RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4990
(130 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 = 116 bits (292), Expect = 3e-35
Identities = 64/78 (82%), Positives = 72/78 (92%)
Query: 6 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 65
V+D EMQEHYD FFE+VF E E+KYGE+EEMNVCDNLGDHLVGNVY+KFRREEDAEKAV
Sbjct: 27 VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVI 86
Query: 66 DLNNRWFGGRPVYAELSP 83
DLNNRWF G+P++AELSP
Sbjct: 87 DLNNRWFNGQPIHAELSP 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 = 93.2 bits (232), Expect = 5e-26
Identities = 26/82 (31%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 8 DEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDL 67
EE +DV EC K+G + + V N GNVY+K A AVN L
Sbjct: 20 TEEEVGWDTEIKDDVIEECN-KHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNAL 75
Query: 68 NNRWFGGRPVYAELSPVTDFRE 89
+ RWF G+ + A P+ +
Sbjct: 76 HGRWFAGKMITAAYVPLPTYHN 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 = 87.8 bits (218), Expect = 7e-24
Identities = 29/93 (31%), Positives = 48/93 (51%), Gaps = 9/93 (9%)
Query: 1 MIISNVTD----EEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRR 56
+II N+ E+ + ED+ VEC K+G+I ++ + D H G + FR
Sbjct: 18 VIIKNMFHPMDFEDDPLVLNEIREDLRVECS-KFGQIRKLLLFDR---HPDGVASVSFRD 73
Query: 57 EEDAEKAVNDLNNRWFGGRPVYAEL-SPVTDFR 88
E+A+ + L+ RWFGGR + A+ TD++
Sbjct: 74 PEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQ 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 = 85.6 bits (212), Expect = 5e-23
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 8/94 (8%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL-----VGNVYIKFR 55
M++ N+ D + + D+ +V EC K+G + + + + ++++F
Sbjct: 23 MVLRNMVDPK--DIDDDLEGEVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS 79
Query: 56 REEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 89
+ KA+ LN RWF GR V AE+ F
Sbjct: 80 IASETHKAIQALNGRWFAGRKVVAEVYDQERFDN 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 = 81.0 bits (200), Expect = 3e-21
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 8 DEEMQEHYDNFFEDVFVECEDKYGEIEEMNV---CDNLGDHLVGNVYIKFRREEDAEKAV 64
+ E Y+ EDV EC KYG ++ + + D + G ++++F D +KA+
Sbjct: 18 ELLDDEEYEEIVEDVRDECS-KYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAM 76
Query: 65 NDLNNRWFGGRPVYAELSPVTDFRE 89
L R F R V + +
Sbjct: 77 QGLTGRKFANRVVVTKYCDPDSYHR 101
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 73.3 bits (180), Expect = 3e-18
Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 5/90 (5%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCD--NLGDHLVGNVYIKFRREE 58
+++ N+ E ++ + ECE KYG++ + + + D ++++F R E
Sbjct: 11 VLLRNMVGAG--EVDEDLEVETKEECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVE 67
Query: 59 DAEKAVNDLNNRWFGGRPVYAELSPVTDFR 88
A KAV DLN R+FGGR V A + FR
Sbjct: 68 SAIKAVVDLNGRYFGGRVVKACFYNLDKFR 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 = 6e-15
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFG 73
DN E + KYGE+EE+ + HL G + F A++ V +L+
Sbjct: 16 DNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL-GLARVLFTSTRGAKETVKNLHLTSVM 74
Query: 74 GRPVYAELSPVTDFREACCRQYEMVL 99
G ++A+L + + YE+++
Sbjct: 75 GNIIHAQLDI---KGQQRMKYYELIV 97
>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 = 7e-09
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 13/85 (15%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD----HLVGNVYIKFRRE 57
+ + D E+ + + F K+G+I ++ + ++ + Y+ + R
Sbjct: 23 LSQRLADPEVLKRPEYF---------GKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
Query: 58 EDAEKAVNDLNNRWFGGRPVYAELS 82
EDA +A+ +NN GR + A L
Sbjct: 74 EDALRAIQCVNNVVVDGRTLKASLG 98
>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 = 2e-07
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 17/74 (22%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
S +TD+ M++ F +G+I E+ V G +++F E A A
Sbjct: 35 SGLTDQLMRQT----FS--------PFGQIMEIRVFPEKG---YS--FVRFSTHESAAHA 77
Query: 64 VNDLNNRWFGGRPV 77
+ +N G V
Sbjct: 78 IVSVNGTTIEGHVV 91
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 45.3 bits (107), Expect = 3e-07
Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 10/78 (12%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
V E++Q G+I ++ V + + G YI F +E A+ V
Sbjct: 40 EVPKEKLQALLYALAS--------SQGDILDIVVDLSDDNS--GKAYIVFATQESAQAFV 89
Query: 65 NDLNNRWFGGRPVYAELS 82
F G P+ S
Sbjct: 90 EAFQGYPFQGNPLVITFS 107
>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 = 3e-07
Identities = 12/78 (15%), Positives = 33/78 (42%), Gaps = 10/78 (12%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ +E+++ F ++G+I ++ V +L + G ++ F+ A A+
Sbjct: 19 KIKKDELKKSLHAIFS--------RFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 65 NDLNNRWFGGRPVYAELS 82
+ F +P+ + +
Sbjct: 69 RSMQGFPFYDKPMRIQYA 86
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dk2_A
Length = 103
Score = 44.6 bits (106), Expect = 4e-07
Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 20/93 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
VT+E +++ F ++G++E + + +I F + A KA+
Sbjct: 22 TVTEEILEKA----FS--------QFGKLERVKKLKDYA-------FIHFDERDGAVKAM 62
Query: 65 NDLNNRWFGGRPVYAELS-PVTDFREACCRQYE 96
++N + G + + P R+ Q +
Sbjct: 63 EEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 45.7 bits (109), Expect = 6e-07
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 13/87 (14%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
++T ++ +E +G +E + G + ++ +++ A +A
Sbjct: 106 SLTQQQFEE----LVR--------PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 64 VNDLNNRWFGGRPVYAELSPVTDFREA 90
+DL + G R +Y + A
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPA 180
Score = 42.3 bits (100), Expect = 1e-05
Identities = 9/74 (12%), Positives = 17/74 (22%), Gaps = 11/74 (14%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
D + + L G +++ E AE+A
Sbjct: 195 GFNDVDA-------LCRAL----SAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQ 243
Query: 65 NDLNNRWFGGRPVY 78
+ GG +
Sbjct: 244 QQADGLSLGGSHLR 257
Score = 38.4 bits (90), Expect = 2e-04
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 83
++ 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 = 45.6 bits (107), Expect = 8e-07
Identities = 16/117 (13%), Positives = 42/117 (35%), Gaps = 11/117 (9%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ +E+++ F ++G+I ++ V +L + G ++ F+ A A+
Sbjct: 20 KIKKDELKKSLYAIFS--------QFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 65 NDLNNRWFGGRPVYAELS-PVTDFREACCRQYEMVLETKNADPVCTREKAKKKMGVY 120
+ F +P+ + + +D + + ++E K V
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQ 126
Score = 29.1 bits (64), Expect = 0.37
Identities = 6/51 (11%), Positives = 16/51 (31%), Gaps = 5/51 (9%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF-GGRPVY 78
++ +E+ + +++F E A A + L +
Sbjct: 230 QFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDALQGFKITQNNAMK 276
>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 = 8e-07
Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 19/78 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+V + E+ E F +G ++E+ + + +++F E A KA+
Sbjct: 42 DVQESELNEI----FG--------PFGPMKEVKILNGFA-------FVEFEEAESAAKAI 82
Query: 65 NDLNNRWFGGRPVYAELS 82
+++ + F +P+ S
Sbjct: 83 EEVHGKSFANQPLEVVYS 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 = 42.7 bits (101), Expect = 1e-06
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 17/76 (22%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 61
I T+ ++ F+ +G I + G +IK+ E A
Sbjct: 35 IPHFATEADLIPL----FQ--------NFGFILDFKHYPEKG---CC--FIKYDTHEQAA 77
Query: 62 KAVNDLNNRWFGGRPV 77
+ L N F GR +
Sbjct: 78 VCIVALANFPFQGRNL 93
>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 = 42.3 bits (100), Expect = 2e-06
Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 15/82 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 63
V+ +E+ + FF Y I + + N G + F ++A A
Sbjct: 26 TVSIDEILD----FFYG--------YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 64 VNDLNNRWFGGRPVYAELSPVT 85
V DLN+R G R V +LS +
Sbjct: 74 VIDLNDRPIGSRKV--KLSGPS 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 = 42.3 bits (100), Expect = 2e-06
Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 13/79 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 63
V+ +E+ + FF Y I + + N G + F ++A A
Sbjct: 26 TVSIDEILD----FFYG--------YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 64 VNDLNNRWFGGRPVYAELS 82
V DLN+R G R V L
Sbjct: 74 VIDLNDRPIGSRKVKLVLG 92
>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 = 43.7 bits (103), Expect = 2e-06
Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 8/92 (8%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-----CDNLGDHLVGNVYIKFR 55
