RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12245
(189 letters)
>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 = 141 bits (356), Expect = 4e-44
Identities = 83/106 (78%), Positives = 94/106 (88%), Gaps = 2/106 (1%)
Query: 28 SQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN 87
SQTI LLN+Y NPQNS++SADG L S V+D EMQEHYD FFE+VF E E+KYGE+EEMN
Sbjct: 1 SQTIALLNIYRNPQNSSQSADG--LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN 58
Query: 88 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
VCDNLGDHLVGNVY+KFRREEDAEKAV DLNNRWF G+P++AELSP
Sbjct: 59 VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104
>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 = 102 bits (257), Expect = 6e-29
Identities = 31/116 (26%), Positives = 45/116 (38%), Gaps = 21/116 (18%)
Query: 24 KPTFSQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEI 83
+P +Q L N++ N EE +DV EC K+G +
Sbjct: 3 QPLATQCFQLSNMF-----------------NPQTEEEVGWDTEIKDDVIEECN-KHGGV 44
Query: 84 EEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 139
+ V N GNVY+K A AVN L+ RWF G+ + A P+ +
Sbjct: 45 IHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHN 97
>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 = 99.4 bits (248), Expect = 1e-27
Identities = 27/117 (23%), Positives = 52/117 (44%), Gaps = 21/117 (17%)
Query: 23 NKPTFSQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGE 82
++ + +++ N++ E+ + ED+ VEC K+G+
Sbjct: 10 SRMRHERVVIIKNMF----------HPMDF------EDDPLVLNEIREDLRVECS-KFGQ 52
Query: 83 IEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL-SPVTDFR 138
I ++ + D H G + FR E+A+ + L+ RWFGGR + A+ TD++
Sbjct: 53 IRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQ 106
>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 = 90.2 bits (224), Expect = 5e-24
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL-----VGNVYIKFRR 106
++ N+ D + + D+ +V EC K+G + + + + ++++F
Sbjct: 24 VLRNMVDPK--DIDDDLEGEVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSI 80
Query: 107 EEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 139
+ KA+ LN RWF GR V AE+ F
Sbjct: 81 ASETHKAIQALNGRWFAGRKVVAEVYDQERFDN 113
>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 = 86.4 bits (214), Expect = 1e-22
Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 21/115 (18%)
Query: 28 SQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN 87
++ + L+N+ + E Y+ EDV EC KYG ++ +
Sbjct: 5 TEVLCLMNMV-----------------LPEELLDDEEYEEIVEDVRDECS-KYGLVKSIE 46
Query: 88 V---CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 139
+ D + G ++++F D +KA+ L R F R V + +
Sbjct: 47 IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR 101
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 79.5 bits (196), Expect = 6e-20
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 5/89 (5%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCD--NLGDHLVGNVYIKFRREED 109
L+ N+ E ++ + ECE KYG++ + + + D ++++F R E
Sbjct: 12 LLRNMVGAG--EVDEDLEVETKEECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVES 68
Query: 110 AEKAVNDLNNRWFGGRPVYAELSPVTDFR 138
A KAV DLN R+FGGR V A + FR
Sbjct: 69 AIKAVVDLNGRYFGGRVVKACFYNLDKFR 97
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 64.7 bits (158), Expect = 3e-14
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRRE 107
+ L NV + +++ KYGE+EE+ + HL G + F
Sbjct: 12 ARLNDNVRETFLKDM----CR--------KYGEVEEVEILLHPRTRKHL-GLARVLFTST 58
Query: 108 EDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 147
A++ V +L+ G ++A+L + + YE+
Sbjct: 59 RGAKETVKNLHLTSVMGNIIHAQLDI---KGQQRMKYYEL 95
>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 = 49.1 bits (117), Expect = 2e-08
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 13/87 (14%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD----HLVGNVYIKFR 105
L + D E+ + + F K+G+I ++ + ++ + Y+ +
Sbjct: 21 VGLSQRLADPEVLKRPEYF---------GKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 71
Query: 106 REEDAEKAVNDLNNRWFGGRPVYAELS 132
R EDA +A+ +NN GR + A L
Sbjct: 72 RSEDALRAIQCVNNVVVDGRTLKASLG 98
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 46.9 bits (112), Expect = 1e-07
Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 20/104 (19%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L + VT+E +++ F ++G++E + + +I F + A
Sbjct: 19 LANTVTEEILEKA----FS--------QFGKLERVKKLKDYA-------FIHFDERDGAV 59
Query: 112 KAVNDLNNRWFGGRPVYAELS-PVTDFREACCRQYEMGECTRSG 154
KA+ ++N + G + + P R+ Q + SG
Sbjct: 60 KAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 46.0 bits (109), Expect = 4e-07
Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 10/78 (12%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
V E++Q G+I ++ V + + G YI F +E A+ V
Sbjct: 40 EVPKEKLQALLYALAS--------SQGDILDIVVDLSDDNS--GKAYIVFATQESAQAFV 89
Query: 115 NDLNNRWFGGRPVYAELS 132
F G P+ S
Sbjct: 90 EAFQGYPFQGNPLVITFS 107
>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 = 45.4 bits (108), Expect = 5e-07
Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 17/76 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
+ S +TD+ M++ F +G+I E+ V G +++F E A
Sbjct: 33 IASGLTDQLMRQT----FS--------PFGQIMEIRVFPEKG---YS--FVRFSTHESAA 75
Query: 112 KAVNDLNNRWFGGRPV 127
A+ +N G V
Sbjct: 76 HAIVSVNGTTIEGHVV 91
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 47.1 bits (112), Expect = 6e-07
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 15/86 (17%)
Query: 58 DEEMQEHYDNFFEDVFVECEDKYGEIE------EMNVCDNLGDHLVGNVYIKFRREEDAE 111
D++++ +V EC K+G + E + + +V ++++F +
Sbjct: 139 DDDLEG-------EVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIV-KIFVEFSIASETH 189
Query: 112 KAVNDLNNRWFGGRPVYAELSPVTDF 137
KA+ LN RWF GR V AE+ F
Sbjct: 190 KAIQALNGRWFAGRKVVAEVYDQERF 215
>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 = 44.5 bits (106), Expect = 7e-07
Identities = 12/78 (15%), Positives = 33/78 (42%), Gaps = 10/78 (12%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ +E+++ F ++G+I ++ V +L + G ++ F+ A A+
Sbjct: 19 KIKKDELKKSLHAIFS--------RFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 115 NDLNNRWFGGRPVYAELS 132
+ F +P+ + +
Sbjct: 69 RSMQGFPFYDKPMRIQYA 86
>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 = 46.1 bits (110), Expect = 1e-06
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 13/87 (14%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
++T ++ +E +G +E + G + ++ +++ A +A
Sbjct: 106 SLTQQQFEE----LVR--------PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 114 VNDLNNRWFGGRPVYAELSPVTDFREA 140
+DL + G R +Y + A
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPA 180
Score = 43.4 bits (103), Expect = 1e-05
Identities = 11/112 (9%), Positives = 21/112 (18%), Gaps = 22/112 (19%)
Query: 17 RCSRIHNKPTFSQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVEC 76
+ L + L D +
Sbjct: 168 YVHWTDAGQLTPALLHSRCLCV-----------DRLPPGFNDVDA-------LCRAL--- 206
Query: 77 EDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+ L G +++ E AE+A + GG +
Sbjct: 207 -SAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLR 257
Score = 38.8 bits (91), Expect = 5e-04
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
++ E AE A+N + R + +L P
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSVQLQP 93
>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 = 46.0 bits (108), Expect = 2e-06
Identities = 16/98 (16%), Positives = 39/98 (39%), Gaps = 21/98 (21%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD 94
+YIN +L + +E+++ F ++G+I ++ V +L
Sbjct: 11 TIYIN-----------NLNEKIKKDELKKSLYAIFS--------QFGQILDILVSRSLK- 50
Query: 95 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
+ G ++ F+ A A+ + F +P+ + +
Sbjct: 51 -MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
Score = 29.1 bits (64), Expect = 0.88
Identities = 6/51 (11%), Positives = 16/51 (31%), Gaps = 5/51 (9%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF-GGRPVY 128
++ +E+ + +++F E A A + L +
Sbjct: 230 QFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDALQGFKITQNNAMK 276
>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 = 43.6 bits (103), Expect = 2e-06
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 17/90 (18%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 110
+L + E+QE F ++G + + + + ++F +A
Sbjct: 17 NLPAGTLAAEIQE----TFS--------RFGSLGRVLLPEG-----GITAIVEFLEPLEA 59
Query: 111 EKAVNDLNNRWFGGRPVYAELSPVTDFREA 140
KA L F P+Y E +P+ F A
Sbjct: 60 RKAFRHLAYSKFHHVPLYLEWAPIGVFGAA 89
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 43.4 bits (103), Expect = 2e-06
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 19/81 (23%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
+V + E+ E F +G ++E+ + + +++F E A
Sbjct: 39 FPLDVQESELNEI----FG--------PFGPMKEVKILNGFA-------FVEFEEAESAA 79
Query: 112 KAVNDLNNRWFGGRPVYAELS 132
KA+ +++ + F +P+ S
Sbjct: 80 KAIEEVHGKSFANQPLEVVYS 100
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 43.1 bits (102), Expect = 3e-06
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 17/76 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
+ T+ ++ F+ +G I + G +IK+ E A
Sbjct: 35 IPHFATEADLIPL----FQ--------NFGFILDFKHYPEKG---CC--FIKYDTHEQAA 77
Query: 112 KAVNDLNNRWFGGRPV 127
+ L N F GR +
Sbjct: 78 VCIVALANFPFQGRNL 93
>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 = 41.9 bits (99), Expect = 7e-06
Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 13/79 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 113
V+ +E+ + FF Y I + + N G + F ++A A
Sbjct: 26 TVSIDEILD----FFYG--------YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 114 VNDLNNRWFGGRPVYAELS 132
