RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780694|ref|YP_003065107.1| probable transcriptional regulator protein, LuxR family [Candidatus Liberibacter asiaticus str. psy62] (246 letters) >1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Length = 99 Score = 77.2 bits (190), Expect = 4e-15 Identities = 17/64 (26%), Positives = 26/64 (40%) Query: 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 D L+ +E E L +EG EIA L S T+++ S M K + Y Sbjct: 32 DKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSS 91 Query: 243 NNIV 246 ++ Sbjct: 92 VSMT 95 >2krf_A Transcriptional regulatory protein COMA; activator, competence, DNA-binding, transcription regulation component regulatory system; NMR {Bacillus subtilis} Length = 73 Score = 76.9 bits (190), Expect = 4e-15 Identities = 18/61 (29%), Positives = 32/61 (52%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 LT RE L + +G T+ EIA L +S+ ++ + SI K +R+ A+ A + + Sbjct: 13 LTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGV 72 Query: 246 V 246 + Sbjct: 73 L 73 >2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus} Length = 91 Score = 76.4 bits (188), Expect = 5e-15 Identities = 21/61 (34%), Positives = 39/61 (63%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 LT RE+E L I++G ++ EIA I+ TV ++++I+ K + R+ A+ YA ++N+ Sbjct: 30 LTEREMEILLLIAKGYSNQEIASASHITIKTVKTHVSNILSKLEVQDRTQAVIYAFQHNL 89 Query: 246 V 246 + Sbjct: 90 I 90 >2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP} Length = 236 Score = 75.3 bits (184), Expect = 1e-14 Identities = 23/122 (18%), Positives = 42/122 (34%) Query: 125 GMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDF 184 G+ + +L + L+ + + Sbjct: 115 GVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIAAKTVLNPKQ 174 Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 L+ RE+ CL W S+GKT+ A + GI+ TV +Y+ K ++ +A A Sbjct: 175 MLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRG 234 Query: 245 IV 246 +V Sbjct: 235 LV 236 >3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Length = 258 Score = 75.5 bits (185), Expect = 1e-14 Identities = 22/61 (36%), Positives = 31/61 (50%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 L+ RE E L I +G +S EIA L IS NTVN + +I+ K + A A + Sbjct: 198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELMKL 257 Query: 246 V 246 + Sbjct: 258 L 258 >1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Length = 82 Score = 75.1 bits (185), Expect = 1e-14 Identities = 18/61 (29%), Positives = 33/61 (54%) Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 +LT RE + L I++G + IA L I+ +TV ++ +++K K+R A + + Sbjct: 21 QLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER 80 Query: 245 I 245 I Sbjct: 81 I 81 >1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A* Length = 234 Score = 73.4 bits (179), Expect = 4e-14 Identities = 23/128 (17%), Positives = 46/128 (35%), Gaps = 4/128 (3%) Query: 123 PAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHW-- 180 G+ + + K I L + + A + + Sbjct: 107 DFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTP 166 Query: 181 --GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIA 238 L +E L WI+ GKT +EIA + G+ N+V + M++ ++++ A Sbjct: 167 TAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTA 226 Query: 239 YAVRNNIV 246 A+R ++ Sbjct: 227 LAIRRKLI 234 >1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Length = 79 Score = 71.3 bits (175), Expect = 2e-13 Identities = 17/61 (27%), Positives = 28/61 (45%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 L+ RE + L+ + G + IA L IS TV + A++M K K+ + A+ Sbjct: 17 LSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLPHLVRMALAGGF 76 Query: 246 V 246 Sbjct: 77 G 77 >1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulator; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Length = 74 Score = 71.3 bits (175), Expect = 2e-13 Identities = 24/61 (39%), Positives = 34/61 (55%) Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 LT RE E + + KT+ EIA L IS TV N+I++ M+K K RS A+ +R Sbjct: 12 LTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGE 71 Query: 246 V 246 + Sbjct: 72 L 72 >2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} Length = 61 Score = 69.7 bits (171), Expect = 5e-13 Identities = 18/58 (31%), Positives = 28/58 (48%) Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 RE + L I EG T+ I+ L IS TV + ++MRK + + A R ++ Sbjct: 2 RERQVLKLIDEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTELLNCARRMRLI 59 >3c57_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A Length = 95 Score = 67.6 bits (165), Expect = 2e-12 Identities = 18/62 (29%), Positives = 32/62 (51%) Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 LT +E L +SEG T+ +IA + ++ TV NY++ ++ K + R+ A +A Sbjct: 27 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELK 86 Query: 245 IV 246 Sbjct: 87 RS 88 >3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A* Length = 225 Score = 60.5 bits (146), Expect = 3e-10 Identities = 19/59 (32%), Positives = 33/59 (55%) Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 +LT RE + + + G ++ EIA L +S NTV ++ ++ +K K R A+ +A N Sbjct: 159 KLTKREQQIIKLLGSGASNIEIADKLFVSENTVKTHLHNVFKKINAKNRLQALIWAKNN 217 >3c3w_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 2.20A {Mycobacterium tuberculosis} Length = 225 Score = 59.6 bits (143), Expect = 6e-10 Identities = 20/81 (24%), Positives = 35/81 (43%) Query: 166 AAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225 AA + LT +E L +SEG T+ +IA + ++ TV NY++ ++ Sbjct: 130 AAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLL 189 Query: 226 RKTATKTRSGAIAYAVRNNIV 246 K + R+ A +A Sbjct: 190 AKLGMERRTQAAVFATELKRS 210 >1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A Length = 215 Score = 52.2 bits (124), Expect = 1e-07 Identities = 18/65 (27%), Positives = 33/65 (50%) Query: 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 +LT RE + L I++G + IA L I+ +TV ++ +++K K+R A + Sbjct: 150 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWV 209 Query: 241 VRNNI 245 + I Sbjct: 210 HQERI 214 >1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A Length = 208 Score = 44.2 bits (103), Expect = 3e-05 Identities = 14/54 (25%), Positives = 26/54 (48%) Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 RE + L G + +IA LGI+ TV + +IM+K ++ + + + Sbjct: 146 REQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRSLANLVHLVEK 199 >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 = 39.9 bits (93), Expect = 6e-04 Identities = 49/281 (17%), Positives = 84/281 (29%), Gaps = 139/281 (49%) Query: 48 RMYAL------TEYVGASHFLLVRWDLFQEQKLDSIVSSDWPF--DLVRCMA-----LS- 93 ++ A+ T+ D F+E L + + DL++ A L Sbjct: 155 QLVAIFGGQGNTD------------DYFEE--LRDLYQTYHVLVGDLIKFSAETLSELIR 200 Query: 94 ---EKDKYY----NV---LQRPTELFCPVFHTLPENITPPAGMDNRY-------CSLTFD 136 + +K + N+ L+ P+ TP D Y C L Sbjct: 201 TTLDAEKVFTQGLNILEWLENPSN-------------TP----DKDYLLSIPISCPL--- 240 Query: 137 VARIRIGLMLL--F----------PKGRIILRDRLWEI-----GLLAAYQANMFKSYDVH 179 IG++ L + P G LR L GL+ A S Sbjct: 241 -----IGVIQLAHYVVTAKLLGFTP-GE--LRSYLKGATGHSQGLVTAVAIAETDS---- 288 Query: 180 WGKDFELTGRE-VECLTWISEG--------KTS-------DEIA----------VILGIS 213 W + F ++ R+ + L +I G TS D + I ++ Sbjct: 289 W-ESFFVSVRKAITVLFFI--GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT 345 Query: 214 RNTVNNYIASIMRKTATKT-----RSGAIAYAVRN---NIV 246 + V +Y+ KT + ++ N N+V Sbjct: 346 QEQVQDYV--------NKTNSHLPAGKQVEISLVNGAKNLV 378 Score = 39.5 bits (92), Expect = 6e-04 Identities = 40/212 (18%), Positives = 57/212 (26%), Gaps = 96/212 (45%) Query: 5 IQQVNIVLNREDEQ--------RTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEY- 55 + + N L +Q + V P +S +Y L Sbjct: 353 VNKTNSHLP-AGKQVEISLVNGAKNLVVSGPPQS------------------LYGLNLTL 