RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3346
(79 letters)
>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 = 86.2 bits (214), Expect = 4e-24
Identities = 47/70 (67%), Positives = 52/70 (74%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
KQT SKILVRNIPFQA Q E+ ELF FGELK VRLPKKM G+G HRGFGFV
Sbjct: 4 GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 69 EFITKNEAKR 78
+FITK +AK+
Sbjct: 64 DFITKQDAKK 73
>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 = 63.5 bits (155), Expect = 2e-14
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 8 VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
V S V + K+ + +P +V+EL +FG LK L K +GL +G+ F
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAF 160
Query: 68 VEFITKNEAKR 78
E++ N +
Sbjct: 161 CEYVDINVTDQ 171
Score = 46.9 bits (112), Expect = 4e-08
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 77
++ V NIPF + + + F A L + P V + F F+EF + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 78 R 78
+
Sbjct: 66 Q 66
>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 = 61.0 bits (149), Expect = 2e-14
Identities = 13/58 (22%), Positives = 33/58 (56%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+K+ + + + + E+F +G++K + +P + + L +G+ +VEF +EA++
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 60.4 bits (147), Expect = 5e-14
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 9 KRKSSNVAK--QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 66
SS + G + +RN+ F +++ + E+ + FG+LK+VR+ + +G
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-TEHSKGCA 60
Query: 67 FVEFITKNEAKR 78
F +F+T+ A++
Sbjct: 61 FAQFMTQEAAQK 72
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 59.2 bits (144), Expect = 1e-13
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
K+ + +PF + E+EE+ KA G +K +RL +G +G +VE+ +++A +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR--AGKPKGLAYVEYENESQASQ 73
>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 = 58.8 bits (143), Expect = 2e-13
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
++ VRN+ + + + ++E+LF A+G L + P + + +GF FV F+ A +
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-TKKPKGFAFVTFMFPEHAVK 65
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 59.4 bits (144), Expect = 3e-13
Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 1/75 (1%)
Query: 3 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 62
+ + S + T + V + + + F FG++ +++P + H
Sbjct: 46 VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKH 104
Query: 63 RGFGFVEFITKNEAK 77
RGF FVEF +A
Sbjct: 105 RGFAFVEFELAEDAA 119
>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 = 57.6 bits (140), Expect = 5e-13
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
SS + V N+ ++ + +F+ +G + V +P++ + RGF FV
Sbjct: 3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH-TKAPRGFAFVR 61
Query: 70 FITKNEAKR 78
F + +A+
Sbjct: 62 FHDRRDAQD 70
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 57.7 bits (140), Expect = 6e-13
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQA 80
>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 = 57.2 bits (139), Expect = 8e-13
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ I V N+ ++++++ELF+ FG + + L K +G +GF F+ F + +A R
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-TGQSKGFAFISFHRREDAAR 72
>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 = 56.8 bits (138), Expect = 9e-13
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
T + V + + + F FG++ +++P + HRGF FVEF +A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAA 63
>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 = 59.2 bits (144), Expect = 2e-12
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
K K ++ A G +I++RN+ + ++ + E F+ FG ++ + +P + F
Sbjct: 199 KSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF 258
Query: 68 VEFITKNEAKR 78
+ F K+ A+R
Sbjct: 259 MVFENKDSAER 269
Score = 55.4 bits (134), Expect = 5e-11
Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITK 73
V+ T + + N P Q + +L + + +RLP + R F +++ +K
Sbjct: 112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT--SRRFAYIDVTSK 169
Query: 74 NEAKR 78
+A+
Sbjct: 170 EDARY 174
Score = 49.6 bits (119), Expect = 6e-09
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
+ + +LV+N+P Q++V + FK G + V + + F +EF + A
Sbjct: 38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD---SLKKNFRFARIEFARYDGA 94
Query: 77 KR 78
Sbjct: 95 LA 96
>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 = 56.1 bits (136), Expect = 2e-12
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
S K+ V + Q + +V LF+ FG + + + G +G FV+F
Sbjct: 7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKFS 64
Query: 72 TKNEAKR 78
+ EA+
Sbjct: 65 SHTEAQA 71
>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 = 57.6 bits (140), Expect = 2e-12
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 8 VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
++R K+ + +P +V+EL +FG LK L K +GL +G+ F
Sbjct: 82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAF 140
Query: 68 VEFITKNEAKRV 79
E++ N +
Sbjct: 141 CEYVDINVTDQA 152
Score = 43.8 bits (104), Expect = 4e-07
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 77
++ V NIPF + + + F A L + P V + F F+EF + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 78 RV 79
+
Sbjct: 66 QA 67
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 57.1 bits (138), Expect = 2e-12
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + V N+ ++ + +F+ +G + V +P+ + RGF FV F K +A+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-TKESRGFAFVRFHDKRDAED 104
>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 = 56.4 bits (136), Expect = 6e-12
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
G + V +I +A++ E++E F +GE+K + L +G +G+ VE+ T +A
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALA 129
>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 = 55.0 bits (133), Expect = 6e-12
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + V + + + + ELF G + +PK V +G H+G+GFVEF+++ +A
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-TGQHQGYGFVEFLSEEDADY 72
>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 = 54.6 bits (132), Expect = 7e-12
Identities = 13/74 (17%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
+ ++ ++ + +L +N+ F + E++E+F+ E++ V G +G
Sbjct: 1 SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKG 54
Query: 65 FGFVEFITKNEAKR 78
++EF ++ +A++
Sbjct: 55 IAYIEFKSEADAEK 68
>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 = 55.1 bits (133), Expect = 8e-12
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQ 78
>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 = 54.6 bits (132), Expect = 9e-12
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
G + V +I +A++ E++E F +GE+K + L +G +G+ VE+ T +A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALA 83
>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 = 9e-12
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
GS ++ +S + T ++ V NIPF+ + ++ ++F FG++ V + GS
Sbjct: 1 GSSGSSGNSESKS----TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-- 54
Query: 62 HRGFGFVEFITKNEAKR 78
+GFGFV F +A R
Sbjct: 55 -KGFGFVTFENSADADR 70
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 54.1 bits (131), Expect = 1e-11
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S + V ++ F + + +F+ FG++ + L K +G +G+GF+ F A+R
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD-TGRSKGYGFITFSDSECARR 62
>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 = 54.2 bits (131), Expect = 1e-11
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 4/76 (5%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
