RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3854
(222 letters)
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 39.3 bits (92), Expect = 1e-04
Identities = 19/102 (18%), Positives = 40/102 (39%), Gaps = 17/102 (16%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+ +++ ++ T L + ++GEV V ++ P +K + F + AK
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEIL---LHPRTRKH-LGL--ARVLFTSTRGAK 62
Query: 99 QVAAQYNNTQIDCR-----------KRSKHYDFIWNFKYLPR 129
+ + T + +R K+Y+ I N Y P+
Sbjct: 63 ETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQ 104
>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 = 36.4 bits (84), Expect = 0.001
Identities = 12/89 (13%), Positives = 38/89 (42%), Gaps = 6/89 (6%)
Query: 25 KDNTENSKKYKKGIIYLSKVPPHM---NVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPA 81
+ + + +K ++++ + + V + E+ +FG++ +V + G + P
Sbjct: 4 GSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP- 62
Query: 82 KQFTEGWIEFLKKKVAKQVAAQYNNTQID 110
++ +++ + A + NN +D
Sbjct: 63 SAS--AYVTYIRSEDALRAIQCVNNVVVD 89
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 35.4 bits (82), Expect = 0.002
Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 15/82 (18%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++S P ++ QL+E+ FG V V + K F +E +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV---------F--AIVEMGDVGARE 59
Query: 99 QVAAQ----YNNTQIDCRKRSK 116
V +Q ++ R R +
Sbjct: 60 AVLSQSQHSLGGHRLRVRPREQ 81
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 35.5 bits (82), Expect = 0.002
Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 12/92 (13%)
Query: 23 KPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAK 82
++ + K ++++ + + L E + FG + V +MPKKR
Sbjct: 8 HMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR--------- 58
Query: 83 QFTEGWIEFLKKKVAKQVAAQYNNTQIDCRKR 114
+ +EF A + QI
Sbjct: 59 ---QALVEFEDVLGACNAVNYAADNQIYIAGH 87
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 34.6 bits (80), Expect = 0.005
Identities = 16/108 (14%), Positives = 36/108 (33%), Gaps = 18/108 (16%)
Query: 6 GSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGR 65
GSS S + + + IY+ +PP + + + ++G +
Sbjct: 1 GSSGSSGMSGGGVIR---GPAGNNDCR------IYVGNLPPDIRTKDIEDVFYKYGAIRD 51
Query: 66 VYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
+ L ++ P F ++EF + A+ + D +
Sbjct: 52 IDLKNRRGGPP-------F--AFVEFEDPRDAEDAVYGRDGYDYDGYR 90
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 34.4 bits (79), Expect = 0.007
Identities = 13/83 (15%), Positives = 32/83 (38%), Gaps = 12/83 (14%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
++++ + + L E + +FG + V +MP KR + +EF A
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------------QALVEFENIDSA 64
Query: 98 KQVAAQYNNTQIDCRKRSKHYDF 120
K+ + + + +++
Sbjct: 65 KECVTFAADVPVYIAGQQAFFNY 87
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 33.2 bits (76), Expect = 0.013
Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 9/82 (10%)
Query: 32 KKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEF 91
K+ + + + +PPH+ L + ++G V + + + +
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN---------VTY 61
Query: 92 LKKKVAKQVAAQYNNTQIDCRK 113
K A+Q + N Q++
Sbjct: 62 SSKDQARQALDKLNGFQLENFT 83
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.8 bits (79), Expect = 0.017
Identities = 37/222 (16%), Positives = 65/222 (29%), Gaps = 37/222 (16%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGE---VGRVYLMPKKRKPGEKKP 80
K N + Y K L ++ P NV + + G+ V K K
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVL--IDGVLGSGKTWVALDVC---LSYKVQCKMD 181
Query: 81 AKQFTEGWIEFLKKKVAKQVAAQYNN--TQIDCRKRSKHYDFIWNFKYLPRFKWIHLNER 138
K F W+ + V QID S+ D N K R I R
Sbjct: 182 FKIF---WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS-DHSSNIKL--RIHSIQAELR 235
