1e-09
Identities = 17/55 (30%), Positives = 25/55 (45%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S ++ + V +P E DL + FS +G V + V +D TG SKG
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG 58
>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 = 50.7 bits (122), Expect = 2e-09
Identities = 9/51 (17%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+F+G + + A+L SE ++ V+ + TG ++
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRK 55
Score = 44.1 bits (105), Expect = 4e-07
Identities = 7/56 (12%), Positives = 19/56 (33%), Gaps = 5/56 (8%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + + + ++ E +L ++F + + G+SKG
Sbjct: 87 KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKG 137
>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 = 50.2 bits (120), Expect = 2e-09
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + V + L ++F +YGRV ++ + RD+ T +S+G
Sbjct: 59 HHHHHHMDVEGMT-SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 113
>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 = 49.2 bits (118), Expect = 2e-09
Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 10/72 (13%)
Query: 21 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK-VTGQSKGKIFEAAF-- 77
K+ V IP ++ ++ ++FS +G + + + + TG +G F F
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG--F--GFVD 64
Query: 78 ---LKIARAAIE 86
+ A+ A
Sbjct: 65 FITKQDAKKAFN 76
>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 = 49.2 bits (118), Expect = 2e-09
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 21 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
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 = 48.3 bits (116), Expect = 2e-09
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + D KMFVG + + DL F+++G V + + D TG+S+G
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRG 54
>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 = 48.4 bits (116), Expect = 3e-09
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 14 VRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + F +F+G + + A+L SE N + D TG ++
Sbjct: 5 LEDPVEGSESTTPF-NLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRK 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 = 48.4 bits (116), Expect = 3e-09
Identities = 9/51 (17%), Positives = 23/51 (45%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQS 68
S + D ++VG + R + E + ++FS+ G + ++ + +
Sbjct: 6 SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP 56
>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 = 48.3 bits (116), Expect = 3e-09
Identities = 11/47 (23%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV-TGQSKG 70
K+ +G++ R++ + + ++FS YG++ I++ +++ SKG
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG 48
>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 = 48.3 bits (116), Expect = 3e-09
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 11/66 (16%)
Query: 28 IKMFVGQIPRSMDEADLTKMFSEYG--RVYNINVLRDKVTGQSKGKIFEAAFLKI----- 80
I +++G + + DLT+ G + I ++ GQSKG F A + +
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG--F--ALVGVGSEAS 57
Query: 81 ARAAIE 86
++ ++
Sbjct: 58 SKKLMD 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 = 49.4 bits (118), Expect = 4e-09
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFL 78
E+ ++VG + E + ++FS+ G + I + DK+ + G F E
Sbjct: 32 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91
Query: 79 KIARAAIE 86
A A+
Sbjct: 92 ADAENAMR 99
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 47.8 bits (114), Expect = 5e-09
Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 4/71 (5%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEA 75
S S+P++ K+ + IP + L + +YG V + + + +
Sbjct: 6 SGSVPKRQRI--RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSS 63
Query: 76 AFLKIARAAIE 86
AR A++
Sbjct: 64 K--DQARQALD 72
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 47.1 bits (113), Expect = 6e-09
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
KMF+G + + L + F ++G V V+RD +T +S+G
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 43
>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 = 49.1 bits (118), Expect = 6e-09
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ D +FVG + ++D+ L F ++ + +V+ D TG S+G
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 130
Score = 47.9 bits (115), Expect = 1e-08
Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+VG + +++ E L + F G + NI ++ DK ++
Sbjct: 4 YVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVN 42
>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 = 47.6 bits (114), Expect = 7e-09
Identities = 13/46 (28%), Positives = 26/46 (56%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
S E+ ++FVG +P + E ++ K+F +YG+ + + +DK
Sbjct: 6 SGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51