GS + A +I V N+P + ++E++F +G ++ + L + G
Sbjct: 4 GSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--- 60
Query: 62 HRGFGFVEFITKNEAK 77
F FVEF +A+
Sbjct: 61 -PPFAFVEFEDPRDAE 75
>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 = 53.8 bits (130), Expect = 2e-11
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S++ V N+P + E+ +LF+ +G+ V + K +GFGF+ T+ A+
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-------DKGFGFIRLETRTLAEI 66
>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 = 54.3 bits (131), Expect = 2e-11
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+TG+K+LV N+ F ++++ELF FG LK + SG G V
Sbjct: 25 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR--SGRSLGTADVH 82
Query: 70 FITKNEAKR 78
F + +A +
Sbjct: 83 FERRADALK 91
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 102
Score = 53.9 bits (130), Expect = 2e-11
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
S+ TG + +R +P++A ++++ F ++ V + G G VE
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGP--DGRVTGEADVE 61
Query: 70 FITKNEAKR 78
F T +A
Sbjct: 62 FATHEDAVA 70
>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 = 53.8 bits (130), Expect = 2e-11
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ V + + + F FG++ +++P + HRGF FVEF +A
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAA 68
>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 = 53.7 bits (129), Expect = 2e-11
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
SS + ++ + IL +N+P +E++E F FG L V LP+ VEF+
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-------GITAIVEFL 54
Query: 72 TKNEAKR 78
EA++
Sbjct: 55 EPLEARK 61
>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 = 54.5 bits (131), Expect = 3e-11
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ + V N+ ++ + +F+ +G + V +P+ + RGF FV F K +A+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-TKESRGFAFVRFHDKRDAE 126
>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 = 53.5 bits (129), Expect = 3e-11
Identities = 13/58 (22%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
++ V ++ F + + +F+ FG ++ ++L +G +G+GF+ F AK+
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE-TGRSKGYGFITFSDSECAKK 83
>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 = 53.4 bits (129), Expect = 3e-11
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 1/69 (1%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
S + K + N+P+ + ++E F+ VRLP++ +GFG+ E
Sbjct: 5 SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAE 63
Query: 70 FITKNEAKR 78
F +
Sbjct: 64 FEDLDSLLS 72
>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 = 53.4 bits (129), Expect = 3e-11
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+TG K+LV N+ F ++++ELF FG LK + SG G V
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVH 76
Query: 70 FITKNEAKR 78
F K +A +
Sbjct: 77 FERKADALK 85
>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 = 55.4 bits (134), Expect = 4e-11
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
T + + V N+P Q + EEL + FG L+ L +G +G+GF E++ K+ A
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-TGQSKGYGFAEYMKKDSAA 151
Query: 78 R 78
R
Sbjct: 152 R 152
Score = 51.1 bits (123), Expect = 1e-09
Identities = 12/70 (17%), Positives = 21/70 (30%), Gaps = 3/70 (4%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
A + V +P + + A F +L G +GF +
Sbjct: 174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ--DGQLKGFAVL 231
Query: 69 EFITKNEAKR 78
E+ T A+
Sbjct: 232 EYETAEMAEE 241
Score = 40.0 bits (94), Expect = 1e-05
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
KIL+R +P EV +L + K ++G FV + +A+
Sbjct: 22 RRKILIRGLPGDVTNQEVHDLLSDYE--------LKYCFVDKYKGTAFVTLLNGEQAEA 72
>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 = 52.7 bits (127), Expect = 4e-11
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEF 70
++ K + I V+N+PF E+ + F + + V L G+ G V F
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE--KGMPTGEAMVAF 64
Query: 71 ITKNEAKR 78
+++EA
Sbjct: 65 ESRDEATA 72
>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 = 52.6 bits (127), Expect = 4e-11
Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
SS + + +K+ V NI E+ F+ +G + + + + FV
Sbjct: 2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---------KDYAFVHME 52
Query: 72 TKNEAKR 78
+A
Sbjct: 53 RAEDAVE 59
>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 = 52.7 bits (127), Expect = 4e-11
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
SS + T + +R PF + V E + +R+ + G+ G+ FV+F
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNAHGN--KTGYIFVDFS 58
Query: 72 TKNEAKR 78
+ E K+
Sbjct: 59 NEEEVKQ 65
>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 = 52.2 bits (126), Expect = 5e-11
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ S + V N+PF +++ +F +G++ V + K + +G F+ F+ K+ A+
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKGVAFILFLDKDSAQN 73
>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 = 53.3 bits (128), Expect = 5e-11
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGF 67
KR S + G + ++ +PF+A+ V + FK ++ + + G G GF
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK--ATGEGF 71
Query: 68 VEFITKNEAKR 78
VEF + + K
Sbjct: 72 VEFRNEADYKA 82
>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 = 53.2 bits (128), Expect = 6e-11
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 1/70 (1%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
+ + + V + + ++ E+F +G + V + S RGF FV
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRRSRGFAFV 93
Query: 69 EFITKNEAKR 78
F ++AK
Sbjct: 94 YFENVDDAKE 103
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 54.1 bits (130), Expect = 6e-11
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
+TG+K+LV N+ F ++++ELF FG LK + SG G V F + +
Sbjct: 84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD--RSGRSLGTADVHFERRAD 141
Query: 76 AKR 78
A +
Sbjct: 142 ALK 144
>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 = 52.2 bits (126), Expect = 6e-11
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
GS ++ R + + + V + + ++ E+F +G + V + S
Sbjct: 1 GSSGSSGNRANPD----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRR 55
Query: 62 HRGFGFVEFITKNEAKR 78
RGF FV F ++AK
Sbjct: 56 SRGFAFVYFENVDDAKE 72
>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 = 51.7 bits (125), Expect = 7e-11
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKR 78
I V N+ + A E+E F G + V + K SG +GF ++EF K +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF--SGHPKGFAYIEFSDKESVRT 63
>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 = 52.9 bits (127), Expect = 7e-11
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 3/70 (4%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
V TG + +R +P++A ++++ F ++ V + G G V
Sbjct: 35 GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGP--DGRVTGEADV 91
Query: 69 EFITKNEAKR 78
EF T EA
Sbjct: 92 EFATHEEAVA 101
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 51.9 bits (125), Expect = 9e-11
Identities = 9/57 (15%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ + +IP+ + ++ +L G + +++ +G +G+ F+EF +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-TGRSKGYAFIEFRDLESSA 58
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 51.6 bits (124), Expect = 1e-10
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAK 77
I++RNI + + L +RL K + +RGF FV+ + +A
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQ-TQQNRGFAFVQLSSAMDAS 67
Query: 78 RV 79
++
Sbjct: 68 QL 69
>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 = 51.5 bits (124), Expect = 1e-10
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEF 70
S+ K + I V+N+PF E+ + F + + V L G+ G V F
