RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13066
(115 letters)
>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 = 151 bits (384), Expect = 2e-49
Identities = 37/87 (42%), Positives = 61/87 (70%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + K+F+GGLD+ TT E+L+++F Q+GE+VD V+MKD T +SRGFGF+ + + V
Sbjct: 12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCV 71
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDVR 98
+++RPH +DGR ++ K PR ++
Sbjct: 72 GTVLASRPHTLDGRNIDPKPCTPRGMQ 98
>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 = 150 bits (382), Expect = 5e-49
Identities = 54/94 (57%), Positives = 70/94 (74%), Gaps = 2/94 (2%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
P + E E RK+FIGGL + TT+ESL+ ++EQWG++ D VVM+DP +KRSRGFGF
Sbjct: 16 PLERKKR--EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73
Query: 63 ITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRD 96
+T+S VD AM+ RPH+IDGRVVE KRAV R+
Sbjct: 74 VTFSSMAEVDAAMAARPHSIDGRVVEPKRAVARE 107
>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 = 147 bits (374), Expect = 9e-48
Identities = 39/98 (39%), Positives = 60/98 (61%), Gaps = 6/98 (6%)
Query: 5 YDDSKCTEP------ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSR 58
+ S P S K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSR
Sbjct: 8 HHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR 67
Query: 59 GFGFITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRD 96
GFGF+T+ + VD ++ H +D + ++ K A PR
Sbjct: 68 GFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRR 105
>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 = 143 bits (363), Expect = 5e-46
Identities = 31/85 (36%), Positives = 48/85 (56%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + K+F+GGL Y TTD SL+ +FE +G+I + VV+ D T +SRG+GF+T ++
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
+ A + IDGR A
Sbjct: 73 ERACKDPNPIIDGRKANVNLAYLGA 97
>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 = 140 bits (354), Expect = 7e-45
Identities = 33/91 (36%), Positives = 57/91 (62%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + K+F+GG+ + + L+ +F+++G + +VV++ D +R RGFGFIT+ +
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+ VD A++ H+I G+ VE KRA PRD +
Sbjct: 62 EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSK 92
>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 = 138 bits (350), Expect = 2e-44
Identities = 33/81 (40%), Positives = 53/81 (65%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E K+F+GGL + T+ + L+ +F ++GE+VD + DP T RSRGFGFI + +A V
Sbjct: 7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASV 66
Query: 72 DDAMSNRPHNIDGRVVETKRA 92
+ + + H +DGRV++ K+A
Sbjct: 67 EKVLDQKEHRLDGRVIDPKKA 87
>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 = 136 bits (345), Expect = 2e-43
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 1/85 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + + GL ++TT++ L+ +F +GE++ V V KD T S+GFGF+ ++E +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
MS H IDGR + K +
Sbjct: 71 VKVMSQ-RHMIDGRWCDCKLPNSKQ 94
>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 = 139 bits (352), Expect = 2e-43
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSRE 93
Score = 115 bits (289), Expect = 7e-34
Identities = 26/96 (27%), Positives = 53/96 (55%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 63 ITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+T+ + VD + + H ++G E ++A+ +
Sbjct: 151 VTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM 186
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 134 bits (340), Expect = 5e-43
Identities = 34/75 (45%), Positives = 54/75 (72%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 RPHNIDGRVVETKRA 92
H +D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
>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 = 132 bits (334), Expect = 6e-41
Identities = 36/83 (43%), Positives = 62/83 (74%), Gaps = 1/83 (1%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+ K+FIGGL++ TT+++L+ +F ++G + D+ +MKDP T RSRGFGF+++ + VD+
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 74 AMSNRPHNIDGRVVETKRAVPRD 96
+ + H +DG+V++ KRA+PRD
Sbjct: 61 VVKTQ-HILDGKVIDPKRAIPRD 82
Score = 110 bits (278), Expect = 2e-32
Identities = 34/84 (40%), Positives = 47/84 (55%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + K+F+GG+ + + FF QWG I+D +M D T +SRGFGF+TY A V
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
D N+ + R +E KRA PR
Sbjct: 143 DRVCQNKFIDFKDRKIEIKRAEPR 166
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 127 bits (321), Expect = 3e-40
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL TT E ++ +FEQ+G++ D ++M D T R RGFGF+T+ +V+
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 78 RPHNIDGRVVETKRA 92
H I+ ++VE K+A
Sbjct: 61 HFHEINNKMVECKKA 75
>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 = 117 bits (296), Expect = 2e-36
Identities = 26/75 (34%), Positives = 41/75 (54%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 78 RPHNIDGRVVETKRA 92
+ HN+ E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>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 = 116 bits (293), Expect = 9e-36
Identities = 27/86 (31%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
KVF+G T E LQ FF Q+GE+VDV + K R F F+T+++ K+
Sbjct: 6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKV 60
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRD 96
I G V A P+
Sbjct: 61 AQSLCG-EDLIIKGISVHISNAEPKH 85
>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 = 111 bits (281), Expect = 5e-34
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
VF+G T++ L+ FF Q+G+++DV + K R F F+T+++ ++
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQ 56
Query: 73 DAMSNRPHNIDGRVVETKRAVPRD 96
I G V A P+
Sbjct: 57 SLCG-EDLIIKGISVHISNAEPKH 79
>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 = 100 bits (252), Expect = 3e-29
Identities = 32/88 (36%), Positives = 50/88 (56%), Gaps = 1/88 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
K+F+GGL + T ++SL+ F ++G+I +VVV+KD T+RSRGFGF+T+
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 72 DDAMSN-RPHNIDGRVVETKRAVPRDVR 98
DAM ++DGR + +A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQAGKSSDN 95
>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 = 99.6 bits (249), Expect = 7e-29
Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++ V + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 78 RPHNIDGRVVETKRAVPRDVR 98
N G+ ++ A+ +
Sbjct: 70 -QINFHGKKLKLGPAIRKQNL 89
>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 = 96.6 bits (241), Expect = 1e-27
Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
++ + VFI L + + +E+L +Q+G++ V V+ P T+ S+G F + +
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 71 VDDAMSNRPHN-------IDGRVVETKRAVPRD 96
++ +DGR ++ AV RD
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 102
>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 = 96.2 bits (240), Expect = 2e-27
Identities = 20/84 (23%), Positives = 37/84 (44%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E R VF L R L+ FF G++ DV ++ D ++RS+G ++ + E + V
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
A+ + G + + +
Sbjct: 81 PLAIGLTGQRLLGVPIIVQASQAE 104
>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 = 96.2 bits (240), Expect = 2e-27
Identities = 27/88 (30%), Positives = 50/88 (56%), Gaps = 2/88 (2%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + K+FIGGL+ T ++ L+A F + G I +V+++KD T +SRGF FIT+
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 72 DDAMSN-RPHNIDGRVVETKRAVPRDVR 98
+A + ++ G+ ++ ++A +
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSFQ 89
>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 = 93.8 bits (234), Expect = 8e-26
Identities = 12/85 (14%), Positives = 33/85 (38%), Gaps = 5/85 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-----VMKDPITKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + + + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
AM+ G+ ++ +R
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQ 89
Score = 86.9 bits (216), Expect = 4e-23
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + +
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 72 DDAMSN-RPHNIDGRVVETKRA 92
D A++ + + + +RA
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQRA 171
>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 = 88.0 bits (219), Expect = 2e-24
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 77 N-RPHNIDGRVVETKRAVPRDVR 98
N + GR + A P ++
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIK 95
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 87.0 bits (216), Expect = 5e-24
Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 5/86 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
LR VF+ G L +F +G + VV+ KD F + + +
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGARE 59
Query: 73 DAMSNRPHNIDGRVVETKRAVPRDVR 98
+S H++ G + + ++ +
Sbjct: 60 AVLSQSQHSLGGHRLRVRPREQKEFQ 85
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 87.5 bits (217), Expect = 1e-23
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+
