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PR00598

Identifier
HTHMARR  [View Relations]  [View Alignment]  
Accession
PR00598
No. of Motifs
4
Creation Date
08-SEP-1996  (UPDATE 16-JUN-1999)
Title
Bacterial regulatory protein MarR family signature
Database References

PROSITE; PS01117 HTH_MARR_FAMILY
PFAM; PF01047 MarR
INTERPRO; IPR000835
Literature References
1. DEHOUX, P. AND COSSART, P.
Homologies between salmolysin and some bacterial regulatory proteins.
MOL.MICROBIOL. 15(3)  591-591 (1995).
 
2. LOMOVSKAYA, O., LEWIS, K. AND MATIN A.
emrR is a negative regulator of the Escherichia coli multidrug resistance
pump emrAB.
J.BACTERIOL. 177(9) 2328-2334 (1995).

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, marR, groups together a range of proteins,
including emrR, hpcR, hpR, marR, pecS, petP, papX, prsX, ywaE, yxaD and yybA.
 
HTHMARR is a 4-element fingerprint that provides a signature for the
multiple antibiotic resistance transcriptional regulator (marR) family.
The fingerprint was derived from an initial alignment of 7 sequences: the
motifs were drawn from short conserved regions spanning virtually the
full alignment length, motifs 2 and 3 spanning the region encoded by
PROSITE pattern HTH_MARR_FAMILY (PS011117). Two iterations on OWL28.1
were required to reach convergence, at which point a true set comprising
11 sequences was identified. A single partial match was also found,
BACYACA36, which makes relatively strong matches with motifs 2 and 3.
 
An update on SPTR37_9f identified a true set of 12 sequences, and 3
partial matches.
Summary Information
  12 codes involving  4 elements
0 codes involving 3 elements
3 codes involving 2 elements
Composite Feature Index
412121212
30000
20330
1234
True Positives
MARR_ECOLI    MARR_SALTY    MPRA_ECOLI    O54521        
PAPX_ECOLI PECS_ERWCH PRSX_ECOLI Q47532
SLYA_ECOLI SLYA_SALTY YXAD_BACSU YYBA_BACSU
True Positive Partials
Codes involving 2 elements
O31564 O82887 P94578
Sequence Titles
MARR_ECOLI  MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARR - ESCHERICHIA COLI. 
MARR_SALTY MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARR - SALMONELLA TYPHIMURIUM.
MPRA_ECOLI TRANSCRIPTIONAL REPRESSOR MPRA (EMRR PROTEIN) - ESCHERICHIA COLI.
O54521 SLYA - SALMONELLA CHOLERAESUIS SEROVAR TYPHI, AND SALMONELLA CHOLERAESUIS SEROVAR CHOLERAESUIS.
PAPX_ECOLI PAPX PROTEIN - ESCHERICHIA COLI.
PECS_ERWCH REGULATORY PROTEIN PECS - ERWINIA CHRYSANTHEMI.
PRSX_ECOLI PRSX PROTEIN - ESCHERICHIA COLI.
Q47532 CYTOPLASMIC PROTEIN - ESCHERICHIA COLI.
SLYA_ECOLI TRANSCRIPTIONAL REGULATOR SLYA - ESCHERICHIA COLI.
SLYA_SALTY TRANSCRIPTIONAL REGULATOR SLYA (SALMOLYSIN) (CYTOLYSIN SLYA) - SALMONELLA TYPHIMURIUM.
YXAD_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN ASNH-GNTR INTERGENIC REGION - BACILLUS SUBTILIS.
YYBA_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN COTF-TETB INTERGENIC REGION - BACILLUS SUBTILIS.

O31564 YFIV PROTEIN - BACILLUS SUBTILIS.
O82887 PAPX PROTEIN - ESCHERICHIA COLI.
P94578 HYPOTHETICAL 16.4 KD PROTEIN - BACILLUS SUBTILIS.
Scan History
OWL28_1    2  100  NSINGLE    
SPTR37_9f 2 35 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
LSPSEISQKLQFTRTNI PRSX_ECOLI 71 71 -
QSQIQLAKAIGIEQPSL SLYA_SALTY 49 49 -
LSPSEISQKLQFTRTNI PAPX_ECOLI 71 71 -
LETRKIAELSGISTATA P25150 78 78 -
IQPSELSCALGSSRTNA EMRR_ECOLI 72 72 -
ARVKELAESFKLDISTL YXAD_BACSU 51 51 -
ITPVELKKVLSVDLGAL MARR_ECOLI 36 36 -

Motif 2 width=16
Element Seqn Id St Int Rpt
TRITDFLEKAGYIKRT PAPX_ECOLI 88 0 -
TRIADELEKRGWIERR EMRR_ECOLI 89 0 -
SNVIKTLEKKSFCRKS P25150 95 0 -
VRTLDQLEDKGLISRQ SLYA_SALTY 66 0 -
TRITDFLEKTGYVKRT PRSX_ECOLI 88 0 -
TRMLDRLVCKGWVERL MARR_ECOLI 53 0 -
SRQAAALEAKELIYRF YXAD_BACSU 68 0 -

