RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17949
(96 letters)
>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 = 104 bits (262), Expect = 4e-31
Identities = 47/62 (75%), Positives = 53/62 (85%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
+ S + QKDTT+TK+FVGGLPYHTTD SLR++F FGDIEEAVVITDRQTGKSRGYG
Sbjct: 3 SGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62
Query: 88 FV 89
FV
Sbjct: 63 FV 64
>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 = 101 bits (254), Expect = 7e-30
Identities = 27/74 (36%), Positives = 46/74 (62%)
Query: 16 GADGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVI 75
G+ G G TL T + +++ + KLF+GGL + TT++SLR ++ +G + + VV+
Sbjct: 1 GSSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVM 60
Query: 76 TDRQTGKSRGYGFV 89
D + +SRG+GFV
Sbjct: 61 RDPASKRSRGFGFV 74
>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 = 98.5 bits (246), Expect = 1e-28
Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ V ++ K+F+GGL + TT + LRE+F FG+++E +V+ D T +SRG+GF
Sbjct: 12 SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 89 V 89
V
Sbjct: 72 V 72
>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 = 95.8 bits (239), Expect = 1e-27
Identities = 25/62 (40%), Positives = 41/62 (66%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G + KLFVGGL + TT ++LR +FS +G++ + V++ D+ T +SRG+G
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 88 FV 89
FV
Sbjct: 62 FV 63
>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 = 95.7 bits (239), Expect = 1e-27
Identities = 22/58 (37%), Positives = 37/58 (63%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
G+S + K+FVGG+P++ + LRE+F FG + E V+I D + + RG+GF++
Sbjct: 1 GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFIT 58
>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 = 95.8 bits (239), Expect = 1e-27
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++ + L V GLP+ TT++ L+E+FS FG++ V D +TG S+G+GFV
Sbjct: 6 SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV 62
>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 = 94.9 bits (237), Expect = 1e-27
Identities = 21/56 (37%), Positives = 38/56 (67%)
Query: 34 NSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
N+ + + K+FVGGL + T+ K L+++F+ FG++ + + D TG+SRG+GF+
Sbjct: 3 NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFI 58
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 92.9 bits (232), Expect = 6e-27
Identities = 19/46 (41%), Positives = 34/46 (73%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
K+FVGGL +TT + ++ +F FG +++A+++ D+ T + RG+GFV
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFV 46
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 92.9 bits (232), Expect = 6e-27
Identities = 23/46 (50%), Positives = 35/46 (76%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
K+F+GGL + TT + LRE+F FG+++E +V+ D T +SRG+GFV
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 47
>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 = 89.5 bits (223), Expect = 2e-25
Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
K+FVGGL T ++ +RE+F FG++E + D +T K RG+ F++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFIT 47
>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 = 88.9 bits (221), Expect = 7e-25
Identities = 24/59 (40%), Positives = 33/59 (55%)
Query: 31 SVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S G+S KD KLF+G +P + +K L+ F FG I E V+ DR TG +G F+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
>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 = 89.9 bits (224), Expect = 1e-24
Identities = 20/46 (43%), Positives = 34/46 (73%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
K+F+GGL + TT+ +LRE+F +G + + ++ D TG+SRG+GF+
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFL 50
Score = 79.1 bits (196), Expect = 2e-20
Identities = 21/47 (44%), Positives = 31/47 (65%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
K+FVGG+ K E FS +G I +A ++ D+ TG+SRG+GFV+
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT 135
>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 = 90.0 bits (224), Expect = 2e-24
Identities = 25/46 (54%), Positives = 34/46 (73%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KLF+GGL + TTD+SLR HF +G + + VV+ D T +SRG+GFV
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Score = 80.4 bits (199), Expect = 1e-20
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
T K+FVGG+ T + LR++F +G IE ++TDR +GK RG+ FV+
Sbjct: 95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152
>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 = 86.4 bits (215), Expect = 3e-24
Identities = 23/48 (47%), Positives = 27/48 (56%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
LFVG L + D++LR F F V+ D QTG SRGYGFVS
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVS 49
>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 = 86.6 bits (215), Expect = 7e-24
Identities = 22/48 (45%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
KLF+GGL T +K L+ F G I E ++I DR T KSRG+ F++
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFIT 54
>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 = 85.8 bits (213), Expect = 8e-24
Identities = 26/46 (56%), Positives = 35/46 (76%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KLFVGGL + T ++SL + FS +G I E VV+ DR+T +SRG+GFV
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 59
>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 = 85.5 bits (212), Expect = 2e-23
Identities = 27/61 (44%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 31 SVGNSQQKDTTW-TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S + Q+KDT+ +FVG L T + ++ F+ FG I +A V+ D TGKS+GYGFV
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 90 S 90
S
Sbjct: 63 S 63
>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 = 85.0 bits (211), Expect = 2e-23
Identities = 21/48 (43%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+FVGG+ + +R F+ +G ++E +ITDR TG S+GYGFVS
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVS 56
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma
cruzi} SCOP: d.58.7.1
Length = 139
Score = 86.3 bits (214), Expect = 2e-23
Identities = 19/62 (30%), Positives = 28/62 (45%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ L V +P + LR+ F +G IE ++ DR+T +SRGYGF
Sbjct: 29 HIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGF 88
Query: 89 VS 90
V
Sbjct: 89 VK 90
>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 = 84.5 bits (210), Expect = 2e-23
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ L++ GL TTD+ L + +G I I D+ T K +GYGFV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVD 53
>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 = 84.6 bits (210), Expect = 2e-23
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++ L V GL +TT++ LRE FS +G I + ++ D+Q+ +SRG+ FV
Sbjct: 6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
>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 = 84.8 bits (210), Expect = 4e-23
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L V GL +TT++ LRE FS +G I + ++ D+Q+ +SRG+ FV
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93
>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 = 83.1 bits (206), Expect = 1e-22
Identities = 22/65 (33%), Positives = 36/65 (55%)
