RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10283
(59 letters)
>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 = 74.2 bits (183), Expect = 9e-20
Identities = 30/44 (68%), Positives = 39/44 (88%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLFVGML+KQQ+E+DV ++F PFG I+ECTVL+GPDG+SK
Sbjct: 13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK 56
>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 = 74.2 bits (183), Expect = 4e-19
Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLF+GM+SK+ E+D+R +F+ FG IEEC +L+GPDG S+
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR 136
Score = 51.8 bits (125), Expect = 2e-10
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
K+FVG + + +E D+R++F +G + E VL+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQ 41
>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 = 62.3 bits (152), Expect = 4e-15
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+ KLF+G + + +E D++ +F FG I E TVLK G K
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHK 55
>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 = 54.1 bits (131), Expect = 2e-11
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
D L+V L + +D + IF +G+I + +L+ G +
Sbjct: 87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 131
Score = 41.0 bits (97), Expect = 2e-06
Identities = 7/35 (20%), Positives = 16/35 (45%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ L V L + + ++ +F G I C +++
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR 37
>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 = 52.7 bits (127), Expect = 3e-11
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+ V + Q N+ ++R++F+ FG ++ + K GT R
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
>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 = 53.0 bits (128), Expect = 6e-11
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
L+V L K + ++ ++F+ +G I +L G S+
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSR 130
Score = 41.0 bits (97), Expect = 2e-06
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
L V L + +++ R +F G IE C +++
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR 36
>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 = 49.2 bits (118), Expect = 6e-10
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
P +L+VG L + + + F FG+I +KG
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
>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 = 49.2 bits (118), Expect = 8e-10
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
KLF+G L+++ NE ++ +F G I E ++K S+
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR 48
>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 = 48.4 bits (116), Expect = 8e-10
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
KL VG +S ++R F +G + EC ++K
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>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 = 50.5 bits (121), Expect = 1e-09
Identities = 10/44 (22%), Positives = 19/44 (43%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
L V LS + + + + F+ FG +E+ V+ G +
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT 137
Score = 41.6 bits (98), Expect = 2e-06
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+LFVG L E+D +++F +G E + +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINR 56
>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 = 48.0 bits (115), Expect = 1e-09
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
K+FVG +S ++R +F G + EC V+K
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 48.5 bits (116), Expect = 1e-09
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P K++ L+ E ++ + +G +EE +L P
Sbjct: 4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL 48
>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 = 47.6 bits (114), Expect = 2e-09
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
+LFVG L E+++RK+F +G E + K
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD 50
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA
recognition motif, RRM, RNA binding domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 47.7 bits (114), Expect = 2e-09
Identities = 9/46 (19%), Positives = 20/46 (43%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+FV L + ++++F+ G + +L+ DG S+
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR 56
>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 = 46.9 bits (112), Expect = 3e-09
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
L+VG L E D+R F FG I TV++
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR 47
>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 = 47.8 bits (114), Expect = 3e-09
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ KL V L ++ D++++FA FGT+++ V G S
Sbjct: 31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 76
>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 = 47.3 bits (113), Expect = 4e-09
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ KL V L ++ D++++FA FGT+++ V G S
Sbjct: 24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL 70
>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 = 46.9 bits (112), Expect = 4e-09
Identities = 12/44 (27%), Positives = 23/44 (52%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+ +FVG L + E+ + ++F G + + T+ K +G K
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK 57
>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 = 47.2 bits (113), Expect = 4e-09
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
L++ L +E ++ + PFG + +L+ GTS+
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 66
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 46.9 bits (112), Expect = 4e-09
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
+ +LFV E ++ +IF PFG ++E +L G
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 66
>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 = 46.4 bits (111), Expect = 5e-09
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
KLF+G L ++ E ++R +F +G + EC ++K
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN 43
>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 = 46.4 bits (111), Expect = 5e-09
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P ++V L +D+ +IF+ +G + + T++K D SK
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK 58
