RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter asiaticus str. psy62] (122 letters) >3iyd_E DNA-directed RNA polymerase subunit omega; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (E:) Length = 90 Score = 93.6 bits (233), Expect = 9e-21 Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 4/81 (4%) Query: 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKP-TVDVGKDKNTVVALREIASGTLSP 60 AR TV+D ++K+ NRF LVL+A+ R R + G K V DK TV+ALREI G ++ Sbjct: 1 ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINN 60 Query: 61 DDLEEDFIHSLQKHVEIDEPD 81 L+ Q+ E + + Sbjct: 61 QILDVR---ERQEQQEQEAAE 78 >2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (E:1-77) Length = 77 Score = 84.9 bits (210), Expect = 3e-18 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 15/77 (19%) Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVG---------------KDKN 45 MA ++ VD+++ L ++ + R + L + + Sbjct: 1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNA 60 Query: 46 TVVALREIASGTLSPDD 62 A++E+ +G L + Sbjct: 61 ETWAMKELLTGRLVFGE 77 >2dc0_A Probable amidase; structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Thermus thermophilus} (A:) Length = 434 Score = 26.7 bits (57), Expect = 1.1 Identities = 7/67 (10%), Positives = 21/67 (31%), Gaps = 1/67 (1%) Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSE 104 ++ + + +G +P L E+ + + + + E + + Sbjct: 2 DLLEAKRLLETGRTTPLALLEEALERAKAFQDRNALAYLDEEAARKEALALTEELRRGQV 61 Query: 105 GDLLEGI 111 L G+ Sbjct: 62 RGPLHGL 68 >2gi3_A Glutamyl-tRNA(Gln) amidotransferase subunit A; TM1272, structural genomics, joint center for structural genomics, JCSG; HET: MSE MPD; 1.80A {Thermotoga maritima} (A:) Length = 476 Score = 25.5 bits (54), Expect = 2.7 Identities = 2/30 (6%), Positives = 12/30 (40%), Gaps = 1/30 (3%) Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKH 74 + + E + + L + + ++++ Sbjct: 8 RKLTIEECLKLSEEEREKLPQLSLETIKRL 37 >1o9p_A Malonamidase E2; malonate; 1.8A {Bradyrhizobium japonicum} (A:) Length = 414 Score = 25.1 bits (53), Expect = 3.1 Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 1/30 (3%) Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKH 74 ++ L+ I +G LSP+ +++ Sbjct: 3 SLADLQRRIETGELSPNAAIAQSHAAIEAR 32 >1m22_A Peptide amidase, PAM; eleven-stranded beta sheet, covered double layers of alpha helices on TOP and bottom, hydrolase; HET: EPE; 1.40A {Stenotrophomonas maltophilia} (A:1-315,A:399-503) Length = 420 Score = 24.0 bits (51), Expect = 6.4 Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 6/53 (11%) Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEAL 97 V L+ + +G L L + ++ + + + P + P+AL Sbjct: 12 DVADLQARMTAGELDSTTLTQAYL----QRIAALDRTGPRLRA-VIELNPDAL 59 >2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K (K:27-95) Length = 69 Score = 24.2 bits (53), Expect = 6.5 Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 10/51 (19%) Query: 26 RTRHLSQGAKPTVDVGKDKNT---VVALREIASGTLS-------PDDLEED 66 R L+ GA +D+ +T +A E G L P+ Sbjct: 13 RALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPNGKIIL 63 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.313 0.132 0.380 Gapped Lambda K H 0.267 0.0619 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 924,403 Number of extensions: 37784 Number of successful extensions: 74 Number of sequences better than 10.0: 1 Number of HSP's gapped: 73 Number of HSP's successfully gapped: 9 Length of query: 122 Length of database: 4,956,049 Length adjustment: 73 Effective length of query: 49 Effective length of database: 2,488,284 Effective search space: 121925916 Effective search space used: 121925916 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: 50 (23.3 bits)