Query: 25 ATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSR 84
+ + N Q+ +L+VG L ++ T+ LR F FG IE ++ D +TG+S+
Sbjct: 9 SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68
Query: 85 GYGFV 89
GYGF+
Sbjct: 69 GYGFI 73
>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 = 82.2 bits (204), Expect = 1e-22
Identities = 22/47 (46%), Positives = 29/47 (61%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+FVG L T ++ F+ FG I +A V+ D TGKS+GYGFVS
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVS 54
>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 = 83.2 bits (206), Expect = 1e-22
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+F+ L + + +++L E FGD++ V+ T S+G F
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62
>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 = 81.8 bits (203), Expect = 2e-22
Identities = 20/47 (42%), Positives = 25/47 (53%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L+VGGL DK L F FGDI + + D +T K RG+ FV
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 54
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 83.7 bits (207), Expect = 2e-22
Identities = 24/61 (39%), Positives = 30/61 (49%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ G S TT L+VGGL DK L F FGDI + + D +T K RG+ F
Sbjct: 50 SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 109
Query: 89 V 89
V
Sbjct: 110 V 110
>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 = 81.8 bits (203), Expect = 2e-22
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ L+VG L ++ T+ LR F FG I+ V++ D TG+S+GYGF+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFI 52
>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 = 81.9 bits (203), Expect = 3e-22
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
G+S + +LFV L Y ++++ L + FS +G + E D T K +G+ FV
Sbjct: 1 GSSGSSGSG--RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFV 55
>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 = 81.9 bits (203), Expect = 3e-22
Identities = 17/61 (27%), Positives = 32/61 (52%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ S G S + + ++V LP+ T+ L FS +G + + ++ D+ T KS+G F
Sbjct: 3 SGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62
Query: 89 V 89
+
Sbjct: 63 I 63
>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 = 81.5 bits (202), Expect = 5e-22
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G +++ D T + V L T + L+E F FG I + D+ TG+S+G+
Sbjct: 2 SSGSSGPNRRADDNAT-IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 88 FVS 90
F+S
Sbjct: 61 FIS 63
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 81.6 bits (202), Expect = 6e-22
Identities = 22/72 (30%), Positives = 31/72 (43%)
Query: 19 GLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDR 78
L + + Q + LF+ LP TD L F FG++ A V D+
Sbjct: 17 PLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK 76
Query: 79 QTGKSRGYGFVS 90
QT S+ +GFVS
Sbjct: 77 QTSLSKCFGFVS 88
>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 = 80.7 bits (200), Expect = 6e-22
Identities = 19/46 (41%), Positives = 29/46 (63%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++VG L Y T + ++E FS FG + +I DR+T K +G+GFV
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV 48
>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 = 81.1 bits (201), Expect = 6e-22
Identities = 23/56 (41%), Positives = 28/56 (50%)
Query: 34 NSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S TT L+VGGL DK L F FGDI + + D +T K RG+ FV
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 81.6 bits (202), Expect = 6e-22
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 23 SLATLTTPSVGNSQQKDTTW--TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQT 80
+ LT S+G + + LF+ LP D+ L + F FG++ A V D+QT
Sbjct: 4 GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63
Query: 81 GKSRGYGFVS 90
S+ +GFVS
Sbjct: 64 NLSKCFGFVS 73
>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 = 82.6 bits (204), Expect = 9e-22
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
T L V L Y T+ +LR F +G + + + DR T +SRG+ FV
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 80.6 bits (199), Expect = 2e-21
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
T L V L Y T+ +LR F +G + + + DR T +SRG+ FV
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
>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 = 79.2 bits (196), Expect = 3e-21
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L V L Y T+ SLR F +G + + + + T RG+ FV
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60
>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 = 81.1 bits (201), Expect = 4e-21
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 34 NSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ Q KLF+GGLP + D ++E + FG ++ ++ D TG S+GY F
Sbjct: 87 DYQPLPGA-HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142
Score = 64.6 bits (158), Expect = 1e-14
Identities = 8/51 (15%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAV-----VITDRQTGKSRGYGFV 89
+L+VG +P+ T++++ + F+ + + Q + + + F+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 80.4 bits (198), Expect = 5e-21
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFV 89
++VG + TTD+ L + G D+ E +R G+S+GY V
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEV 104
>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 = 78.0 bits (193), Expect = 7e-21
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFV 89
L++G L + TTD+ L E G DI E +R G+S+G+ V
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 50
>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 = 78.0 bits (193), Expect = 1e-20
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+++G +PY T++ + + S G + ++ D QTG+S+GY F+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFI 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 = 80.5 bits (199), Expect = 1e-20
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 30 PSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
P V ++ D+ KLF+GGLP + D ++E + FG ++ ++ D TG S+GY F
Sbjct: 103 PGVVSTVVPDSA-HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161
Query: 90 S 90
Sbjct: 162 E 162
Score = 62.0 bits (151), Expect = 1e-13
Identities = 8/51 (15%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDI-----EEAVVITDRQTGKSRGYGFV 89
+L+VG +P+ T++++ + F+ + + Q + + + F+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56
>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 = 81.6 bits (202), Expect = 2e-20
Identities = 18/54 (33%), Positives = 25/54 (46%)
Query: 37 QKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
Q T L V LP T + E FG +E ++ +TG+S+GYGF
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAE 143
Score = 63.8 bits (156), Expect = 6e-14
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 2/48 (4%)
Query: 43 TKLFVGGLPYHTTD-KSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L V LP D +L S + Q G+ +G+ +
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVL 231
Score = 57.7 bits (140), Expect = 1e-11
Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++++ K+ + GLP T++ + + S + + K +G FV
Sbjct: 15 TERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFV 62
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 80.4 bits (199), Expect = 2e-20
Identities = 16/61 (26%), Positives = 31/61 (50%)
Query: 30 PSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
