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PR00036

Identifier
HTHLACI  [View Relations]  [View Alignment]  
Accession
PR00036
No. of Motifs
2
Creation Date
17-SEP-1993  (UPDATE 17-JUN-1999)
Title
LacI bacterial regulatory protein HTH signature
Database References

PROSITE; PS00356 HTH_LACI_FAMILY
PFAM; PF00356 lacI
INTERPRO; IPR000843
PDB; 1LCC
SCOP; 1LCC
CATH; 1LCC
Literature References
1. VARTAK, N.B., REIZER, J., REIZER, A., GRIPP, J.T., GROISMAN, E.A.,
WU, L.-F., TOMICH, J.M. AND SAIER, M.H.
Sequence and evolution of the fruR protein of Salmonella typhimurium -
a pleiotropic transcriptional regulatory protein possessing both activator
and repressor functions which is homologous to the periplasmic ribose-
binding protein.
RES.MICROBIOL. 142(9) 951-963 (1991).
 
2. WEICKERT, M.J. AND ADHYA, S.
A family of bacterial regulators homologous to gal and lac repressors.
J.BIOL.CHEM. 267(22) 15869-15874 (1992).

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
ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR,
rbtR and scrR [1-2]. Within this family, the HTH motif is situated towards
the N-terminus.
 
HTHLACI is a 2-element fingerprint that provides a signature for the HTH
motif of the lacI bacterial regulatory proteins. The fingerprint was
derived from an initial alignment of 6 sequences: the motifs completely
encompass the HTH motif (cf. PROSITE pattern HTH_LACI_FAMILY (PS00356)).
Two iterations on OWL21.1 were required to reach convergence, at which
point a true set comprising 22 sequences was identified. The raffinose
operon, which is not detected by the PROSITE pattern, is similarly not
identified by the fingerprint, as it matches strongly only with the second
motif. The fingerprint also fails to identify the Agrobacterium opnR
protein, which lacks a significant match with the first motif.
 
An update on SPTR37_9f identified a true set of 64 sequences.
Summary Information
64 codes involving  2 elements
Composite Feature Index
26464
12
True Positives
ASCG_ECOLI    CCPA_BACME    CCPA_BACSU    CCPA_STAXY    
CCPA_STRMU CSCR_ECOLI CYTR_ECOLI DEGA_BACSU
EBGR_ECOLI ENDR_PAEPO FRUR_ECOLI FRUR_SALTY
GALR_ECOLI GALR_HAEIN GALS_ECOLI KDGR_BACSU
LACI_ECOLI MALI_ECOLI MALR_CLOBU MALR_STAXY
MALR_STRCO MALR_STRPN O07008 O08352
O31690 O34396 O34829 O68446
O84905 O84915 O86598 O86618
O86795 O87473 O87590 O87600
O87640 O87746 O87853 P72489
PEPR_LACDL PURR_ECOLI PURR_HAEIN Q46479
Q48518 RBSR_BACSU RBSR_ECOLI RBSR_HAEIN
RBTR_KLEAE REGA_CLOAB REGL_STRLI SACR_LACLA
SCRR_KLEPN SCRR_PEDPE SCRR_SALTY SCRR_STAXY
SCRR_STRMU SCRR_VIBAL TRER_ECOLI TRER_SALTY
YAML_STRLM YCJW_ECOLI YVDE_BACSU YYAG_BACSU
Sequence Titles
ASCG_ECOLI  CRYPTIC ASC OPERON REPRESSOR - ESCHERICHIA COLI. 
CCPA_BACME GLUCOSE-RESISTANCE AMYLASE REGULATOR (CATABOLITE CONTROL PROTEIN) - BACILLUS MEGATERIUM.
CCPA_BACSU GLUCOSE-RESISTANCE AMYLASE REGULATOR (CATABOLITE CONTROL PROTEIN) - BACILLUS SUBTILIS.
CCPA_STAXY PROBABLE CATABOLITE CONTROL PROTEIN A - STAPHYLOCOCCUS XYLOSUS.