>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 = 47.7 bits (114), Expect = 7e-09
Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S + + + + S E L ++F + + + G+SKG
Sbjct: 3 SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKG 54
>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 = 47.6 bits (114), Expect = 8e-09
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S + + K+FVG + S + L FS+YG V + +++DK T QS+G
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG 59
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 48.8 bits (116), Expect = 8e-09
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYG--RVYNINVLRDKVTGQSKG 70
++VG + L ++ G V + ++ GQSKG
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKG 100
>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 = 47.6 bits (114), Expect = 8e-09
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 15 RSMSLPEQPD-PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S S ++ + ++V + +D+ L K FS +G + + V+ + G+SKG
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKG 56
>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 = 47.7 bits (114), Expect = 9e-09
Identities = 13/61 (21%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 12 EYVRSMSLPEQP--DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSK 69
+ + ++ L + F K+F+G + E L + ++G++ + V+RD + +S+
Sbjct: 10 KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSR 69
Query: 70 G 70
G
Sbjct: 70 G 70
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 47.3 bits (113), Expect = 1e-08
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 1 MGR-EKRRECTYEYVRSMSLPEQPDP-DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNIN 58
MG + V S + ++ V IP + DL +MF ++G++ ++
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 60
Query: 59 VLRDKVTGQSKG 70
++ ++ SKG
Sbjct: 61 IIFNE--RGSKG 70
>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 = 47.3 bits (113), Expect = 1e-08
Identities = 12/46 (26%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+F+G + R +E L +F ++G + + +++D+ T +S+G
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRG 49
>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 = 46.9 bits (112), Expect = 2e-08
Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S + ++ V IP + DL +MF ++G++ ++ ++ ++ SKG
Sbjct: 6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKG 56
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 46.0 bits (110), Expect = 2e-08
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++FV +P L F+E G V ++ + G+SKG
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKG 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 = 48.1 bits (115), Expect = 3e-08
Identities = 12/49 (24%), Positives = 23/49 (46%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+ E+ ++FVG +P + E D ++F YG + + RD+
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR 58
Score = 44.3 bits (105), Expect = 7e-07
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ V + + L + FS++G V V+ D G++ G
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATG 138
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 45.9 bits (109), Expect = 3e-08
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
+ + + LT +FS+ G+V N+ D+ TG++KG +F E + A+ I+
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>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 = 45.4 bits (108), Expect = 5e-08
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+ V + + +AD+ ++F+E+G + V D+ +G+S G
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLG 71
>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 = 45.3 bits (108), Expect = 5e-08
Identities = 7/51 (13%), Positives = 18/51 (35%), Gaps = 5/51 (9%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + + ++ E +L ++F + + G+SKG
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKG 54
>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 = 44.6 bits (106), Expect = 9e-08
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 3/56 (5%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S P +FV + E L + F R ++ D+ TG SKG
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKG 55
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 44.6 bits (106), Expect = 1e-07
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
S E P +VG +P + + D+ +F + + ++ ++RDK T + KG
Sbjct: 3 SGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKG 57
>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 = 44.6 bits (106), Expect = 1e-07
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV--------YNINVLRDKVTGQSKG 70
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 = 46.2 bits (109), Expect = 1e-07
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYG--RVYNINVLRDKVTGQSKG 70
+ ++ I +++G + + DLT+ G + I ++ GQSKG
Sbjct: 56 AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113
