WORKLIST ENTRIES (1):
HTHLACI View alignment View Structure LacI bacterial regulatory protein HTH signature
Type of fingerprint: COMPOUND with 2 elements
Links:
PRINTS; PR00032 HTHARAC; PR00033 HTHASNC; PR00778 HTHARSR; PR00034 HTHCRP
PRINTS; PR00035 HTHGNTR; PR00037 HTHLACR; PR00038 HTHLUXR; PR00039 HTHLYSR
PRINTS; PR00598 HTHMARR; PR00040 HTHMERR; PR00455 HTHTETR; PR00030 HTHCRO
PRINTS; PR00031 HTHREPRESSR
INTERPRO; IPR000843
PROSITE; PS00356 HTH_LACI_FAMILY
PFAM; PF00356 lacI
PDB; 1LCC 3Dinfo
SCOP; 1LCC
CATH; 1LCC
Creation date 17-SEP-1993; UPDATE 17-JUN-1999
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).
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 FINGERPRINT INDEX
2| 64 64
--+-----------
| 1 2
True positives..
GALR_ECOLI CCPA_STRMU GALS_ECOLI REGA_CLOAB
YCJW_ECOLI DEGA_BACSU CCPA_BACSU O87473
O87746 Q48518 GALR_HAEIN O87853
EBGR_ECOLI RBSR_BACSU PEPR_LACDL CCPA_STAXY
CCPA_BACME KDGR_BACSU PURR_HAEIN RBSR_ECOLI
SCRR_VIBAL O31690 O84905 LACI_ECOLI
Q46479 SCRR_KLEPN O68446 PURR_ECOLI
O34396 SCRR_PEDPE SCRR_STRMU TRER_ECOLI
TRER_SALTY SCRR_SALTY YVDE_BACSU REGL_STRLI
MALR_STRCO SACR_LACLA MALR_STAXY RBSR_HAEIN
MALR_STRPN YYAG_BACSU MALI_ECOLI SCRR_STAXY
CSCR_ECOLI O07008 ASCG_ECOLI MALR_CLOBU
O86795 O34829 O87640 CYTR_ECOLI
O86598 O87590 O86618 YAML_STRLM
O87600 ENDR_PAEPO O84915 FRUR_ECOLI
FRUR_SALTY O08352 RBTR_KLEAE P72489
PROTEIN TITLES
GALR_ECOLI GALACTOSE OPERON REPRESSOR - ESCHERICHIA COLI.
CCPA_STRMU PROBABLE CATABOLITE CONTROL PROTEIN A - STREPTOCOCCUS MUTANS
GALS_ECOLI MGL REPRESSOR AND GALACTOSE ULTRAINDUCTION FACTOR - ESCHERIC
REGA_CLOAB TRANSCRIPTION REGULATORY PROTEIN REGA - CLOSTRIDIUM ACETOBUT
YCJW_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN OMPG-TYRR INTERGEN
DEGA_BACSU DEGRADATION ACTIVATOR - BACILLUS SUBTILIS.
CCPA_BACSU GLUCOSE-RESISTANCE AMYLASE REGULATOR (CATABOLITE CONTROL PRO
O87473 CATABOLITE CONTROL PROTEIN A - LISTERIA MONOCYTOGENES.
O87746 CATABOLITE REGULATOR PROTEIN - ENTEROCOCCUS FAECALIS (STREPT
Q48518 CCPA PROTEIN - LACTOBACILLUS CASEI.
GALR_HAEIN GALACTOSE OPERON REPRESSOR - HAEMOPHILUS INFLUENZAE.
O87853 TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
EBGR_ECOLI EBG OPERON REPRESSOR - ESCHERICHIA COLI.
RBSR_BACSU RIBOSE OPERON REPRESSOR - BACILLUS SUBTILIS.
PEPR_LACDL TRANSCRIPTION REGULATORY PROTEIN PEPR1 - LACTOBACILLUS DELBR
CCPA_STAXY PROBABLE CATABOLITE CONTROL PROTEIN A - STAPHYLOCOCCUS XYLOS
CCPA_BACME GLUCOSE-RESISTANCE AMYLASE REGULATOR (CATABOLITE CONTROL PRO
KDGR_BACSU KDG OPERON REPRESSOR - BACILLUS SUBTILIS.
PURR_HAEIN PURINE NUCLEOTIDE SYNTHESIS REPRESSOR - HAEMOPHILUS INFLUENZ
RBSR_ECOLI RIBOSE OPERON REPRESSOR - ESCHERICHIA COLI.
SCRR_VIBAL SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - V
O31690 YKVZ PROTEIN - BACILLUS SUBTILIS.
O84905 PUTATIVE REPRESSOR PROTEIN - LACTOBACILLUS CASEI.
LACI_ECOLI LACTOSE OPERON REPRESSOR - ESCHERICHIA COLI.
Q46479 LAC REPRESSOR - ESCHERICHIA COLI.
SCRR_KLEPN SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - K
O68446 PURINE NUCLEOTIDE SYNTHESIS REPRESSOR - SALMONELLA TYPHIMURI
PURR_ECOLI PURINE NUCLEOTIDE SYNTHESIS REPRESSOR - ESCHERICHIA COLI.
O34396 LACI REPRESSOR-LIKE PROTEIN - BACILLUS SUBTILIS.
SCRR_PEDPE SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - P
SCRR_STRMU SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - S
TRER_ECOLI TREHALOSE OPERON REPRESSOR - ESCHERICHIA COLI.
TRER_SALTY TREHALOSE OPERON REPRESSOR - SALMONELLA TYPHIMURIUM.
