RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17806
(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 = 110 bits (277), Expect = 6e-33
Identities = 61/73 (83%), Positives = 68/73 (93%)
Query: 1 MQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 60
MQEHYD FFE+VF E E+KYGE+EEMNVCDNLGDHLVGNVY+KFRREEDAEKAV DLNNR
Sbjct: 32 MQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNR 91
Query: 61 WFGGRPVYAELSP 73
WF G+P++AELSP
Sbjct: 92 WFNGQPIHAELSP 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 = 90.9 bits (226), Expect = 5e-25
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 4/77 (5%)
Query: 3 EHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF 62
+DV EC K+G + + V N GNVY+K A AVN L+ RWF
Sbjct: 25 GWDTEIKDDVIEECN-KHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWF 80
Query: 63 GGRPVYAELSPVTDFRE 79
G+ + A P+ +
Sbjct: 81 AGKMITAAYVPLPTYHN 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 = 87.5 bits (217), Expect = 1e-23
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 2 QEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW 61
+ ED+ VEC K+G+I ++ + D H G + FR E+A+ + L+ RW
Sbjct: 33 PLVLNEIREDLRVECS-KFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRW 88
Query: 62 FGGRPVYAEL-SPVTDFR 78
FGGR + A+ TD++
Sbjct: 89 FGGRQITAQAWDGTTDYQ 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 = 84.4 bits (209), Expect = 2e-22
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 3 EHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL-----VGNVYIKFRREEDAEKAVNDL 57
+ D+ +V EC K+G + + + + ++++F + KA+ L
Sbjct: 33 DIDDDLEGEVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 58 NNRWFGGRPVYAELSPVTDFRE 79
N RWF GR V AE+ F
Sbjct: 92 NGRWFAGRKVVAEVYDQERFDN 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 = 80.2 bits (198), Expect = 6e-21
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 3 EHYDNFFEDVFVECEDKYGEIEEMNV---CDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 59
E Y+ EDV EC KYG ++ + + D + G ++++F D +KA+ L
Sbjct: 23 EEYEEIVEDVRDECS-KYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
Query: 60 RWFGGRPVYAELSPVTDFRE 79
R F R V + +
Sbjct: 82 RKFANRVVVTKYCDPDSYHR 101
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 72.9 bits (179), Expect = 3e-18
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 2 QEHYDNFFEDVFVECEDKYGEIEEMNVCD--NLGDHLVGNVYIKFRREEDAEKAVNDLNN 59
E ++ + ECE KYG++ + + + D ++++F R E A KAV DLN
Sbjct: 20 GEVDEDLEVETKEECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG 78
Query: 60 RWFGGRPVYAELSPVTDFR 78
R+FGGR V A + FR
Sbjct: 79 RYFGGRVVKACFYNLDKFR 97
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 63.2 bits (154), Expect = 3e-14
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 6 DNFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFG 63
DN E + KYGE+EE+ + HL G + F A++ V +L+
Sbjct: 16 DNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL-GLARVLFTSTRGAKETVKNLHLTSVM 74
Query: 64 GRPVYAELSPVTDFREACCRQYEM 87
G ++A+L + + YE+
Sbjct: 75 GNIIHAQLDI---KGQQRMKYYEL 95
>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 = 46.0 bits (109), Expect = 4e-07
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 6 DNFFEDVFVECEDKYGEIE------EMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 59
D+ +V EC K+G + E + + +V ++++F + KA+ LN
Sbjct: 140 DDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIV-KIFVEFSIASETHKAIQALNG 197
Query: 60 RWFGGRPVYAELSPVTDF 77
RWF GR V AE+ F
Sbjct: 198 RWFAGRKVVAEVYDQERF 215
>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 = 43.7 bits (103), Expect = 9e-07
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 18 DKYGEIEEMNVCDNLGD----HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
K+G+I ++ + ++ + Y+ + R EDA +A+ +NN GR + A L
Sbjct: 40 GKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98
>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 = 43.0 bits (102), Expect = 5e-06
Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 1/72 (1%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ F E +G +E + G + ++ +++ A +A +DL + G R +Y
Sbjct: 109 QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY 168
Query: 69 AELSPVTDFREA 80
+ A
Sbjct: 169 VHWTDAGQLTPA 180
Score = 41.1 bits (97), Expect = 2e-05
Identities = 8/50 (16%), Positives = 15/50 (30%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ L G +++ E AE+A + GG +
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLR 257
Score = 38.0 bits (89), Expect = 3e-04
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
++ E AE A+N + R + +L P
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSVQLQP 93
>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 = 41.5 bits (98), Expect = 5e-06
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 8/77 (10%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS-PVTDF 77
++G++E + + +I F + A KA+ ++N + G + + P
Sbjct: 34 QFGKLERVKKLKDYA-------FIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86
Query: 78 REACCRQYEMGECTRSG 94
R+ Q + SG
Sbjct: 87 RKERKAQRQAASGPSSG 103
>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 = 40.7 bits (96), Expect = 8e-06
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVT 75
G + F ++A AV DLN+R G R V +LS +
Sbjct: 58 GEAMVAFESRDEATAAVIDLNDRPIGSRKV--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 = 40.7 bits (96), Expect = 9e-06
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
G + F ++A AV DLN+R G R V L
Sbjct: 58 GEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 92
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
YI +EDA V LN G + ++S
Sbjct: 163 YIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 194
Score = 37.7 bits (88), Expect = 4e-04
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 6/60 (10%)
Query: 11 DVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 70
F C G I ++V D+L + I+F R + A A+ + G +
Sbjct: 60 KYFKHC----GPIIHVDVADSLKKNF-RFARIEFARYDGALAAITKTHKV-VGQNEIIVS 113
Score = 35.7 bits (83), Expect = 0.002
Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 10 EDVFVECEDKYGEIEEMNV--CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
E++ E + +G IE++N+ ++ F ++ AE+A+ +N G R +
Sbjct: 225 ENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREI 283
Query: 68 YAELS 72
L+
Sbjct: 284 SVSLA 288
>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 = 40.0 bits (94), Expect = 2e-05
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G+I E+ V G +++F E A A+ +N G V
Sbjct: 48 PFGQIMEIRVFPEKG---YS--FVRFSTHESAAHAIVSVNGTTIEGHVV 91
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 40.8 bits (96), Expect = 3e-05
Identities = 6/28 (21%), Positives = 17/28 (60%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+I++ + + ++ AV+ +N GG+ +
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQYLR 198
Score = 36.5 bits (85), Expect = 0.001
