RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3928
(115 letters)
>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 = 70.6 bits (173), Expect = 7e-17
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ EA+ D I+ F YG++ + L + TG KG+A VE+ T ++A A E LN
Sbjct: 80 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE-ALN 135
>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 = 69.3 bits (170), Expect = 9e-17
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+E GLN
Sbjct: 30 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 85
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 68.4 bits (168), Expect = 1e-16
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+E GLN
Sbjct: 31 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 86
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing,
protein complex, EXON junct complex, signaling protein;
1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB:
2hyi_B* 2j0s_D* 2xb2_D*
Length = 110
Score = 68.5 bits (168), Expect = 1e-16
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ EA+ D I+ F YG++ + L + TG KG+A VE+ T ++A A E LN
Sbjct: 34 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE-ALN 89
>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 = 68.1 bits (167), Expect = 2e-16
Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALE 72
+P +A I +FS +G++ V LPK TG +GF FV+F TK++A KA
Sbjct: 23 IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
>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 = 67.2 bits (165), Expect = 2e-16
Identities = 19/54 (35%), Positives = 29/54 (53%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+ A + +E+ F G V V++ K +G KGFA++EFS KE +L L
Sbjct: 14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
>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 = 67.6 bits (166), Expect = 2e-16
Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + ++ +F +G ++ + L K K+TG+ KGFAF+ F +E+A +A+ G++
Sbjct: 23 LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA-GVS 78
>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 = 67.3 bits (165), Expect = 3e-16
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L D + VF KYG+V V +P+ T +GFAFV F + +A A ++
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA-AMD 76
>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 = 66.0 bits (162), Expect = 6e-16
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L E + + + F +G +T + +P T K +GFAFVEF E+A A++ +N
Sbjct: 15 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-NMN 70
>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 = 67.0 bits (164), Expect = 6e-16
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L ++E + + V ++G + YV + T KG AF +F T+E A K L
Sbjct: 23 LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
>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 = 65.7 bits (161), Expect = 1e-15
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L D + +F +GK+ + L K TG+ KG+ F+ FS E A +ALE LN
Sbjct: 13 LHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE-QLN 68
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 67.1 bits (164), Expect = 1e-15
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L D + VF KYG+V V +P+ + T + +GFAFV F K +A A++ ++
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD-AMD 110
>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 = 65.3 bits (160), Expect = 1e-15
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP ++ + +FSKYGKV V++ K K T K KG AF+ F K+ A +N
Sbjct: 24 LPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR-AIN 79
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 66.7 bits (163), Expect = 1e-15
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L E + + + F +G +T + +P T K +GFAFVEF E+A A++ +N
Sbjct: 71 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-NMN 126
>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 = 65.3 bits (160), Expect = 2e-15
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L E + + + F +G +T + +P T K +GFAFVEF E+A A++ +N
Sbjct: 20 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-NMN 75
>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 = 67.4 bits (165), Expect = 2e-15
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP D ++ + + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 177
Score = 55.0 bits (133), Expect = 1e-10
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEATKALEL 73
+P + + F+ ++ ++ + K FAF+EF + +E T+A+
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 70
>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 = 65.5 bits (160), Expect = 3e-15
Identities = 12/54 (22%), Positives = 28/54 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+ + +E+ FS G + +++ K +G KG+A++EF+ + A+ +
Sbjct: 44 VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
>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 = 64.6 bits (158), Expect = 4e-15
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L D + +F +G++ + L TG+ KG+ F+ FS E A KALE LN
Sbjct: 34 LHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE-QLN 89
>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 = 64.2 bits (157), Expect = 5e-15
Identities = 20/53 (37%), Positives = 27/53 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + +E +FS YG ++ + P T K KGFAFV F E A KA
Sbjct: 16 LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
>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 = 64.3 bits (157), Expect = 6e-15
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
L +E FS GKV V + +++ + KG A+VEF + A+ L
Sbjct: 33 LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 86
>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 = 63.8 bits (156), Expect = 7e-15
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+P + + I + S G V + + TG+ KG+AF+EF E + A+ LN
Sbjct: 10 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR-NLN 65
>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 = 64.9 bits (158), Expect = 9e-15
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L D + VF KYG+V V +P+ + T + +GFAFV F K +A A++ ++
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD-AMD 133
>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 = 63.4 bits (155), Expect = 1e-14
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+P EA + ++ +FS+ G V L + TGK KG+ F E+ +E A A+ LN
Sbjct: 16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR-NLN 71
>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 = 64.0 bits (156), Expect = 1e-14
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + VFSKYG + VS+ + + + +GFAFV F ++A +A E N
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE-RAN 109
>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 = 63.0 bits (154), Expect = 2e-14
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + + +F + G V +PK + TG+ +G+ FVEF ++E+A A++ ++
Sbjct: 23 LDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK-IMD 78
>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 = 62.6 bits (153), Expect = 2e-14
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALELGLN 76
L D+I +FS YGK+ + +P + KG+A+VEF +EA KAL+ ++
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK-HMD 68
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 62.8 bits (153), Expect = 2e-14
Identities = 13/53 (24%), Positives = 24/53 (45%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L +++ + KYG+V V + T K G A V F++ A + ++
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
>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 = 61.8 bits (151), Expect = 3e-14
