RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy518
(81 letters)
>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 = 123 bits (311), Expect = 3e-38
Identities = 57/75 (76%), Positives = 64/75 (85%)
Query: 7 PSVELSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMG 66
VELS YRDQHF+G EQEKLL+ + TLYVGNLS+YTTEEQ+YELFSK GDIK+IIMG
Sbjct: 13 SYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 72
Query: 67 LDKYKKTPCGFCFLE 81
LDK KKT CGFCF+E
Sbjct: 73 LDKMKKTACGFCFVE 87
>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 = 72.3 bits (178), Expect = 1e-18
Identities = 18/44 (40%), Positives = 22/44 (50%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
TLYVGNLS TE + +LFS+ G K M + P F
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
>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 = 66.3 bits (162), Expect = 4e-16
Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 24 AEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ +EK ++YVGN+ Y +T + L FS CG I RI + DK+ P G+ ++E
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIE 84
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 65.4 bits (160), Expect = 6e-16
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+T Y+GN+ ++ TE L LF G I +K G CF++
Sbjct: 26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIK 69
>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 = 64.9 bits (159), Expect = 8e-16
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS + TL V NL+Y T+ + L +F K G + + + + + K P GF F+
Sbjct: 1 GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60
Query: 81 E 81
Sbjct: 61 R 61
>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 = 62.5 bits (153), Expect = 5e-15
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
++YVGN+ Y T E+L F CG + R+ + DK+ P GF ++E
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIE 54
>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 = 62.6 bits (153), Expect = 6e-15
Identities = 20/61 (32%), Positives = 30/61 (49%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS L + ST+YV NL + T LY +FSK G + ++ + DK + G F+
Sbjct: 4 GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63
Query: 81 E 81
Sbjct: 64 L 64
>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 = 62.3 bits (152), Expect = 9e-15
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 34 STLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+T+YVG L +E L+ELF + G + M D+ G+ F+E
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
>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 = 62.4 bits (152), Expect = 1e-14
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
GS + T+++ NLS+ + EE L E+ + GD+K + + L + G F
Sbjct: 3 SGSSGLPSDV-TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 80 LE 81
+
Sbjct: 62 AQ 63
>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 = 62.3 bits (152), Expect = 1e-14
Identities = 10/62 (16%), Positives = 23/62 (37%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ R T++ L+ L + FS G ++ + + D+ + G +
Sbjct: 12 REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71
Query: 80 LE 81
+E
Sbjct: 72 VE 73
>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 = 62.4 bits (152), Expect = 2e-14
Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 4/76 (5%)
Query: 6 SPSVELSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIM 65
S + R G+RA + L V LS YTTE L E+FSK G I + +
Sbjct: 23 SMTGGQQMGRGSRHVGNRANPD----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 78
Query: 66 GLDKYKKTPCGFCFLE 81
D+ + GF F+
Sbjct: 79 VYDQQSRRSRGFAFVY 94
>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 = 61.1 bits (149), Expect = 2e-14
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
G+RA + L V LS YTTE L E+FSK G I + + D+ + GF F+
Sbjct: 7 GNRANPD----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 81 E 81
Sbjct: 63 Y 63
>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 = 61.2 bits (149), Expect = 3e-14
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+YVGNL + + ++F K G I+ I + K ++ F F+E
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVE 67
>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 = 60.7 bits (148), Expect = 3e-14
Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ L+V NLSY ++EE L +LFS G + + +D K P GF F+
Sbjct: 8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVT 56
>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 = 61.0 bits (148), Expect = 4e-14
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS R+ + + NL T ++ E FS+ G + R+++ +
Sbjct: 1 GSSGSSG---RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIV 51
Query: 81 E 81
E
Sbjct: 52 E 52
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 60.4 bits (147), Expect = 4e-14
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCG--DIKRIIMGLDKYKKTPCGFCFLE 81
T+ + N++ +T + + S + I + DK + GF F++
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQ 59
>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 = 60.3 bits (147), Expect = 6e-14
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
R+ +++VGN+ Y TEEQL ++FS+ G + + D+ P G+ F E
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCE 56
>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 = 59.5 bits (145), Expect = 7e-14
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS A ++ LYVG L+ ++ L+ F GDI I + LD + GF F+
Sbjct: 1 GSMATTKR------VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 54
Query: 81 E 81
E
Sbjct: 55 E 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 = 60.5 bits (147), Expect = 9e-14
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
++L V NL+Y T+ + L +F K G + + + D+Y K GF F+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD,
HDAC, histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 59.1 bits (144), Expect = 1e-13
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYK-KTPCGFCFLE 81
+ +++G L+ T++ + E+FS G IK I M +++ G+ ++E
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVE 53
>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 = 59.2 bits (144), Expect = 1e-13
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ +Y+G++ Y TEEQ+ +L S G + + M D G+ F+E
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIE 50
>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 = 60.6 bits (147), Expect = 1e-13
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L+V ++ E+++ E F G+IK I + LD+ G+ +E
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 120
>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 = 59.7 bits (145), Expect = 2e-13
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L+V + TEE +++ F++ G+IK I + LD+ G+ +E
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
>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 = 60.6 bits (147), Expect = 2e-13
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 5/81 (6%)
Query: 1 MTTVISPSVELSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDI 60
T + + H + ++L V NL+Y T+ + L +F K G +
Sbjct: 43 WTYDDATKTFTVTEGSHHHHHHMD-----VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRV 97
Query: 61 KRIIMGLDKYKKTPCGFCFLE 81
+ + D+Y K GF F+
Sbjct: 98 GDVYIPRDRYTKESRGFAFVR 118
>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 = 58.8 bits (143), Expect = 2e-13
