RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1928
(105 letters)
>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 = 92.1 bits (229), Expect = 7e-26
Identities = 46/63 (73%), Positives = 52/63 (82%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 51 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 110
Query: 61 AAD 63
A
Sbjct: 111 VAS 113
>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 = 90.8 bits (226), Expect = 1e-25
Identities = 46/61 (75%), Positives = 53/61 (86%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct: 45 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 104
Query: 61 A 61
Sbjct: 105 V 105
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 88.4 bits (219), Expect = 1e-23
Identities = 46/63 (73%), Positives = 52/63 (82%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 104 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163
Query: 61 AAD 63
A
Sbjct: 164 VAS 166
>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 = 76.6 bits (189), Expect = 8e-20
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ E+FS G + A + D+ G+S G + +E+ +A++A+ +NG L RPM +++
Sbjct: 32 LKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD 91
Query: 62 ADVSVLENTVPRPVARGGRGGASGG 86
+ P R + G S G
Sbjct: 92 ERALPKGDFFPPE--RPQQSGPSSG 114
>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 = 63.3 bits (155), Expect = 3e-14
Identities = 13/58 (22%), Positives = 32/58 (55%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
++ + F GP+ + K+ D++ +++ A + Y + DA A++ NG ++ ++I
Sbjct: 16 ILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKI 73
Score = 56.4 bits (137), Expect = 1e-11
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ F +F S + +D +G S G + + + DA AM G L+GRP++I
Sbjct: 103 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
Query: 60 LAA 62
AA
Sbjct: 163 WAA 165
>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 = 62.5 bits (152), Expect = 6e-14
Identities = 32/106 (30%), Positives = 46/106 (43%), Gaps = 10/106 (9%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
IYELFS+ G +K + D+ + G + Y R+DA AM+ NG LD R ++
Sbjct: 55 QIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 114
Query: 60 LAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTY-RPRGGLKKT 104
A + + GRG + G R+ Y RGG K
Sbjct: 115 WDAG--------FKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKL 152
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 60.1 bits (146), Expect = 2e-13
Identities = 9/64 (14%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ ++ ++G ++ ++ + + LG A +++ A + +K + + G + Q
Sbjct: 22 FLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ 81
Query: 60 LAAD 63
L
Sbjct: 82 LDIK 85
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 60.3 bits (146), Expect = 3e-13
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+Y L S G + + S + G A +++ + A ++ + G P G P+ I +
Sbjct: 50 LYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107
>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 = 61.0 bits (149), Expect = 3e-13
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
LF G ++S KL D+ +G+SLG + Y DA KA+ NG+ L + +++
Sbjct: 18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS 77
Query: 60 LA 61
A
Sbjct: 78 YA 79
Score = 50.3 bits (121), Expect = 3e-09
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQ 57
+ +LFS++G + ++++ D+ +G S G + +++R +A +A+K NG G P+
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163
Query: 58 IQLA 61
++ A
Sbjct: 164 VKFA 167
>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 = 61.5 bits (150), Expect = 3e-13
Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
M+YE FS GP+ S ++ D + RSLG A + +++ +DA +A+ N + G+P++I
Sbjct: 31 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI 89
Score = 54.6 bits (132), Expect = 1e-10
Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 10/100 (10%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+Y+ FS FG + S K+ D S G + +E + A +A+++ NG+ L+ R + +
Sbjct: 119 ALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 61 AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
R G + + P Y G
Sbjct: 178 FK---------SRKEREAELGARAKEFYPYDVPDYAGSSG 208
>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 = 60.7 bits (148), Expect = 3e-13
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+Y LF GP+ + ++ D +G S G A + + D+ +A+K NG+ + + +++
Sbjct: 19 ELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS 78
Query: 60 LA 61
A
Sbjct: 79 YA 80
Score = 51.4 bits (124), Expect = 1e-09
Identities = 17/64 (26%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQ 57
+ +F ++G + + D+ +GR G A + Y +R +A +A+ N V +G +P+
Sbjct: 105 QLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 164
Query: 58 IQLA 61
++LA
Sbjct: 165 VRLA 168
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 58.8 bits (143), Expect = 4e-13
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++YELF + GPL + DR G+ + ++ A+ NG+ L GRP+ +
Sbjct: 32 ILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG 91
Query: 61 AA 62
+
Sbjct: 92 PS 93
>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 = 60.7 bits (148), Expect = 4e-13
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ EL + FGPLK+ L D +G S G A Y + +A+ NG+ L + + +Q
Sbjct: 110 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169
Query: 60 LAA 62
A+
Sbjct: 170 RAS 172
Score = 40.7 bits (96), Expect = 1e-05
Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 7/76 (9%)
Query: 1 MIYELFSEFGPLKSAKLHYDR------SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+ + F+ L + A L + + +AM ++G+ G+
Sbjct: 20 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQ 78
Query: 55 PMQIQLAADVSVLENT 70
++I+ D L
Sbjct: 79 SLKIRRPHDYQPLPGA 94
>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 = 58.4 bits (142), Expect = 5e-13
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 29 LHAIFSRFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>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 = 57.9 bits (141), Expect = 6e-13
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I F+ FG + A++ D +G+S G + + + DA A++Q G L GR ++
Sbjct: 22 AIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 81
Query: 60 LA 61
A
Sbjct: 82 WA 83
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD,
HDAC, histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 57.9 bits (141), Expect = 8e-13
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I E+FS +G +K + +R S G A + +E +A KA+K +G +DG+ +
Sbjct: 20 HIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITA 79
Query: 59 QLA 61
Sbjct: 80 TAV 82
>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 = 58.5 bits (142), Expect = 9e-13
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ LF+ F K + + +GR G A + + + A +A+ NG L G+ + I+
Sbjct: 41 DLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE 100
Query: 60 LA 61
Sbjct: 101 FG 102
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 57.3 bits (139), Expect = 2e-12
Identities = 14/60 (23%), Positives = 32/60 (53%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
E+ G +K +L +R+G+ G A + YE S A +A+ + +G+ + +++ ++
Sbjct: 36 EICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNS 95
>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 = 59.3 bits (144), Expect = 2e-12
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ EL + FGPLK+ L D +G S G A Y + +A+ NG+ L + + +Q
Sbjct: 130 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 189
Query: 60 LA 61
A
Sbjct: 190 RA 191
Score = 41.6 bits (98), Expect = 7e-06
Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 7/83 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDR------SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+ + F+ L + A L + + +AM ++G+ G+