V DLN+R G R V L
Sbjct: 74 VIDLNDRPIGSRKVKLVLG 92
>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 = 42.9 bits (102), Expect = 9e-06
Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 24/95 (25%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLG 93
NL +N +L ++TD E+ F G I + D
Sbjct: 5 NLIVN-----------YLPQDMTDRELYA----LFR--------AIGPINTCRIMRDYKT 41
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+ G ++ F E D+++A+ LN + +
Sbjct: 42 GYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Score = 37.2 bits (87), Expect = 0.001
Identities = 22/96 (22%), Positives = 46/96 (47%), Gaps = 20/96 (20%)
Query: 41 QNSAKSADGSHL-ISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGD 94
+ +S ++L ++N +TD+++ F KYG I + N+ D L
Sbjct: 81 RPGGESIKDTNLYVTNLPRTITDDQLDT----IFG--------KYGSIVQKNILRDKLTG 128
Query: 95 HLVGNVYIKFRREEDAEKAVNDLNNRWFGG--RPVY 128
G ++++ + E+A++A++ LNN G +P+
Sbjct: 129 RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 164
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 17/77 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L ++T+EEM++ FE KYG+ E+ + + G G +I+ AE
Sbjct: 23 LPPDITEEEMRK----LFE--------KYGKAGEVFIHKDKG---FG--FIRLETRTLAE 65
Query: 112 KAVNDLNNRWFGGRPVY 128
A +L+N G+ +
Sbjct: 66 IAKVELDNMPLRGKQLR 82
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 43.5 bits (103), Expect = 1e-05
Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 19/79 (24%)
Query: 54 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREED 109
+++D++++ FE +G+I+ + D G +I++ + +
Sbjct: 135 QDLSDDDIKS----VFE--------AFGKIKSATL---ARDPTTGKHKGYGFIEYEKAQS 179
Query: 110 AEKAVNDLNNRWFGGRPVY 128
++ AV+ +N GG+ +
Sbjct: 180 SQDAVSSMNLFDLGGQYLR 198
Score = 38.1 bits (89), Expect = 6e-04
Identities = 12/75 (16%), Positives = 34/75 (45%), Gaps = 13/75 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
+ ++ +++ F +G I+ +++ D++ G ++++ E A+ A
Sbjct: 39 ELGEDTIRQ----AFA--------PFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 114 VNDLNNRWFGGRPVY 128
+ +N+ GGR +
Sbjct: 87 LEQMNSVMLGGRNIK 101
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 15/82 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 113
V+ +E+ + FF Y I + + N G + F ++A A
Sbjct: 26 TVSIDEILD----FFYG--------YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 114 VNDLNNRWFGGRPVYAELSPVT 135
V DLN+R G R V +LS +
Sbjct: 74 VIDLNDRPIGSRKV--KLSGPS 93
>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 = 41.1 bits (97), Expect = 2e-05
Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 17/81 (20%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L+ + ++E +++ F V + ++ F EDA
Sbjct: 23 LMLSTSEEMIEKE----FN--------NIKPGAVERV-----KKIRDYAFVHFSNREDAV 65
Query: 112 KAVNDLNNRWFGGRPVYAELS 132
+A+ LN + G P+ L+
Sbjct: 66 EAMKALNGKVLDGSPIEVTLA 86
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 11/80 (13%), Positives = 21/80 (26%), Gaps = 15/80 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV--CDNLGDHLVGNVYIKFRREEDAEK 112
+ T +++ + + YI +EDA
Sbjct: 128 SYTQRNIRD----LLQ--------DINVVALSIRLPSLRFNTSR-RFAYIDVTSKEDARY 174
Query: 113 AVNDLNNRWFGGRPVYAELS 132
V LN G + ++S
Sbjct: 175 CVEKLNGLKIEGYTLVTKVS 194
Score = 39.2 bits (92), Expect = 3e-04
Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 14/76 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ ++ + +F+ G I ++V D+L + I+F R + A A+
Sbjct: 52 SYNQNKVYK----YFKH--------CGPIIHVDVADSLKKNF-RFARIEFARYDGALAAI 98
Query: 115 NDLNNRWFGGRPVYAE 130
+ G +
Sbjct: 99 TKTHKV-VGQNEIIVS 113
Score = 38.0 bits (89), Expect = 8e-04
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 14/80 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV--CDNLGDHLVGNVYIKFRREEDAEK 112
+ DE + + F + +G IE++N+ ++ F ++ AE+
Sbjct: 221 ELLDENL-------LRESF----EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 269
Query: 113 AVNDLNNRWFGGRPVYAELS 132
A+ +N G R + L+
Sbjct: 270 ALQ-MNRSLLGNREISVSLA 288
>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 = 42.8 bits (101), Expect = 2e-05
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 17/77 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L +++T+E+ + FE +YGE E+ + + G +I+ AE
Sbjct: 30 LPTDITEEDFKRL----FE--------RYGEPSEVFINRDRG-----FGFIRLESRTLAE 72
Query: 112 KAVNDLNNRWFGGRPVY 128
A +L+ RP+
Sbjct: 73 IAKAELDGTILKSRPLR 89
Score = 33.9 bits (78), Expect = 0.017
Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 18/91 (19%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
V++E +++ F ++G +E+ V D+ G G +++F + A KA
Sbjct: 107 VVSNELLEQ----AFS--------QFGPVEKAVVVVDDRGRAT-GKGFVEFAAKPPARKA 153
Query: 114 VNDLNNRWF----GGRPVYAELSPVTDFREA 140
+ + F RPV E D +
Sbjct: 154 LERCGDGAFLLTTTPRPVIVEPMEQFDDEDG 184
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 16/74 (21%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
N+T++E++E FE EI + G G YI+F+ E DAEK +
Sbjct: 110 NITEDELKE----VFE--------DALEIRLV---SQDG-KSKGIAYIEFKSEADAEKNL 153
Query: 115 NDLNNRWFGGRPVY 128
+ GR V
Sbjct: 154 EEKQGAEIDGRSVS 167
Score = 38.0 bits (89), Expect = 6e-04
Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 13/86 (15%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
N + E++ + ++ V D Y+ F ED EKA+
Sbjct: 24 NKSVAELKV----AIS--------ELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREA 140
+L G + E D ++
Sbjct: 72 -ELTGLKVFGNEIKLEKPKGRDSKKV 96
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 16/119 (13%), Positives = 42/119 (35%), Gaps = 19/119 (15%)
Query: 17 RCSRIHNKPTFSQTILLLNLYINPQNSAKSADGSHLI------SNVTDEEMQEHYDNFFE 70
+ R H+ ++Y+ S D +H + + + D++++E
Sbjct: 81 KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL----LT 136
Query: 71 DVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+G ++ N+ D+ G + ++ ++A+ LN G + +
Sbjct: 137 --------SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 187
Score = 32.3 bits (74), Expect = 0.050
Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 7/74 (9%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+T+E M + FF + D +++FR ++ +A+
Sbjct: 15 GITEEAMMD----FFNAQMRLGGLTQAPGNPVLAVQINQDKNFA--FLEFRSVDETTQAM 68
Query: 115 NDLNNRWFGGRPVY 128
+ F G+ +
Sbjct: 69 A-FDGIIFQGQSLK 81
>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 = 39.8 bits (94), Expect = 4e-05
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
+T + F +G I + V D G ++ F + DAE A
Sbjct: 17 EITTAAIAA----AFA--------PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 114 VNDLNNRWFGGRPV 127
+ + +W GGR +
Sbjct: 65 IQQMGGQWLGGRQI 78
>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 = 40.4 bits (95), Expect = 4e-05
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 20/97 (20%)
Query: 39 NPQNSAKSADGSH-------LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-D 90
+ + K +H L +T E+++ F +G I + V D
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKA----AFA--------PFGRISDARVVKD 50
Query: 91 NLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G ++ F + DAE A+ + +W GGR +
Sbjct: 51 MATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>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 = 41.0 bits (97), Expect = 4e-05
Identities = 23/95 (24%), Positives = 37/95 (38%), Gaps = 24/95 (25%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLG 93
NL +N +L N+T EE + F GEIE + D +
Sbjct: 4 NLIVN-----------YLPQNMTQEEFRS----LFG--------SIGEIESCKLVRDKIT 40
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+G ++ + +DAEKA+N LN + +
Sbjct: 41 GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 75
Score = 34.9 bits (81), Expect = 0.007
Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 26/99 (26%)
Query: 41 QNSAKSADGSHL-ISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDH 95
+ S+ S ++L +S +T +E E +F +YG I + L D
Sbjct: 80 RPSSASIRDANLYVSGLPKTMTQKE--------LEQLF----SQYGRIITSRI---LVDQ 124
Query: 96 LVGNV----YIKFRREEDAEKAVNDLNNRWFGG--RPVY 128
+ G +I+F + +AE+A+ LN + G P+
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163
>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 = 39.5 bits (93), Expect = 5e-05
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
V +E + E F + G + ++ +C D G ++ F+ E A
Sbjct: 27 RVREEILYEL----FL--------QAGPLTKVTICKDREGKPK-SFGFVCFKHPESVSYA 73
Query: 114 VNDLNNRWFGGRPVY 128
+ LN GRP+
Sbjct: 74 IALLNGIRLYGRPIN 88
>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 = 39.1 bits (92), Expect = 7e-05
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 19/82 (23%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 110
++ + T +E++ FE + G + E +V + ++ +E DA
Sbjct: 16 NVSAACTSQELRS----LFE--------RRGRVIECDVVKDYA-------FVHMEKEADA 56
Query: 111 EKAVNDLNNRWFGGRPVYAELS 132
+ A+ LN + G+ + ELS
Sbjct: 57 KAAIAQLNGKEVKGKRINVELS 78
>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 = 39.3 bits (92), Expect = 7e-05
Identities = 12/86 (13%), Positives = 31/86 (36%), Gaps = 14/86 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ + ++++ FF + ++ +++ + GN +KF +D +A+
Sbjct: 27 SAMENDVRD----FFHGL---------RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL 73
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREA 140
N R V + + A
Sbjct: 74 -KRNRMLMIQRYVEVSPATERQWVAA 98
>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 = 39.8 bits (93), Expect = 1e-04
Identities = 13/98 (13%), Positives = 36/98 (36%), Gaps = 17/98 (17%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD 94
+Y+ N L +V +++++ + + + + ++
Sbjct: 47 RIYVK--N---------LAKHVQEKDLKYIFGRYVDF------SSETQRIMFDIRLMKEG 89