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS T LYVG L+ ++ L+ F GDI I + LD + GF F+
Sbjct: 1 GSSGSSGMA-TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
Query: 81 E 81
E
Sbjct: 60 E 60
>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 = 58.4 bits (142), Expect = 3e-13
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS T++VGNL EE LYELF + G + ++ + D+ K P F F+
Sbjct: 4 GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFV 62
Query: 81 E 81
Sbjct: 63 C 63
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 58.4 bits (142), Expect = 3e-13
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 12 SSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYK 71
SS F+ S + ++ L++ L + T+E+L E+ G +K + + ++
Sbjct: 2 SSGSSGVFRYSTSLEKH------KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAG 55
Query: 72 KTPCGFCFLE 81
K P G ++E
Sbjct: 56 K-PKGLAYVE 64
>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 = 58.4 bits (142), Expect = 3e-13
Identities = 20/49 (40%), Positives = 24/49 (48%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+T+ V NLS T E L ELF G I RI + DK GF F+
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 58.6 bits (142), Expect = 7e-13
Identities = 19/61 (31%), Positives = 26/61 (42%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
G T LYVG L+ ++ L+ F GDI I + LD + GF F+
Sbjct: 51 GGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 110
Query: 81 E 81
E
Sbjct: 111 E 111
>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 = 57.3 bits (139), Expect = 8e-13
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS ++ S L+VGNL TEE++ +LF K G + + DK GF F+
Sbjct: 4 GSSGGEKTF-TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFI 56
Query: 81 E 81
Sbjct: 57 R 57
>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 = 57.3 bits (139), Expect = 1e-12
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKK-TPCGFC 78
+ Q +TTS + V N+ + + ++ ELFS G++K + + GF
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 79 FLE 81
F++
Sbjct: 62 FVD 64
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 56.9 bits (138), Expect = 1e-12
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 34 STLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L+V + TEE +++ F++ G+IK I + LD+ G+ +E
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
>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 = 57.4 bits (139), Expect = 1e-12
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
LY+ NL Y T E++Y++F K G I++I +G + G ++
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVV 53
>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 = 60.2 bits (145), Expect = 1e-12
Identities = 20/47 (42%), Positives = 26/47 (55%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
TL+V ++Y TTE +L F G IKRI M K P G+ F+E
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150
>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 = 56.9 bits (138), Expect = 1e-12
Identities = 20/63 (31%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 21 GSRAEQEKLLRTT--STLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
GS + TL + NLSY TEE L E+F K IK G+
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYA 56
Query: 79 FLE 81
F+E
Sbjct: 57 FIE 59
>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 = 56.9 bits (138), Expect = 1e-12
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L+VG LS+ T E+ L ++FSK G I +++ D+ + GF F+
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 56.5 bits (137), Expect = 1e-12
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+YVGNL + +L FS G ++ + + + P GF F+E
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVE 43
>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 = 56.9 bits (138), Expect = 1e-12
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L+V ++ E+++ E F G+IK I + LD+ G+ +E
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 74
>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 = 56.5 bits (137), Expect = 2e-12
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 21 GSRAEQEKLLRT--TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
GS R+ + TL+V LS TTEE L E F RI+ D+ + GF
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA-RIVT--DRETGSSKGFG 57
Query: 79 FLE 81
F++
Sbjct: 58 FVD 60
>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 = 56.2 bits (136), Expect = 2e-12
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIK---RIIMGLDKYKKTPCGFCFLE 81
++L++G+L Y E + F+ G+ +II ++ P G+CF+E
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIR--NRLTGIPAGYCFVE 58
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 58.5 bits (142), Expect = 2e-12
Identities = 22/65 (33%), Positives = 34/65 (52%)
Query: 17 QHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCG 76
Q +GS A+++ L S +YVG++ Y E+ + + F+ G IK I M D G
Sbjct: 12 QMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG 71
Query: 77 FCFLE 81
F F+E
Sbjct: 72 FAFVE 76
Score = 46.5 bits (111), Expect = 6e-08
Identities = 10/58 (17%), Positives = 23/58 (39%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ + R + +YV ++ +++ + +F G IK + D G+ F
Sbjct: 114 IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF 171
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 56.3 bits (136), Expect = 2e-12
Identities = 7/48 (14%), Positives = 18/48 (37%)
Query: 34 STLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ L+ E L ++ K G+++ + + L + G +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVL 54
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 55.3 bits (134), Expect = 4e-12
Identities = 16/49 (32%), Positives = 25/49 (51%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+S LYVG+L + TE+ L +F G I I++ D G+ F+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFIT 53
>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 = 55.4 bits (134), Expect = 4e-12
Identities = 12/67 (17%), Positives = 21/67 (31%), Gaps = 8/67 (11%)
Query: 23 RAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK--------RIIMGLDKYKKTP 74
+T++V L T E + + F + G IK I + D+
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 75 CGFCFLE 81
G +
Sbjct: 63 KGEATVS 69
>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 = 55.5 bits (134), Expect = 5e-12
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKR--------IIMGLDKYKKTPCGFCFLE 81
S +YV L+ T + L + F +CG +K I + LDK P G +
Sbjct: 13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71
>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 = 57.4 bits (138), Expect = 7e-12
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCG--DIKRIIMGLDKYKKTPCGFCFLE 81
LY+GNL+++TT+E L E G DI I ++ GF +
Sbjct: 68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 118
>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 = 55.0 bits (133), Expect = 8e-12
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
T+Y G ++ T++ + + FS G I I + +K G+ F+
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVR 67
>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 = 54.6 bits (132), Expect = 8e-12
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 8/63 (12%)
Query: 21 GSRAE--QEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
GS E + + LYV NL T+EE + + F+ + + +
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYA 54
Query: 79 FLE 81
F+
Sbjct: 55 FVH 57
