RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15193
(106 letters)
>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 = 29.9 bits (68), Expect = 0.056
Identities = 14/31 (45%), Positives = 22/31 (70%), Gaps = 4/31 (12%)
Query: 29 NGTHVQGVKLKVSLARRQLKVAPINDAASST 59
NGT V+ V+LKV++AR+Q P+ D+ S+
Sbjct: 70 NGTQVESVQLKVNIARKQ----PMLDSGPSS 96
>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 = 27.4 bits (61), Expect = 0.53
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 29 NGTHVQGVKLKVSLARRQLKVAPINDAA 56
NGT V+ V+LKV++AR+Q + +
Sbjct: 94 NGTQVESVQLKVNIARKQPMLDAATGKS 121
>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 = 25.7 bits (57), Expect = 1.8
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 29 NGTHVQGVKLKVSLARR 45
NG + +LKV L R
Sbjct: 88 NGFQIGMKRLKVQLKRS 104
>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 = 25.9 bits (57), Expect = 2.5
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 29 NGTHVQGVKLKVSLAR 44
NG ++ +LKV+LA
Sbjct: 105 NGFNILNKRLKVALAA 120
>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 = 25.4 bits (56), Expect = 2.7
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 29 NGTHVQGVKLKVSLARRQLK 48
+G QG KLKVSLAR++
Sbjct: 86 DGKDFQGSKLKVSLARKKPP 105
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 25.2 bits (55), Expect = 3.5
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 26 RKVNGTHVQGVKLKVSLARRQ 46
+ G + L+V+LAR+Q
Sbjct: 74 SCLQGLRLGTDTLRVALARQQ 94
>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 = 24.9 bits (55), Expect = 3.5
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 22 QKLKRKVNGTHVQGVKLKVSLARR 45
+ K +++ ++G +L+V A
Sbjct: 65 EIAKVELDNMPLRGKQLRVRFACH 88
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 25.1 bits (55), Expect = 3.6
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 26 RKVNGTHVQGVKLKVSLARRQ 46
K+NG ++ LKV+ +
Sbjct: 72 DKLNGFQLENFTLKVAYIPDE 92
>1q16_A Respiratory nitrate reductase 1 alpha chain; membrane protein,
electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA
3PH; 1.90A {Escherichia coli} SCOP: b.52.2.2 c.81.1.1
PDB: 3ir7_A* 1y5i_A* 1siw_A* 1y4z_A* 1r27_A* 1y5l_A*
1y5n_A* 3ir6_A* 3ir5_A* 3egw_A*
Length = 1247
Score = 25.4 bits (55), Expect = 4.1
Identities = 7/48 (14%), Positives = 17/48 (35%)
Query: 50 APINDAASSTTWSAIACHQSLKGNHKDKRHQVIYDDDIFGEEPPLEDP 97
N + W + S KG+ ++ + + I G++ +
Sbjct: 702 NGKNHPRNLFIWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGG 749
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 24.5 bits (54), Expect = 4.4
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 26 RKVNGTHVQGVKLKVSLARR 45
R +NG + G ++ V + R
Sbjct: 66 RMMNGMKLSGREIDVRIDRN 85
>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 = 24.5 bits (54), Expect = 4.8
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 26 RKVNGTHVQGVKLKVSLARRQLK 48
+ +NG + G ++V+LA+ K
Sbjct: 69 KALNGKVLDGSPIEVTLAKPVDK 91
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 24.6 bits (54), Expect = 5.2
Identities = 3/22 (13%), Positives = 7/22 (31%)
Query: 25 KRKVNGTHVQGVKLKVSLARRQ 46
+ QG L+ + +
Sbjct: 80 IVALANFPFQGRNLRTGWGKER 101
>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 = 24.5 bits (54), Expect = 5.9
Identities = 4/18 (22%), Positives = 10/18 (55%)
Query: 29 NGTHVQGVKLKVSLARRQ 46
NG ++G +++ A+
Sbjct: 66 NGKDLEGENIEIVFAKPP 83
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 24.6 bits (54), Expect = 6.1
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 29 NGTHVQGVKLKVSLAR 44
NG V +LKV L +
Sbjct: 103 NGFQVGTKRLKVQLKK 118
>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 = 24.1 bits (53), Expect = 6.5
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 26 RKVNGTHVQGVKLKVSLARRQLKVAP 51
R ++ T QG ++ V L+ +L+ A
Sbjct: 62 RGLDNTEFQGKRMHVQLSTSRLRTAS 87
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 24.2 bits (53), Expect = 7.2
Identities = 4/21 (19%), Positives = 9/21 (42%)
Query: 26 RKVNGTHVQGVKLKVSLARRQ 46
+V+G L+V ++
Sbjct: 83 EEVHGKSFANQPLEVVYSKLP 103
>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 = 23.9 bits (52), Expect = 7.2
Identities = 5/30 (16%), Positives = 9/30 (30%)
Query: 22 QKLKRKVNGTHVQGVKLKVSLARRQLKVAP 51
Q + + +G L V L +
Sbjct: 54 QNAIQMFHQYSFRGKDLIVQLQPTDALLCS 83
>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction
potential, iron binding protein electron transport;
1.32A {Pseudomonas aeruginosa}
Length = 82
Score = 23.9 bits (52), Expect = 7.6
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 4 IHFPSNHTEEEITLQAKYQKLKRK 27
I + E + L KY+K+ K
Sbjct: 58 IPLDDANVESKDQLMEKYRKITGK 81
>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP:
d.58.1.1
Length = 80
Score = 24.0 bits (52), Expect = 7.8
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 4 IHFPSNHTEEEITLQAKYQKL 24
I ++ E LQ KY +L
Sbjct: 58 IPDNPDYRETREELQEKYDRL 78
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
0.314 0.129 0.374
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,602,175
Number of extensions: 78752
Number of successful extensions: 141
Number of sequences better than 10.0: 1
Number of HSP's gapped: 141
Number of HSP's successfully gapped: 26
Length of query: 106
Length of database: 6,701,793
Length adjustment: 71
Effective length of query: 35
Effective length of database: 4,719,402
Effective search space: 165179070
Effective search space used: 165179070
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 (22.0 bits)
S2: 51 (23.4 bits)