RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780282|ref|YP_003064695.1| putative transcription regulator protein [Candidatus Liberibacter asiaticus str. psy62] (299 letters) >3mz1_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative, MI center for STR uctural genomics, MCSG; 1.88A {Sinorhizobium meliloti} Length = 300 Score = 203 bits (516), Expect = 6e-53 Identities = 67/286 (23%), Positives = 126/286 (44%), Gaps = 4/286 (1%) Query: 8 LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67 +R F V +G+FT A+ L++ +++++ I GLE + KL R R + +T G+ + Sbjct: 3 MRAFLRVVETGNFTRASASLNMPKATVTNLIQGLEAHLRTKLLNRTTRRVLVTPDGALYY 62 Query: 68 RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI 127 + + L+ L + P G+LR+ T ++ L EF YPDIQI L Sbjct: 63 ERAARLLSDLDELDGSLSTAQSLPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLG 122 Query: 128 LDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELD 187 + ++ ID + DCAIR + SLI R++ + A A+ +L+ P +L+ Sbjct: 123 VSDRTIDYLAENVDCAIRAG-TLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLE 181 Query: 188 KHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDY 247 K+ + L + + I + N + + G G+ P + Sbjct: 182 KNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTMAANESTTYLAAARAGLGVIQAPLF 241 Query: 248 IVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 +V++ N +V ++ D +Y YP + +L+ F +++ Sbjct: 242 MVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWV 287 >3hhg_A Transcriptional regulator, LYSR family; transcription factor, structural genomics, oxford protein production facility, OPPF; 3.20A {Neisseria meningitidis serogroup B} Length = 306 Score = 182 bits (462), Expect = 1e-46 Identities = 74/294 (25%), Positives = 130/294 (44%), Gaps = 9/294 (3%) Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 M + ++L VF V SGSF+ AAEQL ++ S++SR + LE ++G+ L R R L+LT Sbjct: 1 MKTNSEELTVFVQVVESGSFSRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRTTRQLSLT 60 Query: 61 EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120 E+G++ R + ++ + E+ P G L + + + + +LL +F YP Sbjct: 61 EEGAQYFRRAQRILQEMAAAETEMLAVHEIPQGVLSVDSAMPMVLHLLAPLAAKFNERYP 120 Query: 121 DIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREP 180 I++ L+ I++ D A+R + S L R L A+P YL P Sbjct: 121 HIRLSLVSSEGYINLIERKVDIALRAG-ELDDSGLRARHLFDSRFRVIASPEYLAKHGTP 179 Query: 181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG 240 S +EL H + F + P + + L P +S + C+ G G Sbjct: 180 QSTEELAGHQCLGFTE--PGSLNTWAVLDAQGNPYKISPHFT--ASSGEILRSLCLSGCG 235 Query: 241 IALLPDYIVKD---NPNLVRIMEDVITP-SFTVYFCYPEALKNTGKLKAFRNFI 290 I L D++V + L+ ++ + + + Y +L+ F +F+ Sbjct: 236 IVCLSDFLVDNDIAEGKLIPLLAEQTSDKTHPFNAVYYSDKAVNLRLRVFLDFL 289 >1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA binding and regulatory domains, DNA binding protein; 2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB: 1iz1_A Length = 294 Score = 148 bits (374), Expect = 1e-36 Identities = 50/296 (16%), Positives = 104/296 (35%), Gaps = 6/296 (2%) Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 ++ +L+ F VA +G+ AA++LH+SQ I+RQ+ LE ++G+ L R RG+ LT G Sbjct: 2 EFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAG 61 Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123 + + + ++ G+L +A L L+ FL P Sbjct: 62 HAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTAT 121 Query: 124 IQLILD--NKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPL 181 + L ++ ++ + R + + + ++ + Sbjct: 122 VSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTC 181 Query: 182 SIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241 + +L L F + + EPRI V + + + G+ Sbjct: 182 KLADLRAVELTLF-PRGGRPSFADEVIGLFKHAGIEPRI-ARVVEDATAALALTMAGAAS 239 Query: 242 ALLPDYIVK-DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 +++P + P++ + + + K L F + A+D Sbjct: 240 SIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKE-KQPPILARFVEHVRRSAKD 294 >3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR, TSAR, WHTH, DNA- binding, plasmid, transcription; 1.85A {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A Length = 305 Score = 147 bits (372), Expect = 2e-36 Identities = 53/294 (18%), Positives = 92/294 (31%), Gaps = 12/294 (4%) Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 L+ + GS AA+ LHLSQ ++S I LE E+ L R RG++LT G Sbjct: 3 KLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFG 62 Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123 + + + Q E+ + + G + A + + L L F +PD+ Sbjct: 63 QAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVT 122 Query: 124 IQLILDNKDI---DISMDYADCAI-RLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179 + + + D A+ K + L + L + + Sbjct: 