>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 = 46.4 bits (111), Expect = 5e-09
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
L+VG L ED +R IF PFG I+ ++K D G SK
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK 47
>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 = 46.4 bits (111), Expect = 5e-09
Identities = 8/46 (17%), Positives = 20/46 (43%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+ +G L++ +D + +IF+ +G I+ + +
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSK 47
>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 = 48.0 bits (115), Expect = 5e-09
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
PLP KLF+G L N+D V+++ FG ++ ++K G SK
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 136
Score = 37.2 bits (87), Expect = 4e-05
Identities = 8/39 (20%), Positives = 15/39 (38%)
Query: 13 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
L ++L+VG + E+ + F + T G
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39
>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 = 46.5 bits (111), Expect = 6e-09
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
K LFV L+ E+ + K F+ FG +E LK
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>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 = 46.5 bits (111), Expect = 6e-09
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
LF+ L+ E+ ++ +F+ G I+ CT+ K +
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL 48
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 47.9 bits (114), Expect = 6e-09
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ KL V L ++ D++++FA FGT+++ V G S
Sbjct: 84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 129
>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 = 46.0 bits (110), Expect = 7e-09
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P+ L V LS E D+R++F+ +G I + +++ S+
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 57
>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 = 47.7 bits (114), Expect = 8e-09
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
KLF+G L N+D V+++ FG ++ ++K G SK
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156
Score = 34.6 bits (80), Expect = 5e-04
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
++L+VG + E+ + F + T G
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 45.7 bits (109), Expect = 1e-08
Identities = 9/44 (20%), Positives = 20/44 (45%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
KLF+ L ++++ +I GT+++ ++ G K
Sbjct: 15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK 58
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 47.7 bits (114), Expect = 1e-08
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+++V + + ++DD++ +F FG I+ T+ + P G K
Sbjct: 123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHK 167
Score = 41.5 bits (98), Expect = 1e-06
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
L +++VG + + ED +R+ FAPFG I+ + K
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70
>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 = 45.7 bits (109), Expect = 1e-08
Identities = 7/44 (15%), Positives = 19/44 (43%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
LF+G L+ ++ +++ + + V+ GT++
Sbjct: 15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNR 58
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 45.7 bits (109), Expect = 1e-08
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 11 TPLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
+PP +LF+G L + +++D+ +IF+P+G I + +
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 46
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 45.8 bits (109), Expect = 1e-08
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 12 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
P + ++F+G L+ + DV IF+ +G + C+V KG
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG 63
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex;
1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 45.7 bits (109), Expect = 1e-08
Identities = 12/41 (29%), Positives = 24/41 (58%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+FVG + + +E ++R FA +G+++E ++ G SK
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSK 50
>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 = 45.3 bits (108), Expect = 2e-08
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ KLFVG LS NE + ++F+ +G I E V+K
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK 46
>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 = 45.2 bits (107), Expect = 2e-08
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVLKGPDGTSKER 59
+ +LF+G + K + +++ + A + + V K R
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNR 52
>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 = 44.9 bits (107), Expect = 2e-08
Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P + +++G + Q E+ + + + G + ++ P G SK
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSK 44
>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 = 44.4 bits (106), Expect = 3e-08
Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+ L+VG L+++ ++ + F PFG I + + + +
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 49
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 45.5 bits (108), Expect = 3e-08
Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+ L+VG L+++ ++ + F PFG I + + + +
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105
>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 = 44.2 bits (105), Expect = 4e-08
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KL++G LS DD+R++F VL
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 42
>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 = 44.1 bits (105), Expect = 5e-08
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+LFV LS +E+D+ K+F+ +G + E K
Sbjct: 6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK 50
>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 = 44.7 bits (106), Expect = 5e-08
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P+ L V LS E D+R++F+ +G I + +++ S+
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 44.2 bits (105), Expect = 5e-08
Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 12 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