>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 = 46.1 bits (110), Expect = 1e-07
Identities = 7/56 (12%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ + + + + V +P+S ++ + K F G + +++V ++
Sbjct: 29 KKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFR 82
Score = 42.7 bits (101), Expect = 2e-06
Identities = 5/40 (12%), Positives = 13/40 (32%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++ P S + ++ + + V L S+
Sbjct: 121 WMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 160
Score = 38.0 bits (89), Expect = 9e-05
Identities = 8/44 (18%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 29 KMFVGQIPRSM-DEADLTKMFSEYGRVYNINVLRD-KVTGQSKG 70
++ + + + DE L + F +G + IN+ K +
Sbjct: 212 EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 44.6 bits (105), Expect = 2e-07
Identities = 11/45 (24%), Positives = 21/45 (46%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG +P +DE ++T F +G + + + K +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGY 54
>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 = 43.9 bits (104), Expect = 2e-07
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+ V + + +AD+ ++F+E+G + V D+ +G+S G
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLG 77
>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 = 43.8 bits (104), Expect = 2e-07
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 13/64 (20%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG------KIFEAAFLKIAR 82
+F+ + +S+D L FS +G + + V+ D SKG + EA A
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEA-----AE 59
Query: 83 AAIE 86
AIE
Sbjct: 60 RAIE 63
>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 = 43.5 bits (103), Expect = 3e-07
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
Q +FV + + L ++FS G V ++L DK G+S+G
Sbjct: 8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRG 57
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 43.1 bits (102), Expect = 4e-07
Identities = 11/45 (24%), Positives = 19/45 (42%)
Query: 19 LPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+ P ++G IP EADL +F +G + + +K
Sbjct: 19 IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
>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 = 43.0 bits (102), Expect = 4e-07
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ---SKG 70
+F+ + S E L +FS+ G + + + + K S G
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMG 51
>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: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
S D ++VG + ++ E DL F ++G + I V++ +
Sbjct: 3 SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48
>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 = 42.7 bits (101), Expect = 6e-07
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
Q P ++ G I + + + + FS +G++ I V +K
Sbjct: 18 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61
>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 = 42.9 bits (101), Expect = 6e-07
Identities = 8/47 (17%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGR-VYNINVLRD-KVTGQSKGKIF 73
++F+G IP+ ++ + ++ V ++ V +++G F
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAF 56
>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 = 42.2 bits (100), Expect = 7e-07
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 12/65 (18%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYN-INVLRDKVTGQSKG------KIFEAAFLKIA 81
+F+G + +DE L FS +G + ++RD TG SKG F+A +
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA-----S 61
Query: 82 RAAIE 86
AAIE
Sbjct: 62 DAAIE 66
>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 = 42.2 bits (100), Expect = 8e-07
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
K+FVG + + +L +F GRV +V++D
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 42.3 bits (100), Expect = 1e-06
Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 1 MGR-EKRRECTYEYVR---SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYN 56
MG + V M ++ + ++FV P + E++L ++F +G +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60
Query: 57 INVLRD 62
+ +L
Sbjct: 61 VKILNG 66
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 41.5 bits (98), Expect = 1e-06
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+FV PR +D A L++ F +G V ++ + +DK
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK 44
>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 = 41.9 bits (99), Expect = 2e-06
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 9/76 (11%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEA 75
M P +++ + + E DL +F+ + + +TG+ +G
Sbjct: 14 PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG--Q-- 69
Query: 76 AF-----LKIARAAIE 86
AF +IA A+
Sbjct: 70 AFITFPNKEIAWQALH 85
>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 = 41.1 bits (97), Expect = 2e-06
