RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter asiaticus str. psy62] (122 letters) >3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E* Length = 91 Score = 98.8 bits (246), Expect = 3e-22 Identities = 35/89 (39%), Positives = 50/89 (56%), Gaps = 2/89 (2%) Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAK-PTVDVGKDKNTVVALREIASGTLS 59 MAR TV+D ++K+ NRF LVL+A+ R R + G K P V DK TV+ALREI G ++ Sbjct: 1 MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN 60 Query: 60 PDDLEEDFIHSLQKHVEIDEPDSPTENSD 88 L+ Q+ E E + T ++ Sbjct: 61 NQILDVR-ERQEQQEQEAAELQAVTAIAE 88 >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} Length = 90 Score = 93.3 bits (232), Expect = 1e-20 Identities = 34/88 (38%), Positives = 49/88 (55%), Gaps = 2/88 (2%) Query: 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAK-PTVDVGKDKNTVVALREIASGTLSP 60 AR TV+D ++K+ NRF LVL+A+ R R + G K P V DK TV+ALREI G ++ Sbjct: 1 ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINN 60 Query: 61 DDLEEDFIHSLQKHVEIDEPDSPTENSD 88 L+ Q+ E E + T ++ Sbjct: 61 QILDVR-ERQEQQEQEAAELQAVTAIAE 87 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 34.5 bits (79), Expect = 0.006 Identities = 23/98 (23%), Positives = 32/98 (32%), Gaps = 33/98 (33%) Query: 49 ALRE--IASGTLS-----PDD-------LEEDFIHSLQKHVEI----DEPDSPTENS--- 87 + R ++ G+L P L+E F L + E DEP +P E Sbjct: 5 STRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF 64 Query: 88 -DFSWHKPEALSFGQMS----------EGDLLEGINNI 114 + E GQ E LEG N+I Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG-NDI 101 Score = 30.7 bits (69), Expect = 0.090 Identities = 15/108 (13%), Positives = 29/108 (26%), Gaps = 36/108 (33%) Query: 20 VLLASHRTRHLSQGAKPTV-------DVGKDKNTVVA--------------LREIASGTL 58 ++ R +++ VG+ +VA LR++ T Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQ-TY 180 Query: 59 SPDDLEEDFIHSLQKHVEIDEPDSPTENSDF---------SW-HKPEA 96 L D I + + E T +++ W P Sbjct: 181 HV--LVGDLIKFSAETL--SELIRTTLDAEKVFTQGLNILEWLENPSN 224 Score = 29.9 bits (67), Expect = 0.15 Identities = 14/109 (12%), Positives = 25/109 (22%), Gaps = 48/109 (44%) Query: 12 KVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDL-------- 63 K NRFL V H + L + + KD + + + + D+ Sbjct: 415 KFSNRFLPVASPFH-SHLL---VPASDLINKD----LVKNNV---SFNAKDIQIPVYDTF 463 Query: 64 --------EEDFIHSL-----QKHVEIDEPDSPTENSDFSWHKPEALSF 99 + + V+ W F Sbjct: 464 DGSDLRVLSGSISERIVDCIIRLPVK--------------W--ETTTQF 496 >2kxo_A Cell division topological specificity factor; MINE, MIND-binding, to specificity, cell cycle; NMR {Neisseria gonorrhoeae} Length = 95 Score = 28.5 bits (64), Expect = 0.45 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 18/89 (20%) Query: 35 KPTVDVGKDKNTVVALREIASGTLSPDDLE---EDFIHSLQKHVEIDEPDSPTENSDFSW 91 + T V +D+ ++ +E A +PD L + + L K+V + Sbjct: 12 QKTATVARDRLQIIIAQERAQEGQTPDYLPTLRKALMEVLSKYVNVS------------- 58 Query: 92 HKPEALSFGQMSEGDLLEGINNIVTPDKR 120 + + Q + + NI P+++ Sbjct: 59 --LDNIRISQEKQDGMDVLELNITLPEQK 85 >3ke8_A 4-hydroxy-3-methylbut-2-ENYL diphosphate reductase; induced FIT mechanism, FS4-iron-sulfure-cluster, 3Fe-4S, iron, iron-sulfur; HET: EIP; 1.70A {Escherichia coli} PDB: 3ke9_A* 3kef_A* 3kel_A 3kem_A* 3f7t_A Length = 326 Score = 26.8 bits (59), Expect = 1.3 Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 2/40 (5%) Query: 53 IASGTLSPDDLEEDFIHSLQKH--VEIDEPDSPTENSDFS 90 + +G +PD L ++ + LQ+ E + EN F Sbjct: 274 VTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFE 313 >2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K Length = 95 Score = 26.3 bits (58), Expect = 1.8 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 3/47 (6%) Query: 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNT---VVALREIASGTL 