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EKGMPTGEAMVAF 64
Query: 71 ITKNEAKR 78
+++EA
Sbjct: 65 ESRDEATA 72
>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 = 51.3 bits (123), Expect = 2e-10
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
++ + IP K+ E+ E E + V + +RGF FVE+ + A
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 77 KR 78
Sbjct: 66 AM 67
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 52.6 bits (127), Expect = 2e-10
Identities = 13/69 (18%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+ + + +L +N+ F + E++E+F+ E++ V G +G ++E
Sbjct: 89 KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKGIAYIE 142
Query: 70 FITKNEAKR 78
F ++ +A++
Sbjct: 143 FKSEADAEK 151
Score = 46.1 bits (110), Expect = 6e-08
Identities = 9/62 (14%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
T + + N+ +E++ + + +G +R FG+V+F + +
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR--TGTNRKFGYVDFESAEDL 67
Query: 77 KR 78
++
Sbjct: 68 EK 69
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 51.2 bits (123), Expect = 2e-10
Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
A + + NIP A ++++ LF+ FG + + +G F+++ T
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-------EKGCCFIKYDTH 73
Query: 74 NEAKR 78
+A
Sbjct: 74 EQAAV 78
>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 = 51.1 bits (123), Expect = 2e-10
Identities = 15/62 (24%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
++ + V NIP++A + +++++F G + RL +G +G+GF E+ +
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQET 62
Query: 76 AK 77
A
Sbjct: 63 AL 64
>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 = 52.1 bits (125), Expect = 3e-10
Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+ + + V N+ F + ++ ELF G++K + + + GF FVE
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KKTACGFCFVE 87
Query: 70 FITKNEAKR 78
+ ++ +A+
Sbjct: 88 YYSRADAEN 96
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 50.8 bits (122), Expect = 3e-10
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
K+ V N+ A + E+E F +G L+ V + + GF FVEF +A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP------PGFAFVEFEDPRDAE 51
>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 = 51.3 bits (123), Expect = 3e-10
Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 3/79 (3%)
Query: 1 MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGS 59
+E + + + V N+ + + ++E F + G + + + K S
Sbjct: 17 AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF--S 74
Query: 60 GLHRGFGFVEFITKNEAKR 78
G +G+ ++EF +N
Sbjct: 75 GHPKGYAYIEFAERNSVDA 93
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 50.7 bits (122), Expect = 3e-10
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR--GFGFVEFITKNEAK 77
S + ++N+ F + ++ +F G +K + KK +G+ GFGFVE+ +A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 78 R 78
+
Sbjct: 65 K 65
>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 = 50.3 bits (121), Expect = 4e-10
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
S + K + N+P+ + ++E F+ VRLP++ +GFG+
Sbjct: 8 HHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYA 66
Query: 69 EFITKNEAKR 78
EF +
Sbjct: 67 EFEDLDSLLS 76
>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 = 50.8 bits (122), Expect = 4e-10
Identities = 12/61 (19%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ + +RN+P++ E+ ++F +G ++ +R+ + RG +V + +AK
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN----TPETRGTAYVVYEDIFDAK 61
Query: 78 R 78
Sbjct: 62 N 62
>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 = 50.4 bits (121), Expect = 4e-10
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
SS + K+ + IP + +++ LF+ FG++ + + K +G+H+G F+ +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-TGMHKGCAFLTYC 63
Query: 72 TKNEAKR 78
+ A +
Sbjct: 64 ERESALK 70
>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 = 50.5 bits (121), Expect = 4e-10
Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 3/71 (4%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGF 67
+ NIPF + +V + + + V + +G G
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQAL 61
Query: 68 VEFITKNEAKR 78
V+F +++A++
Sbjct: 62 VQFKNEDDARK 72
>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 = 5e-10
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 2 GSEATTVKRKSSNVAKQTGSK---ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG 58
GS T + + +V Q+ K + I + + F FG++ +R+
Sbjct: 4 GSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---- 59
Query: 59 SGLHRGFGFVEFITKNEAKR 78
+G+ FV F T A
Sbjct: 60 ---EKGYSFVRFSTHESAAH 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 = 51.0 bits (122), Expect = 5e-10
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+ K+ V N+ ++E+E F +G L+ V + + GF FVE
Sbjct: 63 HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN------PPGFAFVE 116
Query: 70 FITKNEAK 77
F +A
Sbjct: 117 FEDPRDAA 124
>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 = 50.2 bits (120), Expect = 5e-10
Identities = 9/69 (13%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
++++ ++++V +P ++++ + G++ + + + G G VE
Sbjct: 5 SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 56
Query: 70 FITKNEAKR 78
F+ K +
Sbjct: 57 FVRKEDMTY 65
>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 = 50.4 bits (121), Expect = 5e-10
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 1/77 (1%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
G E + SS + + ++N+ + + ++ LF F E K + +M +G
Sbjct: 7 GEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGR 65
Query: 62 HRGFGFVEFITKNEAKR 78
RG F+ F K A +
Sbjct: 66 MRGQAFITFPNKEIAWQ 82
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 50.0 bits (120), Expect = 5e-10
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 9/68 (13%)
Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
+ + +++ VR P ++SE+ E+F FG +K V++ GF FVEF
Sbjct: 22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---------GFAFVEF 72
Query: 71 ITKNEAKR 78
A +
Sbjct: 73 EEAESAAK 80
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 49.9 bits (120), Expect = 6e-10
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
K+ V + F + +E++F +G++ V + K + RGFGFV F ++AK
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSRGFGFVTFENIDDAKD 69
>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 = 49.6 bits (119), Expect = 7e-10
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
++ + V N+ + ++ + ELF G L V + K G + FGFV F
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD--REGKPKSFGFVCFKHPESV 70
Query: 77 KR 78
Sbjct: 71 SY 72
>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 = 50.3 bits (120), Expect = 8e-10
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 3 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGL 61
+ + R S++ + +R +PF + E+ + F + + LP G
Sbjct: 25 TGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-- 82
Query: 62 HRGFGFVEFITKNEAKR 78
G FV+F ++ A++
Sbjct: 83 ITGEAFVQFASQELAEK 99
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 49.9 bits (119), Expect = 9e-10
Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 6/81 (7%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMV 57
S T + ++K+ + +R +PF A EV F + + +
Sbjct: 5 SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64
Query: 58 GSGLHRGFGFVEFITKNEAKR 78
G G FV F + A+
Sbjct: 65 GR--PTGDAFVLFACEEYAQN 83
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 49.7 bits (119), Expect = 1e-09
Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 15/83 (18%)
Query: 2 GSEATTVKRKSSNVAKQT-----GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKK 55
GS ++K ++SNV + S++ + N+ K+S+VE +F +G + +
Sbjct: 4 GSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--- 60