Query: 95 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
+ G +I E+ A KA+ + N G+P+ + +
Sbjct: 90 RMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA 127
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 38.9 bits (91), Expect = 1e-04
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 56 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 115
+ E N +F K+G+I + G G +++++ A AV
Sbjct: 25 QVGPDRLEKLKNVIHKIF----SKFGKITNDFYPEEDGKTK-GYIFLEYASPAHAVDAVK 79
Query: 116 DLNNRWFGGR 125
+ + +
Sbjct: 80 NADGYKLDKQ 89
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 38.7 bits (91), Expect = 1e-04
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
++E++++ F YG + E++ D+L G ++ F E A KA
Sbjct: 19 TSSEEDLEKL----FS--------AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
Query: 114 VNDLNNRWFGGRPV 127
+++ + F GR +
Sbjct: 67 YAEVDGQVFQGRML 80
>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 = 38.4 bits (90), Expect = 1e-04
Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 16/82 (19%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV---GNVYIKFRREEDA 110
+ T+E ++ F K G I+ + ++ G ++++++ E A
Sbjct: 16 STTEETLKGV----FS--------KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 111 EKAVNDLNNRWFGGRPVYAELS 132
+KA+ L G + +S
Sbjct: 64 QKALKQLQGHTVDGHKLEVRIS 85
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 38.3 bits (90), Expect = 2e-04
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 11/63 (17%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
+F YG I ++N+ + G +I+F + A+ + G+ +
Sbjct: 29 FRIF----SPYGHIMQINIKNAFG-------FIQFDNPQSVRDAIECESQEMNFGKKLIL 77
Query: 130 ELS 132
E+S
Sbjct: 78 EVS 80
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
++ ++ F K+G I E+ + D G +I F DA+ A
Sbjct: 18 ETNEKMLKAV----FG--------KHGPISEVLLIKDRTSKSR-GFAFITFENPADAKNA 64
Query: 114 VNDLNNRWFGGRPVY 128
D+N + G+ +
Sbjct: 65 AKDMNGKSLHGKAIK 79
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 38.6 bits (90), Expect = 2e-04
Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ T ++++E + E G++ + + L G++++ F E A+K V
Sbjct: 22 DATLDDIKE----WLE--------DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 69
Query: 115 NDLNNRWFGGRPVY 128
+ + + +
Sbjct: 70 -ETPGQKYKETDLL 82
>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 = 39.9 bits (93), Expect = 2e-04
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L+SN+ E + + +F+ YG+++ + + N N ++ A+
Sbjct: 7 LVSNLNPERVTP------QSLFILFG-VYGDVQRVKILFNKK----ENALVQMADGNQAQ 55
Query: 112 KAVNDLNNRWFGGRPVYAELS 132
A++ LN G+P+ LS
Sbjct: 56 LAMSHLNGHKLHGKPIRITLS 76
Score = 27.2 bits (60), Expect = 3.1
Identities = 13/84 (15%), Positives = 31/84 (36%), Gaps = 24/84 (28%)
Query: 50 SHLISNVTDEEMQEHYDNFFE----DVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFR 105
S++ +V++E+++ + + F + + K I+
Sbjct: 126 SNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA-------------------LIQMG 166
Query: 106 REEDAEKAVNDLNNRWFG-GRPVY 128
E+A +A+ DL+N G +
Sbjct: 167 SVEEAVQALIDLHNHDLGENHHLR 190
>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 = 38.5 bits (90), Expect = 2e-04
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 11/63 (17%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
E +F KYG + +V ++++ E A AV N R G+ +
Sbjct: 46 ETIF----SKYGRVAGCSVHKGYA-------FVQYSNERHARAAVLGENGRVLAGQTLDI 94
Query: 130 ELS 132
++
Sbjct: 95 NMA 97
>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 = 38.5 bits (90), Expect = 2e-04
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 14/78 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+T EEM + F KYG I ++ V + G Y+ + DA+ AV
Sbjct: 19 KITAEEMYD----IFG--------KYGPIRQIRVGNTPETR--GTAYVVYEDIFDAKNAV 64
Query: 115 NDLNNRWFGGRPVYAELS 132
+ L+ R +
Sbjct: 65 DHLSGFNVSNRYLVVLYY 82
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 37.8 bits (88), Expect = 2e-04
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 56 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 115
+ E N +F K+G+I + G G +++++ A AV
Sbjct: 11 QVGPDRLEKLKNVIHKIF----SKFGKITNDFYPEEDGKTK-GYIFLEYASPAHAVDAVK 65
Query: 116 DLNNRWFGGR 125
+ + +
Sbjct: 66 NADGYKLDKQ 75
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 16/87 (18%), Positives = 26/87 (29%), Gaps = 13/87 (14%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
N + E++ + ++ V D Y+ F ED EKA+
Sbjct: 28 NKSVAELKV----AIS--------ELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREAC 141
+L G + E D C
Sbjct: 76 -ELTGLKVFGNEIKLEKPKGRDGTRGC 101
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 19/81 (23%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
+ T++E++ FE +YG + E ++ + ++ R EDA
Sbjct: 18 ISPTCTNQELRAK----FE--------EYGPVIECDIVKDYA-------FVHMERAEDAV 58
Query: 112 KAVNDLNNRWFGGRPVYAELS 132
+A+ L+N F G+ ++ +LS
Sbjct: 59 EAIRGLDNTEFQGKRMHVQLS 79
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 37.8 bits (88), Expect = 2e-04
Identities = 11/84 (13%), Positives = 27/84 (32%), Gaps = 14/84 (16%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
++ ++ E + +YG +E + D V + + ++
Sbjct: 21 RNIPPHLQWEVLDS----LLV--------QYGVVESCEQVNT--DSETAVVNVTYSSKDQ 66
Query: 110 AEKAVNDLNNRWFGGRPVYAELSP 133
A +A++ LN + P
Sbjct: 67 ARQALDKLNGFQLENFTLKVAYIP 90
>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 = 37.7 bits (88), Expect = 2e-04
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 11/63 (17%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
+F YG I ++N+ +I+F + A+ + G+ +
Sbjct: 41 FRIF----SPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89
Query: 130 ELS 132
E+S
Sbjct: 90 EVS 92
>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 = 37.5 bits (88), Expect = 2e-04
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ F ++DA+ A++ + + GRP+
Sbjct: 47 FVSFTSQDDAQNAMDSMQGQDLNGRPLR 74
>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 = 38.7 bits (91), Expect = 3e-04
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ F ++DA+ A++ + + GRP+
Sbjct: 133 FVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 37.1 bits (87), Expect = 0.001
Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 14/77 (18%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDA 110
L +T++ +++ F G I + + D ++ ++++ + DA
Sbjct: 8 LDKAITEDILKQ--------YFQVG----GPIANIKIMIDKNNKNV-NYAFVEYHQSHDA 54
Query: 111 EKAVNDLNNRWFGGRPV 127
A+ LN + V
Sbjct: 55 NIALQTLNGKQIENNIV 71
>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 = 37.6 bits (88), Expect = 3e-04
Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 17/75 (22%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAEK 112
+VT+ + + +F + G + + +H + Y ++F DA
Sbjct: 26 DVTEVLILQ--------LFSQ----IGPCKSCKMIT---EHTSNDPYCFVEFYEHRDAAA 70
Query: 113 AVNDLNNRWFGGRPV 127
A+ +N R G+ V
Sbjct: 71 ALAAMNGRKILGKEV 85
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 37.6 bits (88), Expect = 3e-04
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNL-GDHLVGNVYIKFRREEDAEK 112
V++ + E +F++ G + ++ D + G H G +++F EEDA+
Sbjct: 26 KVSEPLLWE--------LFLQ----AGPVVNTHMPKDRVTGQHQ-GYGFVEFLSEEDADY 72
Query: 113 AVNDLNNRWFGGRPV 127
A+ ++ G+P+
Sbjct: 73 AIKIMDMIKLYGKPI 87
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 39.4 bits (91), Expect = 3e-04
Identities = 21/143 (14%), Positives = 40/143 (27%), Gaps = 24/143 (16%)
Query: 3 CSFYFKIGACRHGDRCSRIHNKPTFSQTI--------------LLLNLYINPQNSAKSAD 48
C F F G C G +C +H+ P Y S
Sbjct: 73 CLF-FAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFR 131
Query: 49 GSH---LISNVTDEEMQEHY-DNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKF 104
+ + + +H E + G+I+ + ++KF
Sbjct: 132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKF 186
Query: 105 RREEDAEKAVNDLNNRWFGGRPV 127
+ + +AE A ++N+
Sbjct: 187 KYQANAEFAKEAMSNQTLLLPSD 209
Score = 29.0 bits (64), Expect = 0.85
Identities = 6/41 (14%), Positives = 13/41 (31%)
Query: 138 REACCRQYEMGECTRSGFCNFMHLKPISRELRRYLYSRRKR 178
+ C + G C C ++H P ++ +
Sbjct: 69 QLFFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVL 109
>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 = 37.2 bits (87), Expect = 3e-04
Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 19/81 (23%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L T++E++ FE +YG++ E ++ N G ++ + AE
Sbjct: 16 LPREATEQEIRS----LFE--------QYGKVLECDIIKNYG-------FVHIEDKTAAE 56
Query: 112 KAVNDLNNRWFGGRPVYAELS 132
A+ +L++ G + E S
Sbjct: 57 DAIRNLHHYKLHGVNINVEAS 77
>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 = 37.6 bits (88), Expect = 3e-04
Identities = 16/96 (16%), Positives = 34/96 (35%), Gaps = 27/96 (28%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
NLYI S+L ++ ++E++ + +G++ + D+ G
Sbjct: 27 NLYI-----------SNLPLSMDEQELENM----LK--------PFGQVISTRILRDSSG 63
Query: 94 DHL-VGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
VG + + E E + N ++ P
Sbjct: 64 TSRGVG--FARMESTEKCEAVIGHFNGKFIKTPPGV 97
>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 = 37.8 bits (88), Expect = 3e-04
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 14/86 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 113
++T ++ + F E E ++V + +G ++F+ E+DA K+
Sbjct: 26 SITKMDVLQ----FLEG--------IPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73
Query: 114 VNDLNNRWFGGRPVYAELSPVTDFRE 139
L+ + GR + + + D RE
Sbjct: 74 ER-LHRKKLNGREAFVHVVTLEDMRE 98
>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 = 37.2 bits (87), Expect = 4e-04
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ F E+A KAV ++N R +P+Y
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLY 86