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 7/59 (11%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
K+++G + ++ DL ++F + G F + A AIE
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIE 62
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 41.6 bits (98), Expect = 2e-06
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 21 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV--------YNINVLRDKVTGQSKG 70
EQ + D +FV + ++ + F + G + IN+ D+ TG+ KG
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 58
>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 = 41.1 bits (97), Expect = 2e-06
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 17 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
M K+FVG+ M +L + F +YG V ++ + +
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47
>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 = 41.2 bits (97), Expect = 2e-06
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRV--------YNINVLRDKVTGQSKG 70
D D ++V + S+ DL F + G V I++ DK TG+ KG
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 66
>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 = 40.7 bits (96), Expect = 2e-06
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+FVG+ M E +L + FS+YG V ++ + +
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF 41
>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 = 40.7 bits (96), Expect = 2e-06
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
K+ VG I + +L F EYG V ++++D
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>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 = 40.3 bits (95), Expect = 4e-06
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR 61
K+F+G +PR E ++ +F +YG+V ++++
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 41.0 bits (96), Expect = 6e-06
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+ V + + +AD+ ++F+E+G + V D+ +G+S G
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLG 130
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 39.1 bits (91), Expect = 2e-05
Identities = 10/57 (17%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
+ ++P + E ++ + +G+V N+ +L+ K + F E + A +
Sbjct: 20 HIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70
>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 = 38.8 bits (91), Expect = 2e-05
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+VG + + A L + F +G + I+ ++
Sbjct: 21 WVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 38.6 bits (90), Expect = 2e-05
Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKIARAAIE 86
+ + + EADL + E+G + + V+ K + E + A A+
Sbjct: 25 HIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQA-----LVEFEDVLGACNAVN 75
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 39.5 bits (92), Expect = 2e-05
Identities = 10/60 (16%), Positives = 25/60 (41%)
Query: 3 REKRRECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
+ + + P K++VG + + ++ +L + F YG + ++ V R+
Sbjct: 49 TKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN 108
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 38.4 bits (90), Expect = 3e-05
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 21 EQPDPDFIKMFVGQIPRSMDEADLTKMFSE-YGRVYNINVLRDKVTGQSKG 70
P++ +FVG + +D+ L + F + Y V+ D+ TG SKG
Sbjct: 4 GSSGPEY-SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKG 52
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 38.2 bits (89), Expect = 3e-05
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+++ P D+ + + G+V NI + R KG IF
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIF 56
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 38.0 bits (89), Expect = 3e-05
Identities = 9/35 (25%), Positives = 20/35 (57%)
Query: 28 IKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
+K++VG + + +L + FS YG + + + R+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN 35
>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 = 38.4 bits (89), Expect = 3e-05
Identities = 10/57 (17%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
+ ++P + E ++ + +G+V N+ +L+ K + F E + A +
Sbjct: 35 HIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 85
>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 = 3e-05
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
+FV + ++ E L K FS++G++ + L+D
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural
genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 104
Score = 37.9 bits (88), Expect = 4e-05
Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKIARAAIE 86
V + S+ EADL + ++G + + ++ K + E + A+ +
Sbjct: 19 HVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQA-----LVEFENIDSAKECVT 69
>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 = 37.9 bits (88), Expect = 4e-05
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
+ ++P + E ++ + +G+V NI +L+ K + F E A + A +