Sbjct: 20 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQ 78
Query: 55 PMQIQLAADVSVLENTVPRPVAR 77
++I+ D L P
Sbjct: 79 SLKIRRPHDYQPLPGMSENPSVY 101
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 56.9 bits (138), Expect = 2e-12
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I +L S GP+ + K+ +D +GRS G A + + + A++ NG L R ++
Sbjct: 18 QILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 77
Query: 60 LAAD 63
+++
Sbjct: 78 YSSN 81
>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 = 57.0 bits (138), Expect = 4e-12
Identities = 25/85 (29%), Positives = 38/85 (44%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
+F + GP+ L DR+ +S G A + +E +DA A K NG L G+ ++++ A
Sbjct: 26 AVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK 85
Query: 64 VSVLENTVPRPVARGGRGGASGGYR 88
S RP A SG
Sbjct: 86 PSFQSGGRRRPPASSRNRSPSGSLE 110
>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 = 57.4 bits (139), Expect = 4e-12
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ +LF +GP++S K+ DR + +S G + ++ S A +A+ NG + + +++
Sbjct: 58 QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
LAA RP G G +G
Sbjct: 118 LAASGH------QRPGIAGAVGDGNG 137
>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 = 56.5 bits (137), Expect = 5e-12
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+++ELF + GP+ + + DR +G+ G + + DA A+K + + L G+P+++
Sbjct: 31 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 90
Query: 60 LA 61
A
Sbjct: 91 KA 92
>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 = 56.2 bits (136), Expect = 8e-12
Identities = 29/99 (29%), Positives = 45/99 (45%), Gaps = 13/99 (13%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 39 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Query: 61 AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRG 99
R +G R GG R +P R R
Sbjct: 99 CF---------VRGPPKGKRR---GGRRRSRSPDRRRRL 125
>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 = 56.2 bits (136), Expect = 8e-12
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 7/91 (7%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I F+ FG + A++ D +G+S G + + + DA A++Q G L GR ++
Sbjct: 31 DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 90
Query: 60 LAADVSVLENTVPRPVARGGRGGASGGYRNG 90
A P P + G +G
Sbjct: 91 WATRKP------PAPKSTYESNTKQSGPSSG 115
>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 = 55.4 bits (134), Expect = 8e-12
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I + F + + + L Y+ G G A + +E R +A A+ N P+ R +++ L
Sbjct: 32 ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL 91
Query: 61 A 61
Sbjct: 92 G 92
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 55.8 bits (135), Expect = 9e-12
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I E F ++G +K+ L+ DR +G S G A + YE A+ A + NG + G+ +Q+
Sbjct: 42 EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101
Query: 60 LA 61
Sbjct: 102 WC 103
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 55.3 bits (134), Expect = 1e-11
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 39 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
Query: 60 LA 61
Sbjct: 99 WC 100
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 55.0 bits (133), Expect = 1e-11
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
M+ +F FG ++S +L D +GRS G + + A KA++Q NG L GRPM++
Sbjct: 42 MLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG 101
Query: 60 LA 61
Sbjct: 102 HV 103
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 57.7 bits (140), Expect = 1e-11
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
EL FG L+ L Y +G+S G Y ++ A +A G PL R + +
Sbjct: 111 QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 170
Query: 60 LA 61
Sbjct: 171 WT 172
Score = 56.5 bits (137), Expect = 4e-11
Identities = 14/60 (23%), Positives = 25/60 (41%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ S +L + G+ G A L YE A +A +Q +G+ L G +++
Sbjct: 202 LCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 47.3 bits (113), Expect = 8e-08
Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+++L S++ Y + GTA + A A+ ++ L R + +QL
Sbjct: 38 EVHDLLSDYELK------YCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 91
Query: 61 AA 62
Sbjct: 92 QP 93
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 54.5 bits (132), Expect = 2e-11
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
Query: 60 LAA 62
+
Sbjct: 91 GPS 93
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 54.6 bits (132), Expect = 2e-11
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 16/84 (19%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I + F+ P ++ R A + + R DA++AMK NG LDG P+++ LA
Sbjct: 32 IEKEFNNIKPGAVERVKKIR-----DYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
Query: 62 ADVSVLENTVPRPVARGGRGGASG 85
+PV + G +SG
Sbjct: 87 -----------KPVDKDSSGPSSG 99
>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 = 55.6 bits (134), Expect = 2e-11
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 1 MIYELFSEFGPLKSAKLH------YDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+ +F + S + GR G A + A KA+K+ NG L G+
Sbjct: 61 DLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK 120
Query: 55 PMQIQLA 61
PM +Q A
Sbjct: 121 PMVVQFA 127
>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 = 55.1 bits (133), Expect = 2e-11
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+Y++F ++GP++ ++ + GTA ++YE DA A+ +G + R + +
Sbjct: 25 MYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY 82
Query: 62 A 62
Sbjct: 83 N 83
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 54.1 bits (131), Expect = 3e-11
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
M+ + F+E G + A + + +G+S G + +E A +A + NG+ L GR + +++
Sbjct: 24 MLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 82
Query: 61 A 61
Sbjct: 83 D 83
>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 = 54.1 bits (131), Expect = 3e-11
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 12/86 (13%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
M+ +F FG + + L D +GRS G + + A +A++Q NG L GRPM++
Sbjct: 21 MLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVG 80
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
GG G +SG
Sbjct: 81 HV-----------TERLDGGSGPSSG 95
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 55.2 bits (133), Expect = 3e-11
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+++ F FG + ++ D + + G A + +E DA A+ N L GR +++
Sbjct: 79 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
Query: 60 LA 61
LA
Sbjct: 139 LA 140
>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 = 55.6 bits (134), Expect = 3e-11
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I E F ++G +K+ L+ DR +G S G A + YE A+ A + NG + G+ +Q+
Sbjct: 89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
Query: 61 A 61
Sbjct: 149 C 149
>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 = 53.8 bits (130), Expect = 3e-11
Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+Y +FS++G + + D+ + +S G A +++ + A + N L GR ++
Sbjct: 32 DLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS 91
Query: 60 LA 61
+A
Sbjct: 92 IA 93
>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 = 54.2 bits (131), Expect = 4e-11
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+I +LFS+ GP KS K+ + S + + DA A+ NG + G+ +++
Sbjct: 31 LILQLFSQIGPCKSCKMITEHTSNDPYCFVE--FYEHRDAAAALAAMNGRKILGKEVKVN 88
Query: 60 LAAD 63
A
Sbjct: 89 WATT 92
>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 = 53.3 bits (129), Expect = 4e-11
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+++ F FG + ++ D + + G A + +E DA A+ N L GR +++
Sbjct: 23 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 82