Query: 139 LAYEKQAHRQKL-------RAEIAEA-----KREALYFSNNLDVADRIQKKNGKKKTNVP 186
+ + + L A+ A K L + V D + +
Sbjct: 236 RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK--ILLTTRFKQVTDFLSAATTTHISLDH 293
Query: 187 EQSSNKKNDGKGKQIVKKSNTKPVEDRKQ------FLTSLFS 222
+ ++ K ++K + +P + ++ S+ +
Sbjct: 294 HSMTLTPDEVKS-LLLKYLDCRPQDLPREVLTTNPRRLSIIA 334
>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 = 33.9 bits (77), Expect = 0.022
Identities = 16/117 (13%), Positives = 33/117 (28%), Gaps = 6/117 (5%)
Query: 2 TEDAGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFG 61
+ GS + +E P+ +N ++ +++ P + E G
Sbjct: 89 GLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELG 148
Query: 62 EVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRKRSKHY 118
+ K G +E+ K A + N+ Q+ Y
Sbjct: 149 VKRPTSVKVFSGKSERSS------SGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 33.3 bits (77), Expect = 0.028
Identities = 16/95 (16%), Positives = 40/95 (42%), Gaps = 15/95 (15%)
Query: 23 KPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAK 82
P+D + + K I++ + P + + EF S++G + LM K + ++
Sbjct: 79 IPRDEQDKTGK-----IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK----DTGQSR 129
Query: 83 QFTEGWIEFLKKKVAKQVAAQ----YNNTQIDCRK 113
F G++ + +V + + +I+ ++
Sbjct: 130 GF--GFVTYDSADAVDRVCQNKFIDFKDRKIEIKR 162
>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 = 31.8 bits (73), Expect = 0.036
Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ + L S+ G + + KK+ + F G++E+ K + A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTIS-KKKNKAGVLLSMGF--GFVEYKKPEQAQ 64
Query: 99 QVAAQYNNTQIDCRK 113
+ Q +D K
Sbjct: 65 KALKQLQGHTVDGHK 79
>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 = 32.1 bits (73), Expect = 0.036
Identities = 11/77 (14%), Positives = 31/77 (40%), Gaps = 12/77 (15%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
++++ K+P + T++ FG+V + ++ K + ++E ++ A
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------------QAFLELATEEAA 64
Query: 98 KQVAAQYNNTQIDCRKR 114
+ Y+ R +
Sbjct: 65 ITMVNYYSAVTPHLRNQ 81
>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 = 31.9 bits (73), Expect = 0.037
Identities = 14/90 (15%), Positives = 31/90 (34%), Gaps = 6/90 (6%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQ 83
+ +S K +I + +P +++ ++ +F + + + K G
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEK-GMPT---- 57
Query: 84 FTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
E + F + A N+ I RK
Sbjct: 58 -GEAMVAFESRDEATAAVIDLNDRPIGSRK 86
>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 = 31.8 bits (72), Expect = 0.052
Identities = 17/114 (14%), Positives = 40/114 (35%), Gaps = 17/114 (14%)
Query: 1 MTEDAGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRF 60
M + SS G ++ + S+ +I++ K+P + ++ F
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR-----VIHIRKLPIDVTEGEVISLGLPF 55
Query: 61 GEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRKR 114
G+V + ++ K + +IE ++ A + Y + R +
Sbjct: 56 GKVTNLLMLKGKN------------QAFIEMNTEEAANTMVNYYTSVTPVLRGQ 97
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 32.0 bits (73), Expect = 0.053
Identities = 18/110 (16%), Positives = 36/110 (32%), Gaps = 11/110 (10%)
Query: 3 EDAGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGE 62
S +P + E + + + + L ++G
Sbjct: 19 SHMASMTGGQQMGRGSMSYGRPPPDVEGMTS-----LKVDNLTYRTSPDTLRRVFEKYGR 73
Query: 63 VGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
VG VY+ P+ R E ++ F ++ F K+ A+ + +D R
Sbjct: 74 VGDVYI-PRDRYTKE---SRGF--AFVRFHDKRDAEDAMDAMDGAVLDGR 117
>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 = 31.1 bits (71), Expect = 0.080
Identities = 12/82 (14%), Positives = 28/82 (34%), Gaps = 12/82 (14%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ + P+ ++ L RFG + + + F +I++ A+
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTI----------DHVKGDSF--AYIQYESLDAAQ 67