M++ N+ D + + D+ +V EC K+G + + + + ++ ++++F
Sbjct: 127 MVLRNMVDPK--DIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS 183
Query: 56 REEDAEKAVNDLNNRWFGGRPVYAELSPVTDF 87
+ KA+ LN RWF GR V AE+ F
Sbjct: 184 IASETHKAIQALNGRWFAGRKVVAEVYDQERF 215
>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 = 4e-06
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 17/74 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++T+EEM++ FE KYG+ E+ + + G G +I+ AE A
Sbjct: 26 DITEEEMRK----LFE--------KYGKAGEVFIHKDKG---FG--FIRLETRTLAEIAK 68
Query: 65 NDLNNRWFGGRPVY 78
+L+N G+ +
Sbjct: 69 VELDNMPLRGKQLR 82
>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 = 41.7 bits (98), Expect = 4e-06
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 17/86 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
E+QE F ++G + + + + ++F +A KA
Sbjct: 21 GTLAAEIQE----TFS--------RFGSLGRVLLPEG-----GITAIVEFLEPLEARKAF 63
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
L F P+Y E +P+ F A
Sbjct: 64 RHLAYSKFHHVPLYLEWAPIGVFGAA 89
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 42.3 bits (100), Expect = 7e-06
Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 19/79 (24%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREED 59
+++D++++ FE +G+I+ + D G +I++ + +
Sbjct: 135 QDLSDDDIKS----VFE--------AFGKIKSATL---ARDPTTGKHKGYGFIEYEKAQS 179
Query: 60 AEKAVNDLNNRWFGGRPVY 78
++ AV+ +N GG+ +
Sbjct: 180 SQDAVSSMNLFDLGGQYLR 198
Score = 37.3 bits (87), Expect = 4e-04
Identities = 12/75 (16%), Positives = 34/75 (45%), Gaps = 13/75 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+ ++ +++ F +G I+ +++ D++ G ++++ E A+ A
Sbjct: 39 ELGEDTIRQ----AFA--------PFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 64 VNDLNNRWFGGRPVY 78
+ +N+ GGR +
Sbjct: 87 LEQMNSVMLGGRNIK 101
>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 = 40.2 bits (95), Expect = 1e-05
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+T + F +G I + V D G ++ F + DAE A
Sbjct: 17 EITTAAIAA----AFA--------PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 64 VNDLNNRWFGGRPV 77
+ + +W GGR +
Sbjct: 65 IQQMGGQWLGGRQI 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 = 40.1 bits (94), Expect = 1e-05
Identities = 12/86 (13%), Positives = 31/86 (36%), Gaps = 14/86 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ + ++++ FF + ++ +++ + GN +KF +D +A+
Sbjct: 27 SAMENDVRD----FFHGL---------RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL 73
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
N R V + + A
Sbjct: 74 -KRNRMLMIQRYVEVSPATERQWVAA 98
>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 = 40.1 bits (94), Expect = 2e-05
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 19/79 (24%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+ V ++ E +F KYG + +V ++++ E A A
Sbjct: 38 ALVKKSDV--------ETIF----SKYGRVAGCSVHKGYA-------FVQYSNERHARAA 78
Query: 64 VNDLNNRWFGGRPVYAELS 82
V N R G+ + ++
Sbjct: 79 VLGENGRVLAGQTLDINMA 97
>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 = 2e-05
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
+T E+++ F +G I + V D G ++ F + DA
Sbjct: 26 EITTEDIKA----AFA--------PFGRISDARVVK---DMATGKSKGYGFVSFFNKWDA 70
Query: 61 EKAVNDLNNRWFGGRPV 77
E A+ + +W GGR +
Sbjct: 71 ENAIQQMGGQWLGGRQI 87
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 40.0 bits (94), Expect = 2e-05
Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 17/78 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ ++E +++ F V + ++ F EDA +A+
Sbjct: 26 STSEEMIEKE----FN--------NIKPGAVERV-----KKIRDYAFVHFSNREDAVEAM 68
Query: 65 NDLNNRWFGGRPVYAELS 82
LN + G P+ L+
Sbjct: 69 KALNGKVLDGSPIEVTLA 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 = 41.5 bits (98), Expect = 2e-05
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
YI +EDA V LN G + ++S
Sbjct: 163 YIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 194
Score = 37.7 bits (88), Expect = 4e-04
Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 14/76 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ ++ + +F+ G I ++V D+L + I+F R + A A+
Sbjct: 52 SYNQNKVYK----YFKH--------CGPIIHVDVADSLKKNF-RFARIEFARYDGALAAI 98
Query: 65 NDLNNRWFGGRPVYAE 80
+ G +
Sbjct: 99 TKTHKV-VGQNEIIVS 113
Score = 36.5 bits (85), Expect = 0.001
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 14/80 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV--CDNLGDHLVGNVYIKFRREEDAEK 62
+ DE + + F + +G IE++N+ ++ F ++ AE+
Sbjct: 221 ELLDENL-------LRESF----EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 269
Query: 63 AVNDLNNRWFGGRPVYAELS 82
A+ +N G R + L+
Sbjct: 270 ALQ-MNRSLLGNREISVSLA 288
>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 = 41.0 bits (97), Expect = 2e-05
Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 13/75 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
++TD E+ F G I + D + G ++ F E D+++A
Sbjct: 14 DMTDRELYA----LFR--------AIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 64 VNDLNNRWFGGRPVY 78
+ LN + +
Sbjct: 62 IKVLNGITVRNKRLK 76
Score = 35.2 bits (82), Expect = 0.002
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 15/77 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
+TD+++ F KYG I + N+ D L G ++++ + E+A++A
Sbjct: 100 TITDDQLDT----IFG--------KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
Query: 64 VNDLNNRWFGG--RPVY 78
++ LNN G +P+
Sbjct: 148 ISALNNVIPEGGSQPLS 164
>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 = 39.6 bits (93), Expect = 2e-05
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 11/63 (17%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
+F YG I ++N+ +I+F + A+ + G+ +
Sbjct: 41 FRIF----SPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89
Query: 80 ELS 82
E+S
Sbjct: 90 EVS 92
>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 = 39.5 bits (93), Expect = 2e-05
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 19/79 (24%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+ T +E++ FE + G + E +V + ++ +E DA+ A
Sbjct: 19 AACTSQELRS----LFE--------RRGRVIECDVVKDYA-------FVHMEKEADAKAA 59
Query: 64 VNDLNNRWFGGRPVYAELS 82
+ LN + G+ + ELS
Sbjct: 60 IAQLNGKEVKGKRINVELS 78
>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 = 39.6 bits (93), Expect = 3e-05
Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
++ ++ F K+G I E+ + D G +I F DA+ A
Sbjct: 18 ETNEKMLKAV----FG--------KHGPISEVLLIKDRTSKSR-GFAFITFENPADAKNA 64
Query: 64 VNDLNNRWFGGRPVY 78
D+N + G+ +
Sbjct: 65 AKDMNGKSLHGKAIK 79
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 39.1 bits (92), Expect = 3e-05
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 11/63 (17%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
+F YG I ++N+ + G +I+F + A+ + G+ +
Sbjct: 29 FRIF----SPYGHIMQINIKNAFG-------FIQFDNPQSVRDAIECESQEMNFGKKLIL 77
Query: 80 ELS 82
E+S
Sbjct: 78 EVS 80
>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 = 40.3 bits (95), Expect = 3e-05
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 16/74 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N+T++E++E FE EI + G G YI+F+ E DAEK +
Sbjct: 110 NITEDELKE----VFE--------DALEIRLV---SQDG-KSKGIAYIEFKSEADAEKNL 153
Query: 65 NDLNNRWFGGRPVY 78
+ GR V
Sbjct: 154 EEKQGAEIDGRSVS 167
Score = 36.8 bits (86), Expect = 7e-04
Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 13/86 (15%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N + E++ + ++ V D Y+ F ED EKA+
Sbjct: 24 NKSVAELKV----AIS--------ELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
+L G + E D ++
Sbjct: 72 -ELTGLKVFGNEIKLEKPKGRDSKKV 96
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 40.2 bits (94), Expect = 4e-05
Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 12/86 (13%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
V+D ++QE F ++G +++ V + +G + F R DA KA+
Sbjct: 99 GVSDADIQE----LFA--------EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 146
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
GRP+ +L E
Sbjct: 147 KQYKGVPLDGRPMDIQLVASQIDLEH 172
>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 = 39.1 bits (92), Expect = 4e-05
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
++E++++ F YG + E++ D+L G ++ F E A KA
Sbjct: 19 TSSEEDLEKL----FS--------AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
Query: 64 VNDLNNRWFGGRPV 77
+++ + F GR +
Sbjct: 67 YAEVDGQVFQGRML 80
>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 = 40.4 bits (95), Expect = 4e-05
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 17/74 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++T+E+ + FE +YGE E+ + + G +I+ AE A
Sbjct: 33 DITEEDFKRL----FE--------RYGEPSEVFINRDRG-----FGFIRLESRTLAEIAK 75
Query: 65 NDLNNRWFGGRPVY 78