Query: 60 LA 61
LA
Sbjct: 83 LA 84
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 54.0 bits (130), Expect = 4e-11
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+ LFS+ G + + + D +G++ G + +DA K +K ++G LD +
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 53.8 bits (130), Expect = 4e-11
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
+LFS +GPL D + + G A + + A+KA + +G GR + + +
Sbjct: 27 KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86
Query: 63 DVSVLENTVPRPVARGGRGGASG 85
+ G +SG
Sbjct: 87 ---------IKK-EASQSGPSSG 99
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 55.0 bits (133), Expect = 9e-11
Identities = 25/97 (25%), Positives = 36/97 (37%), Gaps = 14/97 (14%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I + F+ FGP+KS + +D + + G A + YE A A++Q N V L GR +
Sbjct: 44 TIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI--- 100
Query: 60 LAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYR 96
V RP G R
Sbjct: 101 ----------KVGRPSNIGQAQPIIDQLAEEARAFNR 127
Score = 51.5 bits (124), Expect = 2e-09
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I +F FG +KSA L D +G+ G + YE+ + A+ N L G+ +++
Sbjct: 141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 200
Query: 60 LA 61
A
Sbjct: 201 KA 202
>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 = 55.7 bits (133), Expect = 9e-11
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+Y +FS+FG + + RS + G A +I++ S A A++ G P +PM+IQ
Sbjct: 29 SLYAIFSQFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Query: 61 A 61
A
Sbjct: 87 A 87
Score = 41.4 bits (96), Expect = 1e-05
Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 5/62 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-DGRPMQIQ 59
M+ LF++F K +L R A + ++ A A G + M+I
Sbjct: 223 MLSMLFNQFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278
Query: 60 LA 61
A
Sbjct: 279 FA 280
>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 = 52.5 bits (127), Expect = 1e-10
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ F +F S + +D +G S G + + + DA AM G L+GRP++I
Sbjct: 17 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 76
Query: 60 LA 61
A
Sbjct: 77 WA 78
>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 = 52.3 bits (126), Expect = 1e-10
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I + F + + + L Y+ G G A + +E R +A A+ N P+ R +++
Sbjct: 32 ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG 91
Query: 61 A 61
Sbjct: 92 P 92
>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 = 52.2 bits (126), Expect = 2e-10
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ ELF FG + L D+ +G+S G A + + RR DA +A+ +G D + ++
Sbjct: 31 DLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE 90
Query: 60 LA 61
A
Sbjct: 91 WA 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 = 52.3 bits (126), Expect = 2e-10
Identities = 12/61 (19%), Positives = 20/61 (32%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ + FG + S ++ D SG S G E + +NG + P
Sbjct: 41 ELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP 100
Query: 61 A 61
Sbjct: 101 T 101
>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 = 53.4 bits (128), Expect = 3e-10
Identities = 21/100 (21%), Positives = 39/100 (39%), Gaps = 9/100 (9%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ LF +G ++ K+ +++ A + + A AM NG L G+P++I L
Sbjct: 20 SLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 75
Query: 61 AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
+ V P G + Y N ++ G
Sbjct: 76 SK-----HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 110
Score = 36.0 bits (83), Expect = 7e-04
Identities = 8/62 (12%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-DGRPMQIQ 59
+ LFS G + + + A + +A++A+ + L + +++
Sbjct: 136 DLKVLFSSNGGVVKGFKFFQKDR---KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192
Query: 60 LA 61
+
Sbjct: 193 FS 194
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 51.3 bits (123), Expect = 3e-10
Identities = 11/63 (17%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 2 IYELFSEFGPLKSAK-LHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ L ++G ++S + ++ D + + Y + A +A+ + NG L+ +++
Sbjct: 32 LDSLLVQYGVVESCEQVNTDSETAVVN---VTYSSKDQARQALDKLNGFQLENFTLKVAY 88
Query: 61 AAD 63
D
Sbjct: 89 IPD 91
>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 = 51.7 bits (124), Expect = 4e-10
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ + ++A + D +G+ LG A + ++ DA K+ + + L+GR + +
Sbjct: 32 VLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV 90
Query: 61 AADVSVLENTVPRPVARGGRGGASG 85
+ E P A+G G +SG
Sbjct: 91 VTLEDMRE-IEKNPPAQGKSGPSSG 114
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 51.6 bits (124), Expect = 4e-10
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 3 YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F FG + SAK+ D+ + S + ++ A A+K NG + + +++QL
Sbjct: 58 ASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
>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 = 51.2 bits (123), Expect = 5e-10
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 18/92 (19%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN------GVPLDG 53
+ E+ +FG LK ++ + S G A + + A K + + G+ LDG
Sbjct: 31 ALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG 90
Query: 54 RPMQIQLAADVSVLENTVPRPVARGGRGGASG 85
R +++ LA V R G +SG
Sbjct: 91 RQLKVDLA---------VTRD--EAASGPSSG 111
>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 = 51.7 bits (124), Expect = 5e-10
Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++
Sbjct: 63 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
Query: 61 A 61
+
Sbjct: 123 S 123
>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 = 50.7 bits (122), Expect = 7e-10
Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 15/86 (17%)
Query: 4 ELFSEFGPLKSAKLHYDRSG----RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+FS+ G +KS + ++ S+G + Y++ A KA+KQ G +DG ++++
Sbjct: 24 GVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR 83
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
++ + G +SG
Sbjct: 84 IS-----------ERATKPASGPSSG 98
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 52.2 bits (126), Expect = 7e-10
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ SE + R+G + + +E D KA+ + G+ + G ++++
Sbjct: 29 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 87
Query: 61 A 61
Sbjct: 88 P 88
Score = 44.5 bits (106), Expect = 4e-07
Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+F + ++ + G+S G A + ++ +DA K +++ G +DGR + +
Sbjct: 115 ELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170
Query: 61 A 61
Sbjct: 171 T 171
>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 = 50.7 bits (122), Expect = 8e-10
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
+F ++G + + + + G A + + R DA A +G LDGR +++Q+A
Sbjct: 32 RVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91
Query: 63 DVSVLENTVPRPVARGGRGG 82
R G G
Sbjct: 92 Y--------GRRDLSGPSSG 103
>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 = 50.4 bits (121), Expect = 8e-10
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG---VPLDGRPMQI 58
+ LF FG + + G S G A + + ++A A+ +G +P + +
Sbjct: 32 VLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV 91
Query: 59 QLA 61
+ A
Sbjct: 92 KFA 94
>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 = 49.9 bits (120), Expect = 1e-09
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 12/86 (13%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+++ F FG + ++ D + + G A + +E DA A+ N L GR +++
Sbjct: 28 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 87
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
LA +P+ G +SG
Sbjct: 88 LA-----------KPMRIKESGPSSG 102