58 R+ + + S R L+ GA +D+ +T +A E G L Sbjct: 28 TRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVL 74 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 25.5 bits (55), Expect = 2.9 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 22/80 (27%) Query: 51 REIASGTLSPDDLE---------EDFIHSLQKHVEIDE-PDSPTENSDFS--------WH 92 +E+ + +DLE E F H V+I E P E ++S + Sbjct: 920 KEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIP----ETGEYSVKLLKGATLY 975 Query: 93 KPEALSFGQMSEGDLLEGIN 112 P+AL F ++ G + G N Sbjct: 976 IPKALRFDRLVAGQIPTGWN 995 >1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X* 1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A* 1ecl_A 1cy9_A* 1cyy_A* Length = 592 Score = 25.5 bits (55), Expect = 3.5 Identities = 3/27 (11%), Positives = 11/27 (40%) Query: 50 LREIASGTLSPDDLEEDFIHSLQKHVE 76 L ++A+ + + F + ++ Sbjct: 550 LDQVANHEAEWKAVLDHFFSDFTQQLD 576 >3kpk_A Sulfide-quinone reductase, putative; oxidoreductases, sulfide:quinone oxidoreductase, C160A mutan oxidoreductase; HET: FAD LMT; 2.05A {Acidithiobacillus ferrooxidans atcc 23} PDB: 3kpg_A* 3kpi_A* Length = 434 Score = 25.2 bits (54), Expect = 3.8 Identities = 7/49 (14%), Positives = 17/49 (34%), Gaps = 3/49 (6%) Query: 28 RHLSQGAKPTVDVGKDKNTVV--ALREIASGTLSPDDLEEDFIHSLQKH 74 L G + T+ + + + + G DD+ H +++ Sbjct: 22 EALGSGHEVTL-ISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERK 69 >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} SCOP: c.117.1.1 PDB: 1m21_A* Length = 503 Score = 25.3 bits (54), Expect = 4.2 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 >1k9a_A Carboxyl-terminal SRC kinase; COOH-terminal SRC kinase, CSK, SFK, signal transduction, SH2, SH3, SRC homology, tyrosine kinase; 2.50A {Rattus norvegicus} SCOP: b.34.2.1 d.93.1.1 d.144.1.7 PDB: 1jeg_A Length = 450 Score = 24.5 bits (53), Expect = 6.2 Identities = 9/47 (19%), Positives = 21/47 (44%) Query: 28 RHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKH 74 + + +G V +G + VA++ I + + L E + + +H Sbjct: 199 QTIGKGEFGDVMLGDYRGNKVAVKCIKNDATAQAFLAEASVMTQLRH 245 >1r42_A Angiotensin I converting enzyme 2; zinc metallopeptidase domain, native or open conformation, chloride ION binding site; HET: NAG; 2.20A {Homo sapiens} SCOP: d.92.1.5 PDB: 1r4l_A* 2ajf_A* 3d0g_A* 3d0h_A* 3d0i_A* Length = 615 Score = 24.0 bits (51), Expect = 8.5 Identities = 6/41 (14%), Positives = 13/41 (31%), Gaps = 1/41 (2%) Query: 52 EIASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWH 92 + G + D + + ++ V + EP E Sbjct: 462 MVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDET-YCDPA 501 >1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F 1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F* 1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F 1y77_F* ... Length = 155 Score = 24.1 bits (52), Expect = 9.7 Identities = 8/45 (17%), Positives = 21/45 (46%), Gaps = 1/45 (2%) Query: 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTL 58 ++ + R +S A VD+ + + + +A++E+A + Sbjct: 86 TKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKI 130 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.313 0.132 0.380 Gapped Lambda K H 0.267 0.0628 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,047,823 Number of extensions: 44286 Number of successful extensions: 90 Number of sequences better than 10.0: 1 Number of HSP's gapped: 87 Number of HSP's successfully gapped: 20 Length of query: 122 Length of database: 5,693,230 Length adjustment: 81 Effective length of query: 41 Effective length of database: 3,729,466 Effective search space: 152908106 Effective search space used: 152908106 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)