+L+ RP+
Sbjct: 76 AELDGTILKSRPLR 89
Score = 32.4 bits (74), Expect = 0.026
Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 18/91 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
V++E +++ F ++G +E+ V D+ G G +++F + A KA
Sbjct: 107 VVSNELLEQ----AFS--------QFGPVEKAVVVVDDRGRAT-GKGFVEFAAKPPARKA 153
Query: 64 VNDLNNRWF----GGRPVYAELSPVTDFREA 90
+ + F RPV E D +
Sbjct: 154 LERCGDGAFLLTTTPRPVIVEPMEQFDDEDG 184
>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 = 39.0 bits (91), Expect = 5e-05
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 14/86 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 63
++T ++ + F E E ++V + +G ++F+ E+DA K+
Sbjct: 26 SITKMDVLQ----FLEG--------IPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73
Query: 64 VNDLNNRWFGGRPVYAELSPVTDFRE 89
L+ + GR + + + D RE
Sbjct: 74 ER-LHRKKLNGREAFVHVVTLEDMRE 98
>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 = 5e-05
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 4/98 (4%)
Query: 30 YGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 89
YG+++ + + N N ++ A+ A++ LN G+P+ LS + +
Sbjct: 28 YGDVQRVKILFNKK----ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQL 83
Query: 90 ACCRQYEMVLETKNADPVCTREKAKKKMGVYEISGVST 127
Q + L + R K I S
Sbjct: 84 PREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 121
Score = 27.2 bits (60), Expect = 1.5
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFG-GRPVY 78
I+ E+A +A+ DL+N G +
Sbjct: 162 LIQMGSVEEAVQALIDLHNHDLGENHHLR 190
>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 = 38.4 bits (90), Expect = 6e-05
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
V +E + E F + G + ++ +C D G ++ F+ E A
Sbjct: 27 RVREEILYEL----FL--------QAGPLTKVTICKDREGKPK-SFGFVCFKHPESVSYA 73
Query: 64 VNDLNNRWFGGRPVY 78
+ LN GRP+
Sbjct: 74 IALLNGIRLYGRPIN 88
>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 = 38.4 bits (90), Expect = 6e-05
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 19/78 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
T++E++ FE +YG + E ++ + ++ R EDA +A+
Sbjct: 21 TCTNQELRAK----FE--------EYGPVIECDIVKDYA-------FVHMERAEDAVEAI 61
Query: 65 NDLNNRWFGGRPVYAELS 82
L+N F G+ ++ +LS
Sbjct: 62 RGLDNTEFQGKRMHVQLS 79
>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 = 37.9 bits (89), Expect = 7e-05
Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 19/78 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
T++E++ FE +YG++ E ++ N G ++ + AE A+
Sbjct: 19 EATEQEIRS----LFE--------QYGKVLECDIIKNYG-------FVHIEDKTAAEDAI 59
Query: 65 NDLNNRWFGGRPVYAELS 82
+L++ G + E S
Sbjct: 60 RNLHHYKLHGVNINVEAS 77
>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 = 39.1 bits (92), Expect = 8e-05
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
N+T EE + F GEIE + D + +G ++ + +DAEKA
Sbjct: 13 NMTQEEFRS----LFG--------SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 64 VNDLNNRWFGGRPVY 78
+N LN + +
Sbjct: 61 INTLNGLRLQTKTIK 75
Score = 32.2 bits (74), Expect = 0.025
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 13/69 (18%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLNNRW 71
E +F +YG I + L D + G +I+F + +AE+A+ LN +
Sbjct: 102 QKELEQLF----SQYGRIITSRI---LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
Query: 72 FGG--RPVY 78
G P+
Sbjct: 155 PSGATEPIT 163
>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 = 38.7 bits (90), Expect = 8e-05
Identities = 10/78 (12%), Positives = 31/78 (39%), Gaps = 6/78 (7%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+V +++++ + + + + ++ + G +I E+ A KA+
Sbjct: 56 HVQEKDLKYIFGRYVDF------SSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
Query: 65 NDLNNRWFGGRPVYAELS 82
+ N G+P+ + +
Sbjct: 110 KEANGYVLFGKPMVVQFA 127
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 38.0 bits (89), Expect = 9e-05
Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 17/75 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAEK 62
+VT+ + + +F + G + + +H + Y ++F DA
Sbjct: 26 DVTEVLILQ--------LFSQ----IGPCKSCKMIT---EHTSNDPYCFVEFYEHRDAAA 70
Query: 63 AVNDLNNRWFGGRPV 77
A+ +N R G+ V
Sbjct: 71 ALAAMNGRKILGKEV 85
>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 = 38.0 bits (89), Expect = 9e-05
Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 16/82 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV---GNVYIKFRREEDA 60
+ T+E ++ F K G I+ + ++ G ++++++ E A
Sbjct: 16 STTEETLKGV----FS--------KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 61 EKAVNDLNNRWFGGRPVYAELS 82
+KA+ L G + +S
Sbjct: 64 QKALKQLQGHTVDGHKLEVRIS 85
>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 = 38.2 bits (89), Expect = 1e-04
Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 17/74 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++T ++ F +G I ++++ ++ + + E A++AV
Sbjct: 48 DMTPTLLRGA----FS--------PFGNIIDLSMDPPRN---CA--FVTYEKMESADQAV 90
Query: 65 NDLNNRWFGGRPVY 78
+LN +
Sbjct: 91 AELNGTQVESVQLK 104
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 38.0 bits (89), Expect = 1e-04
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNL-GDHLVGNVYIKFRREEDAEK 62
V++ + E +F++ G + ++ D + G H G +++F EEDA+
Sbjct: 26 KVSEPLLWE--------LFLQ----AGPVVNTHMPKDRVTGQHQ-GYGFVEFLSEEDADY 72
Query: 63 AVNDLNNRWFGGRPV 77
A+ ++ G+P+
Sbjct: 73 AIKIMDMIKLYGKPI 87
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 10/75 (13%), Positives = 28/75 (37%), Gaps = 13/75 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
+ D++++E +G ++ N+ D+ G + ++ ++A
Sbjct: 125 YLNDDQVKEL----LT--------SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 64 VNDLNNRWFGGRPVY 78
+ LN G + +
Sbjct: 173 IAGLNGMQLGDKKLL 187
Score = 31.9 bits (73), Expect = 0.036
Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 7/74 (9%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+T+E M + FF + D +++FR ++ +A+
Sbjct: 15 GITEEAMMD----FFNAQMRLGGLTQAPGNPVLAVQINQDKNFA--FLEFRSVDETTQAM 68
Query: 65 NDLNNRWFGGRPVY 78
+ F G+ +
Sbjct: 69 A-FDGIIFQGQSLK 81
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 39.2 bits (91), Expect = 1e-04
Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 11/83 (13%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 60
+++SN+ E + + +F+ YG+++ + + N N ++ A
Sbjct: 37 LLVSNLNPERVTP------QSLFILFG-VYGDVQRVKILFNKK----ENALVQMADGNQA 85
Query: 61 EKAVNDLNNRWFGGRPVYAELSP 83
+ A++ LN G+P+ LS
Sbjct: 86 QLAMSHLNGHKLHGKPIRITLSK 108
Score = 27.7 bits (61), Expect = 1.2
Identities = 10/75 (13%), Positives = 25/75 (33%), Gaps = 16/75 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+V++E+++ + + V + I+ E+A +A+
Sbjct: 162 SVSEEDLKVLFSSNGGVVKGFKFFQKDR---------------KMALIQMGSVEEAVQAL 206
Query: 65 NDLNN-RWFGGRPVY 78
DL+N +
Sbjct: 207 IDLHNHDLGENHHLR 221
>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 = 1e-04
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++ F ++DA+ A++ + + GRP+
Sbjct: 133 FVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 36.7 bits (86), Expect = 6e-04
Identities = 11/74 (14%), Positives = 28/74 (37%), Gaps = 14/74 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+T++ +++ F G I + + D ++ ++++ + DA A
Sbjct: 11 AITEDILKQ--------YFQVG----GPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIA 57
Query: 64 VNDLNNRWFGGRPV 77
+ LN + V
Sbjct: 58 LQTLNGKQIENNIV 71
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 37.1 bits (87), Expect = 1e-04
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++ F ++DA+ A++ + + GRP+
Sbjct: 47 FVSFTSQDDAQNAMDSMQGQDLNGRPLR 74
>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 = 37.6 bits (88), Expect = 1e-04
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++ F E+A KAV ++N R +P+Y
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLY 86
>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 = 37.7 bits (88), Expect = 1e-04
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
V+D ++QE F ++G +++ V D G L G + F R DA KA
Sbjct: 46 GVSDADIQE----LFA--------EFGTLKKAAVDYDRSGRSL-GTADVHFERRADALKA 92
Query: 64 VNDLNNRWFGGRPVYAEL 81
+ GRP+ +L
Sbjct: 93 MKQYKGVPLDGRPMDIQL 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 = 38.8 bits (91), Expect = 1e-04
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++ F +E AE+A+ +N R V+
Sbjct: 147 FVHFETQEAAERAIEKMNGMLLNDRKVF 174
Score = 38.0 bits (89), Expect = 2e-04
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+VT+ + E F G I + VC D + +G Y+ F++ DAE+A
Sbjct: 26 DVTEAMLYE--------KFSPA----GPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 64 VNDLNNRWFGGRPV 77
++ +N G+PV
Sbjct: 74 LDTMNFDVIKGKPV 87
>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 = 37.7 bits (88), Expect = 2e-04