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + VFSKYG + VS+ + + + +GFAFV F ++A +A E N
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE-RAN 78
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 61.9 bits (151), Expect = 4e-14
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP + +E + +G V + L + GK KG A+VE+ + +A++A+ ++
Sbjct: 25 LPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM-KMD 79
>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 = 64.1 bits (155), Expect = 5e-14
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+ P +A D I+ G+V + + + KG FV F + E A K +E
Sbjct: 115 KGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 169
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 63.9 bits (156), Expect = 6e-14
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 1 MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
+ +L E + + R+ + + + D I+SVF +GK+ +L + +TGK KG+ F+E
Sbjct: 115 IDQLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173
Query: 61 FSTKEEATKALE 72
+ + + A+
Sbjct: 174 YEKAQSSQDAVS 185
Score = 56.6 bits (137), Expect = 3e-11
Identities = 19/53 (35%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ E D I F+ +G + + + T K KGFAFVE+ E A ALE
Sbjct: 36 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
>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 = 61.1 bits (149), Expect = 7e-14
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + +E VFSKYG+++ V + K + T + +GF FV F ++A A+ +N
Sbjct: 20 LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM-AMN 75
>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 = 61.6 bits (150), Expect = 7e-14
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L E +++VF K+G ++ V L K + T K +GFAF+ F +A A + +N
Sbjct: 15 LNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK-DMN 69
>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 = 64.6 bits (158), Expect = 8e-14
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 20 LPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LPP + D + S T+ L G+LKGFA +E+ T E A +A +
Sbjct: 192 LPPGFNDVDALCRALSAVHSPTFCQLAC-GQDGQLKGFAVLEYETAEMAEEAQQ 244
Score = 64.2 bits (157), Expect = 8e-14
Identities = 15/53 (28%), Positives = 24/53 (45%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LPP E + +G + L + TG+ KG+ F E+ K+ A +A
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Score = 45.7 bits (109), Expect = 4e-07
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 7/53 (13%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + + + + S Y K+ K KG AFV E+A A+
Sbjct: 30 LPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAIN 75
>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 = 64.2 bits (157), Expect = 9e-14
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 20 LPPEA-EHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALEL 73
L E + + + F +G + +++P K AF+ F K+ A +AL++
Sbjct: 218 LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM 273
Score = 57.3 bits (139), Expect = 3e-11
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
PP I + V + LP + FA+++ ++KE+A +E
Sbjct: 125 FPPSYTQRNIRDLLQDINVVALSIRLPS-LRFNTSRRFAYIDVTSKEDARYCVE 177
Score = 55.4 bits (134), Expect = 2e-10
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + + F G + +V + S K FA +EF+ + A A+
Sbjct: 48 NLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAIT 99
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 61.1 bits (149), Expect = 9e-14
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP I+++F + V L + K T K KGF +VEF + +AL
Sbjct: 23 LPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
>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 = 60.6 bits (148), Expect = 1e-13
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L P + + YGK+ K+T K KG+ FV+F + A KA+ L
Sbjct: 13 LQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT-ALK 68
>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 = 61.7 bits (150), Expect = 1e-13
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + I +FSK G + + + K GF FVE+ ++ +A A+ +N
Sbjct: 47 LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR-YIN 102
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 60.5 bits (147), Expect = 2e-13
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
P +A D I+ G+V + + + KG FV F + E A K +E
Sbjct: 19 FPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 71
>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 = 59.8 bits (146), Expect = 2e-13
Identities = 10/57 (17%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + + + + F + + TG +G+ FV F+++++A A++ +
Sbjct: 9 LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD-SMQ 64
>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 = 62.4 bits (151), Expect = 2e-13
Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 1/76 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
P E + + + G S+ F + +E+ +K +A + L LN
Sbjct: 131 APLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF-LNHYQ 189
Query: 80 TDYQSSILTTTSRLSF 95
+ T +L F
Sbjct: 190 MKNPNGPYPYTLKLCF 205
Score = 38.5 bits (89), Expect = 1e-04
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 12 GRVVLKEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
V++ L D + +VF YG V V K K G A VE + +A
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRA 58
Query: 71 LE 72
+
Sbjct: 59 IT 60
>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 = 60.0 bits (146), Expect = 2e-13
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
L P ++ S+ +++ TG + F +V+F + E+ KALEL
Sbjct: 25 LNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALEL 77
>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 = 61.5 bits (150), Expect = 2e-13
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP D ++ + + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 102 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 157
Score = 50.3 bits (121), Expect = 5e-09
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEATKALEL 73
+P + + F+ ++ ++ + K FAF+EF + +E T+A+
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 70
>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 = 61.5 bits (150), Expect = 3e-13
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L D ++ VF ++ V GK KG A++EF ++ +A K LE
Sbjct: 107 LSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 154
Score = 55.3 bits (134), Expect = 6e-11
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
L P ++ S+ +++ TG + F +V+F + E+ KALEL
Sbjct: 21 LNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALEL 73
>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 = 61.0 bits (149), Expect = 3e-13
Identities = 13/54 (24%), Positives = 25/54 (46%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+ P+ E FS++G + L K TG+ +GF FV + + + + +
Sbjct: 95 IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
Score = 51.8 bits (125), Expect = 1e-09
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + D + F KYG VT + + K +TG+ +GF F+ F + ++
Sbjct: 11 LNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
>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 = 60.5 bits (147), Expect = 3e-13
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+P + + +F +YG + V + + T + +G+ FV+F + A +A+ GLN
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA-GLN 105
>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 = 59.7 bits (145), Expect = 4e-13
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L PE + I++ F+ +G+++ + K +TGK KG+ FV F K +A A++
Sbjct: 23 LSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
>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 = 59.6 bits (145), Expect = 4e-13