CCPA_STRMU PROBABLE CATABOLITE CONTROL PROTEIN A - STREPTOCOCCUS MUTANS.
CSCR_ECOLI SUCROSE OPERON REPRESSOR (CSC OPERON REGULATORY PROTEIN) - ESCHERICHIA COLI.
CYTR_ECOLI TRANSCRIPTIONAL REPRESSOR CYTR - ESCHERICHIA COLI.
DEGA_BACSU DEGRADATION ACTIVATOR - BACILLUS SUBTILIS.
EBGR_ECOLI EBG OPERON REPRESSOR - ESCHERICHIA COLI.
ENDR_PAEPO PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN ENDR - PAENIBACILLUS POLYMYXA (BACILLUS POLYMYXA).
FRUR_ECOLI FRUCTOSE REPRESSOR (CATABOLITE REPRESSOR/ACTIVATOR) - ESCHERICHIA COLI.
FRUR_SALTY FRUCTOSE REPRESSOR (CATABOLITE REPRESSOR/ACTIVATOR) - SALMONELLA TYPHIMURIUM.
GALR_ECOLI GALACTOSE OPERON REPRESSOR - ESCHERICHIA COLI.
GALR_HAEIN GALACTOSE OPERON REPRESSOR - HAEMOPHILUS INFLUENZAE.
GALS_ECOLI MGL REPRESSOR AND GALACTOSE ULTRAINDUCTION FACTOR - ESCHERICHIA COLI.
KDGR_BACSU KDG OPERON REPRESSOR - BACILLUS SUBTILIS.
LACI_ECOLI LACTOSE OPERON REPRESSOR - ESCHERICHIA COLI.
MALI_ECOLI MALTOSE REGULON REGULATORY PROTEIN MALI - ESCHERICHIA COLI.
MALR_CLOBU TRANSCRIPTIONAL REGULATORY PROTEIN MALR - CLOSTRIDIUM BUTYRICUM.
MALR_STAXY MALTOSE OPERON TRANSCRIPTIONAL REPRESSOR - STAPHYLOCOCCUS XYLOSUS.
MALR_STRCO MALTOSE OPERON TRANSCRIPTIONAL REPRESSOR - STREPTOMYCES COELICOLOR.
MALR_STRPN MALTOSE OPERON TRANSCRIPTIONAL REPRESSOR - STREPTOCOCCUS PNEUMONIAE.
O07008 HYPOTHETICAL 37.5 KD PROTEIN - BACILLUS SUBTILIS.
O08352 RNA POLYMERASE SIGMA-54 FACTOR - LISTERIA MONOCYTOGENES.
O31690 YKVZ PROTEIN - BACILLUS SUBTILIS.
O34396 LACI REPRESSOR-LIKE PROTEIN - BACILLUS SUBTILIS.
O34829 LACI-FAMILY TRANSCRIPTION REGULATOR - BACILLUS SUBTILIS.
O68446 PURINE NUCLEOTIDE SYNTHESIS REPRESSOR - SALMONELLA TYPHIMURIUM.
O84905 PUTATIVE REPRESSOR PROTEIN - LACTOBACILLUS CASEI.
O84915 GALR-LACI HOMOLOG - PSEUDOMONAS AERUGINOSA.
O86598 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O86618 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O86795 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O87473 CATABOLITE CONTROL PROTEIN A - LISTERIA MONOCYTOGENES.
O87590 TRANSCRIPTION REGULATOR CELR - THERMOMONOSPORA FUSCA.
O87600 PUTATIVE LACI FAMILY REPRESSOR - STREPTOMYCES COELICOLOR.
O87640 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O87746 CATABOLITE REGULATOR PROTEIN - ENTEROCOCCUS FAECALIS (STREPTOCOCCUS FAECALIS).
O87853 TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
P72489 REGR - STREPTOCOCCUS PNEUMONIAE.