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 14/78 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+T EEM + F KYG I ++ V + G Y+ + DA+ AV
Sbjct: 19 KITAEEMYD----IFG--------KYGPIRQIRVGNTPETR--GTAYVVYEDIFDAKNAV 64
Query: 65 NDLNNRWFGGRPVYAELS 82
+ L+ R +
Sbjct: 65 DHLSGFNVSNRYLVVLYY 82
>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 = 37.6 bits (88), Expect = 2e-04
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 14/80 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
V+D ++QE F ++G +++ V D G +G + F R+ DA KA
Sbjct: 40 GVSDADIQEL----FA--------EFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKA 86
Query: 64 VNDLNNRWFGGRPVYAELSP 83
+ N GRP+ +L
Sbjct: 87 MKQYNGVPLDGRPMNIQLVT 106
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 16/87 (18%), Positives = 26/87 (29%), Gaps = 13/87 (14%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N + E++ + ++ V D Y+ F ED EKA+
Sbjct: 28 NKSVAELKV----AIS--------ELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREAC 91
+L G + E D C
Sbjct: 76 -ELTGLKVFGNEIKLEKPKGRDGTRGC 101
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 37.6 bits (87), Expect = 2e-04
Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 10/86 (11%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ + E++Q F D + + ++ G +++ E+D + A+
Sbjct: 28 SCSIEDVQN----FLSDC-----TIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
+ G R + S T+
Sbjct: 79 -KKDRESMGHRYIEVFKSHRTEMDWV 103
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
+I F + ++ A+ +N ++ RP+
Sbjct: 52 FINFASFDASDAAIEAMNGQYLCNRPIT 79
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 36.9 bits (86), Expect = 2e-04
Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 17/74 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++T ++ F +G I ++++ ++ + + E A++AV
Sbjct: 24 DMTPTLLRGA----FS--------PFGNIIDLSMDPPRN---CA--FVTYEKMESADQAV 66
Query: 65 NDLNNRWFGGRPVY 78
+LN +
Sbjct: 67 AELNGTQVESVQLK 80
>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 = 36.9 bits (86), Expect = 2e-04
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++ +++ EDVF KYG I ++++ + G +++F DAE AV
Sbjct: 33 DIRTKDI--------EDVF----YKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAV 78
Query: 65 NDLNNRWFGGRPVYAELS 82
+ + G + E
Sbjct: 79 YGRDGYDYDGYRLRVEFP 96
>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 = 37.1 bits (86), Expect = 3e-04
Identities = 12/87 (13%), Positives = 30/87 (34%), Gaps = 14/87 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 63
++ + + FF+ +E+ + + G +++FR E D + A
Sbjct: 36 EAENKHVID----FFKK--------LDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83
Query: 64 VNDLNNRWFGGRPVYAELSPVTDFREA 90
+ + ++ G R + E
Sbjct: 84 L-CRHKQYMGNRFIQVHPITKKGMLEK 109
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 36.6 bits (85), Expect = 3e-04
Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 14/87 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+ EE+ + FF + M + + G +++F +E AEKA
Sbjct: 26 GCSKEEIVQ----FFSG--------LEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73
Query: 64 VNDLNNRWFGGRPVYAELSPVTDFREA 90
+ + G R + S + R +
Sbjct: 74 L-KKHKERIGHRYIEIFKSSRAEVRTS 99
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 36.9 bits (86), Expect = 3e-04
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
E F YG + + + N G +++F DAE AV L+ + G V
Sbjct: 18 ERAF----SYYGPLRTVWIARNPP----GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69
Query: 80 ELS 82
ELS
Sbjct: 70 ELS 72
>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 = 36.6 bits (85), Expect = 3e-04
Identities = 12/79 (15%), Positives = 27/79 (34%), Gaps = 18/79 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ +E+ D+ + + KY + D ++ E A+ A+
Sbjct: 16 DSNCQEV--------HDLLKDYDLKYCYV----------DRNKRTAFVTLLNGEQAQNAI 57
Query: 65 NDLNNRWFGGRPVYAELSP 83
+ F G+ + +L P
Sbjct: 58 QMFHQYSFRGKDLIVQLQP 76
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 36.3 bits (84), Expect = 3e-04
Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 14/79 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++ E + +YG +E + D V + + ++ A +A+
Sbjct: 26 HLQWEVLDS----LLV--------QYGVVESCEQVNT--DSETAVVNVTYSSKDQARQAL 71
Query: 65 NDLNNRWFGGRPVYAELSP 83
+ LN + P
Sbjct: 72 DKLNGFQLENFTLKVAYIP 90
>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 = 36.5 bits (85), Expect = 4e-04
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 15/73 (20%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ T+E +QE FE K I+ V N G +I+F EDA++A+
Sbjct: 26 SATEETLQE----VFE--------KATFIK---VPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 65 NDLNNRWFGGRPV 77
N N R GR +
Sbjct: 71 NSCNKREIEGRAI 83
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 36.2 bits (84), Expect = 4e-04
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 6 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 65
+ E N +F K+G+I + G G +++++ A AV
Sbjct: 25 QVGPDRLEKLKNVIHKIF----SKFGKITNDFYPEEDGKTK-GYIFLEYASPAHAVDAVK 79
Query: 66 DLNNRWFGGR 75
+ + +
Sbjct: 80 NADGYKLDKQ 89
>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 = 36.5 bits (84), Expect = 6e-04
Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 10/86 (11%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ + E++Q F D + ++ G +++ E+D + A+
Sbjct: 55 SCSVEDVQN----FLSDCTIH-----DGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
+ G R + S T+
Sbjct: 106 -KKDRESMGHRYIEVFKSHRTEMDWV 130
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 36.3 bits (84), Expect = 6e-04
Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
V D+ + F+ +G+I ++ + D + G +++F EDA A
Sbjct: 74 EVDDKVLHA--------AFIP----FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 64 VNDLNNRWFGGRPV 77
++++N GR +
Sbjct: 122 IDNMNESELFGRTI 135
>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 = 36.7 bits (85), Expect = 7e-04
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
T+E++ E F K G+I+++ + D + G ++++ DAE A
Sbjct: 50 YTTEEQIYEL----FS--------KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 64 VNDLNNRWFGGRPVYAELSP 83
+ +N R + +
Sbjct: 98 MRYINGTRLDDRIIRTDWDA 117
>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 = 35.7 bits (83), Expect = 7e-04
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 54 FRREEDAEKAVNDLNNRWFGGRPVY 78
F + +A +A++ N + RP++
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMH 87
>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 = 35.3 bits (82), Expect = 7e-04
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 18/75 (24%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+T+ +++ H F ++GEI + V +I+F + AE A
Sbjct: 22 DTITETDLRNH----FY--------QFGEIRTITVVQRQQ---CA--FIQFATRQAAEVA 64
Query: 64 VND-LNNRWFGGRPV 77
N GR +
Sbjct: 65 AEKSFNKLIVNGRRL 79
>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 = 35.7 bits (83), Expect = 7e-04
Identities = 12/74 (16%), Positives = 22/74 (29%), Gaps = 17/74 (22%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
N + F D++G I D++ YI++ + A+ A
Sbjct: 27 PNTSLAA--------LAREF----DRFGSIRT---IDHVKGD--SFAYIQYESLDAAQAA 69
Query: 64 VNDLNNRWFGGRPV 77
+ GG
Sbjct: 70 CAKMRGFPLGGPDR 83
>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 = 35.2 bits (82), Expect = 7e-04
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 14/75 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV-GNVYIKFRREEDAEK 62
NVT + + E F YG+I+ +++ + + HL G Y++F ++AEK
Sbjct: 15 NVTKDHIMEI----FS--------TYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 63 AVNDLNNRWFGGRPV 77
A+ ++ G+ +
Sbjct: 63 ALKHMDGGQIDGQEI 77
>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 = 36.0 bits (83), Expect = 8e-04
Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 14/86 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEE-MNVCDNLGDHLVGNVYIKFRREEDAEKA 63
T EE+ + FF + + + + + G +++F +E AEKA
Sbjct: 53 GCTKEEIVQ----FFSG--------LEIVPNGITLPVDPEGKITGEAFVQFASQELAEKA 100
Query: 64 VNDLNNRWFGGRPVYAELSPVTDFRE 89
+ + G R + S + R
Sbjct: 101 L-GKHKERIGHRYIEVFKSSQEEVRS 125
>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 = 8e-04
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 22/80 (27%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGN----VYIKFRREEDA 60
N+ +++++ FE ++G+I E+ V L D G ++ + E A
Sbjct: 24 NLDEKDLKP----LFE--------EFGKIYELTV---LKDRFTGMHKGCAFLTYCERESA 68
Query: 61 EKAVNDLNN---RWFGGRPV 77
KA + L+ RP+
Sbjct: 69 LKAQSALHEQKTLPGMNRPI 88
>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 = 35.3 bits (82), Expect = 9e-04
Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
+ + ++QE F +G I + + D G +I F R EDA
Sbjct: 26 DTRETDLQEL----FR--------PFGSISRIYL---AKDKTTGQSKGFAFISFHRREDA 70
Query: 61 EKAVNDLNNRWFGGRPV 77
+A+ ++ + +
Sbjct: 71 ARAIAGVSGFGYDHLIL 87
