RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15515
(242 letters)
>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 = 104 bits (261), Expect = 5e-29
Identities = 38/90 (42%), Positives = 60/90 (66%), Gaps = 3/90 (3%)
Query: 34 NAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDS 93
+ P+ G ++P VFVGGI E E+ F++YG VK+VKI+ DR G+SKGYGF++F +
Sbjct: 1 SLPE-GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
Query: 94 EEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
+ + +++ + I F K+L + PAI+KQ
Sbjct: 60 DVDVQKIVE--SQINFHGKKLKLGPAIRKQ 87
>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 = 90.1 bits (224), Expect = 2e-23
Identities = 29/109 (26%), Positives = 54/109 (49%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
P ++F+GG+ T E L +F ++G + +V ++ DR S+G+ FITF++ +AK K
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 103 DSDNIMFKEKRLNIAPAIKKQGFTGTYDSLPTVTSPVPPVPTSNMYYHN 151
D + K + + A K +G P + P + ++H+
Sbjct: 67 DMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHHH 115
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 86.6 bits (215), Expect = 4e-22
Identities = 21/77 (27%), Positives = 45/77 (58%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
++F+ G+ + T++EL E+ +G VK +++V +RAG KG ++ +++E +A +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 103 DSDNIMFKEKRLNIAPA 119
D + KE + +A +
Sbjct: 77 KMDGMTIKENIIKVAIS 93
>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 = 88.0 bits (219), Expect = 6e-22
Identities = 27/94 (28%), Positives = 50/94 (53%), Gaps = 2/94 (2%)
Query: 31 VNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFI 89
P+ ++FVGGI E E FSQ+G + ++++D+ G S+G+GF+
Sbjct: 75 PKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV 134
Query: 90 TFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
T+DS + R+ ++ I FK++++ I A +
Sbjct: 135 TYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPRH 167
Score = 73.7 bits (182), Expect = 1e-16
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
++F+GG+ TTED L E F +YG V +KI+ D A G S+G+GF++F+ +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 102 KD 103
K
Sbjct: 63 KT 64
>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 = 85.4 bits (212), Expect = 1e-21
Identities = 23/77 (29%), Positives = 36/77 (46%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
+ VFVG + + E+ L ELF Q G + +V I DR G K +GF+ F E
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75
Query: 103 DSDNIMFKEKRLNIAPA 119
+ I + +N++
Sbjct: 76 LLNGIRLYGRPINVSGP 92
>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 = 85.1 bits (211), Expect = 2e-21
Identities = 19/115 (16%), Positives = 45/115 (39%), Gaps = 6/115 (5%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
G P Q++ F + ++ V + ++ ++ ELF+++G
Sbjct: 7 GQQMGRDPDKWQHDLF---DSGCGGGEGVET---GAKLLVSNLDFGVSDADIQELFAEFG 60
Query: 69 IVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
+K+ + DR+G S G + F+ +A + K + + ++I +
Sbjct: 61 TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 115
>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 = 82.2 bits (204), Expect = 9e-21
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA--GISKGYGFITFDSEEEAKRL 100
P +V +G +T T+D + E+FS YG +K + + V+R +SKGY ++ F++ +EA++
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 101 QKDSDNIMFKEKRLNIAPAIKKQ 123
K D + + +
Sbjct: 64 LKHMDGGQIDGQEITATAVLAPW 86
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 82.5 bits (204), Expect = 1e-20
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 1/79 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ V++ G + T D++ E G V +++ KG F+ FDS E AK+ +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 71
Query: 104 SDNIMFKEKRLNIAPAIKK 122
+KE L I
Sbjct: 72 -PGQKYKETDLLILFKDDY 89
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 84.5 bits (209), Expect = 2e-20
Identities = 19/120 (15%), Positives = 45/120 (37%), Gaps = 5/120 (4%)
Query: 3 GAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCE 62
G + S P + F+ ++ V + ++ ++ E
Sbjct: 53 GRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVET-----GAKLLVSNLDFGVSDADIQE 107
Query: 63 LFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKK 122
LF+++G +K+ + DR+G S G + F+ +A + K + + ++I +
Sbjct: 108 LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 82.0 bits (203), Expect = 3e-20
Identities = 28/122 (22%), Positives = 55/122 (45%), Gaps = 15/122 (12%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDEL 60
M +H S+ P + N Q PKR+ V I + +L
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMNTENKSQ--------------PKRLHVSNIPFRFRDPDL 46
Query: 61 CELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAI 120
++F Q+G + V+I+ + G SKG+GF+TF++ +A R ++ + + +++ + A
Sbjct: 47 RQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105
Query: 121 KK 122
+
Sbjct: 106 AR 107
>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 = 81.1 bits (201), Expect = 4e-20
Identities = 24/81 (29%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
R+FV ++ T++E++L +LFS YG + ++ +D KG+ F+TF E A +
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 103 DSDNIMFKEKRLNIAPAIKKQ 123
+ D +F+ + L++ P+ K+
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKK 89
>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 = 81.2 bits (201), Expect = 6e-20
Identities = 26/116 (22%), Positives = 43/116 (37%), Gaps = 11/116 (9%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S + F +Y N +++ ++ TE +L LF+++
Sbjct: 1 GSSGSSGEEIRKIPMFSSYNPGEPNK----------VLYLKNLSPRVTERDLVSLFARFQ 50
Query: 69 IVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
K I G +G FITF ++E A + + K L I K+
Sbjct: 51 EKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 106
>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 = 80.9 bits (200), Expect = 1e-19
Identities = 30/127 (23%), Positives = 60/127 (47%), Gaps = 4/127 (3%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVP---KRVFVGGITSTTTE 57
M +H S+ P + + Q + P + V G++ TTE
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTE 60
Query: 58 DELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNI 116
+L E+FS+YG + V IV D+ S+G+ F+ F++ ++AK ++ ++ + +R+ +
Sbjct: 61 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Query: 117 APAIKKQ 123
+I K+
Sbjct: 121 DFSITKR 127
>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 = 79.6 bits (197), Expect = 1e-19
Identities = 21/57 (36%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ V G++ TTE +L E+FS+YG + V IV D+ S+G+ F+ F++ ++AK
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
>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 = 79.1 bits (196), Expect = 2e-19
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
+++ G+ TT+ +L +L YG + K ++D+ KGYGF+ FDS A++
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 102 KDSDNIMFKEKRLNIA 117
+ + +
Sbjct: 65 TALKASGVQAQMAKQS 80
>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 = 79.6 bits (197), Expect = 2e-19
Identities = 22/111 (19%), Positives = 48/111 (43%), Gaps = 6/111 (5%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GS P Q++ F + A ++ V + ++ ++ ELF+++G
Sbjct: 1 GSRPKQLPDKWQHDLF---DSGFGGGAGVET---GGKLLVSNLDFGVSDADIQELFAEFG 54
Query: 69 IVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
+K+ + DR+G S G + F+ + +A + K + + + +NI
Sbjct: 55 TLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105
>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 = 81.0 bits (200), Expect = 2e-19
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
+FV I EDE+ E F YG +K + + +DR G SKGY + +++ ++A ++
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+ + + + K
Sbjct: 133 ALNGAEIMGQTIQVDWCFVK 152
>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 = 78.7 bits (195), Expect = 2e-19
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+ ++VGG+ + L F +G + ++I +D +G+ F+ F+ E+A
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
>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 = 78.9 bits (195), Expect = 3e-19
Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 26 NYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISK 84
++ AA N + G+ P R++VG + TED L +F +G ++ +++++D G SK
Sbjct: 9 SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68
Query: 85 GYGFITFDSEEEAKR 99
GYGFITF E AK+
Sbjct: 69 GYGFITFSDSECAKK 83
>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 = 82.1 bits (202), Expect = 3e-19
Identities = 28/185 (15%), Positives = 54/185 (29%), Gaps = 11/185 (5%)
Query: 4 AHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKR---VFVGGITSTTTEDEL 60
+ + P AP + +++G +T TT+++L
Sbjct: 26 SPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDL 85
Query: 61 CELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIA 117
E G+ + ++K +RA G SKG+ + SE +K+L + +
Sbjct: 86 TEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT 145
Query: 118 PAIKKQGFTGTYDSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAFFPSNGQSMVPTSPP 177
P K+ + + G P G+ P + P
Sbjct: 146 PVNKQFL-----SQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVP 200
Query: 178 TVPTQ 182
Sbjct: 201 GGDRF 205
>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 = 78.9 bits (195), Expect = 4e-19
Identities = 19/95 (20%), Positives = 42/95 (44%)
Query: 29 AAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGF 88
+ ++ + VFV + +L E+FS G+V + I+ D+ G S+G G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60
Query: 89 ITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
+TF+ EA + + + ++ +++ +
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL 95
>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 = 78.4 bits (194), Expect = 4e-19
Identities = 23/58 (39%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++FVGG++ T E L ++FS+YG + +V +V DR S+G+GF+TF++ ++AK
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
>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 = 80.8 bits (200), Expect = 5e-19
Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 2/92 (2%)
Query: 33 NNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITF 91
++ + K++FVGGI T E L + F QYG ++ ++I+ DR G +G+ F+TF
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 92 DSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
D + ++ + A+ KQ
Sbjct: 154 DDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQ 184
Score = 72.3 bits (178), Expect = 7e-16
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR-L 100
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE +
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Query: 101 QKDSDNIMFKEKRLNIAPAIKKQGFTGTYDS 131
+ + A + + G + +
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLT 103
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 77.1 bits (191), Expect = 6e-19
Identities = 18/60 (30%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
++FVGG++ TT +++ F Q+G V ++ D+ +G+GF+TF+SE+ +++ +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
>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 = 77.6 bits (192), Expect = 7e-19
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
++FVGGI E EL E F ++G+V +V ++ D +G+GFITF+ E+ +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 103 DSDNIMFKEKRLNIAPAIKKQG 124
K++ + A +
Sbjct: 71 M-HFHDIMGKKVEVKRAEPRDS 91
>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 = 77.8 bits (192), Expect = 8e-19
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++F+G I E +L LF ++G + ++ ++ DR G+ KG F+T+ E A +
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALK 70
>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 = 77.3 bits (191), Expect = 8e-19