Identities = 11/51 (21%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+G I+ +++ D++ G ++++ E A+ A+ +N+ GGR +
Sbjct: 51 PFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 101
>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 = 40.2 bits (95), Expect = 3e-05
Identities = 10/60 (16%), Positives = 21/60 (35%), Gaps = 1/60 (1%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ G I + D + G ++ F E D+++A+ LN + +
Sbjct: 17 DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Score = 34.9 bits (81), Expect = 0.003
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG--RPVY 68
KYG I + N+ D L G ++++ + E+A++A++ LNN G +P+
Sbjct: 112 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 164
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 39.5 bits (92), Expect = 3e-05
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
G+I ++ V + + G YI F +E A+ V F G P+ S
Sbjct: 56 SQGDILDIVVDLSDDNS--GKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107
>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 = 39.9 bits (94), Expect = 5e-05
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
YI+F+ E DAEK + + GR V
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEIDGRSVS 167
Score = 34.1 bits (79), Expect = 0.005
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 1/62 (1%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 78
+ ++ V D Y+ F ED EKA+ +L G + E D +
Sbjct: 36 ELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSK 94
Query: 79 EA 80
+
Sbjct: 95 KV 96
>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 = 12/53 (22%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 20 YGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
YG+++ + + N N ++ A+ A++ LN G+P+ LS
Sbjct: 28 YGDVQRVKILFNKK----ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS 76
Score = 27.2 bits (60), Expect = 1.3
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFG-GRPVY 68
I+ E+A +A+ DL+N G +
Sbjct: 162 LIQMGSVEEAVQALIDLHNHDLGENHHLR 190
>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 = 38.6 bits (90), Expect = 6e-05
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 5/62 (8%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 78
++G + + + + ++F +A KA L F P+Y E +P+ F
Sbjct: 33 RFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFG 87
Query: 79 EA 80
A
Sbjct: 88 AA 89
>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 = 37.9 bits (89), Expect = 8e-05
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G I + V D G ++ F + DAE A+ + +W GGR +
Sbjct: 29 PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>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 = 39.5 bits (91), Expect = 1e-04
Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++G+I ++ V +L + G ++ F+ A A+ + F +P+ + +
Sbjct: 36 QFGQILDILVSRSLK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
Score = 28.7 bits (63), Expect = 0.55
Identities = 6/51 (11%), Positives = 16/51 (31%), Gaps = 5/51 (9%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF-GGRPVY 68
++ +E+ + +++F E A A + L +
Sbjct: 230 QFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDALQGFKITQNNAMK 276
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 37.7 bits (88), Expect = 1e-04
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G I + G +IK+ E A + L N F GR +
Sbjct: 50 NFGFILDFKHYPEKG---CC--FIKYDTHEQAAVCIVALANFPFQGRNL 93
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 37.7 bits (88), Expect = 1e-04
Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
+G ++E+ + + +++F E A KA+ +++ + F +P+ S
Sbjct: 54 PFGPMKEVKILNGFA-------FVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
>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 = 38.3 bits (90), Expect = 2e-04
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F ++DA+ A++ + + GRP+
Sbjct: 133 FVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 35.2 bits (82), Expect = 0.002
Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
ED+ + G I + + D ++ ++++ + DA A+ LN + V
Sbjct: 14 EDILKQYFQVGGPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQTLNGKQIENNIV 71
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++G+I ++ V +L + G ++ F+ A A+ + F +P+ + +
Sbjct: 35 RFGQILDILVSRSLK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 38.4 bits (89), Expect = 2e-04
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 20 YGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
YG+++ + + N N ++ A+ A++ LN G+P+ LS
Sbjct: 59 YGDVQRVKILFNKK----ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 108
Score = 26.9 bits (59), Expect = 1.8
Identities = 7/29 (24%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 41 YIKFRREEDAEKAVNDLNN-RWFGGRPVY 68
I+ E+A +A+ DL+N +
Sbjct: 193 LIQMGSVEEAVQALIDLHNHDLGENHHLR 221
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F +E AE+A+ +N R V+
Sbjct: 147 FVHFETQEAAERAIEKMNGMLLNDRKVF 174
Score = 37.3 bits (87), Expect = 5e-04
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
E + E G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 29 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
>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 = 36.7 bits (86), Expect = 2e-04
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F ++DA+ A++ + + GRP+
Sbjct: 47 FVSFTSQDDAQNAMDSMQGQDLNGRPLR 74
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 4/28 (14%), Positives = 12/28 (42%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ ++ ++A+ LN G + +
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLL 187
Score = 28.5 bits (64), Expect = 0.55
Identities = 5/28 (17%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+++FR ++ +A+ + F G+ +
Sbjct: 55 FLEFRSVDETTQAMA-FDGIIFQGQSLK 81
>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 = 38.1 bits (89), Expect = 3e-04
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
E+ F ++YGE E+ + + G +I+ AE A +L+ RP+
Sbjct: 36 EEDFKRLFERYGEPSEVFINRDRG-----FGFIRLESRTLAEIAKAELDGTILKSRPLR 89
Score = 30.8 bits (70), Expect = 0.079
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF----GGRPVYAELSP 73
++G +E+ V D+ G G +++F + A KA+ + F RPV E
Sbjct: 119 QFGPVEKAVVVVDDRGRAT-GKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPME 177
Query: 74 VTDFREA 80
D +
Sbjct: 178 QFDDEDG 184
>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 = 37.0 bits (86), Expect = 3e-04
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 11/63 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
E +F KYG + +V ++++ E A AV N R G+ +
Sbjct: 46 ETIF----SKYGRVAGCSVHKGYA-------FVQYSNERHARAAVLGENGRVLAGQTLDI 94
Query: 70 ELS 72
++
Sbjct: 95 NMA 97
>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 = 36.4 bits (85), Expect = 3e-04
Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 11/63 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+F ++ G + E +V + ++ +E DA+ A+ LN + G+ +