PEPR_LACDL TRANSCRIPTION REGULATORY PROTEIN PEPR1 - LACTOBACILLUS DELBRUECKII (SUBSP. LACTIS).
PURR_ECOLI PURINE NUCLEOTIDE SYNTHESIS REPRESSOR - ESCHERICHIA COLI.
PURR_HAEIN PURINE NUCLEOTIDE SYNTHESIS REPRESSOR - HAEMOPHILUS INFLUENZAE.
Q46479 LAC REPRESSOR - ESCHERICHIA COLI.
Q48518 CCPA PROTEIN - LACTOBACILLUS CASEI.
RBSR_BACSU RIBOSE OPERON REPRESSOR - BACILLUS SUBTILIS.
RBSR_ECOLI RIBOSE OPERON REPRESSOR - ESCHERICHIA COLI.
RBSR_HAEIN RIBOSE OPERON REPRESSOR - HAEMOPHILUS INFLUENZAE.
RBTR_KLEAE RIBITOL OPERON REPRESSOR (RBT OPERON REPRESSOR) - KLEBSIELLA AEROGENES.
REGA_CLOAB TRANSCRIPTION REGULATORY PROTEIN REGA - CLOSTRIDIUM ACETOBUTYLICUM.
REGL_STRLI TRANSCRIPTION REGULATORY PROTEIN REGL - STREPTOMYCES LIVIDANS.
SACR_LACLA SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - LACTOCOCCUS LACTIS (SUBSP. LACTIS) (STREPTOCOCCUS LACTIS).
SCRR_KLEPN SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - KLEBSIELLA PNEUMONIAE.
SCRR_PEDPE SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - PEDIOCOCCUS PENTOSACEUS.
SCRR_SALTY SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - SALMONELLA TYPHIMURIUM.
SCRR_STAXY SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - STAPHYLOCOCCUS XYLOSUS.
SCRR_STRMU SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - STREPTOCOCCUS MUTANS.
SCRR_VIBAL SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - VIBRIO ALGINOLYTICUS.
TRER_ECOLI TREHALOSE OPERON REPRESSOR - ESCHERICHIA COLI.
TRER_SALTY TREHALOSE OPERON REPRESSOR - SALMONELLA TYPHIMURIUM.
YAML_STRLM HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN AML 5'REGION (ORF-S1) - STREPTOMYCES LIMOSUS (STREPTOMYCES ALBIDOFLAVUS).
YCJW_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN OMPG-TYRR INTERGENIC REGION - ESCHERICHIA COLI.
YVDE_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN CLPP-CRH INTERGENIC REGION - BACILLUS SUBTILIS.
YYAG_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN TETL-EXOA INTERGENIC REGION - BACILLUS SUBTILIS.
Scan History
OWL21_1    2  100  NSINGLE    
OWL25_2 1 100 NSINGLE
SPTR37_9f 7 120 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
