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PR00034

Identifier
HTHCRP  [View Relations]  [View Alignment]  
Accession
PR00034
No. of Motifs
2
Creation Date
17-SEP-1993  (UPDATE 29-JUN-1999)
Title
CRP bacterial regulatory protein HTH signature
Database References

PROSITE; PS00042 HTH_CRP_FAMILY
PFAM; PF00325 crp
INTERPRO; IPR001808
PDB; 1CGP
SCOP; 1CGP
CATH; 1CGP
Literature References
1. SPIRO, S. AND GUEST, J.R.
Fnr and its role in oxygen-regulated gene expression in Escherichia coli.
FEMS MICROBIOL.REV. 75(4) 399-428 (1990).
 
2. IRVINE, A.S. AND GUEST, J.R.
Lactobacillus casei contains a member of the crp-fnr family.
NUCLEIC ACIDS RES. 21(3) 753 (1993).
 
3. DE CRECY-LAGARD, V., GLASER, P., LEJEUNE, P., SISMEIRO, O., BARBER,
C.E., DANIELS, M.J. AND DANCHIN, A.
A Xanthomonas campestris pv campestris protein similar to catabolite
activation factor is involved in regulation of phytopathogenicity.
J.BACTERIOL. 172(10) 5877-5883 (1990).

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
anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [1-3]. Within this
family, the HTH motif is situated towards the C-terminus.
 
HTHCRP is a 2-element fingerprint that provides a signature for the HTH
motif of the crp bacterial regulatory proteins. The fingerprint was derived
from an initial alignment of 6 sequences: the motifs completely encompass
the HTH motif, extending a few residues beyond its N- and C-termini (cf.
PROSITE pattern HTH_CRP_FAMILY (PS00042)). Four iterations on OWL21.1 were
required to reach convergence, at which point a true set comprising 27
sequences was identified.
 
