| Literature References | 1. HENIKOFF, S., WALLACE, J.C. AND BROWN, J.P.
Finding protein similarities with nucleotide sequence databases.
METHODS ENZYMOL. 183 111-132 (1990).
2. STOUT, V., TORRES-CABASSA, A., MAURIZI, M.R., GUTNICK, D. AND
GOTTESMAN, S.
Rcsa, an unstable positive regulator of capsular polysaccharide synthesis.
J.BACTERIOL. 173(5) 1738-1747 (1991).
3. KAHN, D. AND DITTA, G.
Modular structure of fixJ - Homology of the transcriptional activator
domain with the -35 binding domain of sigma factors.
MOL.MICROBIOL. 5(4) 987-997 (1991).
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| Documentation | Numerous bacterial transcription regulatory proteins bind DNA via a
helix-turn-helix (HTH) motif. These proteins are very diverse, but for
convenience may be grouped into subfamilies on the basis of sequence
similarity. One such family groups together a range of proteins, including
bvgA, comA, degU, fimZ, fixJ, gerE, lasR, luxR, malT, narL, nodW, rcsA,
sdiA and uhpA [1-3]. Although the sequences belonging to this family differ
somewhat in length, in each case the HTH motif is situated towards the
C-terminus.
HTHLUXR is a 3-element fingerprint that provides a signature for the HTH
motif of the luxR bacterial regulatory proteins. The fingerprint was
derived from an initial alignment of 9 sequences: the motifs completely
encompass the HTH motif, extending a few residues beyond both its N- and C-
termini (cf. PROSITE pattern HTH_LUXR_FAMILY (PS00622)). Three iterations
on OWL21.1 were required to reach convergence, at which point a true set
comprising 46 sequences was identified. Six partial matches were also
found, some of which are simply fragments, while others lack significant
matches with motif 3.
An update on SPTR37_9f identified a true set of 136 sequences, and 35
partial matches.
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| Sequence Titles | BGLJ_ECOLI BGLJ PROTEIN - ESCHERICHIA COLI.
BVGA_BORPE VIRULENCE FACTORS PUTATIVE POSITIVE TRANSCRIPTION REGULATOR BVGA - BORDETELLA PERTUSSIS, BORDETELLA BRONCHISEPTICA, AND BORDETELLA PARAPERTUSSIS.
CARR_ERWCA CARR REGULATORY PROTEIN - ERWINIA CAROTOVORA.
CSGD_ECOLI PROBABLE CSGAB OPERON TRANSCRIPTIONAL REGULATORY PROTEIN - ESCHERICHIA COLI.
CSGD_SALTY PROBABLE CSGAB OPERON TRANSCRIPTIONAL REGULATORY PROTEIN - SALMONELLA TYPHIMURIUM.
DCTR_RHOCA C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTR - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
DEGU_BACBR TRANSCRIPTIONAL REGULATORY PROTEIN DEGU - BACILLUS BREVIS.
DEGU_BACSU TRANSCRIPTIONAL REGULATORY PROTEIN DEGU (PROTEASE PRODUCTION ENHANCER PROTEIN) - BACILLUS SUBTILIS.
ECHR_ERWCH ECHR REGULATORY PROTEIN - ERWINIA CHRYSANTHEMI.
ECNR_CITFR TRANSCRIPTIONAL REGULATORY PROTEIN ENTR (ENTERICIDIN R) - CITROBACTER FREUNDII.
ESAR_ERWST ESAR REGULATORY PROTEIN - ERWINIA STEWARTII.
EVGA_ECOLI PUTATIVE POSITIVE TRANSCRIPTION REGULATOR EVGA - ESCHERICHIA COLI.
EXPR_ERWCA EXPR REGULATORY PROTEIN - ERWINIA CAROTOVORA.
EXPR_ERWCH EXPR REGULATORY PROTEIN - ERWINIA CHRYSANTHEMI.
FIMZ_ECOLI FIMBRIAE Z PROTEIN - ESCHERICHIA COLI.
FIMZ_SALTY FIMBRIAE Z PROTEIN - SALMONELLA TYPHIMURIUM.
FIXJ_AZOCA TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ - AZORHIZOBIUM CAULINODANS.
FIXJ_BRAJA TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ - BRADYRHIZOBIUM JAPONICUM.
FIXJ_RHIME TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ - RHIZOBIUM MELILOTI.
GACA_PSEAE RESPONSE REGULATOR GACA (GLOBAL ACTIVATOR) - PSEUDOMONAS AERUGINOSA.
GACA_PSEFL RESPONSE REGULATOR GACA (GLOBAL ACTIVATOR) (GLOBAL ANTIBIOTIC AND CYANIDE CONTROL PROTEIN) - PSEUDOMONAS FLUORESCENS.