Query: 99 QVAAQYNNTQIDCRKRSKHYDF 120
A+ + R DF
Sbjct: 68 AACAKMRGFPLGGPDRRLRVDF 89
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 30.7 bits (70), Expect = 0.10
Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 16/86 (18%)
Query: 31 SKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIE 90
S +++ + M +L EF S++G+V V++ KP + F ++
Sbjct: 2 SSGSSG--VFVGRCTGDMTEDELREFFSQYGDVMDVFIP---------KPFRAF--AFVT 48
Query: 91 FLKKKVAKQVAAQY---NNTQIDCRK 113
F ++A+ + + +
Sbjct: 49 FADDQIAQSLCGEDLIIKGISVHISN 74
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 31.1 bits (70), Expect = 0.11
Identities = 19/108 (17%), Positives = 39/108 (36%), Gaps = 18/108 (16%)
Query: 8 SNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVP-PHMNVTQLTEFMSRFGEVGRV 66
S+ SS + GK K E + +I+LS +P + + + + +G++
Sbjct: 2 SSGSSGKKPEGKPDQKFDQKQELGR-----VIHLSNLPHSGYSDSAVLKLAEPYGKIKNY 56
Query: 67 YLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRKR 114
LM K + +IE ++ A + + + R
Sbjct: 57 ILMRMKS------------QAFIEMETREDAMAMVDHCLKKALWFQGR 92
>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 = 30.5 bits (69), Expect = 0.13
Identities = 8/72 (11%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGE-VGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
+++ +P ++ E +++ E V V + + + ++E+ + A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGF-----AFVEYESHRAA 65
Query: 98 KQVAAQYNNTQI 109
+ +I
Sbjct: 66 AMARRKLMPGRI 77
>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 = 30.3 bits (69), Expect = 0.13
Identities = 13/77 (16%), Positives = 27/77 (35%), Gaps = 8/77 (10%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFT-EGWIEFLKKKV 96
II + +P +++ ++ +F + + + K T E + F +
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEK-------GMPTGEAMVAFESRDE 69
Query: 97 AKQVAAQYNNTQIDCRK 113
A N+ I RK
Sbjct: 70 ATAAVIDLNDRPIGSRK 86
>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 = 0.18
Identities = 15/109 (13%), Positives = 38/109 (34%), Gaps = 11/109 (10%)
Query: 4 DAGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEV 63
+S G + + N + + + + + + L E S++G +
Sbjct: 19 SHMASMTGGQQMGRGSRHVGNRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPI 73
Query: 64 GRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
V + ++ ++ F ++ F AK+ + N ++D R
Sbjct: 74 ADVSI-VYDQQSRR---SRGF--AFVYFENVDDAKEAKERANGMELDGR 116
>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 = 29.9 bits (68), Expect = 0.19
Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQ 83
P +++ I ++ + T L E FG + R+YL K + G+ +K
Sbjct: 8 PNRRADDNAT-----IRVTNLSEDTRETDLQELFRPFGSISRIYL-AKDKTTGQ---SKG 58
Query: 84 FTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
F +I F +++ A + A + D
Sbjct: 59 F--AFISFHRREDAARAIAGVSGFGYDHL 85
>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 = 30.2 bits (68), Expect = 0.22
Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 13/83 (15%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+ +S +PP + L + M G+V + G +EF++K+
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------------GTGVVEFVRKEDMT 65
Query: 99 QVAAQYNNTQIDCRKRSKHYDFI 121
+ +NT+ + Y +
Sbjct: 66 YAVRKLDNTKFRSHEGETAYIRV 88
>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 = 29.5 bits (67), Expect = 0.22
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+Y+S +P + L S++G+V +V +M K + + +K +I FL K A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIM-KDKDTRK---SKGV--AFILFLDKDSAQ 72
Query: 99 QVAAQYNNTQIDCRK 113
NN Q+ R
Sbjct: 73 NCTRAINNKQLFGRV 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 = 30.8 bits (70), Expect = 0.23
Identities = 22/106 (20%), Positives = 41/106 (38%), Gaps = 9/106 (8%)
Query: 8 SNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVY 67
+E P YV +K +++ +P ++N Q+ E ++ FG +
Sbjct: 89 QPLPGMSENPSVYVPGVVSTVVPDSAHK---LFIGGLPNYLNDDQVKELLTSFGPLKAFN 145
