RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780351|ref|YP_003064764.1| MarR family transcriptional regulator [Candidatus Liberibacter asiaticus str. psy62] (171 letters) >gnl|CDD|128641 smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein. Length = 101 Score = 55.7 bits (135), Expect = 6e-09 Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 4/89 (4%) Query: 54 DVNAVQALLLFNIGDLE-LTAGELRSRGYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSI 112 + Q L+L + + L+ EL R S V+ L +L G I+ S D+RS+ Sbjct: 7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSV 66 Query: 113 RISLTQSGKEIAETISQLYQRHIESIDKV 141 +SLT+ G+E+ I +L + E++ ++ Sbjct: 67 LVSLTEEGREL---IEELLEARHETLAEL 92 >gnl|CDD|184319 PRK13777, PRK13777, transcriptional regulator Hpr; Provisional. Length = 185 Score = 29.6 bits (67), Expect = 0.45 Identities = 12/32 (37%), Positives = 20/32 (62%) Query: 92 KKLIDLGFIKHQRSRIDKRSIRISLTQSGKEI 123 KKL + G++ + DKR+ I LT+ G+E+ Sbjct: 81 KKLEERGYLTFSKKEDDKRNTYIELTEKGEEL 112 >gnl|CDD|168293 PRK05910, PRK05910, type III secretion system protein; Validated. Length = 584 Score = 28.6 bits (64), Expect = 0.76 Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 23/99 (23%) Query: 96 DLGFIKHQRSRIDKRSIRISLTQSGKEIA------------------ETISQLY-QRHIE 136 +LG + + + L SG+E+ E IS+ + +R +E Sbjct: 347 ELGVVFPEEIVVRHVESSPRLIFSGQEVYLRELSCPAILPSLRNLAPEAISERFVKRLVE 406 Query: 137 SIDKVGGLSVDDF----IAMNKLLQRLNRFWGDQIAYRL 171 +V G+S+++ I+ N L+ L ++++ L Sbjct: 407 EFQEVAGISIEEIIPKKISENSLVFLLRALVRERVSLHL 445 >gnl|CDD|130944 TIGR01889, Staph_reg_Sar, staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047. Length = 109 Score = 28.4 bits (64), Expect = 0.94 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%) Query: 85 SNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLT-QSGKEIAETISQLYQR 133 S + +KKL G++ +RS D+R + IS+ + +I IS++ Q Sbjct: 58 SALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEIEQI 107 >gnl|CDD|183170 PRK11512, PRK11512, DNA-binding transcriptional repressor MarR; Provisional. Length = 144 Score = 28.3 bits (63), Expect = 1.0 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 1/69 (1%) Query: 91 LKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQRHIESIDKVGGLSVDDFI 150 L +L+ G+++ + DKR + + LT SG I E QL + + + L+ D+ Sbjct: 75 LDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDLHQ-ELTKNLTADEVA 133 Query: 151 AMNKLLQRL 159 + LL+++ Sbjct: 134 TLEHLLKKV 142 >gnl|CDD|132396 TIGR03353, VI_chp_4, type VI secretion protein, VC_A0114 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. Length = 439 Score = 28.4 bits (64), Expect = 1.1 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 8/52 (15%) Query: 116 LTQSGKEIAETI----SQLYQRHIESIDKVGGLSVDDFIAMNKLLQRLNRFW 163 L Q +E+ + L R ES + G + DF+ LLQ LNR+ Sbjct: 194 LGQRLRELLGLLRARAEALAGRRRESDQQAGSADIADFL----LLQLLNRYE 241 >gnl|CDD|179596 PRK03573, PRK03573, transcriptional regulator SlyA; Provisional. Length = 144 Score = 27.3 bits (61), Expect = 2.3 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 10/75 (13%) Query: 91 LKKLIDLGFIKHQRSRIDKRSIRISLTQSG----KEIAETISQLYQRHIESIDKVGGLSV 146 L +L + G I Q D+R+ RI LT+ E+ I++ + + G+S Sbjct: 67 LDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVINK------TRAEILHGISA 120 Query: 147 DDFIAMNKLLQRLNR 161 ++ + L+ +L + Sbjct: 121 EEIEQLITLIAKLEK 135 >gnl|CDD|179411 PRK02304, PRK02304, adenine phosphoribosyltransferase; Provisional. Length = 175 Score = 26.6 bits (60), Expect = 3.2 Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 39/102 (38%) Query: 78 SRGYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQR---- 133 +RG+ G+ ++Y L +GF+ + K GK ETIS+ Y+ Sbjct: 60 ARGFIFGAALAYKL----GIGFVP-----VRKP---------GKLPRETISESYELEYGT 101 Query: 134 -----HIESI---DKVGGLSVDDFIA----MN---KLLQRLN 160 H ++I D+V L VDD +A + KLL+RL Sbjct: 102 DTLEIHKDAIKPGDRV--LIVDDLLATGGTLEAAIKLLERLG 141 >gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR; Provisional. Length = 441 Score = 26.5 bits (58), Expect = 3.4 Identities = 13/30 (43%), Positives = 17/30 (56%) Query: 139 DKVGGLSVDDFIAMNKLLQRLNRFWGDQIA 168 D + L VDD I+ +LQ L R WG +A Sbjct: 4 DNIDILVVDDDISHCTILQALLRGWGYNVA 33 >gnl|CDD|129416 TIGR00316, cdhC, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex, beta subunit. Nomenclature follows the description for Methanosarcina thermophila. The CO-methylating acetyl-CoA synthase is considered the defining enzyme of the Wood-Ljungdahl pathway, used for acetate catabolism by sulfate reducing bacteria but for acetate biosynthesis by acetogenic bacteria such as oorella thermoacetica (f. Clostridium thermoaceticum). Length = 458 Score = 26.4 bits (58), Expect = 3.5 Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 17/90 (18%) Query: 84 GSNVSYNLKKLID------LGFIK-----HQRS----RIDKRSIRISLTQSGKEIAETIS 128 GSN+ +L+ +I+ L +I+ +QR RI+K + L K I + + Sbjct: 75 GSNLEEDLEGVIERRIHEFLNYIEGVMHLNQRDQIWIRINKNAFNKGLRL--KHIGKAVM 132 Query: 129 QLYQRHIESIDKVGGLSVDDFIAMNKLLQR 158 L++ I+K+ + D + + L++ Sbjct: 133 MLFKEEFPFIEKIEVTIITDPDKVKEELEK 162 >gnl|CDD|162809 TIGR02337, HpaR, homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate. Length = 118 Score = 26.6 bits (59), Expect = 3.9 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 7/80 (8%) Query: 62 LLFNIGDLELTAGELRSRGYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGK 121 +L G +E T +L ++ L +++ L +L G + ++ D+R + ISLT G+ Sbjct: 36 ILAEQGSMEFT--QLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQ 93 Query: 122 ----EIAETISQLYQRHIES 137 ++ I ++Y IE Sbjct: 94 ALYASLSPQIEEIYAA-IEE 112 >gnl|CDD|130205 TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase (isomerizing). The member from Methanococcus jannaschii contains an intein. Length = 607 Score = 26.1 bits (58), Expect = 4.6 Identities = 10/27 (37%), Positives = 20/27 (74%), Gaps = 1/27 (3%) Query: 104 RSRIDKRSIRISLTQSGKEIAETISQL 130 + +DK ++ I+++QSG E A+T++ L Sbjct: 333 KPVVDKDTLVIAISQSG-ETADTLAAL 358 >gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional. Length = 557 Score = 26.1 bits (57), Expect = 4.7 Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%) Query: 113 RISLTQSGKEIAETISQ-LYQRHIESIDKVGGLSVDDFIAMNKLL 156 R++L K+ + I Q LY RHI S++ + L D++ ++ L+ Sbjct: 68 RVNLQMFDKDAVKNIVQYLYNRHISSMNVIDVLKCADYLLIDDLV 112 >gnl|CDD|128695 smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor. Length = 66 Score = 26.0 bits (58), Expect = 5.0 Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 11/64 (17%) Query: 70 ELTAGELRSRGYYLG---SNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAET 126 EL EL LG S VS++LKKL + G ++ SR + + + SLT +++A+ Sbjct: 10 ELCVCEL---AEILGLSQSTVSHHLKKLREAGLVE---SRREGKRVYYSLT--DEKVADL 61 Query: 127 ISQL 130 + +L Sbjct: 62 LEEL 65 >gnl|CDD|172813 PRK14337, PRK14337, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional. Length = 446 Score = 25.8 bits (57), Expect = 5.6 Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 2/39 (5%) Query: 30 RLVER--LHRSLLDVTRDEFERQGRSDVNAVQALLLFNI 66 RL E L SLLD + ER+ V A NI Sbjct: 116 RLAEEPDLRLSLLDFSEHYPEREALWGNGTVPASAFVNI 154 >gnl|CDD|185441 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional. Length = 452 Score = 25.7 bits (57), Expect = 6.6 Identities = 8/27 (29%), Positives = 15/27 (55%) Query: 113 RISLTQSGKEIAETISQLYQRHIESID 139 SL ++ E+ E I + +R IE ++ Sbjct: 12 NQSLKEADPELYELIEKEKERQIEGLE 38 >gnl|CDD|184692 PRK14466, PRK14466, ribosomal RNA large subunit methyltransferase N; Provisional. Length = 345 Score = 25.5 bits (56), Expect = 7.0 Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 3/28 (10%) Query: 119 SGKEIAETISQLYQRHIESIDKVGGLSV 146 + K+IA S LY + + SID++ +S+ Sbjct: 28 AAKQIA---SWLYDKKVTSIDEMTNISL 52 >gnl|CDD|182353 PRK10280, PRK10280, dipeptidyl carboxypeptidase II; Provisional. Length = 681 Score = 25.6 bits (56), Expect = 7.1 Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%) Query: 122 EIAETISQLYQRHIESIDKVGGLSVDD 148 E A SQ QR + + +K GGL V+D Sbjct: 164 EAATLTSQFNQRLLAA-NKSGGLVVND 189 >gnl|CDD|162025 TIGR00759, aceE, pyruvate dehydrogenase