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PR00040

Identifier
HTHMERR  [View Relations]  [View Alignment]  
Accession
PR00040
No. of Motifs
3
Creation Date
17-SEP-1993  (UPDATE 27-JUN-1999)
Title
MerR bacterial regulatory protein HTH signature
Database References

PROSITE; PS00552 HTH_MERR_FAMILY
BLOCKS; BL00552
PFAM; PF00376 merR
INTERPRO; IPR000551
Literature References
1. HELMANN, J.D., WANG, Y., MAHLER, I. AND WALSH, C.T.
Homologous metalloregulatory proteins from both Gram-positive and Gram-
negative bacteria control transcription of mercury resistance operons.
J.BACTERIOL. 171(1) 222-229 (1989).
 
2. SADOWSKY, M.J., CREGAN, P.B., GOTTFERT, M., SHARMA, A., GERHOLD, D.,
RODRIGUEZ-QUINONES, F., KEYSER, H.H., HENNECKE, H. AND STACEY, G.
The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-
specific nodulation of soybeans.
PROC.NATL.ACAD.SCI.U.S.A. 88(2) 637-641 (1991).
 
3. WU, J. AND WEISS, B.
Two divergently transcribed genes, soxR and soxS, control a superoxide
response regulon of Escherichia coli.
J.BACTERIOL. 173(9) 2864-2871 (1991).

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
the mercuric resistance operon regulatory protein merR, Bradyrhizobium
nodulation protein nolA and E.coli soxR protein [1-3]. Within this family,
the HTH motif is situated towards the N-terminus.
 
HTHMERR is a 3-element fingerprint that provides a signature for the HTH
motif of the merR bacterial regulatory proteins. The fingerprint was
derived from an initial alignment of 5 sequences: the first 2 motifs
completely encompass the HTH motif (cf. PROSITE pattern HTH_MERR (PS00552)),
and the third encodes a conserved region immediately beyond its C-terminus.
Two iterations on OWL21.1 were required to reach convergence, at which
point a true set comprising 17 sequences was identified. A single partial
match was also found, namely regulatory protein glnR from Bacillus subtilis.
 
