RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18100
(76 letters)
>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 = 49.4 bits (118), Expect = 1e-09
Identities = 19/34 (55%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 35 NMVGPGEVDSDLEPEVKDECNTKYGEVVRVIIHE 68
NMV P ++D DLE EV +EC K+G V RVII++
Sbjct: 27 NMVDPKDIDDDLEGEVTEECG-KFGAVNRVIIYQ 59
Score = 42.8 bits (101), Expect = 4e-07
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 8 LNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEVKDECNTKYGEVVRVII 66
NMV P ++D DLE EV EEC K+ G V+ + + K +V++ +
Sbjct: 26 RNMVDPKDIDDDLEGEVTEECG-KF-------GAVNRVIIYQEKQGEEEDAEIIVKIFV 76
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 47.1 bits (112), Expect = 3e-08
Identities = 19/34 (55%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 35 NMVGPGEVDSDLEPEVKDECNTKYGEVVRVIIHE 68
NMV P ++D DLE EV +EC K+G V RVII++
Sbjct: 131 NMVDPKDIDDDLEGEVTEEC-GKFGAVNRVIIYQ 163
>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 = 42.7 bits (101), Expect = 5e-07
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 35 NMVGPGEV-----DSDLEPEVKDECNTKYGEVVRVIIHELPTTANV 75
NM P D++++ +V +ECN K+G V+ + + + NV
Sbjct: 14 NMFNPQTEEEVGWDTEIKDDVIEECN-KHGGVIHIYVDKNSAQGNV 58
>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 = 38.1 bits (89), Expect = 2e-05
Identities = 9/72 (12%), Positives = 28/72 (38%), Gaps = 21/72 (29%)
Query: 4 TILDLNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEVKDECNTKYGEVVR 63
++ NM P + + D V +++ +++ EC+ K+G++ +
Sbjct: 17 VVIIKNMFHPMDFEDD--------------------PLVLNEIREDLRVECS-KFGQIRK 55
Query: 64 VIIHELPTTANV 75
+++ +
Sbjct: 56 LLLFDRHPDGVA 67
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 36.7 bits (85), Expect = 8e-05
Identities = 19/27 (70%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 8 LNMVGPGEVDSDLEPEVKEECNTKYGE 34
NMVG GEVD DLE E KEEC KYG+
Sbjct: 14 RNMVGAGEVDEDLEVETKEECE-KYGK 39
>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 = 35.2 bits (81), Expect = 3e-04
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 22/63 (34%)
Query: 8 LNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEVKDECNTKYGEVVRVIIH 67
+NMV P E+ D E E ++ +V+DEC+ KYG V + I
Sbjct: 11 MNMVLPEELLDDEEYE---------------------EIVEDVRDECS-KYGLVKSIEIP 48
Query: 68 ELP 70
Sbjct: 49 RPV 51
>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 = 33.7 bits (77), Expect = 0.001
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 34 ENMVGPGEVDSDLEPEVKDE---CNTKYGEVVRVIIHE 68
+ V E+ + ++ KYGEV + + +
Sbjct: 24 RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCD 61
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 32.7 bits (74), Expect = 0.006
Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 13/65 (20%)
Query: 14 GEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPE----VKDECNTKYGEVVRVIIHEL 69
G P E + YG + PG V + E V + + G +V +
Sbjct: 1790 GMTMQVAVPR-DELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEI----- 1843
Query: 70 PTTAN 74
N
Sbjct: 1844 ---VN 1845
Score = 26.9 bits (59), Expect = 0.58
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 18/65 (27%)
Query: 1 MLATILDLNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEVKDECNTKYGE 60
M+A + PG V + E + + G+ G + +E V N + +
Sbjct: 1809 MIA-------INPGRVAASFSQEALQYVVERVGKRT---GWL---VEI-VNY--NVE-NQ 1851
Query: 61 VVRVI 65
V
Sbjct: 1852 QY-VA 1855
>3u5t_A 3-oxoacyl-[acyl-carrier-protein] reductase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.40A {Sinorhizobium meliloti}
Length = 267
Score = 24.0 bits (53), Expect = 5.8
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 35 NMVGPGEVDSDLEPEVKDE 53
N V PG +DL E K +
Sbjct: 201 NAVAPGPTATDLFLEGKSD 219
>2ztg_A Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthetase,
aminoacyl-tRNA synthetase, ATP-binding, cytoplasm,
ligase; HET: A5A; 2.20A {Archaeoglobus fulgidus}
Length = 739
Score = 23.4 bits (51), Expect = 8.8
Identities = 3/9 (33%), Positives = 5/9 (55%)
Query: 57 KYGEVVRVI 65
G +RV+
Sbjct: 686 PPGRKIRVV 694
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
0.309 0.133 0.378
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,139,082
Number of extensions: 55853
Number of successful extensions: 132
Number of sequences better than 10.0: 1
Number of HSP's gapped: 120
Number of HSP's successfully gapped: 14
Length of query: 76
Length of database: 6,701,793
Length adjustment: 45
Effective length of query: 31
Effective length of database: 5,445,348
Effective search space: 168805788
Effective search space used: 168805788
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 51 (23.6 bits)