Identities = 15/54 (27%), Positives = 31/54 (57%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
++P + ++ +F ++GK+ +++ K + TG KG AF+ + +E A KA
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 58.9 bits (143), Expect = 5e-13
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 20 LPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ P D I + S Y V + L K K T + +GFAFV+ S+ +A++ L+
Sbjct: 17 IAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
>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 = 61.2 bits (149), Expect = 6e-13
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Score = 52.7 bits (127), Expect = 7e-10
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L E + + S F ++G +T + + +T + +GF FV ++T EE A+
Sbjct: 21 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>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 = 58.8 bits (143), Expect = 7e-13
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEEATKALEL 73
LP + + I+ F ++ V LP+ S +LKGF + EF + AL L
Sbjct: 27 LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80
>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 = 58.4 bits (142), Expect = 1e-12
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + + +F +G + ++ + G KG AFV+FS+ EA A+
Sbjct: 23 LNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSHTEAQAAIH 74
>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 = 57.9 bits (141), Expect = 1e-12
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L A + ++ +FS++GKV V L + T K KGF FVE E ++A+ L+
Sbjct: 9 LVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA-KLD 63
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 58.0 bits (141), Expect = 1e-12
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + + +F + G +T V++ K + GK K F FV F E + A+ L LN
Sbjct: 24 LEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIAL-LN 78
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 58.5 bits (142), Expect = 1e-12
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L P + S+F+++ + + TG+++G AF+ F KE A +AL
Sbjct: 33 LSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 57.6 bits (140), Expect = 1e-12
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L PE I + F+ +G+++ + K +TGK KG+ FV F K +A A++
Sbjct: 14 LSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>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 = 59.5 bits (145), Expect = 1e-12
Identities = 18/53 (33%), Positives = 33/53 (62%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP D ++++F KYG + ++ + K TG+ +G AFV ++ +EEA +A+
Sbjct: 97 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Score = 55.7 bits (135), Expect = 4e-11
Identities = 12/53 (22%), Positives = 29/53 (54%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + + ++F G + + + TG G+AFV+F+++ ++ +A++
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
>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 = 57.7 bits (140), Expect = 2e-12
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALEL 73
LP + + I+ F ++ V LP+ S +LKGF + EF + AL L
Sbjct: 23 LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76
>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 = 57.7 bits (140), Expect = 2e-12
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LPP+ IE VF KYG + + L K+ FAFVEF +A A+ G +
Sbjct: 30 LPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVY-GRD 82
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 57.3 bits (139), Expect = 3e-12
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 1 MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
M E R+ ++ P + + + +F +G + V + GFAFVE
Sbjct: 21 MHHRQEGELSNTRLFVR-PFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVE 71
Query: 61 FSTKEEATKALELGLN 76
F E A KA+E ++
Sbjct: 72 FEEAESAAKAIE-EVH 86
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA
recognition motif, RRM, RNP, structural genomics,
NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 57.3 bits (139), Expect = 3e-12
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LPP+ + + +F KYGK V + K KGF F+ T+ A A L+
Sbjct: 23 LPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKV-ELD 72
>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 = 57.3 bits (139), Expect = 3e-12
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
L + + F + G + ++L + TGKLKG A V F A A+
Sbjct: 21 LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAI 80
Query: 72 EL 73
+
Sbjct: 81 DW 82
>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 = 57.0 bits (138), Expect = 4e-12
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP + + + +F KYG + + + T + +G A+V + +A A++ L+
Sbjct: 16 LPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD-HLS 68
>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 = 56.5 bits (137), Expect = 5e-12
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ + I S F++YG V V + TG KG+ FV F + K +E
Sbjct: 17 IDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSFYNDVDVQKIVE 68
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 56.7 bits (137), Expect = 5e-12
Identities = 19/44 (43%), Positives = 28/44 (63%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ S+FSK GKV + P ++TGK KGF FVE + +A K ++
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 56.1 bits (136), Expect = 6e-12
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L EK+ + + ++FS++G++ + + + + K++G AFV F AT AL
Sbjct: 16 LNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALR 69
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 56.6 bits (137), Expect = 7e-12
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
L + + F + G + ++L + TGKLKG A V F A A+
Sbjct: 15 LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAI 74
Query: 72 EL 73
+
Sbjct: 75 DW 76
>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 = 57.6 bits (140), Expect = 7e-12
Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ + + I +FS +G++ + + G +G AFV F+T+ A A++
Sbjct: 103 ISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTTRAMAQTAIK 154
Score = 54.9 bits (133), Expect = 9e-11
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL--KGFAFVEFSTKEEATKALELGLN 76
+P + +F +YG V +++ + +S KG FV F T++ A +A L+
Sbjct: 11 VPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN-ALH 68
>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 = 56.6 bits (137), Expect = 7e-12
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP E + +F +G V + K T K F FV + A A++ +N
Sbjct: 33 LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ-SMN 88
>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 = 57.2 bits (139), Expect = 1e-11
Identities = 10/53 (18%), Positives = 25/53 (47%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + + + F + + TG +G+ FV F+++++A A++
Sbjct: 95 LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147
Score = 49.8 bits (120), Expect = 7e-09
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L D ++ F G + + + K K +AFVE+ +A AL+
Sbjct: 8 LDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 55.8 bits (135), Expect = 1e-11
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP E + S F +G V + K T K F FV F + A A++ +N
Sbjct: 48 LPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK-AMN 103
>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 = 55.5 bits (134), Expect = 1e-11
Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 8/62 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
L D + F + G V + + K TGK KG A V + A A+
Sbjct: 23 LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAV 82
Query: 72 EL 73
E
Sbjct: 83 EW 84