GACA_PSESY RESPONSE REGULATOR GACA (GLOBAL ACTIVATOR) - PSEUDOMONAS SYRINGAE (PV. SYRINGAE).
GACA_PSEVI RESPONSE REGULATOR GACA (GLOBAL ACTIVATOR) - PSEUDOMONAS VIRIDIFLAVA.
GERE_BACSU GERMINATION PROTEIN GERE - BACILLUS SUBTILIS.
LUXR_VIBFI LUXR REGULATORY PROTEIN - VIBRIO FISCHERI.
LUXS_VIBFI LUXR REGULATORY PROTEIN - VIBRIO FISCHERI.
MALT_ECOLI MALT REGULATORY PROTEIN - ESCHERICHIA COLI.
MOAR_KLEAE MONOAMINE REGULON TRANSCRIPTIONAL REGULATOR - KLEBSIELLA AEROGENES.
MOXX_PARDE METHANOL UTILIZATION CONTROL REGULATORY PROTEIN MOXX - PARACOCCUS DENITRIFICANS.
NARL_ECOLI NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL - ESCHERICHIA COLI.
NARP_ECOLI NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARP - ESCHERICHIA COLI.
NARP_HAEIN NITRATE/NITRITE RESPONSE REGULATOR PROTEIN HOMOLOG - HAEMOPHILUS INFLUENZAE.
NODW_BRAJA NODULATION PROTEIN W - BRADYRHIZOBIUM JAPONICUM.
O05202 RESPONSE REGULATOR BPDT - RHODOCOCCUS SP.
O05210 FLCA - AZOSPIRILLUM BRASILENSE.
O07019 HYPOTHETICAL 22.3 KD PROTEIN - BACILLUS SUBTILIS.
O07528 HYPOTHETICAL 24.0 KD PROTEIN - BACILLUS SUBTILIS.
O07832 RESPONSE REGULATOR - PSEUDOMONAS PUTIDA.
O30346 LUXR HOMOLOG - ERWINIA CAROTOVORA SUBSP. BETAVASCULORUM.
O30483 PUTATIVE REGULATORY PROTEIN - STREPTOMYCES HYGROSCOPICUS.
O30760 AUTOINDUCER SYTHESIS REGULATOR - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
O30919 SOLR - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
O30989 RESPONSE REGULATORY PROTEIN - PSEUDOMONAS FLUORESCENS.
O32197 YVQC PROTEIN - BACILLUS SUBTILIS.
O33269 HYPOTHETICAL 87.8 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O33493 STYRENE RESPONSE REGULATOR - PSEUDOMONAS SP.
O34723 SENSOR REGULATOR - BACILLUS SUBTILIS.
O50213 TRANSCRIPTIONAL ACTIVATOR - PSEUDOMONAS SP.
O50326 EXPA PROTEIN - ERWINIA CAROTOVORA.
O51932 CARR - SERRATIA MARCESCENS.
O52160 PUTATIVE DNA-BINDING PROTEIN SALA - PSEUDOMONAS SYRINGAE.
O52592 TRANSCRIPTIONAL ACTIVATOR CARR - ERWINIA CAROTOVORA SUBSP. CAROTOVORA.
O53213 HYPOTHETICAL 120.8 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O53720 TRANSCRIPTIONAL REGULATORY PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O53856 PUTATIVE RESPONSE REGULATOR - MYCOBACTERIUM TUBERCULOSIS.
O54014 FLHR PROTEIN - PARACOCCUS DENITRIFICANS.
O54039 NITRATE/NITRITE REGULATORY PROTEIN - PSEUDOMONAS AERUGINOSA.
O54241 ORF13 - SINORHIZOBIUM MELILOTI.
O54305 SSRB - SALMONELLA TYPHIMURIUM.
O66040 SDIA - SALMONELLA TYPHIMURIUM.
O68318 RESPONSE REGULATOR - VIBRIO CHOLERAE.
O69157 RESPONSE REGULATOR - PSEUDOMONAS FLUORESCENS.
O69816 TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O69859 TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O69961 PUTATIVE TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O70001 PUTATIVE TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O85372 CPRR - RHODOCOCCUS SP.
O85662 RCSB - PROTEUS MIRABILIS.
O85822 RESPONSE REGULATOR YSPR - YERSINIA PSEUDOTUBERCULOSIS.
O86603 TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O86632 PUTATIVE TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O87395 TWO-COMPONENT RESPONSE REGULATOR ORRA - ANABAENA SP. (STRAIN PCC 7120).
O87823 PRHJ - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
O87940 TDIR - THAUERA AROMATICA.
O88023 PUTATIVE TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O88121 WHIK PROTEIN - STREPTOMYCES COELICOLOR.