Identities = 30/86 (34%), Positives = 41/86 (47%), Gaps = 6/86 (6%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G+ VFVG T TEDEL E FSQYG V V I + + F+TF ++ A+
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQ 56
Query: 99 RLQKDSDNIMFKEKRLNIAPAIKKQG 124
L + I K ++I+ A K
Sbjct: 57 SLCGEDLII--KGISVHISNAEPKHN 80
>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 = 78.2 bits (193), Expect = 8e-19
Identities = 26/122 (21%), Positives = 49/122 (40%), Gaps = 27/122 (22%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S S K VF+ ++ + E+ L E+ Q+G
Sbjct: 1 GSSGSSGLPSDVTEG--------------------KTVFIRNLSFDSEEEALGEVLQQFG 40
Query: 69 IVKQVKIVVDRA-GISKGYGFITFDSEEEAKR------LQKDSDNIMFKEKRLNIAPAIK 121
+K V++V+ SKG F F ++E A++ L+ + + ++L + A+
Sbjct: 41 DLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100
Query: 122 KQ 123
+
Sbjct: 101 RD 102
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 77.2 bits (191), Expect = 9e-19
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR--- 99
+ ++VG + T +EL F G V +V I+ D+ G KG+ +I F +E +
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 100 LQKDSDNIMFKEKRLNIAPA 119
L D +F+ +++ + P
Sbjct: 67 L----DESLFRGRQIKVIPK 82
>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 = 79.6 bits (197), Expect = 9e-19
Identities = 18/66 (27%), Positives = 40/66 (60%)
Query: 34 NAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDS 93
++ K V +++F+G I+ TE+++ +FS +G +++ +I+ G+S+G F+TF +
Sbjct: 86 DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT 145
Query: 94 EEEAKR 99
A+
Sbjct: 146 RAMAQT 151
Score = 76.1 bits (188), Expect = 2e-17
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG---ISKGYGFITFDSEEEAKR 99
++FVG + T +E +L ELF QYG V ++ ++ DR+ SKG F+TF + + A
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 100 LQKDSDNIMFKEKRL 114
Q N+
Sbjct: 63 AQNALHNMKVLPGMH 77
>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 = 77.2 bits (191), Expect = 1e-18
Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 3/83 (3%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
+++G +T TT+++L E G+ + ++K +RA G SKG+ + SE +K+L
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 102 KDSDNIMFKEKRLNIAPAIKKQG 124
+ + P+ K +
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEH 85
>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 = 76.8 bits (190), Expect = 1e-18
Identities = 19/60 (31%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
++FVGG++ T E+++ E F +G V+ +++ +D +G+ FITF EE K++ +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 77.8 bits (192), Expect = 1e-18
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 3/87 (3%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
+ V+VG + +T +L FS G + ++ I+ D+ G KGY +I F
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 103 DSDNIMFKEKRLNIAPA-IKKQGFTGT 128
D +F+ + + + P G + T
Sbjct: 97 -MDETVFRGRTIKVLPKRTNMPGISST 122
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 77.4 bits (191), Expect = 1e-18
Identities = 23/107 (21%), Positives = 40/107 (37%), Gaps = 1/107 (0%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEA 97
G + K V + E L ++ +YG V++V+I++ G + F S A
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61
Query: 98 KRLQKDSDNIMFKEKRLNIAPAIKKQGFTGTYDSLPTVTSPVPPVPT 144
K K+ ++ IK Q Y+ + + VPT
Sbjct: 62 KETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPT 108
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 78.3 bits (193), Expect = 1e-18
Identities = 13/84 (15%), Positives = 31/84 (36%), Gaps = 1/84 (1%)
Query: 16 PSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKI 75
+ + + + ++VGG+ + L F +G + ++I
Sbjct: 36 YTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95
Query: 76 VVDRA-GISKGYGFITFDSEEEAK 98
+D +G+ F+ F+ E+A
Sbjct: 96 PLDYETEKHRGFAFVEFELAEDAA 119
>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 = 77.3 bits (191), Expect = 1e-18
Identities = 22/81 (27%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
PKR+ V I + +L ++F Q+G + V+I+ + G SKG+GF+TF++ +A R ++
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRARE 73
Query: 103 DSDNIMFKEKRLNIAPAIKKQ 123
+ + +++ + A +
Sbjct: 74 KLHGTVVEGRKIEVNNATARV 94
>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 = 76.4 bits (189), Expect = 2e-18
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
+FVG + ++ L F + ++ D G S+GYGF++F S+++A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 104 SDNIMFKEKRLNIAPAIKKQ 123
+ L I A K +
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82
>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 = 76.5 bits (189), Expect = 2e-18
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
+VFVG T T +EL + F QYG V V I + + F+TF ++ A+ L
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCG 66
Query: 103 DSDNIMFKEKRLNIAPAIKKQ 123
+ I K ++I+ A K
Sbjct: 67 EDLII--KGISVHISNAEPKH 85
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 77.9 bits (192), Expect = 2e-18
Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 4/126 (3%)
Query: 2 SGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVP---KRVFVGGITSTTTED 58
S H SS S + Q + + + V +T T+ D
Sbjct: 3 SSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPD 62
Query: 59 ELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIA 117
L +F +YG V V I DR S+G+ F+ F + +A+ D + + L +
Sbjct: 63 TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 122
Query: 118 PAIKKQ 123
A +
Sbjct: 123 MARYGR 128
>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 = 76.4 bits (189), Expect = 2e-18
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEA 97
G+ ++VG + TED L +F +G + + ++ D G SKGYGFITF E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 98 KR 99
+R
Sbjct: 61 RR 62
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 78.4 bits (193), Expect = 2e-18
Identities = 25/126 (19%), Positives = 50/126 (39%), Gaps = 3/126 (2%)
Query: 2 SGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELC 61
+ S P P + + N + V+VG + TT+ +L
Sbjct: 14 GTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLI 73
Query: 62 ELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAP 118
++ G+ V ++K +RA G SKGY + SE +L + + +++++ P
Sbjct: 74 QVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP 133
Query: 119 AIKKQG 124
A ++
Sbjct: 134 ATRQNL 139
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
+ V + T+ EL LF G + +I+ D G S GY F+ F SE +++R K
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 105 DNIMFKEKRLNIAPAIKKQ 123
+ I + KRL ++ A
Sbjct: 66 NGITVRNKRLKVSYARPGG 84
Score = 71.5 bits (176), Expect = 8e-16
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++V + T T+D+L +F +YG + Q I+ D+ G +G F+ ++ EEA+
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 79.3 bits (196), Expect = 3e-18
Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 1/96 (1%)
Query: 28 QAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGY 86
QA + R++V + ++D++ +F +G +K + D G KGY
Sbjct: 110 QAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGY 169
Query: 87 GFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKK 122
GFI ++ + ++ + + L + A+
Sbjct: 170 GFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 77.0 bits (190), Expect = 2e-17
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
RV+VG I ED + + F+ +G +K + + D KG+ F+ ++ E A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 102 KDSDNIMFKEKRLNIAPAIKKQ 123
+ +++M + + +
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIG 109
>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 = 78.4 bits (194), Expect = 3e-18
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 31 VNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFI 89
+ ++F+GG+ + +D++ EL + +G +K +V D A G+SKGY F
Sbjct: 82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141
Query: 90 TFDSEEEAKR 99
+ +
Sbjct: 142 EYVDINVTDQ 151
Score = 67.3 bits (165), Expect = 3e-14
Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVK-----IVVDRA-GISKGYGFITFDSEEE 96
+R++VG I TE+ + + F+ + + V+ K + F+ F S +E
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 97 AKRLQKDSDNIMFKEKRLNIAPAIKKQGFTGTY 129
+ D I+F+ + L I Q G +
Sbjct: 64 TTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAH 95
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 76.1 bits (188), Expect = 3e-18
Identities = 16/89 (17%), Positives = 38/89 (42%), Gaps = 1/89 (1%)
Query: 30 AVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFI 89
+ + + P +F+G + + EL S+ + +V R G ++ +G++
Sbjct: 4 MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63
Query: 90 TFDSEEEAKR-LQKDSDNIMFKEKRLNIA 117
F+S E+ ++ L+ + E +L
Sbjct: 64 DFESAEDLEKALELTGLKVFGNEIKLEKP 92
>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 = 77.5 bits (191), Expect = 3e-18
Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 11 SNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIV 70
+P ++ Q + V + + V I +T E +L +LF +YG +
Sbjct: 10 YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69
Query: 71 KQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ VKIV DR S+GYGF+ F S A++
Sbjct: 70 ESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
>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 = 76.1 bits (188), Expect = 3e-18
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+ ++VGG+ + L F +G + ++I +D +G+ F+ F+ E+A
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
>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 = 76.1 bits (188), Expect = 3e-18
Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 26/98 (26%)
Query: 3 GAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCE 62
G+ S G S +PS + V+V + + T ++L
Sbjct: 1 GSSGSSGMSGGLAPSKS-------------------------TVYVSNLPFSLTNNDLYR 35
Query: 63 LFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+FS+YG V +V I+ D+ SKG FI F ++ A+
Sbjct: 36 IFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
>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 = 76.5 bits (189), Expect = 3e-18
Identities = 20/85 (23%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G + +F+ + + L + FS +G + K+V D G SKGYGF+ F+++E A+
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAE 59
Query: 99 RLQKDSDNIMFKEKRLNIAPAIKKQ 123
R + + ++ ++++ + ++
Sbjct: 60 RAIEKMNGMLLNDRKVFVGRFKSRK 84
>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 = 75.3 bits (186), Expect = 5e-18
Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+ ++VG + + T +++ ELFSQ+G V VK++ DR KG+GF+ E ++
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE 57
>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 = 75.4 bits (186), Expect = 5e-18
Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 4/89 (4%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG----ISKGYGFITFDSE 94
G+ +F+ + +TTE+ L +FS+ G +K I + +S G+GF+ +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 95 EEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
E+A++ K +L + + +
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERAT 89
>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 = 75.7 bits (187), Expect = 5e-18
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 32 NNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFIT 90
++ K + V G+ TTE +L E FS +G V V++ D G SKG+GF+
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 91 FDSEEEAKRLQKDSDNI 107
F E ++ I
Sbjct: 64 FTEYETQVKVMSQRHMI 80
>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 = 75.8 bits (187), Expect = 5e-18
Identities = 36/112 (32%), Positives = 46/112 (41%), Gaps = 21/112 (18%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S P S +N V+VGG+ +E L ELF Q G