>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 = 55.3 bits (134), Expect = 2e-11
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL---KGFAFVEFSTKEEATKALE 72
L + ++ VFSK G + ++ K K+ + GF FVE+ E+A KAL+
Sbjct: 13 LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 54.9 bits (133), Expect = 2e-11
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP EA I S+F +YGKV + +K + FV K A A+ L+
Sbjct: 16 LPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAIR-NLH 63
>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 = 54.4 bits (132), Expect = 2e-11
Identities = 17/53 (32%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L P+ + I F +G+V + LP T K +GF F+ F +E K +E
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 55.5 bits (134), Expect = 2e-11
Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L I+ +F+++G + ++ + +G+ G A V F + +A KA++
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 56.4 bits (136), Expect = 2e-11
Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L I+ +F+++G + ++ + +G+ G A V F + +A KA++
Sbjct: 96 LDFGVSDADIQELFAEFGTLKKAAV-DYDRSGRSLGTADVHFERRADALKAMK 147
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 54.6 bits (132), Expect = 3e-11
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L A +E FS YG + V + + GFAFVEF +A A+ GL+
Sbjct: 8 LGTGAGKGELERAFSYYGPLRTVWIAR-----NPPGFAFVEFEDPRDAEDAVR-GLD 58
>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 = 54.6 bits (132), Expect = 3e-11
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+P + +F ++GK+ V + + K GF FV F +A +A E L+
Sbjct: 23 IPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE-KLH 76
>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 = 54.1 bits (131), Expect = 3e-11
Identities = 9/50 (18%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 29 IESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ G + + + ++ G+ KGFA V ++ + K ++ L
Sbjct: 18 LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD-LLP 66
>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 = 54.2 bits (131), Expect = 4e-11
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L D ++ VF ++ V GK KG A++EF ++ +A K LE
Sbjct: 24 LSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 71
>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 = 54.2 bits (131), Expect = 4e-11
Identities = 12/44 (27%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
I+ +F+++G + ++ + +G+ G A V F K +A KA++
Sbjct: 46 IQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 88
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 101
Score = 54.2 bits (131), Expect = 4e-11
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L A + ++ VF K + GK KG+AF+EF++ E+A +AL N
Sbjct: 23 LSYSATEETLQEVFEKATFIKVPQ----NQNGKSKGYAFIEFASFEDAKEALN-SCN 74
>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 = 54.6 bits (132), Expect = 4e-11
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + ++ VFS G V + + K GK +G V F EA +A+
Sbjct: 23 LDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
>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 = 53.9 bits (130), Expect = 5e-11
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 20 LPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L P + ++I F+ G V V + + + TG G+ FVEF+ A K L +N
Sbjct: 17 LEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH-KIN 73
>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 = 53.7 bits (130), Expect = 5e-11
Identities = 12/54 (22%), Positives = 24/54 (44%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+P + F K+G VT V + + +GF F+ F ++ +A+ +
Sbjct: 18 IPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>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 = 53.8 bits (130), Expect = 5e-11
Identities = 15/53 (28%), Positives = 22/53 (41%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+P D I F Y + K+ G G A V F +++EAT A+
Sbjct: 23 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
>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 = 53.8 bits (130), Expect = 6e-11
Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L P + F ++G + + K FA++++ + + A A
Sbjct: 24 GLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71
>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 = 53.4 bits (129), Expect = 6e-11
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 9/57 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ + S+F + G+V + +K +AFV + +A A+ LN
Sbjct: 17 VSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIA-QLN 64
>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 = 53.4 bits (129), Expect = 7e-11
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ P + + + F +YG V + K +AFV E+A +A+ GL+
Sbjct: 18 ISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIR-GLD 65
>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 = 53.4 bits (129), Expect = 8e-11
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + +E FS++GK+ V KLK +AF+ F ++ A KA+E
Sbjct: 19 LANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAME 63
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 53.5 bits (129), Expect = 9e-11
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 12/59 (20%)
Query: 20 LPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + D +E++FSKYG+V S+ K G+AFV++S + A A+ G N
Sbjct: 35 LNTALVKKSD-VETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVL-GEN 83
>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 = 53.1 bits (128), Expect = 9e-11
Identities = 15/53 (28%), Positives = 22/53 (41%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+P D I F Y + K+ G G A V F +++EAT A+
Sbjct: 23 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 52.8 bits (127), Expect = 1e-10
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
V ++L I +FSK+GK+T P+ GK KG+ F+E+++ A A++
Sbjct: 11 QVGPDRLEKLKN--VIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVK 65
>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 = 53.0 bits (128), Expect = 1e-10
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 3/57 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + I +FS+ G + ++ + FVEF +A AL +N
Sbjct: 23 LSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAALA-AMN 76
>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 = 53.0 bits (128), Expect = 1e-10
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + + FS +G +T + G+ KGF FV FS+ EEATKA+
Sbjct: 23 LDDGIDDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSSPEEATKAVT 73
>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 = 53.3 bits (128), Expect = 1e-10
Identities = 18/54 (33%), Positives = 24/54 (44%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP + I FS V GK+ G AFV+F+++E A KAL
Sbjct: 50 LPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK 103
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 52.6 bits (127), Expect = 2e-10
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 12/59 (20%)
Query: 20 LPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP + + D + +FS YG + +++ F F++F + A+E +
Sbjct: 18 LPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE-CES 66
>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 = 54.1 bits (131), Expect = 2e-10
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP +E +FS+YG++ + + TG +G F+ F + EA +A++
Sbjct: 96 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Score = 53.7 bits (130), Expect = 2e-10
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + S+F G++ L + K TG+ G+ FV + ++A KA+
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
>1x5o_A RNA binding motif, single-stranded interacting protein 1;