Query: 56 MVGSGLHRGFGFVEFITKNEAKR 78
H+G+ FV++ + A+
Sbjct: 61 ------HKGYAFVQYSNERHARA 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 = 49.4 bits (118), Expect = 1e-09
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ V +PF A +++V + F + V L K G + G G V+F++ +
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH--VGRNNGNGLVKFLSPQDTFE 71
>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 = 48.7 bits (117), Expect = 1e-09
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 9/57 (15%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
K+ + N+P +A + E+ LF+ +G++ + K +GFV K A+
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK---------NYGFVHIEDKTAAE 56
>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 = 50.2 bits (121), Expect = 1e-09
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 8 VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
KR + KI V I + E EE F +G + +L +G RGFGF
Sbjct: 75 PKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGF 133
Query: 68 VEFITKNEAKRV 79
V + + + RV
Sbjct: 134 VTYDSADAVDRV 145
Score = 44.4 bits (106), Expect = 2e-07
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
K+ + + + + + E F +G + +++ K +G RGFGF+ F + V
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA-TGRSRGFGFLSFEKPSSVDEV 61
>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 = 49.7 bits (119), Expect = 1e-09
Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 1 MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
+ + N ++V IP + ++ +LF+ +G ++ V++ +
Sbjct: 23 QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-TR 81
Query: 61 LHRGFGFVEFITKNEAKR 78
RG+GFV+F + + A++
Sbjct: 82 QSRGYGFVKFQSGSSAQQ 99
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 48.9 bits (117), Expect = 2e-09
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
+ K ++ V NIPF+ + ++ ++F FG++ V + GS +GFGFV
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFV 74
Query: 69 EFITKNEAKR 78
F +A R
Sbjct: 75 TFENSADADR 84
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 48.3 bits (116), Expect = 2e-09
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
+I VRN+PF +++ F G + + + + +G +G G V+F +
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI---KMENGKSKGCGVVKFESPEV 60
Query: 76 AKR 78
A+R
Sbjct: 61 AER 63
>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 = 47.9 bits (115), Expect = 2e-09
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
I V N+ + A +V+ELF FG++ V+L + +GFGFVE ++ ++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEMQEESVSE 57
>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 = 48.7 bits (116), Expect = 2e-09
Identities = 9/69 (13%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+ ++++ ++++V +P ++++ + G++ + + + G G VE
Sbjct: 6 GRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 57
Query: 70 FITKNEAKR 78
F+ K +
Sbjct: 58 FVRKEDMTY 66
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 48.5 bits (116), Expect = 2e-09
Identities = 9/59 (15%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
++ + +++ ++++ + +GE++ V + + H G V F + AK
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR-TRKHLGLARVLFTSTRGAKE 63
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 49.5 bits (119), Expect = 3e-09
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
S K+ + I + ++++ +F +FG+++ R+ + GL RG FV
Sbjct: 84 PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP--DGLSRGCAFV 141
Query: 69 EFITKNEAKR 78
F T+ A+
Sbjct: 142 TFTTRAMAQT 151
Score = 48.4 bits (116), Expect = 8e-09
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRV 79
K+ V +P + ++ ELF+ +G + + + + + +G FV F T+ A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>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 = 48.5 bits (116), Expect = 3e-09
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A + GS + V N+ ++ +++E+F G + + + G RG G V F E
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED--KDGKSRGIGTVTFEQSIE 68
Query: 76 AKR 78
A +
Sbjct: 69 AVQ 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 = 47.6 bits (114), Expect = 3e-09
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 9/66 (13%)
Query: 13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 72
S+ + KI V N+ E+ LF+ G + + + + FV
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECD---------VVKDYAFVHMEK 52
Query: 73 KNEAKR 78
+ +AK
Sbjct: 53 EADAKA 58
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 49.6 bits (119), Expect = 3e-09
Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
++I V ++ +++ +F+AFG++K L + +G H+G+GF+E+ ++
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQSSQD 182
Score = 47.3 bits (113), Expect = 3e-08
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A S++ V +I ++ + + + F FG +K + + V + H+GF FVE+
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV-TMKHKGFAFVEYEVPEA 82
Query: 76 AKRV 79
A+
Sbjct: 83 AQLA 86
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 48.1 bits (114), Expect = 6e-09
Identities = 12/81 (14%), Positives = 23/81 (28%), Gaps = 5/81 (6%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVG 58
G + G + +R +P+ +V+ V G
Sbjct: 26 GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG 85
Query: 59 SGLHRGFGFVEFITKNEAKRV 79
G FVE ++++ K
Sbjct: 86 R--QSGEAFVELGSEDDVKMA 104
>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 = 48.7 bits (117), Expect = 6e-09
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ ++V +P Q E LF + GE++ +L + + +G G+GFV +I +A++
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYIDPKDAEKA 60
Score = 43.3 bits (103), Expect = 5e-07
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 8 VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
V + A + + V +P Q E+E+LF +G + R+ +G+ RG GF
Sbjct: 76 VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGF 134
Query: 68 VEFITKNEAKRV 79
+ F + EA+
Sbjct: 135 IRFDKRIEAEEA 146
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 47.2 bits (113), Expect = 6e-09
Identities = 9/60 (15%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 20 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S++ + N+P + + ++ +F +G + + + FGF++F +
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 60
>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 = 48.3 bits (116), Expect = 6e-09
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ ++V +P E+ LF+A G + R+ + +G G+ FV+F ++ +++R
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-TGYSYGYAFVDFTSEMDSQR 60
Score = 44.1 bits (105), Expect = 2e-07
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 1/71 (1%)
Query: 8 VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
V + + V N+P +++ +F +G + + + + +G RG F
Sbjct: 77 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAF 135
Query: 68 VEFITKNEAKR 78
V + + EA+
Sbjct: 136 VRYNKREEAQE 146
>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 = 47.0 bits (112), Expect = 6e-09
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S ILV+N+P + EV +L K + K ++ FV + +A+
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD--------LKYCYVDRNKRTAFVTLLNGEQAQN 55
>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 = 47.7 bits (114), Expect = 7e-09
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 2/65 (3%)
Query: 15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 74
V K+ + + + + ++ +F G + V L K + RGF F+ F
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR--TSKSRGFAFITFENPA 59
Query: 75 EAKRV 79
+AK
Sbjct: 60 DAKNA 64
>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 = 46.8 bits (112), Expect = 7e-09
Identities = 10/59 (16%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S + +R + ++ +L + +G++ + + +G+GFV+F + + A++
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-TNKCKGYGFVDFDSPSAAQK 62