Sbjct: 59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
Query: 72 DDAMSN 77
A+ N
Sbjct: 119 AAAIDN 124
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 89.3 bits (222), Expect = 1e-23
Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ +V++G + Y +++++ F +G I + + D +T + +GF F+ Y +
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83
Query: 72 DDAMSNR-PHNIDGRVVETKRAVPRDVR 98
A+ + GR ++ R
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPSNIGQA 111
Score = 88.1 bits (219), Expect = 3e-23
Identities = 22/90 (24%), Positives = 49/90 (54%), Gaps = 1/90 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 67 EAKMVDDAMSN-RPHNIDGRVVETKRAVPR 95
+A+ DA+S+ ++ G+ + +AV
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
>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 = 86.7 bits (215), Expect = 2e-23
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
P+ + + GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ +
Sbjct: 41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100
Query: 71 VDDAMS--NRPHNIDGRVVETKRAVPR 95
+A N +DGR + ++ +
Sbjct: 101 AKEAKERANG-MELDGRRIRVDFSITK 126
>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 = 85.1 bits (211), Expect = 4e-23
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + K+FIG + ++ L+ FE++G+I ++ V+KD T +G F+TY E
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 68 AKMVDDAMSN----RPHNIDGRVVETKRAVPR 95
+ A S + R ++ K A
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKPADSE 96
>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 = 85.0 bits (211), Expect = 4e-23
Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + + + + L YRT+ +SL+ FE++G + DV + ++P TK RGF F+ + + +
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 72 DDAMSNRP-HNIDGRVVETKRAVPRDVR 98
DA + +DGR + + A
Sbjct: 69 QDAEAAMDGAELDGRELRVQVARYGRRD 96
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 86.5 bits (214), Expect = 5e-23
Identities = 16/101 (15%), Positives = 40/101 (39%), Gaps = 3/101 (2%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSR 58
P + V++G + TTD+ L G ++V++ ++ +S+
Sbjct: 40 KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99
Query: 59 GFGFITYSEAKMVDDAMSNRP-HNIDGRVVETKRAVPRDVR 98
G+ + + V + P ++G V+ + A +++
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 84.3 bits (209), Expect = 5e-23
Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 7/83 (8%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYS---EAKMV 71
+ + + T +S+ + + ++ ++KD T+++RGF F+ S +A +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 72 DDAMSNR--PHNIDGRVVETKRA 92
+ + P IDG+ + A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92
>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 = 84.2 bits (209), Expect = 6e-23
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
P+ + + GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ +
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 72 DDAMS--NRPHNIDGRVV 87
+A N +DGR +
Sbjct: 71 KEAKERANG-MELDGRRI 87
>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 = 83.8 bits (208), Expect = 8e-23
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
S V++ L + T+ L F ++G++V V +MKD T++S+G FI + +
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 72 DDAMSN 77
+
Sbjct: 72 QNCTRA 77
>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 = 83.3 bits (207), Expect = 1e-22
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 77 N 77
N
Sbjct: 68 N 68
>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 = 82.2 bits (204), Expect = 3e-22
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+G L+ DE+L+ F+ + + VM D T SRG+GF++++ +AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 78 -RPHNIDGRVVETKRAVPRD 96
+ +++GR + A +
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82
>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 = 85.9 bits (212), Expect = 4e-22
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 3/84 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++IG L + TTDE L G +I+++ ++ +S+GF + M
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 76 SNRP-HNIDGRVVETKRAVPRDVR 98
P + G+ + +
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLS 153
>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 = 5e-22
Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+++G L + T++ L+ FE +G+I ++V+MKD T RS+G+GFIT+S+++ A+
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 78 -RPHNIDGRVVETKRAVPRDVR 98
+ GR + R
Sbjct: 67 LNGFELAGRPMRVGHVTERLDG 88
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 82.9 bits (205), Expect = 6e-22
Identities = 26/86 (30%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + +
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 72 DDAMS--NRPHNIDGRVVETKRAVPR 95
+DAM + +DGR + + A
Sbjct: 103 EDAMDAMDG-AVLDGRELRVQMARYG 127
>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 = 81.9 bits (203), Expect = 6e-22
Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+E V++GGLD + ++ L F Q G +V+ + KD +T + +G+GF+ + +
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 71 VDDAMSN-RPHNIDGRVVETKRAVPRDVRL 99
D A+ + G+ + +A + L
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99
>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 = 82.4 bits (204), Expect = 7e-22
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+G L T E ++A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 78 -RPHNIDGRVVETKRAVPR 95
+ GR + T A +
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>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 = 83.0 bits (205), Expect = 9e-22
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + +
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 72 DDAMSN-RPHNIDGRVVETKRAVPR 95
+DAM +DGR + + A
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYG 150
>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 = 81.1 bits (201), Expect = 1e-21
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 77 N-RPHNIDGRVVETKRAVPRDVR 98
N + + R ++ + D+
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDIS 85
>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 = 81.2 bits (201), Expect = 1e-21
Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ +++ + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ +
Sbjct: 11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADA 68
Query: 72 DDAMSNRP-HNIDGRVVETKRAVPRDVR 98
D A ++GR +E A R +
Sbjct: 69 DRAREKLHGTVVEGRKIEVNNATARVMT 96
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 81.2 bits (201), Expect = 2e-21
Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 3/96 (3%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
+ PR +++ + + +R D L+ F Q+G+I+DV ++ + + S+GF
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGF 71
Query: 61 GFITYSEAKMVDDAMSN-RPHNIDGRVVETKRAVPR 95
GF+T+ + D A ++GR +E A R
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 82.4 bits (204), Expect = 4e-21
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
P+S K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + +
Sbjct: 109 VVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168
Query: 71 VDDAMSN-RPHNIDGRVVETKRAVPR 95
D A++ + + + +RA
Sbjct: 169 TDQAIAGLNGMQLGDKKLLVQRASVG 194
Score = 78.1 bits (193), Expect = 2e-19
Identities = 12/87 (13%), Positives = 33/87 (37%), Gaps = 5/87 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-----VMKDPITKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + + + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDVR 98
AM+ G+ ++ +R
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPL 91
>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 = 80.0 bits (198), Expect = 4e-21
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++++G L + T++ L+ FE +G I + +M D T RS+G+GFIT+S+++
Sbjct: 23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 73 DAMSN-RPHNIDGRVVETKRAVPRD 96
A+ + GR ++ R
Sbjct: 83 KALEQLNGFELAGRPMKVGHVTERT 107
>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 = 79.5 bits (197), Expect = 4e-21
Identities = 19/79 (24%), Positives = 38/79 (48%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 77 NRPHNIDGRVVETKRAVPR 95
GR ++
Sbjct: 67 LDESLFRGRQIKVIPKRTN 85
>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 = 79.6 bits (197), Expect = 5e-21
Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 1/93 (1%)
Query: 6 DDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
D + +E + +FIG L+ + L+ + D+ V+ T +R FG++ +
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDF 65
Query: 66 SEAKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
A+ ++ A+ + G ++ ++ RD
Sbjct: 66 ESAEDLEKALELTGLKVFGNEIKLEKPKGRDGT 98
>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 = 79.1 bits (196), Expect = 5e-21
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
++I GL TTD+ L + +G+IV + D T + +G+GF+ + A+
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPR 95
A+ + ++ K++ P
Sbjct: 62 KAVTALKAS--GVQAQMA--KQSGPS 83
>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 = 79.2 bits (196), Expect = 6e-21
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK---RSRGFGFITYS---EAKMV 71
+FI L++ TT+E+L+ F + G I + K S GFGF+ Y +A+