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 54.5 bits (132), Expect = 8e-12
Identities = 21/47 (44%), Positives = 29/47 (61%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+YVGNL Y T EQ+ ELFS+ G + + + D+ K P GF F+E
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE 49
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 54.6 bits (132), Expect = 9e-12
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 21 GSRAEQEKLLRTTS--TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
GS K L T T YVGNL + T + + +F I+ + + DK GFC
Sbjct: 1 GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59
Query: 79 FLE 81
++E
Sbjct: 60 YVE 62
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 55.1 bits (133), Expect = 9e-12
Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 8/56 (14%)
Query: 34 STLYVGNLSYYTTEEQLYELFSKCGDIK--------RIIMGLDKYKKTPCGFCFLE 81
+T++V L T E + + F + G IK I + D+ G +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
>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 = 57.3 bits (139), Expect = 1e-11
Identities = 14/51 (27%), Positives = 22/51 (43%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
T + L V NL T++Q EL G ++R + + G+ F E
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAE 143
Score = 51.5 bits (124), Expect = 1e-09
Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 7/58 (12%)
Query: 24 AEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
E+ R + + L T +++++L S +K + K G F+
Sbjct: 13 EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK------GTAFVT 63
Score = 43.8 bits (104), Expect = 7e-07
Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 3/61 (4%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTE-EQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
+ LL + L V L + + L S + + + GF L
Sbjct: 174 AGQLTPALLHSR-CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ-LKGFAVL 231
Query: 81 E 81
E
Sbjct: 232 E 232
>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 = 54.8 bits (132), Expect = 1e-11
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDI--KRIIMGLDKYKKTPCGFCFLE 81
L++G + E++ E +K + I+ K GF F+E
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVE 58
>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 = 54.2 bits (131), Expect = 1e-11
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPC---GFCFLE 81
+S L++ NL++ TTEE L +FSK G IK I K K GF F+E
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISK--KKNKAGVLLSMGFGFVE 56
>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 = 57.0 bits (138), Expect = 1e-11
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
E+ R L+VGNL TEE LF + G+ + + D+ GF F+
Sbjct: 13 KPGEKTYTQRCR--LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIR 64
Score = 41.2 bits (97), Expect = 6e-06
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRI-IM 65
+ L V NLS + E L + FS+ G +++ ++
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVV 129
>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 = 53.8 bits (130), Expect = 1e-11
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
R TL NLS+ TE++L E+F +I+ L G ++E
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIE 59
>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 = 55.7 bits (135), Expect = 2e-11
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 5/58 (8%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ K +R TL NLS+ TE++L E+F +I+ G +
Sbjct: 88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAY 140
Score = 53.8 bits (130), Expect = 8e-11
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS + T L++GNL+ + +L S+ + + +D T F ++
Sbjct: 1 GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYV 59
Query: 81 E 81
+
Sbjct: 60 D 60
>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 = 54.9 bits (132), Expect = 2e-11
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+YVGNL + +L F G ++ + + + P GF F+E
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVE 116
>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 = 53.8 bits (130), Expect = 2e-11
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 24 AEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+K LYVG+L + TE+ L +F G I+ I + +D G+ F+
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74
>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 = 53.5 bits (129), Expect = 3e-11
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFC 78
GS L++G + E+ L LF + G I ++ D++ G
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK--DRFTGMHKGCA 58
Query: 79 FLE 81
FL
Sbjct: 59 FLT 61
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 53.1 bits (128), Expect = 3e-11
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+++V QL E F G + ++M DK K F +E
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM--DKDKGV---FAIVE 51
>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 = 52.6 bits (127), Expect = 4e-11
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGF 77
T+ L+VG L T+ L F + G I+ I +
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD----SFAY 57
>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 = 53.1 bits (128), Expect = 5e-11
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS E T L+V N+ + + L ++F + G I + + + ++ GF F+
Sbjct: 4 GSSGNSESK-STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFV 60
Query: 81 E 81
Sbjct: 61 T 61
>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 = 54.1 bits (131), Expect = 5e-11
Identities = 13/50 (26%), Positives = 22/50 (44%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ + L V L T+E+ LF G+I+ + DK G+ F+
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVN 50
Score = 41.4 bits (98), Expect = 3e-06
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDI 60
S A + LYV L T+++L +LFS+ G I
Sbjct: 77 SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRI 115
>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 = 52.7 bits (127), Expect = 6e-11
Identities = 13/49 (26%), Positives = 19/49 (38%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
LY+ NLS TE L LF++ + K + G F+
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT 73
>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 = 7e-11
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
R EQ+K T ++VG + ++ E FS+ G I + LDK GF F
Sbjct: 80 PRDEQDK----TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133
Score = 49.8 bits (120), Expect = 2e-09
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ +++G L++ TTE+ L E F K G + + + D GF FL
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLS 51
>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 = 55.0 bits (133), Expect = 7e-11
Identities = 7/49 (14%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 34 STLYVGNLSYYTTEEQLYELFSKCGDIKR-IIMGLDKYKKTPCGFCFLE 81
TL++ N T+ + +L + I + ++ F +++
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT-SRRFAYID 165
Score = 52.3 bits (126), Expect = 6e-10
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 22 SRAEQEKLLRTT--STLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGF 77
S+ E L R +T+ V NL + ++Y+ F CG I + L K F
Sbjct: 28 SKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNF----RF 83
Query: 78 CFLE 81
+E
Sbjct: 84 ARIE 87
Score = 50.4 bits (121), Expect = 3e-09
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 3/63 (4%)