393 Query: 56 --VGASHFLLVRWD----LFQEQKLDSI------VSSDWPFD---LVRCMALSEKD-KYY 99 A L D F E+KL V+S PF LV L KD Sbjct: 394 RKAKAPSGL----DQSRIPFSERKL-KFSNRFLPVAS--PFHSHLLVPASDLINKDLVKN 446 Query: 100 NVLQRPTELFCPVFHT--------LPENITP-------------------PA-------- 124 NV ++ PV+ T L +I+ A Sbjct: 447 NVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGP 506 Query: 125 GMDNRYCSLTFDVARIRIGLMLLFPKG-RIIL 155 G + LT R + G G R+I+ Sbjct: 507 GGASGLGVLT---HRNKDG------TGVRVIV 529 >2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae} Length = 315 Score = 34.6 bits (79), Expect = 0.023 Identities = 8/24 (33%), Positives = 13/24 (54%) Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222 + T +IA LGI R T++ + Sbjct: 20 QDMTQAQIARELGIYRTTISRLLK 43 >3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164 Score = 33.7 bits (76), Expect = 0.041 Identities = 14/57 (24%), Positives = 26/57 (45%) Query: 171 NMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 + + + + E E LT++ G + EIA IL + +++N I I +K Sbjct: 95 LKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRKK 151 >3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative stress, transcription regulation; 2.35A {Mycobacterium tuberculosis} Length = 92 Score = 32.3 bits (74), Expect = 0.100 Identities = 9/29 (31%), Positives = 16/29 (55%) Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227 G ++ +IA LGI+ TV + + +R Sbjct: 52 RGWSTAQIATDLGIAEGTVKSRLHYAVRA 80 >1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Length = 52 Score = 31.2 bits (71), Expect = 0.19 Identities = 7/30 (23%), Positives = 15/30 (50%) Query: 192 ECLTWISEGKTSDEIAVILGISRNTVNNYI 221 + + +G ++A+I GI +T+ Y Sbjct: 13 QISRLLEKGHPRQQLAIIFGIGVSTLYRYF 42 >1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239 Score = 30.7 bits (68), Expect = 0.29 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 1/43 (2%) Query: 186 LTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRK 227 L RE + I E + E+A IL S + V+ A + + Sbjct: 188 LPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALER 230 >1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A Length = 183 Score = 30.5 bits (68), Expect = 0.39 Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 2/44 (4%) Query: 178 VHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221 V +G+ ++ V L +G + I+ + I+R+TV I Sbjct: 138 VVFGRKRKIDRDAV--LNMWQQGLGASHISKTMNIARSTVYKVI 179 >2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus} Length = 209 Score = 30.4 bits (67), Expect = 0.43 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 2/80 (2%) Query: 144 LMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREV--ECLTWISEGK 201 L ++ + R + R + +A + ++ + R + + + EG+ Sbjct: 117 LAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQ 176 Query: 202 TSDEIAVILGISRNTVNNYI 221 +IA + I+R TV Sbjct: 177 AISKIAKEVNITRQTVYRIK 196 >2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc binding transcription factor; 2.40A {Rhodobacter sphaeroides 2} PDB: 2z2s_A Length = 184 Score = 30.0 bits (66), Expect = 0.48 Identities = 6/29 (20%), Positives = 12/29 (41%) Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227 T E+A G+ T+ + I + + Sbjct: 150 GDLTHRELAAETGLPLGTIKSRIRLALDR 178 >1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A Length = 194 Score = 29.8 bits (66), Expect = 0.57 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%) Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 R L + +G + +EIA I+ TV + I Sbjct: 146 RMAITLREL-DGLSYEEIAAIMDCPVGTVRSRIFRAREA 183 >3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus} Length = 144 Score = 29.7 bits (66), Expect = 0.69 Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 1/67 (1%) Query: 162 IGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEG-KTSDEIAVILGISRNTVNNY 220 + +A K ++ GK L+ + L SE ++ +A ++++ + Sbjct: 11 MNTIAKIYRGSIKEFNNRLGKLMNLSYLDFSILKATSEEPRSMVYLANRYFVTQSAITAA 