Sbjct: 19 HIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVN 69
>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 = 38.9 bits (90), Expect = 4e-05
Identities = 5/44 (11%), Positives = 12/44 (27%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ P + E + ++ E G +V +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGL 169
Score = 33.5 bits (76), Expect = 0.004
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 31 FVGQI-PRSMDEADLTKMFSEYGRVYNINVLRDK 63
V + M+ + +F YG V + ++ K
Sbjct: 8 MVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK 41
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 37.5 bits (87), Expect = 6e-05
Identities = 12/48 (25%), Positives = 19/48 (39%)
Query: 14 VRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR 61
S P + P ++VG +PR +DL + E G V +
Sbjct: 6 SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ 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 = 37.3 bits (87), Expect = 7e-05
Identities = 8/35 (22%), Positives = 21/35 (60%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+++VG +P + D+ +F +YG + +I++ +
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR 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 = 38.7 bits (89), Expect = 7e-05
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
Q D F +FV ++ E+ L + F YG + I+++ K +G+ +G
Sbjct: 98 QGDA-FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
>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 = 37.0 bits (86), Expect = 1e-04
Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++ +P + ++ +F +YG + I R T +++G
Sbjct: 12 YIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRG 48
>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 = 36.2 bits (84), Expect = 2e-04
Identities = 11/40 (27%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 23 PDPDFIKMFVGQIPRS-MDEADLTKMFSEYGRVYNINVLR 61
P ++F+G + + + ++D+ +FS+YGRV +V +
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK 62
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 35.6 bits (83), Expect = 2e-04
Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 25 PDFIKMFVGQIP-RSMDEADLTKMFSEYGRVYNINVLR 61
P ++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 45
>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 = 35.5 bits (82), Expect = 2e-04
Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFL--KIARAAIE 86
+ V +P+ + ++ + +Y L+ ++K F L + A+ AI+
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAF-VTLLNGEQAQNAIQ 58
>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 = 35.8 bits (83), Expect = 3e-04
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 23 PDPDFIKMFVGQIP-RSMDEADLTKMFSEYGRVYNINVLR 61
++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>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 = 35.9 bits (83), Expect = 3e-04
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 15 RSMSLPEQPDPDFI-KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
RS S PE+ P ++V M L FS +G + ++++ +
Sbjct: 26 RSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR 73
>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 = 35.7 bits (83), Expect = 3e-04
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 19 LPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV-TGQSKG 70
LP+ P P F+G +P + E + + F + + + R+ + KG
Sbjct: 10 LPKSP-PY--TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG 58
>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 = 35.3 bits (82), Expect = 3e-04
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVT-GQSKG 70
LP+ P P F+G +P + E + + F + + + R+ + KG
Sbjct: 13 RLPKSP-PY--TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG 62
>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 = 34.8 bits (80), Expect = 7e-04
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKIARAAIE 86
+P A++ + FS +G + + + +T I E AR A
Sbjct: 14 LAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITA-----IVEFLEPLEARKAFR 64
>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 = 34.2 bits (79), Expect = 8e-04
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAF-- 77
+P P I V +P ++ ++ F Y + L+ G G+ AF
Sbjct: 10 SGKPGPTVI--KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM-VAFES 66
Query: 78 LKIARAAIE 86
A AA+
Sbjct: 67 RDEATAAVI 75
>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 = 33.7 bits (77), Expect = 0.002
Identities = 7/63 (11%), Positives = 19/63 (30%), Gaps = 1/63 (1%)
Query: 2 GREKRRECTYEYVRSMSLPEQPDPD-FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVL 60
G + +R + + + G + + L + + G V + +
Sbjct: 1 GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60
Query: 61 RDK 63
+K
Sbjct: 61 PNK 63
>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 = 8/54 (14%), Positives = 17/54 (31%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