Sbjct: 1 GSSGSSGPISERNQ--------------------DATVYVGGLDEKVSEPLLWELFLQAG 40
Query: 69 IVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
V + DR G +GYGF+ F SEE+A K D I K + + A
Sbjct: 41 PVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA 92
>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 = 75.5 bits (186), Expect = 9e-18
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 29 AAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYG 87
+ ++ K T VFVG ++ T +++ F+ +G + ++V D A G SKGYG
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 88 FITFDSEEEAKR 99
F++F ++ +A+
Sbjct: 61 FVSFFNKWDAEN 72
>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 = 74.6 bits (184), Expect = 1e-17
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+ V++G I TE+++ +L S G V +K++ D G SKGY FI F E +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 58
>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 = 79.3 bits (196), Expect = 1e-17
Identities = 12/80 (15%), Positives = 31/80 (38%), Gaps = 1/80 (1%)
Query: 44 KRVFVGGITSTTTEDE-LCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
+ + V + + + LC S ++ + G KG+ + +++ E A+ Q+
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 244
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+D + L ++
Sbjct: 245 QADGLSLGGSHLRVSFCAPG 264
Score = 75.0 bits (185), Expect = 3e-16
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 1/80 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
+ V + + T+ + EL +G +++ +V G SKGYGF + ++ A R + D
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 104 SDNIMFKEKRLNIAPAIKKQ 123
+ L + Q
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQ 176
Score = 68.9 bits (169), Expect = 5e-14
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+++ + G+ T E+ +L S Y + K + KG F+T + E+A+
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYEL-KYCFV-----DKYKGTAFVTLLNGEQAEAAINA 76
Query: 104 SDNIMFKEKRLNIAPA 119
+E+ L++
Sbjct: 77 FHQSRLRERELSVQLQ 92
>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 = 76.5 bits (189), Expect = 1e-17
Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
+ V + T++E LF G ++ K+V D+ G S GYGF+ + ++A++
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 105 DNIMFKEKRLNIAPAIKKQ 123
+ + + K + ++ A
Sbjct: 65 NGLRLQTKTIKVSYARPSS 83
Score = 71.8 bits (177), Expect = 6e-16
Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++V G+ T T+ EL +LFSQYG + +I+VD+ G+S+G GFI FD EA+
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 145
>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 = 75.0 bits (185), Expect = 1e-17
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+FV I EDE+ E F YG +K + + +DR G SKGY + +++ ++A
Sbjct: 27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83
>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 = 74.6 bits (184), Expect = 1e-17
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ V ++ T E +L ELF +G + ++ + D+ G SKG+ FI+F E+A R
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
>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 = 77.0 bits (190), Expect = 1e-17
Identities = 22/113 (19%), Positives = 42/113 (37%), Gaps = 1/113 (0%)
Query: 12 NPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVK 71
N V ++F+GG+ + +D++ EL + +G +K
Sbjct: 83 RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLK 142
Query: 72 QVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
+V D A G+SKGY F + + + + +K+L + A
Sbjct: 143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 195
Score = 70.1 bits (172), Expect = 5e-15
Identities = 26/124 (20%), Positives = 44/124 (35%), Gaps = 14/124 (11%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA------GISKGYGFITFDSEEE 96
+R++VG I TE+ + + F+ + + K + F+ F S +E
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 97 AKR-LQKDSDNIMFKEKRLNIAPAIKKQGFTGTYDSLPTVTSPVPPVPTSNMYYHN---- 151
+ + D I+F+ + L I Q G P+V P H
Sbjct: 64 TTQAMAF--DGIIFQGQSLKIRRPHDYQPLPGM-SENPSVYVPGVVSTVVPDSAHKLFIG 120
Query: 152 GLPY 155
GLP
Sbjct: 121 GLPN 124
>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 = 74.7 bits (184), Expect = 2e-17
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 15/91 (16%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S + ++ VN ++PK TV + GGI S T+ + + FS +G
Sbjct: 1 GSSGSSGNTKQLR-----FEDVVNQSSPKNCTV-----YCGGIASGLTDQLMRQTFSPFG 50
Query: 69 IVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ ++++ + KGY F+ F + E A
Sbjct: 51 QIMEIRVFPE-----KGYSFVRFSTHESAAH 76
>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 = 74.6 bits (184), Expect = 2e-17
Identities = 18/77 (23%), Positives = 34/77 (44%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
P +++ + + E EL + +G V +I+ D +G S+G GF +S E+ + +
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 84
Query: 103 DSDNIMFKEKRLNIAPA 119
+ K AP
Sbjct: 85 HFNGKFIKTPPGVSAPT 101
>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 = 74.2 bits (183), Expect = 2e-17
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
+ V +T T+ D L +F +YG V V I + +G+ F+ F +A+
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 74.2 bits (183), Expect = 2e-17
Identities = 17/56 (30%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+FV G+ TE+++ + F++YG +K + + +DR G KGY + +++ +EA+
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 73.9 bits (182), Expect = 2e-17
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 7/83 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKR- 99
+ + I T D + S Y V ++++ D+ ++G+ F+ S +A +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 100 ---LQKDSDNIMFKEKRLNIAPA 119
LQ + K + + A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing,
mRNA splicing, mRNA transport, nonsense-mediated mRNA
decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB:
2j0q_D*
Length = 126
Score = 74.7 bits (184), Expect = 2e-17
Identities = 17/55 (30%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +DR G KGY + +++ +EA+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
>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 = 74.3 bits (183), Expect = 2e-17
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ VF + + +L + FS G V+ V+I+ DR SKG ++ F +
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
>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 = 73.9 bits (182), Expect = 2e-17
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+++FVG + +E+++ LF +G++ + ++ G SKG F+ F S EA+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 73.5 bits (181), Expect = 3e-17
Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 5/80 (6%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ VFV G +L E F +G V V V+D+ + + + +
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKD--KGVFAIVEMGDVGAREAVLSQ 64
Query: 104 SDNIMFKEKRLNIAPAIKKQ 123
RL + P +K+
Sbjct: 65 -SQHSLGGHRLRVRPREQKE 83
>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 = 73.4 bits (181), Expect = 3e-17
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
VFVG ++ T + F+ +G + ++V D A G SKGYGF++F ++ +A+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
>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 = 77.4 bits (191), Expect = 3e-17
Identities = 16/56 (28%), Positives = 32/56 (57%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ V ++ + + L + FSQ+G V++ +VVD G + G GF+ F ++ A++
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARK 152
Score = 77.0 bits (190), Expect = 4e-17
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + + TE++ LF +YG +V I DR G+GFI +S A+ + +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-----GFGFIRLESRTLAEIAKAEL 78
Query: 105 DNIMFKEKRLNIAPA 119
D + K + L I A
Sbjct: 79 DGTILKSRPLRIRFA 93
>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 = 75.7 bits (187), Expect = 3e-17
Identities = 13/57 (22%), Positives = 29/57 (50%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
P +F+G + + EL S+ + +V R G ++ +G++ F+S E+ ++
Sbjct: 13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69
Score = 70.7 bits (174), Expect = 2e-15
Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 4/80 (5%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
+ + ++ TEDEL E+F ++ +V + G SKG +I F SE +A++ +
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLE 154
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+ + +++ +K
Sbjct: 155 EKQGAEIDGRSVSLYYTGEK 174
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 73.5 bits (181), Expect = 3e-17
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FV E EL E+F +G +K+VKI+ G+ F+ F+ E A + ++
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEV 85
Query: 105 DNIMFKEKRLNIAPAIKK 122
F + L + +
Sbjct: 86 HGKSFANQPLEVVYSKLP 103
>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 = 74.8 bits (184), Expect = 5e-17
Identities = 24/121 (19%), Positives = 51/121 (42%), Gaps = 7/121 (5%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDEL 60
MSG S+ S + F K ++VG ++ TTE+++
Sbjct: 1 MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSC----TLYVGNLSFYTTEEQI 56
Query: 61 CELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEK--RLNIA 117
ELFS+ G +K++ + +D+ + G+ F+ + S +A+ + + ++ R +
Sbjct: 57 YELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD 116
Query: 118 P 118
Sbjct: 117 A 117
>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 = 73.1 bits (180), Expect = 5e-17
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + TE+E+ +LF +YG +V I D KG+GFI ++ A+ + +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71
Query: 105 DNIMFKEKRLNIAPAIKK 122
DN+ + K+L + A
Sbjct: 72 DNMPLRGKQLRVRFACHS 89
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 73.1 bits (180), Expect = 5e-17
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQ-YGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+FVG +T + L E F + Y + K+V+D+ G+SKGYGF+ F E E KR +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 104 SDNIMF-KEKRLNIAPAIKKQ 123
+ K + ++ AI K
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKA 91
>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 = 73.5 bits (181), Expect = 5e-17
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
++FVGG+ TT+ L + F +G +++ ++ DR G S+GYGF+T A+R
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 102 KD 103
KD
Sbjct: 77 KD 78
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 73.0 bits (180), Expect = 6e-17
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++V + ++ L + FS +G + K++++ G SKG+GF+ F S EEA + +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 105 DNIMFKEKRLNIAPAIKKQ 123
+ + K L +A A +K+
Sbjct: 76 NGRIVATKPLYVALAQRKE 94
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 76.9 bits (190), Expect = 6e-17
Identities = 16/83 (19%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 44 KRVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDR--AGISKGYGFITFDSEEEAKR- 99
+ + + + T E+ L E F +G ++++ I + + F+ F++++ A+R
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270
Query: 100 LQKDSDNIMFKEKRLNIAPAIKK 122
LQ + + + ++++ A KK
Sbjct: 271 LQM--NRSLLGNREISVSLADKK 291
Score = 74.6 bits (184), Expect = 4e-16
Identities = 8/76 (10%), Positives = 27/76 (35%), Gaps = 2/76 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
V V + + ++++ + F G + V + + + I F + A
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAITK-T 101
Query: 106 NIMFKEKRLNIAPAIK 121
+ + + + ++ +
Sbjct: 102 HKVVGQNEIIVSHLTE 117
Score = 70.4 bits (173), Expect = 1e-14
Identities = 12/96 (12%), Positives = 38/96 (39%), Gaps = 3/96 (3%)
Query: 31 VNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG-IVKQVKIVVDRAGISKGYGFI 89
V N + +++ + T+ + +L + +++ R S+ + +I