E1 component, homodimeric type. WARNING: This family is classified as subfamily rather than equivalog because it includes a counterexample from Pseudomonas putida, MdeB, that is active as an E1 component of an alpha-ketoglutarate dehydrogenase complex rather than a pyruvate dehydrogase complex. The second pyruvate dehydrogenase complex E1 protein from Alcaligenes eutrophus, PdhE, complements an aceE mutant of E. coli but is not part of a pyruvate dehydrogenase complex operon, is more similar to the Pseudomonas putida MdeB than to E. coli AceE, and may have also have a different primary specificity. Length = 885 Score = 25.5 bits (56), Expect = 7.9 Identities = 10/19 (52%), Positives = 13/19 (68%) Query: 66 IGDLELTAGELRSRGYYLG 84 IGDL A + R+RG+ LG Sbjct: 604 IGDLCWAAADQRARGFLLG 622 >gnl|CDD|130874 TIGR01815, TrpE-clade3, anthranilate synthase, alpha proteobacterial clade. This model represents a small clade of anthranilate synthases from alpha proteobacteria and Nostoc (a cyanobacterium). This enzyme is the first step in the pathway for the biosynthesis of tryprophan from chorismate. Length = 717 Score = 25.2 bits (55), Expect = 8.0 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 2/51 (3%) Query: 106 RIDKRSIRISLTQSGKEIAETISQLYQRHIESIDKVGGLSVDDFIAMNKLL 156 R DK R+ S K I +LY R I ++D V G A++ L Sbjct: 355 RNDKS--RVCEPGSVKVIGRRQIELYSRLIHTVDHVEGRLRSGMDALDAFL 403 >gnl|CDD|185053 PRK15098, PRK15098, beta-D-glucoside glucohydrolase; Provisional. Length = 765 Score = 25.4 bits (56), Expect = 8.1 Identities = 14/51 (27%), Positives = 23/51 (45%) Query: 81 YYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLY 131 Y G +SY + D+ R K + +++T +GK T+ QLY Sbjct: 640 YPFGYGLSYTTFTVSDVKLSSPTMKRDGKVTASVTVTNTGKREGATVVQLY 690 >gnl|CDD|181860 PRK09440, avtA, valine--pyruvate transaminase; Provisional. Length = 416 Score = 25.2 bits (56), Expect = 8.7 Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 7/30 (23%) Query: 111 SIRISLTQSGKEI-------AETISQLYQR 133 IR++ Q +EI AE + + Y Sbjct: 386 CIRMNYVQDDEEIEKGIAILAEEVEKAYAE 415 >gnl|CDD|180548 PRK06380, PRK06380, metal-dependent hydrolase; Provisional. Length = 418 Score = 25.2 bits (55), Expect = 8.9 Identities = 8/34 (23%), Positives = 23/34 (67%) Query: 112 IRISLTQSGKEIAETISQLYQRHIESIDKVGGLS 145 + + L+++ KE+ + + + +R +E ++K+G L+ Sbjct: 202 MHMHLSETRKEVYDHVKRTGERPVEHLEKIGFLN 235 >gnl|CDD|147844 pfam05913, DUF871, Bacterial protein of unknown function (DUF871). This family consists of several conserved hypothetical proteins from bacteria and archaea. The function of this family is unknown. Length = 357 Score = 25.2 bits (56), Expect = 9.3 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 13/77 (16%) Query: 95 IDLGFIKHQRSRIDKRSIRISL---TQSGKEIAETISQLYQRHIESID--------KVGG 143 +D GF + + + K ++I L T + + + +S Y + E+++ G Sbjct: 94 LDYGFTGEEIAELSKNPLKIELNASTITTEYLDNLLS--YGANFENLEACHNFYPRPYTG 151 Query: 144 LSVDDFIAMNKLLQRLN 160 LS + F+ N+ ++ Sbjct: 152 LSYEFFLEKNRWFKKYG 168 >gnl|CDD|128802 smart00529, HTH_DTXR, Helix-turn-helix diphteria tox regulatory element. iron dependent repressor. Length = 96 Score = 25.3 bits (56), Expect = 9.4 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 9/51 (17%) Query: 84 GSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQRH 134 V+ LKKL G ++++ R I+LT+ G+ +A +L ++H Sbjct: 13 PPTVTQMLKKLEKDGLVEYEPYR------GITLTEKGRRLAR---RLLRKH 54 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.321 0.138 0.382 Gapped Lambda K H 0.267 0.0836 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,716,834 Number of extensions: 166626 Number of successful extensions: 391 Number of sequences better than 10.0: 1 Number of HSP's gapped: 390 Number of HSP's successfully gapped: 39 Length of query: 171 Length of database: 5,994,473 Length adjustment: 87 Effective length of query: 84 Effective length of database: 4,114,577 Effective search space: 345624468 Effective search space used: 345624468 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: 54 (24.4 bits)