RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7051
(158 letters)
>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 = 120 bits (304), Expect = 2e-36
Identities = 67/102 (65%), Positives = 79/102 (77%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S G P ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+ T+ RGFAFVR
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
F D+RDA+DA AMDG LDGRELRVQ+ARYGR S S G
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103
>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 = 113 bits (284), Expect = 6e-33
Identities = 75/100 (75%), Positives = 84/100 (84%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
+ +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFVR
Sbjct: 59 HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
F DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S S
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158
>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 = 109 bits (274), Expect = 6e-32
Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 1/98 (1%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
P R + +++V NL+ T DL+ +F G + IY+ +D+ T +S+GFAF+ F
Sbjct: 6 SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
+ DA A+ + G D L V+ A+ S S
Sbjct: 66 RREDAARAIAGVSGFGYDHLILNVEWAKP-STNSGPSS 102
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 108 bits (272), Expect = 2e-31
Identities = 83/101 (82%), Positives = 91/101 (90%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S S
Sbjct: 95 RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 135
>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 = 106 bits (267), Expect = 5e-31
Identities = 34/90 (37%), Positives = 47/90 (52%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
+ L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV F
Sbjct: 6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYG 93
+ DA++A + +G LDGR +RV G
Sbjct: 66 NVDDAKEAKERANGMELDGRRIRVSGPSSG 95
>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 = 106 bits (267), Expect = 5e-31
Identities = 30/98 (30%), Positives = 48/98 (48%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
G L V NL+Y ++ +DL ++F G + +++ P D T++ +GFAFV F
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 67 DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
A A +DG++ GR L V + + S S G
Sbjct: 62 HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99
>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 = 100 bits (251), Expect = 1e-28
Identities = 31/90 (34%), Positives = 53/90 (58%), Gaps = 4/90 (4%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MS G P + ++ V NL + T +DL R+F + G+V + I +D+ TR+S+G AF+
Sbjct: 8 MSGGLAPSK----STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
F DK A++ A++ + L GR ++ +A
Sbjct: 64 LFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>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 = 100 bits (251), Expect = 3e-28
Identities = 32/115 (27%), Positives = 54/115 (46%), Gaps = 1/115 (0%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
P R L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRD 118
++A+ A++ ++G+ L G+ + V R P + RGGR R R DR R +
Sbjct: 73 TYKEAQAAMEGLNGQDLMGQPISVDWCFV-RGPPKGKRRGGRRRSRSPDRRRRLE 126
>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 = 97.5 bits (243), Expect = 5e-27
Identities = 35/95 (36%), Positives = 50/95 (52%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+ + L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV
Sbjct: 34 SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRP 95
F + DA++A + +G LDGR +RV + RP
Sbjct: 94 YFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128
>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 = 95.4 bits (238), Expect = 1e-26
Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 6/99 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
L V NL T +++R++FE+ G+ G+++I +D+ GF F+R
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLET 60
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
+ AE A +D L G++LRV+ A + +S S G
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSSG 99
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 95.5 bits (238), Expect = 1e-26
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 5/92 (5%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
G+ P + + L L+ + + GEV ++ I TR+ G A V F
Sbjct: 2 GQIPLK-----EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFT 56
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRP 95
R A++ + + + G + Q+ G+
Sbjct: 57 STRGAKETVKNLHLTSVMGNIIHAQLDIKGQQ 88
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 96.4 bits (240), Expect = 2e-26
Identities = 31/89 (34%), Positives = 38/89 (42%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
G L V L L F G++ DI IP D T + RGFAFV
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
F DA A+D M+ L GR +RV +A
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 94.1 bits (235), Expect = 3e-26
Identities = 29/74 (39%), Positives = 37/74 (50%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L L F G++ DI IP D T + RGFAFV F DA A+D M+
Sbjct: 12 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 71
Query: 78 RMLDGRELRVQMAR 91
L GR +RV +A+
Sbjct: 72 SELFGRTIRVNLAK 85
>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 = 94.6 bits (236), Expect = 3e-26
Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 1/99 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P ++ V L + + L +F + G V + ++P+DR T + +G+ FV F +
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
DA+ A+ MD L G+ +RV A + S G
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKAS-AHNKNLSGPSSG 105
>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 = 92.7 bits (231), Expect = 2e-25
Identities = 33/86 (38%), Positives = 41/86 (47%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L L F G++ DI IP D T + RGFAFV F DA A+D M+
Sbjct: 17 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 76
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
L GR +RV +A+ R S S G
Sbjct: 77 SELFGRTIRVNLAKPMRIKESGPSSG 102
>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 = 92.2 bits (230), Expect = 2e-25
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKRDAEDALDAMD 76
+ LT T D + +F G++ I +P +R S+G+A+V F + +AE AL MD
Sbjct: 9 IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD 68
Query: 77 GRMLDGRELRVQMARYGRP 95
G +DG+E+ P
Sbjct: 69 GGQIDGQEITATAVLAPWP 87
>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 = 95.0 bits (237), Expect = 3e-25
Identities = 34/105 (32%), Positives = 49/105 (46%), Gaps = 2/105 (1%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+ P M SL V +L T L F G + I + RD TR S G+A+V
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
F DAE ALD M+ ++ G+ +R+ ++ R PS +S G
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMWSQ--RDPSLRKSGVGN 105
Score = 66.5 bits (163), Expect = 2e-14
Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 4/105 (3%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
S P R G+ ++ + NL L F G + + D S+G+ FV
Sbjct: 91 WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFV 148
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
F + AE A++ M+G +L+ R++ V R+ G R
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRKVFV--GRFKSRKEREAELGAR 191
>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 = 92.4 bits (230), Expect = 3e-25
Identities = 30/106 (28%), Positives = 51/106 (48%), Gaps = 1/106 (0%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + L T L+ VF + G + ++ + +DR T +SRGFAF+ F + DA++A M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 76 DGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
+G+ L G+ ++V+ A+ S R R R +
Sbjct: 69 NGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHH 114
>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 = 91.0 bits (227), Expect = 5e-25
Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y T ++L F CG V + I D+F+ +GFA++ F DK +L A
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 75 MDGRMLDGRELRVQMARYGRP 95
+D + GR+++V R RP
Sbjct: 67 LDESLFRGRQIKVIPKRTNRP 87
>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 = 90.7 bits (226), Expect = 7e-25
Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L + T D LR +FE G++ +I + +D T S+G+ F+ F D A AL+ ++G
Sbjct: 10 VGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG 69
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
L GR +RV R S G
Sbjct: 70 FELAGRPMRVGHVT-ERLDGGSGPSSG 95
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 90.8 bits (226), Expect = 7e-25
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 1/92 (1%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S G P + E ++ V NL R + L +F + G + + I +DR + + F FV
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFVC 63
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
F A+ ++G L GR + V G
Sbjct: 64 FKHPESVSYAIALLNGIRLYGRPINVSGPSSG 95
>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 = 91.7 bits (228), Expect = 1e-24
Identities = 27/103 (26%), Positives = 49/103 (47%), Gaps = 1/103 (0%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
+ P + + +L V+ + LR++FER G + + I DR TR+SRG+ FV+F
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDR 107
A+ A+ ++G + + L+V +A + D
Sbjct: 94 GSSAQQAIAGLNGFNILNKRLKVALAA-SGHQRPGIAGAVGDG 135
>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 = 89.6 bits (223), Expect = 2e-24
Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 1/87 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L++ T L +VF + G++ ++ + +DR T+ SRGF FV F + DA+DA+ AM+G
Sbjct: 17 VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG 76
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
+ +DGR++RV A + S G
Sbjct: 77 KSVDGRQIRVDQAG-KSSDNRSGPSSG 102
>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 = 90.1 bits (224), Expect = 2e-24
Identities = 27/87 (31%), Positives = 42/87 (48%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
G + L V +L + T D LR +FE G + I + D T S+G+ F+ F D
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMAR 91
A+ AL+ ++G L GR ++V
Sbjct: 78 SECAKKALEQLNGFELAGRPMKVGHVT 104
>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 = 89.3 bits (222), Expect = 5e-24
Identities = 28/86 (32%), Positives = 40/86 (46%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ NL+ R T DL +F R E I T RG AF+ F +K A AL ++G
Sbjct: 30 LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG 89
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
L G+ L ++ + + SS S G
Sbjct: 90 YKLYGKILVIEFGKNKKQRSSGPSSG 115
>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 = 88.1 bits (219), Expect = 8e-24
Identities = 18/88 (20%), Positives = 36/88 (40%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ ++ Y T + + + G V ++ + D T S+G+AF+ F D + A+ ++G
Sbjct: 7 LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGR 105
L R L+ + S
Sbjct: 67 YQLGSRFLKCGYSSNSDISGVSLEHHHH 94
>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 = 89.9 bits (224), Expect = 8e-24
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 4/91 (4%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T ++ R +F GE+ + RD+ T +S G+ FV + D +DAE A++
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
++G L + ++V AR PSS+ R
Sbjct: 64 LNGLRLQTKTIKVSYAR----PSSASIRDAN 90
Score = 74.9 bits (185), Expect = 7e-18
Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 2/91 (2%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
SY RP +L V L T +L ++F + G + I D+ T SRG F+R
Sbjct: 77 SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136
Query: 62 FFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
F + +AE+A+ ++G+ G + V+ A
Sbjct: 137 FDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 87.7 bits (218), Expect = 1e-23
Identities = 28/98 (28%), Positives = 45/98 (45%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
P + S+ V N+ Y T + L+ +F G V + DR T + +G+ F + D+
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 67 DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
A A+ ++GR GR LRV A + +S G
Sbjct: 62 TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99
>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 = 88.8 bits (221), Expect = 2e-23
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 4/90 (4%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T +L +F G + I RD T S G+AFV F + D++ A+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
++G + + L+V AR P +
Sbjct: 65 LNGITVRNKRLKVSYAR----PGGESIKDT 90
Score = 79.2 bits (196), Expect = 1e-19
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 2/91 (2%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
SY RP +L V NL T D L +F + G + I RD+ T RG AFVR
Sbjct: 78 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
Query: 62 FFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
+ + +A++A+ A++ + +G + L V++A
Sbjct: 138 YNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>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 = 86.5 bits (215), Expect = 3e-23
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 3/95 (3%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE---SRGFAFVRFFDKRDA 68
G L + NL + TT + L+ VF + G + I + + S GF FV + A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 69 EDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
+ AL + G +DG +L V+++ P+S S G
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 86.9 bits (216), Expect = 3e-23
Identities = 20/79 (25%), Positives = 40/79 (50%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + T +D+ F GE+ +I++ DR T +G+ V + ++A+ A++ ++G
Sbjct: 28 VTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG 87
Query: 78 RMLDGRELRVQMARYGRPP 96
+ L G+ + V PP
Sbjct: 88 QDLMGQPISVDWCFVRGPP 106
>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 = 85.6 bits (213), Expect = 5e-23
Identities = 25/74 (33%), Positives = 39/74 (52%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L + LR F+ ++ D T SRG+ FV F + DA++A+D+M G
Sbjct: 6 VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 65
Query: 78 RMLDGRELRVQMAR 91
+ L+GR LR+ A
Sbjct: 66 QDLNGRPLRINWAA 79
>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 = 86.7 bits (215), Expect = 7e-23
Identities = 29/88 (32%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y +T DL F CG + I I D+F+ +G+A++ F ++ + A+ A
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSR 102
MD + GR ++V R P SS R
Sbjct: 97 MDETVFRGRTIKVLPKRTNMPGISSTDR 124
>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 = 86.2 bits (214), Expect = 7e-23
Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 1/91 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG L V ++ D+++ F GE+ +I++ DR T S+G+A V +
Sbjct: 20 PQRSVEGW-ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPP 96
+ A A +A++G + G+ ++V P
Sbjct: 79 KQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109
>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 = 85.4 bits (212), Expect = 8e-23
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
GM L + NL+ T DDLR++F +P G+AFV + D+ A
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIR 59
Query: 71 ALDAMDGRM-LDGRELRVQMARYGRPPSSSRSRG 103
A++ + G++ L G+ + V + + SS S G
Sbjct: 60 AIETLSGKVELHGKIMEVDYSVSKKLRSSGPSSG 93
>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 = 86.2 bits (214), Expect = 8e-23
Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 1/104 (0%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
+ V +L+ T +D++ F G + D + +D T +S+G+ FV FF
Sbjct: 6 SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFF 65
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDR 107
+K DAE+A+ M G+ L GR++R A +PP+ + +
Sbjct: 66 NKWDAENAIQQMGGQWLGGRQIRTNWAT-RKPPAPKSTYESNTK 108
>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 = 85.1 bits (211), Expect = 2e-22
Identities = 36/99 (36%), Positives = 43/99 (43%), Gaps = 3/99 (3%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
P + V NL D+ VF + G + DI + R FAFV F D
Sbjct: 14 IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFED 70
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
RDAEDA+ DG DG LRV+ R GR S S G
Sbjct: 71 PRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 84.3 bits (209), Expect = 2e-22
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
++ + N+ T D + V +I + +D+ T+++RGFAFV+ DA L
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 73 DAMDGR----MLDGRELRVQMAR 91
+ +DG+ + V A+
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFAK 93
>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 = 83.7 bits (208), Expect = 3e-22
Identities = 16/76 (21%), Positives = 32/76 (42%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L TT DL ++ + G++ D+ T + +G+ FV F A+ A+ A+
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69
Query: 78 RMLDGRELRVQMARYG 93
+ + + G
Sbjct: 70 SGVQAQMAKQSGPSSG 85
>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 = 85.6 bits (212), Expect = 3e-22
Identities = 28/120 (23%), Positives = 53/120 (44%), Gaps = 1/120 (0%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
++ +L V NL++ TT + + +F + G++ I + D+ + + GF FV
Sbjct: 28 DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
++ + DAE+A+ ++G LD R +R G RG R + + D
Sbjct: 88 YYSRADAENAMRYINGTRLDDRIIRTDWDA-GFKEGRQYGRGRSGGQVRDEYRQDYDAGR 146
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 83.9 bits (208), Expect = 5e-22
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ N+ + T DL +F+ G + D ++ G F+++ A + A+
Sbjct: 32 IGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVALAN 85
Query: 78 RMLDGRELRVQMAR 91
GR LR +
Sbjct: 86 FPFQGRNLRTGWGK 99
>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 = 83.0 bits (206), Expect = 5e-22
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ T + F G + D + +D T +S+G+ FV FF+K DAE+A+ M G
Sbjct: 11 VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70
Query: 78 RMLDGRELRVQMAR 91
+ L GR++R A
Sbjct: 71 QWLGGRQIRTNWAT 84
>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 = 83.5 bits (207), Expect = 6e-22
Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 5/90 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL+ T + ++F + G + + + + FV F++ RDA AL A
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
M+GR + G+E++V A PSS +S
Sbjct: 75 MNGRKILGKEVKVNWA---TTPSSQKSGPS 101
>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 = 83.1 bits (206), Expect = 8e-22
Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 2/99 (2%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRFFDK 65
P+ + + V N+ ++ ++R +F GE+ + +P+ T RGF FV F K
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 66 RDAEDALDAM-DGRMLDGRELRVQMARYGRPPSSSRSRG 103
+DA+ A +A+ L GR L ++ A S S G
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107
>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 = 83.1 bits (206), Expect = 1e-21
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
L R P DL F G+V D+ I DR +R S+G A+V F + + A+ + G
Sbjct: 30 CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTG 88
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
+ L G + VQ ++ + S S G
Sbjct: 89 QRLLGVPIIVQASQAEKNRLSGPSSG 114
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 82.9 bits (205), Expect = 1e-21
Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ + L +F + G+V ++ P D T +++GF FV DA+ + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 77 GRMLDGRE-LRV----QMARYGRP 95
G+ LD + L + + RY
Sbjct: 76 GKRLDLKHRLFLYTMKDVERYNSD 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 = 85.4 bits (212), Expect = 2e-21
Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 2/108 (1%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
+ + M + V ++ Y D +R+ F G + I + D T + +GFAFV +
Sbjct: 20 QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMA--RYGRPPSSSRSRGGRDRDRR 110
A+ AL+ M+ ML GR ++V P + R
Sbjct: 80 PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127
Score = 77.0 bits (190), Expect = 3e-18
Identities = 22/82 (26%), Positives = 43/82 (52%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V ++ + DD++ VFE G++ + RD T + +G+ F+ + + ++DA+ +M+
Sbjct: 130 VASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL 189
Query: 78 RMLDGRELRVQMARYGRPPSSS 99
L G+ LRV A P +
Sbjct: 190 FDLGGQYLRVGKAVTPPMPLLT 211
>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 = 82.4 bits (204), Expect = 2e-21
Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 9/87 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ T +R+ F G++ +I + ++ G++FVRF A A+ +++G
Sbjct: 30 CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSVNG 83
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
++G ++ +G+ S
Sbjct: 84 TTIEGHVVKC---YWGKESPDMTSGPS 107
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 82.0 bits (203), Expect = 2e-21
Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 5/98 (5%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+ + V NL +L R F G + ++I R+ GFAFV F D RDAEDA+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR 55
Query: 74 AMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRR 111
+DG+++ G +RV+++ S R +
Sbjct: 56 GLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEV 93
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 82.4 bits (204), Expect = 2e-21
Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 10/100 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEV--------GDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
V L T + + F++ G + I + DR T + +G A V F D A+
Sbjct: 12 VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 71
Query: 70 DALDAMDGRMLDGRELRVQMA--RYGRPPSSSRSRGGRDR 107
A+D DG+ G ++V A R RGG +
Sbjct: 72 AAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEH 111
>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 = 81.9 bits (203), Expect = 2e-21
Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 6/105 (5%)
Query: 2 SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
S G P S V L+ TT + L+ F I DR T S+GF F
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGF 58
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
V F + DA+ A +AM+ +DG ++ + A+ + S G
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK-PKGEGGSGPSSG 102
>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 = 81.4 bits (202), Expect = 2e-21
Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M ++ V NL Y T + ++ +F + G+V ++ + DR T++ +GF FV ++ +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAI 59
Query: 73 DAMDGRMLDGRELRVQMARYGRPPSSSRSR 102
+D GR +RV A +
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89
>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 = 81.6 bits (202), Expect = 4e-21