Sbjct: 105 VGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYI 164
Query: 90 TFDSEEEAKRLQKDSDNIMFKEKRL--NIAPAIKKQ 123
S+E+A+ + + + + L ++ ++K
Sbjct: 165 DVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS 200
>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 = 74.1 bits (182), Expect = 7e-17
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+ V +T T+ D L +F +YG V V I DR S+G+ F+ F + +A+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 71.8 bits (177), Expect = 7e-17
Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
++F+GG++ TT++ L E F Q+G VK+ ++ D S+G+GF+TF + ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 72.3 bits (178), Expect = 7e-17
Identities = 23/91 (25%), Positives = 34/91 (37%), Gaps = 13/91 (14%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GS P A + +AP T ++G I TE +L LF +G
Sbjct: 1 GSQTIGLPPQVNPQAV----DHIIRSAPPRVT----TAYIGNIPHFATEADLIPLFQNFG 52
Query: 69 IVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ K + KG FI +D+ E+A
Sbjct: 53 FILDFKHYPE-----KGCCFIKYDTHEQAAV 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 = 72.3 bits (178), Expect = 9e-17
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+ VFVG I TE++L ++FS+ G V ++V DR G KGYGF + +E A
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
>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 = 72.3 bits (178), Expect = 9e-17
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 9/85 (10%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQ--------VKIVVDR-AGISKGYGFITFDSE 94
+FV G+ T + + + F Q GI+K + + DR G KG ++FD
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 95 EEAKRLQKDSDNIMFKEKRLNIAPA 119
AK D F + ++ A
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFA 98
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 72.4 bits (178), Expect = 1e-16
Identities = 27/119 (22%), Positives = 48/119 (40%), Gaps = 5/119 (4%)
Query: 3 GAHPSEGSSNPSSPSSTQNNAF-FNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELC 61
P GS++ S S + A AA +F+ + T+ +L
Sbjct: 2 AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGC---NLFIYHLPQEFTDTDLA 58
Query: 62 ELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
F +G V K+ +D+ +SK +GF++FD+ + A+ K + KRL +
Sbjct: 59 STFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 72.4 bits (178), Expect = 1e-16
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 9/92 (9%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQ--------VKIVVDR-AGISKGYGFITFDS 93
+FV G+ T + + + F Q GI+K + + DR G KG ++FD
Sbjct: 7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
Query: 94 EEEAKRLQKDSDNIMFKEKRLNIAPAIKKQGF 125
AK D F + ++ A ++ F
Sbjct: 67 PPSAKAAIDWFDGKEFSGNPIKVSFATRRADF 98
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 71.2 bits (175), Expect = 1e-16
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDS 104
++VGG+ T TE +L F Q+G ++ + +V + FI F + + A+ +K
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSF 69
Query: 105 DNIMFKEKRLNI 116
+ ++ +RLN+
Sbjct: 70 NKLIVNGRRLNV 81
>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 = 71.1 bits (175), Expect = 2e-16
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 7/85 (8%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
++FVG +++ T EL LF + G V + +V K Y F+ + E +AK
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIA 61
Query: 103 DSDNIMFKEKRLNIAPAIKKQGFTG 127
+ K KR+N+ + K Q +G
Sbjct: 62 QLNGKEVKGKRINVELSTKGQKKSG 86
>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 = 71.9 bits (177), Expect = 2e-16
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
+++F+GG++ TTE+ L + Q+G + ++ D A S+G+GF+TF S E
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 102 KDSDNIMFKEKRLNIAPAIKKQ 123
+ + + + A+ ++
Sbjct: 87 AARPHSI-DGRVVEPKRAVARE 107
>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 = 71.6 bits (176), Expect = 2e-16
Identities = 11/82 (13%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ +++ + T +E+ ++F +YG ++Q+++ ++G ++ ++ +AK
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDH 66
Query: 104 SDNIMFKEKRLNIAPAIKKQGF 125
+ L + + F
Sbjct: 67 LSGFNVSNRYLVVLYYNANRAF 88
>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 = 70.7 bits (174), Expect = 2e-16
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
++FVGG++ T++ +L + F+++G V I +D G S+G+GFI F +++
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 102 KDSDNI 107
++
Sbjct: 71 DQKEHR 76
>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 = 72.9 bits (180), Expect = 3e-16
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+FVG + ++ L F + ++ D G S+GYGF++F S+++A+
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Score = 71.8 bits (177), Expect = 6e-16
Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 2/88 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQK 102
+ ++VG + TED L + F G + +KI++D+ + Y F+ + +A LQ
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 103 -DSDNIMFKEKRLNIAPAIKKQGFTGTY 129
+ I ++N A ++ T+
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTF 88
>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 = 71.2 bits (175), Expect = 3e-16
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA--GISKGYGFITFDSEEEAKR- 99
++ V I + E+ ELFS +G +K V++ G +G+GF+ F ++++AK+
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 100 LQKDSDNIMFKEKRLNIAPAIKKQ 123
+ +RL + A +
Sbjct: 75 FNALCHSTHLYGRRLVLEWADSEV 98
>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 = 71.1 bits (175), Expect = 3e-16
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
++F+GG++ TT++ L E F Q+G VK+ ++ D S+G+GF+TF + ++
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 102 KD 103
Sbjct: 85 AQ 86
>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 = 70.3 bits (173), Expect = 4e-16
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
++ VG I+ T T EL F +YG V + IV K Y F+ + E+A +
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIR 62
Query: 103 DSDNIMFKEKRLNIAPA 119
DN F+ KR+++ +
Sbjct: 63 GLDNTEFQGKRMHVQLS 79
>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 = 71.2 bits (175), Expect = 4e-16
Identities = 22/116 (18%), Positives = 47/116 (40%), Gaps = 11/116 (9%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S + Q ++ + +F+ + + +L ++F +G
Sbjct: 1 GSSGSSGLT----------QQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFG 50
Query: 69 IVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
V K+ +D+ +SK +GF+++D+ A+ + + KRL + K
Sbjct: 51 NVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 106
>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 = 70.4 bits (173), Expect = 5e-16
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 33 NNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFD 92
++ P+ ++VG ++ TE + +LFSQ G K K++ + + Y F+ F
Sbjct: 5 SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFY 63
Query: 93 SEEEAKR 99
+A
Sbjct: 64 EHRDAAA 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 = 70.4 bits (173), Expect = 5e-16
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
K +FV + +T TE+ L + FSQ+G +++VK + K Y FI FD + A + ++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEE 64
Query: 104 SDNIMFKEKRLNIAPAIKK 122
+ + + + I A
Sbjct: 65 MNGKDLEGENIEIVFAKPP 83
>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 = 73.1 bits (180), Expect = 5e-16
Identities = 18/79 (22%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+F+ + + L + FS +G + K+V D SKGYGF+ F+++E A+R +
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 105 DNIMFKEKRLNIAPAIKKQ 123
+ ++ ++++ + ++
Sbjct: 164 NGMLLNDRKVFVGRFKSRK 182
Score = 64.6 bits (158), Expect = 7e-13
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 1/92 (1%)
Query: 29 AAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYG 87
+ + P + ++VG + TE L E FS G + +++ D S GY
Sbjct: 1 GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60
Query: 88 FITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
++ F +A+R + + K K + I +
Sbjct: 61 YVNFQQPADAERALDTMNFDVIKGKPVRIMWS 92
>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 = 70.3 bits (173), Expect = 6e-16
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
++FVGG+ +TT++ L FSQYG V I+ D+ S+G+GF+ F +
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
Query: 102 KD 103
Sbjct: 76 AS 77
>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 = 70.0 bits (172), Expect = 7e-16
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 32 NNNAPK--YGTVVP-KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGF 88
+ ++ K YG P R++VGG+ T+ L F ++G ++ + V + +
Sbjct: 3 SGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-----SFAY 57
Query: 89 ITFDSEEEAKR 99
I ++S + A+
Sbjct: 58 IQYESLDAAQA 68
>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 = 69.5 bits (171), Expect = 8e-16
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYG-IVKQVKIVVDR-AGISKGYGFITFDSEEE 96
G+ +F+G + E L + FS +G I++ KI+ D G SKGY FI F S +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 97 AKRLQKDSDNIMFKEKRLNIAPAIKKQG 124
+ + + + + ++ A KK
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSYAFKKDS 88
>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 = 69.6 bits (171), Expect = 9e-16
Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 1/89 (1%)
Query: 32 NNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQ-VKIVVDRAGISKGYGFIT 90
++ G P + V + T + DE+ + F Y ++ V + + G+ G +
Sbjct: 4 GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
Query: 91 FDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
F+S +EA D ++ +++ +
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKLVLG 92
>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 = 69.1 bits (170), Expect = 1e-15
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
++F+G + TE E+ LF QYG V + I+ K YGF+ + + A+ ++
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRN 61
Query: 104 SDNIMFKEKRLNIAPA 119
+ +N+ +
Sbjct: 62 LHHYKLHGVNINVEAS 77
>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 = 69.2 bits (170), Expect = 1e-15
Identities = 14/81 (17%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQ 101
++++G ++ T D+L +LF + ++ + GY F+ + + A R ++
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIE 62
Query: 102 KDSDNIMFKEKRLNIAPAIKK 122
S + K + + ++ K
Sbjct: 63 TLSGKVELHGKIMEVDYSVSK 83
>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 = 69.2 bits (170), Expect = 1e-15
Identities = 12/76 (15%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
K ++V + +T+E+ + + F+ ++ + Y F+ F + E+A K
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKA 70
Query: 104 SDNIMFKEKRLNIAPA 119
+ + + + A
Sbjct: 71 LNGKVLDGSPIEVTLA 86
>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 = 69.3 bits (170), Expect = 1e-15
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 39 GTVVPKRVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
G+ + R+F+G + ++++L +FS YG + Q+ I +GFI FD+ +
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSV 70
Query: 98 KRLQKDSDNIMFKEKRLNIAPA 119
+ + M K+L + +
Sbjct: 71 RDAIEXESQEMNFGKKLILEVS 92
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 68.8 bits (169), Expect = 1e-15
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++FV + T L + F++ G V I ++ G SKG G + F+S E A+R
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAER 63
>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 = 69.2 bits (170), Expect = 1e-15
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 29 AAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYG 87
+ ++ P + K +FV G++ TTE+ L E F + +IV DR G SKG+G
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57