>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 = 49.9 bits (120), Expect = 1e-09
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 12/83 (14%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
++FS++G + + DR + RS G + +E DA AM NG +DGR +++ A
Sbjct: 31 QVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA- 89
Query: 63 DVSVLENTVPRPVARGGRGGASG 85
+ G +SG
Sbjct: 90 ----------GKSSDNRSGPSSG 102
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 50.1 bits (120), Expect = 2e-09
Identities = 20/98 (20%), Positives = 38/98 (38%), Gaps = 18/98 (18%)
Query: 1 MIYELFSEFGPLKSA--------KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPL 51
+ + F + G +K+ L+ DR +G+ G A + ++ A A+ ++G
Sbjct: 23 SVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF 82
Query: 52 DGRPMQIQLAADVSVLENTVPRPVARGGRGGASGGYRN 89
G P+++ A R G G GG +
Sbjct: 83 SGNPIKVSFA---------TRRADFNRGGGNGRGGLEH 111
>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 = 49.6 bits (119), Expect = 2e-09
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ++FSE GP+ S +L YDR +G+ G Y+ + A+ AM+ NG GR +++
Sbjct: 25 LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN 84
Query: 61 AADVSVLENTVPRPVARGGRGGA 83
AA + + GA
Sbjct: 85 AASEK------NKEELKSLGTGA 101
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 48.9 bits (117), Expect = 2e-09
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+I+++FS+FG + + + G++ G L Y + A+ A+K +G LD +
Sbjct: 23 VIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75
>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 = 49.2 bits (118), Expect = 2e-09
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 2 IYELFSEFGPLKSA--------KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
+ + F + G +K+ L+ DR +G+ G A + ++ A A+ ++G
Sbjct: 30 VADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS 89
Query: 53 GRPMQIQLA 61
G P+++ A
Sbjct: 90 GNPIKVSFA 98
>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 = 49.2 bits (118), Expect = 3e-09
Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++F +FG + ++ ++ S G + +E +DA +A ++ +G ++GR +++ A
Sbjct: 34 QMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 90
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 50.2 bits (120), Expect = 3e-09
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ +F ++G + + DR + S G A + + + DA AM +G LDGR +++Q+
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
Query: 61 A 61
A
Sbjct: 147 A 147
>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 = 48.9 bits (117), Expect = 4e-09
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 3 YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++F FG + SAK+ D+ + S + Y+ A A++ NG + + +++QL
Sbjct: 43 LQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 48.9 bits (117), Expect = 5e-09
Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++F +FG + ++ ++ S G + +E +DA +A ++ +G ++GR +++ A
Sbjct: 48 QMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
>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 = 48.5 bits (116), Expect = 5e-09
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQI 58
I ELFS FG LK+ +L +G G + + + DA KA + L GR + +
Sbjct: 32 IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL 91
Query: 59 QLAAD 63
+ A
Sbjct: 92 EWADS 96
>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 = 50.5 bits (120), Expect = 5e-09
Identities = 18/105 (17%), Positives = 35/105 (33%), Gaps = 6/105 (5%)
Query: 2 IYELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ E G + K +R +G+S G A + + + K M L G+ +
Sbjct: 85 LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV 144
Query: 59 QLAADVSVLENTV---PRPVARGGRGGASGGYRNGTAPTYRPRGG 100
+ + + + G G G++ P+GG
Sbjct: 145 TPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGG 189
>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 = 49.9 bits (120), Expect = 5e-09
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG---VPLDGRPMQ 57
I +FS FG ++ ++ G S G A + + R+ A A+K + + PM
Sbjct: 111 DIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170
Query: 58 IQLA 61
++ A
Sbjct: 171 VKFA 174
Score = 45.3 bits (108), Expect = 3e-07
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 2 IYELFSEFGPLKSAKLHYDRSG---RSLGTADLIYERRSDAIKAMKQYNGVPLDG---RP 55
+ ELF ++G + + DRS +S G + + R A++A + + + P
Sbjct: 20 LRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHP 79
Query: 56 MQIQLA 61
+Q++ A
Sbjct: 80 IQMKPA 85
>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 = 48.5 bits (116), Expect = 6e-09
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNG---VPLDGRPM 56
+ LF EFG + + DR +G G A L Y R A+KA + +P RP+
Sbjct: 29 DLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI 88
Query: 57 QIQLA 61
Q++ A
Sbjct: 89 QVKPA 93
>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 = 50.4 bits (121), Expect = 6e-09
Identities = 11/62 (17%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I +L + + + +L R S A + + DA +++ NG+ ++G + +
Sbjct: 133 NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK 192
Query: 60 LA 61
++
Sbjct: 193 VS 194
Score = 48.8 bits (117), Expect = 3e-08
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 1 MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
++ E F FG ++ + + + A +++E + A +A+ Q N L R + +
Sbjct: 227 LLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV 285
Query: 59 QLA 61
LA
Sbjct: 286 SLA 288
Score = 44.6 bits (106), Expect = 8e-07
Identities = 9/63 (14%), Positives = 25/63 (39%), Gaps = 2/63 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+Y+ F GP+ + ++ A + + R A+ A+ + + V + + +
Sbjct: 57 KVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSH 114
Query: 61 AAD 63
+
Sbjct: 115 LTE 117
>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 = 47.6 bits (114), Expect = 1e-08
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 1 MIYELFSEFGP-LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
++Y+ FS FG L++ K+ D +G S G A + + + A++ NG L RP+ +
Sbjct: 21 LLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITV 80
Query: 59 QLA 61
A
Sbjct: 81 SYA 83
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 48.2 bits (115), Expect = 1e-08
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+F ++G + + DR + S G A + + + DA AM +G LDGR +++Q+A
Sbjct: 66 RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 47.4 bits (113), Expect = 2e-08
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+I+++FS+FG + + + G++ G L Y + A+ A+K +G LD +
Sbjct: 37 VIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89
>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 = 47.2 bits (113), Expect = 2e-08
Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 10/87 (11%)
Query: 3 YELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
Y+ FS FG + S K+ D S G + +E + A +A+++ NG+ L+ R + +
Sbjct: 23 YDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF- 80
Query: 63 DVSVLENTVPRPVARGGRGGASGGYRN 89
R G + + N
Sbjct: 81 --------KSRKEREAELGARAKEFTN 99
>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 = 46.6 bits (111), Expect = 3e-08
Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 20/93 (21%)
Query: 2 IYELFSEFGPLKS--------AKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
+ + F + G +K ++ D+ +G+ G A + YE A A++ ++G
Sbjct: 32 LADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ 91
Query: 53 GRPMQIQLAADVSVLENTVPRPVARGGRGGASG 85
G +++ LA R G +SG
Sbjct: 92 GSKLKVSLA-----------RKKPPMNSGPSSG 113
>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 = 47.8 bits (113), Expect = 5e-08
Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ +F +G ++ K + G A + +A+ N + G+ M + +
Sbjct: 21 RVFNVFCLYGNVEKVKFMKSKPG----AAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV 76
