| Identifier | HTHGNTR [View Relations] [View Alignment]
|
| Accession | PR00035 |
| No. of Motifs | 2 |
| Creation Date | 17-SEP-1993 (UPDATE 25-JUN-1999) |
| Title | GntR bacterial regulatory protein HTH signature |
| Database References |
PROSITE; PS00043 HTH_GNTR_FAMILY
BLOCKS; BL00043
PFAM; PF00392 gntR
INTERPRO; IPR000524
|
| Literature References | 1. BUCK, D. AND GUEST, J.R.
Overexpression and site-directed mutagenesis of the succinyl-coA
synthetase of Escherichia coli and nucleotide sequence of a gene
BIOCHEM.J. 260(3) 737-747 (1989).
2. HAYDON, D.J. AND GUEST, J.R.
A new family of bacterial regulatory proteins.
FEMS MICROBIOL.LETT. 79 291-296 (1991).
3. REIZER, A., DEUTSCHER, J., SAIER, M.H. AND REIZER, J.
Analysis of the gluconate (gnt) operon of Bacillus subtilis.
MOL.MICROBIOL. 5(5) 1081-1089 (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
gntR, hutC, korA, and E.coli proteins A, P30, fadR and phnF [1-3]. Within
this family, the HTH motif is situated towards the N-terminus.
HTHGNTR is a 2-element fingerprint that provides a signature for the HTH
motif of the gntR 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_GNTR_FAMILY (PS00043)). Two iterations on
OWL21.1 were required to reach convergence, at which point a true set
comprising 12 sequences was identified. The Streptomyces korA protein,
which is not identified by the PROSITE pattern, also escapes detection by
the fingerprint, as it matches strongly only with motif 1.
An update on SPTR37_9f identified a true set of 66 sequences.
|
| Summary Information | 66 codes involving 2 elements
|
| Composite Feature Index | |
| True Positives | EXUR_ECOLI FADR_ECOLI FADR_HAEIN FARR_ECOLI
GLCC_ECOLI GNTR_BACLI GNTR_BACSU HUTC_KLEAE
HUTC_PSEPU LLDR_ECOLI MOCR_RHIME NTRA_CHEHE
O05509 O06731 O07007 O07578
O07792 O24839 O31459 O33539
O33960 O34712 O34817 O50192
O50196 O50514 O50521 O68050
O68331 O70004 O70026 O82887
O85775 O86331 O87562 O88047
O88071 P73804 P96061 P96570
P96669 P96681 P96711 PDHR_ECOLI
PHNF_ECOLI PTSJ_SALTY Q05077 Q52045
Q53381 TRER_BACSU UXUR_ECOLI UXUR_HAEIN
YCBG_BACSU YCXD_BACSU YDFH_ECOLI YDHC_BACSU
YEGW_ECOLI YHCK_ECOLI YHFR_ECOLI YIDP_ECOLI
YIHL_ECOLI YIN1_STRAM YMFC_BACSU YRDX_RHOSH
YURK_BACSU YV20_MYCTU |
| Sequence Titles | EXUR_ECOLI EXU REGULON TRANSCRIPTIONAL REGULATOR - ESCHERICHIA COLI.
FADR_ECOLI FATTY ACID METABOLISM REGULATOR PROTEIN - ESCHERICHIA COLI.
FADR_HAEIN FATTY ACID METABOLISM REGULATOR PROTEIN - HAEMOPHILUS INFLUENZAE.
FARR_ECOLI FATTY ACYL RESPONSIVE REGULATOR (P30 PROTEIN) - ESCHERICHIA COLI.
GLCC_ECOLI GLC OPERON TRANSCRIPTIONAL ACTIVATOR - ESCHERICHIA COLI.
GNTR_BACLI GLUCONATE OPERON TRANSCRIPTIONAL REPRESSOR (P28 PROTEIN) - BACILLUS LICHENIFORMIS.
GNTR_BACSU GLUCONATE OPERON TRANSCRIPTIONAL REPRESSOR (P28 PROTEIN) - BACILLUS SUBTILIS.
HUTC_KLEAE HISTIDINE UTILIZATION REPRESSOR - KLEBSIELLA AEROGENES.