SCRR_SALTY SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - S
YVDE_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN CLPP-CRH INTERGENI
REGL_STRLI TRANSCRIPTION REGULATORY PROTEIN REGL - STREPTOMYCES LIVIDAN
MALR_STRCO MALTOSE OPERON TRANSCRIPTIONAL REPRESSOR - STREPTOMYCES COEL
SACR_LACLA SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - L
MALR_STAXY MALTOSE OPERON TRANSCRIPTIONAL REPRESSOR - STAPHYLOCOCCUS XY
RBSR_HAEIN RIBOSE OPERON REPRESSOR - HAEMOPHILUS INFLUENZAE.
MALR_STRPN MALTOSE OPERON TRANSCRIPTIONAL REPRESSOR - STREPTOCOCCUS PNE
YYAG_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN TETL-EXOA INTERGEN
MALI_ECOLI MALTOSE REGULON REGULATORY PROTEIN MALI - ESCHERICHIA COLI.
SCRR_STAXY SUCROSE OPERON REPRESSOR (SCR OPERON REGULATORY PROTEIN) - S
CSCR_ECOLI SUCROSE OPERON REPRESSOR (CSC OPERON REGULATORY PROTEIN) - E
O07008 HYPOTHETICAL 37.5 KD PROTEIN - BACILLUS SUBTILIS.
ASCG_ECOLI CRYPTIC ASC OPERON REPRESSOR - ESCHERICHIA COLI.
MALR_CLOBU TRANSCRIPTIONAL REGULATORY PROTEIN MALR - CLOSTRIDIUM BUTYRI
O86795 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR
O34829 LACI-FAMILY TRANSCRIPTION REGULATOR - BACILLUS SUBTILIS.
O87640 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR
CYTR_ECOLI TRANSCRIPTIONAL REPRESSOR CYTR - ESCHERICHIA COLI.
O86598 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR
O87590 TRANSCRIPTION REGULATOR CELR - THERMOMONOSPORA FUSCA.
O86618 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR
YAML_STRLM HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN AML 5'REGION (ORF-
O87600 PUTATIVE LACI FAMILY REPRESSOR - STREPTOMYCES COELICOLOR.
ENDR_PAEPO PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN ENDR - PAENIBACI
O84915 GALR-LACI HOMOLOG - PSEUDOMONAS AERUGINOSA.
FRUR_ECOLI FRUCTOSE REPRESSOR (CATABOLITE REPRESSOR/ACTIVATOR) - ESCHER
FRUR_SALTY FRUCTOSE REPRESSOR (CATABOLITE REPRESSOR/ACTIVATOR) - SALMON
O08352 RNA POLYMERASE SIGMA-54 FACTOR - LISTERIA MONOCYTOGENES.
RBTR_KLEAE RIBITOL OPERON REPRESSOR (RBT OPERON REPRESSOR) - KLEBSIELLA
P72489 REGR - STREPTOCOCCUS PNEUMONIAE.
SCAN HISTORY
OWL21_1 2 100 NSINGLE
OWL25_2 1 100 NSINGLE
SPTR37_9f 7 120 NSINGLE
INITIAL MOTIF SETS
HTHLACI1 Length of motif = 11 Motif number = 1
LacI bacterial regulatory protein HTH motif I - 1
PCODE ST INT
TLYDVAEYAGV LACI_ECOLI 4 4
TIKDVAKRANV PURR_ECOLI 2 2
TLKDIAIEAGV EBGR_ECOLI 2 2
TMLEVAKRAGV ASCG_ECOLI 2 2
TMKDVALKAKV CYTR_ECOLI 10 10
KLDEIARLAGV FRUR_ECOLI 1 1
HTHLACI2 Length of motif = 11 Motif number = 2
LacI bacterial regulatory protein HTH motif II - 1
PCODE ST INT
VSYQTVSRVVN LACI_ECOLI 14 -1
VSTTTVSHVIN PURR_ECOLI 12 -1
VSLATVSRVLN EBGR_ECOLI 12 -1
VSKATVSRVLS ASCG_ECOLI 12 -1
VSTATVSRALM CYTR_ECOLI 20 -1
VSRTTASYVIN FRUR_ECOLI 11 -1
FINAL MOTIF SETS
HTHLACI1 Length of motif = 11 Motif number = 1
LacI bacterial regulatory protein HTH motif I - 7
PCODE ST INT
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 3 3
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 5 5
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 3 3
NIKDIARLSGV MALR_CLOBU 2 2
TLAEIAREAGV O86795 20 20
RIKDIALKAKV O34829 3 3
GIRDVAAAAGV O87640 25 25
TMKDVALKAKV CYTR_ECOLI 11 11
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 2 2
KLDEIARLAGV FRUR_SALTY 2 2
TLKEVAEELGV O08352 332 332
TIYDLAELSGV RBTR_KLEAE 5 5
TIKDIAEMAQT P72489 6 6
HTHLACI2 Length of motif = 11 Motif number = 2
LacI bacterial regulatory protein HTH motif II - 7
PCODE ST INT
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 13 -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 15 -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 13 -1
VGVSTVSRVIN MALR_CLOBU 12 -1
VSAPTVSKVLN O86795 30 -1
VSSATVSRILN O34829 13 -1
VSITTVSDALN O87640 35 -1
VSTATVSRALM CYTR_ECOLI 21 -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 12 -1
VSRTTASYVIN FRUR_SALTY 12 -1
VHESTVSRAVN O08352 342 -1
VSASAVSAILN RBTR_KLEAE 15 -1
TSKTTVSFYLN P72489 16 -1
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