Query: 61 A 61
+
Sbjct: 77 S 77
Score = 40.5 bits (94), Expect = 2e-05
Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+E+ E G + + + L ++ +SDA++ + N +
Sbjct: 139 NFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY 197
>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 = 45.7 bits (109), Expect = 5e-08
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 3 YELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ FS FG + SAK+ + GRS G + + +A KA+ + NG + +P+ + LA
Sbjct: 33 RKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 45.4 bits (108), Expect = 7e-08
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 5/61 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ LF FG + K + ++ G + Y+ A + P GR ++
Sbjct: 43 DLIPLFQNFGFILDFKHYPEK-----GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW 97
Query: 61 A 61
Sbjct: 98 G 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 = 45.2 bits (108), Expect = 7e-08
Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
+ +L +G + S K D+ + + G + ++ S A KA+ + + +
Sbjct: 21 DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK 78
>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 = 46.9 bits (111), Expect = 9e-08
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ LF +G ++ K+ +++ A + + A AM NG L G+P++I L
Sbjct: 51 SLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 106
Query: 61 AADVSV 66
+ +V
Sbjct: 107 SKHQNV 112
Score = 34.6 bits (79), Expect = 0.002
Identities = 8/59 (13%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-DGRPMQI 58
+ LFS G + + + A + +A++A+ + L + +++
Sbjct: 167 DLKVLFSSNGGVVKGFKFFQKDR---KMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 45.1 bits (107), Expect = 1e-07
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 7/60 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
+ E EFGP+ + + A + +E A A+ + G P +
Sbjct: 38 LVEALQEFGPISYVVVMPKK-----RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92
>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 = 44.6 bits (106), Expect = 1e-07
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ E+F + ++ G+S G A + ++ +DA K +++ G +DGR + +
Sbjct: 32 ELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 86
Query: 60 LAADVSVLENTVPRPVARG 78
+ RG
Sbjct: 87 YTG---------EKGGTRG 96
>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 = 44.1 bits (105), Expect = 2e-07
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F+ +G +K K+ DR+G S G + + D K ++ + + G+ +++ A
Sbjct: 28 SFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA 83
>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 = 44.2 bits (105), Expect = 2e-07
Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 16/85 (18%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ + FS FG + ++ ++ G + + + A A+ NG ++G ++
Sbjct: 41 LMRQTFSPFGQIMEIRVFPEK-----GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 95
Query: 61 AADVSVLENTVPRPVARGGRGGASG 85
+ G +SG
Sbjct: 96 G-----------KESPDMTSGPSSG 109
>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 = 46.2 bits (110), Expect = 2e-07
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
LF +G ++ DR G + E R+ A A + +G L RP++I+
Sbjct: 38 DFKRLFERYGEPSEVFINRDR-----GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF 92
Query: 61 A 61
A
Sbjct: 93 A 93
Score = 42.8 bits (101), Expect = 4e-06
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQIQ 59
++ + FS+FGP++ A + D GR+ G + + + A KA+++ +G L +
Sbjct: 112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV 171
Query: 60 LAA 62
+
Sbjct: 172 IVE 174
>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 = 44.2 bits (105), Expect = 2e-07
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 1 MIYELFSEFG-PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I F+ G + S K+ +R +G G + + + A K + + NG PL G
Sbjct: 25 FISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK 84
Query: 59 QL 60
+
Sbjct: 85 RF 86
>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 = 43.7 bits (104), Expect = 3e-07
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 3/61 (4%)
Query: 4 ELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
E G + K +R +G+S G A + + + K M L G+ +
Sbjct: 20 EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP 79
Query: 61 A 61
+
Sbjct: 80 S 80
>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 = 44.4 bits (105), Expect = 3e-07
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ FS FG + + R A + YE+ A +A+ + NG ++ +++ +
Sbjct: 53 LLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 107
Query: 61 A 61
A
Sbjct: 108 A 108
>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 = 43.8 bits (104), Expect = 3e-07
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ SE + R+G + + +E D KA+ + G+ + G ++++
Sbjct: 33 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 91
Query: 61 A 61
Sbjct: 92 P 92
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 43.6 bits (103), Expect = 4e-07
Identities = 9/62 (14%), Positives = 22/62 (35%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I E + G + + ++ G+ ++++ A K ++ G + I
Sbjct: 28 IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET-PGQKYKETDLLILFK 86
Query: 62 AD 63
D
Sbjct: 87 DD 88
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 43.3 bits (103), Expect = 4e-07
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
ELFS+FG + + KL YDR + + G + + +A+ + + GR +++ A
Sbjct: 20 ELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFMGRTIRVTEA 77
>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 = 43.4 bits (103), Expect = 4e-07
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ + FS+FG L+ K D A + ++ R A+KAM++ NG L+G ++I
Sbjct: 27 ILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF 79
Query: 61 A 61
A
Sbjct: 80 A 80
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 44.5 bits (105), Expect = 4e-07
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 1 MIYELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
+ ++ G + K +R +G+S G A+++ + K ++ G L+G +
Sbjct: 71 QLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVD 130
Query: 58 IQLA 61
++ A
Sbjct: 131 VRPA 134
>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 = 43.4 bits (103), Expect = 5e-07
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 16/82 (19%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
+LF ++G +H D+ G + E R+ A A + + +PL G+ ++++ A
Sbjct: 34 KLFEKYGKAGEVFIHKDK-----GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA-- 86
Query: 64 VSVLENTVPRPVARGGRGGASG 85
A G +SG
Sbjct: 87 ---------CHSASLTSGPSSG 99
>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 = 43.0 bits (102), Expect = 6e-07
Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 12/83 (14%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
L F A++ DR +G S G + + DA A + +DG + + A
Sbjct: 31 TLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA- 89
Query: 63 DVSVLENTVPRPVARGGRGGASG 85
+P GG G +SG
Sbjct: 90 ----------KPKGEGGSGPSSG 102
>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 = 42.9 bits (101), Expect = 7e-07
Identities = 9/62 (14%), Positives = 21/62 (33%), Gaps = 7/62 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
+ E +FG + + + A + +E A + + VP + G+
Sbjct: 32 LVEALEKFGTICYVMMMPFK-----RQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN 86
Query: 60 LA 61
+
Sbjct: 87 YS 88
>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 = 42.7 bits (101), Expect = 9e-07
Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+F + +K + +++G+S G A + + DA +A+ N ++GR ++++L
Sbjct: 31 TLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
Query: 61 AAD 63
Sbjct: 88 QGP 90
>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 = 42.9 bits (101), Expect = 9e-07