TLKDIAIEAGV EBGR_ECOLI 2 2 -
TLYDVAEYAGV LACI_ECOLI 4 4 -
TIKDVAKRANV PURR_ECOLI 2 2 -
TMLEVAKRAGV ASCG_ECOLI 2 2 -
TMKDVALKAKV CYTR_ECOLI 10 10 -
KLDEIARLAGV FRUR_ECOLI 1 1 -

Motif 2 width=11
Element Seqn Id St Int Rpt
VSLATVSRVLN EBGR_ECOLI 12 -1 -
VSYQTVSRVVN LACI_ECOLI 14 -1 -
VSTTTVSHVIN PURR_ECOLI 12 -1 -
VSKATVSRVLS ASCG_ECOLI 12 -1 -
VSTATVSRALM CYTR_ECOLI 20 -1 -
VSRTTASYVIN FRUR_ECOLI 11 -1 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
TIKDVARLAGV GALR_ECOLI 3 3 -
TIYDVAREAGV CCPA_STRMU 8 8 -
TIRDVARQAGV GALS_ECOLI 3 3 -
SIKDVAREAGV REGA_CLOAB 4 4 -
TIYDIARVAGV YCJW_ECOLI 4 4 -
TIYDVAKAAGV DEGA_BACSU 4 4 -
TIYDVAREANV CCPA_BACSU 5 5 -
TIYDVAREANV O87473 4 4 -
TIYDVAREANV O87746 7 7 -
TIYDVAREANV Q48518 7 7 -
TIRDVAKLANV GALR_HAEIN 3 3 -
TLEDVAREAGV O87853 7 7 -
TLKDIAIEAGV EBGR_ECOLI 2 2 -
TIKDVAGAAGV RBSR_BACSU 3 3 -
TIYDVAREAKV PEPR_LACDL 7 7 -
TIYDVAREARV CCPA_STAXY 4 4 -
TIYDVAREASV CCPA_BACME 4 4 -
TIKDVAECAGV KDGR_BACSU 10 10 -
TIKDVAKMAGV PURR_HAEIN 3 3 -
TMKDVARLAGV RBSR_ECOLI 2 2 -
SLHDVARLAGV SCRR_VIBAL 3 3 -
NIKDIAEKAGV O31690 3 3 -
TITDIAKAAGV O84905 3 3 -
TLYDVAEYAGV LACI_ECOLI 4 4 -
TLYDVAEYAGV Q46479 5 5 -
TIKDIAELAGV SCRR_KLEPN 7 7 -
TIKDVAKRANV O68446 3 3 -
TIKDVAKRANV PURR_ECOLI 2 2 -
TIKDIAKLANV O34396 3 3 -
KLNDVAKLAGV SCRR_PEDPE 4 4 -
KLTDVAKLAGV SCRR_STRMU 4 4 -
TIKDIARLSGV TRER_ECOLI 6 6 -
TIKDIARLSGV TRER_SALTY 6 6 -
TIKDIAEQAGV SCRR_SALTY 7 7 -
TLSDVAKKANV YVDE_BACSU 3 3 -
RLADIAAQAGV REGL_STRLI 4 4 -
RLADIAAQAGV MALR_STRCO 4 4 -
KLEDVANKAGV SACR_LACLA 3 3 -
TIKDIAQAANV MALR_STAXY 3 3 -
TMKDIARLAQV RBSR_HAEIN 2 2 -
TIKDVAKAAGV MALR_STRPN 3 3 -
NIKEIARLANV YYAG_BACSU 3 3 -
TIHDVALAAGV MALI_ECOLI 8 8 -
NIADIAKIAGV SCRR_STAXY 3 3 -
SLKDVARLAGV CSCR_ECOLI 3 3 -
TIKDIAQEAGF O07008 3 3 -
TMLEVAKRAGV ASCG_ECOLI 2 2 -
NIKDIARLSGV MALR_CLOBU 2 2 -
TLAEIAREAGV O86795 20 20 -
RIKDIALKAKV O34829 3 3 -
GIRDVAAAAGV O87640 25 25 -
TMKDVALKAKV CYTR_ECOLI 10 10 -
TIKDVAAAAGV O86598 9 9 -
TLEMVAALAGV O87590 8 8 -
GMADVARLAGV O86618 27 27 -
RLADIAAQAQV YAML_STRLM 15 15 -
TSRDVAQAAGV O87600 23 23 -
TMKEVAERAGV ENDR_PAEPO 4 4 -