Query: 20 KGSRAEQEKLLRTTS-TLYVGNLSYYTTEEQ-LYELFSKCGDIKRI-IMGLDKYKKTPCG 76
++++ + + NLS +E L E F G I++I I K
Sbjct: 196 PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255
Query: 77 FCF 79
F
Sbjct: 256 CAF 258
>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 = 51.8 bits (125), Expect = 7e-11
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCG--DIKRIIMGLDKYKKTPCGFCFLE 81
LY+GNL+++TT+E L E G DI I ++ GF +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 51
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 53.4 bits (128), Expect = 7e-11
Identities = 12/80 (15%), Positives = 31/80 (38%), Gaps = 10/80 (12%)
Query: 6 SPSVELSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK---- 61
PS + ++ + + + +YVG+ S++TT++QL ++ G
Sbjct: 32 EPSPKPNNKTPAILYTYSGLRNR----RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87
Query: 62 RIIMGLDKYKKTPCGFCFLE 81
+ ++ G+ +
Sbjct: 88 KFAE--NRANGQSKGYAEVV 105
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 52.3 bits (126), Expect = 9e-11
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 12 SSYRDQHFKGSRAEQEKLLRTTST----LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGL 67
S + H G + + L+V N+ + + L ++F + G I + +
Sbjct: 4 SHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF 63
Query: 68 DKYKKTPCGFCFLE 81
+ ++ GF F+
Sbjct: 64 N--ERGSKGFGFVT 75
>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 = 53.8 bits (130), Expect = 1e-10
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 22 SRAEQEKLLR--TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
SR + ++ T ++VG + T E L + F + G I+ I + D+ GF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Score = 52.3 bits (126), Expect = 4e-10
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
S++E K L++G LS+ TT+E L F + G + ++ D K GF F
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 51.9 bits (125), Expect = 1e-10
Identities = 9/47 (19%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L++GNL+ + +L S+ + + +D T F +++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVD 64
>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 = 53.4 bits (129), Expect = 1e-10
Identities = 15/59 (25%), Positives = 25/59 (42%)
Query: 23 RAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
R + L L++G L Y ++Q+ EL + G +K + D G+ F E
Sbjct: 84 RPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142
Score = 51.8 bits (125), Expect = 4e-10
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMG-----LDKYKKTPCGFCFLE 81
LYVGN+ + TEE + + F+ + + L F FLE
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 57
>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 = 52.2 bits (125), Expect = 1e-10
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 17/72 (23%)
Query: 21 GSRAEQEKLLRT---------TSTLYVGN--LSYYTTEEQLYELFSKCGDIKRIIMGLDK 69
GS + LLR T +L V N L + QL + KCG + ++M +K
Sbjct: 4 GSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK 63
Query: 70 YKKTPCGFCFLE 81
+ F
Sbjct: 64 ------PYSFAR 69
>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 = 51.9 bits (125), Expect = 1e-10
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPC-GFCFLE 81
T ++GNL Y TEE + E F I + + + GF + E
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAE 67
>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 = 53.0 bits (128), Expect = 1e-10
Identities = 13/47 (27%), Positives = 19/47 (40%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L V L T+ +LY LF G I + D G+ F++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVD 51
Score = 46.0 bits (110), Expect = 6e-08
Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 15 RDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDI--KRIIMGLDKYKK 72
R++ K S A + LYV NL T++QL +F K G I K I+ DK
Sbjct: 71 RNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR--DKLTG 128
Query: 73 TPCGFCF 79
P G F
Sbjct: 129 RPRGVAF 135
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 53.4 bits (129), Expect = 1e-10
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+LYVG+L TE LYE FS G I I + D + G+ ++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Score = 38.4 bits (90), Expect = 5e-05
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIK 61
+++ NL + LY+ FS G+I
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNIL 131
>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 = 51.1 bits (123), Expect = 2e-10
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGF 77
+T +TLYVG L TE L F + G+I+ I + + C F
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ----CAF 52
>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 = 51.5 bits (124), Expect = 2e-10
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIK-RIIMGLDKYKKTPCGFCFLE 81
T ++GNL Y TEE + E F R+ ++ GF + E
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPER-LKGFGYAE 63
>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 = 51.3 bits (123), Expect = 2e-10
Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 4/47 (8%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
++V L E L E K G I ++M K E
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR----QALVEFE 59
>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 = 50.7 bits (122), Expect = 3e-10
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
T ++VGN+S T ++L LF + G + + K + F+
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV-----VK---DYAFVH 49
>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 = 52.7 bits (127), Expect = 3e-10
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L++G L Y ++Q+ EL + G +K + D G+ F E
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 162
Score = 51.6 bits (124), Expect = 8e-10
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMG-----LDKYKKTPCGFCFLE 81
LYVGN+ + TEE + + F+ + + L F FLE
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 57
>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 = 51.8 bits (125), Expect = 4e-10
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
LYVGNL TE+ L + F G I +I++ DK K + F+E
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMI--DKNNK-NVNYAFVE 47
Score = 39.8 bits (94), Expect = 1e-05
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK 61
+ Q+ T L+VG+L+ +E L F
Sbjct: 76 AFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
>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 = 51.3 bits (123), Expect = 4e-10
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 11 LSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLD 68
L + QH ++ E + L V + E QL +LF + G I+ +I+ D
Sbjct: 22 LQQQQQQHIPPTQMNPEPDVLRN--LMVNYIPTTVDEVQLRQLFERYGPIESVKIVC--D 77
Query: 69 KYKKTPCGFCFLE 81
+ + G+ F++
Sbjct: 78 RETRQSRGYGFVK 90
>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 = 50.8 bits (122), Expect = 5e-10
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 6 SPSVELSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIM 65
+ ++ F E + T + L V NL + ++ + ELF++ G +K+ +
Sbjct: 9 QMGRDPDKWQHDLFDSGCGGGEGV-ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 67
Query: 66 GLDK 69
D+
Sbjct: 68 DYDR 71
>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 = 50.6 bits (121), Expect = 5e-10
Identities = 9/62 (14%), Positives = 21/62 (33%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ R + + L + T+E++ + FS + I + G F