structure genomics, RRM domain, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 52.6 bits (127), Expect = 2e-10
Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP + +E++ +G+V + + S+G +G F + E+ + N
Sbjct: 33 LPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEKCEAVIG-HFN 87
>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 = 54.7 bits (131), Expect = 2e-10
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 20 LPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + G + + + ++ G+ KGFA V ++ + K ++
Sbjct: 76 LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
>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 = 52.4 bits (126), Expect = 3e-10
Identities = 9/54 (16%), Positives = 18/54 (33%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+P + + G+ G A V+F +++A K+ L
Sbjct: 23 IPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 76
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 52.3 bits (126), Expect = 3e-10
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+P + +F ++GK+ V + + K GF FV F +A +A E L+
Sbjct: 37 IPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE-KLH 90
>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 = 54.2 bits (131), Expect = 3e-10
Identities = 13/53 (24%), Positives = 25/53 (47%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L P+ + FS G + + + + T + G+A+V F +A +AL+
Sbjct: 23 LHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Score = 53.1 bits (128), Expect = 8e-10
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L ++ + FS +G + + KG+ FV F T+E A +A+E
Sbjct: 111 LDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 161
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 52.0 bits (125), Expect = 3e-10
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 1 MAELVENNKKYGRVVLKEKLP--PEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLK 54
+ + + V++ + +P + I +FSK+GK+T P+ GK K
Sbjct: 4 LKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTK 61
Query: 55 GFAFVEFSTKEEATKALE 72
G+ F+E+++ A A++
Sbjct: 62 GYIFLEYASPAHAVDAVK 79
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 51.9 bits (125), Expect = 3e-10
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 7/57 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+P A + +F +G + KG F+++ T E+A + L
Sbjct: 35 IPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIV-ALA 84
>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 = 51.5 bits (124), Expect = 4e-10
Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 7/57 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L P D + +F G+AFV++ + A +A+E L+
Sbjct: 16 LSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE-TLS 65
>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 = 54.5 bits (130), Expect = 4e-10
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L EK+ + + ++FS++G++ + + + + K++G AFV F AT AL
Sbjct: 17 LNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALR 70
Score = 46.0 bits (108), Expect = 3e-07
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP E + +F+++ V L + AFVEF + +A A +
Sbjct: 215 LPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 50.9 bits (123), Expect = 4e-10
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + ++ F ++GKV L K+T + +GF FV F +++ K E
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 51.4 bits (124), Expect = 4e-10
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP + ++ F++ G V Y + GK KG V+F + E A +A +N
Sbjct: 16 LPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR-MMN 69
>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 = 54.5 bits (130), Expect = 5e-10
Identities = 11/54 (20%), Positives = 26/54 (48%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
++ + + F YG + + + K +GK +G+AF+E+ + + A +
Sbjct: 109 RVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
>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 = 52.2 bits (125), Expect = 5e-10
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP +A + I + FS V V + G++ G A VEF+T EEA A+
Sbjct: 54 LPYKATENDIYNFFSPLNPVR-VHIEI-GPDGRVTGEADVEFATHEEAVAAMSK 105
>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 = 52.1 bits (125), Expect = 5e-10
Identities = 17/54 (31%), Positives = 23/54 (42%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP EAE+ ++ F K V + GK G FVEF + + AL
Sbjct: 33 LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86
>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 = 51.5 bits (124), Expect = 5e-10
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + IE F+ + K ++ +AFV FS +E+A +A++
Sbjct: 23 LMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMK 69
>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 = 51.3 bits (123), Expect = 6e-10
Identities = 17/54 (31%), Positives = 24/54 (44%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP + I FS V G+ G AFV+F+++E A KAL+
Sbjct: 23 LPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 76
>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 = 52.2 bits (125), Expect = 7e-10
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L +E F YG + V + + GFAFVEF +A A+ L+
Sbjct: 81 LGNNGNKTELERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDAADAVR-ELD 131
>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 = 50.7 bits (122), Expect = 7e-10
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF---KSTGKLKGFAFVEFSTKEEATKALE 72
L PE + + FS +G + + PK TG KG+AF+ F++ + + A+E
Sbjct: 13 LDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 51.4 bits (123), Expect = 9e-10
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ ++P E + ++ S G + + + + G A++ F+T+E A +E
Sbjct: 37 INPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVE 90
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 51.8 bits (124), Expect = 9e-10
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 29 IESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ V G V + + ++ G+ KG+A V +++ K LE L
Sbjct: 72 LIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE-LLP 120
>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 = 53.2 bits (128), Expect = 1e-09
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L P ++ +E FS++G V + G+ G FVEF+ K A KALE
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVV-DDRGRATGKGFVEFAAKPPARKALE 155
Score = 46.2 bits (110), Expect = 2e-07
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + + + +F +YG+ + V + + + GF F+ ++ A A
Sbjct: 30 LPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKA 76
>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 = 50.7 bits (122), Expect = 1e-09
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + + ++ F + + + TG KGF FV+F+++E+A A E +
Sbjct: 23 LSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAKE-AME 75
>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 = 50.9 bits (122), Expect = 1e-09
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ FS +G + +S+ + AFV + E A +A+
Sbjct: 51 PTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVA 91
>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 = 50.4 bits (121), Expect = 1e-09
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+ + FS +G++ + + KG++FV FST E A A+ +N
Sbjct: 33 IASGLTDQLMRQTFSPFGQIMEIRVFP------EKGYSFVRFSTHESAAHAIV-SVN 82
>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 = 50.0 bits (120), Expect = 1e-09
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 20 LPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + + D + +FS YG + +++ F F++F + A+E
Sbjct: 30 LPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 49.0 bits (117), Expect = 4e-09