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 14/80 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
V+D ++QE F ++G +++ V D G +G + F R+ DA KA
Sbjct: 40 GVSDADIQEL----FA--------EFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKA 86
Query: 114 VNDLNNRWFGGRPVYAELSP 133
+ N GRP+ +L
Sbjct: 87 MKQYNGVPLDGRPMNIQLVT 106
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 17/74 (22%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
++T ++ F +G I ++++ ++ + + E A++AV
Sbjct: 24 DMTPTLLRGA----FS--------PFGNIIDLSMDPPRN---CA--FVTYEKMESADQAV 66
Query: 115 NDLNNRWFGGRPVY 128
+LN +
Sbjct: 67 AELNGTQVESVQLK 80
>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 = 38.8 bits (90), Expect = 4e-04
Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 11/97 (11%)
Query: 37 YINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL 96
I A + + L+SN+ E + + +F+ YG+++ + + N
Sbjct: 23 RIAIPGLAGAGNSVLLVSNLNPERVTP------QSLFILFG-VYGDVQRVKILFNKK--- 72
Query: 97 VGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
N ++ A+ A++ LN G+P+ LS
Sbjct: 73 -ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 108
Score = 27.3 bits (60), Expect = 3.3
Identities = 11/80 (13%), Positives = 28/80 (35%), Gaps = 16/80 (20%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
S++ +V++E+++ + + V + I+ E+
Sbjct: 157 SNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR---------------KMALIQMGSVEE 201
Query: 110 AEKAVNDLNN-RWFGGRPVY 128
A +A+ DL+N +
Sbjct: 202 AVQALIDLHNHDLGENHHLR 221
>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 = 37.4 bits (87), Expect = 5e-04
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
V+D ++QE F ++G +++ V + +G + F R DA KA+
Sbjct: 46 GVSDADIQE----LFA--------EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 93
Query: 115 NDLNNRWFGGRPVYAEL 131
GRP+ +L
Sbjct: 94 KQYKGVPLDGRPMDIQL 110
>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 = 38.4 bits (90), Expect = 5e-04
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ F +E AE+A+ +N R V+
Sbjct: 147 FVHFETQEAAERAIEKMNGMLLNDRKVF 174
Score = 37.6 bits (88), Expect = 8e-04
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDA 110
L +VT+ + E F G I + VC D + +G Y+ F++ DA
Sbjct: 23 LHPDVTEAMLYE--------KFSPA----GPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Query: 111 EKAVNDLNNRWFGGRPV 127
E+A++ +N G+PV
Sbjct: 71 ERALDTMNFDVIKGKPV 87
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 38.3 bits (89), Expect = 5e-04
Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 12/86 (13%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
V+D ++QE F ++G +++ V + +G + F R DA KA+
Sbjct: 99 GVSDADIQE----LFA--------EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 146
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREA 140
GRP+ +L E
Sbjct: 147 KQYKGVPLDGRPMDIQLVASQIDLEH 172
>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 = 37.4 bits (87), Expect = 5e-04
Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 17/74 (22%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
++T ++ F +G I ++++ ++ + + E A++AV
Sbjct: 48 DMTPTLLRGA----FS--------PFGNIIDLSMDPPRN---CA--FVTYEKMESADQAV 90
Query: 115 NDLNNRWFGGRPVY 128
+LN +
Sbjct: 91 AELNGTQVESVQLK 104
>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 = 36.5 bits (85), Expect = 5e-04
Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 18/79 (22%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
L +T+ +++ H F ++GEI + V +I+F +
Sbjct: 18 GGLGDTITETDLRNH----FY--------QFGEIRTITVVQRQQ---CA--FIQFATRQA 60
Query: 110 AEKAVND-LNNRWFGGRPV 127
AE A N GR +
Sbjct: 61 AEVAAEKSFNKLIVNGRRL 79
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 36.8 bits (86), Expect = 6e-04
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+I F + ++ A+ +N ++ RP+
Sbjct: 52 FINFASFDASDAAIEAMNGQYLCNRPIT 79
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 37.5 bits (87), Expect = 6e-04
Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
V D+ + F+ +G+I ++ + D + G +++F EDA A
Sbjct: 74 EVDDKVLHA--------AFIP----FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 114 VNDLNNRWFGGRPV 127
++++N GR +
Sbjct: 122 IDNMNESELFGRTI 135
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 37.0 bits (86), Expect = 6e-04
Identities = 16/98 (16%), Positives = 29/98 (29%), Gaps = 30/98 (30%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD 94
NL+I HL TD ++ F +G + V D
Sbjct: 42 NLFIY-----------HLPQEFTDTDLAST----FL--------PFGNVISAKV---FID 75
Query: 95 HLVGNV----YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ F + A+ A+ +N G + +
Sbjct: 76 KQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113
>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 = 36.2 bits (84), Expect = 7e-04
Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 18/83 (21%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 110
+L + +E+ D+ + + KY + D ++ E A
Sbjct: 12 NLPQDSNCQEV--------HDLLKDYDLKYCYV----------DRNKRTAFVTLLNGEQA 53
Query: 111 EKAVNDLNNRWFGGRPVYAELSP 133
+ A+ + F G+ + +L P
Sbjct: 54 QNAIQMFHQYSFRGKDLIVQLQP 76
>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 = 36.8 bits (85), Expect = 7e-04
Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 10/86 (11%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ + E++Q F D + + ++ G +++ E+D + A+
Sbjct: 28 SCSIEDVQN----FLSDC-----TIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREA 140
+ G R + S T+
Sbjct: 79 -KKDRESMGHRYIEVFKSHRTEMDWV 103
>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 = 36.0 bits (84), Expect = 9e-04
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 14/75 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV-GNVYIKFRREEDAEK 112
NVT + + E F YG+I+ +++ + + HL G Y++F ++AEK
Sbjct: 15 NVTKDHIMEI----FS--------TYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 113 AVNDLNNRWFGGRPV 127
A+ ++ G+ +
Sbjct: 63 ALKHMDGGQIDGQEI 77
>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 = 35.9 bits (83), Expect = 0.001
Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 14/87 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 113
+ EE+ + FF + M + + G +++F +E AEKA
Sbjct: 26 GCSKEEIVQ----FFSG--------LEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73
Query: 114 VNDLNNRWFGGRPVYAELSPVTDFREA 140
+ + G R + S + R +
Sbjct: 74 L-KKHKERIGHRYIEIFKSSRAEVRTS 99
>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 = 35.7 bits (83), Expect = 0.001
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 15/73 (20%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ T+E +QE FE K I+ V N G +I+F EDA++A+
Sbjct: 26 SATEETLQE----VFE--------KATFIK---VPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 115 NDLNNRWFGGRPV 127
N N R GR +
Sbjct: 71 NSCNKREIEGRAI 83
>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 = 37.9 bits (87), Expect = 0.002
Identities = 17/149 (11%), Positives = 44/149 (29%), Gaps = 42/149 (28%)
Query: 53 ISNVTDEEMQEHYDNFF---EDVFVE--------CEDKYGEIEE-MNVCDNLG------- 93
++ + E ++ +D + + ++ +N
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422
Query: 94 DHLVG--NVYIKFRREEDAEKAVND-LNNRWFGGRPVYAELS--PVTDFREACCRQYEMG 148
+ + ++Y++ + + + E A++ + + Y D QY
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDH-------YNIPKTFDSDDLIPPYLDQY--- 472
Query: 149 ECTRSGFCNFM--HLKPISRELRRYLYSR 175
F + + HLK I R L+
Sbjct: 473 ------FYSHIGHHLKNIEHPERMTLFRM 495
Score = 31.4 bits (70), Expect = 0.20
Identities = 21/134 (15%), Positives = 40/134 (29%), Gaps = 31/134 (23%)
Query: 4 SFYFKIGACRHGDRCSRIHNKPTFSQTILLLNLYINPQN------SAKSAD-------GS 50
S Y ++ + +H +++ Y P+ D G
Sbjct: 430 SIYLEL--KVKLENEYALHRS--------IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVE---CEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 107
HL + E M F + F+E D ++ + L Y + +
Sbjct: 480 HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL---KFYKPYICD 536
Query: 108 EDA--EKAVNDLNN 119
D E+ VN + +
Sbjct: 537 NDPKYERLVNAILD 550
Score = 31.0 bits (69), Expect = 0.27
Identities = 28/216 (12%), Positives = 54/216 (25%), Gaps = 73/216 (33%)
Query: 18 CSRIHNKPT-FSQTILLLNLYINPQNS--------AKSADGSHLISNVTDEEMQ------ 62
I S T+ L ++ Q + L+S + E+ Q
Sbjct: 51 IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR 110
Query: 63 ---EHYDNFFEDV------FVECEDKYGEIEE---------------M----------NV 88
E D + D V Y ++ + + +V
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV 170
Query: 89 CDNLG--DHLVGNVY-IKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQY 145
C + + ++ + + E + L + P + S
Sbjct: 171 CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS------------- 217
Query: 146 EMGECTRSGFCN-FMHLKPISRELRRYLYSRRKRSS 180
N + + I ELRR L S+ +
Sbjct: 218 -------DHSSNIKLRIHSIQAELRRLLKSKPYENC 246
>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 = 35.3 bits (82), Expect = 0.002
Identities = 25/94 (26%), Positives = 37/94 (39%), Gaps = 21/94 (22%)
Query: 39 NPQNSAKSADGSHL----IS-NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLG 93
+P S K L +S N+T++E++E FE EI +
Sbjct: 6 DPCTSKKVRAARTLLAKNLSFNITEDELKE----VFE--------DALEIRL----VSQD 49
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G YI+F+ E DAEK + + GR V
Sbjct: 50 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 83
>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 = 35.2 bits (82), Expect = 0.002
Identities = 17/94 (18%), Positives = 28/94 (29%), Gaps = 24/94 (25%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
LYI L TD+++ + + YG+I D
Sbjct: 7 GLYI-----------RGLQPGTTDQDLVKL----CQ--------PYGKIVSTKAILDKTT 43
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