+LF+G L + +++D+ +IF+P+G I + +
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 58
>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 = 45.3 bits (108), Expect = 6e-08
Identities = 7/44 (15%), Positives = 19/44 (43%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
LF+G L+ ++ +++ + + V+ GT++
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNR 54
Score = 38.4 bits (90), Expect = 2e-05
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ + L LS ED+++++F I + DG SK
Sbjct: 95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSK 136
>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 = 44.2 bits (105), Expect = 6e-08
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 9 NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
+ P P+K L++ LS + E D+ +FA F + +
Sbjct: 18 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI 57
>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 = 44.9 bits (106), Expect = 6e-08
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
P D K++VG L N+ ++ + F +G + V + P G
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG 111
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.0 bits (104), Expect = 7e-08
Identities = 4/42 (9%), Positives = 15/42 (35%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
++ +++ DD+++ G + + + K
Sbjct: 11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK 52
>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 = 43.4 bits (103), Expect = 8e-08
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+FVG + ED++R+ F+ +G + + + K
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK 39
>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 = 43.4 bits (103), Expect = 8e-08
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ L+VG L+++ ++ + F PFG I + +
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 46
>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 = 45.4 bits (108), Expect = 8e-08
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK-GPDGTSK 57
P D L V L + ++ PFG++E C ++ G SK
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 137
Score = 43.8 bits (104), Expect = 3e-07
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 17 KKLFVGMLSKQQNEDD-VRKIFAPFGTIEECTVLKGPDGTSK 57
+ L V L N+ D + + + + C + G DG K
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLK 226
Score = 33.8 bits (78), Expect = 0.001
Identities = 5/32 (15%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
+K+ + L +V + + + ++ C V
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV 53
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 43.7 bits (103), Expect = 9e-08
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
P + + + L E +V + PFG + +LKG
Sbjct: 14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 51
>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 = 43.3 bits (103), Expect = 1e-07
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+FVG + E ++R+ F FG + E ++ + + R
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE-KQRPR 52
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 43.4 bits (103), Expect = 1e-07
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
K+FVG L + +RK F FG IEE V+
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ 54
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 43.2 bits (102), Expect = 1e-07
Identities = 8/38 (21%), Positives = 13/38 (34%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
P + + L E D+ + FG I V+
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43
inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA;
1.65A {Mus musculus}
Length = 89
Score = 42.6 bits (101), Expect = 1e-07
Identities = 7/35 (20%), Positives = 19/35 (54%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K+FVG ++ +++++ F +G + + + K
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK 45
>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 = 43.1 bits (102), Expect = 1e-07
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+FVG LS + +D++ FAPFG I + V+K G SK
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSK 57
>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 = 43.0 bits (102), Expect = 1e-07
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+ + V LS+ E D++++F PFG+I + K G SK
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK 57
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 43.0 bits (102), Expect = 1e-07
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
K+L V + + + D+R++F FG I + ++ SK
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSK 55
>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 = 43.0 bits (102), Expect = 1e-07
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
+KLF+G LS + E+ +R + +G + +C V++ P
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 64
>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 = 42.6 bits (101), Expect = 2e-07
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+FVG LS ++ D++ F FG + +CT+ P+ T + R
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPN-TGRSR 53
>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 = 44.2 bits (105), Expect = 2e-07
Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+KLF+G LS + ++ +R F +GT+ +C V++ P+ S+
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSR 55
Score = 44.2 bits (105), Expect = 2e-07
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ + K+R
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG-SGKKR 146
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 42.6 bits (101), Expect = 2e-07
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 1/44 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
++FV L ++ F G + + +G SK
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSK 48
>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 = 42.7 bits (101), Expect = 2e-07
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+L+VG L ED +R IF PFG IE ++ + G SK
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68
>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 = 43.7 bits (104), Expect = 2e-07
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
K+FVG + + + F+ +GTI + ++ D
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Score = 43.7 bits (104), Expect = 2e-07