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDVR 98
+ H +DG +E + +
Sbjct: 67 LKQLQG--HTVDGHKLEVRISERATKP 91
>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 = 79.2 bits (196), Expect = 8e-21
Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
++F+ L Y +++E L+ F +G + ++ D +TK+ +GF F+T+ A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 75 MSNRPHNIDGRVVETKRAVPRDVR 98
+ + GR++ + +
Sbjct: 70 VDGQV--FQGRMLHVLPSTIKKEA 91
>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 = 79.4 bits (196), Expect = 1e-20
Identities = 21/94 (22%), Positives = 44/94 (46%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
P+ ++ + R V++G +DY +T + L+A F G I + ++ D + +G+
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 62 FITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
+I ++E VD A++ GR ++
Sbjct: 82 YIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTN 115
>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 = 78.8 bits (195), Expect = 1e-20
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
SLR VF+G + Y T+E L+ F + G +V ++ D T + +G+GF Y + +
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 73 DAMSN-RPHNIDGRVVETKRAVPRDVR 98
AM N GR + A +
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKNK 91
>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 = 80.7 bits (200), Expect = 1e-20
Identities = 18/88 (20%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+E + +FIG L+ + L+ + D+ V+ D T +R FG++ + A+
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAED 66
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRDVR 98
++ A+ + G ++ ++ RD +
Sbjct: 67 LEKALELTGLKVFGNEIKLEKPKGRDSK 94
Score = 66.1 bits (162), Expect = 5e-15
Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 10/87 (11%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
+ + R + L + T++ L+ FE EI +S+G +I + +A
Sbjct: 95 KVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADA 149
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPR 95
+ + IDGR V +
Sbjct: 150 EKNLEEKQG--AEIDGRSVSLYYTGEK 174
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 79.8 bits (197), Expect = 1e-20
Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EP+ LR + + + + L+ FE++G I V ++ D T++SRG+GF+ +
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 72 DDAMS--NRPHNIDGRVVETKRAVPRDVR 98
A++ N NI + ++ A R
Sbjct: 98 QQAIAGLNG-FNILNKRLKVALAASGHQR 125
>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 = 78.0 bits (193), Expect = 1e-20
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+G L T ++ A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 78 -RPHNIDGRVVETKRAVPR 95
+ GR + T A +
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
>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 = 78.0 bits (193), Expect = 2e-20
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 3/86 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + + L T + LQ F +G I + + KD T +S+GF FI++ +
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 72 DDAMS--NRPHNIDGRVVETKRAVPR 95
A++ + D ++ + A P
Sbjct: 71 ARAIAGVSG-FGYDHLILNVEWAKPS 95
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 77.8 bits (192), Expect = 3e-20
Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 5/89 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
L++V L+ + L+ ++GE+ +V ++ P T++ G + ++ AK
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+ + G ++ + + R
Sbjct: 63 ETVKNLHLTS--VMGNIIHAQLDIKGQQR 89
>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 = 77.2 bits (191), Expect = 3e-20
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 3/84 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++IG L + TTDE L G +I+++ ++ +S+GF + M
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 76 SNRP-HNIDGRVVETKRAVPRDVR 98
P + G+ + +
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHH 86
>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 = 77.3 bits (191), Expect = 4e-20
Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ K++IG L T + L+ F + V+ G+ F+ Y +
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAI 58
Query: 73 DAMS--NRPHNIDGRVVETKRAVPRDVR 98
A+ + + G+++E +V + +R
Sbjct: 59 RAIETLSGKVELHGKIMEVDYSVSKKLR 86
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 76.9 bits (189), Expect = 7e-20
Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 9/98 (9%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD--PITKRSRGFGFITYSEA 68
+ RKVF+GGL ++ + A F ++G +V K +G+ F+ + E
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 69 KMVDDAMSNRPH-------NIDGRVVETKRAVPRDVRL 99
V + + ++ K R L
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNL 100
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 76.5 bits (189), Expect = 8e-20
Identities = 14/98 (14%), Positives = 34/98 (34%), Gaps = 2/98 (2%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+ + K+FI GL + T E L+ + G + D+ ++ + + +G
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61
Query: 62 FITYSEAKMVDDAMSNRP-HNIDGRVVETKRAVPRDVR 98
++ Y A+ I +++ +
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99
>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 = 78.4 bits (194), Expect = 1e-19
Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDA 74
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 75 MSNRPHNIDGRVVETKRAVPRDVR 98
+ + V P ++
Sbjct: 64 Q----NALHNMKVLPGMHHPIQMK 83
Score = 73.0 bits (180), Expect = 1e-17
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
++ + DS+ RK+FIG + + T+ ++ F +G+I + +++ P SRG
Sbjct: 80 IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGC 138
Query: 61 GFITYSEAKMVDDAMSN 77
F+T++ M A+
Sbjct: 139 AFVTFTTRAMAQTAIKA 155
>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 = 76.1 bits (188), Expect = 1e-19
Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 4/89 (4%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ + +F+ GL TT+E+L+ F V ++ D T S+GFGF+ ++ +
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 71 VDDAMSN-RPHNIDGRVVETKRAVPRDVR 98
A IDG V A P+
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95
>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 = 76.1 bits (188), Expect = 1e-19
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ E+ R VF+G L+ R +E L F Q G + V + KD + + FGF+ + + V
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESV 70
Query: 72 DDAMSN 77
A++
Sbjct: 71 SYAIAL 76
>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 = 75.3 bits (186), Expect = 2e-19
Identities = 23/84 (27%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+R +++G L Y T E ++ F Q+G++ +V ++ D TK+ +GFGF+ E + +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAI 59
Query: 76 SN-RPHNIDGRVVETKRAVPRDVR 98
+ + GR + A P+
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKSL 83
>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 = 75.0 bits (185), Expect = 3e-19
Identities = 19/96 (19%), Positives = 42/96 (43%), Gaps = 5/96 (5%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDP-ITKRSRGFGFITY 65
+ + ++ K+ + + ++ ++ F +GE+ V + K T RGFGF+ +
Sbjct: 6 SGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
Query: 66 S---EAKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+AK +A+ + H + GR + + A
Sbjct: 66 ITKQDAKKAFNALCHSTH-LYGRRLVLEWADSEVTV 100
>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 = 74.5 bits (184), Expect = 4e-19
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDV-VVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+FIG LD ++ L F +G I+ +M+DP T S+G+ FI ++ D A+
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 77 NRPHN---IDGRVVETKRAVPRDVR 98
N + R + A +D +
Sbjct: 67 AM--NGQYLCNRPITVSYAFKKDSK 89
>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 = 75.0 bits (185), Expect = 4e-19
Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 5/84 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+FI L D+ L F +G +V V D T S+ FGF++Y A+ +
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 75 MSNRPHNIDGRVVETKRAVPRDVR 98
M+ I + ++ + ++
Sbjct: 87 MNGFQ--IGMKRLKVQLKRSKNDS 108
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 75.0 bits (185), Expect = 4e-19
Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 8/103 (7%)
Query: 1 MKPRYD--DSKCTEPESLR-----KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPI 53
M+ YD + EP R +F+ G+ T+E + F ++GEI ++ + D
Sbjct: 1 MREDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60
Query: 54 TKRSRGFGFITYSEAKMVDDAMSN-RPHNIDGRVVETKRAVPR 95
T +G+ + Y K AM ++ G+ + R
Sbjct: 61 TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103
>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 = 76.5 bits (189), Expect = 4e-19
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
S + + L T E ++ F GEI +++D IT +S G+GF+ Y + K + A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 75 MS--NRPHNIDGRVVETKRAVPRD 96
++ N + + ++ A P
Sbjct: 61 INTLNG-LRLQTKTIKVSYARPSS 83
Score = 73.4 bits (181), Expect = 7e-18
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA-- 74
+++ GL T + L+ F Q+G I+ ++ D +T SRG GFI + + ++A
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 75 -MSNRPHNIDGRVVETKRA 92
++ + + + K A
Sbjct: 149 GLNGQKPSGATEPITVKFA 167