HUTC_PSEPU HISTIDINE UTILIZATION REPRESSOR - PSEUDOMONAS PUTIDA.
LLDR_ECOLI PUTATIVE L-LACTATE DEHYDROGENASE OPERON REGULATORY PROTEIN - ESCHERICHIA COLI.
MOCR_RHIME PROBABLE RHIZOPINE CATABOLISM REGULATORY PROTEIN MOCR - RHIZOBIUM MELILOTI.
NTRA_CHEHE NTA OPERON TRANSCRIPTIONAL REGULATOR - CHELATOBACTER HEINTZII.
O05509 K. AEROGENES - BACILLUS SUBTILIS.
O06731 YISV PROTEIN - BACILLUS SUBTILIS.
O07007 HYPOTHETICAL 24.3 KD PROTEIN (YVFI PROTEIN) - BACILLUS SUBTILIS.
O07578 HYPOTHETICAL 52.8 KD PROTEIN - BACILLUS SUBTILIS.
O07792 HYPOTHETICAL 26.5 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O24839 HYPOTHETICAL 28.5 KD PROTEIN - ACINETOBACTER SP. ADP1.
O31459 YBGA PROTEIN - BACILLUS SUBTILIS.
O33539 PUTATIVE REGULATOR OF CATECHOL DEGRADATIVE OPERON - RHODOCOCCUS OPACUS.
O33960 PYRUVATE DEHYDROGENASE COMPLEX REPRESSOR - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O34712 TRANSCRIPTION REGULATOR - BACILLUS SUBTILIS.
O34817 YVOA - BACILLUS SUBTILIS.
O50192 REGULATORY PROTEIN - FRANKIA SP.
O50196 GNTR TRANSCRIPTIONAL REGULATOR HOMOLOG - LACTOBACILLUS RHAMNOSUS.
O50514 TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O50521 TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O68050 POTENTIAL REGULATORY PROTEIN - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O68331 HYPOTHETICAL 23.7 KD PROTEIN - PSEUDOMONAS MARGINALIS PV. ALFALFAE.
O70004 PUTATIVE TWO-COMPONENT REGULATOR - STREPTOMYCES COELICOLOR.
O70026 TRAR PROTEIN - STREPTOMYCES GHANAENSIS.
O82887 PAPX PROTEIN - ESCHERICHIA COLI.
O85775 PUTATIVE REGULATORY PROTEIN MOCR - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
O86331 HYPOTHETICAL 29.0 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O87562 HYPOTHETICAL 13.3 KD PROTEIN - BACILLUS FIRMUS.
O88047 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
O88071 PUTATIVE TRANSCRIPTIONAL REGULATOR - STREPTOMYCES COELICOLOR.
P73804 HYPOTHETICAL 43.0 KD PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P96061 PHNR - SALMONELLA TYPHIMURIUM.
P96570 EPIDEMIC STRAIN MARKER REGULATOR - BURKHOLDERIA CEPACIA (PSEUDOMONAS CEPACIA).
P96669 YDEL PROTEIN - BACILLUS SUBTILIS.
P96681 YDFD PROTEIN - BACILLUS SUBTILIS.
P96711 TRANSCRIPTIONAL REGULATOR (LACI FAMILY) (DNA-BINDING PROTEIN) - BACILLUS SUBTILIS.
PDHR_ECOLI PYRUVATE DEHYDROGENASE COMPLEX REPRESSOR - ESCHERICHIA COLI.
PHNF_ECOLI PHNF PROTEIN - ESCHERICHIA COLI.
PTSJ_SALTY PUTATIVE TRANSCRIPTIONAL REGULATORY PROTEIN PTSJ - SALMONELLA TYPHIMURIUM.
Q05077 HYPOTHETICAL 26.9 KD PROTEIN (ORF-L PROTEIN) (ORFL) - STREPTOMYCES CLAVULIGERUS.
Q52045 HYPOTHETICAL 89.9 KD PROTEIN - HALOBACTERIUM VOLCANII (HALOFERAX VOLCANII).
Q53381 PDHR - ESCHERICHIA COLI.