Identities = 13/86 (15%), Positives = 35/86 (40%), Gaps = 4/86 (4%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ + F + ++ + + Y +G++ G + + +D A+ + + R +Q+
Sbjct: 42 VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP 100
Query: 61 AADVSVLENTVPRPVARGGRGGASGG 86
+LE + + + G S G
Sbjct: 101 ITKKGMLE--KIDMIRKRLQSGPSSG 124
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 42.7 bits (101), Expect = 1e-06
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+F FGP+K K+ G A + +E A KA+++ +G +P+++
Sbjct: 47 ELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
Query: 61 A 61
+
Sbjct: 100 S 100
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 42.0 bits (99), Expect = 1e-06
Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+++L ++ L Y R+ TA + A A++ ++ G+ + +QL
Sbjct: 22 VHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75
>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 = 41.5 bits (98), Expect = 2e-06
Identities = 10/60 (16%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQIQ 59
+ F +FG +++ + + A + + R A A ++ +N + ++GR + ++
Sbjct: 28 DLRNHFYQFGEIRTITVVQRQ-----QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK 82
>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 = 41.5 bits (98), Expect = 2e-06
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 18/82 (21%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
F E+GP+ + A + ER DA++A++ + G+ M +QL+
Sbjct: 29 AKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS-- 79
Query: 64 VSVLENTVPRPVARGGRGGASG 85
R G +SG
Sbjct: 80 ---------TSRLRTASGPSSG 92
>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 = 41.5 bits (98), Expect = 3e-06
Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 10/81 (12%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I ++F ++G ++ L R G A + +E DA A+ +G DG ++++
Sbjct: 39 IEDVFYKYGAIRDIDLKNRRGGP--PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 96
Query: 62 ADVSVLENTVPRPVARGGRGG 82
R G G
Sbjct: 97 --------RSGRGTGSGPSSG 109
>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 = 41.7 bits (98), Expect = 3e-06
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 8/85 (9%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ + F + L D GR+ G + + D +A+K N + + R +++ A
Sbjct: 33 VRDFFHGLRV-DAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPA 90
Query: 62 ADVSVLENTVPRPVARGGRGGASGG 86
+ + G S G
Sbjct: 91 TERQWVA------AGGHITSGPSSG 109
>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 = 41.1 bits (97), Expect = 3e-06
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ FS FG + + R A + YE+ A +A+ + NG ++ +++ +
Sbjct: 29 LLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 61 A 61
A
Sbjct: 84 A 84
>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 = 41.5 bits (98), Expect = 3e-06
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ + FS G ++ ++ DR S RS G A + + A+ G L G P+ +Q
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQA 100
Query: 61 A 61
+
Sbjct: 101 S 101
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 41.2 bits (97), Expect = 3e-06
Identities = 11/69 (15%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 2 IYELFSEFG--PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVP----LDGR 54
I S + + + +L D+ + ++ G A + DA + ++ + +DG+
Sbjct: 26 IMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK 85
Query: 55 PMQIQLAAD 63
+ + A
Sbjct: 86 TIGVDFAKS 94
>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 = 41.0 bits (96), Expect = 4e-06
Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 5/60 (8%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I E FS FG L L TA + + +A KA + P+ ++ A
Sbjct: 27 IQETFSRFGSLGRVLLPEGG-----ITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA 81
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 41.0 bits (96), Expect = 5e-06
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 3 YELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
E F +FG + ++ S +A + Y R DA++A++ N V +DGR ++
Sbjct: 36 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 95
Query: 59 QLA 61
L
Sbjct: 96 SLG 98
>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 = 40.4 bits (95), Expect = 5e-06
Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ E + P + ++ + G G + + + +A+K N + GR +++
Sbjct: 27 VMEFLAPLKP-VAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE 84
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 41.0 bits (96), Expect = 5e-06
Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 7/62 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQ 59
+ L FG + + + + A + A + Y L G+P+ IQ
Sbjct: 33 VISLGLPFGKVTNLLMLKGK-----NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 87
Query: 60 LA 61
+
Sbjct: 88 FS 89
>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 = 41.4 bits (96), Expect = 8e-06
Identities = 9/62 (14%), Positives = 22/62 (35%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I E + G + + ++ G+ ++++ A K ++ G + I
Sbjct: 126 IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK 184
Query: 62 AD 63
D
Sbjct: 185 DD 186
>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 = 40.7 bits (95), Expect = 8e-06
Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 7/62 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
+ L FG + + + + A + A + Y V L G+P+ IQ
Sbjct: 48 VISLGLPFGKVTNLLMLKGK-----NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102
Query: 60 LA 61
+
Sbjct: 103 FS 104
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 40.3 bits (95), Expect = 8e-06
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 1 MIYELFSEFGP-LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG-VPLDGRPMQI 58
M+YE F + P + K+ D++G S G + + + +A+ + G V L +P+++
Sbjct: 25 MLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL 84
Query: 59 QLA 61
+A
Sbjct: 85 SVA 87
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 39.9 bits (94), Expect = 9e-06
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ F FG +++ A + YE A A + G PL G +++
Sbjct: 34 LAREFDRFGSIRTIDHVKGD-----SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR 86
>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 = 40.1 bits (94), Expect = 9e-06
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
IY FS P + GR G AD+ + DA+ AM + + R +++ L
Sbjct: 32 IYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN 89
>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 = 39.8 bits (93), Expect = 1e-05
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
+ L FG + + + + A L AI + Y+ V L +P+ IQ
Sbjct: 32 VIALGLPFGKVTNILMLKGK-----NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ 86
Query: 60 LA 61
+
Sbjct: 87 YS 88
>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 = 39.2 bits (92), Expect = 2e-05
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
+ F FG ++ A + DR +G+S G + R+ A +A K N + +DGR + LA
Sbjct: 36 KYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLAY 94
Query: 63 DVSVLENTVPRPVARGGRGGASGG 86
+ + + G G S G
Sbjct: 95 LGAKPRS--LQTGFAIGVSGPSSG 116
>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 = 38.7 bits (91), Expect = 3e-05
Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 18/84 (21%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I LF ++G + + + E ++ A A++ + L G + ++ +
Sbjct: 25 IRSLFEQYGKVLECDIIK-------NYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS 77
Query: 62 ADVSVLENTVPRPVARGGRGGASG 85
+ ++ G +SG
Sbjct: 78 -----------KNKSKASSGPSSG 90
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 38.3 bits (89), Expect = 5e-05
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 8/88 (9%)
Query: 2 IYELFSEFGPLKSAK----LHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
+ F + P+ K GR G A +++ A A+ + + L R ++