An update on SPTR37_9f identified a true set of 48 sequences.
Summary Information
48 codes involving  2 elements
Composite Feature Index
24848
12
True Positives
AADR_RHOPA    ANR_PSEAE     BTR_BORPE     CRP_ECOLI     
CRP_HAEIN CRP_SALTY CYSR_SYNP7 CYSR_SYNY3
ETRA_SHEPU FIXK_AZOCA FIXK_BRAJA FIXK_RHIME
FLP_LACCA FNRA_PSEST FNRL_RHOSH FNR_ECOLI
FNR_HAEIN FNR_SALTY FX24_RHILV HLYX_ACTPL
LEXA_BACSU NTCA_ANASP NTCA_SYNP7 NTCA_SYNY3
O05689 O06655 O07097 O30778
O31204 O33961 O34015 O52983
O69245 O85222 O86067 O86069
O87372 P94611 P96094 Q44500
Q48301 Q51677 Q51859 Q52775
Q52823 Q53170 Q55322 VFR_PSEAE
Sequence Titles
AADR_RHOPA  ANAEROBIC AROMATIC DEGRADATION REGULATOR - RHODOPSEUDOMONAS PALUSTRIS. 
ANR_PSEAE TRANSCRIPTIONAL ACTIVATOR PROTEIN ANR - PSEUDOMONAS AERUGINOSA.
BTR_BORPE TRANSCRIPTIONAL REGULATORY PROTEIN BTR - BORDETELLA PERTUSSIS.
CRP_ECOLI CATABOLITE GENE ACTIVATOR (CAMP RECEPTOR PROTEIN) (CAMP-REGULATORY PROTEIN) - ESCHERICHIA COLI, AND SHIGELLA FLEXNERI.
CRP_HAEIN CATABOLITE GENE ACTIVATOR (CAMP RECEPTOR PROTEIN) (CAMP-REGULATORY PROTEIN) - HAEMOPHILUS INFLUENZAE.
CRP_SALTY CATABOLITE GENE ACTIVATOR (CAMP RECEPTOR PROTEIN) (CAMP-REGULATORY PROTEIN) - SALMONELLA TYPHIMURIUM, AND KLEBSIELLA AEROGENES.
CYSR_SYNP7 REGULATORY PROTEIN CYSR - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
CYSR_SYNY3 REGULATORY PROTEIN CYSR HOMOLOG - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
ETRA_SHEPU ELECTRON TRANSPORT REGULATOR A - SHEWANELLA PUTREFACIENS (PSEUDOMONAS PUTREFACIENS).
FIXK_AZOCA NITROGEN FIXATION REGULATION PROTEIN FIXK - AZORHIZOBIUM CAULINODANS.
FIXK_BRAJA NITROGEN FIXATION REGULATION PROTEIN FIXK - BRADYRHIZOBIUM JAPONICUM.
FIXK_RHIME NITROGEN FIXATION REGULATION PROTEIN FIXK - RHIZOBIUM MELILOTI.
FLP_LACCA PROBABLE TRANSCRIPTIONAL REGULATOR FLP - LACTOBACILLUS CASEI.
FNRA_PSEST TRANSCRIPTIONAL ACTIVATOR PROTEIN FNRA - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
FNRL_RHOSH TRANSCRIPTIONAL ACTIVATOR PROTEIN FNRL - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
FNR_ECOLI FUMARATE AND NITRATE REDUCTION REGULATORY PROTEIN - ESCHERICHIA COLI.
FNR_HAEIN FUMARATE AND NITRATE REDUCTION REGULATORY PROTEIN HOMOLOG - HAEMOPHILUS INFLUENZAE.
FNR_SALTY FUMARATE AND NITRATE REDUCTION REGULATORY PROTEIN - SALMONELLA TYPHIMURIUM.
FX24_RHILV PROBABLE TRANSCRIPTIONAL ACTIVATOR (ORF-240) - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
HLYX_ACTPL REGULATORY PROTEIN HLYX - ACTINOBACILLUS PLEUROPNEUMONIAE (HAEMOPHILUS PLEUROPNEUMONIAE).
LEXA_BACSU SOS REGULATORY PROTEIN LEXA/DINR - BACILLUS SUBTILIS.
NTCA_ANASP GLOBAL NITROGEN REGULATOR (DNA-BINDING PROTEIN VF1) (NITROGEN- RESPONSIVE REGULATORY PROTEIN) - ANABAENA SP. (STRAIN PCC 7120), AND ANABAENA VARIABILIS.
NTCA_SYNP7 GLOBAL NITROGEN REGULATOR - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
NTCA_SYNY3 GLOBAL NITROGEN REGULATOR - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
O05689 CAMP RECEPTOR PROTEIN - PASTEURELLA MULTOCIDA.
O06655 FNR-TYPE TRANSCRIPTIONAL REGULATOR FNRN2 - RHIZOBIUM LEGUMINOSARUM.
O07097 CRP REGULATORY PROTEIN - ERWINIA CHRYSANTHEMI.
O30778 NITROGEN REGULATOR - SYNECHOCOCCUS SP. (STRAIN WH7803).
O31204 TRANSCRIPTIONAL ACTIVATOR - PASTEURELLA HAEMOLYTICA.
O33961 ANAEROBIC REGULATOR - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O34015 CYCLIC AMP RECEPTOR PROTEIN - VIBRIO CHOLERAE.
O52983 CATABOLITE GENE ACTIVATOR PROTEIN - ESCHERICHIA COLI.
O69245 FIXK2 PROTEIN - BRADYRHIZOBIUM JAPONICUM.
O85222 ANAEROBIC REGULATORY PROTEIN - PSEUDOMONAS FLUORESCENS.
O86067 FNR-TYPE TRANSCRIPTIONAL REGULATOR FNRNC - RHIZOBIUM ETLI.
O86069 FNR-TYPE TRANSCRIPTIONAL REGULATOR FNRND - RHIZOBIUM ETLI.
O87372 PUTATIVE TRANSCRIPTIONAL ACTIVATOR - ACETOBACTER XYLINUM (ACETOBACTER PASTEURIANUS).
P94611 NTCA - CYANOTHECE.
P96094 FNR-LIKE REGULATORY PROTEIN - THIOBACILLUS FERROOXIDANS.
Q44500 CYTOCHROME BD - AZOTOBACTER VINELANDII.
Q48301 CYCLIC AMP RECEPTOR PROTEIN - HAEMOPHILUS SOMNUS.
Q51677 FNRN - PARACOCCUS DENITRIFICANS.
Q51859 CYCLIC AMP RECEPTOR PROTEIN - PASTEURELLA HAEMOLYTICA.
Q52775 FNRN - RHIZOBIUM LEGUMINOSARUM.
Q52823 FIXK - RHIZOBIUM LEGUMINOSARUM.
Q53170 LCRABCDE GENES, COMPLETE CDS'S - RHIZOBIUM SP.
Q55322 PUTATIVE TRANSCRIPTIONAL ACTIVATOR - SYNECHOCOCCUS SP.
VFR_PSEAE CYCLIC AMP RECEPTOR-LIKE PROTEIN - PSEUDOMONAS AERUGINOSA.
Scan History
OWL21_1    4  100  NSINGLE    
OWL25_2 1 100 NSINGLE
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
LAMSRQDIADFLGLTIE FIXK_AZOCA 195 195 -
LPLSRAEIADFLGLTIE FX24_RHILV 186 186 -
LTMTRGDIGNYLGLTIE HLYX_ACTPL 191 191 -
LAMSRNEIGNYLGLAVE ANR_PSEAE 187 187 -
IKITRQEIGQIVGCSRE CRP_SALTY 165 165 -
LKLSHQAIAEAIGSTRV NTCA_SYNP7 170 170 -