>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 = 75.5 bits (186), Expect = 4e-19
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 1/82 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 78 -RPHNIDGRVVETKRAVPRDVR 98
++ G+ + R
Sbjct: 84 LNGQDLMGQPISVDWCFVRGPP 105
>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 = 74.1 bits (183), Expect = 4e-19
Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPI-TKRSRGFGFITYSEAKMVDDAMS 76
KV IG L T + + F +G+I + + + + S+G+ ++ + + A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 77 NRP-HNIDGRVVETKRAVPRDVR 98
+ IDG+ + + R
Sbjct: 66 HMDGGQIDGQEITATAVLAPWPR 88
>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 = 74.2 bits (183), Expect = 7e-19
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+++ LD DE L+ F +G I VM + RS+GFGF+ +S EA
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 75 MSNRPHNIDGRVVETKRAVPRDVR 98
M+ R + + + A ++ R
Sbjct: 75 MNGRI--VATKPLYVALAQRKEER 96
>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 = 73.9 bits (182), Expect = 9e-19
Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 5/89 (5%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
T + + + L Y T+E+LQ FE+ + + +S+G+ FI ++ +
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFED 65
Query: 71 VDDAMSNRP-HNIDGRVVETKRAVPRDVR 98
+A+++ I+GR + + PR
Sbjct: 66 AKEALNSCNKREIEGRAIRLELQGPRGSP 94
>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 = 74.5 bits (183), Expect = 2e-18
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++G L + TT+E + F + G+I +++ D + K + GF F+ Y ++AM
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 77 NRP-HNIDGRVVETKRAVPRD 96
+D R++ T
Sbjct: 100 YINGTRLDDRIIRTDWDAGFK 120
>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 = 72.7 bits (179), Expect = 3e-18
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
RK+F+G L+ + ++E + F+ +G I + V++ P S+G F+ +S A+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIH 74
>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 = 72.7 bits (179), Expect = 4e-18
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 7/89 (7%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P +FI LD +++L F +G I+ V+ D S+G+GF+ + + +
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 59
Query: 73 DAMSNRPHN---IDGRVVETKRAVPRDVR 98
A+ N ++ R V R R R
Sbjct: 60 RAIEK--MNGMLLNDRKVFVGRFKSRKER 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 = 72.3 bits (178), Expect = 4e-18
Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 1/82 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ + ++ +Q F +GEI ++ + D T S+G+ + Y K A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 78 -RPHNIDGRVVETKRAVPRDVR 98
I G+ ++ + +
Sbjct: 88 LNGAEIMGQTIQVDWCFVKGPK 109
>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 = 5e-18
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
VF+ LDY+ + L+ F G +V +++D +SRG G +T+ EA
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAIS 74
Query: 74 AMSNRPHNIDGRVVETKRAVPRDVR 98
+ + + R + K +
Sbjct: 75 MFNGQL--LFDRPMHVKMDERALPK 97
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 72.0 bits (177), Expect = 8e-18
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 10/77 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+FI L TD L + F +G ++ V D T S+ FGF+++ A++ A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 75 MSNRPHNIDGRVVETKR 91
M +G V TKR
Sbjct: 102 M-------NGFQVGTKR 111
>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 = 71.4 bits (175), Expect = 9e-18
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIV-DVVVMKDP-ITKRSRGFGFITYS---EAKMV 71
++FIGG+ E + + E V DV+V ++RGF F+ Y A M
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
+ + G + A P
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPE 92
>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 = 71.5 bits (176), Expect = 1e-17
Identities = 13/84 (15%), Positives = 33/84 (39%), Gaps = 6/84 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
++I L ++ L+ + +G+++ +++D + SRG GF + + V
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH 85
Query: 75 MSNRPHNIDGRVVETKRAVPRDVR 98
+ + I + P +
Sbjct: 86 FNGKF--IKTPPGVSAPTEPLLCK 107
>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 = 74.6 bits (184), Expect = 1e-17
Identities = 12/93 (12%), Positives = 29/93 (31%), Gaps = 5/93 (5%)
Query: 9 KCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS-- 66
+ + + L T + + +G + ++ T +S+G+GF Y
Sbjct: 88 SVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKK 147
Query: 67 -EAKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
A + +P + R + +
Sbjct: 148 DSAARAKSDLLGKP--LGPRTLYVHWTDAGQLT 178
Score = 65.4 bits (160), Expect = 3e-14
Identities = 10/86 (11%), Positives = 21/86 (24%), Gaps = 7/86 (8%)
Query: 17 RKVFIGGLDYRTTD-ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVD 72
R + + L D ++L + + +GF + Y A+
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQ 243
Query: 73 DAMSNRPHNIDGRVVETKRAVPRDVR 98
+ G + P
Sbjct: 244 QQADGLS--LGGSHLRVSFCAPGPPG 267
Score = 51.1 bits (123), Expect = 4e-09
Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 11/91 (12%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + RK+ I GL T++ + + +K + +G F+T +
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQA 70
Query: 72 DDAMS--NRPHNIDGRVVETKRAVPRDVRLY 100
+ A++ ++ + R + + P D L
Sbjct: 71 EAAINAFHQ-SRLRERELSVQLQ-PTDALLC 99
>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 = 74.3 bits (183), Expect = 1e-17
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 6/86 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA--- 74
+ + L ++E L+ F Q+G + VV+ D R+ G GF+ ++ A
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALER 156
Query: 75 MSNRPH--NIDGRVVETKRAVPRDVR 98
+ R V + D
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDE 182
Score = 71.3 bits (175), Expect = 2e-16
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 10/80 (12%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
++F+G L T+E + FE++GE +V + +D RGFGFI +
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLA 71
Query: 72 DDAMSNRPHNIDGRVVETKR 91
+ A +DG +++++
Sbjct: 72 EIAK----AELDGTILKSRP 87
>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 = 71.2 bits (175), Expect = 1e-17
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 6/89 (6%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
E+ K+ + LD+ +D +Q F ++G + V D + RS G + + +A
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADAL 90
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
P +DGR ++ + +
Sbjct: 91 KAMKQYKGVP--LDGRPMDIQLVASQIDL 117
>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 = 72.6 bits (179), Expect = 1e-17
Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ + L TD L A F G I +M+D T S G+ F+ ++ A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 77 --NRPHNIDGRVVETKRAVPR 95
N + + ++ A P
Sbjct: 64 VLNG-ITVRNKRLKVSYARPG 83
Score = 69.1 bits (170), Expect = 3e-16
Identities = 18/66 (27%), Positives = 34/66 (51%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E +++ L TD+ L F ++G IV +++D +T R RG F+ Y++ +
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 72 DDAMSN 77
+A+S
Sbjct: 145 QEAISA 150
>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 = 70.4 bits (173), Expect = 2e-17
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+G L T+E ++ FE++G+ +V + KD +GFGFI + + A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 78 RP-HNIDGRVVETKRAVPRDVR 98
+ G+ + + A
Sbjct: 71 LDNMPLRGKQLRVRFACHSASL 92
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 69.9 bits (172), Expect = 2e-17
Identities = 13/88 (14%), Positives = 35/88 (39%), Gaps = 5/88 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++F+ L + T + L+ F + G ++ + + +S+G G + + ++ +
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62
Query: 73 DAMS--NRPHNIDGRVVETKRAVPRDVR 98
A N + GR ++ +
Sbjct: 63 RACRMMNG-MKLSGREIDVRIDRNASGP 89
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 71.8 bits (176), Expect = 3e-17
Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 1/82 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ + ++ +Q F +GEI ++ + D T S+G+ + Y K A
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 78 -RPHNIDGRVVETKRAVPRDVR 98
I G+ ++ + +
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPK 155
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 69.6 bits (170), Expect = 4e-17
Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 13/97 (13%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQW-----GEIVDVVVMKDPITKRSRGFGFITY 65
+ V + GL DE L +FE G ++ +R G +T+
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTF 54
Query: 66 SEAKMVDDAMSNRPHNIDGRVVETKRAVPRDVRLYLV 102
E + ++ H + G + + A PR L+
Sbjct: 55 REPADAERVLAQADHELHGAQLSLRPAPPRAPARLLL 91
>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 = 69.2 bits (170), Expect = 7e-17
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 8/87 (9%)
Query: 4 RYDDSKC--TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+D E+ K+ + LD+ +D +Q F ++G + V D + RS G
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTA 73
Query: 62 FITYS---EAKMVDDAMSNRPHNIDGR 85
+ + +A + P +DGR