P72402 REDZ GENE (TRANSCRIPTIONAL REGULATOR REDZ) - STREPTOMYCES COELICOLOR.
P72471 RESPONSE REGULATOR HOMOLOG - STREPTOMYCES LIVIDANS.
P73104 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P73686 NITRATE/NITRITE RESPONSE REGULATOR PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P73864 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P74298 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P74670 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P74946 VANR - VIBRIO ANGUILLARUM.
P77080 FIMBRIAE Z PROTEIN - ESCHERICHIA COLI.
P94354 HOMOLOGOUS TO MANY TRANSCRIPTIONAL ACTIVATOR PROTEINS - BACILLUS SUBTILIS.
P94439 YFIK - BACILLUS SUBTILIS.
P95193 HYPOTHETICAL 23.3 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
P95321 DNA-BINDING PROTEIN - MYXOCOCCUS XANTHUS.
P95652 PUTATIVE RESPONSE REGULATOR - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
P96058 SIRA - SALMONELLA TYPHIMURIUM.
P96140 TUTB - THAUERA SP. T1.
P96320 RCSB GENE - ERWINIA AMYLOVORA.
P96686 PROBABLE REGULATORY COMPONENT OF SENSORY TRANSDUCTION SYSTEM - BACILLUS SUBTILIS.
Q02882 HYPOTHETICAL 21.3 KD PROTEIN IN AADA 3'REGION - SALMONELLA CHOLERAE-SUIS (SALMONELLA ENTERICA).
Q07640 TRANSCRIPTIONAL REGULATOR - STREPTOMYCES GRISEUS.
Q11028 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN CY02B10.22 - MYCOBACTERIUM TUBERCULOSIS.
Q44059 DNA FOR AHYI, AHYR, YGGA AND CPDB GENES - AEROMONAS HYDROPHILA, AND AEROMONAS SALMONICIDA.
Q45272 NWSB - BRADYRHIZOBIUM JAPONICUM.
Q45415 VSRC - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
Q45416 VSRD - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
Q46656 MOAR-TRANSCRIPTIONAL POSITIVE REGULATOR - ENTEROBACTER AEROGENES (AEROBACTER AEROGENES).
Q46661 POSITIVE ACTIVATOR OF EXTRACELLULAR POLYSACCHARIDE (AMYLOVORIN) BIOSYNTHESIS (RCSA) - ERWINIA AMYLOVORA.
Q47585 TRANSCRIPTIONAL ACTIVATOR - ESCHERICHIA COLI.
Q48411 ACOK - KLEBSIELLA PNEUMONIAE.
Q52404 RESPONSE REGULATOR PROTEIN CORR - PSEUDOMONAS SYRINGAE.
Q52788 FIXJ - RHIZOBIUM LEGUMINOSARUM.
Q53820 POTENTIAL RESPONSE REGULATOR FOR AERIAL MYCELIUM PRODUCTION - STREPTOMYCES COELICOLOR.
Q54821 REGULATORY PROTEIN - STREPTOMYCES PEUCETIUS.
Q55102 CHO-ORF3 - STREPTOMYCES SP.
Q55104 CHO-ORF1 - STREPTOMYCES SP.
Q55540 TRANSCRIPTIONAL REGULATORY PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q55919 NITRATE/NITRITE RESPONSE REGULATOR PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q55952 PROTEIN KINASE - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
RCSA_ECOLI COLANIC ACID CAPSULAR BIOSYNTHESIS ACTIVATION PROTEIN A - ESCHERICHIA COLI.
RCSA_ERWAM COLANIC ACID CAPSULAR BIOSYNTHESIS ACTIVATION PROTEIN A - ERWINIA AMYLOVORA.
RCSA_ERWST COLANIC ACID CAPSULAR BIOSYNTHESIS ACTIVATION PROTEIN A - ERWINIA STEWARTII.
RCSA_KLEAE COLANIC ACID CAPSULAR BIOSYNTHESIS ACTIVATION PROTEIN A - KLEBSIELLA AEROGENES.
RCSA_SALTI COLANIC ACID CAPSULAR BIOSYNTHESIS ACTIVATION PROTEIN A - SALMONELLA TYPHI.
RCSB_ECOLI CAPSULAR SYNTHESIS REGULATOR COMPONENT B - ESCHERICHIA COLI.
RCSB_SALTI CAPSULAR SYNTHESIS REGULATOR COMPONENT B - SALMONELLA TYPHI.
RHIR_RHILV RHIR REGULATORY PROTEIN - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
RHLR_PSEAE RHLR REGULATORY PROTEIN (ELASTASE MODULATOR) - PSEUDOMONAS AERUGINOSA.