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 35.1 bits (81), Expect = 9e-04
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 6 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 65
+ E N +F K+G+I + G G +++++ A AV
Sbjct: 11 QVGPDRLEKLKNVIHKIF----SKFGKITNDFYPEEDGKTK-GYIFLEYASPAHAVDAVK 65
Query: 66 DLNNRWFGGR 75
+ + +
Sbjct: 66 NADGYKLDKQ 75
>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 = 0.001
Identities = 11/75 (14%), Positives = 29/75 (38%), Gaps = 13/75 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
VT+ ++ + ++ E + + + + G +I F +E A +A
Sbjct: 36 RVTERDLVSLFA------------RFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 83
Query: 64 VNDLNNRWFGGRPVY 78
++ +N G+ +
Sbjct: 84 LHLVNGYKLYGKILV 98
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 35.1 bits (81), Expect = 0.001
Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ T ++++E + E G++ + + L G++++ F E A+K V
Sbjct: 22 DATLDDIKE----WLE--------DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 69
Query: 65 NDLNNRWFGGRPVY 78
+ + + +
Sbjct: 70 -ETPGQKYKETDLL 82
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 35.3 bits (81), Expect = 0.001
Identities = 10/70 (14%), Positives = 27/70 (38%), Gaps = 17/70 (24%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 60
+ + V+ ++ E K G ++ + + N + ++R E++
Sbjct: 34 GLGNGVSRNQLLP----VLE--------KCGLVDALLMPPN-----KPYSFARYRTTEES 76
Query: 61 EKAVNDLNNR 70
++A LN +
Sbjct: 77 KRAYVTLNGK 86
>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 = 35.0 bits (81), Expect = 0.001
Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
NVT++ + E F + + + + N + G +++ F EE+ ++A+
Sbjct: 21 NVTEKNVME----FLAPL---------KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL 67
Query: 65 NDLNNRWFGGRPVYAELSPVT 85
N + GGR + E+
Sbjct: 68 -KCNREYMGGRYI--EVFREK 85
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 35.2 bits (81), Expect = 0.001
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 19/81 (23%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+VT+ E+ +G++ + + +I+ EE A
Sbjct: 26 IDVTEGEVISL----GL--------PFGKVTNLLMLKG-----KNQAFIEMNTEEAANTM 68
Query: 64 VNDL--NNRWFGGRPVYAELS 82
VN G+P+Y + S
Sbjct: 69 VNYYTSVTPVLRGQPIYIQFS 89
>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 = 35.6 bits (82), Expect = 0.001
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
E F YG + + V N G +++F DA AV +L+ R G V
Sbjct: 91 ERAF----GYYGPLRSVWVARNPP----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142
Query: 80 ELS 82
ELS
Sbjct: 143 ELS 145
>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 = 34.8 bits (80), Expect = 0.002
Identities = 16/89 (17%), Positives = 29/89 (32%), Gaps = 10/89 (11%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ T E++ FF D ++ N G+ I+ E+D +KA+
Sbjct: 22 SCTMEDVLN----FFSDC-----RIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREACCR 93
+ + + G R V D
Sbjct: 73 -EKHRMYMGQRYVEVYEINNEDVDALMKS 100
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 34.6 bits (80), Expect = 0.002
Identities = 7/29 (24%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 51 YIKFRREEDAEKAVNDLNNR-WFGGRPVY 78
++KF E + ++A+ + G +PV
Sbjct: 55 FVKFTDELEQKRALTECQGAVGLGSKPVR 83
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 34.9 bits (80), Expect = 0.002
Identities = 17/89 (19%), Positives = 29/89 (32%), Gaps = 9/89 (10%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
T EE+ FF G E + G+ ++ F EE A+ A+
Sbjct: 34 TATAEEVVA----FFGQ----HCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREACCR 93
+ G R + S + ++ R
Sbjct: 86 -RKHKDLLGKRYIELFRSTAAEVQQVLNR 113
>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 = 34.9 bits (81), Expect = 0.002
Identities = 10/76 (13%), Positives = 27/76 (35%), Gaps = 16/76 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHL-VGNVYIKFRREEDAEK 62
++ ++E++ + +G++ + D+ G VG + + E E
Sbjct: 36 SMDEQELENM----LK--------PFGQVISTRILRDSSGTSRGVG--FARMESTEKCEA 81
Query: 63 AVNDLNNRWFGGRPVY 78
+ N ++ P
Sbjct: 82 VIGHFNGKFIKTPPGV 97
>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 = 34.9 bits (80), Expect = 0.002
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 19/81 (23%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+VT+ E+ +G++ + + +I+ EE A
Sbjct: 41 IDVTEGEVISL----GL--------PFGKVTNLLMLKG-----KNQAFIEMNTEEAANTM 83
Query: 64 VND--LNNRWFGGRPVYAELS 82
VN G+P+Y + S
Sbjct: 84 VNYYTSVTPVLRGQPIYIQFS 104
>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 = 34.2 bits (79), Expect = 0.002
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 16/73 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N+T++E++E FE EI + G YI+F+ E DAEK +
Sbjct: 27 NITEDELKE----VFE--------DALEIRL----VSQDGKSKGIAYIEFKSEADAEKNL 70
Query: 65 NDLNNRWFGGRPV 77
+ GR V
Sbjct: 71 EEKQGAEIDGRSV 83
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 34.7 bits (80), Expect = 0.002
Identities = 5/27 (18%), Positives = 12/27 (44%)
Query: 52 IKFRREEDAEKAVNDLNNRWFGGRPVY 78
+ F + A+ A+ +N G + +
Sbjct: 87 VSFDNPDSAQVAIKAMNGFQVGTKRLK 113
>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 = 34.4 bits (79), Expect = 0.002
Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 8/65 (12%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND--LNNRWFGGRPV 77
+V +G++ + + +++ EE A VN +P+
Sbjct: 30 TEVIALGL-PFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI 83
Query: 78 YAELS 82
Y + S
Sbjct: 84 YIQYS 88
>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 = 34.9 bits (81), Expect = 0.003
Identities = 4/28 (14%), Positives = 12/28 (42%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
+ ++ ++A+ LN G + +
Sbjct: 140 FCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Score = 28.7 bits (65), Expect = 0.38
Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 7/73 (9%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+T+E M + FF + D +++FR ++ +A+
Sbjct: 15 GITEEAMMD----FFNAQMRLGGLTQAPGNPVLAVQINQDKNFA--FLEFRSVDETTQAM 68
Query: 65 NDLNNRWFGGRPV 77
+ F G+ +
Sbjct: 69 A-FDGIIFQGQSL 80
>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 = 34.1 bits (79), Expect = 0.003
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++ F +E AE+A+ +N R V+
Sbjct: 49 FVHFETQEAAERAIEKMNGMLLNDRKVF 76
>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 = 34.3 bits (79), Expect = 0.003
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
T+ +++E F KYG I ++++ + D ++ F +DA
Sbjct: 57 YTTERDLREV----FS--------KYGPIADVSI---VYDQQSRRSRGFAFVYFENVDDA 101
Query: 61 EKAVNDLNNRWFGGRPV 77
++A N GR +
Sbjct: 102 KEAKERANGMELDGRRI 118
>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 = 34.1 bits (79), Expect = 0.003
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+I+FR E + AV +LN G R +
Sbjct: 48 FIEFRDLESSASAVRNLNGYQLGSRFL 74
>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 = 33.7 bits (78), Expect = 0.003
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+++F EDA A++++N GR +
Sbjct: 53 FVEFELAEDAAAAIDNMNESELFGRTI 79
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 34.7 bits (80), Expect = 0.003
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
+ + ++ FE KYG + ++ + D +++F + DA
Sbjct: 58 RTSPDTLRRV----FE--------KYGRVGDVYI---PRDRYTKESRGFAFVRFHDKRDA 102
Query: 61 EKAVNDLNNRWFGGRPV 77
E A++ ++ GR +
Sbjct: 103 EDAMDAMDGAVLDGREL 119
>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 = 34.2 bits (79), Expect = 0.003
Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 17/78 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
++E++ F+ +G I+E V G G ++KF +A+ A
Sbjct: 26 QQSEEDVLR----LFQ--------PFGVIDECTVLRGPDGSS-KGCAFVKFSSHTEAQAA 72
Query: 64 VNDLNNRWF---GGRPVY 78
++ L+ +
Sbjct: 73 IHALHGSQTMPGASSSLV 90
>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 = 33.8 bits (78), Expect = 0.003
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
+ ++ +++ F KYG+I E+ V + D ++ F +DA
Sbjct: 23 DTNEQSLEQV----FS--------KYGQISEVVV---VKDRETQRSRGFGFVTFENIDDA 67
Query: 61 EKAVNDLNNRWFGGRPV 77
+ A+ +N + GR +
Sbjct: 68 KDAMMAMNGKSVDGRQI 84
>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 = 33.3 bits (77), Expect = 0.003
Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
TD+++ + + YG+I D + G ++ F A+KA
Sbjct: 16 GTTDQDLVKL----CQ--------PYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 64 VNDLNNRWFGGRPV 77
V L +
Sbjct: 64 VTALKASGVQAQMA 77
>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 = 34.5 bits (80), Expect = 0.004
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 15/69 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV--GNVYIKFRREEDAE 61
++++++E FE +YG + E+NV D + G ++ F + A
Sbjct: 14 TWSEKDLRE----LFE--------QYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 62 KAVNDLNNR 70