123 VNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHP--MAN 180 Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 + EL + N A P L S+L++ Sbjct: 181 ATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLP---EPKLGLVCESFLALPGVVAHSD 237 Query: 240 GIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 + +P + + L I P+ T+Y L T +I Sbjct: 238 LLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWI 291 >3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped structure, DNA binding domain, regulatory domain, DNA-binding; 2.70A {Mycobacterium tuberculosis} Length = 303 Score = 137 bits (346), Expect = 2e-33 Identities = 47/299 (15%), Positives = 99/299 (33%), Gaps = 16/299 (5%) Query: 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 D +L V GSF AAE+LH++ S++S++I LE +VG L R + T Sbjct: 6 LDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVRE-KPCRATTA 64 Query: 63 GSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDI 122 G L R+ ++ E+ ++ ++ IA D + D+ Sbjct: 65 GIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDV 124 Query: 123 QIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYL-KNCREPL 181 +I+ + + A A+ + L + A+ ++ ++ + Sbjct: 125 RIEDQDHSARLLRE-GVAMGAVTTERN-PVPGCRVHPLGEMRYLPVASRPFVQRHLSDGF 182 Query: 182 SIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241 + K + + ++D R I P V + G G Sbjct: 183 TXXXXXKAPSLAWNR--DDGLQDMLVRKAFRRAITRPTH---FVPTTEGFTAAARAGLGW 237 Query: 242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 + P+ + + + VR+ + V + ++ + + + A Sbjct: 238 GMFPEKLAASPLADGSFVRVCD----IHLDVPLYWQCWKLDSPIIARITDTVRAAASGL 292 >3fzv_A Probable transcriptional regulator; LYSR, structural genomics, PSI-2, protein structure initiative; 2.71A {Pseudomonas aeruginosa PA01} Length = 306 Score = 136 bits (343), Expect = 5e-33 Identities = 52/297 (17%), Positives = 111/297 (37%), Gaps = 13/297 (4%) Query: 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR-HARGLTLT 60 S+ +L+ F GS A+ +L+++Q SIS + GLE G++LF R HA+G++LT Sbjct: 3 SYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLT 62 Query: 61 EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120 G++ +R E+ + + +G++ I + L G + F YP Sbjct: 63 PAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYP 122 Query: 121 DIQIQLILDNKDI---DISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNC 177 ++I++ + ++ D A + S+ + + HA + Sbjct: 123 GVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAG 182 Query: 178 REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 + +S+++L +I + ++ +G S + Sbjct: 183 QAQVSLRDLCLEPMILL-----DVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQ 237 Query: 238 GSGIALLPDYIV----KDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 G G +LL D +V + + + + + + T + F ++ Sbjct: 238 GFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYC 294 >1uth_A LYSR-type regulatory protein; transcription regulation, transcriptional regulator; 2.2A {Burkholderia SP} SCOP: c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A Length = 315 Score = 130 bits (328), Expect = 3e-31 Identities = 49/296 (16%), Positives = 83/296 (28%), Gaps = 13/296 (4%) Query: 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 D + L VF + S + A E+L L+Q ++S + L T + LF R ++G+ T Sbjct: 13 DIDLNLLVVFNQLLLDRSVSTAGEKLGLTQPAVSNSLKRLRTALNDDLFLRTSKGMEPTP 72 Query: 62 QGSKLHRVTSEVYHKLETTQIELQ-ESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120 L + L+T + +A T + ++ P Sbjct: 73 YALHLAEPVIYALNTLQTALTTRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAP 132 Query: 121 DIQIQLILDNKD---IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNC 177 IQI + N D+ D A+ L P + QR+L + Sbjct: 133 HIQISTLRPNAGNLKEDMESGAVDLALGLL-PELQTGFFQRRLFRHRYVCMFRKDHPSAK 191 Query: 178 REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 Q + ++ D G R L V +++I Sbjct: 192 SPMSLKQFSELEHVGVVALNTGHGEVDGLL-----ERAGIKRRMRLVVPHFIAIGPILHS 246 Query: 238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 IA +P L P + + R Sbjct: 247 TDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLF 302 >1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine biosynthesis, transcription regulation; 1.80A {Klebsiella aerogenes} SCOP: c.94.1.1 Length = 324 Score = 130 bits (326), Expect = 5e-31 Identities = 65/294 (22%), Positives = 113/294 (38%), Gaps = 11/294 (3%) Query: 4 DWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTE 61 +LR V + + AE L+ SQ IS+Q+ LE E+GI++F R + LT +T Sbjct: 2 KLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTP 61 Query: 62 QGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121 G ++ R+ EV K++ + E + G L +ATT + L G +K F+ YP Sbjct: 62 AGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYPR 121 Query: 122 IQIQLILDNKDIDISM---DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCR 178 + + + + AD AI L+ + P + + Sbjct: 122 VSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLATK 181 Query: 179 EPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 +SI+EL ++ L+T+ + L T G I Y LG Sbjct: 182 GSVSIEELAQYPLVTY----TFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLG 237 Query: 239 SGIALLPDYIVK--DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 G+ ++ V +P+LV++ + I T + + + F Sbjct: 238 LGVGVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRF 291 >2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional activator, LYSR-type transcriptional regulator; 1.80A {Acinetobacter SP} PDB: 2h99_A 2f7a_A* 2f6p_A 2f78_A 2f6g_A* 2f8d_A 2f97_A* Length = 312 Score = 126 bits (317), Expect = 5e-30 Identities = 48/294 (16%), Positives = 103/294 (35%), Gaps = 13/294 (4%) Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 + LR F V SFT AA++L ++Q +SRQI LE E+GI+L R +R + T +G Sbjct: 2 ELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEG 61 Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123 ++ ++ ++ + +RI L LL + + +P+++ Sbjct: 62 HFFYQYAIKLLSNVDQMVSMTKR-IASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLR 120 Query: 124 IQLILDNKDIDISM----DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179 I+L RL+ + + + + +A+ + + Sbjct: 121 IELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDK 180 Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 + + +L ++ + D + + +V + G Sbjct: 181 GVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTK--INEVREVQLALGLVAAGE 238 Query: 240 GIALLPDYIVKDNPN---LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 GI+L+P V +++ +Y ++T + + I Sbjct: 239 GISLVPASTQSIQLFNLSYVPLLDPD--AITPIYIAVRNMEEST-YIYSLYETI 289 >2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A {Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A* Length = 313 Score = 120 bits (302), Expect = 3e-28 Identities = 51/292 (17%), Positives = 93/292 (31%), Gaps = 9/292 (3%) Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 + LR F V S + AAE+L ++Q +SRQI LE E+GI+LF R R +TE G Sbjct: 2 ELRHLRYFVTVVEEQSISKAAEKLCIAQPPLSRQIQKLEEELGIQLFERGFRPAKVTEAG 61 Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123 ++ ++ + + LRI L LL + F P+I Sbjct: 62 MFFYQHAVQILTHTAQASSMAKRIATVSQ-TLRIGYVSSLLYGLLPEIIYLFRQQNPEIH 120 Query: 124 IQLILDNKD---IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLK-NCRE 179 I+LI + D K + A H+L Sbjct: 121 IELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIMLHKEQLKLAIHKHHHLNQFAAT 180 Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 + + ++ ++ + F +G ++ + G Sbjct: 181 GVHLSQIIDEPMLLYPVSQKPNFATFIQSL--FTELGLVPSKLTEIREIQLALGLVAAGE 238 Query: 240 GIALLPDYIVKDN-PNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 G+ ++P + NL+ I + ++ + + Sbjct: 239 GVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNM-DHSNYIPKILACV 289 >2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription, PSI, protein structure initiative, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1 Length = 310 Score = 115 bits (288), Expect = 1e-26 Identities = 37/298 (12%), Positives = 76/298 (25%), Gaps = 14/298 (4%) Query: 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 D + L VF + R + AA +L +S S+ S + L + +LF R + T+ Sbjct: 9 RLDLNLLLVFDALYRHRNVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRMQPTQ 68 Query: 62 QGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121 + L + L E + S + + D L L L Sbjct: 69 RAEHLAAAVAAALRALGEGLEEWRPFVPGQSQRTFVFAATDYTAFALLPPLMNRLQHSAP 128 Query: 122 IQIQLILDNKDIDISMDYADCAIRL------RKPIQSSSLIQRKLVTIHMHAYAAPHYLK 175 +++ + A I + A + + Sbjct: 129 GVRLRLVNAERKLSVEALASGRIDFALGYDEEHERLPEGIQAHDWFADRYVVVARRDHPR 188 Query: 176 NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC 235 P L + + + + D G R +Q+ + L+ + Sbjct: 189 LAGAPTLEGYLAERHAVVTPWNEDSGVIDRLL-----ARSGLRREVAVQLPTVLAALFLA 243 Query: 236 VLGSGIALLPDYIVK---DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 + P + + + L P + + + Sbjct: 244 GSTDFLLTAPRHAARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQL 301 >3hhf_B Transcriptional regulator, LYSR family; transcription factor, structural genomics, oxford protein production facility, OPPF; 2.30A {Neisseria meningitidis serogroup B} Length = 213 Score = 107 bits (267), Expect = 4e-24 Identities = 42/205 (20%), Positives = 75/205 (36%), Gaps = 9/205 (4%) Query: 90 KPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKP 149 P G L + + + + +LL +F YP I++ L+ I++ D A+R + Sbjct: 4 IPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLVSSEGYINLIERKVDIALRAGEL 63 Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209 S L R L A+P YL P S +EL H + F + W Sbjct: 64 DD-SGLRARHLFDSRFRVIASPEYLAKHGTPQSTEELAGHQCLGFTE----PGSLNTWAV 118 Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMED-VITP 265 + +S + C+ G GI L D++V + L+ ++ + Sbjct: 119 LDAQGNPYKISPHFTASSGEILRSLCLSGCGIVCLSDFLVDNDIAEGKLIPLLAEQTSDK 178 Query: 266 SFTVYFCYPEALKNTGKLKAFRNFI 290 + Y +L+ F +F+ Sbjct: 179 THPFNAVYYSDKAVNLRLRVFLDFL 203 >3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich, DNA-binding, transcription regulation; HET: MES; 1.83A {Citrobacter freundii} PDB: 3kot_A Length = 219 Score = 99.0 bits (246), Expect = 1e-21 Identities = 34/207 (16%), Positives = 74/207 (35%), Gaps = 12/207 (5%) Query: 87 SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRL 146 ++ + KL+I L L +F YP I + + N +D + + D IR Sbjct: 6 ATKQTQEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRY 65 Query: 147 RKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN 206 + L + M +P + P ++ K L+ E Sbjct: 66 G-GGAWHDTDAQYLCSALMSPLCSPTLASQIQTP---ADILKFPLLRSYR----RDEWAL 117 Query: 207 WLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVI 263 W+ TV P + + +S +++++ G G+A+ P + + +V+ I Sbjct: 118 WMQTVGEAPPSPTHNVMVFDSSVTMLEAAQAGMGVAIAPVRMFTHLLSSERIVQPFLTQI 177 Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290 + + ++ T ++ F ++ Sbjct: 178 -DLGSYWITRLQSRPETPAMREFSRWL 203 >3fd3_A Chromosome replication initiation inhibitor protein; structural genomics, LYSR, PSI-2, protein structure initiative; HET: MSE P33 PG4; 1.70A {Agrobacterium tumefaciens str} Length = 208 Score = 89.4 bits (221), Expect = 1e-18 Identities = 29/212 (13%), Positives = 62/212 (29%), Gaps = 17/212 (8%) Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKP 149 L IAT D + +F + + +D++D + A+ Sbjct: 2 VTLNIATNADSLGTWFLDAVSKFTGGSD-YLVNIAVDDQDHTVEWLRGGRVLAAVTAH-D 59 Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYL-KNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL 208 L + HA A+P ++ ++ + ++ L + +TF + Sbjct: 60 KPVQGCRVTPLGVLRYHATASPDFMARHFADGVTPAALARAPGLTFNQ-----KDRLQAS 114 Query: 209 ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITP 265 + + S ++ + G G L P +V + LV +M Sbjct: 115 WIRTALGEDVSYPTHWLPSTDGFVKASLAGMGWGLNPVQLVAEHLAAGRLVELMPG---T 171 Query: 266 SFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 + + +L + AR Sbjct: 172 PLDIPLYWQVNRLAAERLAGLTANMVGTARVV 203 >1b9m_A Protein (mode); DNA-binding, gene regulation, winged helix turn helix, molybdate, OB fold; 1.75A {Escherichia coli} SCOP: a.4.5.8 b.40.6.2 b.40.6.2 PDB: 1b9n_A 1o7l_A 1h9s_A 1h9r_A 1h9s_B Length = 265 Score = 81.1 bits (199), Expect = 3e-16 Identities = 32/198 (16%), Positives = 63/198 (31%), Gaps = 10/198 (5%) Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-- 58 + D ++ + +A SGS + A+ +S S I+ + L R G Sbjct: 18 LFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGG 77 Query: 59 ---LTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQ----NLLQGN 111 LT G +L ++ + + L + P L A + Q N G Sbjct: 78 GAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGT 137 Query: 112 LKEFLLLYPDIQIQLILDNKDIDISMDYA-DCAIRLRKPIQSSSLIQRKLVTIHMHAYAA 170 + + ++L + + + RL LI K + + A Sbjct: 138 ITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEA 197 Query: 171 PHYLKNCREPLSIQELDK 188 + + P I +++ Sbjct: 198 VAQNADNQLPGIISHIER 215 >3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type transcriptional regulator, LTTR, redox, structural genomics, OPPF; 2.39A {Neisseria meningitidis} Length = 219 Score = 77.8 bits (191), Expect = 3e-15 Identities = 29/204 (14%), Positives = 64/204 (31%), Gaps = 5/204 (2%) Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149 G ++ + LL + P + + L + + AI + +P Sbjct: 3 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEP 62 Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209 Q ++ L + + +S + L + ++ + + + + Sbjct: 63 FQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCS 122 Query: 210 TVD-RPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK--DNPNLVRIMEDVITPS 266 + + + + LQ +S +I G I++LP + D+ I + PS Sbjct: 123 ELAAKQRIQGLTNTLQGSSINTIRHMVASGLAISVLPATALTENDHMLFSIIPFEGTPPS 182 Query: 267 FTVYFCYPEALKNTGKLKAFRNFI 290 V Y L A + I Sbjct: 183 RRVVLAYRRNFVRPKALSAMKAAI 206 >1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory domain, oxidized form, transcription; 2.30A {Escherichia coli} SCOP: c.94.1.1 PDB: 1i69_A Length = 219 Score = 73.5 bits (179), Expect = 5e-14 Identities = 35/204 (17%), Positives = 62/204 (30%), Gaps = 9/204 (4%) Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149 SG L I +G