Query: 88 FITFDSEEEAK 98
F+ F+SEE+AK
Sbjct: 58 FVDFNSEEDAK 68
>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 = 69.0 bits (169), Expect = 2e-15
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDRA-GISKGYGFITFDSEE 95
++V G+ + T D+L + F Q G+VK + I +D+ G KG ++++
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 96 EAKRLQKDSDNIMFKEKRLNIAPAIKKQ 123
AK + D F+ +L ++ A KK
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKVSLARKKP 104
>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 = 68.1 bits (167), Expect = 4e-15
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
K + + ++ + TE+ L E+F + +K+ ++ G SKGY FI F S E+AK
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGKSKGYAFIEFASFEDAKE 68
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 67.7 bits (166), Expect = 5e-15
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR-L 100
P +VG + T + ++ +F ++ V++V D+ KG+ ++ FD + K L
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Query: 101 QKDSDNIMFKEKRLNIA 117
D + + R++IA
Sbjct: 74 TYDGALLGDRSLRVDIA 90
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 67.7 bits (166), Expect = 5e-15
Identities = 16/92 (17%), Positives = 39/92 (42%), Gaps = 1/92 (1%)
Query: 29 AAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQ-VKIVVDRAGISKGYG 87
+ ++ G P + V + T + DE+ + F Y ++ V + + G+ G
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 88 FITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
+ F+S +EA D ++ +++ ++
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
>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 = 67.6 bits (166), Expect = 6e-15
Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR--AGISKGYGFITFDSEEEAKR- 99
P F+G + TE+ + E F I V++ + KG+G+ F+ +
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLDSLLSA 77
Query: 100 LQKDSDNIMFKEKRLNIA 117
L + +++ + R+++A
Sbjct: 78 LSLNEESLGNRRIRVDVA 95
>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 = 66.5 bits (163), Expect = 1e-14
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ + ++ TEDEL E+F +I + G SKG +I F SE +A++
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEK 68
>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 = 67.5 bits (165), Expect = 1e-14
Identities = 19/99 (19%), Positives = 35/99 (35%), Gaps = 11/99 (11%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDEL 60
M +H S+ P + F + AP+ G ++V G T L
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGN----TLYVYGED--MTPTLL 54
Query: 61 CELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
FS +G + + + + F+T++ E A +
Sbjct: 55 RGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQ 88
>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 = 67.1 bits (164), Expect = 1e-14
Identities = 10/65 (15%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQ-VKIVVDRAGISKGYGFITFDSEEEAKR-LQKD 103
+ I + T+ ++ + + + V ++VD G G + F +E++A++ +
Sbjct: 18 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLH 77
Query: 104 SDNIM 108
+
Sbjct: 78 RKKLN 82
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 66.1 bits (162), Expect = 1e-14
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
R+F+G + ++++L +FS YG + Q+ I +GFI FD+ + + +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 64
Query: 104 SDNIMFKEKRLNIAPA 119
M K+L + +
Sbjct: 65 ESQEMNFGKKLILEVS 80
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 66.2 bits (162), Expect = 2e-14
Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 5/94 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+V+VG + + + EL FS YG ++ V I + G+ F+ F+ +A+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 105 DNIMFKEKRLNIAPAIKKQGFTGTYDSLPTVTSP 138
D + R+ + + +D P
Sbjct: 58 DGKVICGSRVRVELS-TGMPRRSRFDRPPARRKL 90
>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 = 66.6 bits (163), Expect = 2e-14
Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
R++VG + ++ ++F +YG ++ + + R G + F+ F+ +A+
Sbjct: 22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVY 79
Query: 103 DSDNIMFKEKRLNIAPA 119
D + RL +
Sbjct: 80 GRDGYDYDGYRLRVEFP 96
>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 = 65.4 bits (160), Expect = 4e-14
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 42 VPKRVFVGGITSTTTEDELCELFSQYG-IVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ +++G + E+ + F+ G V VKI+ +R GI GY F+ F A++
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
>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 = 65.5 bits (160), Expect = 5e-14
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
RVF+G + T+ + ++ +FS+YG V + KGY F+ + +E A+
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLG 81
Query: 104 SDNIMFKEKRLNIAPA 119
+ + + L+I A
Sbjct: 82 ENGRVLAGQTLDINMA 97
>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 = 66.4 bits (162), Expect = 5e-14
Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+V+VG + + + EL F YG ++ V + + G+ F+ F+ +A ++
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVREL 130
Query: 105 DNIMFKEKRLNIAPA 119
D R+ + +
Sbjct: 131 DGRTLCGCRVRVELS 145
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 65.0 bits (159), Expect = 6e-14
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 4/78 (5%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA--GISKGYGFITFDSEEEAKR- 99
P F+G + TE+ + E F I V++ + + KG+G+ F+ +
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLDSLLSA 73
Query: 100 LQKDSDNIMFKEKRLNIA 117
L + +++ K R+++A
Sbjct: 74 LSLNEESLGNKRIRVDVA 91
>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 = 69.1 bits (168), Expect = 7e-14
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
K +FV + TTE +L F YG +K++ +V R+G +GY FI ++ E + K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 103 DSDNIMFKEKRLNI 116
+D +R+ +
Sbjct: 163 HADGKKIDGRRVLV 176
>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 = 64.2 bits (157), Expect = 9e-14
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 12/97 (12%)
Query: 30 AVNNNAPKYGTVVPKRVFVGGITSTTTEDEL----CELFSQYGIVKQVKIVVDRAGISKG 85
AV P +++ + +DEL +FS++G + I+V R+ +G
Sbjct: 1 AVPETRPN------HTIYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRG 52
Query: 86 YGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKK 122
F+ F A + F +K + I A
Sbjct: 53 QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89
>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 = 65.2 bits (159), Expect = 1e-13
Identities = 23/109 (21%), Positives = 35/109 (32%), Gaps = 8/109 (7%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDEL 60
S GS S Q + V + G+ TE+++
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTT------GHCVHMRGLPYKATENDI 63
Query: 61 CELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDNIM 108
FS V+ V I + G G + F + EEA + KD N+
Sbjct: 64 YNFFSPLNPVR-VHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQ 111
>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 = 64.0 bits (156), Expect = 1e-13
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 32 NNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF 91
++ + + V + G+ TE+++ FS ++ V I + G G + F
Sbjct: 4 GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEF 62
Query: 92 DSEEEAKR-LQKDSDNI 107
+ E+A + KD N+
Sbjct: 63 ATHEDAVAAMAKDKANM 79
>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 = 64.5 bits (157), Expect = 1e-13
Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 7/106 (6%)
Query: 5 HPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELF 64
H S G S ++ + + + ++ G V + G+ T++E+ + F
Sbjct: 9 HHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFV-----RLRGLPFGCTKEEIVQFF 63
Query: 65 SQYGIVKQ-VKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDNIM 108
S IV + + VD G G F+ F S+E A++ L K + I
Sbjct: 64 SGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIG 109
>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 = 63.6 bits (155), Expect = 2e-13
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQ-VKIVVDRAGISKGYGFITFDSEEEAKR-LQKD 103
V + G+ +++E+ + FS IV + + VD G S G F+ F S+E A++ L+K
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 104 SDNIM 108
+ I
Sbjct: 78 KERIG 82
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 64.2 bits (156), Expect = 2e-13
Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 7/96 (7%)
Query: 32 NNNAPKYGTVVP-KRVFVGGITSTTTEDEL----CELFSQYGIVKQVKIVVDRAGISKGY 86
+ P + V + I +++L L S G + IVVD + + G
Sbjct: 17 PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD--IVVDLSDDNSGK 74
Query: 87 GFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKK 122
+I F ++E A+ + F+ L I +
Sbjct: 75 AYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110
>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 = 62.8 bits (153), Expect = 3e-13
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ V + + E+ +L Y + K + +K F+T + E+A+ +
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV-----DRNKRTAFVTLLNGEQAQNAIQM 59
Query: 104 SDNIMFKEKRLNI 116
F+ K L +
Sbjct: 60 FHQYSFRGKDLIV 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 = 62.9 bits (153), Expect = 4e-13
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 5/84 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYG-IVKQVKIVVDRA--GISKGYGFITFDSEEEAKRLQ 101
R+F+GGI +E+ E ++ V V + A ++G+ F+ ++S A +
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 102 K--DSDNIMFKEKRLNIAPAIKKQ 123
+ I ++ + A +
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAEPEI 93
>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 = 61.9 bits (151), Expect = 5e-13
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDS 104
V + G TE + E + V ++IV + G GY F+ F +EEE K+ L+ +
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNR 71
Query: 105 DNIM 108
+ +
Sbjct: 72 EYMG 75
>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 = 65.7 bits (159), Expect = 8e-13
Identities = 27/161 (16%), Positives = 47/161 (29%), Gaps = 16/161 (9%)
Query: 44 KRVFVGGITSTTTEDEL----CELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+++ + +DEL +FSQ+G + + I+V R+ +G F+ F A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 100 LQKDSDNIMFKEKRLNIAPAIKK----------QGFTGTYDSLPTVTSPVPPVPTSNMYY 149
+ F +K + I A S P +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127
Query: 150 HNGLPYTYHNGMAFFPSNGQSMVPTSPPTVPTQVKILLPPG 190
P + P +P Q + PPG
Sbjct: 128 GGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPG 168
Score = 49.9 bits (118), Expect = 2e-07
Identities = 20/99 (20%), Positives = 31/99 (31%), Gaps = 5/99 (5%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDEL 60
G P G + P F+ + T E L
Sbjct: 166 PPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHIL-FLTNLPEETNELML 224
Query: 61 CELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
LF+Q+ K+V++V R F+ FD+E +A
Sbjct: 225 SMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGA 259
>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 = 62.9 bits (153), Expect = 8e-13
Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 6/86 (6%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVK------IVVDRAGISKGYGFITFDSEEEA 97
R++V + E +L +F +Y I + + G KG FI +E+ A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 98 KRLQKDSDNIMFKEKRLNIAPAIKKQ 123
+ K+++ + K + + A +
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARSAR 131
>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 = 60.9 bits (148), Expect = 1e-12
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVK------IVVDRAGISKGYGFITFDSEEEA 97
+R++VG I TE+ + + F+ + + ++ + K + F+ F S +E
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 98 KRLQKDSDNIMFKEKRLNI 116
+ D I+F+ + L I
Sbjct: 67 TQAMA-FDGIIFQGQSLKI 84