+A N L+N
Sbjct: 62 EAQNALHNM 70
Score = 34.1 bits (79), Expect = 0.005
Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 17/82 (20%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREED 59
MI T+ +++ F +G+IEE + G G ++ F
Sbjct: 102 MISKKCTENDIRV----MFS--------SFGQIEECRILRGPDGLS-RGCAFVTFTTRAM 148
Query: 60 AEKAVNDLNNR---WFGGRPVY 78
A+ A+ ++ P+
Sbjct: 149 AQTAIKAMHQAQTMEGCSSPMV 170
>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 = 0.004
Identities = 5/32 (15%), Positives = 11/32 (34%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
+ E ++K ++ L R G+
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPV 147
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 34.0 bits (78), Expect = 0.004
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 80
G ++F EE +A+ LNN F G + E
Sbjct: 68 GTGALEFPSEEILVEALERLNNIEFRGSVITVE 100
>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 = 0.004
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 88
YG +E++ + G ++ ++A+ LNN + G+ + +S
Sbjct: 28 LYGNVEKVKFMKSKP----GAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIM 83
Query: 89 E 89
Sbjct: 84 P 84
Score = 32.0 bits (72), Expect = 0.034
Identities = 10/74 (13%), Positives = 23/74 (31%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
VT+E E + + G +V + + +++ + DA +
Sbjct: 134 EVTEENFFEI----CD--------ELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181
Query: 64 VNDLNNRWFGGRPV 77
+ LN+
Sbjct: 182 LGFLNHYQMKNPNG 195
>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 = 33.8 bits (78), Expect = 0.004
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
N+T++ ++ FE +G IE + + D+ G +I F E A+KA
Sbjct: 37 NITEDMLRG----IFE--------PFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 64 VNDLNNRWFGGRPV 77
+ LN GRP+
Sbjct: 85 LEQLNGFELAGRPM 98
>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 = 33.5 bits (77), Expect = 0.005
Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 19/80 (23%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+ +E + E + ++G+++ + V +H G + +F +E A+K
Sbjct: 26 DSEEEALGEV----LQ--------QFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
Query: 64 VNDLNNRW------FGGRPV 77
+ + GR +
Sbjct: 74 LAAASLEAEGGGLKLDGRQL 93
>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 = 33.3 bits (77), Expect = 0.005
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
T+ +++E F KYG I ++++ + D ++ F +DA
Sbjct: 26 YTTERDLREV----FS--------KYGPIADVSI---VYDQQSRRSRGFAFVYFENVDDA 70
Query: 61 EKAVNDLNNRWFGGRPV 77
++A N GR +
Sbjct: 71 KEAKERANGMELDGRRI 87
>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 = 32.9 bits (76), Expect = 0.005
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
N+T++ ++ FE +G+I+ + + D+ G +I F E A +A
Sbjct: 16 NITEDMLRGI----FE--------PFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 64 VNDLNNRWFGGRPV 77
+ LN GRP+
Sbjct: 64 LEQLNGFELAGRPM 77
>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 = 33.3 bits (77), Expect = 0.005
Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
V D+ + F+ +G+I ++ + D+ +++F EDA
Sbjct: 23 EVDDKVLHA--------AFIP----FGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 67
Query: 61 EKAVNDLNNRWFGGRPV 77
A++++N GR +
Sbjct: 68 AAAIDNMNESELFGRTI 84
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 33.1 bits (75), Expect = 0.006
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 88
G K+ E+A KA LNN ++AE + +
Sbjct: 44 GIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENEVQ 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 = 33.0 bits (76), Expect = 0.006
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+++F DA+ A ++ GR +
Sbjct: 59 FVRFHDRRDAQDAEAAMDGAELDGREL 85
>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 = 33.1 bits (76), Expect = 0.007
Identities = 4/27 (14%), Positives = 11/27 (40%)
Query: 52 IKFRREEDAEKAVNDLNNRWFGGRPVY 78
+ + A+ A+ +N G + +
Sbjct: 72 VSYDNPVSAQAAIQSMNGFQIGMKRLK 98
>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 = 33.0 bits (76), Expect = 0.007
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
D ++++ F ++G+I ++ + N G ++ F DA++A
Sbjct: 26 RFRDPDLRQM----FG--------QFGKILDVEIIFNERGSK-GFGFVTFENSADADRAR 72
Query: 65 NDLNNRWFGGRPVY 78
L+ GR +
Sbjct: 73 EKLHGTVVEGRKIE 86
>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 = 33.7 bits (77), Expect = 0.008
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+++F + DAE A++ ++ GR +
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGREL 142
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 32.9 bits (75), Expect = 0.008
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
++ + A++AV+ L G + L+
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
>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 = 34.1 bits (77), Expect = 0.008
Identities = 6/87 (6%), Positives = 28/87 (32%), Gaps = 21/87 (24%)
Query: 1 MIISNVTDEEMQEHYDNFF---EDVFVE--------CEDKYGEIEE-MNVCDNLG----- 43
++ + E ++ +D + + ++ +N
Sbjct: 361 SSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420
Query: 44 --DHLVG--NVYIKFRREEDAEKAVND 66
+ + ++Y++ + + + E A++
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHR 447
Score = 28.7 bits (63), Expect = 0.68
Identities = 11/97 (11%), Positives = 26/97 (26%), Gaps = 24/97 (24%)
Query: 37 NVCDNLG--DHLVGNVY-IKFRREEDAEKAVNDLNNRWFGGRPVYAELS--------PVT 85
+VC + + ++ + + E + L + P + S +
Sbjct: 169 DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228
Query: 86 DFREA-----CCRQYE---MVLETKNADPVCTREKAK 114
+ + YE +VL V +
Sbjct: 229 SIQAELRRLLKSKPYENCLLVL-----LNVQNAKAWN 260
Score = 27.9 bits (61), Expect = 1.2
Identities = 20/138 (14%), Positives = 39/138 (28%), Gaps = 43/138 (31%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 61
++ +E ++ +Y + E YI+ R +
Sbjct: 78 MVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM---------------YIEQR-----D 117
Query: 62 KAVNDLNNRWFGGRPVYAELSPVTDFREACCRQ--------YEM------VLETKNADPV 107
+ ND N+ F V P R+A + + A V
Sbjct: 118 RLYND--NQVFAKYNVSRL-QPYLKLRQALLELRPAKNVLIDGVLGSGKTWV----ALDV 170
Query: 108 CTREKAKKKM--GVYEIS 123
C K + KM ++ ++
Sbjct: 171 CLSYKVQCKMDFKIFWLN 188
>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 = 32.6 bits (75), Expect = 0.009
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
++ F EEDA+ A + + G V
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKV 84
>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 = 32.8 bits (75), Expect = 0.009
Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 24/82 (29%)
Query: 1 MIISN----VTDEEMQEHYDNFFEDVFVEC-EDKYGEIEEMNVCDNLGDHLVGNVYIKFR 55
+++S + +++++H + + + D G +E F
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVE-------------------FV 58
Query: 56 REEDAEKAVNDLNNRWFGGRPV 77
R+ED AV L+N F
Sbjct: 59 RKEDMTYAVRKLDNTKFRSHEG 80
>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 = 32.4 bits (74), Expect = 0.010
Identities = 11/73 (15%), Positives = 23/73 (31%), Gaps = 14/73 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
T+ ++ FF + +++ + G ++F EDA A+
Sbjct: 26 RATENDIYN----FFSPL---------NPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM 72
Query: 65 NDLNNRWFGGRPV 77
+ R V
Sbjct: 73 -AKDKANMQHRYV 84
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 32.2 bits (74), Expect = 0.010
Identities = 11/82 (13%), Positives = 26/82 (31%), Gaps = 22/82 (26%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAE 61
VT +++++ F V G Y + + + A
Sbjct: 18 PAVTADDLRQ----LFG--------DRKLPLAGQVLLKSG-------YAFVDYPDQNWAI 58
Query: 62 KAVNDLNNRW-FGGRPVYAELS 82
+A+ L+ + G+ + + S
Sbjct: 59 RAIETLSGKVELHGKIMEVDYS 80
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 32.4 bits (74), Expect = 0.011
Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 29 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 75
K G++ M D G ++++ DA+K + + + +
Sbjct: 35 KAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>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 = 32.4 bits (74), Expect = 0.012
Identities = 11/82 (13%), Positives = 28/82 (34%), Gaps = 21/82 (25%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV---------GNVYIKFR 55
+VT +++ + F+ + G ++ H+ G+ + +
Sbjct: 26 SVTLDDLADF----FK--------QCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 56 REEDAEKAVNDLNNRWFGGRPV 77
A+ AV + + F G +
Sbjct: 74 DPPTAKAAVEWFDGKDFQGSKL 95
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 32.4 bits (74), Expect = 0.013
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 21/82 (25%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV---------GNVYIKFR 55
NVT E + + +F+ + G I+ +L G + F
Sbjct: 18 NVTIESVAD----YFK--------QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 56 REEDAEKAVNDLNNRWFGGRPV 77
A+ A++ + + F G P+