>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 = 47.2 bits (113), Expect = 7e-09
Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ V N+ + + +LF G K ++ + + + FVEF +A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS---NDPYCFVEFYEHRDAAA 70
>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 = 46.9 bits (112), Expect = 8e-09
Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
GS ++ S +K +++ N+ + A + ++E+F+ +++P+ +G
Sbjct: 1 GSSGSSGNSTWSGESK----TLVLSNLSYSATEETLQEVFEKATF---IKVPQNQ--NGK 51
Query: 62 HRGFGFVEFITKNEAKR 78
+G+ F+EF + +AK
Sbjct: 52 SKGYAFIEFASFEDAKE 68
>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 = 47.0 bits (112), Expect = 8e-09
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 4/72 (5%)
Query: 9 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFG 66
S N + +R +PF + E+ + F + + LP G G
Sbjct: 3 SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR--STGEA 60
Query: 67 FVEFITKNEAKR 78
FV+F ++ A++
Sbjct: 61 FVQFASQEIAEK 72
>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 = 47.2 bits (112), Expect = 8e-09
Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 5/64 (7%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
G + +R +P+ +V+ + V G G FVE ++++
Sbjct: 16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR--QSGEAFVELESEDD 73
Query: 76 AKRV 79
K
Sbjct: 74 VKLA 77
>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 = 46.9 bits (112), Expect = 9e-09
Identities = 9/60 (15%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 20 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S++ + N+P + + ++ +F +G + + + FGF++F +
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 72
>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 = 48.3 bits (114), Expect = 1e-08
Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ ++ P A +++E + G++ +++ + +G FV F + AK+
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKK 165
>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 = 48.4 bits (116), Expect = 1e-08
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
V ++ ++ + E F G + +R+ + M+ + G+ +V F +A+R
Sbjct: 20 VGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-TRRSLGYAYVNFQQPADAERA 73
Score = 44.2 bits (105), Expect = 4e-07
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
++ ++ K I ++N+ + + F AFG + ++ + +G+GFV
Sbjct: 93 QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV---VCDENGSKGYGFVH 149
Query: 70 FITKNEAKR 78
F T+ A+R
Sbjct: 150 FETQEAAER 158
>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 = 46.9 bits (112), Expect = 1e-08
Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 1/78 (1%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
G + + ++ + + + + ++E+ F A G+++ VR+ S
Sbjct: 7 GKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-SRR 65
Query: 62 HRGFGFVEFITKNEAKRV 79
+G +VEF
Sbjct: 66 SKGIAYVEFCEIQSVPLA 83
>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 = 46.5 bits (111), Expect = 1e-08
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+K+ + N+ ++ +LF ++ L G+ FV++ +N A R
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-------LLKSGYAFVDYPDQNWAIR 59
>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 = 48.1 bits (115), Expect = 1e-08
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
A + + A T KI V I ++ + + F+ +G+++ + + GSG RG
Sbjct: 89 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRG 147
Query: 65 FGFVEFITKNEAKRV 79
F FV F + ++
Sbjct: 148 FAFVTFDDHDSVDKI 162
Score = 43.1 bits (102), Expect = 9e-07
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
K +S +Q K+ + + F+ + F+ +G L + + + RGFGFV
Sbjct: 3 KSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSRGFGFV 60
Query: 69 EFITKNEAKRV 79
+ T E
Sbjct: 61 TYATVEEVDAA 71
>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 = 46.4 bits (110), Expect = 1e-08
Identities = 8/63 (12%), Positives = 19/63 (30%), Gaps = 5/63 (7%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
I + +P+ +V F + G RG +E ++ +
Sbjct: 10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK--RRGDALIEMESEQD 67
Query: 76 AKR 78
++
Sbjct: 68 VQK 70
>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 = 46.5 bits (111), Expect = 2e-08
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 10/84 (11%)
Query: 2 GSEATT-VKRKSSNV-----AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 55
GS ++ +K +Q + + + N+P + E+E + K FG++ R+
Sbjct: 1 GSSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRI--- 57
Query: 56 MV-GSGLHRGFGFVEFITKNEAKR 78
+ SG RG GF + + +
Sbjct: 58 LRDSSGTSRGVGFARMESTEKCEA 81
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 45.1 bits (107), Expect = 5e-08
Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 8/80 (10%)
Query: 1 MGSEATTVKRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 59
MG + K S ++ +R + ++++ E + FG + +V +
Sbjct: 1 MGHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP----- 55
Query: 60 GLHRGFGFVEFITKNEAKRV 79
+ VEF A
Sbjct: 56 --KKRQALVEFEDVLGACNA 73
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 45.1 bits (107), Expect = 5e-08
Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 4/72 (5%)
Query: 7 TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 66
+ S +Q K+ +RNIP + ++ L +G ++ V +
Sbjct: 2 SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ----VNTDSETAVV 57
Query: 67 FVEFITKNEAKR 78
V + +K++A++
Sbjct: 58 NVTYSSKDQARQ 69
>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 = 45.4 bits (108), Expect = 5e-08
Identities = 13/77 (16%), Positives = 32/77 (41%), Gaps = 1/77 (1%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
G ++ S G+ + + ++P + ++ ++F FG + ++ + L
Sbjct: 7 GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ-TNL 65
Query: 62 HRGFGFVEFITKNEAKR 78
+ FGFV + A+
Sbjct: 66 SKCFGFVSYDNPVSAQA 82
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex;
1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 44.9 bits (107), Expect = 5e-08
Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
K + + V I + ++E+ F +G +K V++ +G+ +G+GFV F +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVD 62
Query: 76 AKRV 79
+++
Sbjct: 63 VQKI 66
>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 = 44.9 bits (107), Expect = 5e-08
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
GS ++ S Q + V+ + + E L ++F R+ +G
Sbjct: 1 GSSGSSGPNARS----QPSKTLFVKGLSEDTTE---ETLKESFDGSVRARIVTDRE-TGS 52
Query: 62 HRGFGFVEFITKNEAK 77
+GFGFV+F ++ +AK
Sbjct: 53 SKGFGFVDFNSEEDAK 68
>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 = 45.0 bits (107), Expect = 5e-08
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 21 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
KIL VRN+ + +E+ F R+ K R + FV F + +A
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVE 66
>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 = 44.9 bits (107), Expect = 5e-08
Identities = 8/57 (14%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + N+ +E++ + + G+ R FG+V+F + + ++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN--RKFGYVDFESAEDLEK 73
>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 = 44.3 bits (105), Expect = 7e-08
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 77
++ V NIPF + + + F A L + P V + F F+EF + +E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 78 R 78
+
Sbjct: 68 Q 68
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 44.7 bits (106), Expect = 8e-08
Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFV 68
+ G + + ++P + +++ F FG + ++ + + L + FGFV
Sbjct: 31 AGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV---FIDKQTSLSKCFGFV 87
Query: 69 EFITKNEAKR 78
F + A+
Sbjct: 88 SFDNPDSAQV 97