Sbjct: 74 DVHFERKADALKAMKQYNGVP--LDGR 98
>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 = 68.8 bits (169), Expect = 8e-17
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 6/88 (6%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + R + L + T++ L+ FE E + +S+G +I +
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADA 66
Query: 72 DDAMSNRP-HNIDGRVVETKRAVPRDVR 98
+ + + IDGR V +
Sbjct: 67 EKNLEEKQGAEIDGRSVSLYYTGEKGGT 94
>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 = 69.2 bits (170), Expect = 9e-17
Identities = 14/59 (23%), Positives = 28/59 (47%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+ +++ L R T+ L + F ++ E + +T R RG FIT+ ++ A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 69.0 bits (169), Expect = 1e-16
Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 9/91 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEI--------VDVVVMKDPITKRSRGFGFITYSEA 68
+F+ GL T ES+ +F+Q G I + + D T + +G +++ +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 69 KMVDDAMSN-RPHNIDGRVVETKRAVPRDVR 98
A+ G ++ A R
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFATRRADF 98
>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 = 68.5 bits (168), Expect = 2e-16
Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 11/89 (12%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+ R++D V+ GG+ TD+ ++ F +G+I+++ V + +G+
Sbjct: 11 QLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYS 64
Query: 62 FITYS---EAKMVDDAMSNRPHNIDGRVV 87
F+ +S A +++ I+G VV
Sbjct: 65 FVRFSTHESAAHAIVSVNGTT--IEGHVV 91
>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 = 67.7 bits (166), Expect = 2e-16
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 13/85 (15%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ +F+ L T+E L+ F Q+G++ V +KD + FI + E AM
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 63
Query: 77 NRPHN---IDGRVVETKRAVPRDVR 98
N ++G +E A P D +
Sbjct: 64 E--MNGKDLEGENIEIVFAKPPDQK 86
>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 = 67.2 bits (165), Expect = 2e-16
Identities = 13/87 (14%), Positives = 36/87 (41%), Gaps = 9/87 (10%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ K+F+G + T + L++ FE+ G +++ V+K + F+ +
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAK 57
Query: 73 DAMSNRP-HNIDGRVVETKRAVPRDVR 98
A++ + G+ + + + +
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKK 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 = 67.7 bits (166), Expect = 2e-16
Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 11/90 (12%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
D + P + +IG + + T+ L F+ +G I+D + +G
Sbjct: 12 NPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGC 65
Query: 61 GFITYS---EAKMVDDAMSNRPHNIDGRVV 87
FI Y +A + A++N P GR +
Sbjct: 66 CFIKYDTHEQAAVCIVALANFP--FQGRNL 93
>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 = 67.4 bits (165), Expect = 5e-16
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
PE R ++I L Y+ T E + F ++G I + V P +RG ++ Y +
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAK 61
Query: 73 DAMSNRPH-NIDGR 85
+A+ + N+ R
Sbjct: 62 NAVDHLSGFNVSNR 75
>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 = 67.1 bits (164), Expect = 5e-16
Identities = 16/87 (18%), Positives = 37/87 (42%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + V + GL + + E + FF + + + + RS G F+ ++ ++
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDVR 98
+ A+ I R +E ++ +VR
Sbjct: 71 EKALKKHKERIGHRYIEIFKSSRAEVR 97
>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 = 66.1 bits (162), Expect = 9e-16
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
S++ +++ L T++E ++ F V K+ R + F+ +S +
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAV 65
Query: 73 DAMS--NRPHNIDGRVVETKRAVPRDVR 98
+AM N +DG +E A P D
Sbjct: 66 EAMKALNG-KVLDGSPIEVTLAKPVDKD 92
>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 = 66.8 bits (163), Expect = 9e-16
Identities = 17/93 (18%), Positives = 38/93 (40%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + + V + GL + T E + FF + + + + + G F+ ++
Sbjct: 34 SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRDVRLY 100
++ + A+ I R +E ++ +VR Y
Sbjct: 94 QELAEKALGKHKERIGHRYIEVFKSSQEEVRSY 126
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 65.9 bits (161), Expect = 1e-15
Identities = 10/76 (13%), Positives = 28/76 (36%), Gaps = 1/76 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V+I G T + ++ + E G+++++ + + K +G F+ + + +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70
Query: 77 NRPHNIDGRVVETKRA 92
+
Sbjct: 71 TPGQKYKETDLLILFK 86
>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 = 66.3 bits (162), Expect = 1e-15
Identities = 16/102 (15%), Positives = 35/102 (34%), Gaps = 9/102 (8%)
Query: 6 DDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEI--------VDVVVMKDPITKRS 57
E +++ GL+ T + L FF+Q G + + + D T +
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64
Query: 58 RGFGFITYSEAKMVDDAMSN-RPHNIDGRVVETKRAVPRDVR 98
+G ++Y + A+ + G ++ A +
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
>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 = 65.8 bits (161), Expect = 1e-15
Identities = 10/62 (16%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++G L+ + + F GE V V ++++ +T G+ F+ +++ + +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 76 SN 77
Sbjct: 70 HK 71
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 65.8 bits (161), Expect = 1e-15
Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++G L + T + A F+ I V +++D T + +GF ++ + E + +A++
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 77 NRPHNIDGRVVETKRAVPRDVR 98
+ R + A R
Sbjct: 75 YDGALLGDRSLRVDIAEGRKQD 96
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 67.2 bits (164), Expect = 2e-15
Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 6/90 (6%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
E+ K+ + LD+ +D +Q F ++G + V D + RS G + + +A
Sbjct: 84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADA 142
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
P +DGR ++ + +
Sbjct: 143 LKAMKQYKGVP--LDGRPMDIQLVASQIDL 170
>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 = 65.0 bits (159), Expect = 3e-15
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPI-TKRSRGFGFITYSEAKMVDDAM 75
F+G L Y T+ES++ FF I V + ++P +R +GFG+ + + + A+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
Query: 76 SNRPHNIDGRVVETKRAVPRDVR 98
S ++ + + A +
Sbjct: 75 SLNEESLGNKRIRVDVADQAQDK 97
>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 = 64.1 bits (157), Expect = 4e-15
Identities = 17/85 (20%), Positives = 42/85 (49%), Gaps = 9/85 (10%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ K+FIG L T++ +++ FEQ+G++++ ++K +GF+ + +
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAE 56
Query: 73 DAMSNRP-HNIDGRVVETKRAVPRD 96
DA+ N + + G + + + +
Sbjct: 57 DAIRNLHHYKLHGVNINVEASKNKS 81
>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 = 65.6 bits (161), Expect = 7e-15
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
++ +F+G L+ DE+L+ F+ + + VM D T SRG+
Sbjct: 74 NWAFQSQQSSSDDTF--NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY 131
Query: 61 GFITYSEAKMVDDAMSN 77
GF++++ +AM +
Sbjct: 132 GFVSFTSQDDAQNAMDS 148
Score = 61.0 bits (149), Expect = 4e-13
Identities = 16/74 (21%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
R +++G LD T++ L+ +F+ G I ++ +M D ++ + F+ Y +A +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 74 AMSNRPHNIDGRVV 87
++ + I+ +V
Sbjct: 60 TLNGKQ--IENNIV 71
>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 = 63.9 bits (156), Expect = 7e-15
Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 8/74 (10%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVD--------VVVMKDPITKRSRGFGFI 63
+F+ GL T ES+ +F+Q G I + + D T + +G +
Sbjct: 9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68
Query: 64 TYSEAKMVDDAMSN 77
++ + A+
Sbjct: 69 SFDDPPSAKAAIDW 82
>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 = 63.9 bits (156), Expect = 8e-15
Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++++G L + ++ F ++G I D+ + F F+ + + + +DA+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVY 79
Query: 77 NRP-HNIDGR 85
R ++ DG
Sbjct: 80 GRDGYDYDGY 89
>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 = 63.4 bits (155), Expect = 8e-15
Identities = 14/89 (15%), Positives = 38/89 (42%), Gaps = 11/89 (12%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++ K+ +G + T++ L+A FE++G +++ ++ + + F+ A+
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAV 58
Query: 73 DAMSNR-PHNIDGR--VVETKRAVPRDVR 98
+A+ G+ V+ + R
Sbjct: 59 EAIRGLDNTEFQGKRMHVQLSTSRLRTAS 87
>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 = 63.4 bits (155), Expect = 1e-14
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPIT-KRSRGFGFITYSEAKMVDDAM 75
F+G L Y T+ES++ FF I V + ++P +R +GFG+ + + + A+
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78
Query: 76 SNRPHNIDGRVVETKRAVPRD 96
S ++ R + A
Sbjct: 79 SLNEESLGNRRIRVDVADQAQ 99
>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 = 64.5 bits (157), Expect = 1e-14
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 8/82 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