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+PP + + ++S+ +YG V S V +S+K++A +AL+ LN
Sbjct: 23 IPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALD-KLN 75
>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 = 48.8 bits (117), Expect = 5e-09
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ FS +G + +S+ + AFV + E A +A+
Sbjct: 28 TLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVA 67
>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 = 48.5 bits (116), Expect = 5e-09
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
P + + K + + + + G G+ FV+FS +EE +AL+
Sbjct: 18 APFNVTEKNVMEFLAPL-KPVAIRIVR-NAHGNKTGYIFVDFSNEEEVKQALKC 69
>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 = 48.5 bits (116), Expect = 6e-09
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP A + I + FS V + G++ G A VEF+T E+A A+
Sbjct: 23 LPYRATENDIYNFFSPL-NPMRVHIEI-GPDGRVTGEADVEFATHEDAVAAMAK 74
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation
initiation, RNA-binding, EIF4G-binding translation;
1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 48.8 bits (117), Expect = 6e-09
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L ++ + FS +G + +S KG+ FV F T+E A +A+E +N
Sbjct: 13 LDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERAIE-KMN 66
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 48.1 bits (115), Expect = 7e-09
Identities = 12/55 (21%), Positives = 16/55 (29%), Gaps = 5/55 (9%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
P + + F +G V V + K K FA VE L
Sbjct: 16 FPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLSQS 65
>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 = 48.4 bits (116), Expect = 8e-09
Identities = 18/53 (33%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + ++ FS +G+V V + K TG KGF FV F+ E K +
Sbjct: 23 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 48.0 bits (115), Expect = 8e-09
Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
L + + F ++G++ +++ + + AF++F+T++ A A E N
Sbjct: 20 LGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFN 70
>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 = 48.3 bits (115), Expect = 1e-08
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 7/53 (13%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LPP ++ + G V Y + + G VEF KE+ T A+
Sbjct: 23 LPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVR 68
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 48.3 bits (115), Expect = 1e-08
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTY----VSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP A + + + F ++ +T + G+ G AFV F+ +E A AL
Sbjct: 31 LPFTATAEEVVAFFGQHCPITGGKEGILFVT-YPDGRPTGDAFVLFACEEYAQNALRK 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 = 47.4 bits (113), Expect = 1e-08
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEATKALEL 73
+P + + F+ ++ ++ + K FAF+EF + +E T+A+
Sbjct: 14 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 72
>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 = 48.1 bits (115), Expect = 1e-08
Identities = 12/53 (22%), Positives = 23/53 (43%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP + F +G + + + TGK +G+ FV + + A +A +
Sbjct: 25 LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 47.8 bits (114), Expect = 2e-08
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+P A + + F +V V L K G+ G V+F + ++ +AL+
Sbjct: 24 MPFSAMENDVRDFFHGL-RVDAVHLLK-DHVGRNNGNGLVKFLSPQDTFEALKR 75
>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 = 47.5 bits (113), Expect = 2e-08
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 20 LPPEAEHDYIESVFSKYGK-VTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALE 72
+P + + I +K + V V + K +GFAFVE+ + A A
Sbjct: 16 IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 46.3 bits (111), Expect = 2e-08
Identities = 12/53 (22%), Positives = 23/53 (43%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + + F ++G+V + + T + +GF FV F + K L
Sbjct: 8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>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 = 47.9 bits (114), Expect = 2e-08
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLP-----KFKSTGKLKGFAFVEFSTKEEATKALE 72
L + ++ +F +Y + + + G++KG AF+ ++ A KAL+
Sbjct: 53 LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALK 110
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 46.7 bits (111), Expect = 3e-08
Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 6/60 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
VV L + ++G ++YV + K A VEF A A+
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVN 75
>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 = 48.4 bits (115), Expect = 3e-08
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 10/81 (12%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
+PP + ++ +FS G V FK K + A ++ + EEA +AL L+
Sbjct: 128 IPPSVSEEDLKVLFSSNGGVV----KGFKFFQKDRKMALIQMGSVEEAVQALI-DLHNHD 182
Query: 80 TDYQSSILTTTSRLSFGITPL 100
+ R+SF + +
Sbjct: 183 LGENHHL-----RVSFSKSTI 198
Score = 37.6 bits (87), Expect = 2e-04
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 20 LPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L PE + +F YG V V K K A V+ + +A A+
Sbjct: 11 LNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLAMS 59
>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 = 46.0 bits (110), Expect = 4e-08
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + ++ F+K+G+V ++ +TG+ +GF F+ F K L+
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71
>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 = 46.7 bits (111), Expect = 4e-08
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 7/53 (13%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LPP ++ + G V Y + + G VEF KE+ T A+
Sbjct: 24 LPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVR 69
>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 = 46.3 bits (110), Expect = 4e-08
Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
VV L + K+G + YV + F K A VEF + A + +
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVT 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 = 46.5 bits (111), Expect = 5e-08
Identities = 12/53 (22%), Positives = 23/53 (43%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + + F ++G+V + + T + +GF FV F + K L
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
>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 = 46.4 bits (110), Expect = 5e-08
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 30 ESVFSKYGKVTYVSLPKFKSTGKLK---GFAFVEFSTKEEATKALE 72
F K+GK+ V + S + A+V + E+A +A++
Sbjct: 36 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQ 81
>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 = 48.1 bits (114), Expect = 6e-08
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+PP + ++ +FS G V V KF + A ++ + EEA +AL
Sbjct: 159 IPPSVSEEDLKVLFSSNGGV--VKGFKFFQKDR--KMALIQMGSVEEAVQALI 207
Score = 38.4 bits (89), Expect = 1e-04
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 12 GRVVLKEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
V+L L PE + +F YG V V K K A V+ + +A A
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLA 88
Query: 71 LE 72
+
Sbjct: 89 MS 90
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 45.6 bits (108), Expect = 8e-08
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP +A ++ + G V P + + AF+ + A +A+ L
Sbjct: 27 LPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVS-CLQ 77
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 46.0 bits (109), Expect = 8e-08
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 6/53 (11%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP I+ FS++G + V LP+ A VEF EA KA