Sbjct: 27 RSLF----ERRGRVIECDVVKDYA-------FVHMEKEADAKAAIAQLNGKEVKGKRINV 75
Query: 70 ELS 72
ELS
Sbjct: 76 ELS 78
>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 = 36.5 bits (85), Expect = 3e-04
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++ F EDA +A+ LN + G P+ L+
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>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 = 36.8 bits (86), Expect = 3e-04
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F E+A KAV ++N R +P+Y
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLY 86
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 36.4 bits (85), Expect = 3e-04
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+I F + ++ A+ +N ++ RP+
Sbjct: 52 FINFASFDASDAAIEAMNGQYLCNRPIT 79
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 36.4 bits (85), Expect = 3e-04
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 11/63 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+F YG I ++N+ + G +I+F + A+ + G+ +
Sbjct: 29 FRIF----SPYGHIMQINIKNAFG-------FIQFDNPQSVRDAIECESQEMNFGKKLIL 77
Query: 70 ELS 72
E+S
Sbjct: 78 EVS 80
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 36.2 bits (84), Expect = 3e-04
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 65
K+G+I + G G +++++ A AV + + +
Sbjct: 30 KFGKITNDFYPEEDGKTK-GYIFLEYASPAHAVDAVKNADGYKLDKQ 75
>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 = 36.5 bits (85), Expect = 3e-04
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 11/63 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+F YG I ++N+ +I+F + A+ + G+ +
Sbjct: 41 FRIF----SPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89
Query: 70 ELS 72
E+S
Sbjct: 90 EVS 92
>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 = 36.5 bits (85), Expect = 3e-04
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
KYG+ E+ + + G G +I+ AE A +L+N G+ +
Sbjct: 38 KYGKAGEVFIHKDKG---FG--FIRLETRTLAEIAKVELDNMPLRGKQLR 82
>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 = 36.6 bits (85), Expect = 4e-04
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
++ F + DAE A+ + +W GGR +
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQI 87
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA
complex, AU-rich element, transcription/RNA complex;
1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB:
1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 36.8 bits (86), Expect = 5e-04
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F GEIE + D + +G ++ + +DAEKA+N LN + +
Sbjct: 16 QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 75
Score = 32.2 bits (74), Expect = 0.023
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 13/69 (18%)
Query: 6 DNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLNNRW 61
E +F +YG I + L D + G +I+F + +AE+A+ LN +
Sbjct: 102 QKELEQLF----SQYGRIITSRI---LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
Query: 62 FGG--RPVY 68
G P+
Sbjct: 155 PSGATEPIT 163
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 35.9 bits (83), Expect = 5e-04
Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
+YG +E + D V + + ++ A +A++ LN + P
Sbjct: 38 QYGVVESCEQVNT--DSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP 90
>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 = 35.7 bits (83), Expect = 6e-04
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
+ F R+ DA KA+ N GRP+ +L
Sbjct: 74 DVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 35.5 bits (82), Expect = 8e-04
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 65
K+G+I + G G +++++ A AV + + +
Sbjct: 44 KFGKITNDFYPEEDGKTK-GYIFLEYASPAHAVDAVKNADGYKLDKQ 89
>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 = 35.5 bits (82), Expect = 0.001
Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 10/74 (13%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 66
+FF + ++ +++ + GN +KF +D +A+ N R
Sbjct: 35 DFFHGL---------RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRY 84
Query: 67 VYAELSPVTDFREA 80
V + + A
Sbjct: 85 VEVSPATERQWVAA 98
>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 = 34.9 bits (81), Expect = 0.001
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F+ E A+ LN GRP+
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPIN 88
>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 = 35.3 bits (82), Expect = 0.001
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAEKAVNDLNNRWFGGRPV 67
+ G + + +H + Y ++F DA A+ +N R G+ V
Sbjct: 38 QIGPCKSCKMIT---EHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEV 85
>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 = 34.9 bits (81), Expect = 0.001
Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
F ++YG + E ++ + ++ R EDA +A+ L+N F G+ ++
Sbjct: 28 RAKF----EEYGPVIECDIVKDYA-------FVHMERAEDAVEAIRGLDNTEFQGKRMHV 76
Query: 70 ELS 72
+LS
Sbjct: 77 QLS 79
>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 = 34.9 bits (81), Expect = 0.001
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
YG + E++ D+L G ++ F E A KA +++ + F GR +
Sbjct: 31 AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML 80
>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 = 35.5 bits (82), Expect = 0.001
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 79
G ++F+ E+DA K+ L+ + GR + + + D RE
Sbjct: 58 GQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMRE 98
>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 = 34.9 bits (81), Expect = 0.001
Identities = 13/63 (20%), Positives = 28/63 (44%), Gaps = 11/63 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+F ++YG++ E ++ N G ++ + AE A+ +L++ G +
Sbjct: 26 RSLF----EQYGKVLECDIIKNYG-------FVHIEDKTAAEDAIRNLHHYKLHGVNINV 74
Query: 70 ELS 72
E S
Sbjct: 75 EAS 77
>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 = 34.9 bits (81), Expect = 0.001
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++++++ E A+KA+ L G + +S
Sbjct: 54 FVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS 85
>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 = 35.0 bits (81), Expect = 0.001
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
K+G I E+ + D G +I F DA+ A D+N + G+ +
Sbjct: 30 KHGPISEVLLIKDRTSKSR-GFAFITFENPADAKNAAKDMNGKSLHGKAIK 79
>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 = 35.0 bits (81), Expect = 0.001
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
+ F R DA KA+ GRP+ +L
Sbjct: 80 DVHFERRADALKAMKQYKGVPLDGRPMDIQL 110
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 35.1 bits (81), Expect = 0.002
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 10 EDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
F+ +G+I ++ + D + G +++F EDA A++++N GR +
Sbjct: 81 HAAFIP----FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
>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: 42 IKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ F + A+ A+ +N G + +