Sbjct: 40 VVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIE 98
Query: 58 IQLAADVSVLENTVPRPVARGGRGGASG 85
+ + + E G +SG
Sbjct: 99 LFRS---TAAEVQQVLNRFSSASGPSSG 123
>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 = 38.7 bits (91), Expect = 6e-05
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
E FS++G + A+L D+ +G+S G + Y+ + + + R ++I+
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIK 161
Query: 60 LA 61
A
Sbjct: 162 RA 163
Score = 36.7 bits (86), Expect = 3e-04
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E F ++G + K+ D +GRS G L +E+ S + +K + LDG+ + + A
Sbjct: 22 EYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHI--LDGKVIDPKRA 78
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 37.7 bits (88), Expect = 7e-05
Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 15/87 (17%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ FS +GPL++ + + G A + +E DA A++ +G + G ++++L+
Sbjct: 17 LERAFSYYGPLRTVWI----ARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72
Query: 62 ADVSVLENTVPRPVARGGRGGASGGYR 88
+ R R R
Sbjct: 73 -----------TGMPRRSRFDRPPARR 88
>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 = 37.4 bits (87), Expect = 1e-04
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I + FS + + L D GRS G A + + + A KA+K + + R ++I
Sbjct: 32 IVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK 90
Query: 61 A 61
+
Sbjct: 91 S 91
>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 = 38.4 bits (90), Expect = 1e-04
Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 11/86 (12%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ + F ++G ++ ++ DR SG+ G A + ++ K + Q ++G +++
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
A + + G
Sbjct: 179 KA---------LSKQEMASASSSQRG 195
Score = 34.6 bits (80), Expect = 0.002
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
F ++G L + D + RS G + Y + AM +DGR ++ + A
Sbjct: 32 SHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV 90
>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 = 36.8 bits (86), Expect = 1e-04
Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 16/79 (20%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
LF G + + A + E+ +DA A+ Q NG + G+ + ++L+
Sbjct: 28 SLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST- 79
Query: 64 VSVLENTVPRPVARGGRGG 82
G G
Sbjct: 80 --------KGQKKSGPSSG 90
>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 = 36.8 bits (86), Expect = 1e-04
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 17/86 (19%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG-VPLDGRPMQIQ 59
+ +LF + + + G A + Y ++ AI+A++ +G V L G+ M++
Sbjct: 24 DLRQLFGDRKLPLAG-----QVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD 78
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
+ G +SG
Sbjct: 79 YS-----------VSKKLRSSGPSSG 93
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 36.9 bits (85), Expect = 1e-04
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ E F+ G +KS +L + A + E DAI A+ + + + + + L
Sbjct: 29 LLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL 86
Query: 61 AADVS 65
A S
Sbjct: 87 ATGAS 91
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 36.5 bits (85), Expect = 2e-04
Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 12/82 (14%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +F + ++S +L D+ + + G + ++ +A+ Y+G L R +++ +
Sbjct: 32 IDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDI 89
Query: 61 AADVSVLENTVPRPVARGGRGG 82
A R + G
Sbjct: 90 AE---------GRKQDKSGPSS 102
>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 = 36.0 bits (84), Expect = 2e-04
Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ F G + + D+ SG G A + + + ++ + GR +++
Sbjct: 23 LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIP 81
Query: 61 A 61
Sbjct: 82 K 82
>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 = 36.7 bits (85), Expect = 2e-04
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
IY FS P + GR G AD+ + +A+ AM + + R +++ L
Sbjct: 63 IYNFFSPLNP-VRVHIEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLN 120
>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 = 36.1 bits (84), Expect = 2e-04
Identities = 5/60 (8%), Positives = 23/60 (38%), Gaps = 7/60 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS +G + + + ++ A++ + G+ + ++++
Sbjct: 40 LFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS 92
>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 = 36.6 bits (85), Expect = 3e-04
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ FS G + + D+ SG G A + + R+ A+ + GR +++
Sbjct: 53 LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLP 111
Query: 61 A 61
Sbjct: 112 K 112
>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 = 36.4 bits (84), Expect = 3e-04
Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I + FS + + L D G+ G A + + + A KA+ + + R +++
Sbjct: 59 IVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK 117
Query: 61 A 61
+
Sbjct: 118 S 118
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 36.2 bits (84), Expect = 3e-04
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 15/81 (18%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ +FS++G + +H G A + Y A A+ NG L G+ + I +A
Sbjct: 45 VETIFSKYGRVAGCSVHK-------GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97
Query: 62 ADVSVLENTVPRPVARGGRGG 82
+ P+P G G
Sbjct: 98 GE--------PKPDRSGPSSG 110
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 35.6 bits (83), Expect = 3e-04
Identities = 9/83 (10%), Positives = 30/83 (36%), Gaps = 14/83 (16%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS +G + + + ++ A++ + G+ + ++++
Sbjct: 28 LFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS 80
Query: 62 ADVSVLENTVPRPVARGGRGGAS 84
++ RP G G +
Sbjct: 81 -------SSNARPQFDHGDHGTN 96
>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 = 36.4 bits (84), Expect = 4e-04
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ F +GPL+S + + G A + +E DA A+++ +G L G ++++L+
Sbjct: 90 LERAFGYYGPLRSVWV----ARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B;
protein biosynthesis, RNA recognition motif, RNA
binding domain, RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 35.3 bits (82), Expect = 5e-04
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 4/63 (6%)
Query: 2 IYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I E F + +L + R G +E + A+ N L R +++
Sbjct: 36 IKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVD 93
Query: 60 LAA 62
+A
Sbjct: 94 VAD 96
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 34.6 bits (79), Expect = 0.002
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 7/73 (9%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQI 58
+++++FS+FG + + A L Y A A +G + ++I
Sbjct: 44 VLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 100
Query: 59 QLA--ADVSVLEN 69
+ ++V N
Sbjct: 101 DFSKLTSLNVKYN 113
>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 = 34.8 bits (79), Expect = 0.002
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ F +GP+K + Y RSG+ G A + YE D A K +G +DGR + + +
Sbjct: 119 LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 178
Query: 61 AADVSV 66
+V
Sbjct: 179 ERGRTV 184
>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 = 33.8 bits (78), Expect = 0.002
Identities = 14/86 (16%), Positives = 26/86 (30%), Gaps = 15/86 (17%)
Query: 2 IYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I E F + +L + R G +E + A+ N L + +++
Sbjct: 32 IKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD 89
Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
+A G +SG
Sbjct: 90 VAD---------QAQ--DKDSGPSSG 104
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 33.9 bits (77), Expect = 0.003
Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQI 58
++Y + + G ++ + +++ + +E A KA NG + ++I
Sbjct: 41 VLYTVCNPVGKVQRIVIFKRNGIQAM----VEFESVLCAQKAKAALNGADIYAGCCTLKI 96
Query: 59 QLA--ADVSVLEN 69
+ A ++V+ N
Sbjct: 97 EYARPTRLNVIRN 109
>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 = 34.3 bits (78), Expect = 0.003
Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 7/74 (9%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQI 58
+++++FS+FG + + A L Y A A +G + ++I
Sbjct: 62 VLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 118
Query: 59 QLA--ADVSVLENT 70
+ ++V N
Sbjct: 119 DFSKLTSLNVKYNN 132
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 33.3 bits (76), Expect = 0.003
Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 4/58 (6%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E G + A L Y + A +A+ G+ L +++ LA
Sbjct: 38 RALRELGSVPLRL----TWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
>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 = 33.7 bits (77), Expect = 0.003
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 6/88 (6%)
Query: 2 IYELFSEF---GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ S+ + Y R GR G A + E D A+ + + + R +++
Sbjct: 34 VQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL-KKDRESMGHRYIEV 92
Query: 59 QLAADVSVLENTVPRPVARGGRGGASGG 86
+ + + V + G S G
Sbjct: 93 FKSHRTEM--DWVLKHSGPNSASGPSSG 118
>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 = 33.2 bits (76), Expect = 0.004
Identities = 16/97 (16%), Positives = 30/97 (30%), Gaps = 22/97 (22%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
+ E G + A ++ D GT + + R+ D A+++ + +
Sbjct: 34 DHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI-- 85
Query: 64 VSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
R G R + G R+ P G
Sbjct: 86 ---------RVKVDGPRSPSYGRSRS-----SGPSSG 108
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 33.0 bits (75), Expect = 0.005
Identities = 5/48 (10%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG 48
+ + + G + + + ++ + Y ++ +A NG
Sbjct: 43 QLLPVLEKCGLVDALLMPPNK-----PYSFARYRTTEESKRAYVTLNG 85
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 32.1 bits (73), Expect = 0.008
Identities = 12/60 (20%), Positives = 28/60 (46%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+ ++G ++ + + +G + + R DA KA+ N +G+P+ +L
Sbjct: 43 VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 31.3 bits (72), Expect = 0.010
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 6 FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F +FG + A L +D+ + R G + +E K + + ++ + ++ + A
Sbjct: 20 FEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECKKA 75
>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 = 32.3 bits (73), Expect = 0.010
Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 4/63 (6%)
Query: 2 IYELFSEF---GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ S+ Y R GR G A + D A+ + + + R +++
Sbjct: 61 VQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEV 119
Query: 59 QLA 61
+
Sbjct: 120 FKS 122
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 31.7 bits (72), Expect = 0.015
Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 9/87 (10%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
+ E G + A ++ D GT + + R+ D A+++ + + A
Sbjct: 35 DHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET---AY 85
Query: 64 VSVLENTVPRPVARGGRGGASGGYRNG 90
+ V + P R + R+
Sbjct: 86 IRVKVDGPRSPSYGRSRSRSRSRSRSR 112
>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 = 31.4 bits (72), Expect = 0.015
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 13/83 (15%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
E F +FG + + YD R G + +E +A+ + + G+ ++++ A
Sbjct: 29 EYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM-HFHDIMGKKVEVKRA- 86
Query: 63 DVSVLENTVPRPVARGGRGGASG 85
PR G +SG
Sbjct: 87 --------EPRDSK--SSGPSSG 99
>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 = 31.4 bits (71), Expect = 0.018
Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 2 IYELFSEF---GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ FS+ +R G+ G A + E D KA+ + + + + R +++
Sbjct: 28 VLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL-EKHRMYMGQRYVEV 86
Query: 59 QLA 61
Sbjct: 87 YEI 89
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 31.0 bits (70), Expect = 0.029
Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 10/74 (13%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
+L E + R G + + ++A+++ N + G
Sbjct: 47 DLARENSLETTFSSVNTRDFDGTGALE--FPSEEILVEALERLNNIEFRGSV-------- 96
Query: 64 VSVLENTVPRPVAR 77
++V + P P+ R
Sbjct: 97 ITVERDDNPPPIRR 110
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 30.9 bits (69), Expect = 0.042
Identities = 7/63 (11%), Positives = 20/63 (31%), Gaps = 5/63 (7%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +FS G + + + + ++ +++A A + + L +
Sbjct: 159 RIRFVFSRLGDIDRIRYVESK-----NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWD 213
Query: 61 AAD 63
Sbjct: 214 DRR 216
>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 = 29.4 bits (67), Expect = 0.050
Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E F FG ++S +L D + + G + ++ K M++ + +I++A
Sbjct: 18 EYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA 75
>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 = 29.7 bits (67), Expect = 0.059
Identities = 9/64 (14%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 1 MIYELFSEFGPLKSAK------LHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+ + F+ L + + + A L + + +AM ++G+ G+
Sbjct: 22 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQ 80
Query: 55 PMQI 58
++I
Sbjct: 81 SLKI 84
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 27.5 bits (61), Expect = 0.41
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 2/58 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGR--SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
E ++G + + L +ER AIKA+ NG GR ++
Sbjct: 30 TKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVK 87
>3okf_A 3-dehydroquinate synthase; structural genomics, center for
structural genomics of infec diseases, csgid, NAD,
lyase; HET: NAD; 2.50A {Vibrio cholerae o1 biovar
eltor}
Length = 390
Score = 26.1 bits (58), Expect = 2.7
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 18 HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENTVPRPVAR 77
H+ SG LGT +L ++ + K M++ V L R I + A + N ++
Sbjct: 5 HHHSSGVDLGTENLYFQSNAMECKTMERIT-VNLGERSYPISIGAG--LFANPALLSLSA 61
Query: 78 GGR 80
+
Sbjct: 62 KQK 64
>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 = 26.2 bits (57), Expect = 3.0
Identities = 33/128 (25%), Positives = 46/128 (35%), Gaps = 55/128 (42%)
Query: 6 FSE--------FGPLKSAKLH--YDRSGRSLGTA-DLIYERRSDAIKAMKQYNG----VP 50
FSE F P+ ++ H L A DLI + D +K +N +P
Sbjct: 409 FSERKLKFSNRFLPV-ASPFHSHL------LVPASDLINK---DLVKNNVSFNAKDIQIP 458
Query: 51 L----DGRPMQIQLAADVSVLENTVP----RPV-------ARG------GRGGASG-G-- 86
+ DG ++ S+ E V PV + G GGASG G
Sbjct: 459 VYDTFDGSDLR---VLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVL 515
Query: 87 -YRN--GT 91
+RN GT
Sbjct: 516 THRNKDGT 523
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 24.8 bits (54), Expect = 3.9
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRS---LGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
+ + S++G +KS ++ G G + + D KAM+ G R +
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 90
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
0.317 0.137 0.400
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: 1,640,749
Number of extensions: 90205
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 192
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.4 bits)