Identities = 23/106 (21%), Positives = 45/106 (42%), Gaps = 4/106 (3%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S G + + L + + DL+ +FE G++ ++ + +DRFT +G AF+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 62 FFDKRDAEDALDAMDGRML---DGRELRVQMARYGRPPSSSRSRGG 104
+ ++ A A A+ + R ++V+ A S G
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPAD-SESRGGSGPSSG 106
>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 = 81.1 bits (201), Expect = 4e-21
Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 7/89 (7%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
P ++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIF 58
Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQMAR 91
+ A +AL +M G + +R+Q A+
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAK 87
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 81.2 bits (201), Expect = 4e-21
Identities = 31/104 (29%), Positives = 53/104 (50%), Gaps = 4/104 (3%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
S G + L V N+ +R DLR++F + G++ D+ I + R S+GF FV
Sbjct: 4 GSSGNSESKSTPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 60
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
F + DA+ A + + G +++GR++ V A R ++S G
Sbjct: 61 TFENSADADRAREKLHGTVVEGRKIEVNNAT-ARVMTNSGPSSG 103
>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 = 80.7 bits (200), Expect = 6e-21
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
++L + NLT+ TT +DL G ++ +I +R +S+GFA V + ++
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 72 LDAMDGRMLDGRELRVQMAR 91
+D + R L G+ V +
Sbjct: 62 MDLLPKRELHGQNPVVTPSN 81
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 80.8 bits (200), Expect = 6e-21
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 2/87 (2%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
R +E L + L + T ++L + + G V D+ + +R + +G A+V + +
Sbjct: 10 RYSTSLEKH-KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYEN 67
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMAR 91
+ A A+ MDG + ++V ++
Sbjct: 68 ESQASQAVMKMDGMTIKENIIKVAISN 94
>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 = 80.8 bits (200), Expect = 7e-21
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRFFDKRDAE 69
V L T + + F++ G + I + DR T + +G A V F D A+
Sbjct: 18 VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 77
Query: 70 DALDAMDGRMLDGRELRVQMA 90
A+D DG+ G ++V A
Sbjct: 78 AAIDWFDGKEFSGNPIKVSFA 98
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 81.3 bits (201), Expect = 7e-21
Identities = 22/74 (29%), Positives = 36/74 (48%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ +L T DL F G V + D+ T S+ F FV F + A+ A+ AM+G
Sbjct: 45 IYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
Query: 78 RMLDGRELRVQMAR 91
+ + L+VQ+ +
Sbjct: 105 FQVGTKRLKVQLKK 118
>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 = 82.2 bits (204), Expect = 1e-20
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 3/91 (3%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L V NL T D L++ F+ G + +I I D+ ++ +AFV + DA AL
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
++G+ ++ +++ A + SS
Sbjct: 61 LNGKQIENNIVKINWAF--QSQQSSSDDTFN 89
Score = 76.0 bits (188), Expect = 3e-18
Identities = 26/90 (28%), Positives = 44/90 (48%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
++ + +L V +L + LR F+ ++ D T SRG+ FV
Sbjct: 75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
F + DA++A+D+M G+ L+GR LR+ A
Sbjct: 135 SFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 80.5 bits (199), Expect = 1e-20
Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 8/94 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEV--------GDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
V L T DDL F++CG V I+I D+ T + +G A V + D A+
Sbjct: 20 VQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAK 79
Query: 70 DALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
A++ DG+ G +L+V +AR P +S S G
Sbjct: 80 AAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113
>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 = 79.6 bits (197), Expect = 1e-20
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
++ +L NL++ T D+L+ VFE E+ +S+G A++ F
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKS 62
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMAR 91
+ DAE L+ G +DGR + +
Sbjct: 63 EADAEKNLEEKQGAEIDGRSVSLYYTG 89
>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 = 83.9 bits (208), Expect = 2e-20
Identities = 19/85 (22%), Positives = 31/85 (36%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T + G + ++ T +S+G+ F + K A A +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 76 DGRMLDGRELRVQMARYGRPPSSSR 100
G+ L R L V G+ +
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALL 182
Score = 71.9 bits (177), Expect = 6e-16
Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 6/103 (5%)
Query: 16 LKVDNLTYRTT-PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L VD L D L R + + + +GFA + + AE+A
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ-LKGFAVLEYETAEMAEEAQQQ 245
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSR 117
DG L G LRV + P RS + + +R
Sbjct: 246 ADGLSLGGSHLRV---SFCAPGPPGRSMLAALIAAQA-TALNR 284
Score = 69.2 bits (170), Expect = 4e-15
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 7/74 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L T ++ + + F + +G AFV + AE A++A
Sbjct: 27 IRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQ 79
Query: 78 RMLDGRELRVQMAR 91
L REL VQ+
Sbjct: 80 SRLRERELSVQLQP 93
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 79.7 bits (197), Expect = 2e-20
Identities = 27/109 (24%), Positives = 50/109 (45%), Gaps = 5/109 (4%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
R PP + L + NL Y+ T +++ +F + G + I + T E+RG A+V + D
Sbjct: 2 RLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYED 56
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR 113
DA++A+D + G + R L V R ++ ++ +
Sbjct: 57 IFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 105
>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 = 79.3 bits (196), Expect = 3e-20
Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 7/106 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
P + ++ + NL++ + + L V ++ G++ + + T S+G AF +F
Sbjct: 7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 66
Query: 65 KRDAEDALDAMD------GRMLDGRELRVQMARYGRPPSSSRSRGG 104
+ A+ L A G LDGR+L+V +A R ++S G
Sbjct: 67 QEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV-TRDEAASGPSSG 111
>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 = 79.3 bits (196), Expect = 4e-20
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ +L DL ++F G V + D+ T S+ F FV + + A+ A+ +M+G
Sbjct: 30 IYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
+ + L+VQ+ R + S S G
Sbjct: 90 FQIGMKRLKVQLKR-SKNDSKSGPSSG 115
>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 = 78.1 bits (193), Expect = 7e-20
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL T+ + + + F + + R +AFV F ++ DA +A+ A++G
Sbjct: 20 VRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNG 73
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
++LDG + V +A+ SS S G
Sbjct: 74 KVLDGSPIEVTLAKPVDKDSSGPSSG 99
>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 = 81.7 bits (201), Expect = 7e-20
Identities = 23/137 (16%), Positives = 47/137 (34%), Gaps = 3/137 (2%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVR 61
++L + NLT+ TT +DL G ++ +I +R +S+GFA V
Sbjct: 59 NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 118
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
+ ++ +D + R L G+ V + S + + + +
Sbjct: 119 VGSEASSKKLMDLLPKRELHGQNPVVTPVN-KQFLSQFEMQSRKTTQSGQMSGEGKAGPP 177
Query: 122 TRSRSFSSRSRSGSKSP 138
S + +
Sbjct: 178 GGSSRAAFPQGGRGRGR 194
>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 = 79.9 bits (197), Expect = 8e-20
Identities = 25/102 (24%), Positives = 46/102 (45%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
P R L V ++ D+++ F GE+ +I++ DR T S+G+A V +
Sbjct: 63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
+ A A +A++G + G+ ++V P +S R
Sbjct: 123 THKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRR 164
>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 = 77.2 bits (191), Expect = 1e-19
Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 8/92 (8%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
GMV L + NL T ++R +FE+ G+V + I + + FV DK AEDA
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAEDA 58
Query: 72 LDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
+ + L G + V+ ++ SS S G
Sbjct: 59 IRNLHHYKLHGVNINVEASKNKSKASSGPSSG 90
>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 = 77.3 bits (191), Expect = 1e-19
Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + NL+Y T + L+ VFE+ + + +S+G+AF+ F DA++AL++
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFI-KVP---QNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
+ R ++GR +R+++ R +S G
Sbjct: 73 CNKREIEGRAIRLELQG-PRGSPNSGPSSG 101
>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 = 76.1 bits (188), Expect = 4e-19
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 2/86 (2%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
+L + NL + +L+ D+ + D T +R F +V F
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESA 68
Query: 66 RDAEDALDAMDGRMLDGRELRVQMAR 91
D E AL+ + G + G E++++ +
Sbjct: 69 EDLEKALE-LTGLKVFGNEIKLEKPK 93
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 77.7 bits (191), Expect = 4e-19
Identities = 21/98 (21%), Positives = 45/98 (45%), Gaps = 3/98 (3%)
Query: 18 VDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V + ++ TT L +V G +V ++ +R +S+G+A V + L+ +
Sbjct: 60 VGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELL 119
Query: 76 DGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR 113
G++L+G ++ V+ A + S ++ + R R
Sbjct: 120 PGKVLNGEKVDVRPAT-RQNLSQFEAQARKRECVRVPR 156
>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 = 76.2 bits (188), Expect = 5e-19
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 1/86 (1%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
+E L V NL + + D++ +F G + + DR R S G A V F
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFER 79
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMA 90
K DA A+ +G LDGR + +Q+
Sbjct: 80 KADALKAMKQYNGVPLDGRPMNIQLV 105
>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 = 76.2 bits (188), Expect = 5e-19
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 11/97 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL T + L + F + G++ + +D +AF+ F ++ A A++ M+G
Sbjct: 16 VRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNG 67
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRS 114
+ L+G + + A +PP R R S
Sbjct: 68 KDLEGENIEIVFA---KPPDQKRKERKAQRQAASGPS 101
>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 = 77.2 bits (190), Expect = 6e-19
Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+ V NL +L R F G + +++ R+ GFAFV F D RDA DA+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127
Query: 73 DAMDGRMLDGRELRVQMARYGR 94
+DGR L G +RV+++ +
Sbjct: 128 RELDGRTLCGCRVRVELSNGEK 149
>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 = 78.1 bits (193), Expect = 7e-19
Identities = 17/73 (23%), Positives = 33/73 (45%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L D ++ + G + + +D T S+G+AF + D + A+ ++G
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 78 RMLDGRELRVQMA 90
L ++L VQ A
Sbjct: 179 MQLGDKKLLVQRA 191