An update on SPTR37_9f identified a true set of 40 sequences, and 9
partial matches.
Summary Information
  40 codes involving  3 elements
9 codes involving 2 elements
Composite Feature Index
3404040
2288
123
True Positives
MERD_ACICA    MERD_ENTAG    MERD_PSEAE    MERD_SERMA    
MERD_SHIFL MERR_BACSR MERR_PSEAE MERR_SERMA
MERR_SHIFL MERR_STAAU NOLA_BRAJA NOLA_BRASN
O05606 O05612 O07300 O07304
O07935 O54316 O66018 O66022
O70107 O86214 P77071 Q44190
Q44191 Q46655 Q52395 Q53442
Q56281 Q56287 Q56448 Q57106
Q57492 Q60233 Q99092 Q99093
SOXR_ECOLI SOXR_PSEAE SOXR_SALTY TIPA_STRLI
True Positive Partials
Codes involving 2 elements
O07586 O53384 O54191 O66920
O86531 P95838 Q55938 YYAN_BACSU
ZNTR_ECOLI
Sequence Titles
MERD_ACICA  MERCURIC RESISTANCE PROTEIN MERD - ACINETOBACTER CALCOACETICUS. 
MERD_ENTAG MERCURIC RESISTANCE PROTEIN MERD - ENTEROBACTER AGGLOMERANS.
MERD_PSEAE MERCURIC RESISTANCE PROTEIN MERD - PSEUDOMONAS AERUGINOSA.
MERD_SERMA MERCURIC RESISTANCE PROTEIN MERD - SERRATIA MARCESCENS.
MERD_SHIFL MERCURIC RESISTANCE PROTEIN MERD - SHIGELLA FLEXNERI.
MERR_BACSR MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - BACILLUS SP. (STRAIN RC607).
MERR_PSEAE MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - PSEUDOMONAS AERUGINOSA, AND PSEUDOMONAS FLUORESCENS.
MERR_SERMA MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - SERRATIA MARCESCENS.
MERR_SHIFL MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - SHIGELLA FLEXNERI.
MERR_STAAU MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - STAPHYLOCOCCUS AUREUS.
NOLA_BRAJA NODULATION PROTEIN NOLA - BRADYRHIZOBIUM JAPONICUM.
NOLA_BRASN NODULATION PROTEIN NOLA - BRADYRHIZOBIUM SP. (STRAIN NC92).
O05606 REPRESSOR/INDUCER PROTEIN - PSEUDOMONAS SP.
O05612 TRANSPOSON TN5041 DNA - PSEUDOMONAS SP.
O07300 MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - PSEUDOMONAS SP.
O07304 MERT, MERR AND PARTIAL MERP GENES - PSEUDOMONAS SP.
O07935 DNA, MOSAIC MERCURY RESISTANCE TRANSPOSABLE ELEMENT (MER-OPERON), 3624 BP - ESCHERICHIA COLI, AND ENTEROBACTER CLOACAE.
O54316 REGULATORY PROTEIN MER R - THIOBACILLUS SP.
O66018 MERD - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
O66022 MERCURY OPERON COREGULATOR PROTEIN - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
O70107 REGULATORY PROTEIN - BACILLUS CEREUS.
O86214 REGULATORY PROTEIN - EXIGUOBACTERIUM SP.
P77071 MERR - ESCHERICHIA COLI, AND PSEUDOMONAS SP. K-62.
Q44190 REGULATORY PROTEIN - ALCALIGENES FAECALIS.
Q44191 REGULATORY PROTEIN - AGROBACTERIUM RADIOBACTER.
Q46655 REGULATORY PROTEIN - ENTEROBACTER AEROGENES (AEROBACTER AEROGENES).
Q52395 ORGANOMERCURIAL RESISTANCE REGULATORY PROTEIN - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
Q53442 SOXR - ESCHERICHIA COLI.
Q56281 MERR AND MERC GENES - THIOBACILLUS FERROOXIDANS.
Q56287 MERR AND MERC GENES - THIOBACILLUS FERROOXIDANS.
Q56448 MERCURIC RESISTANCE PROTEIN MERD - UNIDENTIFIED.
Q57106 REGULATORY PROTEIN - ACINETOBACTER CALCOACETICUS, ESCHERICHIA COLI, ALCALIGENES SP., ENTEROBACTER AGGLOMERANS, AND ENTEROBACTER CLOACAE.
Q57492 REGULATORY PROTEIN - ENTEROBACTER CLOACAE, AND KLEBSIELLA OXYTOCA.
Q60233 MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - ALCALIGENES SP., PSEUDOMONAS FLUORESCENS, COMAMONAS TESTOSTERONI (PSEUDOMONAS TESTOSTERONI), AND UNIDENTIFIED.
Q99092 MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - ACINETOBACTER SP.
Q99093 MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - ACINETOBACTER CALCOACETICUS.
SOXR_ECOLI SOXR PROTEIN - ESCHERICHIA COLI.
SOXR_PSEAE SOXR PROTEIN - PSEUDOMONAS AERUGINOSA.
SOXR_SALTY SOXR PROTEIN - SALMONELLA TYPHIMURIUM.
TIPA_STRLI TRANSCRIPTIONAL ACTIVATOR TIPA - STREPTOMYCES LIVIDANS.

O07586 HYPOTHETICAL 16.4 KD PROTEIN - BACILLUS SUBTILIS.
O53384 REGULATORY PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O54191 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O66920 TRANSCRIPTIONAL REGULATOR (MERR FAMILY) - AQUIFEX AEOLICUS.
O86531 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
P95838 MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
Q55938 MERCURIC RESISTANCE OPERON REGULATORY PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
YYAN_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN TETL-EXOA INTERGENIC REGION - BACILLUS SUBTILIS.
ZNTR_ECOLI ZN(II)-RESPONSIVE REGULATOR OF ZNTA - ESCHERICHIA COLI.
Scan History
OWL21_1    2  125  NSINGLE    
OWL25_2 1 100 NSINGLE
SPTR37_9f 3 100 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
RIGELADKCGVN MERR_BACSR 3 3 -
RIGELAEATGVT NOLA_BRAJA 11 11 -
TIGKVATLAGVS MERR_THIFE 6 6 -
TIGVFAKAAGVN MERR_SERMA 8 8 -
TIGVFAKAAGVN MERR_SHIFL 8 8 -

Motif 2 width=14
Element Seqn Id St Int Rpt
NVETIRFYQRKGLL MERR_SERMA 19 -1 -
STDTLRYYEKEHLI MERR_THIFE 17 -1 -
NVETIRFYQRKGLL MERR_SHIFL 19 -1 -
NKETIRYYERLGLI MERR_BACSR 14 -1 -
TVRTLHHYEHTGLL NOLA_BRAJA 22 -1 -