KV++G L L+ F +G + V V ++P GF F+ + + + DA+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVR 128
Query: 77 NRP-HNIDGR--VVETKRAVPR 95
+ G VE R
Sbjct: 129 ELDGRTLCGCRVRVELSNGEKR 150
>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 = 66.5 bits (163), Expect = 1e-14
Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 2/81 (2%)
Query: 17 RKVFIGGLDYRTTDE-SLQAFFEQWGEIVDVVVMKD-PITKRSRGFGFITYSEAKMVDDA 74
R++ I L DE L+ FE +G I + + + F+ + + A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270
Query: 75 MSNRPHNIDGRVVETKRAVPR 95
+ + R + A +
Sbjct: 271 LQMNRSLLGNREISVSLADKK 291
Score = 64.2 bits (157), Expect = 1e-13
Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 5/83 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
+++ T +++ + + + + SR F +I + +A+ +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 74 AMSNRPHNIDGRVVETKRAVPRD 96
++ I+G + TK + P +
Sbjct: 178 KLNGLK--IEGYTLVTKVSNPLE 198
Score = 61.9 bits (151), Expect = 8e-13
Identities = 11/75 (14%), Positives = 24/75 (32%), Gaps = 2/75 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V + L + +F+ G I+ V V K++ F I ++ A++
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101
Query: 79 PHNIDGRVVETKRAV 93
+ +
Sbjct: 102 HKVVGQNEIIVSHLT 116
>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 = 62.3 bits (152), Expect = 2e-14
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDD 73
+++GGL T+ L+ F Q+GEI + V++ + FI + A++ +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAE 66
Query: 74 AMSNRPHNIDGRVV 87
N+ ++GR +
Sbjct: 67 KSFNK-LIVNGRRL 79
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 62.7 bits (153), Expect = 2e-14
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KV++G L L+ F +G + V + ++P GF F+ + + + +DA+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 78 RP-HNIDGR--VVETKRAVPR 95
I G VE +PR
Sbjct: 57 LDGKVICGSRVRVELSTGMPR 77
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 62.7 bits (153), Expect = 2e-14
Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 11/100 (11%)
Query: 2 KPRYDDSKCTEPESL--RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRG 59
PR + L ++F+ + L F +G + +V ++ G
Sbjct: 15 VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------G 66
Query: 60 FGFITYSEAKMVDDAMSNRP-HNIDGRVVETKRAVPRDVR 98
F F+ + EA+ A+ + + +E + R
Sbjct: 67 FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106
>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 = 62.1 bits (151), Expect = 5e-14
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 13/79 (16%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
P +++ G D T L+ F +G I+D+ + R F+TY A
Sbjct: 35 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESA 86
Query: 69 KMVDDAMSNRPHNIDGRVV 87
++ ++ +
Sbjct: 87 DQAVAELNGT--QVESVQL 103
>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 = 61.1 bits (149), Expect = 9e-14
Identities = 10/66 (15%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ R +++G L T+ + F Q G ++ + + + F+ + E +
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDA 68
Query: 72 DDAMSN 77
A++
Sbjct: 69 AAALAA 74
>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 = 63.5 bits (155), Expect = 9e-14
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SE 67
+ +++G L T+ L F G I+ + V +D IT+RS G+ ++ + ++
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 68 AKMVDDAMSNRPHNIDGRVV 87
A+ D M+ I G+ V
Sbjct: 70 AERALDTMNFDV--IKGKPV 87
Score = 62.3 bits (152), Expect = 2e-13
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 7/83 (8%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FI LD +++L F +G I+ V+ D S+G+GF+ + + + A+
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK- 162
Query: 79 PHN---IDGRVVETKRAVPRDVR 98
N ++ R V R R R
Sbjct: 163 -MNGMLLNDRKVFVGRFKSRKER 184
>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 = 61.8 bits (150), Expect = 1e-13
Identities = 12/88 (13%), Positives = 35/88 (39%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ E+ V++ GL + ++ + FF++ + D + + ++ G GF+ +
Sbjct: 20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 79
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRDVR 98
A+ + R ++ + +
Sbjct: 80 YKAALCRHKQYMGNRFIQVHPITKKGML 107
>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 = 60.4 bits (147), Expect = 1e-13
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
P +++ G D T L+ F +G I+D+ + R F+TY + +
Sbjct: 11 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESA 62
Query: 72 DDAMSNRPHNIDGRVVETKR 91
D A++ ++G VE+ +
Sbjct: 63 DQAVA----ELNGTQVESVQ 78
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 60.4 bits (147), Expect = 2e-13
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 4/83 (4%)
Query: 19 VFIGGLDYRTTDESLQAFF-EQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS- 76
+F+G L D L FF + + V+ D T S+G+GF+ +++ A++
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 77 -NRPHNIDGRVVETKRAVPRDVR 98
+ + V A+P+ R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
>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 = 59.6 bits (145), Expect = 3e-13
Identities = 10/83 (12%), Positives = 24/83 (28%), Gaps = 1/83 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ + + + + + + FF + I V +K G + +
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71
Query: 73 DAMSNRP-HNIDGRVVETKRAVP 94
A+ + I R V+
Sbjct: 72 AAVIDLNDRPIGSRKVKLVLGSG 94
>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 = 59.8 bits (145), Expect = 4e-13
Identities = 10/82 (12%), Positives = 22/82 (26%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
I + + T + F E + V + + G + + +
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75
Query: 77 NRPHNIDGRVVETKRAVPRDVR 98
++GR D+R
Sbjct: 76 LHRKKLNGREAFVHVVTLEDMR 97
>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 = 59.4 bits (144), Expect = 4e-13
Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 2/80 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V + G+ + + ++ FF + V ++KD R+ G G + + + +A+
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 79 PHNIDGRVVETKRAVPRDVR 98
+ R VE A R
Sbjct: 77 RMLMIQRYVEVSPATERQWV 96
>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 = 62.9 bits (152), Expect = 5e-13
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 3/100 (3%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
P D + + + +F+ ++Y TT+ L+ FE +G I + ++ + + RG+
Sbjct: 90 DPHNDPNAQGDAF--KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 62 FITYSEAKMVDDAMSNRPH-NIDGRVVETKRAVPRDVRLY 100
FI Y + + A + IDGR V R V+ +
Sbjct: 148 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGW 187
>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 = 58.5 bits (142), Expect = 7e-13
Identities = 10/77 (12%), Positives = 24/77 (31%), Gaps = 1/77 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ + + + + + + FF + I V +K G + +
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71
Query: 73 DAMSNRP-HNIDGRVVE 88
A+ + I R V+
Sbjct: 72 AAVIDLNDRPIGSRKVK 88
>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 = 58.7 bits (142), Expect = 1e-12
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 11/80 (13%)
Query: 19 VFIGGLDYRTTDESL---QAFFEQWGEIVDVVVMKDPIT---KRSRGFGFITYS---EAK 69
VF+ GL R D + +F ++G+I VV+ + ++TY +A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 70 MVDDAMSNRPHNIDGRVVET 89
++N +DGR ++
Sbjct: 78 RAIQCVNNVV--VDGRTLKA 95
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 56.3 bits (136), Expect = 5e-12
Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 11/89 (12%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
YDD T V I GL + L +++G I VVVM +
Sbjct: 9 MENYDDPHKTPAS--PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQA 60
Query: 62 FITY---SEAKMVDDAMSNRPHNIDGRVV 87
+ + A + ++ I G
Sbjct: 61 LVEFEDVLGACNAVNYAADNQIYIAGHPA 89
>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 = 56.1 bits (136), Expect = 6e-12
Identities = 14/65 (21%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 17 RKVFIGGLDYRTTDESLQ----AFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++I L+ + + L+ A F ++G+I+D++V + + RG F+ + E
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 65
Query: 73 DAMSN 77
+A+ +
Sbjct: 66 NALRS 70
>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 = 55.4 bits (134), Expect = 9e-12
Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 2/82 (2%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ + V + G + T++++ F + V + ++++ G+ F+ +S +
Sbjct: 5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAP-LKPVAIRIVRNA-HGNKTGYIFVDFSNEEE 62
Query: 71 VDDAMSNRPHNIDGRVVETKRA 92
V A+ + GR +E R
Sbjct: 63 VKQALKCNREYMGGRYIEVFRE 84
>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 = 55.5 bits (134), Expect = 1e-11
Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 2/87 (2%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + V + GL YR T+ + FF + V + P R G + ++ +
Sbjct: 11 QSTTGHCVHMRGLPYRATENDIYNFFSP-LNPMRVHIEIGP-DGRVTGEADVEFATHEDA 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDVR 98
AM+ N+ R VE
Sbjct: 69 VAAMAKDKANMQHRYVELFLNSTAGTS 95
>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 = 54.9 bits (133), Expect = 2e-11