Score = 69.7 bits (171), Expect = 1e-15
Identities = 18/109 (16%), Positives = 36/109 (33%), Gaps = 7/109 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
V N+ + T + + F +G + + + FAF+ F + A+
Sbjct: 9 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68
Query: 73 DAMDGRMLDGRELRVQMAR-YGRPPSSSRSRGGRDRDRRRDRSRSRDRR 120
A DG + G+ L+++ Y P S + +
Sbjct: 69 -AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 76.1 bits (187), Expect = 9e-19
Identities = 20/112 (17%), Positives = 41/112 (36%), Gaps = 10/112 (8%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAF 59
G PP E + + N+ + L+ + G++ DI + + ++ G A+
Sbjct: 20 GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAY 76
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRR 111
+ F + A+ ++A G G L + + P S + G
Sbjct: 77 IVFATQESAQAFVEAFQGYPFQGNPLVIT---FSETPQSQVAEDGSLEHHHH 125
>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 = 79.0 bits (195), Expect = 9e-19
Identities = 31/89 (34%), Positives = 44/89 (49%), Gaps = 6/89 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
L V NL T +D +R+FER GE +++I RDR GF F+R
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLES 67
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYG 93
+ AE A +DG +L R LR++ A +G
Sbjct: 68 RTLAEIAKAELDGTILKSRPLRIRFATHG 96
Score = 58.2 bits (141), Expect = 4e-11
Identities = 21/104 (20%), Positives = 35/104 (33%), Gaps = 2/104 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL+ + + L + F + G V + D R + G FV F K A AL+
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGR-ATGKGFVEFAAKPPARKALERC 157
Query: 76 DGRM-LDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRD 118
L R + + + + + R+
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKERE 201
>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 = 75.9 bits (187), Expect = 9e-19
Identities = 25/97 (25%), Positives = 38/97 (39%), Gaps = 1/97 (1%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
+E L V NL + + D++ +F G + + DR R S G A V F
Sbjct: 27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFER 85
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
+ DA A+ G LDGR + +Q+
Sbjct: 86 RADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122
>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 = 74.9 bits (185), Expect = 1e-18
Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N++ T +LR +FER G V + + + +AFV + DA+ A+ ++G
Sbjct: 14 VGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNG 65
Query: 78 RMLDGRELRVQMARYGRPPSSSRS 101
+ + G+ + V+++ G+ S S
Sbjct: 66 KEVKGKRINVELSTKGQKKSGPSS 89
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 75.0 bits (185), Expect = 1e-18
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 3/90 (3%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S+ + + L V N+ +R DLR++F + G++ D+ I + R S+GF FV
Sbjct: 19 SHMNTENKSQPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVT 75
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
F + DA+ A + + G +++GR++ V A
Sbjct: 76 FENSADADRAREKLHGTVVEGRKIEVNNAT 105
>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 = 75.2 bits (185), Expect = 2e-18
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 23 YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
TP LR F G + D+ + R AFV + A+ A+ ++G ++
Sbjct: 47 EDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVES 100
Query: 83 RELRVQMARYGRPPSSSRSRG 103
+L+V +AR + P + G
Sbjct: 101 VQLKVNIAR--KQPMLDAATG 119
>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 = 74.7 bits (184), Expect = 2e-18
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
SL + +L + + R F GE V + I R+R T G+ FV F D AE L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 74 AMDGRMLDG----RELRVQMARYGRPPS 97
++G+ L G + ++ A Y P S
Sbjct: 71 KINGKPLPGATPAKRFKLNYATYSGPSS 98
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 73.8 bits (182), Expect = 3e-18
Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 9/90 (10%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ NL + +DL R+F G + I I F F++F + + DA++
Sbjct: 15 IGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECES 66
Query: 77 GRMLDGRELRVQMARYGRPPSSSRSRGGRD 106
M G++L ++++ P G +
Sbjct: 67 QEMNFGKKLILEVSSSNARPQFDHGDHGTN 96
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 73.8 bits (182), Expect = 3e-18
Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 2/91 (2%)
Query: 8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
G + V NL + T L+ F CG V I + +S+G V+F
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEV 60
Query: 68 AEDALDAMDGRMLDGRELRVQMARYGRPPSS 98
AE A M+G L GRE+ V++ R PSS
Sbjct: 61 AERACRMMNGMKLSGREIDVRIDRNASGPSS 91
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 75.7 bits (187), Expect = 3e-18
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 2/88 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE--SRGFAFVRFFDKRDAEDALDAM 75
V + + DLR +FE+ G V +I + RDR S+G FV F+ ++ A +A +A+
Sbjct: 8 VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67
Query: 76 DGRMLDGRELRVQMARYGRPPSSSRSRG 103
+ + ++
Sbjct: 68 HNMKVLPGMHHPIQMKPADSEKNNAVED 95
Score = 66.9 bits (164), Expect = 7e-15
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ ++ + T +D+R +F G++ + I R SRG AFV F + A+ A+ AM
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ 158
Query: 78 RML---DGRELRVQMA 90
+ V+ A
Sbjct: 159 AQTMEGCSSPMVVKFA 174
>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 = 75.3 bits (186), Expect = 4e-18
Identities = 19/86 (22%), Positives = 36/86 (41%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
+ G L + L D ++ + G + + +D T S+G+AF + D
Sbjct: 86 HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMA 90
+ A+ ++G L ++L VQ A
Sbjct: 146 INVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 69.2 bits (170), Expect = 1e-15
Identities = 16/87 (18%), Positives = 34/87 (39%), Gaps = 6/87 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
V N+ + T + + F +G + + + FAF+ F + A+
Sbjct: 9 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68
Query: 73 DAMDGRMLDGRELRVQMARYGRPPSSS 99
A DG + G+ L+++ +P +
Sbjct: 69 -AFDGIIFQGQSLKIRRPHDYQPLPGA 94
>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 = 73.0 bits (180), Expect = 5e-18
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N++ T +LR FE G V + I + +AFV DA +A+ +D
Sbjct: 15 VGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDN 66
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
G+ + VQ++ +S S G
Sbjct: 67 TEFQGKRMHVQLSTSRLRTASGPSSG 92
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 73.4 bits (181), Expect = 5e-18
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 3/87 (3%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + LR+ F G + + + S+GF FV F +A A+ M+G
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
R++ + L V +A+ + S G
Sbjct: 78 RIVATKPLYVALAQ-RKEERQSGPSSG 103
>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 = 73.3 bits (180), Expect = 6e-18
Identities = 17/100 (17%), Positives = 34/100 (34%), Gaps = 6/100 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+ NL T +++ F R G +G + +P E A V F + +A A
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRH 65
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRS 114
+ L ++ A G ++ + + +
Sbjct: 66 LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105
>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 = 72.3 bits (178), Expect = 1e-17
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 6/79 (7%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
TP LR F G + D+ + R AFV + A+ A+ ++G ++ +
Sbjct: 25 MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVESVQ 78
Query: 85 LRVQMARYGRPPSSSRSRG 103
L+V +AR S S G
Sbjct: 79 LKVNIARKQPMLDSGPSSG 97
>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 = 72.3 bits (178), Expect = 1e-17
Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 11/99 (11%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+ YG+ P L V L T+ L R F+R G + I + FA++
Sbjct: 9 IGYGKANPTT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYI 58
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
++ A+ A M G L G + R+++ + + SS
Sbjct: 59 QYESLDAAQAACAKMRGFPLGGPDRRLRV-DFAKSGPSS 96
>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 = 76.2 bits (188), Expect = 2e-17
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ N T ++R + + V I +P RF SR FA++ K DA ++ ++
Sbjct: 122 MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT-SRRFAYIDVTSKEDARYCVEKLN 180
Query: 77 GRMLDGRELRVQMAR 91
G ++G L +++
Sbjct: 181 GLKIEGYTLVTKVSN 195
Score = 70.4 bits (173), Expect = 2e-15
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 14 VSLKVDNLTYRTTPDD-LRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKRDAEDA 71
+ + NL+ ++ LR FE G + I IP + + AF+ F +K AE A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270
Query: 72 LDAMDGRMLDGRELRVQMA 90
L M+ +L RE+ V +A
Sbjct: 271 L-QMNRSLLGNREISVSLA 288
Score = 69.6 bits (171), Expect = 4e-15
Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 3/84 (3%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
R + ++ V NL + + + F+ CG + + + +++ FA + F
Sbjct: 32 NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFA 89
Query: 64 DKRDAEDALDAMDGRMLDGRELRV 87
A A+ ++ E+ V
Sbjct: 90 RYDGALAAITKTHK-VVGQNEIIV 112
>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 = 71.8 bits (177), Expect = 2e-17
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ NL L F G + I RD T S+G+AF+ F ++ A++AM+
Sbjct: 10 IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69
Query: 77 GRMLDGRELRVQMARYGRPPSSSRSRGG 104
G+ L R + V A + + S G
Sbjct: 70 GQYLCNRPITVSYA-FKKDSKGSGPSSG 96
>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 = 73.4 bits (181), Expect = 3e-17
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
GR ++ +L NL++ T D+L+ VFE E I +S+G A++
Sbjct: 88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIE 142
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
F + DAE L+ G +DGR + +
Sbjct: 143 FKSEADAEKNLEEKQGAEIDGRSVSLYYT 171
Score = 72.3 bits (178), Expect = 7e-17
Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 2/90 (2%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S+ +L + NL + +L+ D+ + R T +R F +V
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVD 60
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
F D E AL+ + G + G E++++ +
Sbjct: 61 FESAEDLEKALE-LTGLKVFGNEIKLEKPK 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 = 71.9 bits (177), Expect = 3e-17
Identities = 23/105 (21%), Positives = 40/105 (38%), Gaps = 16/105 (15%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ NL L F G + + D S+G+ FV F + AE A++ M+G
Sbjct: 10 IKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYT 122
+L+ R++ V + R R +R + +T
Sbjct: 68 MLLNDRKVFVGRFKS--------------RKEREAELGARAKEFT 98
>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 = 70.8 bits (174), Expect = 4e-17
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L T DLR F + GE+ I + + + AF++F ++ AE A +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEK 67
Query: 75 M-DGRMLDGRELRVQMAR 91
+ +++GR L V+ R
Sbjct: 68 SFNKLIVNGRRLNVKWGR 85
>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 = 73.4 bits (180), Expect = 4e-17
Identities = 26/110 (23%), Positives = 47/110 (42%), Gaps = 8/110 (7%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
V NL R TP L +F G+V + I + + A V+ D A+ A+ ++