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
K+F+G L+ ED++R+ F +GT+ + ++K P G S+
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSR 45
>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 = 43.6 bits (103), Expect = 2e-07
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
L L+VG LS E+ + ++F+ G I++ + T+
Sbjct: 35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC 81
>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 = 42.1 bits (100), Expect = 2e-07
Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
L++ L + D+ K+ P+G I + K
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK 47
>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 = 42.7 bits (101), Expect = 3e-07
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P LF+ L ++ + D+ ++F PFG + V SK
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 42.3 bits (100), Expect = 3e-07
Identities = 3/50 (6%), Positives = 16/50 (32%), Gaps = 3/50 (6%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGT--IEECTVLKGPD-GTSK 57
+ + ++ D + +P+ + + ++K ++
Sbjct: 4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNR 53
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 105
Score = 42.2 bits (100), Expect = 3e-07
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
KLFVG L ++ +R F+ +G + +C ++K
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT 53
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 42.3 bits (100), Expect = 3e-07
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
K+L V + + + D+R++F FG I + ++ G SK
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SK 69
>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 = 42.2 bits (100), Expect = 3e-07
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
K+F+G LS Q ++ +R+ F FG ++EC V++ P
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62
>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 = 42.3 bits (100), Expect = 3e-07
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
K +F+ LS E+ + ++ FG ++ V+ PD SK
Sbjct: 14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK 57
>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 = 42.1 bits (99), Expect = 3e-07
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
P + L + L + E +V + PFG + +LKG
Sbjct: 13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG 50
>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 = 41.8 bits (99), Expect = 3e-07
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
PL +FVG LS + + FAPFG I + V+K G SK
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSK 48
>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 = 42.8 bits (101), Expect = 3e-07
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ L V + +E +R++F +G IE ++
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC 76
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 41.3 bits (98), Expect = 4e-07
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
K+F+G LS Q ++ +R+ F FG ++EC V++ P
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 37
>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 = 42.2 bits (99), Expect = 4e-07
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
P + + + L E +V + PFG + +LKG
Sbjct: 29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66
>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 = 41.9 bits (99), Expect = 4e-07
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
K L + LS E+ ++++F I+ V + +G SK
Sbjct: 13 GESKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSK 53
>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 = 41.3 bits (98), Expect = 4e-07
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
LFVG L+ +++ +R F F + V+ G+S+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 43
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 41.5 bits (98), Expect = 4e-07
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 7/44 (15%)
Query: 8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
T ++G + E D+ +F FG I +
Sbjct: 26 RVTT-------AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE 62
>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 = 40.9 bits (97), Expect = 5e-07
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+FVG LS E+ +R+ F FG +E + T+K R
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK-TNKRR 41
>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 = 41.7 bits (98), Expect = 5e-07
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
+ + V L + E D+ + FGTI ++
Sbjct: 10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF 50
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 41.6 bits (98), Expect = 6e-07
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
P LF+ L ++ + D+ F PFG + V SK
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK 82
>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 = 41.5 bits (98), Expect = 6e-07
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
NCT ++ G ++ + +R+ F+PFG I E V
Sbjct: 24 KNCT-------VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
>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 = 41.1 bits (97), Expect = 7e-07
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
L V L + E D+++ F+ FG + V K
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK 52
>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 = 41.1 bits (97), Expect = 7e-07
Identities = 7/36 (19%), Positives = 18/36 (50%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
L V L+ + + D +R++F +G + + + +
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR 47
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 40.5 bits (96), Expect = 7e-07
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+FVG LS +DV+ F FG +++ ++ T++ R
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT-TNRHR 41
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 41.2 bits (97), Expect = 8e-07
Identities = 9/43 (20%), Positives = 17/43 (39%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
D +++VG L D+ +F +G I + + G
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG 60
>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 = 40.6 bits (96), Expect = 8e-07
Identities = 7/34 (20%), Positives = 18/34 (52%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ ++VG L + V+++F+ FG + ++