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++++GGL T+ +L F+++G I + + F +I Y A +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAACA 71
Query: 77 N 77
Sbjct: 72 K 72
>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 = 55.6 bits (134), Expect = 2e-11
Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 2/97 (2%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+ D + + V + GL Y+ T+ + FF V V + P R G
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEA 89
Query: 62 FITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+ ++ + AMS N+ R +E
Sbjct: 90 DVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGAS 126
>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 = 57.2 bits (137), Expect = 4e-11
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 12/89 (13%)
Query: 17 RKVFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
++I L+ + + SL A F Q+G+I+D++V + + + RG F+ + A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+M P + + + A
Sbjct: 67 NALRSMQGFP--FYDKPMRIQYAKTDSDI 93
Score = 39.1 bits (90), Expect = 1e-04
Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 8/80 (10%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
+E +F+ L T + L F Q+ +V ++
Sbjct: 192 PGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDI 246
Query: 61 GFITYS---EAKMVDDAMSN 77
F+ + +A DA+
Sbjct: 247 AFVEFDNEVQAGAARDALQG 266
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 54.0 bits (130), Expect = 5e-11
Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 4/76 (5%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + +RK+ I + E L + Q+G + + +TYS
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVVNVTYSSKDQA 67
Query: 72 DDAMSNRP-HNIDGRV 86
A+ ++
Sbjct: 68 RQALDKLNGFQLENFT 83
>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 = 53.9 bits (130), Expect = 6e-11
Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 10/84 (11%)
Query: 17 RKVFIGGLDY-RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+VFIG L+ ++ F ++G + V K G+ F+ YS + A+
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAV 79
Query: 76 SNRP-HNIDGRVVETKRAVPRDVR 98
+ G+ ++ A
Sbjct: 80 LGENGRVLAGQTLDINMAGEPKPD 103
>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 = 53.2 bits (128), Expect = 6e-11
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 5/80 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVM-KDPI----TKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + +P+ + + F F+ +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 72 DDAMSNRPHNIDGRVVETKR 91
AM+ G+ ++ +R
Sbjct: 67 TQAMAFDGIIFQGQSLKIRR 86
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 53.4 bits (128), Expect = 2e-10
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 7/79 (8%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKR 56
M S E + V I ++ E L A G+I+D+VV +
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDD 70
Query: 57 SRGFGFITYSEAKMVDDAM 75
+ G +I ++ + +
Sbjct: 71 NSGKAYIVFATQESAQAFV 89
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 53.4 bits (128), Expect = 2e-10
Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 3/89 (3%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEI---VDVVVMKDPITKRSRGFGFITYSEAK 69
E+ V + GL + T E + AFF Q I + ++ R G F+ ++ +
Sbjct: 20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEE 79
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+A+ + R +E R+ +V+
Sbjct: 80 YAQNALRKHKDLLGKRYIELFRSTAAEVQ 108
>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 = 53.0 bits (127), Expect = 2e-10
Identities = 12/89 (13%), Positives = 34/89 (38%), Gaps = 10/89 (11%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
DS+ S R + I L T+ + + +G++ +++++ + +
Sbjct: 18 GSHMGDSRSAGVPS-RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 70
Query: 62 FITY---SEAKMVDDAMSNRPHNIDGRVV 87
FI A + + ++ + G+ +
Sbjct: 71 FIEMNTEEAANTMVNYYTSVTPVLRGQPI 99
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 51.8 bits (125), Expect = 3e-10
Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 15/93 (16%)
Query: 11 TEPESLR---KVFIGGLDYRTTDES-LQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
TE ++ ++FIG L + + L F +G I+ + + FGFI +
Sbjct: 2 TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD 53
Query: 67 EAKMVDDAMSNRP-HNIDGR--VVETKRAVPRD 96
+ V DA+ G+ ++E + R
Sbjct: 54 NPQSVRDAIECESQEMNFGKKLILEVSSSNARP 86
>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 = 3e-10
Identities = 18/109 (16%), Positives = 37/109 (33%), Gaps = 19/109 (17%)
Query: 3 PRYDDSKCTE-PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
R++ + V GGL + L E+ G + +++ + + +
Sbjct: 13 LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYS 66
Query: 62 FITYS---EAKMVDDAMSNRPHNIDGRVVETKRAVPRDVRLYLVFCVSV 107
F Y E+K ++ + E + + + LYL F V
Sbjct: 67 FARYRTTEESKRAYVTLNGK---------EVVDDLGQKITLYLNFVEKV 106
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 51.7 bits (124), Expect = 3e-10
Identities = 10/58 (17%), Positives = 24/58 (41%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
I ++L + F + G++V++ D T +++GF F+ + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
>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 = 51.8 bits (124), Expect = 4e-10
Identities = 17/90 (18%), Positives = 28/90 (31%), Gaps = 2/90 (2%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSEA 68
E + + + GL + T E + FF + + + RG I
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
+ V A+ + R VE DV
Sbjct: 66 QDVQKALEKHRMYMGQRYVEVYEINNEDVD 95
>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 = 51.5 bits (124), Expect = 4e-10
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 12/83 (14%)
Query: 17 RKVFIGGLDYRTTDES-LQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++FIG L + + L F +G I+ + + FGFI + + V DA+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 74
Query: 76 SNRP-HNIDGR--VVETKRAVPR 95
G+ ++E + R
Sbjct: 75 EXESQEMNFGKKLILEVSSSNAR 97
>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 = 49.4 bits (118), Expect = 4e-09
Identities = 14/88 (15%), Positives = 26/88 (29%), Gaps = 11/88 (12%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
V + GL + L E++G I V++M +
Sbjct: 4 GSSGSHHKVSVS--PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQAL 55
Query: 63 ITY---SEAKMVDDAMSNRPHNIDGRVV 87
+ + AK ++ P I G+
Sbjct: 56 VEFENIDSAKECVTFAADVPVYIAGQQA 83
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 49.5 bits (118), Expect = 4e-09
Identities = 10/74 (13%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDD 73
R + I L T+ + + +G++ +++++K + FI A + +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70
Query: 74 AMSNRPHNIDGRVV 87
++ + G+ +
Sbjct: 71 YYTSVTPVLRGQPI 84
>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 = 49.5 bits (118), Expect = 4e-09
Identities = 15/89 (16%), Positives = 30/89 (33%), Gaps = 4/89 (4%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQ---WGEIVDVVVMKDPITKRSRGFGFITYSEA 68
E V + GL + + E +Q F + V + R G F+
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESE 71
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPRDV 97
V A+ ++ R +E ++ ++
Sbjct: 72 DDVKLALKKDRESMGHRYIEVFKSHRTEM 100
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 48.7 bits (116), Expect = 5e-09
Identities = 11/86 (12%), Positives = 25/86 (29%), Gaps = 6/86 (6%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
V++G L L+ + G + + + R F+ Y ++
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLT-----WQGPRRRAFLHYPDSAA 68
Query: 71 VDDAMSNRP-HNIDGRVVETKRAVPR 95
A+S + + A +
Sbjct: 69 AQQAVSCLQGLRLGTDTLRVALARQQ 94
>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 = 49.1 bits (117), Expect = 9e-09
Identities = 17/111 (15%), Positives = 37/111 (33%), Gaps = 21/111 (18%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEI--------VDVVVMKDPIT 54
+ + EP ++++ L ++ L+ F ++ + D+ +MK
Sbjct: 34 SVFRSYEPGEPNC--RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK---E 88
Query: 55 KRSRGFGFITYS---EAKMVDDAMSNRPHNIDGR---VVETKRAVPRDVRL 99
R +G FI A + + G+ V + A P+
Sbjct: 89 GRMKGQAFIGLPNEKAAAKALKEANGYV--LFGKPMVVQFARSARPKQDPK 137
>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 = 47.5 bits (113), Expect = 2e-08
Identities = 10/74 (13%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDD 73
R + I L T+ + A +G++ +++++K + F+ A + +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVN 69
Query: 74 AMSNRPHNIDGRVV 87
S ++ + +
Sbjct: 70 YYSAVTPHLRNQPI 83
>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 = 48.1 bits (114), Expect = 2e-08
Identities = 16/100 (16%), Positives = 30/100 (30%), Gaps = 4/100 (4%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQ---WGEIVDVVVMKDPITKRSR 58
R E V + GL + + E +Q F V + R
Sbjct: 30 MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQS 88
Query: 59 GFGFITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDVR 98
G F+ V A+ ++ R +E ++ ++
Sbjct: 89 GEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMD 128
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 47.0 bits (112), Expect = 3e-08
Identities = 11/76 (14%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 17 RKVFIGGLDYRTTD------ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ + + D + F ++G+I + ++ +++G+ F+ Y+