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPI 87
>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 = 0.014
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
+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 = 0.015
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 17/77 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV---CDNLGDHLVGNVYIKFRREEDAE 61
E++E F +GE++ + + G H G ++ F ++DA+
Sbjct: 26 QANQREIRE----LFS--------TFGELKTVRLPKKMTGTGAHR-GFGFVDFITKQDAK 72
Query: 62 KAVNDLNN-RWFGGRPV 77
KA N L + GR +
Sbjct: 73 KAFNALCHSTHLYGRRL 89
>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 = 0.018
Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 14/74 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKA 63
+ T EE++E + +G ++++ V + G G Y+++ E A +A
Sbjct: 28 SCTKEELEE----ICK--------AHGTVKDLRLVTNRAG-KPKGLAYVEYENESQASQA 74
Query: 64 VNDLNNRWFGGRPV 77
V ++ +
Sbjct: 75 VMKMDGMTIKENII 88
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 32.6 bits (74), Expect = 0.019
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+ E K + L + G V
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKV 129
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 31.9 bits (73), Expect = 0.021
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
D ++++ F ++G+I ++ + N G ++ F DA++A
Sbjct: 40 RFRDPDLRQM----FG--------QFGKILDVEIIFN-ERGSKGFGFVTFENSADADRAR 86
Query: 65 NDLNNRWFGGRPVY 78
L+ GR +
Sbjct: 87 EKLHGTVVEGRKIE 100
>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 = 31.4 bits (72), Expect = 0.024
Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
++T+ ++ F KYG++ ++ + + D +I F ++ A
Sbjct: 27 SLTNNDLYR----IFS--------KYGKVVKVTI---MKDKDTRKSKGVAFILFLDKDSA 71
Query: 61 EKAVNDLNNRWFGGRPV 77
+ +NN+ GR +
Sbjct: 72 QNCTRAINNKQLFGRVI 88
>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 = 31.1 bits (71), Expect = 0.027
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 21/82 (25%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV---------GNVYIKFR 55
NVT E + + +F+ + G I+ +L G + F
Sbjct: 24 NVTIESVAD----YFK--------QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 56 REEDAEKAVNDLNNRWFGGRPV 77
A+ A++ + + F G P+
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPI 93
>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 = 31.7 bits (72), Expect = 0.029
Identities = 9/73 (12%), Positives = 23/73 (31%), Gaps = 14/73 (19%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
T+ ++ FF + +++ + G ++F E+A A+
Sbjct: 57 KATENDIYN----FFSPL---------NPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM 103
Query: 65 NDLNNRWFGGRPV 77
+ R +
Sbjct: 104 -SKDRANMQHRYI 115
>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 = 31.6 bits (72), Expect = 0.030
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 14/74 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKA 63
T ++++ H F G I + +CD H G YI+F + A
Sbjct: 47 GSTAQDLEAH----FS--------SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 64 VNDLNNRWFGGRPV 77
V ++ F GR +
Sbjct: 95 VA-MDETVFRGRTI 107
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 31.3 bits (71), Expect = 0.030
Identities = 14/80 (17%), Positives = 23/80 (28%), Gaps = 19/80 (23%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
V + ++ E F G I + V ++F A AV
Sbjct: 32 GVVEADLVEALQEF------------GPISYVVVMPKKRQ-----ALVEFEDVLGACNAV 74
Query: 65 NDLNNR--WFGGRPVYAELS 82
N + + G P + S
Sbjct: 75 NYAADNQIYIAGHPAFVNYS 94
>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 = 31.3 bits (71), Expect = 0.030
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 54 FRREEDAEKAVNDLNNRWFGGRPV 77
F R+ED AV L+N F
Sbjct: 58 FVRKEDMTYAVRKLDNTKFRSHEG 81
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 31.1 bits (71), Expect = 0.034
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 19/77 (24%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDA 60
T+E++ D F E YGEI+ +++ NL D G + +++ ++A
Sbjct: 34 EATEEDIH--------DKFAE----YGEIKNIHL--NL-DRRTGYLKGYTLVEYETYKEA 78
Query: 61 EKAVNDLNNRWFGGRPV 77
+ A+ LN + G+P+
Sbjct: 79 QAAMEGLNGQDLMGQPI 95
>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 = 0.058
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRP 76
+++F AEK ++ +N + G
Sbjct: 56 FVEFADLATAEKCLHKINGKPLPGAT 81
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 31.3 bits (70), Expect = 0.068
Identities = 10/76 (13%), Positives = 25/76 (32%), Gaps = 6/76 (7%)
Query: 3 ISNVTDEEMQEHY-DNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 61
+ + +H E + G+I+ + ++KF+ + +AE
Sbjct: 139 VGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANAE 193
Query: 62 KAVNDLNNRWFGGRPV 77
A ++N+
Sbjct: 194 FAKEAMSNQTLLLPSD 209
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.7 bits (66), Expect = 0.11
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 15/84 (17%)
Query: 8 DEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV--- 64
++E + Y +DV + KYGE+ + + G ++F + AE AV
Sbjct: 22 EDESKGGYS---KDVLLRLLQKYGEVLNLVLSSKKP----GTAVVEFATVKAAELAVQNE 74
Query: 65 -----NDLNNRWFGGRPVYAELSP 83
N L W G+P A
Sbjct: 75 VGLVDNPLKISWLEGQPQDASGPS 98
>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 = 30.2 bits (68), Expect = 0.12
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 29 KYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
YGEI+ ++ D G +++ + A A LN G+ +
Sbjct: 95 DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 145
>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 = 0.14
Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 12/74 (16%)
Query: 7 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGN-------VYIKFRREED 59
+ ++ + N E + + ++ E++ V L ++ V+ +F E +
Sbjct: 199 IETLLKCEFSNDCEVIARK---RFREVDA--VLSWLLEYAPSRLTGTGACVFAEFDTESE 253
Query: 60 AEKAVNDLNNRWFG 73
A + + G
Sbjct: 254 ARQVLEQAPEWLNG 267
>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 = 29.0 bits (66), Expect = 0.14
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 14/74 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
T EE++ H F G + + + CD H G YI+F +E +
Sbjct: 17 GATAEELEAH----FHG--------CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 64 VNDLNNRWFGGRPV 77
+ L+ F GR +
Sbjct: 65 L-ALDESLFRGRQI 77
>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 = 29.6 bits (67), Expect = 0.15
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 11/62 (17%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLNNRWFGGR 75
D F E YGEI+ +++ NL D G + +++ ++A+ A+ LN + G+
Sbjct: 40 HDKFAE----YGEIKNIHL--NL-DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 92
Query: 76 PV 77
P+
Sbjct: 93 PI 94
>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 = 29.8 bits (66), Expect = 0.17
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
G++ + + L G++++ F E A+K V + + +
Sbjct: 132 DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK-YKETDLLILFK 184
>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 = 29.3 bits (66), Expect = 0.19
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 52 IKFRREEDAEKAVNDLNNRWFGGRP 76
+KF+ A++A+ LN +
Sbjct: 89 VKFQSGSSAQQAIAGLNGFNILNKR 113
>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 = 0.20
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
Y +F + A++ LN G + +
Sbjct: 61 YAEFEDLDSLLSALS-LNEESLGNKRIR 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 = 0.20
Identities = 11/74 (14%), Positives = 27/74 (36%), Gaps = 14/74 (18%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKA 63
+ ++++ FF G++ ++ + D G Y++F + A
Sbjct: 36 RIRPRDLED----FFS--------AVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 83
Query: 64 VNDLNNRWFGGRPV 77
+ L + G P+
Sbjct: 84 IG-LTGQRLLGVPI 96
>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 = 0.29
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 16/71 (22%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
T+++++E+ F +GE+ + V D H G +++F E K
Sbjct: 26 KTTEQDLKEY----FS--------TFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 64 VND---LNNRW 71
++ ++ RW
Sbjct: 74 MSQRHMIDGRW 84
>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 = 28.4 bits (64), Expect = 0.31
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 21 DVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLNNRWFGGRP 76
+ F + YGEI+ +++ NL D G +++ + A A LN G+
Sbjct: 45 EKFCD----YGEIKNIHL--NL-DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 97
Query: 77 V 77
+
Sbjct: 98 I 98
>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 = 29.3 bits (66), Expect = 0.32
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 25 ECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF----GGRPVYAE 80
E E E+ E + DN DH +G +Y++ R + + + G +