Sbjct: 18 LPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFR 64
>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 = 45.3 bits (108), Expect = 1e-07
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L + + S FS+YG+V + K K+T + +GF FV+F L
Sbjct: 24 LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
>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 = 45.3 bits (107), Expect = 1e-07
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
VV L + + V K G V + +P K ++F + T EE+ +A
Sbjct: 29 VVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYV 81
>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 = 44.5 bits (106), Expect = 2e-07
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ D + FS+YG V V +PK + FAFV F+ + A
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60
>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 = 46.2 bits (109), Expect = 2e-07
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
E L D + +FSK+G V + + + A ++++ A A
Sbjct: 52 ENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 102
>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 = 45.3 bits (108), Expect = 2e-07
Identities = 13/53 (24%), Positives = 28/53 (52%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L E + + + + ++GK+T + + ++ + +GF FV FS+ E A+
Sbjct: 35 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 45.4 bits (107), Expect = 2e-07
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
E L D + +FSK+G V + + + A ++++ A A
Sbjct: 34 ENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 84
>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 = 45.3 bits (107), Expect = 2e-07
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ KLP + + S+ +GKVT + + K K AF+E +T+E A +
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 85
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 44.5 bits (105), Expect = 3e-07
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ KLP + + S+ +GKVT + + K K AF+E +T+E A +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70
>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 = 43.6 bits (103), Expect = 4e-07
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 7/53 (13%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP ++ + + Y K+ + K AFV E+A A++
Sbjct: 13 LPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 43.8 bits (104), Expect = 5e-07
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 20 LPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
L P+ + + F K Y + + TG KG+ FV+F+ + E +AL
Sbjct: 17 LTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69
>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 = 43.0 bits (102), Expect = 6e-07
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ + ++ F +YG+V V +PK + FAFV F+ + A
Sbjct: 19 CTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSLCG 66
>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 = 43.3 bits (102), Expect = 7e-07
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
RV+ KLP E + ++ +GKVT + + K K AF+E +T+E A +
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMV 68
Query: 72 E 72
Sbjct: 69 N 69
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 43.8 bits (103), Expect = 8e-07
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 4/68 (5%)
Query: 9 KKYGRVVLKEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFSTKE 65
G VV LP + +++ S V G+ G AFVE +++
Sbjct: 41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY-TREGRQSGEAFVELGSED 99
Query: 66 EATKALEL 73
+ AL+
Sbjct: 100 DVKMALKK 107
>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 = 42.2 bits (99), Expect = 3e-06
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 20 LPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP + +++ S V V G+ G AFVE ++++ AL+
Sbjct: 25 LPWSCSIEDVQNFLSDCTIHDGVAGVHFIY-TREGRQSGEAFVELESEDDVKLALKK 80
>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 = 41.8 bits (98), Expect = 3e-06
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 4/72 (5%)
Query: 5 VENNKKYGRVVLKEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEF 61
+E ++ + LP + + + FS + GK +G A +E
Sbjct: 4 LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLL-NRDGKRRGDALIEM 62
Query: 62 STKEEATKALEL 73
++++ KALE
Sbjct: 63 ESEQDVQKALEK 74
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 40.5 bits (94), Expect = 7e-06
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 13/82 (15%)
Query: 6 ENNKKYGRVVLKEKLPPEAE------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFV 59
+ + ++ LK K E E D + + KYG+V + L K G A V
Sbjct: 5 SSGQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVV 59
Query: 60 EFSTKEEATKAL--ELGLNPCP 79
EF+T + A A+ E+GL P
Sbjct: 60 EFATVKAAELAVQNEVGLVDNP 81
>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 = 40.2 bits (94), Expect = 9e-06
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
E + + KYG+V +++ L G +V+F +E+A KA+ LN
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKFRREEDAEKAVI-DLN 89
>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 = 40.4 bits (95), Expect = 1e-05
Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 17 KEKLPPEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+ + + + + V +K+G V ++ + K + G +V+ + A A+
Sbjct: 19 QTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVN- 73
Query: 74 GLN 76
L+
Sbjct: 74 ALH 76
>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 = 39.9 bits (93), Expect = 2e-05
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 9/69 (13%)
Query: 6 ENNKKYGRVVLKEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 63
+ ++ GRV+ LP + + + YGK+ L ++K AF+E T
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSA-VLKLAEPYGKIKNYIL------MRMKSQAFIEMET 71
Query: 64 KEEATKALE 72
+E+A ++
Sbjct: 72 REDAMAMVD 80
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 39.0 bits (91), Expect = 3e-05
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 20 LPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP ++ + + + T+ S+ +T G +EF ++E +ALE
Sbjct: 36 LPEGCSWQDLKDLARENSLETTFSSV----NTRDFDGTGALEFPSEEILVEALE 85
>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 = 3e-05
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 20 LPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LPP+ + D I + F ++G + + + KS KG+AF+ F + ++
Sbjct: 16 LPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
>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 = 38.5 bits (90), Expect = 5e-05
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 22 PEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
P ++ E + SK+G++ + L G A V F EEA ++ L+
Sbjct: 33 PLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQ-TLD 85
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 38.5 bits (89), Expect = 6e-05
Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ D + +V + GKV + + A VEF + A KA
Sbjct: 31 QNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKA 80
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 39.4 bits (91), Expect = 6e-05
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 6/55 (10%)
Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ L P I VFS+ G + + + K FV+F + A A E
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKE 197
>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 = 8e-05
Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
+L + L + + + ++ ++G + + G A +++T+EEA KA ++
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ------GIALCKYTTREEANKA-QMA 62
Query: 75 LNPCP 79
LN C
Sbjct: 63 LNNCV 67