P + ++ + +++V + +D ++ F FG I+ A + D TGK +GYGF+
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172
Query: 90 S 90
Sbjct: 173 E 173
Score = 78.1 bits (193), Expect = 1e-19
Identities = 15/54 (27%), Positives = 29/54 (53%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
Q ++++VG + Y + ++R+ F+ FG I+ + D T K +G+ FV
Sbjct: 22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
>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 = 77.8 bits (192), Expect = 2e-20
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++K+ ++VG + Y +T + L HFS G I ++ D+ +G +GY ++
Sbjct: 29 EEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83
>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 = 76.8 bits (190), Expect = 2e-20
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQ-TGKSRGYGFV 89
TK+ +G L + T + E FS +G I+ + +R S+GY +V
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYV 52
>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 = 77.3 bits (191), Expect = 2e-20
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+FVG +PY T++ L++ FS G + ++ DR+TGK +GYGF
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFC 55
>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 = 76.5 bits (189), Expect = 4e-20
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDI-EEAVVITDRQTGKSRGYGFVS 90
+F+G L +K L + FS FG I + ++ D TG S+GY F++
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFIN 54
>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 = 78.0 bits (193), Expect = 6e-20
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
T L V LP + T + R F G+IE ++ D+ TG+S GYGFV
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFV 49
Score = 76.8 bits (190), Expect = 1e-19
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L+V GLP T K L + FS +G I + ++ D+ TG SRG GF+
Sbjct: 82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136
>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 = 75.6 bits (187), Expect = 6e-20
Identities = 11/47 (23%), Positives = 24/47 (51%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++VG + Y T + L HF G + ++ D+ +G +G+ ++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI 53
>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 = 77.6 bits (192), Expect = 9e-20
Identities = 19/47 (40%), Positives = 23/47 (48%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
T L V LP TD+ L F G I ++ D +TG S GY FV
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFV 50
Score = 77.2 bits (191), Expect = 1e-19
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ T L+V LP TD L F +G I + ++ D+ TG+ RG FV
Sbjct: 83 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
>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 = 75.4 bits (186), Expect = 1e-19
Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 3/47 (6%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
LFV GL TT+++L+E F A ++TDR+TG S+G+GFV
Sbjct: 16 KTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFV 59
>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 = 75.9 bits (187), Expect = 1e-19
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
LFV G+ T++ + + F+ +G+I+ + DR+TG +GY V
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69
>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 = 75.0 bits (185), Expect = 1e-19
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGK---SRGYGFV 89
+ LF+ L + TT+++L+ FS G I+ + + S G+GFV
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFV 55
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 74.7 bits (184), Expect = 2e-19
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 32 VGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFV 89
+G+ + + + HT S+ S + + +I D+QT ++RG+ FV
Sbjct: 1 MGHHHHHHMD--TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFV 58
>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 = 76.8 bits (189), Expect = 2e-19
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
LFV + + ++E F +G+I+ + DR+TG S+GY V
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 74.6 bits (184), Expect = 2e-19
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
LFV G+ T++ + + F+ +G+I+ + DR+TG +GY V
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70
>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 = 74.6 bits (184), Expect = 3e-19
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L++ L T++ L F+ F + + + TG+ RG F++
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT 73
>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 = 74.7 bits (184), Expect = 3e-19
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 16 GADGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVI 75
G+ G G + +++D +F L + L + FS G + + +I
Sbjct: 1 GSSGSSGKSPVREPVDNLSPEERDAR--TVFCMQLAARIRPRDLEDFFSAVGKVRDVRII 58
Query: 76 TDRQTGKSRGYGFV 89
+DR + +S+G +V
Sbjct: 59 SDRNSRRSKGIAYV 72
>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 = 74.3 bits (183), Expect = 3e-19
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDR-QTGKSRGY 86
++ S G +K TT +K+ V +P+ + +RE FS FG+++ + TG RG+
Sbjct: 2 SSGSSGQVPKKQTT-SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 87 GFV 89
GFV
Sbjct: 61 GFV 63
>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 = 74.2 bits (183), Expect = 4e-19
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S GNS+ K T +L V +P+ D LR+ F FG I + +I + + S+G+G
Sbjct: 2 SSGSSGNSESKSTP-KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFG 58
Query: 88 FV 89
FV
Sbjct: 59 FV 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 = 74.2 bits (183), Expect = 4e-19
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+Q++ T L++ LP ++ L FG + ++ D +G SRG GF
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFAR 72
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 73.9 bits (182), Expect = 4e-19
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KLF+ GLP+ T + L E G +++ ++T+R GK +G +V
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63
>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 = 75.7 bits (187), Expect = 5e-19
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTG--KSRGYGFV 89
K+FVG +P ++K LRE F +G + E V+ DR +S+G FV
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 52
Score = 72.6 bits (179), Expect = 7e-18
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
KLF+G + T+ +R FS FG IEE ++ G SRG FV+
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVT 142
>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 = 73.8 bits (182), Expect = 5e-19
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G +++ ++VGGL ++ L E F G + + DR TG+ +GYG
Sbjct: 2 SSGSSGPISERNQD-ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
Query: 88 FV 89
FV
Sbjct: 61 FV 62
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 73.9 bits (182), Expect = 5e-19
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+L V +P+ D LR+ F FG I + +I + S+G+GFV
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 74
>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 = 77.0 bits (190), Expect = 6e-19
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L V L +++ L + FS FG +E+AVV+ D G++ G GFV
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVE 143
Score = 66.3 bits (162), Expect = 8e-15
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 30 PSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ ++ T +LFVG LP T++ + F +G+ E + + RG+GF+