Sbjct: 87 VSFDNPDSAQVAIKAMNGFQVGTKRLK 113
>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 = 34.5 bits (80), Expect = 0.002
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREAC 81
Y+ F ED EKA+ +L G + E D C
Sbjct: 62 YVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTRGC 101
>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 = 34.3 bits (79), Expect = 0.002
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 10/64 (15%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
D+ + + KY + D ++ E A+ A+ + F G+ +
Sbjct: 23 HDLLKDYDLKYCYV----------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV 72
Query: 70 ELSP 73
+L P
Sbjct: 73 QLQP 76
>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 = 34.7 bits (80), Expect = 0.002
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 5/50 (10%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+G I ++++ ++ + + E A++AV +LN +
Sbjct: 60 PFGNIIDLSMDPPRN---CA--FVTYEKMESADQAVAELNGTQVESVQLK 104
>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 = 34.6 bits (80), Expect = 0.002
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 44 FRREEDAEKAVNDLNNRWFGGRPVY 68
F + +A +A++ N + RP++
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMH 87
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation
initiation, RNA-binding, EIF4G-binding translation;
1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 34.5 bits (80), Expect = 0.002
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F +E AE+A+ +N R V+
Sbjct: 49 FVHFETQEAAERAIEKMNGMLLNDRKVF 76
>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 = 34.2 bits (79), Expect = 0.002
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ + + E A++AV +LN +
Sbjct: 53 FVTYEKMESADQAVAELNGTQVESVQLK 80
>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 = 34.3 bits (79), Expect = 0.002
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
KYG I ++ V + G Y+ + DA+ AV+ L+ R +
Sbjct: 31 KYGPIRQIRVGNTPETR--GTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY 82
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 35.2 bits (81), Expect = 0.002
Identities = 14/62 (22%), Positives = 25/62 (40%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 78
++G +++ V + +G + F R DA KA+ GRP+ +L
Sbjct: 111 EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170
Query: 79 EA 80
E
Sbjct: 171 EH 172
>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: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++F EDA A++++N GR +
Sbjct: 53 FVEFELAEDAAAAIDNMNESELFGRTI 79
>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: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ ++ ++A+ LN G + +
Sbjct: 140 FCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Score = 27.2 bits (61), Expect = 1.2
Identities = 5/27 (18%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++FR ++ +A+ + F G+ +
Sbjct: 55 FLEFRSVDETTQAMA-FDGIIFQGQSL 80
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 33.9 bits (78), Expect = 0.003
Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 65
K G++ M D G ++++ DA+K + + + +
Sbjct: 35 KAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 33.8 bits (78), Expect = 0.003
Identities = 7/29 (24%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNR-WFGGRPVY 68
++KF E + ++A+ + G +PV
Sbjct: 55 FVKFTDELEQKRALTECQGAVGLGSKPVR 83
>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 = 33.8 bits (78), Expect = 0.004
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNL-GDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
++F++ G + ++ D + G H G +++F EEDA+ A+ ++ G+P+
Sbjct: 33 WELFLQ----AGPVVNTHMPKDRVTGQHQ-GYGFVEFLSEEDADYAIKIMDMIKLYGKPI 87
>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: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 78
YG +E++ + G ++ ++A+ LNN + G+ + +S
Sbjct: 28 LYGNVEKVKFMKSKP----GAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIM 83
Query: 79 E 79
Sbjct: 84 P 84
Score = 30.8 bits (69), Expect = 0.086
Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 1/63 (1%)
Query: 6 DNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 64
E+ F E D+ G +V + + +++ + DA + + LN+
Sbjct: 133 LEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKN 192
Query: 65 RPV 67
Sbjct: 193 PNG 195
>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 = 33.8 bits (78), Expect = 0.004
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 42 IKFRREEDAEKAVNDLNNRWFGGRPVY 68
I F +E A +A++ +N G+ +
Sbjct: 72 ITFPNKEIAWQALHLVNGYKLYGKILV 98
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 34.4 bits (79), Expect = 0.004
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
G +I E+ A KA+ + N G+P+ + +
Sbjct: 93 GQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA 127
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 33.5 bits (76), Expect = 0.004
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 78
G K+ E+A KA LNN ++AE + +
Sbjct: 44 GIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENEVQ 84
>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 = 33.5 bits (77), Expect = 0.005
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 19 KYGEIEEMNVCDNLGDHLVGN----VYIKFRREEDAEKAVNDLNN---RWFGGRPV 67
++G+I E+ V L D G ++ + E A KA + L+ RP+
Sbjct: 36 EFGKIYELTV---LKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI 88
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 33.3 bits (76), Expect = 0.005
Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 8/65 (12%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND--LNNRWFGGRPV 67
+V +G++ + + +++ EE A VN +P+
Sbjct: 30 TEVIALGL-PFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI 83
Query: 68 YAELS 72
Y + S
Sbjct: 84 YIQYS 88
>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 = 33.0 bits (76), Expect = 0.005
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
YI+F+ E DAEK + + GR V
Sbjct: 57 YIEFKSEADAEKNLEEKQGAEIDGRSV 83
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 33.3 bits (76), Expect = 0.006
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 8/65 (12%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDL--NNRWFGGRPV 67
+V +G++ + + +I+ EE A VN G+P+
Sbjct: 31 GEVISLGL-PFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI 84
Query: 68 YAELS 72
Y + S
Sbjct: 85 YIQFS 89
>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 = 33.4 bits (77), Expect = 0.006
Identities = 4/27 (14%), Positives = 8/27 (29%)
Query: 42 IKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ E E + N ++ P
Sbjct: 71 ARMESTEKCEAVIGHFNGKFIKTPPGV 97
>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 = 33.0 bits (76), Expect = 0.006
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+I F R EDA +A+ ++ + +
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLIL 87
