RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5725
(117 letters)
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 107 bits (267), Expect = 2e-28
Identities = 46/85 (54%), Positives = 59/85 (69%)
Query: 25 GVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGE 84
G+ EL+ K I G D++++ NATLLFQ L+RS K V YRL+ AFEW++GE
Sbjct: 992 GLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLNKVAFEWIMGE 1051
Query: 85 IENRFQQAQCAPGEMVGALAAQSLG 109
+E RFQQA +PGEMVG LAAQS+G
Sbjct: 1052 VEARFQQAVVSPGEMVGTLAAQSIG 1076
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 102 bits (254), Expect = 1e-26
Identities = 37/85 (43%), Positives = 60/85 (70%)
Query: 25 GVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGE 84
GV++L E +++ G++++ + A +A LF CL+RS L T+ V + YRL+ +AF+W++
Sbjct: 989 GVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSN 1048
Query: 85 IENRFQQAQCAPGEMVGALAAQSLG 109
IE +F ++ PGEMVG LAAQS+G
Sbjct: 1049 IEAQFLRSVVHPGEMVGVLAAQSIG 1073
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 86.3 bits (213), Expect = 2e-21
Identities = 14/76 (18%), Positives = 33/76 (43%)
Query: 34 VIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQ 93
VI + ++ + A+ + + L + + ++ + + + + +
Sbjct: 4 VIDEKDKSYLEEKVKQASNILPQKIVEDLKNLISNKEVLVTRDEIDKIFDLAIKEYSEGL 63
Query: 94 CAPGEMVGALAAQSLG 109
APGE +G +AAQS+G
Sbjct: 64 IAPGEAIGIVAAQSVG 79
>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 = 36.6 bits (84), Expect = 0.001
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 4 SVRNSPAQY--SGSARRIIGLNIGVRELLEKCVIVAGEDQLSK 44
S+ N SG + + GLN+ +R+ K +G DQ S+
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGLNLTLRKA--KA--PSGLDQ-SR 406
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 26.1 bits (58), Expect = 3.3
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 97 GEMVGALAAQSLG 109
GE +G +AAQS+G
Sbjct: 912 GEAIGVIAAQSIG 924
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 25.9 bits (57), Expect = 3.7
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 97 GEMVGALAAQSLG 109
GE VG +AAQS+G
Sbjct: 1218 GEAVGIVAAQSIG 1230
>3mkt_A Multi antimicrobial extrusion protein (Na(+)/drug antiporter)
MATE-like MDR efflux...; multidrug transporter,
cation-bound, transport protein; 3.65A {Vibrio cholerae}
PDB: 3mku_A
Length = 460
Score = 25.7 bits (57), Expect = 4.4
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 5/24 (20%)
Query: 99 MVG-----ALAAQSLGTSTYFPFL 117
M G +AA S+ S + P +
Sbjct: 38 MAGGVSAIDMAAVSIAASIWLPSI 61
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 25.7 bits (57), Expect = 5.2
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 97 GEMVGALAAQSLG 109
GE VG +AA+S+G
Sbjct: 959 GEAVGVVAAESIG 971
>2zxr_A Single-stranded DNA specific exonuclease RECJ; DNA repair,
hydrolase; 2.15A {Thermus thermophilus} PDB: 2zxo_A
2zxp_A 1ir6_A
Length = 666
Score = 25.0 bits (55), Expect = 7.6
Identities = 6/24 (25%), Positives = 10/24 (41%), Gaps = 2/24 (8%)
Query: 10 AQYSGSARRIIGLNIGVRELLEKC 33
AQ G+ R + ++ E L
Sbjct: 363 AQGKGTVRSLAPISA--VEALRSA 384
>3s4w_B Protein FACD2, fanconi anemia group D2 protein homolog; DNA repair,
DNA binding protein; 3.41A {Mus musculus}
Length = 1323
Score = 24.9 bits (53), Expect = 8.6
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 39 EDQLSKQANENATLLFQCLVRSTLCTKL-------VAENYRLSSEAFEWLVGEIENRFQQ 91
+ Q L+ C S + L + + +L+ + EW+ I N FQ
Sbjct: 569 SSEQRTQVTSLLQLVHSCTEHSPWASSLYYDEFANLIQERKLAPKTLEWVGQTIFNDFQD 628
Query: 92 A 92
A
Sbjct: 629 A 629
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
0.319 0.132 0.376
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,643,229
Number of extensions: 81906
Number of successful extensions: 152
Number of sequences better than 10.0: 1
Number of HSP's gapped: 152
Number of HSP's successfully gapped: 11
Length of query: 117
Length of database: 6,701,793
Length adjustment: 80
Effective length of query: 37
Effective length of database: 4,468,113
Effective search space: 165320181
Effective search space used: 165320181
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 (21.8 bits)
S2: 51 (23.9 bits)