+ G ++ F A+KAV L +
Sbjct: 44 NKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 35.7 bits (82), Expect = 0.002
Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 17/69 (24%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L + V+ ++ E K G ++ + + N + ++R E+++
Sbjct: 35 LGNGVSRNQLLP----VLE--------KCGLVDALLMPPN-----KPYSFARYRTTEESK 77
Query: 112 KAVNDLNNR 120
+A LN +
Sbjct: 78 RAYVTLNGK 86
>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 = 35.4 bits (82), Expect = 0.002
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 22/80 (27%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGN----VYIKFRREEDA 110
N+ +++++ FE ++G+I E+ V L D G ++ + E A
Sbjct: 24 NLDEKDLKP----LFE--------EFGKIYELTV---LKDRFTGMHKGCAFLTYCERESA 68
Query: 111 EKAVNDLNN---RWFGGRPV 127
KA + L+ RP+
Sbjct: 69 LKAQSALHEQKTLPGMNRPI 88
>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 = 35.2 bits (82), Expect = 0.002
Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
V D+ + F+ +G+I ++ + D+ +++F EDA
Sbjct: 18 EVDDKVLHA--------AFIP----FGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 62
Query: 111 EKAVNDLNNRWFGGRPV 127
A++++N GR +
Sbjct: 63 AAAIDNMNESELFGRTI 79
>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 = 35.6 bits (82), Expect = 0.002
Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 10/89 (11%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ T E++ FF D + ++ N G+ I+ E+D +KA+
Sbjct: 22 SCTMEDVLN----FFSDCRIR-----NGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREACCR 143
+ + + G R V D
Sbjct: 73 -EKHRMYMGQRYVEVYEINNEDVDALMKS 100
>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 = 36.4 bits (85), Expect = 0.002
Identities = 16/116 (13%), Positives = 34/116 (29%), Gaps = 22/116 (18%)
Query: 22 HNKPTFSQTILLLNLYINPQNSAKSADGSHL-ISN----VTDEEMQEHYDNFFEDVFVEC 76
HN + + + + L I T+ +++ F
Sbjct: 68 HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV----MFS------ 117
Query: 77 EDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR---WFGGRPVY 128
+G+IEE + G G ++ F A+ A+ ++ P+
Sbjct: 118 --SFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170
Score = 36.4 bits (85), Expect = 0.002
Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 26/89 (29%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
+++ + ++++++E FE +YG + E+NV D
Sbjct: 5 KMFVG-----------QVPRTWSEKDLRE----LFE--------QYGAVYEINVLRDRSQ 41
Query: 94 DHLV--GNVYIKFRREEDAEKAVNDLNNR 120
+ G ++ F + A +A N L+N
Sbjct: 42 NPPQSKGCCFVTFYTRKAALEAQNALHNM 70
>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 = 35.4 bits (82), Expect = 0.002
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 104 FRREEDAEKAVNDLNNRWFGGRPVY 128
F + +A +A++ N + RP++
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMH 87
>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 = 35.3 bits (82), Expect = 0.002
Identities = 14/95 (14%), Positives = 34/95 (35%), Gaps = 24/95 (25%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
LY+ +L VT+ ++ + ++ E + + +
Sbjct: 27 VLYLK-----------NLSPRVTERDLVSLFA------------RFQEKKGPPIQFRMMT 63
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+ G +I F +E A +A++ +N G+ +
Sbjct: 64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV 98
>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 = 35.6 bits (82), Expect = 0.003
Identities = 12/87 (13%), Positives = 30/87 (34%), Gaps = 14/87 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 113
++ + + FF+ +E+ + + G +++FR E D + A
Sbjct: 36 EAENKHVID----FFKK--------LDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83
Query: 114 VNDLNNRWFGGRPVYAELSPVTDFREA 140
+ + ++ G R + E
Sbjct: 84 L-CRHKQYMGNRFIQVHPITKKGMLEK 109
>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 = 35.4 bits (81), Expect = 0.003
Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 10/86 (11%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ + E++Q F D + ++ G +++ E+D + A+
Sbjct: 55 SCSVEDVQN----FLSDCTIH-----DGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREA 140
+ G R + S T+
Sbjct: 106 -KKDRESMGHRYIEVFKSHRTEMDWV 130
>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 = 35.0 bits (81), Expect = 0.003
Identities = 14/98 (14%), Positives = 29/98 (29%), Gaps = 30/98 (30%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD 94
NL+I HL D+++ + F +G + V D
Sbjct: 27 NLFIY-----------HLPQEFGDQDLLQM----FM--------PFGNVVSAKV---FID 60
Query: 95 HLVGNV----YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ + A+ A+ +N G + +
Sbjct: 61 KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK 98
>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 = 34.9 bits (81), Expect = 0.003
Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
+ + ++QE F +G I + + D G +I F R EDA
Sbjct: 26 DTRETDLQEL----FR--------PFGSISRIYL---AKDKTTGQSKGFAFISFHRREDA 70
Query: 111 EKAVNDLNNRWFGGRPV 127
+A+ ++ + +
Sbjct: 71 ARAIAGVSGFGYDHLIL 87
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 34.6 bits (80), Expect = 0.003
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
E F YG + + + N G +++F DAE AV L+ + G V
Sbjct: 18 ERAF----SYYGPLRTVWIARNPP----GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69
Query: 130 ELS 132
ELS
Sbjct: 70 ELS 72
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 34.6 bits (80), Expect = 0.004
Identities = 7/29 (24%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 101 YIKFRREEDAEKAVNDLNNR-WFGGRPVY 128
++KF E + ++A+ + G +PV
Sbjct: 55 FVKFTDELEQKRALTECQGAVGLGSKPVR 83
>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 = 34.5 bits (80), Expect = 0.004
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEMGECTRSGFCN 157
++ F +E AE+A+ +N R V+ V F+ R+ E+G F N
Sbjct: 49 FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAELGA-RAKEFTN 99
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 34.3 bits (79), Expect = 0.004
Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 79 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 125
K G++ M D G ++++ DA+K + + + +
Sbjct: 35 KAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>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 = 35.3 bits (82), Expect = 0.004
Identities = 4/28 (14%), Positives = 12/28 (42%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+ ++ ++A+ LN G + +
Sbjct: 140 FCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Score = 29.1 bits (66), Expect = 0.52
Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 7/73 (9%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+T+E M + FF + D +++FR ++ +A+
Sbjct: 15 GITEEAMMD----FFNAQMRLGGLTQAPGNPVLAVQINQDKNFA--FLEFRSVDETTQAM 68
Query: 115 NDLNNRWFGGRPV 127
+ F G+ +
Sbjct: 69 A-FDGIIFQGQSL 80
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 34.6 bits (80), Expect = 0.004
Identities = 15/98 (15%), Positives = 32/98 (32%), Gaps = 28/98 (28%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
L++ L ++E++ F+ +G I+E V G
Sbjct: 17 KLFV-----------GMLNKQQSEEDVLR----LFQ--------PFGVIDECTVLRGPDG 53
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWF---GGRPVY 128
G ++KF +A+ A++ L+ +
Sbjct: 54 SS-KGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV 90
>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 = 34.1 bits (79), Expect = 0.004
Identities = 13/76 (17%), Positives = 23/76 (30%), Gaps = 17/76 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L N + F D++G I D++ YI++ + A+
Sbjct: 25 LGPNTSLAA--------LAREF----DRFGSIRT---IDHVKGD--SFAYIQYESLDAAQ 67
Query: 112 KAVNDLNNRWFGGRPV 127
A + GG
Sbjct: 68 AACAKMRGFPLGGPDR 83
>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 = 34.6 bits (80), Expect = 0.004
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
EDVF KYG I ++++ + G +++F DAE AV + + G +
Sbjct: 40 EDVF----YKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93
Query: 130 ELS 132
E
Sbjct: 94 EFP 96
>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 = 34.6 bits (80), Expect = 0.005
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
N+T++ ++ FE +G IE + + D+ G +I F E A+KA
Sbjct: 37 NITEDMLRG----IFE--------PFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 114 VNDLNNRWFGGRPV 127
+ LN GRP+
Sbjct: 85 LEQLNGFELAGRPM 98
>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 = 33.8 bits (78), Expect = 0.005
Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
NVT++ + E F + + + + N + G +++ F EE+ ++A+
Sbjct: 21 NVTEKNVME----FLAPL---------KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL 67
Query: 115 NDLNNRWFGGRPVYAELSPVT 135
N + GGR + E+
Sbjct: 68 -KCNREYMGGRYI--EVFREK 85
>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 = 33.7 bits (78), Expect = 0.007
Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
V D+ + F+ +G+I ++ + D+ +++F EDA
Sbjct: 23 EVDDKVLHA--------AFIP----FGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 67
Query: 111 EKAVNDLNNRWFGGRPV 127
A++++N GR +
Sbjct: 68 AAAIDNMNESELFGRTI 84
>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 = 33.7 bits (78), Expect = 0.007
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+I+FR E + AV +LN G R +
Sbjct: 48 FIEFRDLESSASAVRNLNGYQLGSRFL 74
>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 = 33.9 bits (78), Expect = 0.007
Identities = 11/82 (13%), Positives = 28/82 (34%), Gaps = 21/82 (25%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV---------GNVYIKFR 105
+VT +++ + F+ + G ++ H+ G+ + +
Sbjct: 26 SVTLDDLADF----FK--------QCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 106 REEDAEKAVNDLNNRWFGGRPV 127
A+ AV + + F G +
Sbjct: 74 DPPTAKAAVEWFDGKDFQGSKL 95