70 Query: 221 IASIMRK 227 + + K Sbjct: 71 VDKLEAK 77 >1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A Length = 192 Score = 29.6 bits (66), Expect = 0.75 Identities = 6/26 (23%), Positives = 13/26 (50%) Query: 197 ISEGKTSDEIAVILGISRNTVNNYIA 222 ++G + +IA G+S+ V + Sbjct: 21 KNDGMSQKDIAAKEGLSQAKVTRALQ 46 >1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 Length = 141 Score = 29.0 bits (64), Expect = 1.00 Identities = 6/46 (13%), Positives = 17/46 (36%), Gaps = 1/46 (2%) Query: 181 GKDFELTGRE-VECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225 + L+ E + + E++ + SR+ + Y+ + Sbjct: 2 PRGSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPV 47 >1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1 Length = 178 Score = 28.9 bits (64), Expect = 1.0 Identities = 6/30 (20%), Positives = 14/30 (46%) Query: 193 CLTWISEGKTSDEIAVILGISRNTVNNYIA 222 +++GK +IA +G S + ++ Sbjct: 45 IGRELAKGKKKGDIAKEIGKSPAFITQHVT 74 >1upi_A DTDP-4-dehydrorhamnose 3,5-epimerase; rhamnose pathway, PSI, protein structure initiative, TB structural genomics consortium, TB; HET: CME; 1.7A {Mycobacterium tuberculosis} SCOP: b.82.1.1 PDB: 2ixc_A* 1pm7_A* Length = 225 Score = 28.9 bits (64), Expect = 1.1 Identities = 9/58 (15%), Positives = 17/58 (29%), Gaps = 7/58 (12%) Query: 40 DCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDK 97 + MY + + D ++ DWP +LS++D Sbjct: 142 LALQDNSTVMYLCSAEYNPQREHTICAT-------DPTLAVDWPLVDGAAPSLSDRDA 192 >3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A* Length = 189 Score = 28.9 bits (64), Expect = 1.1 Identities = 5/23 (21%), Positives = 7/23 (30%) Query: 200 GKTSDEIAVILGISRNTVNNYIA 222 +A ISR + I Sbjct: 42 AGNISALADAENISRKIITRCIN 64 >1ep0_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; racemase, DTDP-4-dehydrorhamnose epimerase, structural genomics, PSI; 1.50A {Methanothermobacterthermautotrophicus} SCOP: b.82.1.1 PDB: 1epz_A* Length = 185 Score = 29.0 bits (65), Expect = 1.2 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 7/49 (14%) Query: 49 MYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDK 97 Y TE + + WD D + DWP ++V + +SEKD+ Sbjct: 132 NYKCTELYHPEYDSGIPWD-------DPDIGIDWPLEMVDDLIISEKDR 173 >1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Length = 243 Score = 28.6 bits (63), Expect = 1.2 Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 1/44 (2%) Query: 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 EL RE + + +T E+A LGIS+ ++ I++ Sbjct: 198 ELDERERLIVYLRYYKDQTQSEVASRLGISQVQMSRLEKKILQH 241 >1nt2_B Conserved hypothetical protein; adeMet, binding motif, coiled coil, RNA binding protein; HET: SAM; 2.90A {Archaeoglobus fulgidus} SCOP: a.183.1.1 Length = 258 Score = 28.6 bits (64), Expect = 1.2 Identities = 10/36 (27%), Positives = 18/36 (50%) Query: 69 FQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQR 104 F+E L + S PF++ A + YY +L++ Sbjct: 21 FEESFLKAENPSPLPFNVSEVGAKALGKDYYRILRK 56 >3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A Length = 151 Score = 28.2 bits (63), Expect = 1.7 Identities = 7/47 (14%), Positives = 21/47 (44%), Gaps = 1/47 (2%) Query: 182 KDFELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRK 227 ++ ++ + L +S E T +I G+++ V+ + ++ Sbjct: 32 TEYGISAEQSHVLNMLSIEALTVGQITEKQGVNKAAVSRRVKKLLNA 78 >2v79_A DNA replication protein DNAD; primosome, DNA remodelling, oligomerization domain, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis} Length = 135 Score = 28.0 bits (62), Expect = 1.8 Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 7/53 (13%) Query: 182 KDFELTGREVECL----TWISEGK---TSDEIAVILGISRNTVNNYIASIMRK 227 K L E+ L + +G T +++ + IS N + ++K Sbjct: 26 KQLGLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQK 78 >2i3f_A Glycolipid transfer-like protein; GLTP superfamily, GLTP-like, protein structure initiative, PSI; 1.38A {Galdieria