TINQVAEAAGV O84915 13 13 -
KLDEIARLAGV FRUR_ECOLI 1 1 -
KLDEIARLAGV FRUR_SALTY 2 2 -
TLKEVAEELGV O08352 332 332 -
TIYDLAELSGV RBTR_KLEAE 5 5 -
TIKDIAEMAQT P72489 6 6 -

Motif 2 width=11
Element Seqn Id St Int Rpt
VSVATVSRVIN GALR_ECOLI 13 -1 -
VSMATVSRVVN CCPA_STRMU 18 -1 -
VSVATVSRVLN GALS_ECOLI 13 -1 -
VSIATVSRVLN REGA_CLOAB 14 -1 -
VSKSTVSRVLN YCJW_ECOLI 14 -1 -
VSITTVSRVIN DEGA_BACSU 14 -1 -
VSMATVSRVVN CCPA_BACSU 15 -1 -
VSMATVSRVVN O87473 14 -1 -
VSMATVSRVVN O87746 17 -1 -
VSMATVSRVVN Q48518 17 -1 -
VSVATVSRVLN GALR_HAEIN 13 -1 -
VSRATVSRVVN O87853 17 -1 -
VSLATVSRVLN EBGR_ECOLI 12 -1 -
VSVATVSRNLN RBSR_BACSU 13 -1 -
VSMATVSRVVN PEPR_LACDL 17 -1 -
VSMATVSRVVN CCPA_STAXY 14 -1 -
VSMATVSRVVN CCPA_BACME 14 -1 -
VSKSTVSRYIN KDGR_BACSU 20 -1 -
VSTTTVSHVIN PURR_HAEIN 13 -1 -
VSTSTVSHVIN RBSR_ECOLI 12 -1 -
VSKSTVSRVIN SCRR_VIBAL 13 -1 -
VSVTTVSRVIN O31690 13 -1 -
VSIATVSRILN O84905 13 -1 -
VSYQTVSRVVN LACI_ECOLI 14 -1 -
VSYQTVSRVVN Q46479 15 -1 -
VSKATASLVLN SCRR_KLEPN 17 -1 -
VSTTTVSHVIN O68446 13 -1 -
VSTTTVSHVIN PURR_ECOLI 12 -1 -
VSHTTVSRALN O34396 13 -1 -
VSATTVSRVIN SCRR_PEDPE 14 -1 -
VSPTTVSRVIN SCRR_STRMU 14 -1 -
VGKSTVSRVLN TRER_ECOLI 16 -1 -
VGKSTVSRVLN TRER_SALTY 16 -1 -
VSKATASLVLN SCRR_SALTY 17 -1 -
VSKMTVSRVIN YVDE_BACSU 13 -1 -
VSEATVSRVLN REGL_STRLI 14 -1 -
VSEATVSRVLN MALR_STRCO 14 -1 -
VSVTTVSRVIN SACR_LACLA 13 -1 -
VSTSTVSRVIS MALR_STAXY 13 -1 -
VSTSTVSHVIN RBSR_HAEIN 12 -1 -
VSPSTVTRVIQ MALR_STRPN 13 -1 -
VSVSTVSRVLN YYAG_BACSU 13 -1 -
VSVSTVSLVLS MALI_ECOLI 18 -1 -
VSKSTVSRYLN SCRR_STAXY 13 -1 -
VSMMTVSRVMH CSCR_ECOLI 13 -1 -
FSISTVSRVLN O07008 13 -1 -
VSKATVSRVLS ASCG_ECOLI 12 -1 -
VGVSTVSRVIN MALR_CLOBU 12 -1 -
VSAPTVSKVLN O86795 30 -1 -
VSSATVSRILN O34829 13 -1 -
VSITTVSDALN O87640 35 -1 -
VSTATVSRALM CYTR_ECOLI 20 -1 -
VSKGAVSLAFN O86598 19 -1 -
VGRGTVSRVIN O87590 18 -1 -
VSAQTVSRTLA O86618 37 -1 -
VSEATASRVLN YAML_STRLM 25 -1 -
VSQAAVSLVLG O87600 33 -1 -
VSKSTVSQFLQ ENDR_PAEPO 14 -1 -
VSKASVSRYIG O84915 23 -1 -
VSRTTASYVIN FRUR_ECOLI 11 -1 -
VSRTTASYVIN FRUR_SALTY 12 -1 -
VHESTVSRAVN O08352 342 -1 -
VSASAVSAILN RBTR_KLEAE 15 -1 -
TSKTTVSFYLN P72489 16 -1 -