>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 = 33.8 bits (78), Expect = 0.007
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 21/82 (25%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV---------GNVYIKFR 105
NVT E + + +F+ + G I+ +L G + F
Sbjct: 24 NVTIESVAD----YFK--------QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 106 REEDAEKAVNDLNNRWFGGRPV 127
A+ A++ + + F G P+
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPI 93
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 34.1 bits (78), Expect = 0.007
Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 14/86 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 113
T EE+ + FF + + + + + G +++F +E AEKA
Sbjct: 53 GCTKEEIVQ----FFSG--------LEIVPNGITLPVDPEGKITGEAFVQFASQELAEKA 100
Query: 114 VNDLNNRWFGGRPVYAELSPVTDFRE 139
+ + G R + S + R
Sbjct: 101 L-GKHKERIGHRYIEVFKSSQEEVRS 125
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 33.7 bits (77), Expect = 0.007
Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 19/83 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L +VT+ E+ +G++ + + +I+ EE A
Sbjct: 24 LPIDVTEGEVISL----GL--------PFGKVTNLLMLKG-----KNQAFIEMNTEEAAN 66
Query: 112 KAVNDL--NNRWFGGRPVYAELS 132
VN G+P+Y + S
Sbjct: 67 TMVNYYTSVTPVLRGQPIYIQFS 89
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 34.1 bits (78), Expect = 0.008
Identities = 16/89 (17%), Positives = 29/89 (32%), Gaps = 9/89 (10%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
T EE+ F + G E + G+ ++ F EE A+ A+
Sbjct: 34 TATAEEVVAF--------FGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 115 NDLNNRWFGGRPVYAELSPVTDFREACCR 143
+ G R + S + ++ R
Sbjct: 86 -RKHKDLLGKRYIELFRSTAAEVQQVLNR 113
>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 = 33.9 bits (78), Expect = 0.009
Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 19/80 (23%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
+ +E + E + ++G+++ + V +H G + +F +E A+K
Sbjct: 26 DSEEEALGEV----LQ--------QFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
Query: 114 VNDLNNRW------FGGRPV 127
+ + GR +
Sbjct: 74 LAAASLEAEGGGLKLDGRQL 93
>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 = 33.6 bits (77), Expect = 0.009
Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 19/83 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L VT+ E+ +G++ + + +++ EE A
Sbjct: 23 LPGEVTETEVIAL----GL--------PFGKVTNILMLKG-----KNQAFLELATEEAAI 65
Query: 112 KAVND--LNNRWFGGRPVYAELS 132
VN +P+Y + S
Sbjct: 66 TMVNYYSAVTPHLRNQPIYIQYS 88
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 33.4 bits (77), Expect = 0.009
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
+ ++ +++ F KYG+I E+ V + D ++ F +DA
Sbjct: 23 DTNEQSLEQV----FS--------KYGQISEVVV---VKDRETQRSRGFGFVTFENIDDA 67
Query: 111 EKAVNDLNNRWFGGRPV 127
+ A+ +N + GR +
Sbjct: 68 KDAMMAMNGKSVDGRQI 84
>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 = 34.1 bits (78), Expect = 0.009
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
E F YG + + V N G +++F DA AV +L+ R G V
Sbjct: 91 ERAF----GYYGPLRSVWVARNPP----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142
Query: 130 ELS 132
ELS
Sbjct: 143 ELS 145
>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 = 34.7 bits (79), Expect = 0.010
Identities = 8/57 (14%), Positives = 20/57 (35%), Gaps = 3/57 (5%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV---YAELSPVTDFREACCRQYEMGECTRSG 154
+ E ++K ++ L R G+ ++ F + + G+ + G
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172
>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 = 34.7 bits (79), Expect = 0.010
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 138
YG +E++ + G ++ ++A+ LNN + G+ + +S
Sbjct: 28 LYGNVEKVKFMKSKP----GAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIM 83
Query: 139 E 139
Sbjct: 84 P 84
Score = 32.0 bits (72), Expect = 0.071
Identities = 10/79 (12%), Positives = 24/79 (30%), Gaps = 13/79 (16%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREE 108
+ VT+E E + + G +V + + +++ +
Sbjct: 129 FNAPLEVTEENFFEI----CD--------ELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176
Query: 109 DAEKAVNDLNNRWFGGRPV 127
DA + + LN+
Sbjct: 177 DALETLGFLNHYQMKNPNG 195
>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 = 33.3 bits (77), Expect = 0.010
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
N+T++ ++ FE +G+I+ + + D+ G +I F E A +A
Sbjct: 16 NITEDMLRGI----FE--------PFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 114 VNDLNNRWFGGRPV 127
+ LN GRP+
Sbjct: 64 LEQLNGFELAGRPM 77
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 33.1 bits (76), Expect = 0.013
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 21/82 (25%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV---------GNVYIKFR 105
NVT E + + +F+ + G I+ +L G + F
Sbjct: 18 NVTIESVAD----YFK--------QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 106 REEDAEKAVNDLNNRWFGGRPV 127
A+ A++ + + F G P+
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPI 87
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 32.6 bits (75), Expect = 0.016
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
D ++++ F ++G+I ++ + N G ++ F DA++A
Sbjct: 26 RFRDPDLRQM----FG--------QFGKILDVEIIFNERGSK-GFGFVTFENSADADRAR 72
Query: 115 NDLNNRWFGGRPVY 128
L+ GR +
Sbjct: 73 EKLHGTVVEGRKIE 86
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 32.7 bits (74), Expect = 0.016
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 138
G K+ E+A KA LNN ++AE + +
Sbjct: 44 GIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENEVQ 84
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 33.0 bits (75), Expect = 0.016
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 19/83 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L +VT+ E+ F G++ + + +I+ EE A
Sbjct: 39 LPIDVTEGEVISLGLPF------------GKVTNLLMLKG-----KNQAFIEMNTEEAAN 81
Query: 112 KAVND--LNNRWFGGRPVYAELS 132
VN G+P+Y + S
Sbjct: 82 TMVNYYTSVTPVLRGQPIYIQFS 104
>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 = 32.6 bits (75), Expect = 0.016
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
T+ +++E F KYG I ++++ + D ++ F +DA
Sbjct: 26 YTTERDLREV----FS--------KYGPIADVSI---VYDQQSRRSRGFAFVYFENVDDA 70
Query: 111 EKAVNDLNNRWFGGRPV 127
++A N GR +
Sbjct: 71 KEAKERANGMELDGRRI 87
>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 = 33.2 bits (76), Expect = 0.019
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
T+E++ E F K G+I+++ + D + G ++++ DAE A
Sbjct: 50 YTTEEQIYEL----FS--------KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 114 VNDLNNRWFGGRPVYAELSP 133
+ +N R + +
Sbjct: 98 MRYINGTRLDDRIIRTDWDA 117
>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 = 33.3 bits (76), Expect = 0.021
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+++F + DAE A++ ++ GR +
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGREL 142
>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 = 32.2 bits (74), Expect = 0.021
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
++ F EEDA+ A + + G V
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKV 84
>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 = 32.2 bits (74), Expect = 0.023
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+++F DA+ A ++ GR +
Sbjct: 59 FVRFHDRRDAQDAEAAMDGAELDGREL 85
>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 = 32.8 bits (75), Expect = 0.023
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 14/74 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKA 113
T ++++ H F G I + +CD H G YI+F + A
Sbjct: 47 GSTAQDLEAH----FS--------SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 114 VNDLNNRWFGGRPV 127
V ++ F GR +
Sbjct: 95 VA-MDETVFRGRTI 107
>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 = 32.2 bits (74), Expect = 0.025
Identities = 11/82 (13%), Positives = 26/82 (31%), Gaps = 22/82 (26%)
Query: 54 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAE 111
VT +++++ F V G Y + + + A
Sbjct: 18 PAVTADDLRQ----LFG--------DRKLPLAGQVLLKSG-------YAFVDYPDQNWAI 58
Query: 112 KAVNDLNNRW-FGGRPVYAELS 132
+A+ L+ + G+ + + S
Sbjct: 59 RAIETLSGKVELHGKIMEVDYS 80
>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 = 31.8 bits (73), Expect = 0.027
Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
++T+ ++ F KYG++ ++ + + D +I F ++ A
Sbjct: 27 SLTNNDLYR----IFS--------KYGKVVKVTI---MKDKDTRKSKGVAFILFLDKDSA 71
Query: 111 EKAVNDLNNRWFGGRPV 127
+ +NN+ GR +
Sbjct: 72 QNCTRAINNKQLFGRVI 88
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 31.8 bits (73), Expect = 0.027
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
+KF E AE+A +N GR +
Sbjct: 52 VVKFESPEVAERACRMMNGMKLSGREID 79
>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 = 32.3 bits (74), Expect = 0.029
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 17/77 (22%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV---CDNLGDHLVGNVYIKFRREEDAE 111
E++E F +GE++ + + G H G ++ F ++DA+
Sbjct: 26 QANQREIRE----LFS--------TFGELKTVRLPKKMTGTGAHR-GFGFVDFITKQDAK 72
Query: 112 KAVNDLNN-RWFGGRPV 127
KA N L + GR +
Sbjct: 73 KAFNALCHSTHLYGRRL 89
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 32.1 bits (73), Expect = 0.030
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 130
G ++F EE +A+ LNN F G + E
Sbjct: 68 GTGALEFPSEEILVEALERLNNIEFRGSVITVE 100
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 31.7 bits (72), Expect = 0.033
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
++ + A++AV+ L G + L+
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 31.9 bits (73), Expect = 0.035
Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 14/74 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKA 113
+ T EE++E + +G ++++ V + G G Y+++ E A +A
Sbjct: 28 SCTKEELEE----ICK--------AHGTVKDLRLVTNRAG-KPKGLAYVEYENESQASQA 74
Query: 114 VNDLNNRWFGGRPV 127
V ++ +
Sbjct: 75 VMKMDGMTIKENII 88
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 31.8 bits (73), Expect = 0.039
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
T+E++ D F E YGEI+ +++ NL D G + +++ ++A
Sbjct: 34 EATEEDIH--------DKFAE----YGEIKNIHL--NL-DRRTGYLKGYTLVEYETYKEA 78
Query: 111 EKAVNDLNNRWFGGRPV 127
+ A+ LN + G+P+
Sbjct: 79 QAAMEGLNGQDLMGQPI 95
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 32.0 bits (73), Expect = 0.044
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+++F + DAE A++ ++ GR +
Sbjct: 93 FVRFHDKRDAEDAMDAMDGAVLDGREL 119
>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 = 31.6 bits (72), Expect = 0.045
Identities = 11/73 (15%), Positives = 23/73 (31%), Gaps = 14/73 (19%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
T+ ++ FF + +++ + G ++F EDA A+
Sbjct: 26 RATENDIYN----FFSPL---------NPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM 72
Query: 115 NDLNNRWFGGRPV 127
+ R V
Sbjct: 73 -AKDKANMQHRYV 84
>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 = 31.6 bits (72), Expect = 0.052
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
++ F +DA++A N GR +
Sbjct: 92 FVYFENVDDAKEAKERANGMELDGRRI 118
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 31.5 bits (72), Expect = 0.054
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
D ++++ F ++G+I ++ + N G ++ F DA++A
Sbjct: 40 RFRDPDLRQM----FG--------QFGKILDVEIIFN-ERGSKGFGFVTFENSADADRAR 86
Query: 115 NDLNNRWFGGRPVY 128
L+ GR +
Sbjct: 87 EKLHGTVVEGRKIE 100
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 31.3 bits (70), Expect = 0.059
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 15/84 (17%)
Query: 58 DEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV--- 114
++E + Y +DV + KYGE+ + + G ++F + AE AV
Sbjct: 22 EDESKGGYS---KDVLLRLLQKYGEVLNLVLSSKKP----GTAVVEFATVKAAELAVQNE 74
Query: 115 -----NDLNNRWFGGRPVYAELSP 133
N L W G+P A
Sbjct: 75 VGLVDNPLKISWLEGQPQDASGPS 98
>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 = 31.6 bits (72), Expect = 0.073
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 24/93 (25%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
NL +N ++ + V + ++++ FE +YG IE + + CD
Sbjct: 44 NLMVN-----------YIPTTVDEVQLRQL----FE--------RYGPIESVKIVCDRET 80
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 126
G ++KF+ A++A+ LN +
Sbjct: 81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 31.4 bits (71), Expect = 0.084
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+ E K + L + G V
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKV 129
>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 = 30.9 bits (70), Expect = 0.086
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 20/79 (25%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVEC-EDKYGEIEEMNVCDNLGDHLVGNVYIKFRREE 108
S L + + +++++H + + + D G +E F R+E
Sbjct: 21 SGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVE-------------------FVRKE 61
Query: 109 DAEKAVNDLNNRWFGGRPV 127
D AV L+N F
Sbjct: 62 DMTYAVRKLDNTKFRSHEG 80
>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1
Length = 98
Score = 30.8 bits (69), Expect = 0.090
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 3 CSFYFKIGACRHGDRCSRIHNKPTFSQTILL 33
C Y G C +GD C H+ T LL
Sbjct: 39 CKLYHTTGNCINGDDCMFSHDPLTEETRELL 69
Score = 26.2 bits (57), Expect = 2.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 142 CRQYEMGECTRSGFCNFMH 160
C+ Y G C R+ C +MH
Sbjct: 16 CKFYITGFCARAENCPYMH 34
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 30.5 bits (69), Expect = 0.095
Identities = 16/83 (19%), Positives = 25/83 (30%), Gaps = 19/83 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
LI V + ++ E F G I + V ++F A
Sbjct: 29 LIDGVVEADLVEALQEF------------GPISYVVVMPKKRQ-----ALVEFEDVLGAC 71
Query: 112 KAVNDLNNR--WFGGRPVYAELS 132
AVN + + G P + S
Sbjct: 72 NAVNYAADNQIYIAGHPAFVNYS 94
>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 = 30.2 bits (69), Expect = 0.10
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 14/74 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
T EE++ H F G + + + CD H G YI+F +E +
Sbjct: 17 GATAEELEAH----FHG--------CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 114 VNDLNNRWFGGRPV 127
+ L+ F GR +
Sbjct: 65 L-ALDESLFRGRQI 77
>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 = 30.4 bits (69), Expect = 0.11
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRP 126
+++F AEK ++ +N + G
Sbjct: 56 FVEFADLATAEKCLHKINGKPLPGAT 81
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 31.3 bits (70), Expect = 0.12
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
G++ + + L G++++ F E A+K V + + +
Sbjct: 132 DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK-YKETDLLILFK 184
>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding
protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A
Length = 77
Score = 29.5 bits (66), Expect = 0.16
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 3 CSFYFKIGACRHGDRCSRIHNK 24
C + G C +G RC IHN
Sbjct: 53 CHKFKLQGRCPYGSRCHFIHNP 74
Score = 28.4 bits (63), Expect = 0.46
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 3 CSFYFKIGACRHGDRCSRIHNK 24
C Y + G CR+G +C H
Sbjct: 15 CRTYSESGRCRYGAKCQFAHGL 36
>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 = 30.6 bits (69), Expect = 0.17
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 79 KYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
YGEI+ ++ D G +++ + A A LN G+ +
Sbjct: 95 DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 145
>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 = 29.6 bits (66), Expect = 0.19
Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 15/96 (15%)
Query: 42 NSAKSADGSHL-ISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL 96
+S S +G+ + +SN ++ +E+Q+ F ++G+++ + + + L
Sbjct: 2 SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFA--------RHGKVKSVELSPHTDYQL 53
Query: 97 VGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
V + +DA AVN L+ G + + L+
Sbjct: 54 KAVV--QMENLQDAIGAVNSLHRYKIGSKKILVSLA 87
>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 = 29.2 bits (66), Expect = 0.29
Identities = 11/74 (14%), Positives = 27/74 (36%), Gaps = 14/74 (18%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKA 113
+ ++++ FF G++ ++ + D G Y++F + A
Sbjct: 36 RIRPRDLED----FFS--------AVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 83
Query: 114 VNDLNNRWFGGRPV 127
+ L + G P+
Sbjct: 84 IG-LTGQRLLGVPI 96
>2zue_A Arginyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase, nucleotide-binding, protein
biosynthesis, ligase/RNA complex; HET: ANP; 2.00A
{Pyrococcus horikoshii} PDB: 2zuf_A
Length = 629
Score = 30.4 bits (69), Expect = 0.30
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 75 ECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF----GGRPVYAE 130
E E E+ E + DN DH +G +Y++ R + + + G +
Sbjct: 185 EFERIMNELRERGLKDNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRK 244
Query: 131 L 131
L
Sbjct: 245 L 245
>2ww4_A 4-diphosphocytidyl-2C-methyl-D-erythritol kinase; non-mevalonate
pathway, isoprenoid biosynthesis, transferase; HET: ADP;
2.00A {Escherichia coli} PDB: 1oj4_A*
Length = 283
Score = 30.3 bits (69), Expect = 0.30
Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 12/74 (16%)
Query: 57 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGN-------VYIKFRREED 109
+ ++ + N E + + ++ E++ V L ++ V+ +F E +
Sbjct: 199 IETLLKCEFSNDCEVIARK---RFREVDA--VLSWLLEYAPSRLTGTGACVFAEFDTESE 253
Query: 110 AEKAVNDLNNRWFG 123
A + + G
Sbjct: 254 ARQVLEQAPEWLNG 267
>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 = 29.2 bits (66), Expect = 0.31
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 110
++E+Q + F + YGEI+ +++ NL D G +++ + A
Sbjct: 37 EAQEDEIQ--------EKFCD----YGEIKNIHL--NL-DRRTGFSKGYALVEYETHKQA 81
Query: 111 EKAVNDLNNRWFGGRPV 127
A LN G+ +
Sbjct: 82 LAAKEALNGAEIMGQTI 98
>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 = 29.4 bits (66), Expect = 0.33
Identities = 9/73 (12%), Positives = 23/73 (31%), Gaps = 14/73 (19%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
T+ ++ FF + +++ + G ++F E+A A+
Sbjct: 57 KATENDIYN----FFSPL---------NPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM 103
Query: 115 NDLNNRWFGGRPV 127
+ R +
Sbjct: 104 -SKDRANMQHRYI 115
>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 = 28.8 bits (65), Expect = 0.45
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
Y +F + A++ LN G + +
Sbjct: 61 YAEFEDLDSLLSALS-LNEESLGNKRIR 87
>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 = 28.6 bits (64), Expect = 0.51
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 104 FRREEDAEKAVNDLNNRWFGGRPV 127
F R+ED AV L+N F
Sbjct: 58 FVRKEDMTYAVRKLDNTKFRSHEG 81
>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 = 28.3 bits (64), Expect = 0.54
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 16/71 (22%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
T+++++E+ F +GE+ + V D H G +++F E K
Sbjct: 26 KTTEQDLKEY----FS--------TFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 114 VND---LNNRW 121
++ ++ RW
Sbjct: 74 MSQRHMIDGRW 84
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 28.1 bits (63), Expect = 0.62