P + V +P ++ ++ F Y + L+ G G+
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61
>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 = 0.003
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 16 SMSLPEQPDPDFIK-MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
S S E+ P ++V M L FS +G + ++++ +
Sbjct: 3 SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR 49
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 32.8 bits (75), Expect = 0.004
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 11/64 (17%)
Query: 19 LPEQPDPDFI---KMFVGQIPRSMDE------ADLTKMFSEYGRVYNINVLRDKVTGQSK 69
L ++P + V +P+ + + K+FS++G++ N + G++K
Sbjct: 4 LKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTK 61
Query: 70 GKIF 73
G IF
Sbjct: 62 GYIF 65
>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 = 32.8 bits (75), Expect = 0.004
Identities = 9/57 (15%), Positives = 18/57 (31%)
Query: 17 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
S + + + IP S+ + D+ + N + GQ G+
Sbjct: 5 SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 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 = 32.8 bits (75), Expect = 0.004
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
++ V +P S DL E G V +V RD
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 50
>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 = 32.2 bits (74), Expect = 0.005
Identities = 7/43 (16%), Positives = 14/43 (32%)
Query: 21 EQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
E ++V + S E + K F+ V + +
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR 51
>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 = 32.5 bits (74), Expect = 0.005
Identities = 9/54 (16%), Positives = 19/54 (35%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ + + +P + ++ + FS V N L G+ G+ F
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88
>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 = 0.006
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 7 RECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 66
R + + ++ + D +++ P D+ + + G+V NI + R
Sbjct: 89 RRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HK 147
Query: 67 QSKGKIF 73
KG IF
Sbjct: 148 AFKGSIF 154
>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 = 32.5 bits (74), Expect = 0.006
Identities = 7/43 (16%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 31 FVGQIPRSMDEADLTK---MFSEYGRVYNINVLRDKVTGQSKG 70
FV + + + + ++ K F ++G+++ + + S+G
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQG 61
>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 = 32.9 bits (75), Expect = 0.006
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 30 MFVGQI-PRSMDEADLTKMFSEYGRVYNINVLRDK 63
+ V + P + L +F YG V + +L +K
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 40
Score = 32.2 bits (73), Expect = 0.010
Identities = 12/48 (25%), Positives = 17/48 (35%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ 67
+ P + + IP S+ E DL +FS G V K
Sbjct: 113 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM 160
>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 = 0.008
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
LP PD ++ V +P S E D+ F RV +++L+D G++ G
Sbjct: 6 SGKPLPINPDDLYV--SVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGL 60
>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 = 32.3 bits (73), Expect = 0.009
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 17 MSLPEQPDPDFIKMFVGQI-PRSMDEADLTKMFSEYGRVYNINVLRDK 63
+++P + V + P + L +F YG V + +L +K
Sbjct: 24 IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 71
Score = 31.9 bits (72), Expect = 0.014
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+ IP S+ E DL +FS G V K
Sbjct: 155 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 30.8 bits (70), Expect = 0.012
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 41 EADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
+ + K+FS++G++ N + G++KG IF E A A A++
Sbjct: 21 KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVK 65
>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 = 31.3 bits (71), Expect = 0.013
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
++ V +P S DL E G V +V RD
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 51
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 31.7 bits (71), Expect = 0.016
Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 12 EYVRSMSLPEQPDPDFIKMFVGQIPRSMD---------EADLTKMFSEYGRVYNINVLRD 62
+Y M ++VG I +++ E+ + +FS G + I +
Sbjct: 119 DYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES 178
Query: 63 K 63
K
Sbjct: 179 K 179
>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 = 0.018
Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 1/68 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF-EAAFL 78
P +++ +P + + F + V + + G++ G+ F E