Sbjct: 29 QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88
Query: 80 LE 81
++
Sbjct: 89 VQ 90
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 50.4 bits (121), Expect = 5e-10
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 34 STLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L++G L+ T E+ L +F K G I +++ D+ K+ GF F+
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR-GFAFIT 54
>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 = 49.9 bits (120), Expect = 6e-10
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L++GNL TE+++ LF + G + + K + F+
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI-----IK---NYGFVH 48
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 50.0 bits (120), Expect = 6e-10
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 9/63 (14%)
Query: 20 KGSRAEQEKLLRTTST-LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
+GS + ++T L+V E +L E+F G +K + K GF
Sbjct: 17 RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEV--------KILNGFA 68
Query: 79 FLE 81
F+E
Sbjct: 69 FVE 71
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 51.4 bits (123), Expect = 6e-10
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 17 QHFKGSRAEQEKLLRTTST-LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPC 75
QH T L V NL + ++ + ELF++ G +K+ + D+ +
Sbjct: 71 QHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SL 129
Query: 76 GFCFLE 81
G +
Sbjct: 130 GTADVH 135
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 50.2 bits (120), Expect = 6e-10
Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 6/61 (9%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
+ +++ L TE ++ L G + ++M K F+
Sbjct: 4 SHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFI 57
Query: 81 E 81
E
Sbjct: 58 E 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 = 50.0 bits (120), Expect = 6e-10
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L+V NL+ TEE L + FS+ G ++R+ K + F+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIH 51
>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 = 49.5 bits (119), Expect = 7e-10
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ ++ L+VGN+S T ++L F + G + + K + F+
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI-----VK---DYAFVH 50
>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 = 49.6 bits (119), Expect = 7e-10
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ LY+GNLS T + L +LF + L G+ F++
Sbjct: 7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVD 50
>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 = 49.6 bits (119), Expect = 1e-09
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKR 62
R ST++V NL Y ++L E+FS G + R
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVR 44
>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 = 49.2 bits (118), Expect = 1e-09
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 15 RDQHFKGSRAEQEKLLRTTST-LYVGNLSYYTTEEQLYELFSKCGDIKR 62
+ QH T L V NL + ++ + ELF++ G +K+
Sbjct: 10 KWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKK 58
>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 = 50.3 bits (121), Expect = 1e-09
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTP--CGFCFLE 81
++VG + +E+ L ELF + G + I + D+ + P G CF+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVT 53
Score = 43.4 bits (103), Expect = 6e-07
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCF 79
+ +E+ + L++G +S TE + +FS G I+ RI+ G D + G F
Sbjct: 85 ADSEKNNAVEDRK-LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR---GCAF 140
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 49.0 bits (117), Expect = 1e-09
Identities = 10/69 (14%), Positives = 22/69 (31%), Gaps = 7/69 (10%)
Query: 13 SYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKK 72
+ H + + K + +++ L E L E + G I +++ K
Sbjct: 2 GHHHHHHMENYDDPHKT-PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK--- 57
Query: 73 TPCGFCFLE 81
+E
Sbjct: 58 ---RQALVE 63
>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 = 48.6 bits (116), Expect = 2e-09
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMG-----LDKYKKTPCGFCFLE 81
LYVGN+ + TEE + + F+ + + L F FLE
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 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 = 48.3 bits (116), Expect = 2e-09
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
+S LY+ L TT++ L +L G I + I+ DK G+ F++
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL--DKTTNKCKGYGFVD 53
>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 = 49.1 bits (117), Expect = 2e-09
Identities = 9/62 (14%), Positives = 19/62 (30%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
R+ +Y+ L + + + + F K ++ I G F
Sbjct: 12 GQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 71
Query: 80 LE 81
+E
Sbjct: 72 VE 73
>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 = 48.4 bits (116), Expect = 2e-09
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 22 SRAEQEKLLRTTST-LYVGNLSYYTTEEQLYELFSKCGDIK--RIIM 65
S + +++ R LYV NL +E+L + FS G I +++M
Sbjct: 3 SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM 49
>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 = 48.0 bits (115), Expect = 3e-09
Identities = 10/50 (20%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+T++VG + E ++ F++ G +K + + D+ G+ F+
Sbjct: 8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV-SKGYGFVS 56
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 99
Score = 48.0 bits (115), Expect = 3e-09
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
++VG + + E +L E F K G + ++M D K+ P GF F+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFIT 58
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 47.8 bits (114), Expect = 4e-09
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 37 YVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ + ++ L LFSK G + + +D+ GF F+E
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60
>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 = 48.0 bits (115), Expect = 4e-09
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 20 KGSRAEQEKLLRTTST-LYVGNLSYYTTEEQLYELFSKCGDIK--RIIM 65
G +A+ K T LY+ NL E++L + G + RI+
Sbjct: 11 SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILR 59
>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 = 48.4 bits (115), Expect = 4e-09
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 10/67 (14%)
Query: 15 RDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTP 74
R H SR+ + +++ L TE ++ L G + ++M K
Sbjct: 17 RGSHMGDSRSAGVP----SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK----- 67
Query: 75 CGFCFLE 81
F+E
Sbjct: 68 -NQAFIE 73
>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 = 49.6 bits (118), Expect = 5e-09
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 12 SSYRDQHFKGSRAEQ-EKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKY 70
+ FK ++ + + ++TL++ N+ +EE L LFS G + + K
Sbjct: 129 GNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD 188
Query: 71 KKTPCGFCFLE 81
+ ++
Sbjct: 189 R----KMALIQ 195
Score = 40.0 bits (93), Expect = 2e-05
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 33 TSTLYVGNLSYYT-TEEQLYELFSKCGDIKRI-IMGLDKYKKTPCGF 77
S L V NL+ T + L+ LF GD++R+ I+ + K
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL----FNKKENAL 76