sulphuraria} PDB: 2q52_A Length = 224 Score = 27.9 bits (62), Expect = 2.2 Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 6/57 (10%) Query: 26 LPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRW-DLFQEQKLDSIVSSD 81 P+R ++ P + E++ H L F +++L+ D Sbjct: 152 APSRERFYRKLHPDLNIAKAKIE-----EFLIELHDPLCCIVQFFFQRELEDQCWGD 203 >1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28 Length = 144 Score = 27.9 bits (62), Expect = 2.3 Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 2/48 (4%) Query: 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227 K+ LT + L + E G ++IA ++ + R T I + + Sbjct: 23 KELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ 70 >3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A* Length = 138 Score = 27.6 bits (61), Expect = 2.9 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 2/48 (4%) Query: 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227 LT +V CL I G DE+A + + T+ + + Sbjct: 23 GHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEES 70 >1xd7_A YWNA; structural genomics, protein structure initiative, winged helix DNA binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55 Length = 145 Score = 27.3 bits (60), Expect = 3.5 Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 2/56 (3%) Query: 191 VECLTWISEGK--TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 + L+ IS + +S+ IA + + V I+ + + +R+G +++ + Sbjct: 12 IHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGASLKKD 67 >1jid_A Signal recognition particle 19 kDa protein; signal recognition particle (SRP), protein-RNA complex, GGAG tetraloop, signaling protein/RNA complex; HET: 5BU A23; 1.80A {Homo sapiens} SCOP: d.201.1.1 PDB: 1mfq_B* 1ry1_B* 2go5_B 2j37_B Length = 128 Score = 27.1 bits (60), Expect = 3.6 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 9/80 (11%) Query: 155 LRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGI-S 213 ++D +GL + N K Y W +D + GR L K D ++ S Sbjct: 49 IQDVCSAVGLNVFLEKN--KMYSREWNRDVQYRGRVRVQL------KQEDGSLCLVQFPS 100 Query: 214 RNTVNNYIASIMRKTATKTR 233 R +V Y A ++ K T+T+ Sbjct: 101 RKSVMLYAAEMIPKLKTRTQ 120 >3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A Length = 250 Score = 26.9 bits (58), Expect = 4.5 Identities = 13/70 (18%), Positives = 24/70 (34%) Query: 168 YQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 N + + G+ V I+ + I I G+ TV+ +AS+ R+ Sbjct: 145 NTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRE 204 Query: 228 TATKTRSGAI 237 + I Sbjct: 205 NILDKKKNKI 214 >2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426} Length = 128 Score = 26.8 bits (59), Expect = 4.5 Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 7/53 (13%) Query: 182 KDFELTGREVECL----TWISEGK---TSDEIAVILGISRNTVNNYIASIMRK 227 K L E+ L ++ EG T E+A + +S + +++K Sbjct: 26 KQLGLGEGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQK 78 >3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28 Length = 166 Score = 26.8 bits (59), Expect = 4.9 Identities = 10/49 (20%), Positives = 21/49 (42%), Gaps = 3/49 (6%) Query: 182 KDFELTGREVECLTWISE---GKTSDEIAVILGISRNTVNNYIASIMRK 227 K ELT L I + ++ ++A +GI + ++ + + K Sbjct: 47 KPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDK 95 >3onq_A Regulator of polyketide synthase expression; structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Bifidobacterium adolescentis} Length = 262 Score = 26.5 bits (58), Expect = 5.1 Identities = 8/34 (23%), Positives = 14/34 (41%) Query: 195 TWISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 T++ G + + A L + NTV + T Sbjct: 204 TFLKYGSSLENTAKELNVHPNTVRYRLKRAAETT 237 >2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus} Length = 244 Score = 26.6 bits (58), Expect = 5.3 Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 2/45 (4%) Query: 185 ELTGREVECLTWISEGK--TSDEIAVILGISRNTVNNYIASIMRK 227 + + E++ L + E K E+A +L S T+ N IA + + Sbjct: 149 DYSREEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF 193 >2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn- helix motif; 3.00A {Mycobacterium tuberculosis H37RV} Length = 70 Score = 26.7 bits (59), Expect = 5.3 Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 1/39 (2%) Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 RE LT + G + + A + G T+ + +A Sbjct: 21 REALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDA 58 >2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein structure initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1 Length = 170 Score = 26.4 bits (58), Expect = 5.4 Identities = 8/21 (38%), Positives = 10/21 (47%) Query: 200 GKTSDEIAVILGISRNTVNNY 220 + A LGISR V+ Y Sbjct: 103 NLSLTTAAEALGISRRMVSYY 123 >2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H 1ku2_A Length = 423 Score = 26.8 bits (58), Expect = 5.4 Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 5/48 (10%) Query: 185 ELTGREVECLTW-----ISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 +L+ RE L T +E+ G++R + +RK Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRK 407 >1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438 Score = 26.4 bits (57), Expect = 6.5 Identities = 6/29 (20%), Positives = 12/29 (41%) Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227 T +E+ G++R + +RK Sbjct: 394 REHTLEEVGAYFGVTRERIRQIENKALRK 422 >2o0m_A Transcriptional regulator, SORC family; structural genomics, PSI-2, protein structure initiative; 1.60A {Enterococcus faecalis V583} SCOP: c.124.1.8 Length = 345 Score = 26.4 bits (58), Expect = 6.6 Identities = 2/24 (8%), Positives = 8/24 (33%) Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222 + ++ +GI+ + Sbjct: 33 QPIGRRSLSETMGITERVLRTETD 56 >1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28 Length = 138 Score = 26.4 bits (58), Expect = 6.9 Identities = 9/73 (12%), Positives = 24/73 (32%), Gaps = 2/73 (2%) Query: 157 DRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISE--GKTSDEIAVILGISR 214 + + +G L + ++T + + L I T E+ +L + Sbjct: 3 NEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDL 62 Query: 215 NTVNNYIASIMRK 227 + + ++ K Sbjct: 63 GALTRMLDRLVCK 75 >2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A Length = 146 Score = 26.2 bits (57), Expect = 8.2 Identities = 7/47 (14%), Positives = 19/47 (40%), Gaps = 1/47 (2%) Query: 182 KDFELTGREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRK 227 + L+ + L S+G KT +A ++++ + + + Sbjct: 31 GELNLSYLDFLVLRATSDGPKTMAYLANRYFVTQSAITASVDKLEEM 77 >3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua} Length = 143 Score = 25.8 bits (57), Expect = 8.6 Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 2/48 (4%) Query: 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227 +++T + L I + EIA+ TVN + ++RK Sbjct: 31 ASYDVTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRK 78 >2kfs_A Conserved hypothetical regulatory protein; WHTH, DNA binding, phosphorylation, DNA-binding protein; NMR {Mycobacterium tuberculosis} Length = 148 Score = 25.7 bits (56), Expect = 9.5 Identities = 4/20 (20%), Positives = 9/20 (45%) Query: 202 TSDEIAVILGISRNTVNNYI 221 +A +LG+ + V + Sbjct: 33 DLPRVAELLGVPVSKVAQQL 52 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 0.324 0.137 0.423 Gapped Lambda K H 0.267 0.0694 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,142,765 Number of extensions: 96685 Number of successful extensions: 548 Number of sequences better than 10.0: 1 Number of HSP's gapped: 546 Number of HSP's successfully gapped: 85 Length of query: 246 Length of database: 5,693,230 Length adjustment: 90 Effective length of query: 156 Effective length of database: 3,511,270 Effective search space: 547758120 Effective search space used: 547758120 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 (21.6 bits) S2: 55 (25.0 bits)