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
Query: 79 KIARAAIE 86
+AA+
Sbjct: 78 ADYKAALC 85
>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 = 31.1 bits (70), Expect = 0.020
Identities = 8/34 (23%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 31 FVGQIPRS-MDEADLTKMFSEYGRVYNINVLRDK 63
+ +P S ++ + K+ YG++ N ++R K
Sbjct: 29 HLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
>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 = 31.4 bits (70), Expect = 0.023
Identities = 13/58 (22%), Positives = 32/58 (55%), Gaps = 9/58 (15%)
Query: 17 MSLPEQPDPDFIKMFVGQIPRSMDEADLTK----MFSEYGRVYNINVLRDKVTGQSKG 70
M++PE P+ +++ + + + +L K +FS++G++ +I V R + + +G
Sbjct: 1 MAVPETR-PNHT-IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRG 53
Score = 27.1 bits (59), Expect = 0.84
Identities = 5/34 (14%), Positives = 18/34 (52%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+F+ +P +E L+ +F+++ + ++ +
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR 243
>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 = 30.1 bits (68), Expect = 0.034
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINV 59
+VG IP + E + F+ R+ +
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQ 38
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 30.4 bits (68), Expect = 0.054
Identities = 19/104 (18%), Positives = 34/104 (32%), Gaps = 31/104 (29%)
Query: 8 ECTYEYVRSMSL------PEQ-PDPDFIKMFVGQIPRSMDEADLTKMFSEY---GRVYNI 57
+ + + +++ P PD D++ IP S + + + Y ++
Sbjct: 204 DAEKVFTQGLNILEWLENPSNTPDKDYLL----SIPISCPLIGVIQ-LAHYVVTAKLLGF 258
Query: 58 NV--LRDK---VTGQSKGKIFEAA----------FLKIARAAIE 86
LR TG S+G + A F R AI
Sbjct: 259 TPGELRSYLKGATGHSQG-LVTAVAIAETDSWESFFVSVRKAIT 301
Score = 24.2 bits (52), Expect = 8.2
Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 26/75 (34%)
Query: 16 SMSLPEQPD-----------PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV 64
+ LPE + + + F+G + ++ + + ++ +V N+ L +
Sbjct: 38 NKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKV----GQFDQVLNL-CLTE-- 90
Query: 65 TGQSKGKIFEAAFLK 79
FE +L+
Sbjct: 91 --------FENCYLE 97
>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 = 28.7 bits (65), Expect = 0.11
Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 31 FVGQIPRSMDEADLTK----MFSEYGRVYNINVLRDKVTGQSKG 70
++ + + + +L K +FS +G++ +I V R + + +G
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRG 52
>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 = 28.3 bits (63), Expect = 0.18
Identities = 10/57 (17%), Positives = 22/57 (38%), Gaps = 6/57 (10%)
Query: 31 FVGQIPRSM-DEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKIARAAIE 86
+ R L ++ +G + N +L ++ E A + A+AA++
Sbjct: 19 HIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEA---FIEMATTEDAQAAVD 70
>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 = 28.6 bits (64), Expect = 0.19
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRV-----YNINVLRDKVTGQSKGKIF 73
+++V + + + E DL +F Y + +R G+ KG+ F
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAF 96
>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 = 28.1 bits (62), Expect = 0.28
Identities = 8/53 (15%), Positives = 18/53 (33%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ 67
+ +++ V + + L ++FS++G V I Q
Sbjct: 34 VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ 86
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 28.1 bits (62), Expect = 0.30
Identities = 8/36 (22%), Positives = 14/36 (38%)
Query: 32 VGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQ 67
V + + L ++FS++G V I Q
Sbjct: 33 VENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ 68
>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 = 26.9 bits (59), Expect = 0.58
Identities = 6/40 (15%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 28 IKMFVGQIPRSMDEAD----LTKMFSEYGRVYNINVLRDK 63
+ V I + + L + F+ +G+V ++ +
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT 49
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 26.8 bits (59), Expect = 0.65
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 7/47 (14%)
Query: 31 FVGQIPRSMDEADLTK----MFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ I + + L + S G + +I V + + GK +
Sbjct: 33 LITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAY 76
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 26.3 bits (57), Expect = 0.85
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 39 MDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKIARAAIE 86
+ L ++ +YG V N+ VL K G + + E A +K A A++
Sbjct: 29 YSKDVLLRLLQKYGEVLNL-VLSSKKPGTA---VVEFATVKAAELAVQ 72
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 26.3 bits (58), Expect = 0.94
Identities = 8/56 (14%), Positives = 16/56 (28%), Gaps = 4/56 (7%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
R + + P + ++ + +P DL + E T G