>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 = 37.8 bits (88), Expect = 1e-04
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 21 PPEAEHDYIESVF---SKYGKVTYVSLPK----FKSTGKLKGFAFVEFSTKEEATKALE 72
P + + D V K+G V V + + + ++ FVEFS E KA++
Sbjct: 31 PKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 89
>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 = 35.9 bits (83), Expect = 4e-04
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK--STGKLKGFAFVEFSTKEEATKALE 72
L + E + + SKYG V + +P+ G FVEF++ + KA++
Sbjct: 19 LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQ 77
>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 = 35.1 bits (80), Expect = 0.003
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ V K G V + +P K ++F + T EE+ +A
Sbjct: 37 LLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYV 74
>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 = 33.3 bits (76), Expect = 0.005
Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 9/63 (14%)
Query: 12 GRVVLKEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
RVV + + + +G ++ + + AF+E +T E+A
Sbjct: 15 RRVVHIMDFQRGKNLRYQ-LLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQA 67
Query: 70 ALE 72
A++
Sbjct: 68 AVD 70
>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 = 32.3 bits (73), Expect = 0.011
Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ +L + ++ F+++GKV V L + A V+ ++A A+
Sbjct: 17 IDYRLSRKELQQLLQEAFARHGKVKSVEL---SPHTDYQLKAVVQMENLQDAIGAVN 70
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 31.7 bits (72), Expect = 0.017
Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 21 PPEAEHDYIESVF---SKYGKVTYVSLPKFKSTGK-LKGFAFVEFSTKEEATKALE 72
E + D KYGKV + + F+EF E A KA+
Sbjct: 19 AGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVV 74
>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 = 29.8 bits (66), Expect = 0.18
Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 16/92 (17%)
Query: 7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG---KLKGFA------ 57
+ + L D ++S+ KY LP+ T +L A
Sbjct: 282 SAATTTHISLDHHSMTL-TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340
Query: 58 -----FVEFSTKEEATKALELGLNPC-PTDYQ 83
+ ++ T +E LN P +Y+
Sbjct: 341 LATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 28.4 bits (63), Expect = 0.27
Identities = 10/67 (14%), Positives = 21/67 (31%), Gaps = 3/67 (4%)
Query: 6 ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 65
+ G V LPP + + F + + ++ +L + F
Sbjct: 2 SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ---RLGCGGVLTFREPA 58
Query: 66 EATKALE 72
+A + L
Sbjct: 59 DAERVLA 65
>2qtw_A Proprotein convertase subtilisin/kexin type 9 Pro; coronary heart
disease, hypercholest low density lipoprotein receptor,
autocatalytic cleavage; HET: NAG; 1.90A {Homo sapiens}
PDB: 3m0c_A 2pmw_A 3h42_A 3bps_P 3gcw_P 3gcx_P 3p5b_P
3p5c_P
Length = 124
Score = 28.5 bits (63), Expect = 0.28
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 65
VVLKE+ + ++ + Y++ G L GF V+ S
Sbjct: 52 VVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFL-VKMSGDL 102
>2w2n_P Proprotein convertase subtilisin/kexin type 9; hydrolase-receptor
complex, PCSK9, proprotein converta low-density
lipoprotein receptor, EGF; 2.30A {Homo sapiens} PDB:
2w2m_P 2w2o_P 2w2p_P 2w2q_P 2xtj_P
Length = 114
Score = 28.1 bits (62), Expect = 0.37
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 65
VVLKE+ + ++ + Y++ G L GF V+ S
Sbjct: 42 VVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFL-VKMSGDL 92
>1v5i_B POIA1, IA-1=serine proteinase inhibitor; protease-inhibitor
complex, subtilisin, hydrolase-Pro binding complex;
1.50A {Pleurotus ostreatus} SCOP: d.58.3.2 PDB: 1itp_A
Length = 76
Score = 26.4 bits (58), Expect = 1.0
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFA 57
V+ K + + + + V ++ G +T + +KGFA
Sbjct: 7 VIFKNDVSEDKIRETKDEVIAEGGTITNEY-----NMPGMKGFA 45
>2p4e_P Proprotein convertase subtilisin/kexin type 9; protease, LDL
receptor, LDL, endocytosis, hydrol; 1.98A {Homo sapiens}
Length = 692
Score = 27.3 bits (60), Expect = 1.2
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
VVLKE+ + ++ + Y++ G L GF V+ S + +
Sbjct: 80 VVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFL-VKMS--GDLLELA 134
>2i9x_A Putative septation protein spovg; APC86317.1, staphylococcus
epidermidis ATCC 12228, ST genomics, PSI-2, protein
structure initiative; 1.80A {Staphylococcus
epidermidis} SCOP: d.366.1.1
Length = 87
Score = 26.3 bits (58), Expect = 1.3
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 38 KVTYVSLPKFKSTGKLKGFAFVEF 61
KVT V L K ++ G++K +
Sbjct: 5 KVTDVRLRKIQTDGRMKALVSITL 28
>2i9z_A Putative septation protein spovg; APC86317, staphylococcus
epidermidis ATCC 12228, STRU genomics, PSI-2, protein
structure initiative; 2.30A {Staphylococcus
epidermidis} SCOP: d.366.1.1
Length = 105
Score = 26.0 bits (57), Expect = 1.7
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 38 KVTYVSLPKFKSTGKLKGFAFVEF 61
KVT V L K ++ G++K +
Sbjct: 5 KVTDVRLRKIQTDGRMKALVSITL 28
>2ia9_A Putative septation protein spovg; APC85465, bacillus subtilis
subsp. subtilis STR. 168, structural genomics, PSI-2;
3.00A {Bacillus subtilis} SCOP: d.366.1.1
Length = 100
Score = 26.0 bits (57), Expect = 1.9
Identities = 6/24 (25%), Positives = 13/24 (54%)
Query: 38 KVTYVSLPKFKSTGKLKGFAFVEF 61
+VT V L + + G+++ A +
Sbjct: 5 EVTDVRLRRVNTDGRMRAIASITL 28
>1jln_A STEP-like ptpase, protein tyrosine phosphatase, receptor type, R;
PTP-SL, PTPBR7, ERK2-MAP kinase regulation, hydrolase;
1.81A {Mus musculus} SCOP: c.45.1.2 PDB: 2a8b_A
Length = 297
Score = 24.9 bits (55), Expect = 6.5
Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 10/38 (26%)
Query: 2 AELVENNKK--YG--------RVVLKEKLPPEAEHDYI 29
++ + K Y RV L+ K ++ YI
Sbjct: 51 IDIPRHGTKNRYKTILPNPLSRVCLRPKNITDSLSTYI 88
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 121
Score = 24.6 bits (53), Expect = 7.7
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ L + + + +FS +G++ ++ + G + F KE+A +AL
Sbjct: 21 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEG------IILF--KEKAKEALG 71
>1jpd_X L-Ala-D/L-Glu epimerase; enolase superfamily, muconate lactonizing
enzyme subgroup, alpha/beta barrel, structural genomics,
isomerase; 2.60A {Escherichia coli} SCOP: c.1.11.2
d.54.1.1
Length = 324
Score = 24.9 bits (55), Expect = 8.2
Identities = 8/40 (20%), Positives = 15/40 (37%)
Query: 1 MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVT 40
MA + G +LK KL + + ++ + T
Sbjct: 136 MANSASTLWQAGAKLLKVKLDNHLISERMVAIRTAVPDAT 175
>4agy_A VP1 protein; picornavirus, enterovirus, HEV-A; 6.09A {Human
coxsackievirus A7} PDB: 4agx_A
Length = 181
Score = 24.6 bits (53), Expect = 8.9
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
I + +S+ G V V++ + T KGFA
Sbjct: 3 ITNFYSRAGLVGVVNM-PVQGTSNTKGFAKWGIDIMGFV 40
>2shp_A SHP-2, SYP, SHPTP-2; tyrosine phosphatase, insulin signaling, SH2
protein; HET: CAT; 2.00A {Homo sapiens} SCOP: c.45.1.2
d.93.1.1 d.93.1.1
Length = 525
Score = 24.8 bits (54), Expect = 9.1
Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 10/38 (26%)
Query: 2 AELVENNKK--YG--------RVVLKEKLPPEAEHDYI 29
+ EN K Y RVVL + P E DYI
Sbjct: 268 GQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYI 305
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
0.314 0.132 0.389
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,745,436
Number of extensions: 88652
Number of successful extensions: 526
Number of sequences better than 10.0: 1
Number of HSP's gapped: 421
Number of HSP's successfully gapped: 232
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.4 bits)