Sbjct: 8 VSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLN 62
Query: 77 GRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
G L G+ +R+ ++++ G D+ +D S R+ + S
Sbjct: 63 GHKLHGKPIRITLSKHQNVQ--LPREGQEDQGLTKDYGNSPLHRFKKPGS 110
Score = 61.8 bits (150), Expect = 1e-12
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + N+ + +DL+ +F G V + +F ++ R A ++ +A AL +
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 178
Query: 76 DG-RMLDGRELRVQMAR 91
+ + LRV ++
Sbjct: 179 HNHDLGENHHLRVSFSK 195
>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 = 70.8 bits (174), Expect = 5e-17
Identities = 27/107 (25%), Positives = 43/107 (40%), Gaps = 8/107 (7%)
Query: 2 SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
S G G K V L + + +D+ R+F+ G + + + R S+G AF
Sbjct: 2 SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAF 60
Query: 60 VRFFDKRDAEDALDAMDGRML---DGRELRVQMARYGRPPSSSRSRG 103
V+F +A+ A+ A+ G L V+ A S S G
Sbjct: 61 VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFAD--TDKESGPSSG 105
>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 = 70.5 bits (173), Expect = 9e-17
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ NL T D+ +F + G V + + G+AFV++ ++R A A+ +
Sbjct: 32 IGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVLGEN 83
Query: 77 GRMLDGRELRVQMARYGRPPSSSRSRG 103
GR+L G+ L + MA +P S S G
Sbjct: 84 GRVLAGQTLDINMAGEPKPDRSGPSSG 110
>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 = 70.4 bits (173), Expect = 1e-16
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L Y TT LR+ FE G++ + + DR T +SRG+ FV D+ AE A +
Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP 81
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
++DGR+ V +A G P S ++
Sbjct: 82 -IIDGRKANVNLAYLGAKPRSLQTGFA 107
>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 = 72.7 bits (178), Expect = 2e-16
Identities = 28/128 (21%), Positives = 50/128 (39%), Gaps = 8/128 (6%)
Query: 4 GRPPPRIEGMVSLKVDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
P G L V NL R TP L +F G+V + + + A V+
Sbjct: 25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQM 79
Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYT 122
D A+ A+ ++G L G+ +R+ +++ G D+ +D S R+
Sbjct: 80 ADGNQAQLAMSHLNGHKLHGKPIRITLSK--HQNVQLPREGQEDQGLTKDYGNSPLHRFK 137
Query: 123 RSRSFSSR 130
+ S + +
Sbjct: 138 KPGSKNFQ 145
Score = 60.0 bits (145), Expect = 9e-12
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + N+ + +DL+ +F G V + +F ++ R A ++ +A AL +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 209
Query: 76 DGRML-DGRELRVQMAR 91
L + LRV ++
Sbjct: 210 HNHDLGENHHLRVSFSK 226
>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 = 71.4 bits (176), Expect = 2e-16
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L + TT D+LR F + G V D+ I +D T SRGF F+ F ++ +
Sbjct: 8 IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ-- 65
Query: 78 RMLDGRELRVQMA 90
+LDG+ + + A
Sbjct: 66 HILDGKVIDPKRA 78
Score = 69.1 bits (170), Expect = 1e-15
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 3/88 (3%)
Query: 5 RPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
R PR E + K V + P + F + G + D + D+ T +SRGF FV +
Sbjct: 77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQMA 90
+ R++ ++ A
Sbjct: 137 DSADAVDRVC-QNKFIDFKDRKIEIKRA 163
>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 = 69.6 bits (171), Expect = 2e-16
Identities = 28/117 (23%), Positives = 43/117 (36%), Gaps = 7/117 (5%)
Query: 2 SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
S G G + V NL Y+ L+ VF G V I D+ + SRG
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGT 60
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRS 116
V F +A A+ +G++L R + V+M P + ++ S
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP----KGDFFPPERPQQSGPSS 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 = 72.0 bits (176), Expect = 2e-16
Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 6/110 (5%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
V L + D + VF G V + + + G A V D + A+ ++
Sbjct: 9 VYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLN 63
Query: 77 GRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
+ G+++ V +++ +D S SR+ R++
Sbjct: 64 NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQ 113
Score = 66.7 bits (162), Expect = 2e-14
Identities = 8/70 (11%), Positives = 19/70 (27%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
N T ++ + + G + E + + K DA + L ++
Sbjct: 128 FFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNH 187
Query: 78 RMLDGRELRV 87
+
Sbjct: 188 YQMKNPNGPY 197
>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 = 69.6 bits (171), Expect = 2e-16
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 1/74 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ NL +L + + G+V I RD + SRG F R E + +G
Sbjct: 30 ISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNG 88
Query: 78 RMLDGRELRVQMAR 91
+ +
Sbjct: 89 KFIKTPPGVSAPTE 102
>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 = 68.8 bits (169), Expect = 3e-16
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 2/87 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + + +LR F++ G V ++ + D + RGF F+ F D++ + A+ M
Sbjct: 15 VGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHF 73
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGG 104
+ G+++ V+ A R SS G
Sbjct: 74 HDIMGKKVEVKRAE-PRDSKSSGPSSG 99
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 68.9 bits (169), Expect = 3e-16
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 8/74 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L +F G + ++ I GFAFV F + A A++ + G
Sbjct: 36 VRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEEVHG 87
Query: 78 RMLDGRELRVQMAR 91
+ + L V ++
Sbjct: 88 KSFANQPLEVVYSK 101
>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 = 69.5 bits (170), Expect = 4e-16
Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 6/93 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEV-----GDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
V NL DL+ +F R + ++ R +G AF+ +++ A AL
Sbjct: 50 VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
Query: 73 DAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
+G +L G+ + VQ AR P G R
Sbjct: 110 KEANGYVLFGKPMVVQFAR-SARPKQDPKEGKR 141
>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 = 67.5 bits (166), Expect = 4e-16
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L+ T + +R F GEV I +P D T + RGF F+ F ++ + +
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKY 62
Query: 78 RMLDGRELRVQMA 90
+ + +++A
Sbjct: 63 HNVGLSKCEIKVA 75
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 68.4 bits (168), Expect = 4e-16
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 2/99 (2%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
E + V NL + T D+ +F+ + + + RD+ T + +GF +V F +
Sbjct: 7 GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDE 65
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
++AL DG +L R LRV +A + S S G
Sbjct: 66 VDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPSSG 103
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 68.4 bits (168), Expect = 5e-16
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L ++TT DL+ F GEV + + +D T S+GF FVRF + +
Sbjct: 20 VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH- 78
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
M+DGR ++ + S S G
Sbjct: 79 -MIDGRWCDCKLPNSKQSQDSGPSSG 103
>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 = 68.1 bits (167), Expect = 5e-16
Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 3/93 (3%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
G +KV N+ + + D++ F + + G A V F +
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSS 98
+A A+ ++ R + R++++ + PSS
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKLVLG---SGPSS 97
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 67.5 bits (166), Expect = 5e-16
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L+ TT +D++ FE+ G+V D + D+ T RGF FV F + E +
Sbjct: 4 VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHF 62
Query: 78 RMLDGRELRVQMA 90
++ + + + A
Sbjct: 63 HEINNKMVECKKA 75
>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 = 67.7 bits (166), Expect = 6e-16
Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 5/92 (5%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S G+P P + +KV N+ + + D++ F + + G A V
Sbjct: 9 SSGKPGPTV-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
F + +A A+ ++ R + R++++ G
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95
>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 = 71.8 bits (175), Expect = 6e-16
Identities = 29/141 (20%), Positives = 59/141 (41%), Gaps = 10/141 (7%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVR 61
P ++ ++NL + D+L++ +F + G++ DI + R + + RG AFV
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVI 58
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
F + A +AL +M G + +R+Q A + S ++ R + R +
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQYA---KTDSDIIAKMKGTFVERDRKREKRKPKS 115
Query: 122 TRSRSFSSRSRSGSKSPRKAR 142
+ + + G +P
Sbjct: 116 QETPATKKAVQGGGATPVVGA 136
Score = 53.3 bits (127), Expect = 3e-09
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 6/73 (8%)
Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG-R 78
NL T L +F + ++ + R AFV F ++ A A DA+ G +
Sbjct: 214 NLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFK 268
Query: 79 MLDGRELRVQMAR 91
+ +++ A+
Sbjct: 269 ITQNNAMKISFAK 281
>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 = 68.0 bits (166), Expect = 1e-15
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 10/91 (10%)
Query: 18 VDNLTYRTTPDDLRR---VFERCGEVGDIYIPRDRFTRESR---GFAFVRFFDKRDAEDA 71
V L+ R ++ + F + G++ + I S+ A+V + DA A
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79
Query: 72 LDAMDGRMLDGRELRVQMA--RY--GRPPSS 98
+ ++ ++DGR L+ + +Y PSS
Sbjct: 80 IQCVNNVVVDGRTLKASLGTTKYCSYSGPSS 110
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 66.4 bits (163), Expect = 2e-15
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L+++TT + LR F + GEV + + RD T+ SRGF FV F D+ + L A L
Sbjct: 8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHEL 66
Query: 81 DGRELRVQMA 90
D + + ++A
Sbjct: 67 DSKTIDPKVA 76
>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 = 69.2 bits (170), Expect = 2e-15
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MS P E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
+ + + A+ +DGR + + A
Sbjct: 61 TYATVEEVDAAM-NARPHKVDGRVVEPKRA 89
Score = 66.5 bits (163), Expect = 2e-14
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + T LR FE+ G++ I I DR + + RGFAFV F D + +
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKY 167
Query: 78 RMLDGRELRVQMA--RYGRPPSSSRSRG 103
++G V+ A + +SS RG
Sbjct: 168 HTVNGHNCEVRKALSKQEMASASSSQRG 195
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 66.1 bits (162), Expect = 3e-15
Identities = 27/70 (38%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L++ T+ DL+ F + GEV D I D T SRGF F+ F D E LD + L
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRL 77
Query: 81 DGRELRVQMA 90
DGR + + A
Sbjct: 78 DGRVIDPKKA 87
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 65.9 bits (161), Expect = 3e-15
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+V + + ++F + G++ + + P + +++G+ F+ + A DA+ D
Sbjct: 11 QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNAD 68