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFI 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 = 74.8 bits (184), Expect = 7e-19
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L+VG L ++TT++ + E FS GDI++ ++ D+ + G+ FV
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86
>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 = 73.5 bits (181), Expect = 7e-19
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
LFV + + ++E F +G+I+ + DR+TG S+GY V
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 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 = 73.0 bits (180), Expect = 8e-19
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 33 GNSQQKDTTW--TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
G+S + T + L+V L D+ LR+ FS FG I A V+ + G+S+G+GFV
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVC 61
>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 = 76.3 bits (187), Expect = 9e-19
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFVS 90
L++G L + TTD+ L E G DI E +R G+S+G+ V
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 118
>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 = 72.6 bits (179), Expect = 9e-19
Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 34 NSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S +K+FVG T + L++ F +G++ + + R + FV
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFV 53
>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 = 73.4 bits (181), Expect = 1e-18
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+F+ L +K+L + FS FG+I V+ D S+GYGFV
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVH 51
Score = 24.5 bits (54), Expect = 4.5
Identities = 2/26 (7%), Positives = 9/26 (34%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKS 58
+ +T +++ +T +
Sbjct: 88 AELGARAKEFTNVYIKNFGPGSTRAA 113
>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 = 72.7 bits (179), Expect = 1e-18
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L + L Y T+++L+E F + + Q GKS+GY F+
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFI 58
>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 = 72.7 bits (179), Expect = 1e-18
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KL V L + +D ++E F+ FG +++A V DR +G+S G V
Sbjct: 30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADV 75
>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 = 72.3 bits (178), Expect = 2e-18
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 37 QKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ TT LF+G L + + L+ S + + D +TG +R +G+V
Sbjct: 12 SESTTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVD 64
>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 = 77.6 bits (190), Expect = 2e-18
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
LFV + Y TT+ LR F V+G I+ ++ +++GK RGY F+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
>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 = 71.9 bits (177), Expect = 2e-18
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G ++ +FVG L ++ L E F G + + + DR GK + +G
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFG 60
Query: 88 FV 89
FV
Sbjct: 61 FV 62
>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 = 72.8 bits (179), Expect = 2e-18
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KL V L + +D ++E F+ FG +++A V DR +G+S G V
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADV 81
>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 = 72.3 bits (178), Expect = 2e-18
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ +FV L Y K L+E FS+ G + A ++ D+ GKSRG G V+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVT 62
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 72.4 bits (178), Expect = 2e-18
Identities = 9/48 (18%), Positives = 21/48 (43%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
++ L + + L++ +G++EE ++ +T K G V
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVL 54
>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 = 71.5 bits (176), Expect = 3e-18
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 5/61 (8%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ +K L L ++ T+ L+E F + + Q GKS+G +
Sbjct: 3 MLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAY 57
Query: 89 V 89
+
Sbjct: 58 I 58
>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 = 71.5 bits (176), Expect = 4e-18
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S+ + KLFVG L +++ + F FG I+E V+ G S+G FV
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFV 61
>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 = 72.6 bits (179), Expect = 6e-18
Identities = 23/47 (48%), Positives = 27/47 (57%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
LFVG L + D++LR F F V+ D QTG SRGYGFVS
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVS 135
Score = 58.7 bits (143), Expect = 2e-12
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L+VG L T+ L+++F V G I ++ D+ K+ Y FV
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFV 46
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 70.3 bits (173), Expect = 1e-17
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++FV LP+ T K L++ F+ G + A + + GKS+G G V
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVV 53
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 70.1 bits (172), Expect = 2e-17
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAV--------VITDRQTGKSRGYG 87
+Q ++ +FV GL + T +S+ ++F G I+ + TDR+TGK +G
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 88 FVS 90
VS
Sbjct: 61 TVS 63
>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 = 69.6 bits (171), Expect = 2e-17
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ +FVG T+ LRE FS +GD+ + + R + FV
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFV 47
>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 = 69.3 bits (170), Expect = 2e-17
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 34 NSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAV--------VITDRQTGKSRG 85
+ + +FV GL + T +S+ ++F G I+ + TDR+TGK +G
Sbjct: 5 HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 64
Query: 86 YGFVS 90
VS
Sbjct: 65 EATVS 69
>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 = 69.9 bits (172), Expect = 7e-17
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 37 QKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ TT LF+G L + + L+ S + V+ D +TG +R +G+V
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYV 59
Score = 66.9 bits (164), Expect = 1e-15
Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+K L L ++ T+ L+E F +I Q GKS+G ++
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIE 142
>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 = 67.0 bits (164), Expect = 2e-16
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFG-DIEEAVVITDRQTGKSRGYGFVS 90
G+S L++G L + + + F+ G + +I +R TG GY FV
Sbjct: 1 GSSGSSGMA-ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVE 58
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 68.7 bits (168), Expect = 3e-16
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KL V L + +D ++E F+ FG +++A V DR +G+S G V
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADV 134
>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 = 70.0 bits (172), Expect = 4e-16