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 73
Query: 71 VDDAMSNR-PHNIDGR 85
DA+ N + +D +
Sbjct: 74 AVDAVKNADGYKLDKQ 89
>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 = 46.3 bits (110), Expect = 5e-08
Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 10/80 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS- 76
+V + GL + + L+ + G++ V +D G G + + + + A+
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69
Query: 77 -NRPHNIDGRVVETKRAVPR 95
+ ET +
Sbjct: 70 LDN-TKFRSHEGETAYIRVK 88
>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 = 5e-08
Identities = 7/70 (10%), Positives = 24/70 (34%), Gaps = 8/70 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ + L + + + + + +K R++ F+T + +A+
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 77 NR-PHNIDGR 85
++ G+
Sbjct: 59 MFHQYSFRGK 68
>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 = 47.1 bits (111), Expect = 9e-08
Identities = 10/90 (11%), Positives = 29/90 (32%), Gaps = 1/90 (1%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
+ R V+I G T + ++ + E G+++++ + + K +G
Sbjct: 94 KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGS 152
Query: 61 GFITYSEAKMVDDAMSNRPHNIDGRVVETK 90
F+ + + + +
Sbjct: 153 IFVVFDSIESAKKFVETPGQKYKETDLLIL 182
>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 = 46.8 bits (111), Expect = 1e-07
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 19 VFIGGLD-YRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+ + L+ R T +SL F +G++ V ++ + + + ++ AMS+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Score = 41.0 bits (96), Expect = 1e-05
Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 7/64 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+ + + ++E L+ F G +V + R I EA +
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDL 178
Query: 76 SNRP 79
N
Sbjct: 179 HNHD 182
>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 = 46.2 bits (109), Expect = 2e-07
Identities = 6/78 (7%), Positives = 20/78 (25%), Gaps = 5/78 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+ T+E+ ++ G V G + + +A +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 76 SNRPHNIDGRVVETKRAV 93
++ + + +
Sbjct: 186 NH--YQMKNPNGPYPYTL 201
Score = 44.3 bits (104), Expect = 1e-06
Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 19 VFIGGLDY-RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+ + GLD + + + F +G + V MK G + ++ VD A+++
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 44.8 bits (106), Expect = 2e-07
Identities = 11/86 (12%), Positives = 28/86 (32%), Gaps = 6/86 (6%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P ++ + L + + L+ + T+ G G + + +++
Sbjct: 25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILV 81
Query: 73 DAMS--NRPHNIDGRVVETKRAVPRD 96
+A+ N G V+ +R
Sbjct: 82 EALERLNN-IEFRGSVITVERDDNPP 106
>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 = 46.1 bits (109), Expect = 2e-07
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 19 VFIGGLD-YRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+ + L+ R T +SL F +G++ V ++ + + + ++ AMS+
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 91
Score = 43.4 bits (102), Expect = 2e-06
Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 7/64 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+ + + ++E L+ F G +V ++ R I EA +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQALIDL 209
Query: 76 SNRP 79
N
Sbjct: 210 HNHD 213
>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 = 43.3 bits (102), Expect = 1e-06
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 10/81 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+V + GL + + L+ + G++ V +D G G + + + + A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 69
Query: 77 --NRPHNIDGRVVETKRAVPR 95
+ ET +
Sbjct: 70 KLDN-TKFRSHEGETAYIRVK 89
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 42.4 bits (100), Expect = 1e-06
Identities = 9/65 (13%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 19 VFIGGL------DYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ + + + F ++G+I + ++ +++G+ F+ Y+
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61
Query: 73 DAMSN 77
DA+ N
Sbjct: 62 DAVKN 66
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 44.4 bits (104), Expect = 1e-06
Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 18/75 (24%)
Query: 17 RKVFIGGLDY---------RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY-- 65
+ +++GG+D + ++ F + G+I + ++ S+ GF+ +
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKY 188
Query: 66 -SEAKMVDDAMSNRP 79
+ A+ +AMSN+
Sbjct: 189 QANAEFAKEAMSNQT 203
>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 = 42.1 bits (99), Expect = 2e-06
Identities = 10/70 (14%), Positives = 21/70 (30%), Gaps = 6/70 (8%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + S + L T +Q F ++G + V++ + + E
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLE 55
Query: 68 AKMVDDAMSN 77
A +
Sbjct: 56 PLEARKAFRH 65
>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 = 38.4 bits (89), Expect = 5e-05
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 12 EPESLRKVFIGGLDY-RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ E R + + L + +D ++ E +G+I + ++M+ + FI +
Sbjct: 21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETRED 74
Query: 71 VDDAMS---NRPHNIDGRVV 87
+ + GR V
Sbjct: 75 AMAMVDHCLKKALWFQGRCV 94
>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 = 36.2 bits (83), Expect = 7e-04
Identities = 10/60 (16%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+ + L Y T + L F ++G ++ ++ TK ++ + Y++ A +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLSL 104
>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 = 36.0 bits (82), Expect = 0.001
Identities = 17/114 (14%), Positives = 35/114 (30%), Gaps = 35/114 (30%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
F+ D + + ++ + EI +++ KD ++ R F + + +MV
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 74 AMS--------------------------------NRPHNIDGRVVETKRAVPR 95
+ +R +N D +V K V R
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN-DNQVF-AKYNVSR 133
>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 = 34.6 bits (79), Expect = 0.004
Identities = 23/118 (19%), Positives = 43/118 (36%), Gaps = 28/118 (23%)
Query: 6 DDSKCTEPESLRKVFIGGLDYRTTDESLQAF----------FEQ---WG-EIVDVVV--M 49
DD T E + K F+G + + F FE G +I + +
Sbjct: 51 DDEPTTPAELVGK-FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLL 109
Query: 50 KDPITKRSRGFGFI-TYSEAKMVDDAMSNRPHNIDGRVVETK--RAVPR-DVRLYLVF 103
++ T + I Y A+++ + RP + + + RAV + +L +F
Sbjct: 110 QENDTTLVKTKELIKNYITARIM----AKRPFD---KKSNSALFRAVGEGNAQLVAIF 160
>2hzl_A Trap-T family sorbitol/mannitol transporter, periplasmic binding
protein, SMOM; trap transporter, periplasmic subunit,
ligand binding; 1.40A {Rhodobacter sphaeroides 2} PDB:
2hzk_A
Length = 365
Score = 30.1 bits (68), Expect = 0.11
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 26 YRTTDESLQAFFEQWGEIVDVVVMKDPITKR 56
+ E LQA FE E+ + +P K+
Sbjct: 299 RPFSPEILQACFEAANEVYAEMEASNPAFKK 329
>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 = 27.0 bits (59), Expect = 1.6
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 12/81 (14%)
Query: 4 RYDDSKCTEPESLRKVFI--GGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
R++ + + + + + GGL + L E+ G VD ++M ++ +
Sbjct: 7 RHEGIETVS-YATQSLVVANGGLGNGVSRNQLLPVLEKCGL-VDALLMPP-----NKPYS 59
Query: 62 FITYS---EAKMVDDAMSNRP 79
F Y E+K ++ +
Sbjct: 60 FARYRTTEESKRAYVTLNGKE 80
>2koj_A Partitioning defective 3 homolog; PDZ domain, structural
genomics, alternative splicing, cell cycle, cell
division, cell junction, coiled coil; NMR {Mus
musculus} PDB: 2ogp_A
Length = 111
Score = 25.4 bits (56), Expect = 2.9
Identities = 5/25 (20%), Positives = 12/25 (48%), Gaps = 5/25 (20%)
Query: 38 EQWGEIVDVVVMKDPITKRSRGFGF 62
++ G+ +++ + K G GF
Sbjct: 7 KKVGKRLNIQLKKGT-----EGLGF 26
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT,
cytoplasmic vesicle, membrane, Ca structural protein;
7.94A {Bos taurus}
Length = 190
Score = 25.1 bits (54), Expect = 5.4
Identities = 6/7 (85%), Positives = 7/7 (100%)
Query: 12 EPESLRK 18
EPES+RK
Sbjct: 83 EPESIRK 89
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 25.1 bits (54), Expect = 5.4
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 28 TTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D S++ +F+++GEI DP + I Y+
Sbjct: 18 IQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYA 56
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 121
Score = 24.6 bits (53), Expect = 7.1
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDV 46
F G LD +T E L F GEI +
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWI 49
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
0.324 0.140 0.417
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: 1,806,968
Number of extensions: 99112
Number of successful extensions: 636
Number of sequences better than 10.0: 1
Number of HSP's gapped: 504
Number of HSP's successfully gapped: 203
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)