Query: 77 GRMLDGRE-LRV 87
G LD + RV
Sbjct: 69 GYKLDKQHTFRV 80
>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 = 65.4 bits (160), Expect = 5e-15
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 18 VDNLTYRT-TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ NL + + +DL R+F G + I I F F++F + + DA++
Sbjct: 27 IGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXES 78
Query: 77 GRMLDGRELRVQMARYGR 94
M G++L ++++
Sbjct: 79 QEMNFGKKLILEVSSSNA 96
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 65.4 bits (160), Expect = 7e-15
Identities = 24/103 (23%), Positives = 43/103 (41%), Gaps = 4/103 (3%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFV 60
S G P+ + + NL Y T + ++ F + + +PR+ E +GF +
Sbjct: 5 SSGSRLPK-SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 62
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
F D AL +++ L + +RV +A + S S G
Sbjct: 63 EFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPSSG 104
>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 = 64.9 bits (159), Expect = 8e-15
Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + R ++R F R G V ++ I DR T S+G+ FV F++ D + ++
Sbjct: 14 VGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQ 70
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGR 105
G++L++ A + S+ R
Sbjct: 71 INFHGKKLKLGPAI-RKQNLSTYHVQPR 97
>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 = 64.7 bits (158), Expect = 1e-14
Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 7/86 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + ++ + + + + ++ AFV + A++A+
Sbjct: 10 VKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQ 62
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
G++L VQ+ S S G
Sbjct: 63 YSFRGKDLIVQLQPTDALLCSGPSSG 88
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 64.4 bits (157), Expect = 1e-14
Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 3/84 (3%)
Query: 8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
P+ + + L++ N+ + L + + G V V + K
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD---SETAVVNVTYSSKDQ 66
Query: 68 AEDALDAMDGRMLDGRELRVQMAR 91
A ALD ++G L+ L+V
Sbjct: 67 ARQALDKLNGFQLENFTLKVAYIP 90
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 64.5 bits (157), Expect = 2e-14
Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 5/81 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+ V NL DL+R G V P + R AF+ + D A+ A+
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75
Query: 75 MDGRMLDGRELRVQMARYGRP 95
+ G L LRV +AR R
Sbjct: 76 LQGLRLGTDTLRVALARQQRD 96
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 63.6 bits (155), Expect = 3e-14
Identities = 15/75 (20%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+V + + ++F + G++ + + P + +++G+ F+ + A DA+ D
Sbjct: 25 QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNAD 82
Query: 77 GRMLDGRE-LRVQMA 90
G LD + RV +
Sbjct: 83 GYKLDKQHTFRVNLF 97
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 63.7 bits (155), Expect = 4e-14
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 4/83 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGE-VGDIYIPRD-RFTRESRGFAFVRFFDKRDAEDALDAM 75
+ + +++ + E V D+ + ++RGFAFV + R A A +
Sbjct: 13 IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL 72
Query: 76 --DGRMLDGRELRVQMARYGRPP 96
L G ++ V A
Sbjct: 73 MPGRIQLWGHQIAVDWAEPEIDV 95
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 63.0 bits (154), Expect = 6e-14
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L+++TT + LR F + GEV + + RD T+ SRGF FV F D+ + L A L
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHEL 91
Query: 81 DGRELRVQMA 90
D + + ++A
Sbjct: 92 DSKTIDPKVA 101
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 62.6 bits (153), Expect = 8e-14
Identities = 30/83 (36%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L + TT + LR F + GEV D I +D+ T +SRGF FV+F D L A L
Sbjct: 24 LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-ASRPHTL 82
Query: 81 DGRELRVQMARYGRPPSSSRSRG 103
DGR + + S S G
Sbjct: 83 DGRNIDPKPCTPRGMQPSGPSSG 105
>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 = 62.1 bits (151), Expect = 2e-13
Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 9/108 (8%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S G+P P + + V + + +D+R F V +++ +D R + G V+
Sbjct: 5 SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR-NNGNGLVK 62
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRV------QMARYGRPPSSSRSRG 103
F +D +AL + ++ R + V Q G +S S G
Sbjct: 63 FLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109
>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 = 62.1 bits (151), Expect = 2e-13
Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 9/108 (8%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFD 64
V + N+ + T D+ + E +++ D + G A V+F +
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ-GLGQALVQFKN 66
Query: 65 KRDAEDALDAMDGRMLDGRELRV------QMARYGRPPSSSRSRGGRD 106
+ DA + + + L+GRE V M + P + G
Sbjct: 67 EDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSS 113
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 61.9 bits (151), Expect = 2e-13
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L++ TT + LR +E+ G++ D + RD ++ SRGF FV F + + A+ A +
Sbjct: 35 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSI 93
Query: 81 DGRELRVQMARYGRPPSSSRSRGG 104
DGR + + A R S S G
Sbjct: 94 DGRVVEPKRAV-AREESGSGPSSG 116
>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 = 61.5 bits (150), Expect = 2e-13
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFVRFFDKRDAEDALD 73
+ + NL Y T + ++ F + + +PR+ E +GF + F D AL
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 78
Query: 74 AMDGRMLDGRELRVQMAR 91
+++ L R +RV +A
Sbjct: 79 SLNEESLGNRRIRVDVAD 96
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 59.9 bits (146), Expect = 6e-13
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V T T D+LR F + G+V D++IP+ R FAFV F D + A+ +
Sbjct: 10 VGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC--GED 62
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRG 103
++ G + + A +S S G
Sbjct: 63 LIIKGISVHISNAEPKHNSNSGPSSG 88
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 61.8 bits (150), Expect = 7e-13
Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 1/97 (1%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
+E L V NL + + D++ +F G + + DR + S G A V F
Sbjct: 80 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER 138
Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
+ DA A+ G LDGR + +Q+
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 59.6 bits (145), Expect = 1e-12
Identities = 22/95 (23%), Positives = 36/95 (37%), Gaps = 8/95 (8%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
G+ S+ V L F G V + + +D+ FA V D A +
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDV-GARE 59
Query: 71 ALDAMDGRMLDGRELRVQMA--RYGRPPSSSRSRG 103
A+ + L G LRV+ + + P+S +G
Sbjct: 60 AVLSQSQHSLGGHRLRVRPREQKEFQSPASKSPKG 94
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 58.6 bits (142), Expect = 2e-12
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 2/74 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ T DD++ E G+V +I + R + +G FV F A+ + G
Sbjct: 16 IKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV-ETPG 73
Query: 78 RMLDGRELRVQMAR 91
+ +L +
Sbjct: 74 QKYKETDLLILFKD 87
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43
inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA;
1.65A {Mus musculus}
Length = 89
Score = 57.2 bits (139), Expect = 6e-12
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V T T ++L++ F + GEV D++IP+ R FAFV F D + A+ +
Sbjct: 16 VGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC--GED 68
Query: 78 RMLDGRELRVQMA 90
++ G + + A
Sbjct: 69 LIIKGISVHISNA 81
>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 = 59.8 bits (144), Expect = 6e-12
Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 2/90 (2%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
S+ + T DD++ E G+V +I + R + +G FV
Sbjct: 97 PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFV 155
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
F A+ ++ G+ +L +
Sbjct: 156 VFDSIESAKKFVETP-GQKYKETDLLILFK 184
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 58.5 bits (141), Expect = 6e-12
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V+NL Y T D L ++F + G V I FT+ ++ A +++ D A+ A ++DG
Sbjct: 33 VENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSLDG 88
Query: 78 RML--DGRELRVQMARYGRPPSSSRSRGGRD 106
+ + LR+ ++ + RD
Sbjct: 89 QNIYNACCTLRIDFSKLTSLNVKYNNDKSRD 119
>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 = 56.9 bits (137), Expect = 2e-11
Identities = 12/61 (19%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM 79
L + + L V E+CG V + +P ++ ++F R+ +++ A ++G+
Sbjct: 34 GLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKE 87
Query: 80 L 80
+
Sbjct: 88 V 88
>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 = 56.2 bits (136), Expect = 2e-11
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 5/84 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
++K+ + T ++ V I I R+ G+ FV F ++ + + AL
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGN-KTGYIFVDFSNEEEVKQALK- 68
Query: 75 MDGRMLDGRELRVQMARYGRPPSS 98
+ + GR + V + PSS
Sbjct: 69 CNREYMGGRYIEVFREK--SGPSS 90
>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 = 56.0 bits (135), Expect = 3e-11
Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 11/91 (12%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM-- 75
V L DL E+ G + + + + A V F + A++ +
Sbjct: 20 VRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAAD 73
Query: 76 DGRMLDGRELRVQMARY---GRPPSSSRSRG 103
+ G++ + RP +S S G
Sbjct: 74 VPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 55.4 bits (134), Expect = 4e-11
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
SL V +LT L F + + D+ T S+G+ FV+F D+ + + AL
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69
Query: 74 AMDGRM-LDGRELRVQMA 90
G + L + +R+ +A
Sbjct: 70 ECQGAVGLGSKPVRLSVA 87
>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 = 54.4 bits (131), Expect = 8e-11
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
V N+ + T + + F +G + + + FAF+ F + A+
Sbjct: 11 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 70
Query: 73 DAMDGRMLDGRELRVQMARYGRP 95
A DG + G+ L++ RP
Sbjct: 71 -AFDGIIFQGQSLKI-----RRP 87
>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 = 54.8 bits (132), Expect = 1e-10
Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 3/97 (3%)
Query: 8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFDKR 66
P +++ L + + +++ + F V + +P D R S G AFV+F +
Sbjct: 10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR-STGEAFVQFASQE 68
Query: 67 DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
AE AL + R + + + +S S G
Sbjct: 69 IAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPSSG 104
>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 = 55.9 bits (134), Expect = 1e-10
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 6/93 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
+ V+NL Y T D L ++F + G V I FT+ ++ A +++ D A+ A ++
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSL 104
Query: 76 DGRML--DGRELRVQMARYGRPPSSSRSRGGRD 106
DG+ + LR+ ++ + RD
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRD 137