>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 = 45.2 bits (108), Expect = 9e-08
Identities = 8/55 (14%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
V N+ + +++ F+ G + +++ + + + FVE+ ++A
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDK--NNKNVNYAFVEYHQSHDANIA 57
Score = 45.2 bits (108), Expect = 1e-07
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 1/69 (1%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
+S + + V ++ + FK F + M +G RG+GFV
Sbjct: 77 FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ-TGSSRGYGFVS 135
Query: 70 FITKNEAKR 78
F ++++A+
Sbjct: 136 FTSQDDAQN 144
>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 = 44.1 bits (105), Expect = 9e-08
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 3/70 (4%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
+ + + V+N+ + + F FG + ++ M+ G +GFGFV
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV---MMEGGRSKGFGFV 60
Query: 69 EFITKNEAKR 78
F + EA +
Sbjct: 61 CFSSPEEATK 70
>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 = 44.2 bits (105), Expect = 1e-07
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 9/67 (13%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
S + + VRN+ + +E+ F FG+L+ V+ K + F+ F
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---------DYAFIHFD 53
Query: 72 TKNEAKR 78
++ A +
Sbjct: 54 ERDGAVK 60
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.3 bits (105), Expect = 1e-07
Identities = 10/58 (17%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ ++ P A +++E + G++ +++ + +G FV F + AK+
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKF 68
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 43.8 bits (104), Expect = 1e-07
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
V N+PF Q +++ +FK ++ VRL + + +GF +VEF + K
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKE 71
>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 = 44.3 bits (105), Expect = 1e-07
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ V ++ + +++ F FG + R+ K M +G +G+GFV F K +A+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAEN 72
>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 = 43.4 bits (103), Expect = 2e-07
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
+ S+ GSK+ V E+++ F +GE+ V +PK R F FV F
Sbjct: 2 RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTF 55
Query: 71 ITKNEAKRV 79
A+ +
Sbjct: 56 ADDKVAQSL 64
>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 = 43.3 bits (103), Expect = 2e-07
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ V ++ + FK F + M +G RG+GFV F ++++A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQN 58
>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 = 43.2 bits (102), Expect = 2e-07
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 12 SSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
S + K + S ++ VR + ++++ E + FG + +V + + VEF
Sbjct: 6 SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-------FKRQALVEF 58
Query: 71 ITKNEAKR 78
+ AK
Sbjct: 59 ENIDSAKE 66
>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 = 43.4 bits (102), Expect = 3e-07
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 9 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
+ + S+++ +R +P + EV L FG++ + + K + F
Sbjct: 19 SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAF 71
Query: 68 VEFITKNEAKRV 79
+E T+ A +
Sbjct: 72 IEMNTEEAANTM 83
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 42.8 bits (101), Expect = 5e-07
Identities = 14/65 (21%), Positives = 22/65 (33%), Gaps = 9/65 (13%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFIT 72
+ I V+ + V + FK G +K + L +G +G V F
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-TGKLKGEATVSFDD 66
Query: 73 KNEAK 77
AK
Sbjct: 67 PPSAK 71
>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 = 43.9 bits (103), Expect = 5e-07
Identities = 8/59 (13%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + N+ + ++ E + G ++ ++ + +G +GF V ++ +K+
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKK 127
>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 = 43.9 bits (104), Expect = 6e-07
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEA 76
G+ + V+N+ +E+ F FG ++ + +V G G GFVEF K A
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV---VVDDRGRATGKGFVEFAAKPPA 150
Query: 77 KRV 79
++
Sbjct: 151 RKA 153
Score = 41.2 bits (97), Expect = 5e-06
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
++ V N+P + + + LF+ +GE V + + RGFGF+ ++ A+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-------RGFGFIRLESRTLAEIA 74
>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 = 41.8 bits (99), Expect = 6e-07
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
S + V + E+ E F +G++ V +PK R F FV F
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQI 54
Query: 76 AKRV 79
A+ +
Sbjct: 55 AQSL 58
>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 = 41.9 bits (99), Expect = 7e-07
Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 7/75 (9%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV---GSGLH 62
+ + + I V+ + V + FK G +K P + +G
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 63 RGFGFVEFITKNEAK 77
+G V F AK
Sbjct: 63 KGEATVSFDDPPSAK 77
>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 = 43.5 bits (102), Expect = 7e-07
Identities = 12/73 (16%), Positives = 29/73 (39%), Gaps = 1/73 (1%)
Query: 6 TTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF 65
+T ++ + N + + + N P + + E+ G + + K G
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV-KVFSGKSERSSS 167
Query: 66 GFVEFITKNEAKR 78
G +E+ +K++A
Sbjct: 168 GLLEWDSKSDALE 180
Score = 31.6 bits (71), Expect = 0.014
Identities = 10/60 (16%), Positives = 19/60 (31%), Gaps = 7/60 (11%)
Query: 20 GSKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
++V + + V +F +G ++ V+ K G VE R
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS------KPGAAMVEMADGYAVDR 57
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 41.8 bits (98), Expect = 8e-07
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 21 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S+++ +R +P + EV L FG++ + + K + F+E T+ A
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAFIEMNTEEAANT 67
>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 = 42.0 bits (99), Expect = 9e-07
Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 11/83 (13%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV 57
GS ++ S I V+ + ++ + FK G +K P +
Sbjct: 1 GSSGSSGDPDED----SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY 56
Query: 58 ---GSGLHRGFGFVEFITKNEAK 77
+G +G V + AK
Sbjct: 57 LDKETGKPKGDATVSYEDPPTAK 79
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 42.6 bits (100), Expect = 9e-07
Identities = 10/80 (12%), Positives = 31/80 (38%), Gaps = 5/80 (6%)
Query: 3 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV---GS 59
+ T + + + + + V + + ++ ++ ++ G V L K +
Sbjct: 38 NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL--KFAENRAN 95
Query: 60 GLHRGFGFVEFITKNEAKRV 79
G +G+ V ++N ++
Sbjct: 96 GQSKGYAEVVVASENSVHKL 115
>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 = 41.4 bits (98), Expect = 1e-06
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
SS + +KI V IP ++E+ E FK FG + V + RGFGF+ F
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA-EKQRPRGFGFITFE 60
Query: 72 TKNEAKRV 79
+ +
Sbjct: 61 DEQSVDQA 68
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 41.4 bits (97), Expect = 1e-06
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 6/78 (7%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
GS ++ + + V N+P A+ S+++ + G +P ++ G
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGS-----VPLRLTWQG- 54