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIY 35
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 41.7 bits (98), Expect = 8e-07
Identities = 7/37 (18%), Positives = 18/37 (48%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
L V L+ + + D +R++F +G + + + +
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 40.7 bits (96), Expect = 9e-07
Identities = 8/37 (21%), Positives = 19/37 (51%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
K++VG L + ++ + F+ +G + + + P G
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG 38
>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 = 41.9 bits (99), Expect = 1e-06
Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 17 KKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+++ + LS + +E+ +R+ F FG+IE+ + G S
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNN 254
Score = 38.8 bits (91), Expect = 2e-05
Identities = 5/43 (11%), Positives = 14/43 (32%), Gaps = 1/43 (2%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
+ L++ + ++R + + L TS+
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSR 159
Score = 38.8 bits (91), Expect = 2e-05
Identities = 10/36 (27%), Positives = 13/36 (36%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
+ V L K N++ V K F G I V
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK 79
>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 = 40.3 bits (95), Expect = 1e-06
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE 44
+ + L LS ED+++++F I
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIR 44
>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 = 40.3 bits (95), Expect = 2e-06
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
L+V L +++ +RK F+PFGTI V+ G SK
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSK 55
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 40.0 bits (94), Expect = 2e-06
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ +FV + + + + F FG + + K
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK 42
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 39.9 bits (94), Expect = 2e-06
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
LFV + ++ E+D+ FA +G I+ + G K
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
>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 = 40.0 bits (94), Expect = 2e-06
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
LFV + ++ ED++++ F +G I+ +
Sbjct: 24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHL 58
>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 = 41.4 bits (96), Expect = 2e-06
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K LFV ++ E +R+ F +G I+ ++
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
>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 = 40.0 bits (94), Expect = 2e-06
Identities = 10/40 (25%), Positives = 14/40 (35%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
K L+V L +E+ + K F V K D
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD 52
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 39.7 bits (93), Expect = 2e-06
Identities = 5/34 (14%), Positives = 14/34 (41%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+KL + + + + + +G +E C +
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN 49
>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 = 40.6 bits (95), Expect = 2e-06
Identities = 7/36 (19%), Positives = 18/36 (50%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
L V L+ + + D +R++F +G + + + +
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104
>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 = 39.5 bits (93), Expect = 3e-06
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECT-VLKGPD-GTSK 57
+F+G L + +E + F+ FG I + +++ PD G SK
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK 48
>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 = 40.0 bits (94), Expect = 3e-06
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
LFV + ++ E+D+ FA +G I+ + G K
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
>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 = 40.2 bits (94), Expect = 3e-06
Identities = 11/50 (22%), Positives = 21/50 (42%)
Query: 9 NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKE 58
+ P P+ +++V L+K E D++ IF + T D +
Sbjct: 38 SYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK 87
>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 = 40.6 bits (94), Expect = 4e-06
Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 52
P+ +++ L+++ +D+++K IF+ FG I + V +
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL 49
Score = 32.5 bits (73), Expect = 0.003
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 9 NCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
+ PP+ LF+ L ++ NE + +F F +E ++ G
Sbjct: 200 PLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD 245
>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 = 40.2 bits (95), Expect = 4e-06
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
LFVG L+ +++ +R F F + V+ G+S+
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 129
Score = 34.8 bits (81), Expect = 4e-04
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ L+VG L K ED +++ F G I ++ + +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV 41
>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 = 39.8 bits (93), Expect = 5e-06
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
LFV + ++ ED++++ F +G I+ + G SK
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 39.2 bits (91), Expect = 5e-06
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+K+FVG L +ED++ F FG + K +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYF 49
>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 = 38.8 bits (91), Expect = 6e-06
Identities = 8/36 (22%), Positives = 18/36 (50%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
D ++VG L ++ +E + ++F G + + K
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK 49
>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 = 38.8 bits (91), Expect = 6e-06
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ L+VG LS+ E + ++F+ G + C ++
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT 49
>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 = 39.2 bits (92), Expect = 1e-05