SDIA_ECOLI SDIA REGULATORY PROTEIN - ESCHERICHIA COLI.
SGAR_HYPME PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN SGAR - HYPHOMICROBIUM METHYLOVORUM.
UHPA_ECOLI TRANSCRIPTIONAL REGULATORY PROTEIN UHPA - ESCHERICHIA COLI.
UHPA_SALTY TRANSCRIPTIONAL REGULATORY PROTEIN UHPA - SALMONELLA TYPHIMURIUM.
UVRY_ECOLI UVRY PROTEIN - ESCHERICHIA COLI.
Y4QH_RHISN HYPOTHETICAL TRANSCRIPTIONAL REGULATOR Y4QH - RHIZOBIUM SP. (STRAIN NGR234).
YENR_YEREN YENR REGULATORY PROTEIN - YERSINIA ENTEROCOLITICA.
YEXN_AERSA HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN EXEN 3'REGION (ORF2) - AEROMONAS SALMONICIDA.
YGEK_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN KDUI-LYSS INTERGENIC REGION - ESCHERICHIA COLI.
YHJB_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN TREF-KDGK INTERGENIC REGION - ESCHERICHIA COLI.
YKGK_ECOLI HYPOTHETICAL 23.3 KD PROTEIN IN INTF-EAEH INTERGENIC REGION - ESCHERICHIA COLI.
YXJL_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN GALE-PEPT INTERGENIC REGION - BACILLUS SUBTILIS.
YZ18_MYCTU PUTATIVE REGULATORY PROTEIN RV0890C - MYCOBACTERIUM TUBERCULOSIS.
AGMR_PSEAE GLYCEROL METABOLISM ACTIVATOR (AGMR PROTEIN) - PSEUDOMONAS AERUGINOSA.
ALKS_PSEOL REGULATORY PROTEIN ALKS - PSEUDOMONAS OLEOVORANS.
BRPA_STRHY BIALAPHOS BIOSYNTHETIC PATHWAY REGULATORY PROTEIN - STREPTOMYCES HYGROSCOPICUS.
CMA1_BACSU COMA OPERON PROTEIN 1 - BACILLUS SUBTILIS.
LASR_PSEAE LASR REGULATORY PROTEIN - PSEUDOMONAS AERUGINOSA.
O05478 LIPA TRANSCRIPTIONAL ACTIVATOR - STREPTOMYCES SP.
O30798 MXAB - METHYLOBACTERIUM EXTORQUENS.
O33515 HYPOTHETICAL PROTEIN - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O54240 ORF12 - SINORHIZOBIUM MELILOTI.
O54452 TRANSCRIPTIONAL ACTIVATOR HOMOLOG - RHIZOBIUM ETLI.
O69403 RCSV GENE - ERWINIA AMYLOVORA.
O86078 DMSO REDUCTASE REGULATORY PROTEIN DORX - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
P72557 PUTATIVE NARL HOMOLOG - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
P72781 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P73431 RNA POLYMERASE SIGMA-E FACTOR - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
PHZR_PSEAR TRANSCRIPTIONAL ACTIVATOR PHZR - PSEUDOMONAS AUREOFACIENS.
PHZR_PSEFL TRANSCRIPTIONAL ACTIVATOR PHZR - PSEUDOMONAS FLUORESCENS.
Q04825 HYPOTHETICAL 12.7 KD PROTEIN IN PEFI 3'REGION (ORF7) - SALMONELLA TYPHIMURIUM.
Q08859 FIMK PROTEIN - KLEBSIELLA PNEUMONIAE.
Q44232 PUTATIVE TRANSCRIPTION FACTOR - ANABAENA SP.
Q52466 EPSR - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
Q53894 ABSA2 - STREPTOMYCES COELICOLOR.
Q54307 REGULATOR OF CHOLESTEROL OXIDASE - STREPTOMYCES HYGROSCOPICUS.
Q55192 HYPOTHETICAL 20.8 KD PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
TRAR_RHISN PROBABLE TRANSCRIPTIONAL ACTIVATOR TRAR - RHIZOBIUM SP. (STRAIN NGR234).
YAHA_ECOLI HYPOTHETICAL 40.7 KD PROTEIN IN BETT-PRPR INTERGENIC REGION - ESCHERICHIA COLI.
YC29_CYAPA PROBABLE TRANSCRIPTIONAL REGULATOR YCF29 - CYANOPHORA PARADOXA.
YC29_PORPU PROBABLE TRANSCRIPTIONAL REGULATOR YCF29 - PORPHYRA PURPUREA.
YJJQ_ECOLI HYPOTHETICAL 27.0 KD PROTEIN IN DNAT-BGLJ INTERGENIC REGION (O241) - ESCHERICHIA COLI.
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