Identities = 6/48 (12%), Positives = 20/48 (41%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L++ P T +++R+ + ++ + + SR + ++
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYID 165
Score = 67.3 bits (165), Expect = 4e-15
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 43 TKLFVGGLPYHTTD-KSLREHFSVFGDIEEAVVITDRQ-TGKSRGYGFVS 90
++ + L D LRE F FG IE+ + ++ + F+
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMV 260
Score = 61.9 bits (151), Expect = 4e-13
Identities = 9/47 (19%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
T + V LP + ++F G I V K+ + +
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARI 86
>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 = 63.8 bits (156), Expect = 4e-15
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++ T ++LFVG LP T++ +R+ F +G E + D +G+GF+
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFI 56
>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 = 64.0 bits (156), Expect = 4e-15
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 8/66 (12%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAV--------VITDRQTGKSR 84
+D+ + ++V GL T L + F G ++ + D++TGK +
Sbjct: 6 SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65
Query: 85 GYGFVS 90
G VS
Sbjct: 66 GDATVS 71
>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 = 63.8 bits (156), Expect = 5e-15
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ + D L+VG L T+ + + FS G + +IT+ + Y F
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCF 59
Query: 89 V 89
V
Sbjct: 60 V 60
>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 = 65.8 bits (161), Expect = 7e-15
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 31 SVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
S + + + +F+ L +K+L + FS FG+I V+ D S+GYGFV
Sbjct: 92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVH 149
Score = 65.0 bits (159), Expect = 1e-14
Identities = 18/47 (38%), Positives = 22/47 (46%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L+VG L T+ L E FS G I V D T +S GY +V
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
>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 = 62.7 bits (153), Expect = 7e-15
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S +D T T L+VGGL T+ LR HF FG+I V+ + F+
Sbjct: 5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFI 53
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 63.1 bits (154), Expect = 8e-15
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+VG LP++T + F I ++ D+ T K +G+ +V
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61
>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 = 63.2 bits (154), Expect = 9e-15
Identities = 12/61 (19%), Positives = 21/61 (34%), Gaps = 2/61 (3%)
Query: 31 SVGNSQQKDT--TWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
S G+S + D + +P+ T + + E AV + G+ G
Sbjct: 2 SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61
Query: 89 V 89
V
Sbjct: 62 V 62
>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 = 61.2 bits (149), Expect = 3e-14
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G S K T + V +P+ + + + F + I +V + + G G
Sbjct: 2 SSGSSGASSGKPGP-TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 88 FV 89
V
Sbjct: 61 MV 62
>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 = 62.2 bits (151), Expect = 4e-14
Identities = 12/62 (19%), Positives = 23/62 (37%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
G++ + + GLP+ T + + + FS + + + GK G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87
Query: 88 FV 89
FV
Sbjct: 88 FV 89
>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 = 61.1 bits (149), Expect = 4e-14
Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 9/58 (15%)
Query: 33 GNSQQKDTT-WTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
G+S LFV L T++ L + FS FG +E + + Y F+
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFI 50
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 61.1 bits (149), Expect = 5e-14
Identities = 21/47 (44%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 45 LFVGGLPYHTTDKSLREHFS-VFGDIEEAVVITDRQTGKSRGYGFVS 90
LFVG L D L E F V+ V+ D QTG S+GYGFV
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVK 57
>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 = 60.8 bits (148), Expect = 5e-14
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 1/62 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G+S K T + V +P+ + + + F + I +V + + G G
Sbjct: 2 SSGSSGSSSGKPGP-TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 88 FV 89
V
Sbjct: 61 MV 62
>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 = 61.2 bits (149), Expect = 5e-14
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L++ LPY T + + + F +G I + V T ++RG +V
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYV 52
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 60.4 bits (147), Expect = 9e-14
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ Q+ + + T+LFV P + L E F FG ++E ++ G+ FV
Sbjct: 22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFV 70
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 60.8 bits (147), Expect = 1e-13
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITD--RQTGKSRGYGFV 89
K+FVGGLP + + F FG + + +GY F+
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFL 57
>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 = 59.9 bits (146), Expect = 1e-13
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQT-GKSRGYGFV 89
F+G LPY T++S++E F I + + + +G+G+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 66
>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 = 59.6 bits (145), Expect = 1e-13
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 31 SVGNSQQKDT--TWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
S G+S +DT + L+V L T+++ + + F+ V K R Y F
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAF 55
Query: 89 V 89
V
Sbjct: 56 V 56
>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 = 59.6 bits (145), Expect = 2e-13
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
G+S TKL VG + T++ LR F +G + E ++ + Y FV
Sbjct: 1 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFV 49
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 59.3 bits (144), Expect = 2e-13
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+FV G P L E+F FG + V+ D+ G + V
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVAS--VVMDKDKGV---FAIVE 51
>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 = 59.6 bits (145), Expect = 2e-13
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
F+G LPY T++S++E F + + +G+G+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA 62
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 59.2 bits (144), Expect = 2e-13
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 6/55 (10%)
Query: 36 QQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ T ++G +P+ T+ L F FG I + + +G F+
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIK 69
>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 = 58.9 bits (143), Expect = 4e-13
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 16 GADGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVI 75
G+ G G+ L V N Q ++ GG+ TD+ +R+ FS FG I E V
Sbjct: 1 GSSGSSGNTKQLRFEDVVN--QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF 58
Query: 76 TDRQTGKSRGYGFV 89
+ +GY FV