Query: 68 LMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
L+ K G K + + E++ V Q A N Q+ +K
Sbjct: 146 LV-KDSATGLS---KGY--AFCEYVDINVTDQAIAGLNGMQLGDKK 185
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 29.8 bits (67), Expect = 0.23
Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 12/77 (15%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
+I++ K+P + ++ FG+V + ++ K + +IE ++ A
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN------------QAFIEMNTEEAA 65
Query: 98 KQVAAQYNNTQIDCRKR 114
+ Y + R +
Sbjct: 66 NTMVNYYTSVTPVLRGQ 82
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 29.1 bits (66), Expect = 0.28
Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 16/92 (17%)
Query: 25 KDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQF 84
+ + + K +++ + M +L +F ++GEV V++ KP + F
Sbjct: 2 RGSHHHHHHGSK--VFVGRCTEDMTAEELQQFFCQYGEVVDVFIP---------KPFRAF 50
Query: 85 TEGWIEFLKKKVAKQVAAQY---NNTQIDCRK 113
++ F KVA+ + + +
Sbjct: 51 --AFVTFADDKVAQSLCGEDLIIKGISVHISN 80
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 30.0 bits (67), Expect = 0.32
Identities = 9/71 (12%), Positives = 24/71 (33%), Gaps = 10/71 (14%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
I + + + + L + S+FG V ++ K + + +++ A+
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ----------FQALLQYADPVSAQ 80
Query: 99 QVAAQYNNTQI 109
+ I
Sbjct: 81 HAKLSLDGQNI 91
>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 = 29.0 bits (65), Expect = 0.41
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 13/75 (17%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+ +S +PP + L + M G+V + G +EF++K+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------------TGVVEFVRKEDMT 64
Query: 99 QVAAQYNNTQIDCRK 113
+ +NT+ +
Sbjct: 65 YAVRKLDNTKFRSHE 79
>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 = 28.9 bits (65), Expect = 0.46
Identities = 14/96 (14%), Positives = 32/96 (33%), Gaps = 14/96 (14%)
Query: 23 KPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAK 82
P ++++NS IY+ + + + L +F + G V + +P
Sbjct: 8 DPDEDSDNSA------IYVQGLNDSVTLDDLADFFKQCGVVKMN---KRTGQPMIHIYLD 58
Query: 83 QFT-----EGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
+ T + + + AK ++ K
Sbjct: 59 KETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSK 94
>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 = 28.7 bits (65), Expect = 0.49
Identities = 11/74 (14%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ ++ ++ + E S +G++ + + ++ P +K + ++EF A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPH---LSKGY--AYVEFENPDEAE 61
Query: 99 QVAAQYNNTQIDCR 112
+ + QID +
Sbjct: 62 KALKHMDGGQIDGQ 75
>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 = 29.4 bits (66), Expect = 0.52
Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 9/106 (8%)
Query: 10 ESSPAEEPGKYVLK--PKDNTENSKKYKKGI-IYLSKVPPHMNVTQLTEFMSRFGEVGRV 66
S E +Y + DN E K KK +Y+ + + Q+ E S+ G++ ++
Sbjct: 10 RSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI 69
Query: 67 YLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
M + KK A F ++E+ + A+ N T++D R
Sbjct: 70 I-MGLDK---MKKTACGF--CFVEYYSRADAENAMRYINGTRLDDR 109
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 29.6 bits (67), Expect = 0.59
Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 12/95 (12%)
Query: 23 KPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAK 82
+ KK I++ + L ++ ++G++ + +M + +
Sbjct: 93 EDSQRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR----GSGKKR 146
Query: 83 QFTEGWIEFLKKKVAKQVAAQY----NNTQIDCRK 113
F ++ F ++ Q N + RK
Sbjct: 147 GF--AFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 28.5 bits (64), Expect = 0.66
Identities = 12/96 (12%), Positives = 34/96 (35%), Gaps = 18/96 (18%)
Query: 25 KDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYL-------MPKKRKPGE 77