>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 = 47.1 bits (113), Expect = 5e-09
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
T L+VG+L+ +E L F ++ D + G+ F+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQTGSSRGYGFVS 49
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 47.1 bits (112), Expect = 7e-09
Identities = 6/49 (12%), Positives = 15/49 (30%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ L + N+ + E L L + G ++ + +
Sbjct: 13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTY 61
>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 = 47.0 bits (112), Expect = 1e-08
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIK--RIIM 65
++VG+LS T E + F+ G I R++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVK 49
>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 = 11/44 (25%), Positives = 22/44 (50%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFC 78
++V NL + T + L + F++CG + + ++ K CG
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVV 53
>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 = 46.5 bits (111), Expect = 1e-08
Identities = 7/50 (14%), Positives = 18/50 (36%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ + V N+ + + +++ + F I + K P G +
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
>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 = 45.6 bits (109), Expect = 1e-08
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
++VG LS T EE++ E F G+++ I + +D GFCF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCF 45
>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 = 46.7 bits (111), Expect = 2e-08
Identities = 4/61 (6%), Positives = 18/61 (29%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
+ + + ++ N+ + T+ + + + + L G +
Sbjct: 3 SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALV 62
Query: 81 E 81
+
Sbjct: 63 Q 63
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 46.3 bits (110), Expect = 2e-08
Identities = 9/47 (19%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
++Y+ T + + E G + I M K G F+
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVV 58
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 46.8 bits (111), Expect = 2e-08
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 33 TSTLYVGNLSYYTTEEQL----YELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ + + N++ +E+L Y L S GDI I++ L G +
Sbjct: 29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNS---GKAY 76
>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 = 47.6 bits (113), Expect = 2e-08
Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 4/70 (5%)
Query: 12 SSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYK 71
+S + K + + ++TL++ N+ +EE L LFS G + + K +
Sbjct: 99 NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 158
Query: 72 KTPCGFCFLE 81
++
Sbjct: 159 ----KMALIQ 164
Score = 39.9 bits (93), Expect = 2e-05
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 33 TSTLYVGNLSYYT-TEEQLYELFSKCGDIKRIIMGLDK 69
S L V NL+ T + L+ LF GD++R+ + +K
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 40
>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 = 45.8 bits (109), Expect = 2e-08
Identities = 7/50 (14%), Positives = 18/50 (36%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ + V N+ + + +++ + F I + K P G +
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
>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 = 46.1 bits (110), Expect = 2e-08
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
L+VG L+ +EE + LF G I ++ G D K G F++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK---GCAFVK 62
>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 = 45.9 bits (109), Expect = 2e-08
Identities = 7/61 (11%), Positives = 20/61 (32%), Gaps = 2/61 (3%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS + + + V + + E + + F + + + D + G +
Sbjct: 4 GSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR-NNGNGLV 61
Query: 81 E 81
+
Sbjct: 62 K 62
>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 = 45.6 bits (109), Expect = 2e-08
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIK--RIIM 65
++VG+LS T + F+ G I R++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVK 40
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 45.6 bits (108), Expect = 3e-08
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L++ L TE ++ L G + I+M K FLE
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLE 57
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 45.5 bits (108), Expect = 4e-08
Identities = 8/62 (12%), Positives = 22/62 (35%), Gaps = 1/62 (1%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
GS + + L + ++E++ + FS + + ++ G F
Sbjct: 3 SGSSGNSPDT-ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 80 LE 81
++
Sbjct: 62 VQ 63
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 45.2 bits (107), Expect = 4e-08
Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 5/51 (9%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ +YVGNL L + G + L + P FL
Sbjct: 17 PLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGPRRRAFLH 62
>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 = 45.3 bits (108), Expect = 5e-08
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIM 65
+ +++ NL + LY+ FS G+I +++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 39
Score = 25.3 bits (56), Expect = 1.9
Identities = 5/28 (17%), Positives = 10/28 (35%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQ 49
AE + + +Y+ N +T
Sbjct: 86 REAELGARAKEFTNVYIKNFGPGSTRAA 113
>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 = 45.1 bits (107), Expect = 6e-08
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ + + R +TLYV T L FS G+I + M + F
Sbjct: 26 RSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAF 77
Query: 80 LE 81
+
Sbjct: 78 VT 79
>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 = 45.1 bits (107), Expect = 6e-08
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 31 RTTSTLYVGNLSY-YTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
S +++GNL+ + + +FSK G + + K G+ F++
Sbjct: 25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----HK---GYAFVQ 68
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 45.1 bits (107), Expect = 6e-08
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
L++ +L T+ L F G++ ++ + DK F F+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFI--DKQTSLSKCFGFVS 88
>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 = 44.6 bits (106), Expect = 6e-08
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 9/61 (14%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
GS E+ + TLYV T L FS G+I + M + F+
Sbjct: 4 GSSGERRAPRKGN-TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFV 54
Query: 81 E 81
Sbjct: 55 T 55
>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 = 44.6 bits (106), Expect = 7e-08
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 10/72 (13%)
Query: 11 LSSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYT-TEEQLYELFSKCGDIKRIIMGLDK 69
+ S H S S L++GNL ++E L+ +FS G I +I +
Sbjct: 1 MGSSHHHHHHSSGLVPRGS-HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---- 55
Query: 70 YKKTPCGFCFLE 81
K F F++
Sbjct: 56 -KN---AFGFIQ 63
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 43.6 bits (104), Expect = 8e-08