Motif 3 width=21
Element Seqn Id St Int Rpt
RMYDRESGQRVHQIRALRELG NOLA_BRAJA 46 10 -
RRYGEADVTRVRFVKSAQRLG MERR_SERMA 43 10 -
RLYNDEAVRRIRFIKTAQHCG MERR_THIFE 41 10 -
RRYGEADVVRVKFVKSAQRLG MERR_SHIFL 43 10 -
RMYSQQTVDRLHFIKRMQELG MERR_BACSR 38 10 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
TIGVFAKAAGVN Q99093 9 9 -
TIGVFAKAAGVN Q99092 9 9 -
TIGVFAKAAGVN Q57492 9 9 -
TIGVFAKAAGVN Q57106 9 9 -
TIGVFAKAAGVN Q44191 9 9 -
TIGVFAKAAGVN O07304 9 9 -
TIGVFAKAAGVN MERR_SERMA 8 8 -
TIGVFAKAAGVN MERR_PSEAE 9 9 -
TIGVFAKAAGVN Q52395 9 9 -
TIGVFAKAAGVN P77071 9 9 -
TIGVFAKAAGVN MERR_SHIFL 8 8 -
TIGVFAKAAGVN O07300 9 9 -
TIGVFAKAAGVN Q44190 9 9 -
TIGAFAKAAGVN Q46655 9 9 -
TIGVFAKVAGVN O54316 9 9 -
TIGVFARTAGVN Q60233 9 9 -
TIGAFAKAAGVN O05606 9 9 -
TIGALAASAGVH Q56281 5 5 -
TIGALAASAGVH Q56287 5 5 -
TVSRLALDAGVS Q56448 5 5 -
TVSRLALDAGVS O66022 5 5 -
TVSRLALDAGVS O66018 5 5 -
TVSRLALDAGVS O07935 5 5 -
TVSRLALDAGVS MERD_SERMA 5 5 -
TVSRLALDAGVS MERD_ACICA 5 5 -
TVSRLALDAGVS MERD_ENTAG 5 5 -
PVSRLALDAGVS MERD_PSEAE 5 5 -
TVSQLAHNAGVS MERD_SHIFL 5 5 -
RIGELADKCGVN MERR_BACSR 3 3 -
RIGELADKCGVN O86214 4 4 -
SISRLAEDAGVS O05612 5 5 -
KISELAKACDVN MERR_STAAU 4 4 -
RIGELAEKCSVN O70107 4 4 -
SVGELARRAGVA SOXR_PSEAE 11 11 -
TPGEVAKRSGVA SOXR_ECOLI 13 13 -
RIGELAEATGVT NOLA_BRAJA 11 11 -
TPGEVAKRSGVA SOXR_SALTY 13 13 -
TPGEVAKCSGVA Q53442 13 13 -
RIGELAGATGVT NOLA_BRASN 12 12 -
SVGQVAGFAGVT TIPA_STRLI 4 4 -

Motif 2 width=14
Element Seqn Id St Int Rpt
NVETIRFYQRKGLL Q99093 20 -1 -
NVETIRFYQRKGLL Q99092 20 -1 -
NVETIRFYQRKGLL Q57492 20 -1 -
NVETIRFYQRKGLL Q57106 20 -1 -
NVETIRFYQRKGLL Q44191 20 -1 -
NVETIRFYQRKGLL O07304 20 -1 -
NVETIRFYQRKGLL MERR_SERMA 19 -1 -
NVETIRFYQRKGLL MERR_PSEAE 20 -1 -
NVETIRFYQRKGLL Q52395 20 -1 -
NVETIRFYQRKGLL P77071 20 -1 -
NVETIRFYQRKGLL MERR_SHIFL 19 -1 -
NVETIRFYQRKGLL O07300 20 -1 -
NVETIRFYQRKGLL Q44190 20 -1 -
NVETIRFYQRKGLL Q46655 20 -1 -
NVETIRFYQRRGLL O54316 20 -1 -
NVETIRFYQRKGLL Q60233 20 -1 -
NVETIRFYQRKALL O05606 20 -1 -
HVETVRFYQRKGLL Q56281 16 -1 -
HVETVRFYQRKGLL Q56287 16 -1 -
SVHIVRDYLLRGLL Q56448 16 -1 -
SVHIVRDYLLRGLL O66022 16 -1 -
SVHIVRDYLLRGLL O66018 16 -1 -
SVHIVRDYLLRGLL O07935 16 -1 -
SVHIVRDYLLRGLL MERD_SERMA 16 -1 -
SVHIVRDYLLRGLL MERD_ACICA 16 -1 -
SVHIVRDYLLRGLL MERD_ENTAG 16 -1 -
SVHIVRDYLLRGLL MERD_PSEAE 16 -1 -
SVHIVRDYLVRGLL MERD_SHIFL 16 -1 -
NKETIRYYERLGLI MERR_BACSR 14 -1 -
NKETIRYYERLGLI O86214 15 -1 -
SVHIVRDYMLRGLL O05612 16 -1 -
NKETVRYYERKGLI MERR_STAAU 15 -1 -
NKETIRYYERLGLI O70107 15 -1 -
AVSALHFYETKGLI SOXR_PSEAE 22 -1 -
AVSALHFYESKGLI SOXR_ECOLI 24 -1 -
TVRTLHHYEHTGLL NOLA_BRAJA 22 -1 -
AVSPLHFYESKGLI SOXR_SALTY 24 -1 -
AVSALHFYESKGLI Q53442 24 -1 -
TVRTLHHYEHTGLL NOLA_BRASN 23 -1 -
TVRTLHHYDDIGLL TIPA_STRLI 15 -1 -