>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 = 53.2 bits (128), Expect = 4e-10
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
+ + L YR T +D+ F + ++I R G A V F DA A+ A
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGR-VTGEADVEFATHEDAVAAM-AK 74
Query: 76 DGRMLDGRELRV 87
D + R + +
Sbjct: 75 DKANMQHRYVEL 86
>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 = 52.9 bits (127), Expect = 4e-10
Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
+ + E+ GEV ++ + + G +V+F + DAE A+ ++ R +G+ +
Sbjct: 42 EVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Query: 88 Q 88
+
Sbjct: 101 E 101
>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 = 52.5 bits (126), Expect = 8e-10
Identities = 21/118 (17%), Positives = 39/118 (33%), Gaps = 11/118 (9%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAF 59
R E + + L + + F++ V IYI + + G F
Sbjct: 13 QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGF 71
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSR 117
V F ++ D + AL + + R ++V ++ D R R +S
Sbjct: 72 VEFRNEADYKAAL-CRHKQYMGNRFIQVHP--------ITKKGMLEKIDMIRKRLQSG 120
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 52.2 bits (125), Expect = 9e-10
Identities = 14/107 (13%), Positives = 37/107 (34%), Gaps = 13/107 (12%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
P R+ + + L T ++ + G+V ++ + + + AF+
Sbjct: 9 HHGSGVPSRV-----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFI 57
Query: 61 RFFDKRDAEDALDA--MDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
+ A ++ +L G+ + +Q + + + S R
Sbjct: 58 EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQAR 104
>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 = 52.2 bits (125), Expect = 1e-09
Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 15/112 (13%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERC---GEVGDIYIPRDRFTRESRGFAFVR 61
P +K+ L + + +D++ C V ++ R R G AFV
Sbjct: 9 MLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGEAFVE 67
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRV----------QMARYGRPPSSSRSRG 103
+ D + AL D + R + V + G +S S G
Sbjct: 68 LESEDDVKLAL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118
>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 = 52.2 bits (125), Expect = 1e-09
Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 3/91 (3%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAF 59
M G +++ L + T +++ + F V I +P D + G AF
Sbjct: 30 MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAF 88
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
V+F + AE AL + R + V +
Sbjct: 89 VQFASQELAEKALG-KHKERIGHRYIEVFKS 118
>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 = 51.7 bits (124), Expect = 1e-09
Identities = 30/116 (25%), Positives = 38/116 (32%), Gaps = 8/116 (6%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
PP + V L + DL+ G+V + RD G V F
Sbjct: 7 RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV 59
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDR 119
K D A+ +D E R + GR R R R RSRSR R
Sbjct: 60 RKEDMTYAVRKLDNTKFRSHEGETAYIRV-KVDGPRSPSYGRSRSRSRSRSRSRSR 114
>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 = 51.7 bits (124), Expect = 1e-09
Identities = 25/116 (21%), Positives = 32/116 (27%), Gaps = 12/116 (10%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
PP + V L + DL+ G+V + RD G V
Sbjct: 4 GSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVE 56
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSR 117
F K D A+ +D E R S S G R R S
Sbjct: 57 FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYG-----RSRSSGPSS 107
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 50.5 bits (121), Expect = 3e-09
Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 8/77 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L DL + G + + + + A V F D A +A++
Sbjct: 26 IRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAAD 79
Query: 78 R--MLDGRELRVQMARY 92
+ G V +
Sbjct: 80 NQIYIAGHPAFVNYSTS 96
>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 = 50.6 bits (121), Expect = 4e-09
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 4/82 (4%)
Query: 10 IEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPR--DRFTRESRGFAFVRFFDK 65
+ MV + +D+ Y +D+R + G V I IPR D G FV F
Sbjct: 10 LMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSV 69
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
D + A+ + GR R +
Sbjct: 70 FDCQKAMQGLTGRKFANRVVVT 91
>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 = 50.3 bits (120), Expect = 6e-09
Identities = 12/90 (13%), Positives = 33/90 (36%), Gaps = 8/90 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD--AM 75
+ L T ++ + G+V ++ + + + AF+ + A ++
Sbjct: 36 IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS 89
Query: 76 DGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
+L G+ + +Q + + + S R
Sbjct: 90 VTPVLRGQPIYIQFSNHKELKTDSSPNQAR 119
>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 = 49.8 bits (119), Expect = 7e-09
Identities = 13/88 (14%), Positives = 33/88 (37%), Gaps = 8/88 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD--AM 75
+ L T ++ + G+V +I + + + AF+ + A ++ +
Sbjct: 20 IRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSA 73
Query: 76 DGRMLDGRELRVQMARYGRPPSSSRSRG 103
L + + +Q + + +S S G
Sbjct: 74 VTPHLRNQPIYIQYSNHKELKTSGPSSG 101
>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 = 50.6 bits (121), Expect = 7e-09
Identities = 19/104 (18%), Positives = 35/104 (33%), Gaps = 6/104 (5%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
+ + + L Y+ T +D+ F V ++I R G A V F
Sbjct: 37 SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGR-VTGEADVEFA 94
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYG---RPPSSSRSRGG 104
+A A+ + D + R + + + SS+ G
Sbjct: 95 THEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQG 137
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 50.3 bits (120), Expect = 7e-09
Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 6/91 (6%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD----IYIPRDRFTRESRGFAF 59
E V +++ L + T +++ F + + I R G AF
Sbjct: 14 VAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAF 72
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
V F + A++AL +L R + + +
Sbjct: 73 VLFACEEYAQNAL-RKHKDLLGKRYIELFRS 102
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 49.5 bits (118), Expect = 9e-09
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVG---DIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
++ L + T +D+ F C I+ +R + RG A + ++D + AL
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK-RRGDALIEMESEQDVQKAL 72
Query: 73 DAMDGRMLDGRELRV 87
+ R + V
Sbjct: 73 -EKHRMYMGQRYVEV 86
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 48.9 bits (117), Expect = 2e-08
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
+DLR + G++ + + R G A V F D +A+ + +DGR GR++
Sbjct: 41 EDLRVECSKFGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Query: 88 QM 89
Q
Sbjct: 97 QA 98
>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 = 48.5 bits (115), Expect = 2e-08
Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 14 VSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
++V N+ YR + +L++ F R G+V + + + + A V+ + +DA
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAI 66
Query: 70 DALDAMDGRMLDGRELRVQMARYGRPPSS 98
A++++ + +++ V +A PSS
Sbjct: 67 GAVNSLHRYKIGSKKILVSLATGASGPSS 95
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 47.0 bits (112), Expect = 1e-07
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 6/80 (7%)
Query: 10 IEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
+ M + + + DD+ + G V IY+ + ++G +V+
Sbjct: 12 LSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDK----NSAQGNVYVKCPSIAA 67
Query: 68 AEDALDAMDGRMLDGRELRV 87
A A++A+ GR G+ +
Sbjct: 68 AIAAVNALHGRWFAGKMITA 87
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 46.7 bits (111), Expect = 1e-07
Identities = 14/96 (14%), Positives = 28/96 (29%), Gaps = 3/96 (3%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
+ + NL + DL+ + TR+ G + F
Sbjct: 19 SHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRDFDGTGALEFP 75
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
+ +AL+ ++ G + V+ P S
Sbjct: 76 SEEILVEALERLNNIEFRGSVITVERDDNPPPIRRS 111
>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 = 46.5 bits (110), Expect = 2e-07
Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 5/90 (5%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD---IYIPRDRFTRESRGFAFV 60
P +K+ L + + +D++ C ++ R R G AFV
Sbjct: 35 MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-QSGEAFV 93
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
+ D + AL D + R + V +
Sbjct: 94 ELGSEDDVKMALK-KDRESMGHRYIEVFKS 122
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 46.2 bits (109), Expect = 3e-07
Identities = 21/91 (23%), Positives = 32/91 (35%), Gaps = 7/91 (7%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ N Y T D L V G+V R + + A V F A+ A A++G
Sbjct: 30 IQNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKAALNG 84
Query: 78 RMLDGRE--LRVQMARYGRPPSSSRSRGGRD 106
+ L+++ AR R D
Sbjct: 85 ADIYAGCCTLKIEYARPTRLNVIRNDNDSWD 115
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 46.3 bits (109), Expect = 6e-07
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L +L +R VF R G++ I + FV+F + +AE A +A
Sbjct: 145 ALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKEA 198
Query: 75 MDGRMLDGRELRVQMAR 91
M + L + R
Sbjct: 199 MSNQTLLLPSDKEWDDR 215
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 44.0 bits (104), Expect = 1e-06
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 28 DDLRRVFERCGEVGDIYIPR----DRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR 83
++ + G V + I + + E FV F + A+ A++GR GR
Sbjct: 40 GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR 99
Query: 84 ELRV 87
++
Sbjct: 100 KVVA 103
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 41.9 bits (98), Expect = 8e-06
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRD--RFTRESRGFAFVRFFDKRDAEDALDA 74
V L D++ F R G + + + + +G+AF+ F ++ + +DA
Sbjct: 13 VGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA 71
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 39.4 bits (92), Expect = 5e-05
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 28 DDLRRVFERCGEVGDIYIPR-DRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
+ + E+ G+VG I + F+ F A A+ ++GR GR ++
Sbjct: 28 VETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVK 87
Query: 87 V 87
Sbjct: 88 A 88
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 41.0 bits (95), Expect = 6e-05
Identities = 20/116 (17%), Positives = 41/116 (35%), Gaps = 10/116 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
VDN + D + + + E+ I + +D + R F + + + ++ +
Sbjct: 30 VDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE--EV 86
Query: 78 RMLDGRELRVQMARYGRPPS-------SSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
++ + L + R PS R R D + SR + Y + R
Sbjct: 87 LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ 142
Score = 33.3 bits (75), Expect = 0.031
Identities = 11/88 (12%), Positives = 29/88 (32%), Gaps = 24/88 (27%)
Query: 9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCG---EVGDIYIPRDRFTR---ESRGFAFVRF 62
++ ++ ++ L P + R++F+R +IP + +
Sbjct: 354 KLTTIIESSLNVLE----PAEYRKMFDRLSVFPP--SAHIPTILLSLIWFDV-------- 399