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
++VG LS TT E + F + G + ++ DK GF F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGF 45
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 44.1 bits (105), Expect = 9e-08
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 9/53 (16%)
Query: 30 LRTTSTLYVGNLSYYT-TEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ S L++GNL ++E L+ +FS G I +I + K F F++
Sbjct: 7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KN---AFGFIQ 51
>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 = 44.6 bits (106), Expect = 1e-07
Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
L++ +L ++ L ++F G++ ++ + DK F F+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI--DKQTNLSKCFGFVS 73
>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 = 46.0 bits (108), Expect = 1e-07
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 35 TLYVGNLSYYTTEEQL----YELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
T+Y+ NL+ +++L Y +FS+ G I I++ + G F+
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVI 58
Score = 39.1 bits (90), Expect = 4e-05
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
L++ NL T E L LF++ K + + ++ F+E
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH-----DIAFVE 250
>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 = 43.9 bits (104), Expect = 1e-07
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 2/60 (3%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+ T +++ L Y TE +Y FS R+ + + + G +E
Sbjct: 4 GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGR-VTGEADVE 61
>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 = 43.8 bits (104), Expect = 1e-07
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
T T+ + + TE+ + E + I + + + G+ F++
Sbjct: 9 TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGN-KTGYIFVD 56
>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 = 43.4 bits (103), Expect = 1e-07
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+GS S ++VG + T E+L + F + G++ + + K F F
Sbjct: 2 RGSHHHHHH----GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAF 52
>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 = 44.4 bits (105), Expect = 2e-07
Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 5/80 (6%)
Query: 5 ISPSVELSSYRDQHFKG---SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK 61
+ ++S G +E T +++ L Y TE +Y FS
Sbjct: 15 VPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PV 73
Query: 62 RIIMGLDKYKKTPCGFCFLE 81
R+ + + + G +E
Sbjct: 74 RVHIEIGPDGR-VTGEADVE 92
>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 = 45.1 bits (106), Expect = 2e-07
Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 1/68 (1%)
Query: 15 RDQHFKGSR-AEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKT 73
R+ F A + ++ ++ L+ N TEE +E+ + G + + + K
Sbjct: 104 RNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSE 163
Query: 74 PCGFCFLE 81
LE
Sbjct: 164 RSSSGLLE 171
Score = 43.2 bits (101), Expect = 9e-07
Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 33 TSTLYVGNLSY-YTTEEQLYELFSKCGDIKRIIMGLDK 69
+ L V L ++++ +F G+++++ K
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK 41
>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 = 43.4 bits (103), Expect = 2e-07
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 33 TSTLYVGNLSYYTTEEQL----YELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
T+Y+ NL+ +++L + +FS+ G I I++ + G F
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAF 55
>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 = 43.4 bits (103), Expect = 2e-07
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 32 TTSTLYVGNLSYYTTEEQLYELFSKCGDIK--RIIMGLDKYKKTPCGFCFLE 81
T + ++VG L Y+TT+ L + F GDI+ +I D+ G+ F+
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVIT--DRQTGKSRGYGFVT 65
>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 = 43.0 bits (102), Expect = 3e-07
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDI---KRIIM 65
+S +++GNL E+ LY+ FS G I +I+
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR 40
>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 = 43.0 bits (102), Expect = 3e-07
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+ ++ ++ TS L V L + TTE+ L E FS G++ + + D GF F
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 43.0 bits (102), Expect = 4e-07
Identities = 17/60 (28%), Positives = 29/60 (48%)
Query: 20 KGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
G + + +++G LS+ TT+E L E F + G++K ++ D K GF F
Sbjct: 12 SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
>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 = 42.4 bits (100), Expect = 4e-07
Identities = 8/49 (16%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
+S + V NL + +++++L +K + +K F+
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK------RTAFVT 46
>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 = 42.6 bits (101), Expect = 5e-07
Identities = 18/59 (30%), Positives = 26/59 (44%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
GS L+VG L + TT+E L FS+ G++ ++ DK GF F
Sbjct: 4 GSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62
>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 = 42.6 bits (101), Expect = 5e-07
Identities = 15/58 (25%), Positives = 26/58 (44%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+++ L++G LS+ TTEE L + + G + ++ D K GF F
Sbjct: 16 PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73
>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 = 42.5 bits (100), Expect = 5e-07
Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 7/51 (13%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
R+ + + V L + + L + + GD+ + D G +E
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVE 56
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 42.6 bits (100), Expect = 8e-07
Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 3/64 (4%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIK---RIIMGLDKYKKTPCGF 77
+ Q + + L + T E++ F + I I+ + P G
Sbjct: 11 SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70
Query: 78 CFLE 81
F+
Sbjct: 71 AFVL 74
>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 = 41.8 bits (98), Expect = 1e-06
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 12/69 (17%)
Query: 17 QHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQL---YELFSKCGDIKRIIMGLDKY--- 70
R Q+ L+ +V LS + ++ E F K G I ++++
Sbjct: 5 SSGASVRVVQKNLV------FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG 58
Query: 71 KKTPCGFCF 79
+ P +
Sbjct: 59 SQGPSASAY 67
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 41.4 bits (97), Expect = 1e-06
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKC---GDIKRIIMGLDKYKKTPCGF 77
GS+ E+E + + L + T E + FS C I L++ K G
Sbjct: 1 GSKLEEE--VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK-RRGD 57
Query: 78 CFLE 81
+E
Sbjct: 58 ALIE 61
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 40.2 bits (95), Expect = 2e-06
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCF 79
+++G LS+ TT+E L E F + G++K ++ D K GF F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 46
>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 = 40.3 bits (95), Expect = 2e-06
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKR-IIMGLDKYKKTPCGFCF 79