+DN++N+ I++ + ++ + + ++ + G + + R+ G+
Sbjct: 2 QDNSDNNT------IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 55
Query: 78 KKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
K E + F AK ++ +
Sbjct: 56 LK-----GEATVSFDDPPSAKAAIDWFDGKEFSGNP 86
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 29.3 bits (65), Expect = 0.70
Identities = 9/71 (12%), Positives = 24/71 (33%), Gaps = 10/71 (14%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
I + + + + L + S+FG V ++ K + + +++ A+
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ----------FQALLQYADPVSAQ 98
Query: 99 QVAAQYNNTQI 109
+ I
Sbjct: 99 HAKLSLDGQNI 109
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 28.7 bits (64), Expect = 0.74
Identities = 11/107 (10%), Positives = 36/107 (33%), Gaps = 13/107 (12%)
Query: 10 ESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFM----SRFGEVGR 65
E++ A+ +++ P + ++ ++ + P + +L + S G++
Sbjct: 3 ETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD 62
Query: 66 VYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
+ + G + +I F ++ A+ +
Sbjct: 63 IVVDLSDDNSG---------KAYIVFATQESAQAFVEAFQGYPFQGN 100
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 27.8 bits (62), Expect = 0.99
Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 6/78 (7%)
Query: 37 GIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKV 96
G + + LT S+ G+V + P G+ K ++E
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNME-FPIDEATGKTK-----GFLFVECGSMND 66
Query: 97 AKQVAAQYNNTQIDCRKR 114
AK++ ++ ++D + R
Sbjct: 67 AKKIIKSFHGKRLDLKHR 84
>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 = 28.3 bits (64), Expect = 1.2
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 9/93 (9%)
Query: 21 VLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKP 80
+ +P D +K +++ +P ++N Q+ E ++ FG + L+ K G
Sbjct: 82 IRRPHDYQPLPGAHK---LFIGGLPNYLNDDQVKELLTSFGPLKAFNLV-KDSATGLS-- 135
Query: 81 AKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
K + + E++ V Q A N Q+ +K
Sbjct: 136 -KGY--AFCEYVDINVTDQAIAGLNGMQLGDKK 165
>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 = 27.7 bits (62), Expect = 1.3
Identities = 10/98 (10%), Positives = 32/98 (32%), Gaps = 18/98 (18%)
Query: 23 KPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYL-------MPKKRKP 75
+++N+ I++ + ++ + + ++ + G + + R+
Sbjct: 6 HHHSHSDNNT------IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59
Query: 76 GEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
G+ K E + F AK ++ +
Sbjct: 60 GKLK-----GEATVSFDDPPSAKAAIDWFDGKEFSGNP 92
>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 = 27.6 bits (62), Expect = 1.4
Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 10/90 (11%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQ 83
N+E+ K+ +++S +P L + +FG++ V ++ +R K
Sbjct: 5 SSGNSESKSTPKR--LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS------KG 56
Query: 84 FTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
F G++ F A + + + T ++ RK
Sbjct: 57 F--GFVTFENSADADRAREKLHGTVVEGRK 84
>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 = 27.9 bits (62), Expect = 1.4
Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 12/73 (16%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
+I +P ++ E SRFG +GRV L +EFL+ A
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------------ITAIVEFLEPLEA 59
Query: 98 KQVAAQYNNTQID 110
++ ++
Sbjct: 60 RKAFRHLAYSKFH 72
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 27.6 bits (61), Expect = 1.4
Identities = 11/74 (14%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 27 NTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTE 86
+ S+K +++ +PP ++ ++T RFG + + + K F
Sbjct: 4 GSSGSRK-----VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAF-- 56
Query: 87 GWIEFLKKKVAKQV 100
+ F ++ + +
Sbjct: 57 --LLFQEESSVQAL 68