Motif 3 width=21
Element Seqn Id St Int Rpt
RRYGEADVTRVRFVKSAQRLG Q99093 44 10 -
RRYGEADVTRVRFVKSAQRLG Q99092 44 10 -
RRYGEADVTRVRFVKSAQRLG Q57492 44 10 -
RRYGEADVTRVRFVKSAQRLG Q57106 44 10 -
RRYGEADVTRVRFVKSAQRLG Q44191 44 10 -
RRYGEADVTRVRFVKSAQRLG O07304 44 10 -
RRYGEADVTRVRFVKSAQRLG MERR_SERMA 43 10 -
RRYGEADVTRVRFVKSAQRLG MERR_PSEAE 44 10 -
RRYGDADVARVRFVKSAQRLG Q52395 44 10 -
RRYGAADVTRVRFVKSAQRLG P77071 44 10 -
RRYGEADVVRVKFVKSAQRLG MERR_SHIFL 43 10 -
RRYGEADVVRVKFVKSAQRLG O07300 44 10 -
RRYGEADVVRVKFVKSAQRLG Q44190 44 10 -
RRYGAADVTRVRFVKSAQRLG Q46655 44 10 -
RRYGEVDVTRLRFVKSAQRLG O54316 44 10 -
RRYGETDVTRVRFVKSAQRLG Q60233 44 10 -
RRYGEADVARVKFVKSAQRLG O05606 44 10 -
RRYGQSDLERLHFVKSAKGLG Q56281 40 10 -
RRYGQSDLERLHFVKSAKGLG Q56287 40 10 -
GLFDDAALQRLCFVRAAFEAG Q56448 40 10 -
GLFDDAALQRLCFVRAAFEAG O66022 40 10 -
GLFDDAALQRLCFVRAAFEAG O66018 40 10 -
GLFDDTALQRVRFVRAAFEAG O07935 40 10 -
GLFDDAALQRLCFVRAAFEAG MERD_SERMA 40 10 -
GLFDDTALQRLRFVRAAFEAG MERD_ACICA 40 10 -
GLFDDTALQRLRFVRAAFEAG MERD_ENTAG 40 10 -
GLFDDAALQRLCFVRAAFEAG MERD_PSEAE 40 10 -
GVFDDAALQRLCFVRAAFEAG MERD_SHIFL 40 10 -
RMYSQQTVDRLHFIKRMQELG MERR_BACSR 38 10 -
RMYSQQTVDRLHFIKRMQELG O86214 39 10 -
GIFDERSLARLCFVRAAFESG O05612 40 10 -
RIYSEETADRVRFIKRMKELD MERR_STAAU 39 10 -
RMYSEQTVDRLNFIKRMQELD O70107 39 10 -
RRFSRETLRRVVVIKVAQRVG SOXR_PSEAE 45 9 -
RRYKRDVLRYVAIIKIAQRIG SOXR_ECOLI 47 9 -
RMYDRESGQRVHQIRALRELG NOLA_BRAJA 46 10 -
RRYKRDVLRYVAIIKIAQRIG SOXR_SALTY 47 9 -
RRYKRDVLRYVAIIKIAQRIG Q53442 47 9 -
RMYDRESIQRVHQIRALRELG NOLA_BRASN 47 10 -
RRYSDADLDRLQQILFYRELG TIPA_STRLI 39 10 -