Motif 2 width=16
Element Seqn Id St Int Rpt
ETVSRTLTYLEEQGTI FIXK_AZOCA 211 -1 -
ETVSRQMTRLRKIGVI FX24_RHILV 202 -1 -
ETISRLLGRFQKSGMI HLYX_ACTPL 207 -1 -
ETVSRVFTRFQQNGLI ANR_PSEAE 203 -1 -
ETVGRILKMLEDQNLI CRP_SALTY 181 -1 -
VTVTRLLGDLRESKLI NTCA_SYNP7 186 -1 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
LPLSRAEIADFLGLTIE O86069 187 187 -
LPLSRAEIADFLGLTIE O06655 187 187 -
LPLSRAEIADFLGLTIE Q52775 187 187 -
LAMSRQDIADFLGLTIE FIXK_AZOCA 195 195 -
LPLSRAEIADFLGLTIE FX24_RHILV 186 186 -
LPLSRAEIADFLGLTIE O86067 187 187 -
LPMSRQDIADYLGLTIE FIXK_BRAJA 185 185 -
LPMSRQDIADYLGLTIE FIXK_RHIME 159 159 -
LTMTRGDIGNYLGLTVE ETRA_SHEPU 193 193 -
LPMGRQDIADFLGLTIE AADR_RHOPA 187 187 -
LTMTRGDIGNYLGLTIE HLYX_ACTPL 191 191 -
LTMTRGDIGNYLGLTIE O31204 192 192 -
LTMTRGDIGNYLGLTVE FNR_HAEIN 196 196 -
LAMSRNEIGNYLGLAVE ANR_PSEAE 187 187 -
VRMSREEIGNYLGLTLE BTR_BORPE 186 186 -
IKITRQEIGQIVGCSRE CRP_ECOLI 166 166 -
IKITRQEIGQIVGCSRE O07097 166 166 -
IKITRQEIGQIVGCSRE CRP_SALTY 165 165 -
LPLTREEMADYLGLTLE FNRL_RHOSH 187 187 -
IKITRQEIGQIVGCSRE O34015 166 166 -
LPMSRNEIGNYLGLAVE FNRA_PSEST 188 188 -
LTMTRGDIGNYLGLTVE FNR_ECOLI 193 193 -
LTMTRGDIGNYLGLTVE FNR_SALTY 193 193 -
LPLTREAMADYLGLTLE Q51677 188 188 -
IKITRQEIGQMVGCSRE O05689 165 165 -
IKITRQEIGQMVGCSRE Q48301 170 170 -
IKITRQEIGQMVGCSRE Q51859 180 180 -
LSMSRNEIGNYLGLAVE O85222 188 188 -
LPLTREAMADYLGLTLE O33961 187 187 -
VPMSRQDIADHLGLTIE Q52823 185 185 -
LAMSRNEIGNYLGLAVE Q44500 188 188 -
LPMTRLDVADYLGMTIE Q53170 175 175 -
LPMCRRDIGDYLGLTLE O69245 180 180 -
IKITRQEIGQMVGCSRE CRP_HAEIN 180 180 -
PSISRADMADFLGLTTE O87372 154 154 -
IKITRQEIGQIVGCSRQ O52983 166 166 -
LKLSHQAIAEAIGSTRV NTCA_SYNP7 170 170 -
IKITRQEIGRIVGCSRE VFR_PSEAE 170 170 -
VPMAWTQLADYLGTTPE FLP_LACCA 168 168 -
LKLSHQAIAEAIGSTRV P94611 175 175 -
LKLSHQAIAEAIGSTRV NTCA_SYNY3 174 174 -
LKLSHQAIAEAIGSTRV NTCA_ANASP 172 172 -
LRLSHQAIAEAIGSTRV O30778 173 173 -
IPLTHQVIAELSGSTRV CYSR_SYNP7 152 152 -
LPAKKAMIAARLGLTPE P96094 179 179 -
LRLTHQEMASALSTTRV Q55322 177 177 -
VRLTHQMLANAIGTTRV CYSR_SYNY3 160 160 -
YPPSVREIGEAVGLASS LEXA_BACSU 24 24 -