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 27.3 bits (61), Expect = 1.6
Identities = 10/72 (13%), Positives = 18/72 (25%), Gaps = 12/72 (16%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
Y+ +P L FG + P+ K +I++ + A
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE----------KGC--CFIKYDTHEQAA 77
Query: 99 QVAAQYNNTQID 110
N
Sbjct: 78 VCIVALANFPFQ 89
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.2 bits (62), Expect = 1.6
Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 14/76 (18%)
Query: 131 KWIHLNERLAYEKQAHRQKLRAEIAEAKREALYFSNNLDVADRIQKKNGKKKTNVPEQSS 190
KW R E+Q R + ++ + D+ + Q+++ + + N + +
Sbjct: 89 KW-----R---EEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKN---KIN 137
Query: 191 NKKNDGKGKQIVKKSN 206
N+ D K ++ +
Sbjct: 138 NRIAD---KAFYQQPD 150
>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 = 27.2 bits (61), Expect = 1.7
Identities = 13/90 (14%), Positives = 36/90 (40%), Gaps = 11/90 (12%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQ 83
+ N + + + + + + L E S++G + V ++ ++ ++
Sbjct: 8 NRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADVSIV-YDQQSRR---SRG 58
Query: 84 FTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
F ++ F AK+ + N ++D R+
Sbjct: 59 F--AFVYFENVDDAKEAKERANGMELDGRR 86
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 27.3 bits (61), Expect = 1.8
Identities = 5/35 (14%), Positives = 13/35 (37%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKR 73
+Y+ + +L S +G + V++
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP 37
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 27.1 bits (60), Expect = 2.0
Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 13/91 (14%)
Query: 26 DNTENSKKYKKGIIYLSKVPPHMNV-TQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQF 84
+ + + + ++++ N+ QL + + FG + ++ K
Sbjct: 5 SSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN----------- 53
Query: 85 TEGWIEFLKKKVAKQVAAQYNNTQIDCRKRS 115
E +IE + A+ Y T +
Sbjct: 54 -EAFIEMATTEDAQAAVDYYTTTPALVFGKP 83
>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 = 27.5 bits (61), Expect = 2.2
Identities = 18/111 (16%), Positives = 37/111 (33%), Gaps = 11/111 (9%)
Query: 2 TEDAGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFG 61
E + G + + E + + + + L ++G
Sbjct: 41 GEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS-----LKVDNLTYRTSPDTLRRVFEKYG 95
Query: 62 EVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
VG VY+ P+ R E ++ F ++ F K+ A+ + +D R
Sbjct: 96 RVGDVYI-PRDRYTKE---SRGF--AFVRFHDKRDAEDAMDAMDGAVLDGR 140
>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 = 26.8 bits (60), Expect = 2.3
Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+ + + + L ++G VG VY+ P++ + F ++ F ++ A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYI-PREPHTKAP---RGF--AFVRFHDRRDAQ 69
Query: 99 QVAAQYNNTQIDCR 112
A + ++D R
Sbjct: 70 DAEAAMDGAELDGR 83
>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 = 26.9 bits (60), Expect = 2.8
Identities = 7/71 (9%), Positives = 23/71 (32%), Gaps = 7/71 (9%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ + + + FG + ++ G +K +++F A+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVL-----RGPDGSSKGC--AFVKFSSHTEAQ 70
Query: 99 QVAAQYNNTQI 109
+ +Q
Sbjct: 71 AAIHALHGSQT 81
>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 = 27.6 bits (61), Expect = 3.1
Identities = 13/72 (18%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
++LS +PP ++ L S G V + + +K + I+ + A
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM----------ALIQMGSVEEA 171
Query: 98 KQVAAQYNNTQI 109
Q +N +
Sbjct: 172 VQALIDLHNHDL 183
>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 = 26.6 bits (59), Expect = 3.1
Identities = 8/90 (8%), Positives = 32/90 (35%), Gaps = 7/90 (7%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQ 83
+ E K +++ +P + + +F+ + G+