Sbjct: 185 EFERIMNELRERGLKDNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRK 244
Query: 81 L 81
L
Sbjct: 245 L 245
>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 = 28.4 bits (63), Expect = 0.32
Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 14/84 (16%)
Query: 3 ISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREE 58
+SN ++ +E+Q+ F ++G+++ + + + L V + +
Sbjct: 14 VSNIDYRLSRKELQQLLQEAFA--------RHGKVKSVELSPHTDYQLKAVV--QMENLQ 63
Query: 59 DAEKAVNDLNNRWFGGRPVYAELS 82
DA AVN L+ G + + L+
Sbjct: 64 DAIGAVNSLHRYKIGSKKILVSLA 87
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 28.1 bits (63), Expect = 0.35
Identities = 4/36 (11%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 51 YIKFRREEDAEKAVNDLNNR----WFGGRPVYAELS 82
+++ DA + + L + G+ + + +
Sbjct: 57 FVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>3gja_A CYTC3; halogenase, beta barrel, biosynthetic protein; 2.20A
{Streptomyces} PDB: 3gjb_A*
Length = 319
Score = 28.9 bits (64), Expect = 0.48
Identities = 9/66 (13%), Positives = 18/66 (27%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 61
+ EEM ++ + Y + N HL ++ + +
Sbjct: 28 PVKIFEPEEMTRRWNIIRRQLLDRSLAIYPDSNGKANISNYDRHLDIDLLAEHIMRPEIV 87
Query: 62 KAVNDL 67
V L
Sbjct: 88 DRVGSL 93
>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 = 0.55
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
Y +F + A++ LN G R +
Sbjct: 65 YAEFEDLDSLLSALS-LNEESLGNRRIR 91
>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 = 0.59
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+ 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 = 27.2 bits (61), Expect = 0.76
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+ +++ +E A A+ +LN R F GR +
Sbjct: 54 FCEYQDQETALSAMRNLNGREFSGRAL 80
>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens}
Length = 354
Score = 27.9 bits (61), Expect = 0.88
Identities = 7/65 (10%), Positives = 21/65 (32%)
Query: 7 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND 66
++ + + ++ V C K + DH+ ++ D+ +
Sbjct: 26 NSTSIKYNLEELYQAVENLCSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKK 85
Query: 67 LNNRW 71
++ W
Sbjct: 86 IDRCW 90
>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 = 26.8 bits (60), Expect = 0.98
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 16/75 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKA 63
+ + E++ FF +YG ++E+ + D G G ++ F + D +K
Sbjct: 20 RMDETEIRS----FFA--------RYGSVKEVKIITDRTGVSK-GYGFVSFYNDVDVQKI 66
Query: 64 VNDLNNRWFGGRPVY 78
V N F G+ +
Sbjct: 67 VESQIN--FHGKKLK 79
>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 = 27.1 bits (60), Expect = 1.1
Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 11/75 (14%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
EE+ E E V ++ + + G ++++ A A
Sbjct: 19 MKKREEILEEIAKVTEGVL--------DVIVYASAADKMKN-RGFAFVEYESHRAAAMAR 69
Query: 65 NDLNNR--WFGGRPV 77
L G +
Sbjct: 70 RKLMPGRIQLWGHQI 84
>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 = 27.5 bits (62), Expect = 1.4
Identities = 6/31 (19%), Positives = 7/31 (22%), Gaps = 1/31 (3%)
Query: 54 FRREEDAEKAVNDLNNRWFGGRPVYAELSPV 84
A L+ R V PV
Sbjct: 265 CTSASSAIDVGAQLSGAGV-CRTVRVATGPV 294
>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 = 27.7 bits (61), Expect = 1.4
Identities = 19/100 (19%), Positives = 33/100 (33%), Gaps = 15/100 (15%)
Query: 4 SNVTDEE----MQEHYDNFFEDVFVE--CEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 57
+N T E N ++ FVE C D + N+ +G+ R
Sbjct: 131 TNTTRERRAMIFNFGEQNGYKTFFVESICVD------PEVIAANIVQVKLGSPDYVNR-- 182
Query: 58 EDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 97
D+++A D R Y L D + + ++
Sbjct: 183 -DSDEATEDFMRRIECYENSYESLDEEQDRDLSYIKIMDV 221
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI,
protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 26.6 bits (58), Expect = 1.5
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 29 KYGEIEEMNVCDNLGDHLVGN-VYIKFRREEDAEKAVNDLNNRWFGGR 75
+YG I + + + GN ++I+++ + A KA++ + R FG
Sbjct: 46 QYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGES 86
>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 = 1.6
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 57 EEDAEKAVNDLNNRWFGGRPV 77
EE +A+ L+N F GR +
Sbjct: 52 EESVSEAIAKLDNTDFMGRTI 72
>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 = 27.3 bits (60), Expect = 1.6
Identities = 8/59 (13%), Positives = 16/59 (27%), Gaps = 1/59 (1%)
Query: 22 VFVECEDKYGEIEEMNVCDNLGDHLVGNV-YIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
+ V+ E + + V + R + AE+ + G R
Sbjct: 52 IAVQARAGRDETAFLLELACDEARIAAVVGWEDLRAPQLAERVAEWRGTKLRGFRHQLQ 110
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 25.7 bits (57), Expect = 2.5
Identities = 5/27 (18%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
Y++F + ++A+ + G R +
Sbjct: 60 YVEFDEVDSLKEALT-YDGALLGDRSL 85
>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 = 26.2 bits (58), Expect = 4.1
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 43 GDHLVGNVYIKFRREEDAEKA 63
DH G Y++ ++ + E+
Sbjct: 176 YDHFAGRAYVRLHQDPEYERL 196
>2ep5_A 350AA long hypothetical aspartate-semialdehyde dehydrogenase;
oxidoreductase, structural genomics, NPPSFA; 2.40A
{Sulfolobus tokodaii}
Length = 350
Score = 25.6 bits (57), Expect = 5.1
Identities = 11/63 (17%), Positives = 19/63 (30%), Gaps = 7/63 (11%)
Query: 50 VYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL-----SPVTDFREACCRQYEMVLETKNA 104
+ I + E+ L N F P L P+ E Q + + ++
Sbjct: 248 INIVTNERINIEEIKKTLKN--FKSLPQQKNLPTAPKQPIIVRDEEDRPQPIIDVNAESG 305
Query: 105 DPV 107
V
Sbjct: 306 MAV 308
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 25.0 bits (54), Expect = 5.8
Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 70
DV + G+++ + + G ++F A+KA LN
Sbjct: 39 VDVLYTVCNPVGKVQRIVIFKRNGIQ----AMVEFESVLCAQKAKAALNGA 85
>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 = 6.5
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 9 EEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDH 45
E + +H D + + E+ ++C++L DH
Sbjct: 39 ESLHDHADELYRSCLASFKKNGQIDEQADICESLHDH 75
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 25.0 bits (54), Expect = 6.6
Identities = 7/51 (13%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 70
DV + K+G + ++ + +++ A+ A L+ +
Sbjct: 42 LDVLHQIFSKFGTVLKIITFT---KNNQFQALLQYADPVSAQHAKLSLDGQ 89
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 25.0 bits (54), Expect = 7.5
Identities = 8/39 (20%), Positives = 12/39 (30%), Gaps = 4/39 (10%)
Query: 75 RPVYAELSPVTDFREAC--CRQY--EMVLETKNADPVCT 109
P + C C+ Y ++V D VC
Sbjct: 8 DKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCA 46
>3gwc_A TS, tsase, thymidylate synthase THYX; FAD, fdump, flavoprotein,
methyltransferase, nucleotid biosynthesis, transferase;
HET: FAD UFP; 1.90A {Mycobacterium tuberculosis} PDB:
3hzg_A* 2af6_A* 2gq2_A*
Length = 258
Score = 25.0 bits (55), Expect = 7.8
Identities = 4/37 (10%), Positives = 9/37 (24%)
Query: 3 ISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC 39
I + + Y + + D+ I
Sbjct: 131 ILTEAADAARATYSELLAKLEAKFADQPNAILRRKQA 167
>2z1n_A Dehydrogenase; reductase, SDR, oxidoreductase; 1.80A {Aeropyrum
pernix}
Length = 260
Score = 24.8 bits (55), Expect = 8.6
Identities = 5/30 (16%), Positives = 11/30 (36%)
Query: 49 NVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
+ + R E E A + + + G +
Sbjct: 33 RLLLFSRNREKLEAAASRIASLVSGAQVDI 62
>3h7h_B Transcription elongation factor SPT5; helices surrounding beta
sheet, activator, ME binding, nucleus, repressor,
transcription regulation; 1.55A {Homo sapiens}
Length = 106
Score = 24.5 bits (53), Expect = 9.2
Identities = 5/26 (19%), Positives = 16/26 (61%)
Query: 44 DHLVGNVYIKFRREEDAEKAVNDLNN 69
+H+ G +Y++ ++ ++A+ + N
Sbjct: 48 EHVKGYIYVEAYKQTHVKQAIEGVGN 73
>2jxd_A Serine protease inhibitor kazal-type 2; anti-parallel beta sheet,
beta-bulge, disulfide bond, alpha helix, pyrrolidone
carboxylic acid, secreted; NMR {Homo sapiens}
Length = 62
Score = 23.7 bits (51), Expect = 9.3
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 80 ELSPVTDFREACCRQYEMVLETKNADPVC 108
+ + +R C QY + ++ +PVC
Sbjct: 2 QFGLFSKYRTPNCSQYRLPGCPRHFNPVC 30
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.135 0.402
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: 2,105,875
Number of extensions: 119812
Number of successful extensions: 513
Number of sequences better than 10.0: 1
Number of HSP's gapped: 494
Number of HSP's successfully gapped: 206
Length of query: 130
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,384,350
Effective search space: 206064450
Effective search space used: 206064450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (23.7 bits)