LL + +P +++ L + A+ L Sbjct: 4 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV 63 Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209 +S + I+ L M + RE + + +L L+ D + + Sbjct: 64 KESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFC- 122 Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITPS 266 G + + S ++ GSGI LLP V +V + P Sbjct: 123 ---FEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPR 179 Query: 267 FTVYFCYPEALKNTGKLKAFRNFI 290 T+ Y + + I Sbjct: 180 RTIGLVYRPGSPLRSRYEQLAEAI 203 >2qsx_A Putative transcriptional regulator, LYSR family; the putative transcriptional regulator, PSI-2; 1.64A {Vibrio parahaemolyticus rimd 2210633} Length = 218 Score = 73.2 bits (178), Expect = 6e-14 Identities = 27/223 (12%), Positives = 73/223 (32%), Gaps = 13/223 (5%) Query: 77 LETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDIS 136 ++ L +++ L + T L N+ +F +P+I+++++ + + Sbjct: 4 IQHATASLIQTN-TDQELLVVDVTPSFASLWLVPNINDFHQRHPNIRVKILTGDGAVKNI 62 Query: 137 MDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGD 196 +D +R P+ + + L + + K Q + + I Sbjct: 63 HGESDLHVRCL-PLSTHYEYSQLLCEETLLLIGNTNLPKLSD----NQAISHYPFIPQTT 117 Query: 197 LIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NP 253 + + + + + + + G+ALLPD++ + Sbjct: 118 ----RPQLWEQFKQENDLECPITYHSVGFEHFYLACEAVRMEKGLALLPDFMAQFSILRG 173 Query: 254 NLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 ++ I + + Y P + K+ F +++ K Sbjct: 174 DIQHIGNLKLHSGYGYYVVIPNFRLTSRKVALFHDWLKDKLTH 216 >3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio regulation; 1.58A {Porphyromonas gingivalis} Length = 232 Score = 70.5 bits (172), Expect = 5e-13 Identities = 26/213 (12%), Positives = 59/213 (27%), Gaps = 11/213 (5%) Query: 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYA 140 E Q+S +G+L IA + LL + ++I + + + Sbjct: 4 EEQQS---LTGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGE 60 Query: 141 DCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPK 200 + ++ L L Y + ++ + E++ H L + Sbjct: 61 IDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCF 120 Query: 201 CMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVR 257 + + R + S + M+ G GI +P V+ + + Sbjct: 121 RDQLVRFCQMKGL---HERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELV 177 Query: 258 IMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 + P V + + + Sbjct: 178 RPFGMPRPVREVRLAVRQDYSRRKLREQLIGLL 210 >2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural genomics, DNA-binding protein, PSI-2; 2.30A {Agrobacterium tumefaciens str} Length = 135 Score = 70.5 bits (172), Expect = 5e-13 Identities = 16/107 (14%), Positives = 34/107 (31%), Gaps = 8/107 (7%) Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----AR 55 K+ + ++A +GS + A + +S + L + Sbjct: 22 ERLGHGKVELMQLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGG 81 Query: 56 GLTLTEQGSKLHRVTSEVYHKLETT---QIELQESSVKPSGKLRIAT 99 G LT G++L + ++ I+ E++ P L Sbjct: 82 GAALTVFGAELLERYRGMEERMNEALREDIDWLEANRNPQDALNRDR 128 >2ql3_A Probable transcriptional regulator, LYSR family protein; APC7314, rhodococcus SP. RHA1, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.05A {Rhodococcus SP} Length = 209 Score = 68.2 bits (165), Expect = 2e-12 Identities = 34/207 (16%), Positives = 65/207 (31%), Gaps = 13/207 (6%) Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD---IDISMDYADCAIRLRK 148 +G + + LG +L L F YP ++ D ++ + D AI Sbjct: 4 AGPIAVGCYPALGPTILPSMLYAFTAEYPRASVEFREDTQNRLRTQLEGGELDVAIVYDL 63 Query: 149 PIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL 208 + + M A H L P+ + +L +H ++ N Sbjct: 64 DLSPEWQTVPLMTREPMVVLGAEHPLAGVDGPVRLADLAEHPMVLL-----DAPPSTNHA 118 Query: 209 ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKDNPN-----LVRIMEDVI 263 V R G + ++ + + G G LL D +V+ + + Sbjct: 119 MDVCREAGFAPRVAYRTANFETARAFVGRGLGWTLLLQRPRVDVTYEGLPVVVKPIAEPK 178 Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290 S V + + + +AF F+ Sbjct: 179 PASVAVVVAWHQEATLSRVARAFIRFV 205 >2hxr_A HTH-type transcriptional regulator CYNR; CYNR transcriptional regulator LYSR structural genomics, PSI-2, protein structure initiative; 2.05A {Escherichia coli K12} PDB: 3hfu_A Length = 238 Score = 57.1 bits (136), Expect = 4e-09 Identities = 39/244 (15%), Positives = 73/244 (29%), Gaps = 22/244 (9%) Query: 49 LFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLL 108 ++ ++A +L + + + + G LRIA T + Sbjct: 2 VWRQYAS----------------RALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFI 45 Query: 109 QGNLKEFLLLY--PDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMH 166 + +F Y +Q+Q + K D+ P+ S L L+T + Sbjct: 46 GPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLA 105 Query: 167 AYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVN 226 A H+ E +++ L L+ + G ++ N Sbjct: 106 LVVAQHHPLAVHEQVALSRLHDEKLVLL----SAEFATREQIDHYCEKAGLHPQVVIEAN 161 Query: 227 SYLSIMQYCVLGSGIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAF 286 S ++++ S LLP I + L I T + T KAF Sbjct: 162 SISAVLELIRRTSLSTLLPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAF 221 Query: 287 RNFI 290 + Sbjct: 222 LHMA 225 >2fyi_A HTH-type transcriptional regulator CBL; Lys-R family, cofactor-binding domain, cysteine biosynthesis; 2.80A {Escherichia coli K12} SCOP: c.94.1.1 Length = 228 Score = 55.6 bits (132), Expect = 1e-08 Identities = 34/202 (16%), Positives = 62/202 (30%), Gaps = 3/202 (1%) Query: 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI 150 SG L IATT + L +K F L+P+++++LI ++ A Sbjct: 12 TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE 71 Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT 210 + S+ Q ++ + +S L+ Sbjct: 72 RLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDA 131 Query: 211 VDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD--NPNLVRIMEDVITPSFT 268 R I +S + Y LG GI L+ + + NL+R+ + + T Sbjct: 132 FARKGLLADIVLSAQDSDVIKT-YVALGLGIGLVAEQSSGEQEEENLIRLDTRHLFDANT 190 Query: 269 VYFCYPEALKNTGKLKAFRNFI 290 V+ + F Sbjct: 191 VWLGLKRGQLQRNYVWRFLELC 212 >3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2 Length = 230 Score = 46.1 bits (109), Expect = 9e-06 Identities = 31/201 (15%), Positives = 69/201 (34%), Gaps = 21/201 (10%) Query: 1 MSFD-----WDKLRVFYVVARSG-----SFTHAAEQLHLSQSSISRQISGLETEVGI-KL 49 MS + + ++ A + + + A+ L +SQ S SR I LE I + Sbjct: 1 MSLETDDQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRT 60 Query: 50 FYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQ 109 + + L +TE+G + ++ + + + SG + Q ++Q Sbjct: 61 VTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEGRYYVARKQYIIQ 120 Query: 110 GNLKEFLLLYP-DIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAY 168 K ++ Y + I++ + + I + R ++ Sbjct: 121 FQEKLGIIPYLGTLNIKVDQASLPELRKIRGFR-GIHIEGFKTED----RTFGSVK---- 171 Query: 169 AAPHYLKNCREPLSIQELDKH 189 A P ++N + + E + Sbjct: 172 AFPAKIQNIPCFVIMPERTVY 192 >3oxn_A Putative transcriptional regulator, LYSR family; structural genomics, PSI-2, protein structure initiative; 2.70A {Vibrio parahaemolyticus} Length = 241 Score = 45.0 bits (106), Expect = 2e-05 Identities = 25/205 (12%), Positives = 50/205 (24%), Gaps = 11/205 (5%) Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149 IATT Q +L L P++ + D D R Sbjct: 18 DQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPT 77 Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209 L L + + + + +E S+ + H L Sbjct: 78 GPVEPLRSEILGRVGVLCLLSKQHPLANQEM-SLDDYLSHPHAMIAISDGVKALIEQALI 136 Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVRIMEDVITPS 266 R L+ + + I +P + + +LV Sbjct: 137 D-----KPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTP 191 Query: 267 FTVYFCYPEALKNTGKLKAFRNFIF 291 F + +++ + R+ + Sbjct: 192 FDYSMIWHARCEHSPAQEWLRSVVR 216 >2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus} Length = 244 Score = 39.7 bits (92), Expect = 8e-04 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 3/85 (3%) Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSK 65 +++ V+ + A+ L S+ ++ +I+ L+ GI R + L E G Sbjct: 155 MKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF-GILTQKGKDRKVELNELGLN 213 Query: 66 LHRVTSEVYHKLETTQIELQESSVK 90 + ++ V ++++ ++E+ K Sbjct: 214 VIKLNKSVIESSKSSEELVKENKGK 238 >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 = 36.0 bits (83), Expect = 0.011 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 7/78 (8%) Query: 8 LRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLE----TEVGIKLFYRHARGLTLT 60 + + + S A+ + + Q S+ R + LE R A+ + LT Sbjct: 56 WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLT 115 Query: 61 EQGSKLHRVTSEVYHKLE 78 E+ L EV HK Sbjct: 116 EKAEPLIAEMEEVIHKTR 133 >3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A* Length = 138 Score = 35.7 bits (82), Expect = 0.012 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 6/77 (7%) Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTE 61 + + R A H+ + +I+R + LE I+ R L +T Sbjct: 32 VACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTR 91 Query: 62 QGSKLHRVTSEVYHKLE 78 +G ++ + +V + E Sbjct: 92 RGEEIIPLILKVEERWE 108 >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 = 35.4 bits (82), Expect = 0.016 Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 6/76 (7%) Query: 9 RVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTEQ 62 V + + + A +++R + L + I R L+LT++ Sbjct: 41 SVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDK 100 Query: 63 GSKLHRVTSEVYHKLE 78 G K ++ Sbjct: 101 GRKETTELRDIVEASC 116 >3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcriptional regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A Length = 140 Score = 34.5 bits (79), Expect = 0.030 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 6/77 (7%) Query: 8 LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGI----KLFYRHARGLTLTE 61 V + + E++ L +++ + LE + + + ++LTE Sbjct: 39 YIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTE 98 Query: 62 QGSKLHRVTSEVYHKLE 78 QG + +E+ K+ Sbjct: 99 QGKAIKSPLAEISVKVF 115 >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 = 32.9 bits (75), Expect = 0.083 Identities = 8/75 (10%), Positives = 27/75 (36%), Gaps = 6/75 (8%) Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKL----FYRHARGLTLTE 61 +V + + T + L + +++R + L + ++ + + LT Sbjct: 37 FKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTT 96 Query: 62 QGSKLHRVTSEVYHK 76 G+ + ++ + Sbjct: 97 GGAAICEQCHQLVGQ 111 >2vh1_A FTSQ, cell division protein FTSQ; potra, membrane, septation, cell cycle, transmembrane, inner membrane; 2.7A {Escherichia coli} Length = 220 Score = 32.8 bits (74), Expect = 0.094 Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 3/63 (4%) Query: 99 TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDID-ISMDYAD-CAIRLRKPIQSSSLI 156 ++LG+ L F+ LYP +Q Q D K I + + Y A+ P+ Sbjct: 151 IKLNLGRGDTMKRLARFVELYPVLQQQAQTDGKRISYVDLRYDSGAAVGW-APLPPEEST 209 Query: 157 QRK 159 Q++ Sbjct: 210 QQQ 212 >2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, structural genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28 Length = 207 Score = 32.7 bits (74), Expect = 0.11 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 6/76 (7%) Query: 9 RVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLE----TEVGIKLFYRHARGLTLTEQ 62 + ++ + S + A+ + S+ LE +L + + LTE+ Sbjct: 52 HILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEE 111 Query: 63 GSKLHRVTSEVYHKLE 78 G+++ E + Sbjct: 112 GTEVFWSLLEEFDPTR 127 >2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28 Length = 145 Score = 32.3 bits (73), Expect = 0.14 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 6/77 (7%) Query: 8 LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTE 61 + + G + L +++S+++ + LE + + R A L +T Sbjct: 36 FDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITR 95 Query: 62 QGSKLHRVTSEVYHKLE 78 +G ++ E Sbjct: 96 KGEEVIEKVIERRENFI 112 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 31.9 bits (71), Expect = 0.17 Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 11/32 (34%) Query: 105 QNL--LQGNLKEFLLLY-----PDIQIQLILD 129 Q L LQ +LK LY P + I+ ++ Sbjct: 20 QALKKLQASLK----LYADDSAPALAIKATME 47 >2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28 Length = 142 Score = 31.8 bits (72), Expect = 0.18 Identities = 11/77 (14%), Positives = 24/77 (31%), Gaps = 6/77 (7%) Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTE 61 V ++ +L L ++S + +E IK + + LT+ Sbjct: 40 FLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTD 99 Query: 62 QGSKLHRVTSEVYHKLE 78 + + S K+ Sbjct: 100 KSETIRPELSNASDKVA 116 >3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, structural genomics; 2.38A {Bacillus cereus atcc 10987} Length = 139 Score = 31.1 bits (70), Expect = 0.33 Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 6/77 (7%) Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTE 61 V V+A+SG + + E + S+++ I ++ + + + + LT+ Sbjct: 36 FGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTK 95 Query: 62 QGSKLHRVTSEVYHKLE 78 +G + + Y Sbjct: 96 KGEETKKQVDVQYSDFL 112 >2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, PSI, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 Length = 146 Score = 30.4 bits (68), Expect = 0.45 Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 4/59 (6%) Query: 24 AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTEQGSKLHRVTSEVYHKLE 78 A+ + + +++R + GLE++ ++ R A+ + LT + L + + Sbjct: 59 AQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVR 117 >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 = 29.5 bits (66), Expect = 0.85 Identities = 22/187 (11%), Positives = 46/187 (24%), Gaps = 81/187 (43%) Query: 166 HAYAAPHYLKNCREPLSIQELDKH-----------------------NLITFGDLIPKCM 202 + P + + L+ +++ + NL+ G P+ + Sbjct: 330 NNEGVPSPMLSISN-LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGP--PQSL 386 Query: 203 EDFN-WLATVDRPIGE-----------PRISCLQVNSYLSIMQYCVLGSGIALLP---DY 247 N L P G + S N +L + P Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFS----NRFLPVA-----------SPFHSHL 