Query: 62 HRGFGFVEFITKNEAKRV 79
R F+ + A++
Sbjct: 55 PRRRAFLHYPDSAAAQQA 72
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 41.0 bits (97), Expect = 1e-06
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + V ++ + + + F FG + R+ K M +G +G+GFV F K +A+
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAEN 63
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 41.4 bits (97), Expect = 1e-06
Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 6/70 (8%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFV 68
+ +I ++N+P ++++L + E F V + G G +
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSS-----VNTRDFDGTGAL 72
Query: 69 EFITKNEAKR 78
EF ++
Sbjct: 73 EFPSEEILVE 82
>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 = 41.1 bits (97), Expect = 2e-06
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 25 VRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ N+ + K+ E+++ +F FG++ + + + S RG FV F + A
Sbjct: 13 INNLNEKIKKDELKKSLHAIFSRFGQILDILVSR----SLKMRGQAFVIFKEVSSATN 66
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 40.8 bits (96), Expect = 2e-06
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 6/58 (10%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ V P +++ E F AFG + V + K F VE + V
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD------KGVFAIVEMGDVGAREAV 61
>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 = 41.0 bits (96), Expect = 2e-06
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 11 KSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
S + S++L +R +P + ++EV L FG++ + + K + F+E
Sbjct: 5 SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-------GKNQAFLE 57
Query: 70 FITKNEAKRV 79
T+ A +
Sbjct: 58 LATEEAAITM 67
>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 = 42.5 bits (99), Expect = 2e-06
Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ V + + +S++ F+ +G +K + + SG RG+ F+E+ + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVY-SKRSGKPRGYAFIEYEHERDMHS 159
>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 = 40.3 bits (95), Expect = 2e-06
Identities = 9/54 (16%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
V + ++++ F FGE++ + + ++ + F++F T+ A+
Sbjct: 17 VGGLGDTITETDLRNHFYQFGEIRTITVVQR-------QQCAFIQFATRQAAEV 63
>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 = 40.3 bits (95), Expect = 2e-06
Identities = 8/59 (13%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + N+ + ++ E + G ++ ++ + +G +GF V ++ +K+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKK 60
>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 = 40.5 bits (95), Expect = 4e-06
Identities = 10/63 (15%), Positives = 20/63 (31%), Gaps = 9/63 (14%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A + G+ + V + + F FG + + + R FV +
Sbjct: 35 APRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMES 85
Query: 76 AKR 78
A +
Sbjct: 86 ADQ 88
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 39.9 bits (94), Expect = 4e-06
Identities = 7/54 (12%), Positives = 20/54 (37%), Gaps = 7/54 (12%)
Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
V + + + F FG ++ + K F ++++ + + A+
Sbjct: 22 VGGLGPNTSLAALAREFDRFGSIRTIDHVK-------GDSFAYIQYESLDAAQA 68
>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 = 39.9 bits (94), Expect = 5e-06
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
I ++N+ + + F AFG + K + +G+GFV F T+ A+R
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGN---ILSCKVVCDENGSKGYGFVHFETQEAAER 60
>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 = 39.6 bits (93), Expect = 6e-06
Identities = 12/68 (17%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFI 71
S+ + + + + ++ ++ + F GE + V++ + + +G+ G+ FVEF
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL-TGIPAGYCFVEFA 60
Query: 72 TKNEAKRV 79
A++
Sbjct: 61 DLATAEKC 68
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 39.3 bits (92), Expect = 9e-06
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 20 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
I+V P + + LF G++ + P +G +GF FVE +
Sbjct: 6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA-TGKTKGFLFVECGSM 64
Query: 74 NEAKR 78
N+AK+
Sbjct: 65 NDAKK 69
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 38.6 bits (90), Expect = 2e-05
Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 9/65 (13%)
Query: 20 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
S I+V N+P + ++ + ++F FG++ P++ G +G+ F+E+ +
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASP 71
Query: 74 NEAKR 78
A
Sbjct: 72 AHAVD 76
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 38.7 bits (90), Expect = 2e-05
Identities = 11/79 (13%), Positives = 30/79 (37%), Gaps = 8/79 (10%)
Query: 4 EATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE----VEELFKAFGELKFVRLPKKMVGS 59
+ S+ + +L+ NI + + + + L + G++ + + S
Sbjct: 13 HMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL----S 68
Query: 60 GLHRGFGFVEFITKNEAKR 78
+ G ++ F T+ A+
Sbjct: 69 DDNSGKAYIVFATQESAQA 87
>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 = 38.4 bits (89), Expect = 2e-05
Identities = 7/56 (12%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + ++++ + + G + + +P ++ + F + T E+KR
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-------NKPYSFARYRTTEESKR 78
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 37.8 bits (88), Expect = 2e-05
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 9/64 (14%)
Query: 21 SKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 74
S I+V N+P + ++ + ++F FG++ P++ G +G+ F+E+ +
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASPA 58
Query: 75 EAKR 78
A
Sbjct: 59 HAVD 62
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 37.1 bits (87), Expect = 3e-05
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
KI V + + ++ E F FGE++ + LP + RGF F+ F + K++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD-NKTNKRRGFCFITFKEEEPVKKI 57
>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 = 38.7 bits (89), Expect = 5e-05
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 23 ILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
I + N+ + K+ E+++ +F FG++ + + + S RG FV F + A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR----SLKMRGQAFVIFKEVSSATN 67
Score = 37.5 bits (86), Expect = 1e-04
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 6/54 (11%)
Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ N+P + + + LF F K VRL FVEF + +A
Sbjct: 212 LTNLPEETNELMLSMLFNQFPGFKEVRLVPG------RHDIAFVEFDNEVQAGA 259
>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 = 37.3 bits (87), Expect = 5e-05
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 1 MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
M TV + K+ K+ + + F+ + + ++ +G+L + + S
Sbjct: 8 MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV-MRDPASK 66
Query: 61 LHRGFGFVEFITKNEAKRV 79
RGFGFV F + E
Sbjct: 67 RSRGFGFVTFSSMAEVDAA 85
>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 = 36.8 bits (86), Expect = 6e-05
Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 78
S I + N+ + + + + F AFG + ++ PK M +G +G+ F+ F + + +
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
>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 = 37.1 bits (86), Expect = 7e-05
Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 5/59 (8%)
Query: 25 VRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 78
V + + EV E F FG++ V + GS +V +I +A R
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALR 78
>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 = 37.1 bits (86), Expect = 1e-04
Identities = 8/63 (12%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMVGSGLHRGFGFVEFITKNE 75
+I V+N+ ++ +++ +F + + + + +++ G +G F+ +