Sbjct: 59 PE------KGYSFV 66
>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 = 59.0 bits (143), Expect = 4e-13
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 32 VGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGD-IEEAVVITDRQ-TGKSRGYGFV 89
S +LF+GG+P + + E + + + + +V K+RG+ FV
Sbjct: 2 SSGSSGNC----RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFV 57
Query: 90 S 90
Sbjct: 58 E 58
>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 = 58.4 bits (142), Expect = 4e-13
Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 6/47 (12%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KL++G L T LR+ F + Q GY FV
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFV 49
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 59.9 bits (145), Expect = 4e-13
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 5/47 (10%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
K++VG L + L F +G + V + G+ FV
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFV 115
>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 = 58.4 bits (142), Expect = 5e-13
Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 8/55 (14%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S K+FVG + T + LR F G + E V+ + Y FV
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFV 48
>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 = 59.1 bits (143), Expect = 5e-13
Identities = 14/55 (25%), Positives = 27/55 (49%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S+ +++ GLP+ +K + + F +E+++ I GK+ G GFV
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 72
>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 = 59.1 bits (143), Expect = 6e-13
Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 5/53 (9%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVV-----ITDRQTGKSRGYGFVS 90
+++V L H +K L+ F + D I + G+ +G F+
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIG 98
>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 = 58.1 bits (141), Expect = 9e-13
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+++VG LP K + + F +G I + + R + FV
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFV 66
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 57.8 bits (140), Expect = 9e-13
Identities = 9/53 (16%), Positives = 18/53 (33%), Gaps = 1/53 (1%)
Query: 37 QKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ D +++ G P T ++E G + + +G FV
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFV 57
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 57.7 bits (140), Expect = 9e-13
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
K++VG L L FS +G + + + G+ FV
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFV 42
>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 = 56.9 bits (138), Expect = 2e-12
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
T+L+VGGL +T+ +L F FG I + + ++
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYI 58
>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 = 57.1 bits (138), Expect = 2e-12
Identities = 10/61 (16%), Positives = 23/61 (37%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
+ + + + GLP+ + + + + FS + + + G+S G F
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 89 V 89
V
Sbjct: 62 V 62
>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 = 54.9 bits (133), Expect = 1e-11
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
KLF+G LP T++ +R F +G + E +I + YGFV
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFV 47
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 54.0 bits (130), Expect = 3e-11
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 6/53 (11%)
Query: 43 TKLFVGGLPY------HTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ V G P K+L FS G + D TGK++G+ FV
Sbjct: 7 QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 53.6 bits (129), Expect = 4e-11
Identities = 10/64 (15%), Positives = 22/64 (34%), Gaps = 1/64 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G+ ++ KL + +P H + L +G +E +
Sbjct: 2 SSGSSGSVPKRQRI-RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Query: 88 FVSP 91
+ S
Sbjct: 61 YSSK 64
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 52.4 bits (126), Expect = 2e-10
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 9/75 (12%)
Query: 16 GADGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKS-LREHFSVFGDIEEAVV 74
G+ G G L +V N + +++F+G L KS + FS +G + V
Sbjct: 1 GSSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60
Query: 75 ITDRQTGKSRGYGFV 89
+GY FV
Sbjct: 61 --------HKGYAFV 67
>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 = 51.5 bits (124), Expect = 2e-10
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 10/62 (16%)
Query: 31 SVGNSQQKDTTW--TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGF 88
S G+S ++ L+V G T LR FS FG+ I D R F
Sbjct: 2 SSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGN------IIDLSMDPPRNCAF 53
Query: 89 VS 90
V+
Sbjct: 54 VT 55
>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 = 51.7 bits (124), Expect = 3e-10
Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 8/58 (13%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
++ L+V G T LR FS FG+I + + R FV+
Sbjct: 30 FPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVT 79
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 51.4 bits (123), Expect = 4e-10
Identities = 12/64 (18%), Positives = 22/64 (34%), Gaps = 3/64 (4%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDI---EEAVVITDRQTGKSRG 85
T + + + GLP+ T + + F I +E ++ G+ G
Sbjct: 10 TSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG 69
Query: 86 YGFV 89
FV
Sbjct: 70 DAFV 73
>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 = 50.5 bits (121), Expect = 4e-10
Identities = 8/51 (15%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVV-----ITDRQTGKSRGYGFV 89
+L+VG +P+ T++++ + F+ + + Q + + + F+
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 58
>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 = 50.8 bits (122), Expect = 5e-10
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
G+S TT + + G P++ T+K++ E + A+ I G GY FV
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK--PVAIRIVRNAHGNKTGYIFV 55
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 50.5 bits (121), Expect = 8e-10
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 43 TKLFVGGLPYHTTDKS------LREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ + V +P D+ + + FS FG I + GK++GY F+
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFL 66
>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 = 51.6 bits (123), Expect = 1e-09
Identities = 10/72 (13%), Positives = 17/72 (23%)
Query: 18 DGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITD 77
D +TP + L P T+++ E G V
Sbjct: 99 DFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVF 158
Query: 78 RQTGKSRGYGFV 89
+ G +
Sbjct: 159 SGKSERSSSGLL 170
Score = 39.7 bits (92), Expect = 3e-05
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 6/47 (12%)
Query: 45 LFVGGL-PYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L V GL + F ++G++E+ + + G V
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVE 48
>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 = 49.5 bits (118), Expect = 2e-09
Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 34 NSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFV 89