Sbjct: 3 SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN-GQGL---- 57
Query: 84 FTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
+ ++F + A++ + + + +++ R+
Sbjct: 58 -GQALVQFKNEDDARK-SERLHRKKLNGRE 85
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 27.1 bits (60), Expect = 3.7
Identities = 14/110 (12%), Positives = 33/110 (30%), Gaps = 11/110 (10%)
Query: 5 AGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVG 64
+ P + ++ L + +S + ++ + E + FG +
Sbjct: 57 PAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLK 116
Query: 65 RVYLM--PKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
+ + R G + F ++ A + QY +D R
Sbjct: 117 KAAVDYDRSGRSLGT---------ADVHFERRADALKAMKQYKGVPLDGR 157
>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 = 27.3 bits (61), Expect = 3.9
Identities = 11/81 (13%), Positives = 29/81 (35%), Gaps = 6/81 (7%)
Query: 33 KYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFL 92
+ ++++ PP + + + V +P R ++F +I+
Sbjct: 114 HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR---FNTS-RRF--AYIDVT 167
Query: 93 KKKVAKQVAAQYNNTQIDCRK 113
K+ A+ + N +I+
Sbjct: 168 SKEDARYCVEKLNGLKIEGYT 188
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 25.8 bits (57), Expect = 4.3
Identities = 8/62 (12%), Positives = 23/62 (37%), Gaps = 8/62 (12%)
Query: 53 LTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCR 112
+ + S+FG++ + + K K + ++E+ A + ++D +
Sbjct: 24 IHKIFSKFGKITNDFYPEEDGKT------KGY--IFLEYASPAHAVDAVKNADGYKLDKQ 75
Query: 113 KR 114
Sbjct: 76 HT 77
>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 = 26.1 bits (58), Expect = 4.9
Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 25/108 (23%)
Query: 6 GSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGR 65
GSS S A + GK +++ + N L + S++G++
Sbjct: 1 GSSGSSGMASDEGK-------------------LFVGGLSFDTNEQSLEQVFSKYGQISE 41
Query: 66 VYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
V ++ K R+ ++ F G++ F AK N +D R+
Sbjct: 42 VVVV-KDRETQR---SRGF--GFVTFENIDDAKDAMMAMNGKSVDGRQ 83
>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 = 25.7 bits (57), Expect = 4.9
Identities = 6/35 (17%), Positives = 18/35 (51%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKR 73
+Y+ + + T L +FGE+ + ++ +++
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ 49
>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 = 26.9 bits (59), Expect = 5.0
Identities = 13/72 (18%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
++LS +PP ++ L S G V + + +K + I+ + A
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM----------ALIQMGSVEEA 202
Query: 98 KQVAAQYNNTQI 109
Q +N +
Sbjct: 203 VQALIDLHNHDL 214
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 26.1 bits (58), Expect = 5.2
Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 10/91 (10%)
Query: 23 KPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAK 82
NTEN + K+ +++S +P L + +FG++ V ++ +R K
Sbjct: 18 GSHMNTENKSQPKR--LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS------K 69
Query: 83 QFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
F G++ F A + + + T ++ RK
Sbjct: 70 GF--GFVTFENSADADRAREKLHGTVVEGRK 98
>2wan_A Pullulanase; hydrolase, glycoside hydrolase, polysaccharide,
amylase, starch, carbohydrate; 1.65A {Bacillus
acidopullulyticus}
Length = 921
Score = 27.1 bits (60), Expect = 5.6
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 7 SSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYL 41
S + +S + GKY+ + T+ K GI L
Sbjct: 444 SIDANSGMKNKGKYLAFTEHGTKGPDHVKTGIDSL 478
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 25.8 bits (57), Expect = 5.9
Identities = 8/65 (12%), Positives = 23/65 (35%), Gaps = 8/65 (12%)
Query: 50 VTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQI 109
+ + S+FG++ + + K K + ++E+ A + ++
Sbjct: 35 KNVIHKIFSKFGKITNDFYPEEDGKT------KGY--IFLEYASPAHAVDAVKNADGYKL 86