>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 = 61.7 bits (150), Expect = 1e-12
Identities = 17/90 (18%), Positives = 40/90 (44%), Gaps = 2/90 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDS 104
V V G+ + E+++ + F + V ++ D G + G G + F S ++ L+++
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRVD-AVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNR 77
Query: 105 DNIMFKEKRLNIAPAIKKQGFTGTYDSLPT 134
++ + ++ A + G S P+
Sbjct: 78 MLMIQRYVEVSPATERQWVAAGGHITSGPS 107
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 61.9 bits (150), Expect = 1e-12
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 3/70 (4%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA---GISKGYGFITFDSEEEAKRL 100
++VFVGG+ EDE+ F ++G + + KGY F+ F E + L
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 101 QKDSDNIMFK 110
K
Sbjct: 69 IDACLEEDGK 78
>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 = 61.8 bits (150), Expect = 2e-12
Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 12/101 (11%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S S + + + + + + G V ++ G+ + + F +
Sbjct: 1 GSSGSSGKSPS------GQKRSRSRSPHEAGFCV----YLKGLPFEAENKHVIDFFKKLD 50
Query: 69 IVK-QVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDNI 107
IV+ + I G + G GF+ F +E + K L + +
Sbjct: 51 IVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYM 91
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 60.2 bits (146), Expect = 3e-12
Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+++ + I + L L QYG+V+ + V + +T+ S+++A++
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNVTYSSKDQARQ 69
>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 = 61.8 bits (149), Expect = 6e-12
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ V++ G + T D++ E G V +++ KG F+ FDS E AK+ +
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169
Query: 104 SDNIMFKEKRLNI 116
+KE L I
Sbjct: 170 -PGQKYKETDLLI 181
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 59.5 bits (144), Expect = 8e-12
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIV----KQVKIVVDRAGISKGYGFITFDSEEEAKR-L 100
V + G+ T T +E+ F Q+ + + + V G G F+ F EE A+ L
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 101 QKDSDNIM------FKEKRLNIAPAIKKQGFTGTYDS 131
+K D + F+ + + + S
Sbjct: 86 RKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSS 122
>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 = 61.3 bits (148), Expect = 1e-11
Identities = 20/135 (14%), Positives = 41/135 (30%), Gaps = 7/135 (5%)
Query: 46 VFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+ V G+ S D + +F YG V++VK + + G + R
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHL 62
Query: 105 DNIMFKEKRLNIAPAIKKQGFTGTYDSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAFF 164
+N +++N+ + + G L + S + N +
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI--Q 120
Query: 165 PSNGQSMVPTSPPTV 179
+ +P V
Sbjct: 121 HPSNVLHFFNAPLEV 135
Score = 57.8 bits (139), Expect = 2e-10
Identities = 13/120 (10%), Positives = 32/120 (26%), Gaps = 3/120 (2%)
Query: 5 HPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPK--RVFVGGITSTTTEDELCE 62
P + S ++ + + + TE+ E
Sbjct: 83 MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFE 142
Query: 63 LFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIK 121
+ + G+ + + V G + +DS+ +A ++ K +K
Sbjct: 143 ICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202
>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 = 58.4 bits (141), Expect = 2e-11
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 9/86 (10%)
Query: 14 SSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQV 73
SS SS + ++ + VV GG+ + + ++L + + G+V +
Sbjct: 2 SSGSSGAKHTLLRHEGIETVSYATQSLVV----ANGGLGNGVSRNQLLPVLEKCGLVDAL 57
Query: 74 KIVVDRAGISKGYGFITFDSEEEAKR 99
+ + K Y F + + EE+KR
Sbjct: 58 LMPPN-----KPYSFARYRTTEESKR 78
>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 = 57.7 bits (140), Expect = 3e-11
Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++V G T L FS +G + + + + F+T++ E A +
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQ 64
>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 = 57.9 bits (140), Expect = 3e-11
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 7/89 (7%)
Query: 41 VVPKRVFVGGITSTTTEDELC---ELFSQYGIVKQVKIVVDRAG----ISKGYGFITFDS 93
V VFV G++ + E+ E F ++G + +V I + ++T+
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72
Query: 94 EEEAKRLQKDSDNIMFKEKRLNIAPAIKK 122
E+A R + +N++ + L + K
Sbjct: 73 SEDALRAIQCVNNVVVDGRTLKASLGTTK 101
>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 = 57.2 bits (138), Expect = 5e-11
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 10/89 (11%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI---VKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQ 101
V + G+ + + +++ S I V V + R G G F+ +SE++ K L+
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79
Query: 102 KDSDNIM------FKEKRLNIAPAIKKQG 124
KD +++ FK R + +K G
Sbjct: 80 KDRESMGHRYIEVFKSHRTEMDWVLKHSG 108
>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 = 57.7 bits (139), Expect = 6e-11
Identities = 20/113 (17%), Positives = 40/113 (35%), Gaps = 5/113 (4%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKR-VFVGGITSTTTEDE 59
M +H S+ P + + Q + V + G+ + + ++
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVED 60
Query: 60 LCELFSQYGI---VKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDNIM 108
+ S I V + R G G F+ SE++ K L+KD +++
Sbjct: 61 VQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMG 113
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 56.7 bits (137), Expect = 6e-11
Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 4/80 (5%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSD 105
+ + L LFS+ G V ++ +D A G +KG+ F+ S +AK++ K
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 106 NIMFKEK---RLNIAPAIKK 122
K L +++
Sbjct: 76 GKRLDLKHRLFLYTMKDVER 95
>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 = 56.7 bits (137), Expect = 7e-11
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
RV V G+ + + +L + + G V + G G + F +E+ +
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKL 70
Query: 105 DNIMFKEKRLNIAPA 119
DN F+ A
Sbjct: 71 DNTKFRSHEGETAYI 85
>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 = 56.8 bits (137), Expect = 8e-11
Identities = 17/113 (15%), Positives = 42/113 (37%), Gaps = 9/113 (7%)
Query: 13 PSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQ 72
S ++ + + ++ + V + + + + TE E+ L +G V
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGDS--RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN 60
Query: 73 VKIVVDRAGISKGYGFITFDSEEEAKRLQKD--SDNIMFKEKRLNIAPAIKKQ 123
+ ++ K FI ++EE A + S + + + + I + K+
Sbjct: 61 LLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 108
>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 = 55.6 bits (134), Expect = 2e-10
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
RV V G+ + + +L + + G V + G G + F +E+ +
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKL 71
Query: 105 DNIMFKEKRLNIAPA 119
DN F+ A
Sbjct: 72 DNTKFRSHEGETAYI 86
>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 = 54.5 bits (131), Expect = 4e-10
Identities = 14/87 (16%), Positives = 37/87 (42%), Gaps = 10/87 (11%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI---VKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQ 101
+ G+ + T +++ FS I + +++R G +G I +SE++ ++ L+
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73
Query: 102 KDSDNIM------FKEKRLNIAPAIKK 122
K + ++ ++ +K
Sbjct: 74 KHRMYMGQRYVEVYEINNEDVDALMKS 100
>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 = 56.4 bits (136), Expect = 5e-10
Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 3/95 (3%)
Query: 5 HPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELF 64
+ N+ + + + + + I + +E++L LF
Sbjct: 82 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLF 141
Query: 65 SQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
S G V + + + I S EEA +
Sbjct: 142 SSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQ 173
Score = 54.1 bits (130), Expect = 3e-09
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 5/78 (6%)
Query: 46 VFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+ V + T L LF YG V++VKI+ + K + +A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 61
Query: 105 DNIMFKEKRLNIAPAIKK 122
+ K + I + +
Sbjct: 62 NGHKLHGKPIRITLSKHQ 79
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 53.7 bits (129), Expect = 1e-09
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+ + + + +L +L + + V R G G + F SEE +
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD--FDGTGALEFPSEEILVEALERL 87
Query: 105 DNIMFKEKRLNI 116
+NI F+ + +
Sbjct: 88 NNIEFRGSVITV 99
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 52.9 bits (127), Expect = 2e-09
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 8/81 (9%)
Query: 39 GTVVPKRV-FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
G+ VP RV + + TE E+ L +G V + ++ K FI ++EE A
Sbjct: 11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAA 65
Query: 98 KRLQKD--SDNIMFKEKRLNI 116
+ S + + + + I
Sbjct: 66 NTMVNYYTSVTPVLRGQPIYI 86
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 52.4 bits (126), Expect = 2e-09
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 9/81 (11%)
Query: 36 PKYGTVVPKRVFVGGITSTTTE------DELCELFSQYGIVKQVKIVVDRA-GISKGYGF 88
P+ + + V + + + + ++FS++G + G +KGY F
Sbjct: 8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIF 65
Query: 89 ITFDSEEEAKRLQKDSDNIMF 109
+ + S A K++D
Sbjct: 66 LEYASPAHAVDAVKNADGYKL 86
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 52.1 bits (125), Expect = 2e-09
Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 4/88 (4%)
Query: 32 NNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF 91
+ P G + V+VG + +L + G V +++ + F+ +
Sbjct: 8 PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQG---PRRRAFLHY 63
Query: 92 DSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
A++ + L +A A
Sbjct: 64 PDSAAAQQAVSCLQGLRLGTDTLRVALA 91
>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 = 54.6 bits (131), Expect = 3e-09
Identities = 20/123 (16%), Positives = 35/123 (28%), Gaps = 14/123 (11%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGI-TSTTTEDE 59
M +H S+ P P + V + T
Sbjct: 1 MGSSHHHHHHSSGLVPRG---------SHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQS 51
Query: 60 LCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
L LF YG V++VKI+ + K + +A+ + K + I +
Sbjct: 52 LFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS 107
Query: 120 IKK 122
+
Sbjct: 108 KHQ 110
Score = 54.2 bits (130), Expect = 4e-09
Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 3/95 (3%)
Query: 5 HPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELF 64
+ N+ + + + + + I + +E++L LF
Sbjct: 113 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLF 172
Query: 65 SQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
S G V + + + I S EEA +
Sbjct: 173 SSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQ 204
>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 = 51.7 bits (124), Expect = 5e-09
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 5/71 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+ + + T E+ E FS++G + +V + + F EA++ +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHLA 67
Query: 106 NIMFKEKRLNI 116
F L +
Sbjct: 68 YSKFHHVPLYL 78
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 51.3 bits (123), Expect = 5e-09
Identities = 10/56 (17%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