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 33.0 bits (76), Expect = 0.006
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+I+FR E + AV +LN G R +
Sbjct: 48 FIEFRDLESSASAVRNLNGYQLGSRFL 74
>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 = 33.9 bits (77), Expect = 0.007
Identities = 8/57 (14%), Positives = 20/57 (35%), Gaps = 3/57 (5%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV---YAELSPVTDFREACCRQYEMGECTRSG 94
+ E ++K ++ L R G+ ++ F + + G+ + G
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172
>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 = 33.0 bits (76), Expect = 0.007
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+I+F EDA++A+N N R GR +
Sbjct: 57 FIEFASFEDAKEALNSCNKREIEGRAI 83
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 32.8 bits (75), Expect = 0.008
Identities = 8/51 (15%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 18 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ G++ + + L G++++ F E A+K V + + + +
Sbjct: 33 EDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLL 82
>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 = 33.0 bits (75), Expect = 0.008
Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 6/74 (8%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 66
NF D + + ++ G +++ E+D + A+ + G R
Sbjct: 36 NFLSDC-----TIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL-KKDRESMGHRY 89
Query: 67 VYAELSPVTDFREA 80
+ S T+
Sbjct: 90 IEVFKSHRTEMDWV 103
>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 = 0.009
Identities = 4/27 (14%), Positives = 11/27 (40%)
Query: 42 IKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ + A+ A+ +N G + +
Sbjct: 72 VSYDNPVSAQAAIQSMNGFQIGMKRLK 98
>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 = 32.6 bits (75), Expect = 0.009
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 18 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
D++G I D++ YI++ + A+ A + GG
Sbjct: 39 DRFGSIRT---IDHVKGD--SFAYIQYESLDAAQAACAKMRGFPLGGPDR 83
>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 = 32.9 bits (75), Expect = 0.010
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREA 80
G +++FR E D + A+ + ++ G R + E
Sbjct: 68 GEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEK 109
>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 = 33.4 bits (77), Expect = 0.010
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 19 KYGEIEEMNV-CDNLGDHLV--GNVYIKFRREEDAEKAVNDLNNR 60
+YG + E+NV D + G ++ F + A +A N L+N
Sbjct: 26 QYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNM 70
Score = 32.2 bits (74), Expect = 0.021
Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 6 DNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR---W 61
+N +F +G+IEE + G G ++ F A+ A+ ++
Sbjct: 109 ENDIRVMF----SSFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIKAMHQAQTME 163
Query: 62 FGGRPVY 68
P+
Sbjct: 164 GCSSPMV 170
>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 = 32.2 bits (74), Expect = 0.011
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++F EDA A++++N GR +
Sbjct: 58 FVEFELAEDAAAAIDNMNESELFGRTI 84
>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 = 32.1 bits (74), Expect = 0.012
Identities = 13/51 (25%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 19 KYGEIEEMNV-CDNLGDHLV-GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
YG+I+ +++ + + HL G Y++F ++AEKA+ ++ G+ +
Sbjct: 27 TYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
>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 = 32.6 bits (74), Expect = 0.013
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 8/65 (12%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND--LNNRWFGGRPV 67
+V +G++ + + +I+ EE A VN G+P+
Sbjct: 46 GEVISLGL-PFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI 99
Query: 68 YAELS 72
Y + S
Sbjct: 100 YIQFS 104
>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 = 32.2 bits (73), Expect = 0.016
Identities = 8/54 (14%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 60
+ + +K G ++ + + N + ++R E++++A LN +
Sbjct: 38 GVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGK 86
>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 = 31.9 bits (73), Expect = 0.016
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
EDVF KYG I ++++ + G +++F DAE AV + + G +
Sbjct: 40 EDVF----YKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93
Query: 70 ELS 72
E
Sbjct: 94 EFP 96
>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 = 31.5 bits (72), Expect = 0.017
Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND-LNNRWFGGRPV 67
++GEI + V +I+F + AE A N GR +
Sbjct: 35 QFGEIRTITVVQRQQ---CA--FIQFATRQAAEVAAEKSFNKLIVNGRRL 79
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 31.9 bits (73), Expect = 0.018
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
E F YG + + + N G +++F DAE AV L+ + G V
Sbjct: 18 ERAF----SYYGPLRTVWIARNPP----GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69
Query: 70 ELS 72
ELS
Sbjct: 70 ELS 72
>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 = 31.6 bits (72), Expect = 0.019
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREA 80
G +++F +E AEKA+ + G R + S + R +
Sbjct: 58 GEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRTS 99
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 31.4 bits (72), Expect = 0.024
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+KF E AE+A +N GR +
Sbjct: 52 VVKFESPEVAERACRMMNGMKLSGREID 79
>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 = 31.1 bits (71), Expect = 0.025
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVT 75
G +++ F EE+ ++A+ N + GGR + E+
Sbjct: 51 GYIFVDFSNEEEVKQAL-KCNREYMGGRYI--EVFREK 85
>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 = 31.8 bits (72), Expect = 0.026
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 79
G +++F +E AEKA+ + G R + S + R
Sbjct: 85 GEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEEVRS 125
>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 = 31.4 bits (71), Expect = 0.026
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 6/77 (7%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 66
NFF D ++ N G+ I+ E+D +KA+ + + + G R
Sbjct: 30 NFFSDC-----RIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL-EKHRMYMGQRY 83
Query: 67 VYAELSPVTDFREACCR 83
V D
Sbjct: 84 VEVYEINNEDVDALMKS 100
>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 = 31.5 bits (72), Expect = 0.026
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
++ F EEDA+ A + + G V
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKV 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 = 31.0 bits (71), Expect = 0.027
Identities = 6/27 (22%), Positives = 10/27 (37%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
++ F A+KAV L +
Sbjct: 51 FVDFDSPSAAQKAVTALKASGVQAQMA 77