+++ + GLP+ T + + FS + E + + GK RG +
Sbjct: 3 KLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60
>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 = 48.8 bits (117), Expect = 2e-09
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 45 LFVGGLPYHTTDKSLREH----FSVFGDIEEAVVITDRQTGKSRGYGFV 89
+++ L L++ FS FG I + +V ++ K RG FV
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFV 56
>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 = 51.4 bits (122), Expect = 2e-09
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 45 LFVGGLPYHTTDKSLREH----FSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+++ L L++ FS FG I + +V ++ K RG FV
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVI 58
Score = 39.5 bits (91), Expect = 4e-05
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 42 WTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
LF+ LP T + L F+ F +E ++ R FV
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVE 250
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 48.7 bits (116), Expect = 5e-09
Identities = 9/65 (13%), Positives = 23/65 (35%), Gaps = 7/65 (10%)
Query: 29 TPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREH----FSVFGDIEEAVVITDRQTGKSR 84
+P +G++ + + + + L+ S GDI + I + +
Sbjct: 16 SPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNS 72
Query: 85 GYGFV 89
G ++
Sbjct: 73 GKAYI 77
>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 = 48.3 bits (115), Expect = 5e-09
Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
G+S + T + LP T ++E FS FG + ++ + V
Sbjct: 1 GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIV 51
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 47.6 bits (114), Expect = 7e-09
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 9/48 (18%)
Query: 43 TKLFVGGLPYHTTDKS-LREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++LF+G LP K L FS +G I + + +GF+
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFI 50
>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 = 47.7 bits (114), Expect = 7e-09
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 9/48 (18%)
Query: 43 TKLFVGGLPYHTTDKS-LREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++LF+G LP K L FS +G I + + +GF+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFI 62
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 47.0 bits (112), Expect = 8e-09
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 43 TKLFVGGLPYHTTDK------SLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ + V +P D+ + + FS FG I + GK++GY F+
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFL 52
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 47.4 bits (113), Expect = 1e-08
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ + GL + L E FG I VV+ + V
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALV 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 = 47.4 bits (113), Expect = 1e-08
Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
++ S G + + V G+P+ + +R+ F ++ ++ D G++ G G
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNG 59
Query: 88 FV 89
V
Sbjct: 60 LV 61
>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 = 47.4 bits (113), Expect = 1e-08
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
S + TT + + GLPY T+ + FS V I G+ G V
Sbjct: 6 SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADV 60
>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 = 47.9 bits (114), Expect = 1e-08
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ TT + + GLPY T+ + FS + V I G+ G V
Sbjct: 39 FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRVTGEADV 91
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 46.7 bits (111), Expect = 2e-08
Identities = 6/46 (13%), Positives = 15/46 (32%), Gaps = 3/46 (6%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++ + LP + + L++ + T G G +
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDGTGAL 72
>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 = 46.7 bits (111), Expect = 2e-08
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++ V GLP + + L++H GD+ A V D G G V
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 55
>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 = 46.8 bits (111), Expect = 3e-08
Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 30 PSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+G+S+ + + LP T+ + FG + +++ K + F+
Sbjct: 19 SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFI 72
Query: 90 S 90
Sbjct: 73 E 73
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 45.9 bits (109), Expect = 3e-08
Identities = 5/47 (10%), Positives = 16/47 (34%), Gaps = 7/47 (14%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ + V LP + + + + + + +++ FV
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFV 45
>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 = 45.6 bits (108), Expect = 7e-08
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
++ V GLP + + L++H GD+ A V D G G V
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 56
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 44.8 bits (106), Expect = 9e-08
Identities = 7/46 (15%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ + LP T+ + FG + +++ K + F+
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIE 58
>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 = 44.5 bits (105), Expect = 2e-07
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 6/52 (11%)
Query: 45 LFVGGLPYHTTDKSL---REHFSVFGDIEEAVVITDRQTGKSR---GYGFVS 90
+FV GL D + E+F FG I + V+ S+ +V+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVT 69
>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 = 45.0 bits (106), Expect = 2e-07
Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFV 89
+ + + GLP+ + + ++ S D V + G+ G FV
Sbjct: 37 LGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFV 93
>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 = 44.0 bits (104), Expect = 2e-07
Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ V GL + L E FG I +++ + V
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALV 56
>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 = 43.8 bits (103), Expect = 3e-07
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFG--DIEEAVVITDRQTGKSRGYGFV 89
+ + GLP+ + + ++ S D V + G+ G FV
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFV 66
>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 = 44.5 bits (105), Expect = 5e-07
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
P N Q L + +P +++ L+ FS G VV + K R
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG----GVVKGFKFFQKDRKMA 161
Query: 88 FV 89
+
Sbjct: 162 LI 163
Score = 44.1 bits (104), Expect = 6e-07
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 45 LFVGGL-PYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L V L P T +SL F V+GD++ ++ + + V
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQ 47
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 43.8 bits (103), Expect = 1e-06
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYG 87
P N Q L + +P +++ L+ FS G VV + K R
Sbjct: 137 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG----GVVKGFKFFQKDRKMA 192
Query: 88 FV 89
+
Sbjct: 193 LI 194
Score = 41.5 bits (97), Expect = 6e-06
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 45 LFVGGL-PYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L V L P T +SL F V+GD++ ++ + V