431 Query: 248 IVKDNPNLVRIMEDVITPSFTVYFCYPEALK------NTGKLKAFRNF-----------I 290 +V + I +D++ + + F + ++ G R I Sbjct: 432 LVPASD---LINKDLVKNNVS--FN-AKDIQIPVYDTFDG--SDLRVLSGSISERIVDCI 483 Query: 291 FLKARDW 297 W Sbjct: 484 IRLPVKW 490 >2vh2_A FTSQ, cell division protein FTSQ; potra, cell cycle; 3.4A {Yersinia enterocolitica} Length = 255 Score = 29.4 bits (65), Expect = 1.00 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%) Query: 99 TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYAD-CAIRLR 147 ++LG++ G L+ F+ LYP +Q Q +D + Y AI Sbjct: 177 VRLELGRDDRMGRLQRFIELYPMLQQQPDKRVSYVD--LRYETGAAIGWA 224 >3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structural genomics, protein structure initiative; HET: GOL; 2.00A {Rhodococcus jostii RHA1} Length = 150 Score = 28.4 bits (63), Expect = 2.0 Identities = 12/77 (15%), Positives = 21/77 (27%), Gaps = 7/77 (9%) Query: 9 RVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKL----FYRHARGLTLTE 61 V + + A + L S I + LE + R + + TE Sbjct: 43 SVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATE 102 Query: 62 QGSKLHRVTSEVYHKLE 78 +G +L Sbjct: 103 EGRRLRDDAKARVDAAH 119 >1fjm_A Protein serine/threonine phosphatase-1 (alpha isoform, type 1); hydrolase, complex (hydrolase/toxin) complex; HET: ADD; 2.10A {Oryctolagus cuniculus} SCOP: d.159.1.3 Length = 330 Score = 28.1 bits (62), Expect = 2.2 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 9/67 (13%) Query: 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFG--DLIPKCMEDFNWLATVD--- 212 R+LVT+ ++AP+Y ++ +D+ + +F K + + ++ Sbjct: 261 RQLVTL----FSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGG 316 Query: 213 RPIGEPR 219 RPI PR Sbjct: 317 RPITPPR 323 >1z91_A Organic hydroperoxide resistance transcriptional regulator; OHRR, MARR family, bacterial transcription factor, DNA binding protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A* Length = 147 Score = 27.3 bits (60), Expect = 4.0 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 4/59 (6%) Query: 24 AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTEQGSKLHRVTSEVYHKLE 78 EQL+L +++ + +E + I + ++LTE G+ L ++ + Sbjct: 61 GEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTIL 119 >2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima} Length = 112 Score = 27.3 bits (60), Expect = 4.8 Identities = 10/73 (13%), Positives = 29/73 (39%), Gaps = 3/73 (4%) Query: 44 EVGIKL-FYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLR-IATTI 101 E+G R R +TL + + + ++E ++ ++ V ++ + + Sbjct: 7 ELGETFRKKREERRITLLDASLFTN-INPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFL 65 Query: 102 DLGQNLLQGNLKE 114 +L + + +E Sbjct: 66 ELSPDEMLKLYEE 78 >3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: FDA; 2.10A {Mycobacterium thermoresistibile} Length = 393 Score = 27.1 bits (60), Expect = 4.9 Identities = 8/41 (19%), Positives = 17/41 (41%) Query: 133 IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHY 173 +D ++ Y + +P+ + +Q L + M AA Sbjct: 271 LDAAIAYTKERKQFGRPVSDNQGVQFMLADMAMKIEAARLM 311 >1z05_A Transcriptional regulator, ROK family; structural genomics, PSI, protein structure initiative; 2.00A {Vibrio cholerae o1 biovar eltor str} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 Length = 429 Score = 27.2 bits (59), Expect = 5.4 Identities = 7/38 (18%), Positives = 19/38 (50%), Gaps = 2/38 (5%) Query: 9 RVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETE 44 RV+ ++ + G + +++ L+ +SI++ L Sbjct: 43 RVYKLIDQKGPISRIDLSKESELAPASITKITRELIDA 80 >1qgc_4 Protein (inmunoglobuline); virus-antibody complex, icosahedral virus, virus/immune system complex; 30.00A {Mus musculus} SCOP: i.6.1.1 Length = 438 Score = 26.9 bits (59), Expect = 6.3 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 15/56 (26%) Query: 57 LTLT-EQGSKLHRVTSEVYHKLETT-----------QIELQES---SVKPSGKLRI 97 LTLT ++ + + T E HK T+ ++ L ES VKP G L++ Sbjct: 183 LTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECEVMLVESGGGLVKPGGSLKL 238 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 0.323 0.138 0.410 Gapped Lambda K H 0.267 0.0642 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,556,784 Number of extensions: 114819 Number of successful extensions: 354 Number of sequences better than 10.0: 1 Number of HSP's gapped: 322 Number of HSP's successfully gapped: 54 Length of query: 299 Length of database: 5,693,230 Length adjustment: 92 Effective length of query: 207 Effective length of database: 3,462,782 Effective search space: 716795874 Effective search space used: 716795874 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 56 (25.5 bits)