V + G+ E +L E ++G + V ++ K + F+ A
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACN 72
>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 = 50.2 bits (120), Expect = 2e-08
Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 7/82 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK- 102
V V G+ + E +L E ++G + V ++ K + F++ + AK
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70
Query: 103 -DSDNIMFKEKRLNIAPAIKKQ 123
+ ++ + K+
Sbjct: 71 AADVPVYIAGQQAFFNYSTSKR 92
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 48.9 bits (117), Expect = 2e-08
Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 7/74 (9%)
Query: 46 VFVGGITSTTTE------DELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ V + + + + ++FS++G + + G +KGY F+ + S A
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 62
Query: 100 LQKDSDNIMFKEKR 113
K++D ++
Sbjct: 63 AVKNADGYKLDKQH 76
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 49.4 bits (118), Expect = 3e-08
Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 7/75 (9%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ + + + TE E+ L +G V + ++ K F+ +EE A +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNY 70
Query: 104 --SDNIMFKEKRLNI 116
+ + + + I
Sbjct: 71 YSAVTPHLRNQPIYI 85
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 49.3 bits (117), Expect = 7e-08
Identities = 27/139 (19%), Positives = 48/139 (34%), Gaps = 15/139 (10%)
Query: 10 SSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGI 69
S N + +S AAV+ G R+ V + T D L ++FS++G
Sbjct: 4 SGNLALAAS---------AAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGT 54
Query: 70 VKQVKIVVDRAGISKGYGFITFDSEEEAKR--LQKDSDNIMFKEKRLNIAPAIKKQGFTG 127
V ++ + + A+ L D NI L I + K
Sbjct: 55 VLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS-KLTSLNV 110
Query: 128 TYDSLPTVTSPVPPVPTSN 146
Y++ + P +P+ +
Sbjct: 111 KYNNDKSRDYTRPDLPSGD 129
>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 = 47.4 bits (112), Expect = 4e-07
Identities = 27/138 (19%), Positives = 41/138 (29%), Gaps = 16/138 (11%)
Query: 28 QAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYG 87
AAV+ G R+ V + T D L ++FS++G V ++
Sbjct: 31 AAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQA 87
Query: 88 FITFDSEEEAKR--LQKDSDNIMFKEKRLNIAPAIKKQ---------GFTGTYDSLPTVT 136
+ + A+ L D NI L I + T LP +
Sbjct: 88 LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLP--S 145
Query: 137 SPVPPVPTSNMYYHNGLP 154
P M GL
Sbjct: 146 GDSQPSLDQTMAAAFGLS 163
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 46.7 bits (110), Expect = 1e-06
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 46 VFVGGITSTTT---------EDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEE 96
++VGGI E + +FS+ G + +++ V SK GF+ F +
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQAN 191
Query: 97 AKR 99
A+
Sbjct: 192 AEF 194
>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 = 47.5 bits (112), Expect = 2e-06
Identities = 33/227 (14%), Positives = 68/227 (29%), Gaps = 46/227 (20%)
Query: 37 KYGTVVP--KRVFVGGITSTTTEDELCELFSQYGIVKQVK-IVVDRAGISKGYG-FITFD 92
+Y ++ + FV +D + S+ +++ I++ + +S F T
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQDMPKSILSK----EEIDHIIMSKDAVSGTLRLFWTLL 72
Query: 93 S--EEEAKR-----LQKDSDNIMFKEKRLNIAPAIKKQGFTGTYDSLPTVTSPVPP--VP 143
S EE ++ L+ + +M K P++ + + D L V
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 144 TSNMYY--HNGL----PYTY---HNGMAFFPSNGQS-MVPTSPPTVPTQVKILLPPGVLL 193
Y L P G+ G++ + + + L V
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLID-GVLGS---GKTWVA----------LDVCLSYKVQC 178
Query: 194 CGICLIFLITLALAPTIKRPS--LKPLNSSQCKIKQSRGRLLSRACS 238
IF + L P L+ L +I + + +
Sbjct: 179 KMDFKIFWLNLK---NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Score = 32.5 bits (73), Expect = 0.14
Identities = 22/171 (12%), Positives = 38/171 (22%), Gaps = 77/171 (45%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+ + + T T DE+ L +Y D E
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKY------------LDCR------PQDLPREVL 323
Query: 99 -----------RLQKD----SDNI--MFKEKRLNIAPAIKKQGFTGTYDSLPTVTSPVPP 141
+D DN + +K I I+ + + L P
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI---IES-----SLNVL-------EP 368
Query: 142 VPTSNMYYHNGLPYTYHNGMAFFPSNGQSMVPTSPPTVPTQVKILLPPGVL 192
M+ ++ FP + I P +L
Sbjct: 369 AEYRKMFDR----------LSVFPPS---------------AHI--PTILL 392
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 39.1 bits (91), Expect = 2e-04
Identities = 10/43 (23%), Positives = 23/43 (53%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
E+ E+ +YG V+++ + + G ++ F EE+A++
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEK 83
>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 = 37.6 bits (87), Expect = 6e-04
Identities = 15/101 (14%), Positives = 37/101 (36%), Gaps = 10/101 (9%)
Query: 28 QAAVNNNAPKY-GTVVPKRV-FVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISK 84
+ K+ RV + + S ++ + +L YG +K ++ K
Sbjct: 8 KKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MK 62
Query: 85 GYGFITFDSEEEAKRLQK--DSDNIMFKEKRLNIAPAIKKQ 123
FI ++ E+A + + F+ + + + + K +
Sbjct: 63 SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK 103
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 36.9 bits (85), Expect = 0.001
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 2/61 (3%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G+ V V G+ ++ L F ++ + G +TF +A+
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--RLGCGGVLTFREPADAE 61
Query: 99 R 99
R
Sbjct: 62 R 62
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 34.7 bits (79), Expect = 0.006
Identities = 21/110 (19%), Positives = 36/110 (32%), Gaps = 16/110 (14%)
Query: 9 GSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYG 68
GSS S T+ N + P G V + + T D L + + G
Sbjct: 1 GSSGSSGKRITRPG---------NTDDPSGGNKV-LLLSIQNPLYPITVDVLYTVCNPVG 50
Query: 69 IVKQVKIVVDRAGISKGYGFITFDSEEEAK--RLQKDSDNIMFKEKRLNI 116
V+++ I + F+S A+ + + +I L I
Sbjct: 51 KVQRIVIFKRN----GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI 96
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 34.1 bits (78), Expect = 0.007
Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 7/73 (9%)
Query: 30 AVNNNAPKYGTVVPKRV-FVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYG 87
+ ++ + G V +RV + +L +L +G++ I+
Sbjct: 1 GSSGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-----NKINEA 55
Query: 88 FITFDSEEEAKRL 100
FI + E+A+
Sbjct: 56 FIEMATTEDAQAA 68
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 35.1 bits (80), Expect = 0.016
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 49 GGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
GG+ + + ++L + + G+V + +K Y F + + EE+KR
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDALL-----MPPNKPYSFARYRTTEESKRA 72
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 31.7 bits (72), Expect = 0.060
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGIS---KGYGFITFDSEEEAKR 99
+++ + S+YG+VK ++I G+ G F+ F S + ++
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQK 74
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 33.5 bits (76), Expect = 0.062
Identities = 40/227 (17%), Positives = 61/227 (26%), Gaps = 88/227 (38%)
Query: 4 AHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVG-GITSTTTEDELCE 62
A +S A F +A NA +F G G T +EL +
Sbjct: 129 ARIMAKRPFDKKSNS----ALF--RAVGEGNAQLVA------IFGGQGNTDDYF-EELRD 175
Query: 63 LFSQY-GIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIK 121
L+ Y +V I + A+ L L
Sbjct: 176 LYQTYHVLVGD---------------LI----KFSAETLS-----------ELIRTTLDA 205
Query: 122 KQGFTGTYDSLPTVTSP--VPPVPTSNMYYHNGLPYTYHNGMAFFPSNGQSMVPTS-PPT 178
++ FT + L + +P P + S +P S P
Sbjct: 206 EKVFTQGLNILEWLENPSNTPDKD-------------------YLLS-----IPISCPLI 241
Query: 179 VPTQV-------KIL-LPPGVL---LCGI--CLIFLIT---LALAPT 209
Q+ K+L PG L L G L+T +A +
Sbjct: 242 GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDS 288
Score = 31.6 bits (71), Expect = 0.30
Identities = 7/49 (14%), Positives = 15/49 (30%), Gaps = 13/49 (26%)
Query: 30 AVNNNAPKYGTVVPKRVFVGGITSTTTE--DELCELFSQYGIVKQVKIV 76
VN N V G D + + + + +++ I+
Sbjct: 1843 IVNYNVE-NQQYV-----AAG----DLRALDTVTNVLNFIKL-QKIDII 1880
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 31.1 bits (70), Expect = 0.085
Identities = 9/67 (13%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 51 ITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFK 110
++ + L E F+++G VK V++ + + ++ ++A
Sbjct: 21 LSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIG 78
Query: 111 EKRLNIA 117
K++ ++
Sbjct: 79 SKKILVS 85
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 31.2 bits (71), Expect = 0.10
Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++L S++G ++++ + G ++F EEA
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRH---PDGVASVSFRDPEEADY 79
>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf
transcription; HET: HEM; 1.90A {Lactococcus lactis}
PDB: 3vox_A 3vok_A*
Length = 189
Score = 31.2 bits (70), Expect = 0.17
Identities = 5/36 (13%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 62 ELFSQYGIVK-QVKIVVDRAGISKGYGFITFDSEEE 96
F + + ++ +V I +G + F+ ++
Sbjct: 23 NEFQTHSFHEAKIMHIVKALDIPRGSFYQYFEDLKD 58
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif,
RRM, RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 30.1 bits (68), Expect = 0.27
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISK-----GYGFITFDSEEEAKR 99
E E+ E ++G V +V I ++ G + F+ F E +
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHK 86
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 30.0 bits (67), Expect = 0.29
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA---KRLQKD 103
F G + T ++L LFS +G +K + V G +G I F + + K +
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFV---RGAKEGI--ILFKEKAKEALGKAKDAN 77
Query: 104 SDNIMFKEKRL 114
+ N+ + K +
Sbjct: 78 NGNLQLRNKEV 88
>3nrg_A TETR family transcriptional regulator; structural genomics, joint
center for structural genomics, J protein structure
initiative, PSI-2; 2.56A {Chloroflexus aurantiacus}
Length = 217
Score = 30.6 bits (69), Expect = 0.36
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 11/41 (26%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG----YGFITFDSEEE 96
+ F+Q V I + +RAGI+KG Y F +++
Sbjct: 24 DEFAQND-YDSVSINRITERAGIAKGSFYQY----FADKKD 59
>1rkt_A Protein YFIR; transcription regulator, structural genomics, PSI,
protein S initiative, midwest center for structural
genomics, MCSG; 1.95A {Bacillus subtilis} SCOP: a.4.1.9
a.121.1.1
Length = 205
Score = 30.1 bits (68), Expect = 0.44
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 11/41 (26%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG----YGFITFDSEEE 96
+F + G + + VV+ +G S+G Y F S EE
Sbjct: 23 TVFKRKG-FELTTMKDVVEESGFSRGGVYLY----FSSTEE 58
>3jsj_A Putative TETR-family transcriptional regulator; DNA-binding,
transcription regulation; 2.10A {Streptomyces
avermitilis ma-4680}
Length = 190
Score = 30.2 bits (68), Expect = 0.44
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 62 ELFSQYGIVKQVKIVVDRAGISKG--YGFITFDSEEE 96
L + G+ V+ + AG+SK Y F+S++E
Sbjct: 20 ALTYRDGVGIGVEALCKAAGVSKRSMYQL--FESKDE 54
>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus
subtilis subsp}
Length = 197
Score = 30.0 bits (68), Expect = 0.47
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 11/41 (26%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG----YGFITFDSEEE 96
E+ S+ G + + I +V +AG ++G Y F S+
Sbjct: 21 EVISEKG-LDKASISDIVKKAGTAQGTFYLY----FSSKNA 56