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQ 78
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 43.6 bits (102), Expect = 1e-06
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 15/57 (26%)
Query: 43 TKLFVGGLPYHTTDKS---------LREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
L+VGG+ K +R FS GDI+ + +S+ GFV
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVK 185
>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 = 42.2 bits (99), Expect = 1e-06
Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 6/74 (8%)
Query: 16 GADGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVI 75
G+ G G+ TL + T + GGL + L G ++ ++
Sbjct: 1 GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60
Query: 76 TDRQTGKSRGYGFV 89
+ + Y F
Sbjct: 61 PN------KPYSFA 68
>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 = 41.7 bits (98), Expect = 1e-06
Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 45 LFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
L + LP T+ + FG + +++ K + F+
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFL 56
>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 = 42.1 bits (98), Expect = 3e-06
Identities = 9/53 (16%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 37 QKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
+ D +++ G P T ++E G + + + +G FV
Sbjct: 104 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQV-LNIQMRRTLHKAFKGSIFV 155
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 40.2 bits (94), Expect = 6e-06
Identities = 9/65 (13%), Positives = 18/65 (27%), Gaps = 5/65 (7%)
Query: 25 ATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSR 84
++ ++ + ++VG LP L+ G V R
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGPR 56
Query: 85 GYGFV 89
F+
Sbjct: 57 RRAFL 61
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.0 bits (80), Expect = 0.001
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 33 GNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFV 89
G + + ++ V L Y T L + FS FG + + + T ++ +
Sbjct: 19 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALL 71
>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 = 35.1 bits (80), Expect = 0.001
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 4/85 (4%)
Query: 6 ALGTAESVLGGADGLVGSLATLTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSV 65
A ++V G + A+ G + + ++ V L Y T L + FS
Sbjct: 10 AQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSK 69
Query: 66 FGDIEEAVVITDRQTGKSRGYGFVS 90
FG + + + T ++ +
Sbjct: 70 FGTVLKIITFTK----NNQFQALLQ 90
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 32.6 bits (74), Expect = 0.005
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 44 KLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGYGFVS 90
+ V GLP D+ L +F V++ + + G ++
Sbjct: 10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ---RLGCGGVLT 53
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 29.3 bits (65), Expect = 0.099
Identities = 9/63 (14%), Positives = 17/63 (26%), Gaps = 5/63 (7%)
Query: 27 LTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGY 86
+T P + L + Y T L + G ++ V ++
Sbjct: 10 ITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIV-----IFKRNGIQ 64
Query: 87 GFV 89
V
Sbjct: 65 AMV 67
>1pjz_A Thiopurine S-methyltransferase; polymorphism, S-adenosylmethionine,
drug metabolism; NMR {Pseudomonas syringae PV} SCOP:
c.66.1.36
Length = 203
Score = 29.0 bits (64), Expect = 0.19
Identities = 7/52 (13%), Positives = 14/52 (26%), Gaps = 3/52 (5%)
Query: 48 GGLPYHTTDKSLREHFSVFGDI---EEAVVITDRQTGKSRGYGFVSPSFYLI 96
G P+ L S ++ + G G + Y++
Sbjct: 149 EGPPFSVPQTWLHRVMSGNWEVTKVGGQDTLHSSARGLKAGLERMDEHVYVL 200
>1gpj_A Glutamyl-tRNA reductase; tRNA-dependent tetrapyrrole
biosynthesis; HET: GMC CIT; 1.95A {Methanopyrus
kandleri} SCOP: a.151.1.1 c.2.1.7 d.58.39.1
Length = 404
Score = 29.1 bits (66), Expect = 0.19
Identities = 4/44 (9%), Positives = 11/44 (25%), Gaps = 11/44 (25%)
Query: 43 TKLFVGGLPYHTTDKSLREHFSV-----------FGDIEEAVVI 75
L G+ + + E + +V++
Sbjct: 2 EDLVSVGITHKEAEVEELEKARFESDEAVRDIVESFGLSGSVLL 45
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 121
Score = 27.3 bits (60), Expect = 0.55
Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 4/41 (9%)
Query: 46 FVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRGY 86
F G L T + L FS G+ + D G G
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGE----IKWIDFVRGAKEGI 59
>1s1g_A Potassium voltage-gated channel subfamily D membe; K+ channels,
tetramerization domain, T1 domain, transport PR; 2.60A
{Homo sapiens} SCOP: d.42.1.2
Length = 124
Score = 26.3 bits (58), Expect = 1.1
Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 27 LTTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSL-REHFSVFGDIEEAVVITDRQ 79
+ P+ + ++ L V G + T +L R ++ G E+ +
Sbjct: 1 MLAPA--DKNKRQDELIVLNVSGRRFQTWRTTLERYPDTLLGSTEKEFFFNEDT 52
>2nz0_B Potassium voltage-gated channel subfamily D membe; KV4.3, kchip1,
membrane protein; 3.20A {Homo sapiens} PDB: 2i2r_A
Length = 140
Score = 26.3 bits (58), Expect = 1.5
Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 1/53 (1%)
Query: 28 TTPSVGNSQQKDTTWTKLFVGGLPYHTTDKSL-REHFSVFGDIEEAVVITDRQ 79
+ + ++ L V G + T +L R ++ G E+ +
Sbjct: 22 MPLAPADKNKRQDELIVLNVSGRRFQTWRTTLERYPDTLLGSTEKEFFFNEDT 74
>2bu3_A ALR0975 protein; phytochelatin synthase, PCS, acyl-enzyme
intermedia nostoc, glutathione metabolism, cysteine
protease, transfer; HET: 3GC; 1.4A {Anabaena SP} SCOP:
d.3.1.14 PDB: 2btw_A* 2btw_B
Length = 254
Score = 25.9 bits (56), Expect = 2.1
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 71 EAVVITDRQTGKSRGYGFVSPS 92
+A+ D + K+RG+ FVS +
Sbjct: 230 KAMNTVDSVSQKTRGFVFVSKT 251
>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 = 2.9
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 12/53 (22%)
Query: 13 VLGGA----DGLVGSLATLTTPS------VGNSQQK-DTTWTKLFVGGLPYHT 54
V+ G GL +L PS + S++K + L V P+H+
Sbjct: 378 VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA-SPFHS 429
>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure
initiative, NE structural genomix research consortium,
nysgxrc; 2.35A {Pichia guilliermondii}
Length = 132
Score = 25.1 bits (54), Expect = 3.6
Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 35 SQQKDTTWTKLFVGGLPYHTTDKSLREHFSVFGDIEEAVVITDRQTGKSRG 85
S +F G P ++ + +F FG I E + + + G
Sbjct: 2 SLSNGELAILVF--GYPETMANQVIA-YFQEFGTILEDFEVLRKPQAMTVG 49
>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2,
protein structure initiative, northeast structural
genomics consortium; 2.00A {Colwellia psychrerythraea}
Length = 124
Score = 24.4 bits (54), Expect = 5.0
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 59 LREHFSVFGDIEEAVVITDRQ 79
L++ F + +A+V+TD Q
Sbjct: 6 LKQRAKAFDYVFDAIVVTDLQ 26
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
0.316 0.135 0.395
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: 1,439,568
Number of extensions: 69975
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 331
Number of HSP's successfully gapped: 215
Length of query: 96
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 34
Effective length of database: 4,970,691
Effective search space: 169003494
Effective search space used: 169003494
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.4 bits)