Identities = 4/36 (11%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 101 YIKFRREEDAEKAVNDLNNR----WFGGRPVYAELS 132
+++ DA + + L + G+ + + +
Sbjct: 57 FVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase
(phospho), phosphatase, hydrolase (phosp glycolysis,
bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus}
SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A*
1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A
Length = 469
Score = 29.6 bits (66), Expect = 0.66
Identities = 20/104 (19%), Positives = 35/104 (33%), Gaps = 15/104 (14%)
Query: 54 SNVTDEE----MQEHYDNFFEDVFVE--CEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 107
+N T E N ++ FVE C D + N+ +G+ R
Sbjct: 131 TNTTRERRAMIFNFGEQNGYKTFFVESICVD------PEVIAANIVQVKLGSPDYVNR-- 182
Query: 108 EDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEMGECT 151
D+++A D R Y L D + + ++G+
Sbjct: 183 -DSDEATEDFMRRIECYENSYESLDEEQDRDLSYIKIMDVGQSY 225
>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 = 28.2 bits (63), Expect = 0.70
Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 11/75 (14%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
EE+ E E V ++ + + G ++++ A A
Sbjct: 19 MKKREEILEEIAKVTEGVL--------DVIVYASAADKMKN-RGFAFVEYESHRAAAMAR 69
Query: 115 NDLNNR--WFGGRPV 127
L G +
Sbjct: 70 RKLMPGRIQLWGHQI 84
>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 = 28.5 bits (64), Expect = 0.78
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+YGEI+ +++ NL D G + +++ ++A+ A+ LN + G+P+
Sbjct: 45 EYGEIKNIHL--NL-DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 94
>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 = 28.0 bits (63), Expect = 0.79
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 16/75 (21%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 113
+ + E++ FF +YG ++E+ + D G G ++ F + D +K
Sbjct: 20 RMDETEIRS----FFA--------RYGSVKEVKIITDRTGVSK-GYGFVSFYNDVDVQKI 66
Query: 114 VNDLNNRWFGGRPVY 128
V N F G+ +
Sbjct: 67 VESQIN--FHGKKLK 79
>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 = 27.5 bits (62), Expect = 0.99
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+ E ++K ++ L R G+
Sbjct: 49 LVGVGSEASSKKLMDLLPKRELHGQNP 75
>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 = 27.6 bits (62), Expect = 1.0
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+ +++ +E A A+ +LN R F GR +
Sbjct: 54 FCEYQDQETALSAMRNLNGREFSGRAL 80
>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 = 27.6 bits (62), Expect = 1.0
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
Y +F + A++ LN G R +
Sbjct: 65 YAEFEDLDSLLSALS-LNEESLGNRRIR 91
>3rfw_A Cell-binding factor 2; SURA-like, chaperone; 2.20A {Campylobacter
jejuni}
Length = 252
Score = 28.2 bits (63), Expect = 1.4
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 19/65 (29%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ +++ YD +DKY + + H I E++A+ +
Sbjct: 90 KIDAAKVKAFYDQN--------KDKYVKPARVQA-----KH------ILVATEKEAKDII 130
Query: 115 NDLNN 119
N+L
Sbjct: 131 NELKG 135
>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 = 28.5 bits (63), Expect = 1.6
Identities = 32/190 (16%), Positives = 51/190 (26%), Gaps = 71/190 (37%)
Query: 6 YFKIGACRHGDRCSRIHNKPTFSQTILLLNLYINPQNSAKSADGSHLIS------NVTD- 58
Y A R +K + S L A + L++ N D
Sbjct: 126 YIT--ARIMAKRPF---DKKSNS---ALFR--------AVGEGNAQLVAIFGGQGNTDDY 169
Query: 59 -EEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN-- 115
EE+++ Y + V ++ + L + R DAEK
Sbjct: 170 FEELRDLYQTYHV--LVG-----------DLIKFSAETLSELI----RTTLDAEKVFTQG 212
Query: 116 -DLNNRWFGG---RP-----VYAELS-P---VTDFREACCRQYEMGECTRSGFCNFMHLK 162
++ W P + +S P V Y + +
Sbjct: 213 LNI-LEWLENPSNTPDKDYLLSIPISCPLIGVIQL-----AHYVV-------TAKLLGFT 259
Query: 163 PISRELRRYL 172
P ELR YL
Sbjct: 260 P--GELRSYL 267
>3gja_A CYTC3; halogenase, beta barrel, biosynthetic protein; 2.20A
{Streptomyces} PDB: 3gjb_A*
Length = 319
Score = 28.1 bits (62), Expect = 1.8
Identities = 9/62 (14%), Positives = 17/62 (27%)
Query: 56 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 115
EEM ++ + Y + N HL ++ + + V
Sbjct: 32 FEPEEMTRRWNIIRRQLLDRSLAIYPDSNGKANISNYDRHLDIDLLAEHIMRPEIVDRVG 91
Query: 116 DL 117
L
Sbjct: 92 SL 93
>3pyf_A 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; transferase;
HET: ANP; 1.70A {Mycobacterium tuberculosis} PDB:
3pyd_A* 3pye_A* 3pyg_A* 4ed4_A* 4dxl_A* 4emd_A*
Length = 306
Score = 27.9 bits (63), Expect = 2.2
Identities = 6/31 (19%), Positives = 7/31 (22%), Gaps = 1/31 (3%)
Query: 104 FRREEDAEKAVNDLNNRWFGGRPVYAELSPV 134
A L+ R V PV
Sbjct: 265 CTSASSAIDVGAQLSGAGV-CRTVRVATGPV 294
>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 = 26.4 bits (59), Expect = 2.2
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 107 EEDAEKAVNDLNNRWFGGRPV 127
EE +A+ L+N F GR +
Sbjct: 52 EESVSEAIAKLDNTDFMGRTI 72
>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens}
Length = 354
Score = 27.9 bits (61), Expect = 2.4
Identities = 7/65 (10%), Positives = 21/65 (32%)
Query: 57 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND 116
++ + + ++ V C K + DH+ ++ D+ +
Sbjct: 26 NSTSIKYNLEELYQAVENLCSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKK 85
Query: 117 LNNRW 121
++ W
Sbjct: 86 IDRCW 90
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4;
influenza A, nonstructural protein, viral protein: HOST
complex, Zn finger; 1.95A {Homo sapiens}
Length = 72
Score = 26.0 bits (57), Expect = 2.8
Identities = 9/23 (39%), Positives = 10/23 (43%), Gaps = 1/23 (4%)
Query: 3 CSFYFKIGACRHGDRCSRIHNKP 25
C FY K G C C +H P
Sbjct: 47 CYFYSKFGECS-NKECPFLHIDP 68
Score = 25.6 bits (56), Expect = 3.8
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 142 CRQYEMGECTRSGFCNFMHLKPISR 166
C+ + G C + C F+H +++
Sbjct: 19 CKHWLRGLCKKGDQCEFLHEYDMTK 43
>4do7_A Amidohydrolase 2; enzyme function initiative, EFI, structural
TIM-barrel fold, putative lactonase; 1.70A {Burkholderia
multivorans} PDB: 4dlm_A 4dnm_A* 4dlf_A
Length = 303
Score = 27.0 bits (59), Expect = 4.5
Identities = 8/59 (13%), Positives = 16/59 (27%), Gaps = 1/59 (1%)
Query: 72 VFVECEDKYGEIEEMNVCDNLGDHLVGNV-YIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
+ V+ E + + V + R + AE+ + G R
Sbjct: 52 IAVQARAGRDETAFLLELACDEARIAAVVGWEDLRAPQLAERVAEWRGTKLRGFRHQLQ 110
>1iq0_A Arginyl-tRNA synthetase; riken structural genomics/proteomics
initiative, RSGI, structural genomics, ligase; 2.30A
{Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 d.67.2.1
Length = 592
Score = 26.9 bits (60), Expect = 4.8
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 93 GDHLVGNVYIKFRREEDAEKA 113
DH G Y++ ++ + E+
Sbjct: 176 YDHFAGRAYVRLHQDPEYERL 196
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 25.7 bits (57), Expect = 5.4
Identities = 5/27 (18%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
Y++F + ++A+ + G R +
Sbjct: 60 YVEFDEVDSLKEALT-YDGALLGDRSL 85
>3h7h_B Transcription elongation factor SPT5; helices surrounding beta
sheet, activator, ME binding, nucleus, repressor,
transcription regulation; 1.55A {Homo sapiens}
Length = 106
Score = 25.6 bits (56), Expect = 6.6
Identities = 5/26 (19%), Positives = 16/26 (61%)
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNN 119
+H+ G +Y++ ++ ++A+ + N
Sbjct: 48 EHVKGYIYVEAYKQTHVKQAIEGVGN 73
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit;
CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 77
Score = 24.9 bits (54), Expect = 8.0
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 142 CRQYEMGECTRSGFCNFMHLKPISRE 167
C+ + G C + C F+H +++
Sbjct: 13 CKHWLRGLCKKGDQCEFLHEYDMTKM 38
>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative
splicing, cytoplasm, metal-binding, nucleus,
RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}
Length = 89
Score = 24.8 bits (53), Expect = 8.1
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 132 SPVTDFREACCRQYEMGECTRSGFCNFMHLKP 163
V + R C G C+R C ++H
Sbjct: 44 CQVENGRVIACFDSLKGRCSREN-CKYLHPPT 74
>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform
1, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 98
Score = 24.8 bits (53), Expect = 8.6
Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 126 PVYAELSPVTDFREACCRQYEMGECTRSGFCNFMHLKPISRELRRYLYSRRKRSSRRS 183
P + + +D C Y G C R C + H L+ + + + ++++ +
Sbjct: 43 PADSTMIDTSDNTVTVCMDYIKGRCMREK-CKYFHPPA---HLQAKIKAAQHQANQAA 96
>3p3b_A Mandelate racemase/muconate lactonizing protein; enolase
superfamily fold, galacturonate dehydratase, D-tartr
galacturonate, lyase; HET: TAR; 1.65A {Geobacillus SP}
PDB: 3ops_A* 3n4f_A* 3qpe_A*
Length = 392
Score = 26.2 bits (58), Expect = 8.7
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVE 75
HL + V + E E+ D E + V
Sbjct: 324 HLSAAVRNFEFVEYDDITIEGMDVS 348
>1yo7_A Regulatory protein ROP; protein design, RE-engineering of
topology, four-helix bundle, replication regulator;
2.80A {Escherichia coli}
Length = 120
Score = 25.1 bits (54), Expect = 9.3
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 59 EEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDH 95
E + +H D + + E+ ++C++L DH
Sbjct: 39 ESLHDHADELYRSCLASFKKNGQIDEQADICESLHDH 75
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
0.322 0.137 0.426
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: 2,993,322
Number of extensions: 172854
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 223
Length of query: 189
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 101
Effective length of database: 4,244,745
Effective search space: 428719245
Effective search space used: 428719245
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)