Query: 63 FDKRDAEDALDAMDGRML---DGRELRV 87
K D ++ + L +E +
Sbjct: 400 -IKSDVMVVVNKLHKYSLVEKQPKESTI 426
Score = 27.9 bits (61), Expect = 1.8
Identities = 21/123 (17%), Positives = 34/123 (27%), Gaps = 43/123 (34%)
Query: 58 AFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSR--------------- 102
AFV FD +D +D + +L E+ + S +
Sbjct: 28 AFVDNFDCKDVQDMPKS----ILSKEEID---HIIMSKDAVSGTLRLFWTLLSKQEEMVQ 80
Query: 103 ---GGRDRD---------RRRDRSRS---------RDRRYTRSRSFSSRSRSGSKSPRKA 141
R + R S RDR Y ++ F+ + S + K
Sbjct: 81 KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL 140
Query: 142 RSK 144
R
Sbjct: 141 RQA 143
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 37.7 bits (87), Expect = 2e-04
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
G L + NLT + LR + + G + + ++G A ++ + +A A
Sbjct: 6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKA 59
Query: 72 LDAMDGRMLDGRELRVQMA 90
A++ +L + +
Sbjct: 60 QMALNNCVLANTTIFAESP 78
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 35.9 bits (82), Expect = 8e-04
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 9/79 (11%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
+ D L R+ ++ GEV ++ + + G A V F + AE A+ G + +
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVGLV----DN 80
Query: 86 RVQMARYGRPPSSSRSRGG 104
++++ P +
Sbjct: 81 PLKISWLEGQPQDASGPSS 99
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 37.1 bits (85), Expect = 0.001
Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
+ + L V E+CG V + +P ++ ++F R+ +++ A ++G+ +
Sbjct: 33 SRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKEVVDDLG 86
Query: 86 RVQMARY 92
+
Sbjct: 87 QKITLYL 93
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 33.0 bits (75), Expect = 0.011
Identities = 19/85 (22%), Positives = 29/85 (34%), Gaps = 14/85 (16%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERC-----GEVGDIYIPRDRFTRESRGFAFVRFFDK 65
G V+++V L + L FE G V + + F +
Sbjct: 6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFREP 57
Query: 66 RDAEDALDAMDGRMLDGRELRVQMA 90
DAE L D L G +L ++ A
Sbjct: 58 ADAERVLAQAD-HELHGAQLSLRPA 81
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 32.0 bits (72), Expect = 0.021
Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 13/90 (14%)
Query: 16 LKVDNLTYRTTP----DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
L V NL + LRR+ + CG + + A +RF ++ AE A
Sbjct: 12 LYVYNLPANKDGKSVSNRLRRLSDNCG---------GKVLSITGCSAILRFINQDSAERA 62
Query: 72 LDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
M+ + G + V R +
Sbjct: 63 QKRMENEDVFGNRIIVSFTPKNRELCETSG 92
>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate
bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa}
SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A
Length = 239
Score = 31.2 bits (71), Expect = 0.097
Identities = 14/51 (27%), Positives = 21/51 (41%)
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFS 128
R L G+ A YG P S+ R R+ R + R+ + + RS
Sbjct: 50 RFLKGQGQGWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLR 100
>3ui3_A Immunoglobulin G-binding protein G, virulence-ASS protein D;
ferrodoxin-like fold, virulence associated protein D,
ribonu RNA binding protein; 2.80A {Streptococcus}
Length = 160
Score = 30.1 bits (67), Expect = 0.22
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 3/52 (5%)
Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCG---EVGDIYIPRDRFTRESRGFA 58
++ + K Y DDLR+ E G G +Y+ + ++ +
Sbjct: 66 LKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYK 117
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 30.4 bits (68), Expect = 0.29
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 22/81 (27%)
Query: 12 GM-VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
GM + L Y+T+ + V+ R D +++ GF+ +
Sbjct: 1630 GMGMDL------YKTSKA-AQDVWNRA----------DNHFKDTYGFSILDIVINNPVNL 1672
Query: 71 AL--DAMDGRMLDGRELRVQM 89
+ G+ + RE M
Sbjct: 1673 TIHFGGEKGKRI--RENYSAM 1691
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 28.6 bits (64), Expect = 0.66
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 59 FVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
FV F + A+ A++GR GR++ ++
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVAEV 209
>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 = 28.7 bits (63), Expect = 0.93
Identities = 38/153 (24%), Positives = 62/153 (40%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P + + +L V + Y TT LRR FE G + I++ + + + RG+AF+ + +
Sbjct: 95 PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSR 125
RD A DG+ +DGR + V + R R G R + R++
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214
Query: 126 SFSSRSRSGSKSPRKARSKSIDRDNKHERNGRS 158
S SP R + DR+ + R
Sbjct: 215 DTSRYDERPGPSPLPHRDRDRDRERERRERSRE 247
>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus
subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A
Length = 245
Score = 28.0 bits (63), Expect = 1.2
Identities = 6/39 (15%), Positives = 14/39 (35%)
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRS 116
L G A Y P ++ + ++ + + R+
Sbjct: 49 PFLRGGGKGWITAEYSMLPQATNQQTIQESSKGKISGRT 87
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 26.5 bits (58), Expect = 1.8
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 9/83 (10%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
+ + R FE D F R + F + A DA + G+E+
Sbjct: 19 SESETRAKFESLFRTYDKDTTFQYFKSFKR--VRINFSNPLSAADARLRLHKTEFLGKEM 76
Query: 86 RVQMA-------RYGRPPSSSRS 101
++ A + PP+ +S
Sbjct: 77 KLYFAQTLHIGSSHLAPPNPDKS 99
>3c8w_A Acetoacetate decarboxylase ADC; YP_094708.1, structural GE joint
center for structural genomics, JCSG, protein structu
initiative; HET: LCK CIT; 1.60A {Legionella pneumophila
subsp} SCOP: d.347.1.1
Length = 255
Score = 27.3 bits (60), Expect = 2.2
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 3/41 (7%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD 42
+Y P R + Y T PD L+ + E+ +
Sbjct: 29 TYPAGPYRFINREFFII---AYETDPDLLQAILPPDMELLE 66
>1xoc_A Oligopeptide-binding protein APPA; oligopeptide, APPA, transport,
transport protein; 1.55A {Bacillus subtilis} SCOP:
c.94.1.1
Length = 520
Score = 27.3 bits (61), Expect = 2.3
Identities = 6/29 (20%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 17 KVDNLTYRTTPDDLRRVFE-RCGEVGDIY 44
+D +TY+ PD + + G++ + +
Sbjct: 213 YLDTVTYKVIPDANAAEAQLQAGDI-NFF 240
>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural
genomics/proteomics initiative structural genomics;
2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB:
1udq_A 1uds_A 1udo_A
Length = 255
Score = 27.0 bits (60), Expect = 2.6
Identities = 9/39 (23%), Positives = 16/39 (41%)
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRS 116
L G+ A Y P +++ R R+ + R R+
Sbjct: 49 NWLKGKGQGWITAEYSMLPRATQQRTIRESVQGRIGGRT 87
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 26.7 bits (59), Expect = 3.7
Identities = 16/83 (19%), Positives = 24/83 (28%), Gaps = 2/83 (2%)
Query: 46 PRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
+ +R G A D + + D R R +
Sbjct: 493 DKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDYDDEPF 552
Query: 106 DR--DRRRDRSRSRDRRYTRSRS 126
R + RR SRS D+ SR+
Sbjct: 553 RRSNNNRRSFSRSNDKNNYSSRN 575
>3bgt_A ADC, AAD, probable acetoacetate decarboxylase; lyase, schiff
base; HET: MSE; 2.10A {Chromobacterium violaceum} PDB:
3bh3_A
Length = 246
Score = 26.6 bits (58), Expect = 4.0
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD 42
++ P R + +TYRT P + V ++ +
Sbjct: 19 AFPPGPYRFVNREYM---IITYRTDPAAIEAVLPEPLQMAE 56
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif,
hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 25.2 bits (56), Expect = 4.1
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 57 FAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
++V L M + G++L+V A
Sbjct: 42 ASYVEI-LNGKGPHVLKVMKNTTVKGKQLKVNKAN 75
>2r8u_A Microtubule-associated protein RP/EB family member 1; cytoskeleton,
acetylation, cell cycle, cell division, cytoplasm,
mitosis, phosphorylation; 1.35A {Homo sapiens} SCOP:
a.40.1.1 PDB: 1vka_A 1txq_B 1wu9_A 2hkq_A 2hl5_A 3tq7_A
3gjo_A 1yib_A 1yig_A
Length = 268
Score = 26.3 bits (57), Expect = 4.3
Identities = 17/120 (14%), Positives = 33/120 (27%), Gaps = 8/120 (6%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTR----ESRGFA--FVRFFDKRDAEDALDAMDGRMLDGR 83
L+ F+R G D IP D+ + ++ F F +FFD D + R
Sbjct: 78 LQAGFKRMGV--DKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQGQET 135
Query: 84 ELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARS 143
+ + +R ++ ++ +A
Sbjct: 136 AVAPSLVAPALNKPKKPLTSSSAAPQRPISTQRTAAAPKAGPGVVRKNPGVGNGDDEAAE 195
>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH.,
transferase; 1.70A {Bacillus anthracis}
Length = 255
Score = 26.2 bits (58), Expect = 4.8
Identities = 7/39 (17%), Positives = 14/39 (35%)
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRS 116
+ G A Y P ++ R R+ + + R+
Sbjct: 59 PFMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRT 97
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 26.4 bits (58), Expect = 5.4
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 102 RGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSK 136
R G D+ + + +R T + SSR R +K
Sbjct: 446 RSGEVFDKDLSKLKRNRKRITNQMTDSSRERPITK 480
>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen,
blood clotting; HET: NDG NAG; 2.70A {Gallus gallus}
SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*
Length = 464
Score = 26.1 bits (57), Expect = 6.0
Identities = 13/59 (22%), Positives = 20/59 (33%)
Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
+D + +DA R LD R+ R PP S R + + + Y
Sbjct: 6 YDNEEDSPQIDARAHRPLDKRQEAAPTLRPVAPPISGTGYQPRPPKQDKQAMKKGPIIY 64
>3rqt_A Putative uncharacterized protein; ligand binding component,
ABC-type import system, nickel, SI DI-peptides,
structural genomics; HET: MSE HIS EPE; 1.50A
{Staphylococcus aureus}
Length = 486
Score = 26.1 bits (58), Expect = 7.1
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 17 KVDNLTYRTTPDDLRRVFE-RCGEVGDI 43
K+D++T D RV + D+
Sbjct: 194 KLDHITVTYQEDGNNRVRNLESQKD-DL 220
>3ry3_A Putative solute-binding protein; structural genomics, IDP00509,
center for structural genomic infectious diseases,
csgid, transport prote; 2.43A {Yersinia pestis}
Length = 528
Score = 25.8 bits (57), Expect = 7.6
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIP 46
D L + +D + G++G + IP
Sbjct: 207 DFDKLIFVFLDEDSAFAAAQSGQLGVVRIP 236
>1uqw_A Putative binding protein YLIB; Zn binding protein, transport,
lipoprotein, bacterial targets at IGS-CNRS, france,
BIGS, structural genomics; 2.72A {Escherichia coli}
SCOP: c.94.1.1
Length = 509
Score = 25.7 bits (57), Expect = 8.7
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 17 KVDNLTYRTTPDDLRRVFE-RCGEVGDI 43
K+D++T+R D+ R + GE
Sbjct: 211 KLDSITWRPVADNNTRAAMLQTGEA-QF 237
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
0.321 0.136 0.396
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,506,732
Number of extensions: 147790
Number of successful extensions: 1042
Number of sequences better than 10.0: 1
Number of HSP's gapped: 802
Number of HSP's successfully gapped: 295
Length of query: 158
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 72
Effective length of database: 4,300,587
Effective search space: 309642264
Effective search space used: 309642264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)