Motif 2 width=16
Element Seqn Id St Int Rpt
ETVSRQLTRLRKEGVI O86069 203 -1 -
ETVSRKLTKLRKSGVI O06655 203 -1 -
ETVSRQMTRLRKSGVI Q52775 203 -1 -
ETVSRTLTYLEEQGTI FIXK_AZOCA 211 -1 -
ETVSRQMTRLRKIGVI FX24_RHILV 202 -1 -
ETVSRQMTRLRKWGVI O86067 203 -1 -
ETVSRTFTKLERHGAI FIXK_BRAJA 201 -1 -
ETVSRVVTKLKERSLI FIXK_RHIME 175 -1 -
ETISRLLGRFQKSGLI ETRA_SHEPU 209 -1 -
ETVSRTFTKLEREKLI AADR_RHOPA 203 -1 -
ETISRLLGRFQKSGMI HLYX_ACTPL 207 -1 -
ETISRLLGRFQKSGMI O31204 208 -1 -
ETISRLLGRFQKLGVI FNR_HAEIN 212 -1 -
ETVSRVFTRFQQNGLI ANR_PSEAE 203 -1 -
ETVSRLFSRFGREGLI BTR_BORPE 202 -1 -
ETVGRILKMLEDQNLI CRP_ECOLI 182 -1 -
ETVGRILKMLEDQNLI O07097 182 -1 -
ETVGRILKMLEDQNLI CRP_SALTY 181 -1 -
ETVSRQVSALKRDGVI FNRL_RHOSH 203 -1 -
ETVGRILKMLEEQNLI O34015 182 -1 -
ETVSRVFTRFQQNGLL FNRA_PSEST 204 -1 -
ETISRLLGRFQKSGML FNR_ECOLI 209 -1 -
ETISRLLGRFQKSGML FNR_SALTY 209 -1 -
ETVSRQMSALKREGVI Q51677 204 -1 -
ETVGRILKMLEDQHLI O05689 181 -1 -
ETVGRILKMLEDQHLI Q48301 186 -1 -
ETVGRIIKMLEDEGLI Q51859 196 -1 -
ETVSRVFTRFQQNELI O85222 204 -1 -
ETVSRQMSALKRDGVI O33961 203 -1 -
ETVSRTLTKLASRNVV Q52823 201 -1 -
ETVSRVFSRFQQNELI Q44500 204 -1 -
ETVSRTITKLAGSGVI Q53170 191 -1 -
ETVSRALSQLHTQGIL O69245 196 -1 -
ETVGRIIKMLEDQNLI CRP_HAEIN 196 -1 -
ETVSRLLSAFHREQLI O87372 170 -1 -
QTVGRILKMLEDQNLI O52983 182 -1 -
VTVTRLLGDLRESKLI NTCA_SYNP7 186 -1 -
EMVGRVLKSLEEQGLV VFR_PSEAE 186 -1 -
ETVSRTLKRLAEEKLI FLP_LACCA 184 -1 -
VTVTRLLGDLRQEEMI P94611 191 -1 -
VTVTRLLGDLREGNMI NTCA_SYNY3 190 -1 -
VTVTRLLGDLREKKMI NTCA_ANASP 188 -1 -
VTITRLLGDLRNSGLV O30778 189 -1 -
VTTTRLLGEFRQAGRI CYSR_SYNP7 168 -1 -
ETFSRVLKRLREEHLI P96094 195 -1 -
VTVTRVIGLLRDEGWL Q55322 193 -1 -
VTVTRLLGEFQTQGKV CYSR_SYNY3 176 -1 -
STVHGHLARLETKGLI LEXA_BACSU 41 0 -