++VG + TE++L E FS+ GD+ I + F F
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR------AFAF 46
>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 = 40.2 bits (95), Expect = 2e-06
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFL 80
++VG LS+ T+++ L + F+K G++ + +D GF F+
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFI 58
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
Length = 118
Score = 41.1 bits (96), Expect = 3e-06
Identities = 8/64 (12%), Positives = 18/64 (28%), Gaps = 4/64 (6%)
Query: 21 GSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKC---GDIKRIIMGLDKYKKTPCGF 77
S + + L + + E + S C + + + + G
Sbjct: 5 SSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGE 63
Query: 78 CFLE 81
F+E
Sbjct: 64 AFVE 67
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B
protein; 2.50A {Homo sapiens}
Length = 143
Score = 41.4 bits (97), Expect = 3e-06
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 33 TSTLYVGNLSYYTTEEQLYELFSKCGDI 60
+YV NL+ + E+ L +F + D
Sbjct: 45 NCRIYVKNLAKHVQEKDLKYIFGRYVDF 72
>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 = 40.1 bits (93), Expect = 1e-05
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYK 71
+ V NL Y T + L+++FSK G + +II +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ 84
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 38.8 bits (90), Expect = 2e-05
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKT--PCGFCFL 80
+ ++VG L E+++ F + G + + K P G+ FL
Sbjct: 6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFL 57
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 38.6 bits (90), Expect = 2e-05
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 34 STLYVGNLSYYTTE------EQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
S + V N+ + ++++FSK G I + G+ FLE
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLE 67
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 38.9 bits (90), Expect = 2e-05
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYK 71
+ V NL Y T + L+++FSK G + +II +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ 66
>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 = 38.3 bits (89), Expect = 3e-05
Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 7/51 (13%)
Query: 31 RTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
R+ + + V L + + L + + GD+ + D G +E
Sbjct: 14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVE 57
>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 = 38.4 bits (89), Expect = 4e-05
Identities = 7/63 (11%), Positives = 16/63 (25%), Gaps = 4/63 (6%)
Query: 22 SRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKC---GDIKRIIMGLDKYKKTPCGFC 78
+ + L + + E + S C + + + G
Sbjct: 33 GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-QSGEA 91
Query: 79 FLE 81
F+E
Sbjct: 92 FVE 94
>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 = 37.9 bits (87), Expect = 7e-05
Identities = 9/47 (19%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
++Y+ T + + E G + I M K G F+
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVV 156
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 36.3 bits (84), Expect = 1e-04
Identities = 9/70 (12%), Positives = 18/70 (25%), Gaps = 3/70 (4%)
Query: 12 SSYRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDKYK 71
+ + KL + + NL + + L +L +
Sbjct: 7 HHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNT 63
Query: 72 KTPCGFCFLE 81
+ G LE
Sbjct: 64 RDFDGTGALE 73
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 35.8 bits (83), Expect = 1e-04
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 34 STLYVGNL------SYYTTEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
S + V N+ + ++++FSK G I + G+ FLE
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLE 53
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 37.1 bits (85), Expect = 2e-04
Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 13/74 (17%)
Query: 14 YRDQHFKGSRAEQEKLLRTTSTLYVGNLSYYTT---------EEQLYELFSKCGDIKRII 64
+ ++ + TLYVG + E ++ +FS+ GDI RI
Sbjct: 115 EKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIR 174
Query: 65 MGLDKYKKTPCGFC 78
+ CGF
Sbjct: 175 Y----VESKNCGFV 184
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 35.3 bits (82), Expect = 3e-04
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 35 TLYVGNLSYYTTEEQLYELFSKC-GDIK--RIIMGLDKYKKTPCGFCF 79
+L+VG+L+ + LYE F K + ++++ K G+ F
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSK---GYGF 55
>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 = 33.4 bits (76), Expect = 0.002
Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 8/72 (11%)
Query: 12 SSYRDQHFKGSRAEQEKLLRTTS-TLYVGNLSY-YTTEEQLYELFSKCGDIKRIIMGLDK 69
S + +G ++ + +++ NL + ++ + +L G IK I+ K
Sbjct: 3 SGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
Query: 70 YKKTPCGFCFLE 81
F+E
Sbjct: 63 ------SQAFIE 68
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 33.5 bits (76), Expect = 0.002
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 36 LYVGNLSYYTTEEQLYELFSKCGDIKRIIMGLDK 69
L + N Y T + LY + + G ++RI++
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN 61
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 31.3 bits (70), Expect = 0.017
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 8/51 (15%)
Query: 33 TSTLYVGNLSYYT--TEEQLYELFSKCGDIKRIIMGLDKYKKTPCGFCFLE 81
T +L V N + QL + KCG + ++M +K + F
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFAR 62
>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 = 27.5 bits (61), Expect = 0.27
Identities = 5/36 (13%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 35 TLYVGNLSY-YTTEEQLYELFSKCGDIKRIIMGLDK 69
+++ + QL +L G I ++
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI 52
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 27.4 bits (60), Expect = 0.31
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 46 TEEQLYELFSKCGDIKRIIMGLDK 69
+++ L L K G++ +++ K
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKK 53
>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 = 27.5 bits (60), Expect = 0.46
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 14/48 (29%)
Query: 28 KLLRTTS----TLYVGNLSYYT----------TEEQLYELFSKCGDIK 61
K+L TT T ++ + T +++ L K D +
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
>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 = 25.8 bits (56), Expect = 1.8
Identities = 5/10 (50%), Positives = 7/10 (70%)
Query: 65 MGLDKYKKTP 74
MG+D YK +
Sbjct: 1631 MGMDLYKTSK 1640
Score = 24.6 bits (53), Expect = 5.1
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 8/30 (26%)
Query: 35 TLYVGNLSY--------YTTEEQLYELFSK 56
TL G+L + + QL E F+K
Sbjct: 10 TLSHGSLEHVLLVPTASFFIASQLQEQFNK 39
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.135 0.393
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: 1,155,800
Number of extensions: 52101
Number of successful extensions: 336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 321
Number of HSP's successfully gapped: 201
Length of query: 81
Length of database: 6,701,793
Length adjustment: 50
Effective length of query: 31
Effective length of database: 5,305,743
Effective search space: 164478033
Effective search space used: 164478033
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)