>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted
DNA-binding transcriptional regulator TETR/ACRR family;
2.10A {Clostridium acetobutylicum atcc 824}
Length = 203
Score = 30.1 bits (68), Expect = 0.48
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG--YGFITFDSEEE 96
++F G + + ++++ GISKG Y + F S+EE
Sbjct: 22 DIFIANGY-ENTTLAFIINKLGISKGALYHY--FSSKEE 57
>2id6_A Transcriptional regulator, TETR family; 1.75A {Thermotoga
maritima} SCOP: a.4.1.9 a.121.1.1 PDB: 3ih2_A 3ih3_A
3ih4_A 1zkg_A* 2iek_A* 1z77_A*
Length = 202
Score = 29.7 bits (67), Expect = 0.68
Identities = 7/26 (26%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG 85
E+F + G + + ++AG++KG
Sbjct: 16 EVFGKKG-YDRATTDEIAEKAGVAKG 40
>3egq_A TETR family transcriptional regulator; DNA-binding, transcription
regulation, bacterial regulatory DNA/RNA-binding
3-helical bundle fold; HET: MSE PE8; 2.55A
{Archaeoglobus fulgidus}
Length = 170
Score = 29.5 bits (66), Expect = 0.69
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKGYGFITFDSEEE 96
L+ + +V I + A +SK F F+S+++
Sbjct: 15 RLYMKKP-PHEVSIEEIAREAKVSKSLIFYHFESKQK 50
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 28.3 bits (63), Expect = 0.80
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISKGYG--FITFDSEEEAKR 99
E E E +YG V + I F+ F+ E A +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIK 71
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 28.2 bits (62), Expect = 0.86
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++D L L +YG V + + + G + F + + A+
Sbjct: 30 SKDVLLRLLQKYGEVLNLVL----SSKKPGTAVVEFATVKAAEL 69
>3f0c_A TETR-molecule A, transcriptional regulator; MCSG,PSI, SAD,
structural genomics, protein structure initiative;
2.96A {Cytophaga hutchinsonii}
Length = 216
Score = 29.0 bits (65), Expect = 1.1
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 62 ELFSQYGIVK-QVKIVVDRAGISKG--YGFITFDSEEE 96
+ F+ YG+ K + + G+ K Y + F +E
Sbjct: 22 KRFAHYGLCKTTMNEIASDVGMGKASLYYY--FPDKET 57
>2eh3_A Transcriptional regulator; all alpha proteins, tetracyclin
repressor-like, C-terminal D homeodomain-like,
DNA/RNA-binding 3-helical bundle; 1.55A {Aquifex
aeolicus}
Length = 179
Score = 28.6 bits (64), Expect = 1.2
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 7/39 (17%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG--YGFITFDSEEE 96
ELF + G + + +V RA +SKG Y F S+EE
Sbjct: 13 ELFFEKG-YQGTSVEEIVKRANLSKGAFYFH--FKSKEE 48
>3geu_A Intercellular adhesion protein R; TETR family, intercellular
adhesion regulator, IDP00851, DNA repressor,
transcription; HET: MSE; 1.90A {Staphylococcus aureus}
Length = 189
Score = 28.7 bits (64), Expect = 1.3
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 11/41 (26%)
Query: 62 ELFSQYGIVKQVKI--VVDRAGISKG----YGFITFDSEEE 96
LFS+ G + + I K + FDS++
Sbjct: 14 TLFSEKG-YDGTTLDDIAKSVNIKKASLYYH----FDSKKS 49
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 27.7 bits (61), Expect = 1.4
Identities = 10/51 (19%), Positives = 21/51 (41%)
Query: 81 GISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQGFTGTYDS 131
I+ + F +++ A+R QK +N R+ ++ K + T
Sbjct: 43 SITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCETSGP 93
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 27.7 bits (62), Expect = 1.4
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+D++ E +++G V + I VD+ ++G ++ S A
Sbjct: 31 KDDVIEECNKHGGV--IHIYVDKNS-AQGNVYVKCPSIAAAIA 70
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 91
Score = 27.3 bits (60), Expect = 1.5
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 58 DELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIA 117
DEL + F+ +G V ++ V D+ ++TF A + + + + IA
Sbjct: 30 DELLQQFASFGEVILIRFVEDKM-------WVTFLEGSSALNVL-SLNGKELLNRTITIA 81
Query: 118 P 118
Sbjct: 82 L 82
>3csk_A Probable dipeptidyl-peptidase 3; Zn-hydrolase, aminodipeptidase,
hexxgh-motif, aminopeptidase hydrolase, metal-binding,
metalloprotease; 1.95A {Saccharomyces cerevisiae}
Length = 711
Score = 28.7 bits (63), Expect = 2.1
Identities = 7/51 (13%), Positives = 17/51 (33%), Gaps = 1/51 (1%)
Query: 78 DRAGISKGY-GFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQGFTG 127
+ +GI + + ++E + +N L + +K F
Sbjct: 329 EPSGIIGEFESLVAIQNKERTAKFSSLVNNAEEFISLLPWSKDYEKPIFNP 379
>3sqr_A Laccase; multicopper oxidase, glycosylation, oxidoreductase; HET:
NAG BMA MAN; 1.67A {Botrytis aclada}
Length = 580
Score = 28.6 bits (64), Expect = 2.1
Identities = 7/62 (11%), Positives = 20/62 (32%), Gaps = 3/62 (4%)
Query: 130 DSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAFFPSNGQSMVPTSPPTVPTQVKILLPP 189
+ + ++ + + + N + N S++ + PT +KI
Sbjct: 371 EPVASLVPHLALDVGGYSLVDEQVSSAFTNYFTWTI-NSSSLLL--DWSSPTTLKIFNNE 427
Query: 190 GV 191
+
Sbjct: 428 TI 429
>3fvy_A Dipeptidyl-peptidase 3; SGC, DPP3, alternative splicing,
aminopeptidase, cytoplasm, hydrolase, metal-binding,
metalloprotease, phosphoprotein; 1.90A {Homo sapiens}
PDB: 3t6b_A 3t6j_A
Length = 728
Score = 28.7 bits (63), Expect = 2.3
Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 2/68 (2%)
Query: 78 DRAGISKGY-GFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQGFTG-TYDSLPTV 135
D G + GF+ ++ + + ++ + K L P +K F + SL +
Sbjct: 322 DPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVL 381
Query: 136 TSPVPPVP 143
T +P
Sbjct: 382 TFAGSGIP 389
>2pfm_A Adenylosuccinate lyase; PURB, purine biosynthesis, B anthracis;
2.00A {Bacillus anthracis} PDB: 1f1o_A 2x75_A*
Length = 444
Score = 28.1 bits (63), Expect = 2.9
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 51 ITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKG 85
ITS T++E+ E F+ ++ V + +R G+++
Sbjct: 410 ITSKLTQEEINECFNYEHHMQHVDTIFERLGLNEA 444
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc,
OB fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 26.1 bits (58), Expect = 3.4
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 83 SKGYGFITFDSEEE 96
KG+GFI ++ +
Sbjct: 13 DKGFGFIKDENGDN 26
>3o0d_A YALI0A20350P, triacylglycerol lipase; alpha/beta-hydrolase, lipids
binding, glycosylation, extracellular, hydrolase; HET:
NAG; 1.70A {Yarrowia lipolytica}
Length = 301
Score = 27.3 bits (60), Expect = 4.4
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 138 PVPPVPTSNMYYHNGLPYTYHNGMAFFPSN 167
VP VP + Y H + P +
Sbjct: 231 IVPQVPFWDGYQHCSGEVFIDWPLIHPPLS 260
>1fzc_B Fibrin; blood coagulation, plasma protein, crosslinking; HET: NAG
MAN; 2.30A {Homo sapiens} SCOP: d.171.1.1 h.1.8.1 PDB:
1fzb_B* 1fza_B* 1fze_B* 1fzf_B* 1fzg_B* 1n86_B* 1n8e_B
2h43_B* 2hlo_B* 2hod_B* 2hpc_B* 2q9i_B* 2xnx_B 2xny_B
3e1i_B* 2z4e_B* 2oyh_B* 1ltj_B* 1rf0_B* 1lt9_B* ...
Length = 328
Score = 27.2 bits (60), Expect = 5.1
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 10/41 (24%)
Query: 124 GFTGT-YDSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAF 163
+ GT ++L S + + T HNGM F
Sbjct: 211 KYRGTAGNALMDGASQLMGENRT---------MTIHNGMFF 242
>1h1n_A Endo type cellulase ENGI; hydrolase, glycosyl hydrolase, family 5,
subtype, thermophilic, thermophIle, endoglucanase; 1.12A
{Thermoascus aurantiacus} SCOP: c.1.8.3 PDB: 1gzj_A
Length = 305
Score = 27.2 bits (60), Expect = 5.6
Identities = 6/37 (16%), Positives = 11/37 (29%)
Query: 152 GLPYTYHNGMAFFPSNGQSMVPTSPPTVPTQVKILLP 188
+ ++ SM P + + IL P
Sbjct: 267 WTGAIWWAAGPWWGDYIFSMEPDNGIAYQQILPILTP 303
>3ghg_B Fibrinogen beta chain; triple-stranded coiled coil, beta sheets,
alpha helices, AMY amyloidosis, blood coagulation,
disease mutation, glycoprot phosphoprotein; HET: NAG NDG
BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_B*
1deq_B 2a45_H*
Length = 461
Score = 26.9 bits (59), Expect = 6.3
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 10/41 (24%)
Query: 124 GFTGT-YDSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAF 163
+ GT ++L S + + T HNGM F
Sbjct: 344 KYRGTAGNALMDGASQLMGENRT---------MTIHNGMFF 375
>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR,
cell cycle, protein turnover COM ligase-ligase inhibitor
complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1
c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A
Length = 336
Score = 26.8 bits (59), Expect = 6.4
Identities = 17/79 (21%), Positives = 28/79 (35%), Gaps = 1/79 (1%)
Query: 161 MAFFPSNGQSMVPTSPPTVPTQVKILLPPGVLLCGICLIFLITLALAPTIKRPSLKPLNS 220
+A S Q++ T P LL GV+ C + LA ++ ++
Sbjct: 42 LASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFR-CPRSFMDQPLAEHFSPFRVQHMDL 100
Query: 221 SQCKIKQSRGRLLSRACSS 239
S I+ S + CS
Sbjct: 101 SNSVIEVSTLHGILSQCSK 119
>1lwu_B Fibrinogen beta chain; heterotrimer, protein-peptide complex, blood
clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon
marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_B*
Length = 323
Score = 26.8 bits (59), Expect = 7.2
Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 10/41 (24%)
Query: 124 GFTGT-YDSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAF 163
++G ++L + + + T HNGM F
Sbjct: 208 DYSGNAGNALLEGATQLMGDNRT---------MTIHNGMQF 239
>1lgy_A Lipase, triacylglycerol lipase; hydrolase (carboxylic ester); 2.20A
{Rhizopus niveus} SCOP: c.69.1.17 PDB: 1tic_A
Length = 269
Score = 26.8 bits (59), Expect = 7.2
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 138 PVPPVPTSNM-YYHNGLPYTYHNGMAFF 164
VP VP + + H G+ +G +
Sbjct: 205 IVPHVPPQSFGFLHPGVESWIKSGTSNV 232
>3gwj_A Arylphorin; mono-glucosylated N-glycan, stability, glycosyla
glycoprotein, secreted, storage protein, oxygen
transport; HET: NAG BMA MAN GLC; 2.43A {Antheraea
pernyi}
Length = 674
Score = 26.8 bits (59), Expect = 7.5
Identities = 6/29 (20%), Positives = 12/29 (41%), Gaps = 3/29 (10%)
Query: 21 NNAFFNYQAAVNNNAPKYGTVVPKRVFVG 49
N+ FN + + V ++F+G
Sbjct: 484 NHQPFNINIDIKADVATDAVV---KIFMG 509
>1tib_A Lipase; hydrolase(carboxylic esterase); 1.84A {Thermomyces
lanuginosus} SCOP: c.69.1.17 PDB: 1dt3_A 1dt5_A 1du4_A
1ein_A* 1dte_A 4dyh_A* 4ea6_A 1gt6_A*
Length = 269
Score = 26.4 bits (58), Expect = 7.8
Identities = 7/33 (21%), Positives = 11/33 (33%), Gaps = 1/33 (3%)
Query: 138 PVPPVPTSNM-YYHNGLPYTYHNGMAFFPSNGQ 169
VP +P Y H+ Y +G +
Sbjct: 202 IVPRLPPREFGYSHSSPEYWIKSGTLVPVTRND 234
>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen,
blood clotting; HET: NDG NAG; 2.70A {Gallus gallus}
SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*
Length = 464
Score = 26.9 bits (59), Expect = 7.8
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 10/41 (24%)
Query: 124 GFTGT-YDSLPTVTSPVPPVPTSNMYYHNGLPYTYHNGMAF 163
+ G ++L S + + T HNGM F
Sbjct: 348 NYKGNAGNALMEGASQLYGENRT---------MTIHNGMYF 379
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure initiative;
NMR {Homo sapiens}
Length = 97
Score = 25.1 bits (55), Expect = 9.6
Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 7/70 (10%)
Query: 56 TEDELCELFSQYGIV-----KQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFK 110
T+++L E + + S+ Y I F + ++ + D +F
Sbjct: 22 TKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAY--INFRNPDDILLFRDRFDGYIFL 79
Query: 111 EKRLNIAPAI 120
+ + PA+
Sbjct: 80 DSKGLEYPAV 89
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
0.315 0.132 0.386
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: 3,609,778
Number of extensions: 213231
Number of successful extensions: 962
Number of sequences better than 10.0: 1
Number of HSP's gapped: 781
Number of HSP's successfully gapped: 238
Length of query: 242
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 151
Effective length of database: 4,160,982
Effective search space: 628308282
Effective search space used: 628308282
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)