TRER_BACSU TREHALOSE OPERON TRANSCRIPTIONAL REPRESSOR - BACILLUS SUBTILIS.
UXUR_ECOLI UXU OPERON TRANSCRIPTIONAL REGULATOR - ESCHERICHIA COLI.
UXUR_HAEIN UXU OPERON REGULATOR - HAEMOPHILUS INFLUENZAE.
YCBG_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN GLTP-CWLJ INTERGENIC REGION (ORF6) - BACILLUS SUBTILIS.
YCXD_BACSU HYPOTHETICAL 50.8 KD PROTEIN IN SRFA4-SFP INTERGENIC REGION (ORF8) - BACILLUS SUBTILIS.
YDFH_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN DCP-NOHA INTERGENIC REGION - ESCHERICHIA COLI.
YDHC_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN DINB-PHOB INTERGENIC REGION - BACILLUS SUBTILIS.
YEGW_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN FBAB-THID INTERGENIC REGION - ESCHERICHIA COLI.
YHCK_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN NANA-SSPB INTERGENIC REGION - ESCHERICHIA COLI.
YHFR_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN CYSG-TRPS INTERGENIC REGION - ESCHERICHIA COLI.
YIDP_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN ILVO-IBPB INTERGENIC REGION - ESCHERICHIA COLI.
YIHL_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN GLNA-RBN INTERGENIC REGION - ESCHERICHIA COLI.
YIN1_STRAM HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN INSTABLE DNA LOCUS (ORF 1) - STREPTOMYCES AMBOFACIENS.
YMFC_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN SPOIIIE-PGSA INTERGENIC REGION - BACILLUS SUBTILIS.
YRDX_RHOSH HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN RDXA 3'REGION - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
YURK_BACSU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN HOM-MRGA INTERGENIC REGION - BACILLUS SUBTILIS.
YV20_MYCTU HYPOTHETICAL TRANSCRIPTIONAL REGULATOR CY20G9.20 - MYCOBACTERIUM TUBERCULOSIS.
|
| Scan History | OWL21_1 2 200 NSINGLE
OWL25_2 1 150 NSINGLE
SPTR37_9f 3 200 NSINGLE
|
| Initial Motifs | Motif 1 width=15
Element Seqn Id St Int Rpt
LPPERELAKQFDVSR A_ECOLI 33 33 -
LPTESALQTEFGVSR P30_ECOLI 28 28 -
IPSEAELVAQFGFSR HUTC_KLEAE 35 35 -
LPAERELSELIGVTR FADR_ECOLI 30 30 -
LPAEQQLAARFEVNR PHNF_ECOLI 34 34 -
ILSENTIAAEFSVSR GNTR_BACSU 40 40 -
Motif 2 width=17
Element Seqn Id St Int Rpt
RHTLRRAIDQLVEKGWV PHNF_ECOLI 48 -1 -
RSPVREALKILASEKII GNTR_BACSU 54 -1 -
RPSLREAIQRLEAKGLL A_ECOLI 47 -1 -
RVTVRQALRQLVEQQIL P30_ECOLI 42 -1 -
RMTINRALRELTDEGLL HUTC_KLEAE 49 -1 -
RTTLREVLQRLARDGWL FADR_ECOLI 44 -1 -
|
| Final Motifs | Motif 1 width=15
Element Seqn Id St Int Rpt
