RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14809
(90 letters)
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus
radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 35.1 bits (81), Expect = 0.001
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 1 MLRRNIDVSMGLVNGSI--VYDLEC--VTTKFEVLPRAYVHREQF-SLCLEYAITIHKCQ 55
+ +N D + + NG++ V E +T F+ + +L L YA+T+H+ Q
Sbjct: 443 VQTKN-DYNNEIFNGTLGMVLKAEGARLTVDFDGNVVEL-TGAELFNLQLGYALTVHRAQ 500
Query: 56 G 56
G
Sbjct: 501 G 501
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain,
PIN-tower interface, coupling hydrolysis to DNA
unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Length = 459
Score = 31.5 bits (71), Expect = 0.022
Identities = 10/49 (20%), Positives = 16/49 (32%)
Query: 19 YDLECVTTKFEVLPRAYVHREQFSLCLEYAITIHKCQGLSMNNALMDIG 67
Y K + + A T HK QG+S++ A +
Sbjct: 383 YKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGMSVDRAFIYTP 431
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 30.5 bits (69), Expect = 0.054
Identities = 6/10 (60%), Positives = 9/10 (90%)
Query: 47 YAITIHKCQG 56
+A+T+HK QG
Sbjct: 534 WAMTVHKSQG 543
>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell
division inhibitor, MINC, MINE, cell hydrolase; HET:
ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*
Length = 260
Score = 27.2 bits (61), Expect = 0.61
Identities = 8/18 (44%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 4 RNIDVSMGLVNGSIVYDL 21
RN+D+ MG +VYD
Sbjct: 44 RNLDLIMGCER-RVVYDF 60
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 25.2 bits (56), Expect = 3.0
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 4 RNIDVS-MGLVNGSIVYDLECVTTKFEVLPRAYVHR 38
R IDVS + LV + YD+ + P+ Y+HR
Sbjct: 419 RGIDVSQVNLV---VNYDMP-LDQAGRPDPQTYLHR 450
>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 240
Score = 25.2 bits (56), Expect = 3.2
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 8 VSMGLVNGSIVYDL 21
+ G V +V DL
Sbjct: 162 CAAGKVGDQVVLDL 175
>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural
genomics/proteomics initiative structural genomics;
2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB:
1udq_A 1uds_A 1udo_A
Length = 255
Score = 25.1 bits (55), Expect = 3.5
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 8 VSMGLVNGSIVYDL 21
VS+G+VN I+ DL
Sbjct: 162 VSVGIVNDRILLDL 175
>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 = 25.0 bits (54), Expect = 4.5
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 12 LVNGSIVYDLECVTTKFEVLPRAYVHREQFSLCLE 46
L +GS+ + L V T A +EQF+ L
Sbjct: 11 LSHGSLEHVLL-VPT--ASFFIASQLQEQFNKILP 42
Score = 24.2 bits (52), Expect = 8.5
Identities = 7/35 (20%), Positives = 9/35 (25%), Gaps = 16/35 (45%)
Query: 2 LRRNIDVSMGLVNGSIVYDLECVTTKFEVLPRAYV 36
L V + LVNG + V
Sbjct: 360 LPAGKQVEISLVNG----------------AKNLV 378
>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate
bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa}
SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A
Length = 239
Score = 24.7 bits (54), Expect = 5.6
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 8 VSMGLVNGSIVYDL 21
VS+G+ G V DL
Sbjct: 163 VSVGIYQGVPVLDL 176
>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial
cell division, cell cycle; 2.60A {Archaeoglobus
fulgidus} SCOP: c.37.1.10
Length = 263
Score = 24.5 bits (54), Expect = 5.8
Identities = 3/18 (16%), Positives = 9/18 (50%), Gaps = 2/18 (11%)
Query: 4 RNIDVSMGLVNGSIVYDL 21
N+++ +G+ + L
Sbjct: 44 ANLELILGMEG--LPVTL 59
>2po1_A Probable exosome complex exonuclease 1; RNAse PH,
hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*
Length = 249
Score = 24.2 bits (53), Expect = 7.9
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 8 VSMGLVNGSIVYDL 21
+ G + G IV DL
Sbjct: 162 CAAGKIEGEIVLDL 175
>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B
2c37_B* 2c38_B* 2c39_B* 3l7z_B
Length = 250
Score = 23.7 bits (52), Expect = 9.7
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 8 VSMGLVNGSIVYDL 21
V++G +G I+ DL
Sbjct: 166 VAVGKADGVIILDL 179
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
0.326 0.135 0.413
Gapped
Lambda K H
0.267 0.0491 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,292,696
Number of extensions: 59980
Number of successful extensions: 118
Number of sequences better than 10.0: 1
Number of HSP's gapped: 118
Number of HSP's successfully gapped: 16
Length of query: 90
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 33
Effective length of database: 5,110,296
Effective search space: 168639768
Effective search space used: 168639768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.0 bits)