Sbjct: 45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104
Query: 76 AKR 78
A +
Sbjct: 105 AAK 107
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 36.1 bits (84), Expect = 1e-04
Identities = 7/43 (16%), Positives = 13/43 (30%), Gaps = 7/43 (16%)
Query: 36 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ F FG + + + R FV + A +
Sbjct: 29 LLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMESADQ 64
>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 = 36.0 bits (84), Expect = 1e-04
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
A Q S ++V +P++ + +++E F FGE+ V++ KK + +G +GFGFV
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHSKGFGFVR 63
Query: 70 FITKNEAKRV 79
F +V
Sbjct: 64 FTEYETQVKV 73
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif,
RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2adb_A
Length = 164
Score = 36.6 bits (84), Expect = 2e-04
Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 11 KSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFG 66
+ +A S +L V N+ + + ++F FG LK + K +
Sbjct: 34 VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN------QFQA 87
Query: 67 FVEFITKNEAKR 78
+++ A+
Sbjct: 88 LLQYADPVSAQH 99
>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 = 35.2 bits (82), Expect = 2e-04
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
K+ V + + + ++++ F FGE+ + K +G RGFGF+ F ++V
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI-KMDPNTGRSRGFGFILFKDAASVEKV 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 = 35.3 bits (82), Expect = 3e-04
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
+G K+ + + +Q Q + E F FGE+K + + + RGFGFV F+ +
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAG 79
Query: 76 AKRV 79
+V
Sbjct: 80 VDKV 83
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 34.8 bits (81), Expect = 3e-04
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
KI V + +V+ F+ FG++ L + HRGFGFV F +++ ++V
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-TTNRHRGFGFVTFESEDIVEKV 57
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 35.4 bits (81), Expect = 3e-04
Identities = 13/80 (16%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 2 GSEATTVKRKSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG 58
GS + R + G+K+L ++N + + + G+++ + + K+
Sbjct: 4 GSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--- 60
Query: 59 SGLHRGFGFVEFITKNEAKR 78
+ VEF + A++
Sbjct: 61 ---NGIQAMVEFESVLCAQK 77
>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 = 35.0 bits (81), Expect = 4e-04
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 78
+KI V +P+ + + + F+ FG+++ + + +G RG+GFV + A+R
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV---ITDRQTGKSRGYGFVTMADRAAAER 74
Query: 79 V 79
Sbjct: 75 A 75
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 35.3 bits (81), Expect = 4e-04
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRV 79
K+ V +P + E+ F+ FG L K +G+ F+ F ++ + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 34.4 bits (80), Expect = 4e-04
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
K+ + + +Q Q + E F FGE+K + + + RGFGFV F+ + +V
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAGVDKV 58
>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 = 34.9 bits (80), Expect = 4e-04
Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSG 60
G + + + ++ G I + N+P S V +L + +G++K L +
Sbjct: 7 GKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------ 60
Query: 61 LHRGFGFVEFITKNEAKRV 79
+ F+E T+ +A +
Sbjct: 61 -MKSQAFIEMETREDAMAM 78
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 35.0 bits (80), Expect = 8e-04
Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ + NIP + +++ LF + G +K + +K R ++ + EA +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMGSVEEAVQ 204
Score = 34.2 bits (78), Expect = 0.002
Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 20 GSKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
S +LV N+ P + + LF +G+++ V++ + V+ N+A+
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK------KENALVQMADGNQAQL 87
>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 = 34.5 bits (79), Expect = 0.001
Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 25 VRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ NIP + +++ LF + G +K + +K R ++ + EA +
Sbjct: 125 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMGSVEEAVQ 173
Score = 33.3 bits (76), Expect = 0.003
Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 23 ILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+LV N+ P + + LF +G+++ V++ + V+ N+A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK------KENALVQMADGNQAQL 56
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 33.8 bits (77), Expect = 0.002
Identities = 10/70 (14%), Positives = 26/70 (37%), Gaps = 8/70 (11%)
Query: 12 SSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
+ +A S +L V N+ + + ++F FG + + K ++ +
Sbjct: 17 DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALL 71
Query: 69 EFITKNEAKR 78
++ A+
Sbjct: 72 QYADPVSAQH 81
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 33.6 bits (76), Expect = 0.003
Identities = 9/53 (16%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 26 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+++ +S + +F G++ +R + + GFV+F + A+
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVES-------KNCGFVKFKYQANAEF 194
>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 = 32.2 bits (74), Expect = 0.004
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
K+ V + + Q + F +GE+ + K + RGFGFV+F N V
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI-MKDKTTNQSRGFGFVKFKDPNCVGTV 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 = 31.0 bits (69), Expect = 0.027
Identities = 12/77 (15%), Positives = 28/77 (36%), Gaps = 8/77 (10%)
Query: 6 TTVKRKSSN---VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGL 61
TT R ++ T + I + + EV+ L + + + LP++++ +
Sbjct: 271 TT--RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 62 HRGFGFVEFITKNEAKR 78
E I ++
Sbjct: 329 RLS-IIAESI-RDGLAT 343
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 29.6 bits (67), Expect = 0.038
Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 38 EELFKAFGELKF--VRLPKKMV-GSGLHRGFGFVEFITKNEAKR 78
L++ F + + R K ++ +G+ +G+GFV+F + E KR
Sbjct: 24 GMLYEFFVK-VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKR 66
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 26.5 bits (58), Expect = 0.70
Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 14/67 (20%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAF-----GELKFVRLPKKMVGSGLHRGFGFVEFIT 72
G + VR +P + F+ G + + G + F
Sbjct: 6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL---------GCGGVLTFRE 56
Query: 73 KNEAKRV 79
+A+RV
Sbjct: 57 PADAERV 63
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 23.6 bits (50), Expect = 6.6
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 34 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ + L + +GE+ + L K G+ + VEF T A+
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSSKKPGTAV------VEFATVKAAELA 70
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.133 0.358
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: 1,089,540
Number of extensions: 53909
Number of successful extensions: 482
Number of sequences better than 10.0: 1
Number of HSP's gapped: 312
Number of HSP's successfully gapped: 194
Length of query: 79
Length of database: 6,701,793
Length adjustment: 48
Effective length of query: 31
Effective length of database: 5,361,585
Effective search space: 166209135
Effective search space used: 166209135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.4 bits)