>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 = 31.0 bits (71), Expect = 0.027
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
++ F +DA++A N GR +
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRI 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 = 31.0 bits (71), Expect = 0.029
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+I F E A +A+ LN GRP+
Sbjct: 51 FITFSDSECARRALEQLNGFELAGRPM 77
>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 = 31.0 bits (71), Expect = 0.030
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+I F ++ A+ +NN+ GR +
Sbjct: 62 FILFLDKDSAQNCTRAINNKQLFGRVI 88
>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 = 31.1 bits (71), Expect = 0.032
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF---GGRPVY 68
+G I+E V G G ++KF +A+ A++ L+ +
Sbjct: 38 PFGVIDECTVLRGPDGSS-KGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV 90
>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 = 31.1 bits (71), Expect = 0.032
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
++ F DA++A L+ GR +
Sbjct: 59 FVTFENSADADRAREKLHGTVVEGRKIE 86
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 31.5 bits (71), Expect = 0.033
Identities = 11/74 (14%), Positives = 23/74 (31%), Gaps = 6/74 (8%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 66
NF D + ++ G +++ E+D + A+ + G R
Sbjct: 63 NFLSDCTIH-----DGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRY 116
Query: 67 VYAELSPVTDFREA 80
+ S T+
Sbjct: 117 IEVFKSHRTEMDWV 130
>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 = 31.8 bits (72), Expect = 0.034
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
+++F DA AV +L+ R G V ELS
Sbjct: 114 FVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>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 = 31.7 bits (72), Expect = 0.035
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++F + DAE A++ ++ GR +
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGREL 142
>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 = 31.0 bits (71), Expect = 0.036
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++F DA+ A ++ GR +
Sbjct: 59 FVRFHDRRDAQDAEAAMDGAELDGREL 85
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 31.0 bits (70), Expect = 0.036
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++ + A++AV+ L G + L+
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 31.4 bits (71), Expect = 0.037
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCR 83
G+ ++ F EE A+ A+ + G R + S + ++ R
Sbjct: 69 GDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAEVQQVLNR 113
>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 = 31.1 bits (71), Expect = 0.037
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G IE + + D+ G +I F E A+KA+ LN GRP+
Sbjct: 49 PFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 98
>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 = 30.7 bits (70), Expect = 0.041
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
++ F +DA+ A+ +N + GR +
Sbjct: 58 FVTFENIDDAKDAMMAMNGKSVDGRQI 84
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 30.9 bits (69), Expect = 0.047
Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 12/80 (15%)
Query: 2 QEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV------- 54
E + +DV + KYGE+ + + G ++F + AE AV
Sbjct: 23 DESKGGYSKDVLLRLLQKYGEVLNLVLSSKKP----GTAVVEFATVKAAELAVQNEVGLV 78
Query: 55 -NDLNNRWFGGRPVYAELSP 73
N L W G+P A
Sbjct: 79 DNPLKISWLEGQPQDASGPS 98
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 30.6 bits (69), Expect = 0.062
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 70
G ++F EE +A+ LNN F G + E
Sbjct: 68 GTGALEFPSEEILVEALERLNNIEFRGSVITVE 100
>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 = 30.9 bits (70), Expect = 0.062
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
K G+I+++ + D + G ++++ DAE A+ +N R + +
Sbjct: 62 KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117
>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 = 30.0 bits (68), Expect = 0.068
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRP 66
+++F AEK ++ +N + G
Sbjct: 56 FVEFADLATAEKCLHKINGKPLPGAT 81
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 30.5 bits (69), Expect = 0.070
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++F + DAE A++ ++ GR +
Sbjct: 93 FVRFHDKRDAEDAMDAMDGAVLDGREL 119
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 30.7 bits (69), Expect = 0.070
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ E K + L + G V
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKV 129
>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 = 30.5 bits (69), Expect = 0.072
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
++ F +DA++A N GR +
Sbjct: 92 FVYFENVDDAKEAKERANGMELDGRRI 118
>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 = 30.0 bits (68), Expect = 0.081
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 19 KYGEIEEMNV---CDNLGDHLVGNVYIKFRREEDAEKAVNDLNN-RWFGGRPV 67
+GE++ + + G H G ++ F ++DA+KA N L + GR +
Sbjct: 38 TFGELKTVRLPKKMTGTGAHR-GFGFVDFITKQDAKKAFNALCHSTHLYGRRL 89
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 29.9 bits (68), Expect = 0.090
Identities = 5/27 (18%), Positives = 12/27 (44%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
Y+++ E A +AV ++ +
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENII 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 = 30.0 bits (68), Expect = 0.090
Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 9/58 (15%)
Query: 19 KYGEIEEMNVCDNLGDHLV---------GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ G I+ +L G + F A+ A++ + + F G P+
Sbjct: 36 QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 93
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 29.9 bits (68), Expect = 0.094
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLNNRWFGGR 65
D F E YGEI+ +++ D G + +++ ++A+ A+ LN + G+
Sbjct: 41 HDKFAE----YGEIKNIHL---NLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 93
Query: 66 PV 67
P+
Sbjct: 94 PI 95
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 29.6 bits (67), Expect = 0.11
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 44 FRREEDAEKAVNDLNNRWFGGRPVY 68
F DA++A L+ GR +
Sbjct: 76 FENSADADRAREKLHGTVVEGRKIE 100
>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 = 29.5 bits (67), Expect = 0.11
Identities = 5/33 (15%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRW-FGGRPVYAELS 72
++ + + A +A+ L+ + G+ + + S
Sbjct: 48 FVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS 80
>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 = 30.2 bits (67), Expect = 0.12
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
G++ + + L G++++ F E A+K V + + +
Sbjct: 132 DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK-YKETDLLILFK 184