Sbjct: 17 RGSHMSKLPAKRY-RITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDG 68
>3gla_A Low molecular weight heat shock protein; HSPA, SHP, SHSP, high
resolution, stress response, chaperone; 1.64A
{Xanthomonas axonopodis PV} PDB: 3gt6_A 3guf_A
Length = 100
Score = 25.9 bits (58), Expect = 1.2
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 6 RRECTY-EYVRSMSLPEQPDPDFIK 29
R E Y + R +LP+ D D I
Sbjct: 58 RIERRYGSFHRRFALPDSADADGIT 82
>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 = 25.3 bits (56), Expect = 1.8
Identities = 8/43 (18%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 31 FVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ P ++ E ++ + + I ++R+ G G IF
Sbjct: 14 KLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIF 54
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 25.3 bits (54), Expect = 2.6
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 6/25 (24%)
Query: 67 QSKGKIFEAAFLKIARAAIEPQKAP 91
Q+ K+ +A+ LK+ AP
Sbjct: 20 QALKKL-QAS-LKL----YADDSAP 38
>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 = 25.2 bits (55), Expect = 2.7
Identities = 7/54 (12%), Positives = 16/54 (29%), Gaps = 2/54 (3%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ + +P E D+ FS +++ G+ G+
Sbjct: 39 FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEAD 90
>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 = 25.4 bits (54), Expect = 3.1
Identities = 4/31 (12%), Positives = 11/31 (35%)
Query: 17 MSLPEQPDPDFIKMFVGQIPRSMDEADLTKM 47
M D + ++ P + +A+ +
Sbjct: 1 MDFETNEDINGVRFTWNVFPSTRSDANSNVV 31
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 25.0 bits (54), Expect = 3.1
Identities = 8/61 (13%), Positives = 18/61 (29%), Gaps = 2/61 (3%)
Query: 15 RSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLR--DKVTGQSKGKI 72
R + + + + +P S D+ S+ + G+ G+
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 73 F 73
F
Sbjct: 92 F 92
>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 = 3.2
Identities = 8/52 (15%), Positives = 17/52 (32%), Gaps = 3/52 (5%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
Q + + +P E D+ FS +++ G+ G+
Sbjct: 11 QSTTGHC-VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEAD 59
>3nct_A Protein PSIB; DNA binding protein, chaperone; 2.20A {Escherichia
coli}
Length = 144
Score = 24.8 bits (53), Expect = 4.0
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 2 GREKRRECTYEYVRSMSLPEQ--PDPDFIKMFVGQIP 36
G ++RRE T+ +R + P+ + ++ F G P
Sbjct: 25 GSDERRELTHAVMRELDAPDNWTMNGEYGSEFGGFFP 61
>1gme_A Heat shock protein 16.9B; small heat shock protein, chaperone,
alpha-crystallin; 2.70A {Triticum aestivum} SCOP:
b.15.1.1 PDB: 2h50_A 2h53_A 2byu_A
Length = 151
Score = 24.2 bits (53), Expect = 6.5
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 6 RRECTY-EYVRSMSLPEQPDPDFIK 29
R E + ++VR L E + +K
Sbjct: 98 RVERSSGKFVRRFRLLEDAKVEEVK 122
>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA
replication, MCM complex, AAA+ Pro ATP-binding,
DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}
Length = 595
Score = 24.5 bits (54), Expect = 6.9
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 7 RECTYEYVRSMSLPEQPDPDFIKMFVGQIPRSMD---EADLT 45
+ + + E+P+ ++ GQ+PR ++ E DL
Sbjct: 179 EKTKLIDWQKAVIQERPE----EVPSGQLPRQLEIILEDDLV 216
>2e7j_A SEP-tRNA:Cys-tRNA synthase; seven-stranded BETE-strand, lyase,
structural genomics; HET: PLP; 2.40A {Archaeoglobus
fulgidus} SCOP: c.67.1.9 PDB: 2e7i_A*
Length = 371
Score = 24.3 bits (53), Expect = 7.1
Identities = 6/53 (11%), Positives = 18/53 (33%), Gaps = 7/53 (13%)
Query: 33 GQIPRSMDEADLTKMFSEYGRVYNINVLR--DKVTGQSKGKIFEAAFLKIARA 83
G++ +A E+G Y++ ++ I + ++ +
Sbjct: 19 GKLTEEARQA-----LLEWGDGYSVCDFCTTGRLDEIKTPPIHDFIHNQLPKF 66
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 23.7 bits (51), Expect = 8.0
Identities = 5/54 (9%), Positives = 18/54 (33%), Gaps = 3/54 (5%)
Query: 23 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNIN---VLRDKVTGQSKGKIF 73
+ + + + +P + ++ F ++ + + G+ G F
Sbjct: 19 SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAF 72
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 24.0 bits (51), Expect = 9.7
Identities = 6/35 (17%), Positives = 12/35 (34%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+ + P + E K S++G + N
Sbjct: 54 RTVLIHCPEKISENKFLKYLSQFGPINNHFFYESF 88
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 0.136 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: 1,446,130
Number of extensions: 76620
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 379
Number of HSP's successfully gapped: 204
Length of query: 91
Length of database: 6,701,793
Length adjustment: 58
Effective length of query: 33
Effective length of database: 5,082,375
Effective search space: 167718375
Effective search space used: 167718375
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)