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+F+ L K + + F+ FG I C V+ SK
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSK 143
Score = 34.9 bits (81), Expect = 4e-04
Identities = 12/40 (30%), Positives = 17/40 (42%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
P P L+VG L E + + F+P G I V +
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR 49
>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 = 38.2 bits (89), Expect = 1e-05
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ ++VG + D+ F+ G+I T+L
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70
>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 = 37.5 bits (88), Expect = 1e-05
Identities = 6/34 (17%), Positives = 16/34 (47%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ ++VG + +++ F G++ T+L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILC 40
>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 = 37.7 bits (88), Expect = 2e-05
Identities = 7/44 (15%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
+ +F L+ + D+ F+ G + + ++ + SK
Sbjct: 24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67
>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 = 37.2 bits (87), Expect = 3e-05
Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 52
P+ +++ L+++ +D+++K IF+ FG I + V +
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL 48
>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 = 37.2 bits (87), Expect = 3e-05
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+F+ L K + + F+ FG I C V+ SK
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSK 45
>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 = 36.9 bits (86), Expect = 4e-05
Identities = 7/37 (18%), Positives = 18/37 (48%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ +FVG + + E+ ++ IF+ G + ++
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY 42
>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 = 36.3 bits (84), Expect = 8e-05
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 9/44 (20%)
Query: 8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
T L+V +R F+PFG I + ++
Sbjct: 38 KGNT-------LYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPP 72
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 36.7 bits (84), Expect = 9e-05
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 9/47 (19%)
Query: 14 PPDKKLFVGMLS---------KQQNEDDVRKIFAPFGTIEECTVLKG 51
+K L+VG + Q E +R +F+ G I+ ++
Sbjct: 132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES 178
>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 = 36.4 bits (84), Expect = 1e-04
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
PP L + + +E+D++ +F+ G + + D
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 158
Score = 29.9 bits (67), Expect = 0.022
Identities = 6/38 (15%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 19 LFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKGPDGT 55
L V L+ ++ + +F +G ++ +L
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN 43
>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 = 35.8 bits (83), Expect = 1e-04
Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 13 LPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
LPP+ + L++ L + +++ IF +G I + V ++
Sbjct: 3 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETR 47
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 35.8 bits (83), Expect = 1e-04
Identities = 8/40 (20%), Positives = 13/40 (32%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
+ +FV L + + V F G I+ P
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPM 44
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 35.6 bits (82), Expect = 1e-04
Identities = 4/46 (8%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 52
P + + + ++ + ++ ++ + + G I + V
Sbjct: 24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD 69
>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 = 35.3 bits (81), Expect = 1e-04
Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 2/39 (5%)
Query: 15 PDKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
+ L V G L + + + + G ++ +
Sbjct: 24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 62
>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 = 34.6 bits (80), Expect = 2e-04
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 9/44 (20%)
Query: 8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
T L+V +R F+PFG I + ++
Sbjct: 14 KGNT-------LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP 48
>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 = 34.6 bits (80), Expect = 2e-04
Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
P + V + + D++ F + I L G
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57
>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 = 35.4 bits (81), Expect = 3e-04
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
PP L + + +E+D++ +F+ G + + D
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 189
Score = 33.4 bits (76), Expect = 0.002
Identities = 6/43 (13%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 14 PPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKGPDGT 55
+ L V L+ ++ + +F +G ++ +L
Sbjct: 32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN 74
>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 = 34.2 bits (79), Expect = 4e-04
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
P P F+G L E+ +++ F I + + P + +
Sbjct: 11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 57
>3n9u_C Cleavage and polyadenylation specificity factor S;
protein-protein complex, coexpression, heterotetramer,
mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 34.9 bits (80), Expect = 4e-04
Identities = 4/28 (14%), Positives = 11/28 (39%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIE 44
++VG S + + ++ G +
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYD 83
>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 = 34.0 bits (78), Expect = 4e-04
Identities = 4/33 (12%), Positives = 13/33 (39%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
+ L ++++ F+ FG++ +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL 42
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 33.8 bits (78), Expect = 4e-04