>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 = 0.12
Identities = 10/70 (14%), Positives = 26/70 (37%), Gaps = 12/70 (17%)
Query: 1 MQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGN-------VYIKFRREEDAEKA 53
++ + N E + + ++ E++ V L ++ V+ +F E +A +
Sbjct: 203 LKCEFSNDCEVIARK---RFREVDA--VLSWLLEYAPSRLTGTGACVFAEFDTESEARQV 257
Query: 54 VNDLNNRWFG 63
+ G
Sbjct: 258 LEQAPEWLNG 267
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 29.3 bits (66), Expect = 0.13
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 8/65 (12%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR--WFGGRPV 67
D+ + ++G I + V ++F A AVN + + G P
Sbjct: 36 ADLVEALQ-EFGPISYVVVMPKKRQ-----ALVEFEDVLGACNAVNYAADNQIYIAGHPA 89
Query: 68 YAELS 72
+ S
Sbjct: 90 FVNYS 94
>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 = 29.3 bits (66), Expect = 0.16
Identities = 8/58 (13%), Positives = 19/58 (32%), Gaps = 9/58 (15%)
Query: 19 KYGEIEEMNVCDNLGDHLV---------GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ G ++ H+ G+ + + A+ AV + + F G +
Sbjct: 38 QCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKL 95
>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 = 29.3 bits (66), Expect = 0.17
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
G ++F EDA A+ + R V
Sbjct: 56 GEADVEFATHEDAVAAM-AKDKANMQHRYV 84
>2zue_A Arginyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase, nucleotide-binding, protein
biosynthesis, ligase/RNA complex; HET: ANP; 2.00A
{Pyrococcus horikoshii} PDB: 2zuf_A
Length = 629
Score = 30.1 bits (68), Expect = 0.17
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 15 ECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF----GGRPVYAE 70
E E E+ E + DN DH +G +Y++ R + + + G +
Sbjct: 185 EFERIMNELRERGLKDNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRK 244
Query: 71 L 71
L
Sbjct: 245 L 245
>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 = 29.2 bits (66), Expect = 0.19
Identities = 10/56 (17%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW------FGGRPV 67
++G+++ + V +H G + +F +E A+K + + GR +
Sbjct: 38 QFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL 93
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 28.9 bits (65), Expect = 0.21
Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 9/58 (15%)
Query: 19 KYGEIEEMNVCDNLGDHLV---------GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ G I+ +L G + F A+ A++ + + F G P+
Sbjct: 30 QIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 87
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 29.8 bits (66), Expect = 0.21
Identities = 9/54 (16%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 78 REACCRQYEMGECTRSGFCNFMHLKPISRELRRY-LYSRRKRSSRRSSRSRSRD 130
+ C + G C C ++H P ++ + L + R + R+
Sbjct: 69 QLFFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYRE 122
Score = 29.0 bits (64), Expect = 0.38
Identities = 8/49 (16%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 19 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ G+I+ + ++KF+ + +AE A ++N+
Sbjct: 166 RLGDIDRIRYV-----ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD 209
>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 = 28.6 bits (64), Expect = 0.27
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 44 FRREEDAEKAVNDLNNRWFGGRPV 67
F R+ED AV L+N F
Sbjct: 57 FVRKEDMTYAVRKLDNTKFRSHEG 80
>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 = 28.9 bits (65), Expect = 0.29
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 42 IKFRREEDAEKAVNDLNNRWFGGRP 66
+KF+ A++A+ LN +
Sbjct: 89 VKFQSGSSAQQAIAGLNGFNILNKR 113
>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 = 28.6 bits (64), Expect = 0.43
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 19 KYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
YGEI+ ++ D G +++ + A A LN G+ +
Sbjct: 95 DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 145
>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 = 28.3 bits (63), Expect = 0.52
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
G ++F E+A A+ + R +
Sbjct: 87 GEADVEFATHEEAVAAM-SKDRANMQHRYI 115
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 27.7 bits (62), Expect = 0.52
Identities = 4/36 (11%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 41 YIKFRREEDAEKAVNDLNNR----WFGGRPVYAELS 72
+++ DA + + L + G+ + + +
Sbjct: 57 FVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase
(phospho), phosphatase, hydrolase (phosp glycolysis,
bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus}
SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A*
1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A
Length = 469
Score = 28.8 bits (64), Expect = 0.54
Identities = 17/93 (18%), Positives = 31/93 (33%), Gaps = 11/93 (11%)
Query: 1 MQEHYDNFFEDVFVE--CEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
N ++ FVE C D + N+ +G+ R D+++A D
Sbjct: 142 FNFGEQNGYKTFFVESICVD------PEVIAANIVQVKLGSPDYVNR---DSDEATEDFM 192
Query: 59 NRWFGGRPVYAELSPVTDFREACCRQYEMGECT 91
R Y L D + + ++G+
Sbjct: 193 RRIECYENSYESLDEEQDRDLSYIKIMDVGQSY 225
>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 = 27.6 bits (62), Expect = 0.56
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
Y +F + A++ LN G + +
Sbjct: 61 YAEFEDLDSLLSALS-LNEESLGNKRIR 87
>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 = 28.7 bits (63), Expect = 0.61
Identities = 14/98 (14%), Positives = 28/98 (28%), Gaps = 24/98 (24%)
Query: 27 NVCDNLG--DHLVGNVY-IKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCR 83
+VC + + ++ + + E + L + P + S
Sbjct: 169 DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS----------- 217
Query: 84 QYEMGECTRSGFCN-FMHLKPISRELRRYLYSRRKRSS 120
N + + I ELRR L S+ +
Sbjct: 218 ---------DHSSNIKLRIHSIQAELRRLLKSKPYENC 246
>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 = 27.6 bits (62), Expect = 0.62
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++ + A A LN G+ +
Sbjct: 72 LVEYETHKQALAAKEALNGAEIMGQTI 98
>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 = 27.4 bits (61), Expect = 0.97
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 19 KYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
G I + +CD H G YI+F + AV ++ F GR +
Sbjct: 59 SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTI 107
>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 = 1.0
Identities = 6/31 (19%), Positives = 7/31 (22%), Gaps = 1/31 (3%)
Query: 44 FRREEDAEKAVNDLNNRWFGGRPVYAELSPV 74
A L+ R V PV
Sbjct: 265 CTSASSAIDVGAQLSGAGV-CRTVRVATGPV 294
>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 = 26.8 bits (60), Expect = 1.1
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ 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 = 26.8 bits (60), Expect = 1.2
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+ +++ +E A A+ +LN R F GR +
Sbjct: 54 FCEYQDQETALSAMRNLNGREFSGRAL 80