Motif 3 width=17
Element Seqn Id St Int Rpt
NDRRCLHLQLTEKGHEF EMRR_ECOLI 108 3 -
SDRRAKRIKLTEKAEPL SLYA_SALTY 85 3 -
EDRRTKKISLTSEGMFF PAPX_ECOLI 107 3 -
EDRRAKKISLTSEGMFF PRSX_ECOLI 107 3 -
NDKRGVLVKLTTGGAAI MARR_ECOLI 72 3 -
SDGRVSLFTITKLGKQL YXAD_BACSU 87 3 -
RDRRLVFVSITDSGKQA P25150 114 3 -

Motif 4 width=21
Element Seqn Id St Int Rpt
QLWSALSTTEKDQLEQITRKL EMRR_ECOLI 138 13 -
EIWGYLTHDEQELFEVINKKL PRSX_ECOLI 137 13 -
ELTKNLTADEVATLEYLLKKV MARR_ECOLI 103 14 -
QMLKEWSTQEKEMFGELLQRM YXAD_BACSU 117 13 -
ELWSNLTCDECEMFEVISKKL PAPX_ECOLI 137 13 -
EILAGISSEEIELLIKLIAKL SLYA_SALTY 115 13 -
ELIAGMTKDEQKILTGLLRKV P25150 144 13 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
QSQIQLAKAIGIEQPSL SLYA_SALTY 49 49 -
QSQIQLAKAIGIEQPSL O54521 47 47 -
QSQIQLAKAIGIEQPSL SLYA_ECOLI 49 49 -
LSPSEISQKLQFTRTNI Q47532 71 71 -
LSPSEISQKLQFTRTNI PAPX_ECOLI 71 71 -
LSPSEISQKLQFTRTNI PRSX_ECOLI 71 71 -
ITPVELKKVLSVDLGAL MARR_SALTY 55 55 -
ITPVELKKVLSVDLGAL MARR_ECOLI 36 36 -
IQPSELSCALGSSRTNA MPRA_ECOLI 72 72 -
YSPSQIVNALMINNSTL PECS_ERWCH 72 72 -
IIQEKLAEMIKVDRTTA YYBA_BACSU 45 45 -
ARVKELAESFKLDISTL YXAD_BACSU 51 51 -

Motif 2 width=16
Element Seqn Id St Int Rpt
VRTLDQLEDKGLISRQ SLYA_SALTY 66 0 -
VRTLDQLEDKGLISRQ O54521 64 0 -
VRTLDQLEEKGLISRQ SLYA_ECOLI 66 0 -
TRITDFLEKAGYVKRT Q47532 88 0 -
TRITDFLEKAGYIKRT PAPX_ECOLI 88 0 -
TRITDFLEKTGYVKRT PRSX_ECOLI 88 0 -
TRMLDRLLCKGWIERL MARR_SALTY 72 0 -
TRMLDRLVCKGWVERL MARR_ECOLI 53 0 -
TRIADELEKRGWIERR MPRA_ECOLI 89 0 -
TSRLDRLEQAGWLRRM PECS_ERWCH 89 0 -
ARAIKKLEMQGFIQKL YYBA_BACSU 62 0 -
SRQAAALEAKELIYRF YXAD_BACSU 68 0 -

Motif 3 width=17
Element Seqn Id St Int Rpt
SDRRAKRIKLTEKAEPL SLYA_SALTY 85 3 -
SDRRAKRIKLTEKAEPL O54521 83 3 -
SDRRAKRIKLTEKAEPL SLYA_ECOLI 85 3 -
EDRRAKKISLTSEGMFF Q47532 107 3 -
EDRRTKKISLTSEGMFF PAPX_ECOLI 107 3 -
EDRRAKKISLTSEGMFF PRSX_ECOLI 107 3 -
NDKRGVLVKLTPDGAAI MARR_SALTY 91 3 -
NDKRGVLVKLTTGGAAI MARR_ECOLI 72 3 -
NDRRCLHLQLTEKGHEF MPRA_ECOLI 108 3 -
GDRRSVNIQLTDEGFAL PECS_ERWCH 108 3 -
QNKKIKKLFPTEKGKKV YYBA_BACSU 81 3 -
SDGRVSLFTITKLGKQL YXAD_BACSU 87 3 -

Motif 4 width=21
Element Seqn Id St Int Rpt
EILAGISSEEIELLIKLIAKL SLYA_SALTY 115 13 -
EILAGISSEEIELLIKLVAKL O54521 113 13 -
EILHGISAEELEQLITLIAKL SLYA_ECOLI 115 13 -
EIWDYLTHDEQELFEVINKKL Q47532 137 13 -
ELWSNLTCDECEMFEVISKKL PAPX_ECOLI 137 13 -
EIWGYLTHDEQELFEVINKKL PRSX_ECOLI 137 13 -
ELTKNLTADEVATLEYLLKKI MARR_SALTY 122 14 -
ELTKNLTADEVATLEYLLKKV MARR_ECOLI 103 14 -
QLWSALSTTEKDQLEQITRKL MPRA_ECOLI 138 13 -
DILSPFSEEEKTHLRALLGRV PECS_ERWCH 138 13 -
VALSGFTSEEKETISALLHRV YYBA_BACSU 111 13 -
QMLKEWSTQEKEMFGELLQRM YXAD_BACSU 117 13 -