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIF-APFGTIEECTVLKGPDGTSK 57
P+ LFVG L+ ++ + + F + + V+ G SK
Sbjct: 8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSK 51
>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 = 34.1 bits (78), Expect = 6e-04
Identities = 6/48 (12%), Positives = 16/48 (33%), Gaps = 1/48 (2%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
D + + L ++++ + F+ + L P+G
Sbjct: 37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKIT 84
>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 = 33.3 bits (77), Expect = 7e-04
Identities = 5/27 (18%), Positives = 13/27 (48%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIE 44
L++G L+ ++D+ + G +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVND 29
>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 = 33.4 bits (77), Expect = 7e-04
Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
P + V + + D++ F + I L G
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 33.4 bits (77), Expect = 8e-04
Identities = 8/31 (25%), Positives = 11/31 (35%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFG 41
P P +VG L + D+ IF
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS 40
>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 = 33.9 bits (77), Expect = 0.001
Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 1/46 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
P L + E++ +I G +V K G S+
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV-KVFSGKSERS 165
Score = 33.5 bits (76), Expect = 0.002
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 14 PPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKGPDGT 55
L V L + + N D V +F +G +E+ +K G
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGA 44
>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 = 33.0 bits (76), Expect = 0.001
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
P P F+G L E+ +++ F I + + P + +
Sbjct: 15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 61
>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 = 33.7 bits (76), Expect = 0.001
Identities = 4/50 (8%), Positives = 15/50 (30%)
Query: 8 WNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
++ +++ DD+++ G + + + K
Sbjct: 101 DEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK 150
>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 = 32.7 bits (75), Expect = 0.001
Identities = 8/39 (20%), Positives = 13/39 (33%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
+ +FV L + + V F G I+ P
Sbjct: 11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQP 49
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 32.5 bits (74), Expect = 0.001
Identities = 8/41 (19%), Positives = 17/41 (41%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
P ++VG L + D+++ G++ +GP
Sbjct: 17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR 57
>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 = 32.0 bits (73), Expect = 0.002
Identities = 6/34 (17%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+ V L + N +V + + ++ C V +
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR 38
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 32.0 bits (73), Expect = 0.002
Identities = 4/43 (9%), Positives = 12/43 (27%), Gaps = 1/43 (2%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP-DGTSK 57
+ + + + +F+ G + G +K
Sbjct: 12 NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTK 54
>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 = 32.8 bits (74), Expect = 0.002
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIE--ECTVLKGPD-GTSK 57
L++G L+ ++D+ + G + E + G SK
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK 112
>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 = 32.5 bits (74), Expect = 0.002
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ + L + E+D+ F+P + GPDG
Sbjct: 44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVT 86
>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 = 32.1 bits (73), Expect = 0.002
Identities = 8/48 (16%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 11 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPDGTSK 57
+P +++ L + V F +E+ + GP+G +
Sbjct: 20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67
>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 = 31.5 bits (72), Expect = 0.004
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFG 41
L++G L +E+ + + FA G
Sbjct: 7 GMAASLWMGDLEPYMDENFISRAFATMG 34
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 112
Score = 31.4 bits (71), Expect = 0.006
Identities = 6/39 (15%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 14 PPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 51
+ + + L ++ V K+ P+G I+ +++
Sbjct: 23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM 61
>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 = 31.1 bits (71), Expect = 0.006
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFG 41
P K LFV LS+ E+ +++ F
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFDGSV 40
>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 = 31.2 bits (71), Expect = 0.006
Identities = 6/45 (13%), Positives = 11/45 (24%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPDGTSK 57
+ + + DV + E VL +G
Sbjct: 13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGL 57
>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 = 30.8 bits (70), Expect = 0.007
Identities = 7/36 (19%), Positives = 13/36 (36%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 53
++V L+ DD+ F G ++ P
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPM 52
>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 = 30.5 bits (69), Expect = 0.011
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
P D + V + E+DVR F ++ +LK G +
Sbjct: 14 PDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNN 56
>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 = 30.1 bits (68), Expect = 0.014
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ + L + E+D+ F+P + GPDG
Sbjct: 13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVT 55
>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 = 29.2 bits (66), Expect = 0.023
Identities = 5/43 (11%), Positives = 12/43 (27%), Gaps = 1/43 (2%)
Query: 15 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