>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 = 26.9 bits (59), Expect = 1.2
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++ +DA AVN L+ G + + L+
Sbjct: 56 VVQMENLQDAIGAVNSLHRYKIGSKKILVSLA 87
>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 = 27.0 bits (59), Expect = 1.4
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 19 KYGEIEEMNVCDNLGDHLVGN-VYIKFRREEDAEKAVNDLNNRWFGGR 65
+YG I + + + GN ++I+++ + A KA++ + R FG
Sbjct: 46 QYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGES 86
>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 = 26.4 bits (59), Expect = 1.5
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPVY 68
Y +F + A++ LN G R +
Sbjct: 65 YAEFEDLDSLLSALS-LNEESLGNRRIR 91
>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 = 26.6 bits (59), Expect = 1.6
Identities = 6/27 (22%), Positives = 16/27 (59%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
+++ ++A+ A+ LN + G+P+
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLMGQPI 94
>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 = 26.5 bits (59), Expect = 1.9
Identities = 6/27 (22%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
Y++F + A+ L + G P+
Sbjct: 71 YVEFCEIQSVPLAIG-LTGQRLLGVPI 96
>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 = 26.3 bits (58), Expect = 2.0
Identities = 21/85 (24%), Positives = 27/85 (31%), Gaps = 27/85 (31%)
Query: 44 FRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEMGECTRSGFCNFMHLKP 103
F R+ED AV L+N F G ++ +K
Sbjct: 58 FVRKEDMTYAVRKLDNTKFRSHE---------------------------GETAYIRVKV 90
Query: 104 ISRELRRYLYSRRKRSSRRSSRSRS 128
Y SR + SR SRSRS
Sbjct: 91 DGPRSPSYGRSRSRSRSRSRSRSRS 115
>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1
Length = 98
Score = 26.2 bits (57), Expect = 2.2
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 82 CRQYEMGECTRSGFCNFMH 100
C+ Y G C R+ C +MH
Sbjct: 16 CKFYITGFCARAENCPYMH 34
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4;
influenza A, nonstructural protein, viral protein: HOST
complex, Zn finger; 1.95A {Homo sapiens}
Length = 72
Score = 25.6 bits (56), Expect = 2.4
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 82 CRQYEMGECTRSGFCNFMHLKPISR 106
C+ + G C + C F+H +++
Sbjct: 19 CKHWLRGLCKKGDQCEFLHEYDMTK 43
>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 = 26.5 bits (59), Expect = 2.9
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 33 GDHLVGNVYIKFRREEDAEKA 53
DH G Y++ ++ + E+
Sbjct: 176 YDHFAGRAYVRLHQDPEYERL 196
>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 = 25.6 bits (57), Expect = 2.9
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 47 EEDAEKAVNDLNNRWFGGRPV 67
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 = 26.6 bits (58), Expect = 3.0
Identities = 8/59 (13%), Positives = 16/59 (27%), Gaps = 1/59 (1%)
Query: 12 VFVECEDKYGEIEEMNVCDNLGDHLVGNV-YIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+ V+ E + + V + R + AE+ + G R
Sbjct: 52 IAVQARAGRDETAFLLELACDEARIAAVVGWEDLRAPQLAERVAEWRGTKLRGFRHQLQ 110
>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 = 25.5 bits (56), Expect = 3.8
Identities = 8/54 (14%), Positives = 18/54 (33%), Gaps = 5/54 (9%)
Query: 19 KYGE-IEEMNVCDNLGDHLVGNVY--IKFRREEDAEKAVNDLNNR--WFGGRPV 67
K E + ++ V + D + + +++ A A L G +
Sbjct: 31 KVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI 84
>2z1n_A Dehydrogenase; reductase, SDR, oxidoreductase; 1.80A {Aeropyrum
pernix}
Length = 260
Score = 25.6 bits (57), Expect = 5.0
Identities = 5/30 (16%), Positives = 11/30 (36%)
Query: 39 NVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+ + R E E A + + + G +
Sbjct: 33 RLLLFSRNREKLEAAASRIASLVSGAQVDI 62
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit;
CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 77
Score = 24.9 bits (54), Expect = 5.0
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 82 CRQYEMGECTRSGFCNFMHLKPISRE 107
C+ + G C + C F+H +++
Sbjct: 13 CKHWLRGLCKKGDQCEFLHEYDMTKM 38
>3h7h_B Transcription elongation factor SPT5; helices surrounding beta
sheet, activator, ME binding, nucleus, repressor,
transcription regulation; 1.55A {Homo sapiens}
Length = 106
Score = 25.2 bits (55), Expect = 5.1
Identities = 5/26 (19%), Positives = 16/26 (61%)
Query: 34 DHLVGNVYIKFRREEDAEKAVNDLNN 59
+H+ G +Y++ ++ ++A+ + N
Sbjct: 48 EHVKGYIYVEAYKQTHVKQAIEGVGN 73
>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative
splicing, cytoplasm, metal-binding, nucleus,
RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}
Length = 89
Score = 24.8 bits (53), Expect = 5.2
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 72 SPVTDFREACCRQYEMGECTRSGFCNFMHLKP 103
V + R C G C+R C ++H
Sbjct: 44 CQVENGRVIACFDSLKGRCSREN-CKYLHPPT 74
Score = 24.4 bits (52), Expect = 8.2
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 82 CRQYEMGECTRS-GFCNFMH 100
CRQ++ G C+RS C F H
Sbjct: 20 CRQFQRGTCSRSDEECKFAH 39
>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 = 24.8 bits (55), Expect = 5.8
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 19 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
G + + + CD H G YI+F +E ++ L+ F GR +
Sbjct: 29 GCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQI 77
>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform
1, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 98
Score = 24.8 bits (53), Expect = 6.0
Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 66 PVYAELSPVTDFREACCRQYEMGECTRSGFCNFMHLKPISRELRRYLYSRRKRSSRRS 123
P + + +D C Y G C R C + H L+ + + + ++++ +
Sbjct: 43 PADSTMIDTSDNTVTVCMDYIKGRCMREK-CKYFHPPA---HLQAKIKAAQHQANQAA 96
>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens}
Length = 354
Score = 25.6 bits (55), Expect = 6.6
Identities = 7/57 (12%), Positives = 18/57 (31%)
Query: 5 YDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW 61
+ ++ V C K + DH+ ++ D+ + ++ W
Sbjct: 34 LEELYQAVENLCSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKKIDRCW 90
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 24.5 bits (54), Expect = 7.2
Identities = 5/27 (18%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 41 YIKFRREEDAEKAVNDLNNRWFGGRPV 67
Y++F + ++A+ + G R +
Sbjct: 60 YVEFDEVDSLKEALT-YDGALLGDRSL 85
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 24.6 bits (53), Expect = 8.0
Identities = 7/51 (13%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 60
DV + K+G + ++ + +++ A+ A L+ +
Sbjct: 42 LDVLHQIFSKFGTVLKIITFT---KNNQFQALLQYADPVSAQHAKLSLDGQ 89
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.138 0.430
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: 2,111,867
Number of extensions: 118313
Number of successful extensions: 522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 506
Number of HSP's successfully gapped: 209
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (23.7 bits)