Query: 110 DCRKR 114
D +
Sbjct: 87 DKQHT 91
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 25.9 bits (57), Expect = 6.2
Identities = 11/91 (12%), Positives = 28/91 (30%), Gaps = 11/91 (12%)
Query: 24 PKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFG-EVGRVYLMPKKRKPGEKKPAK 82
P+ + + K+ I + +P + L + E + +
Sbjct: 16 PRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFD-------- 67
Query: 83 QFTEGWIEFLKKKVAKQVAAQYNNTQIDCRK 113
G +EF +++ + + NN +
Sbjct: 68 --GTGALEFPSEEILVEALERLNNIEFRGSV 96
>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 = 25.3 bits (56), Expect = 7.7
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+YL +P Q+ + S G V + +M + G + K + +IEF + +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMM-FDPQTG--RS-KGY--AFIEFRDLESSA 58
Query: 99 QVAAQYNNTQIDCR 112
N Q+ R
Sbjct: 59 SAVRNLNGYQLGSR 72
>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 = 26.2 bits (58), Expect = 7.8
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 11/88 (12%)
Query: 31 SKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLM--PKKRKPGEKKPAKQFTEGW 88
+ + + P ++ L + S+FG V + ++ + R G +G+
Sbjct: 91 RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG---------KGF 141
Query: 89 IEFLKKKVAKQVAAQYNNTQIDCRKRSK 116
+EF K A++ + + +
Sbjct: 142 VEFAAKPPARKALERCGDGAFLLTTTPR 169
>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 = 25.6 bits (56), Expect = 8.1
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 7/76 (9%)
Query: 37 GIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKV 96
G + L +P ++ +F S V +P + K E +++F +++
Sbjct: 43 GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPE------GKITGEAFVQFASQEL 96
Query: 97 AKQVAAQYNNTQIDCR 112
A++ A + +I R
Sbjct: 97 AEK-ALGKHKERIGHR 111
>1qg8_A Protein (spore coat polysaccharide biosynthesis P SPSA);
glycosyltransferase, transferase; 1.50A {Bacillus
subtilis} SCOP: c.68.1.1 PDB: 1h7q_A* 1h7l_A 1qgq_A*
1qgs_A*
Length = 255
Score = 26.2 bits (58), Expect = 8.2
Identities = 13/89 (14%), Positives = 34/89 (38%), Gaps = 4/89 (4%)
Query: 92 LKKKVAKQVAAQYNNTQIDCRKRSKHYDFIWNFKYLPRFKWIHLNERLAY----EKQAHR 147
+ V ++V ++ + + + D + ++ + + L+E L ++ H
Sbjct: 163 HRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHF 222
Query: 148 QKLRAEIAEAKREALYFSNNLDVADRIQK 176
Q E E R N ++ + ++K
Sbjct: 223 QLFELEKNEFVRNLPPQRNCRELRESLKK 251
>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 = 25.6 bits (56), Expect = 8.7
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKR 73
+Y+ + + N T+L +G + V++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP 110
>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 = 25.2 bits (56), Expect = 8.8
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLM 69
IY+ V +L G V RV ++
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTIL 39
>2vq8_A RNAse ZF-1A; evolution, zebrafish, polymorphism, ribonucleases,
hydrolase; 1.35A {Danio rerio} PDB: 3ljd_A 3ln8_A
Length = 139
Score = 25.7 bits (56), Expect = 9.1
Identities = 10/53 (18%), Positives = 19/53 (35%), Gaps = 5/53 (9%)
Query: 82 KQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRKRSKHYDFIWNFKYLPRFKWIH 134
+ E + FL + V ++ Q N++I R I K ++
Sbjct: 14 EHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNR-----KITLSGTDNGCKPVN 61
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
0.312 0.129 0.370
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,255,841
Number of extensions: 184091
Number of successful extensions: 466
Number of sequences better than 10.0: 1
Number of HSP's gapped: 459
Number of HSP's successfully gapped: 99
Length of query: 222
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,188,903
Effective search space: 552935196
Effective search space used: 552935196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.8 bits)