+ + E +V + AP +++ G
Sbjct: 9 TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKT 50
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 102
Score = 29.4 bits (66), Expect = 0.024
Identities = 6/40 (15%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 13 LPPDKKLFVGMLSKQQN-EDDVRKIFAPFGTIEECTVLKG 51
+ + + + + +N + ++ PFG I +L
Sbjct: 12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK 51
>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 = 28.5 bits (64), Expect = 0.046
Identities = 9/41 (21%), Positives = 16/41 (39%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
PL ++L+VG + E+ + F + T G
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN 42
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 28.5 bits (64), Expect = 0.051
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 16 DKKLFVGML------SKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D + V + ++ ++ + KIF+ FG I DG +K
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND-FYPEEDGKTK 61
>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 = 28.2 bits (63), Expect = 0.077
Identities = 6/45 (13%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 57
D + + L +++++ + F+ + L G S
Sbjct: 13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRST 57
>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 = 27.8 bits (61), Expect = 0.14
Identities = 8/49 (16%), Positives = 16/49 (32%), Gaps = 2/49 (4%)
Query: 9 NCTPLPPDKKLFVGM--LSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT 55
L + + L D + +IF+ FGT+ + +
Sbjct: 37 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 85
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 27.3 bits (60), Expect = 0.16
Identities = 7/49 (14%), Positives = 16/49 (32%), Gaps = 2/49 (4%)
Query: 9 NCTPLPPDKKLFVGMLSKQQ--NEDDVRKIFAPFGTIEECTVLKGPDGT 55
L + + + D + +IF+ FGT+ + +
Sbjct: 19 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 67
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 27.0 bits (60), Expect = 0.18
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 21 VGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
VG ++ ++ + KIF+ FG I DG +K
Sbjct: 12 VGPDRLEKLKNVIHKIFSKFGKITND-FYPEEDGKTK 47
>2wd5_B Structural maintenance of chromosomes protein 3; DNA damage, cell
cycle, cell division; 2.70A {Mus musculus}
Length = 213
Score = 26.5 bits (59), Expect = 0.43
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 2 LPLDLIWNCTPLPPDKKLFVGMLSKQQNEDDVRKIFAP-FGTI 43
LPL+ + P+ + M+SK + K F FG
Sbjct: 105 LPLNKLDVRDTAYPETNDAIPMISKLRYNPRFDKAFKHVFGKT 147
>2kyc_A Parvalbumin-3, parvalbumin, thymic CPV3; EF-hand protein, calcium
binding protein; NMR {Gallus gallus} PDB: 2kyf_A
Length = 108
Score = 26.1 bits (58), Expect = 0.43
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 5/34 (14%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPF-----GTIEE 45
KK F +++ +++IF G IEE
Sbjct: 27 KKFFQISGMSKKSSSQLKEIFRILDNDQSGFIEE 60
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 25.2 bits (55), Expect = 1.1
Identities = 6/33 (18%), Positives = 9/33 (27%), Gaps = 4/33 (12%)
Query: 29 NEDDVRKIFAPFGTIEEC----TVLKGPDGTSK 57
++V F I + PDG
Sbjct: 36 TAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT 68
>1rwy_A Parvalbumin alpha; EF-hand, calcium-binding, calcium-binding
protein; HET: PG4; 1.05A {Rattus norvegicus} SCOP:
a.39.1.4 PDB: 1rtp_1* 2jww_A 3f45_A 1s3p_A 1xvj_A
1rjv_A 1rk9_A 1g33_A
Length = 109
Score = 24.9 bits (55), Expect = 1.3
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPF-----GTIEE 45
KK F + K+++ DDV+K+F G IEE
Sbjct: 27 KKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEE 60
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 25.0 bits (54), Expect = 1.5
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 3 PLDLIWNCTPLPPDK-KLFVGMLSKQQNEDD 32
P +I P+PP + + + + EDD
Sbjct: 237 PDWMIITVLPVPPPSVRPSISVDGTSRGEDD 267
>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker
complexed with non-BRCT protein, three-helix bundle,
parallel beta sheet; 2.50A {Homo sapiens} SCOP:
c.15.1.4 c.15.1.4 PDB: 1gzh_B
Length = 259
Score = 24.8 bits (53), Expect = 1.6
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 11 TPLPPDKKLFVGM---LSKQQNEDDVRKI 36
PLP +K LF+G L+ D +
Sbjct: 7 GPLPLNKTLFLGYAFLLTMATTSDKLASR 35
>1bu3_A Calcium-binding protein; 1.65A {Merluccius bilinearis} SCOP:
a.39.1.4
Length = 109
Score = 24.1 bits (53), Expect = 2.6
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 5/34 (14%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPF-----GTIEE 45
K F + ++ DD++K F G IEE
Sbjct: 28 KAFFAKVGLTAKSADDIKKAFFVIDQDKSGFIEE 61
>3fs7_A Parvalbumin, thymic; calcium-binding protein, EF-hand,
acetylation, calcium, metal binding protein; 1.95A
{Gallus gallus} PDB: 2kqy_A
Length = 109
Score = 23.8 bits (52), Expect = 3.4
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 5/34 (14%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPF-----GTIEE 45
K F + + D ++K+F G IEE
Sbjct: 28 KSFFSTVGLSSKTPDQIKKVFGILDQDKSGFIEE 61
>2pvb_A Protein (parvalbumin); calcium binding protein, metal binding
protein; 0.91A {Esox lucius} SCOP: a.39.1.4 PDB: 1pvb_A
2pal_A 1pal_A 3pal_A 4pal_A 4cpv_A 1cdp_A 5cpv_A 1b8r_A
1b9a_A 1b8l_A 1b8c_A 1a75_B 1a75_A
Length = 108
Score = 23.3 bits (51), Expect = 4.3
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 5/34 (14%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPF-----GTIEE 45
K+ F + ++ DDV+K F G IEE
Sbjct: 27 KEFFAKVGLASKSLDDVKKAFYVIDQDKSGFIEE 60
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 23.5 bits (51), Expect = 5.4
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 3 PLDLIWNCTPLPP-DKKLFVGMLSKQQNEDD 32
P ++ P+PP + + + + + EDD
Sbjct: 271 PEWMVLTVLPVPPVTARPSITLETGIRAEDD 301
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.141 0.442
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 910,554
Number of extensions: 37258
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 196
Length of query: 59
Length of database: 6,701,793
Length adjustment: 30
Effective length of query: 29
Effective length of database: 5,864,163
Effective search space: 170060727
Effective search space used: 170060727
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 (21.7 bits)
S2: 51 (23.4 bits)