LPSERRLAELLGVSR O07792 34 34 -
LPSEREYAEQFGISR O34817 34 34 -
LPPERELAKQFDVSR PDHR_ECOLI 34 34 -
LPPERELAKQFDVSR Q53381 34 34 -
LPAERELAERLGISR O88071 40 40 -
LPSERELSERLAVSR O33960 34 34 -
LPTEPELAAELGISR O68331 35 35 -
LPAERQLAMQLGVSR LLDR_ECOLI 31 31 -
LPSEFELSKKLGVSR YMFC_BACSU 33 33 -
LPSERELMAFFNVGR YHCK_ECOLI 55 55 -
LPGERDLSQLTGVSR YEGW_ECOLI 47 47 -
LPGEKKLAEEFAVSR YIDP_ECOLI 25 25 -
LPTESEFCEQYDVSR O31459 27 27 -
LPPEREIAEMLDVTR UXUR_ECOLI 33 33 -
LPSEHELTAQYGTSR TRER_BACSU 28 28 -
ALSENELAASMGVSR YIN1_STRAM 31 31 -
RLTEELLARRYGVSR O50514 26 26 -
IPSEAELVAQFGFSR HUTC_KLEAE 35 35 -
LPSERDLADKIGVTR FADR_HAEIN 36 36 -
LPSERAMVTRYAVSR O50521 36 36 -
VPSESELVNELGFSR HUTC_PSEPU 43 43 -
LPSERELIDRSGLSR O86331 45 45 -
LPTENELCTKYNVSR YURK_BACSU 33 33 -
LDSVQALAESFQVSR O07007 13 13 -
IPTENELMQQFGVSR P96711 49 49 -
LPTEREISEKFGVSR UXUR_HAEIN 48 48 -
LPAERELSELIGVTR FADR_ECOLI 30 30 -
LPTLVELMARYQASR O50192 28 28 -
LPPERDLAERLGVNR YV20_MYCTU 49 49 -
LPSERELGELLGIKR YIHL_ECOLI 30 30 -
LPTEMELMDILHVSR YCBG_BACSU 41 41 -
LPSERELCAIFNTTR P96061 33 33 -
LPAERFIADEKNVSR EXUR_ECOLI 32 32 -
LPTESALQTEFGVSR FARR_ECOLI 29 29 -
RINEVELAAQLKVSR NTRA_CHEHE 12 12 -
IPTENELCTQYNVSR YHFR_ECOLI 35 35 -
IPSQRTLAKDFQVNR P96681 37 37 -
LPSSRALVDRFRVSP O88047 15 15 -
RINETQLAKSFGVSR YDHC_BACSU 34 34 -
LPAEQQLAARFEVNR PHNF_ECOLI 34 34 -
LPSERRLCEKLGFSR GLCC_ECOLI 31 31 -
IPDEVSLAKEFNSSR O05509 26 26 -
LNKEAELQQMFNVSR P96570 49 49 -
LPPVRELASELKVNR PTSJ_SALTY 29 29 -
IPSQRTLADMFQVNR O06731 39 39 -
ILSENKLAAEFSVSR GNTR_BACLI 41 41 -
LPPTRLMAEDLGVSR O85775 35 35 -
LPPTRMMAEDLGVSR MOCR_RHIME 35 35 -
RIAEIPTAELLGVSR O24839 25 25 -
PLSEKEVSVRFNVSR YDFH_ECOLI 35 35 -
LPAEPVLMERYQVTR O50196 29 29 -
ILSENTIAAEFSVSR GNTR_BACSU 40 40 -
NPTLAELATEAGLSR O33539 28 28 -
LPSKRLLANQLSISQ P96669 38 38 -
LPSTRQLAMMTGLHR P73804 82 82 -
LPSIRQLSARYQVSK YCXD_BACSU 26 26 -
RMSITELAHAAQVSR O68050 20 20 -
LPSKRRLSSLLDVST O07578 38 38 -
CLSSTELSERLDVSR O82887 13 13 -
PLSAQEIAERTGVSR O70004 174 174 -
IPSDRNIAQEWGISR Q05077 33 33 -
LPSIRALSKDLACSV O87562 38 38 -
LPSVRELATIIIANP O34712 35 35 -
SLSKTELAEKAGIST Q52045 737 737 -
IPSVRDLATEWSISQ O70026 33 33 -
LPPQRAIAEALGVDL YRDX_RHOSH 36 36 -
Motif 2 width=17
Element Seqn Id St Int Rpt
RPAVREALKRLSAAGLV O07792 48 -1 -
RMTVRQALSNLVNEGLL O34817 48 -1 -
RPSLREAIQRLEAKGLL PDHR_ECOLI 48 -1 -
RPSLREAIQRLEAKGLL Q53381 48 -1 -
RVTLREVLRVLQDQGLV O88071 54 -1 -
RPSLREAVAELQQEGLL O33960 48 -1 -
RNTVREAMRVLAFSGLI O68331 49 -1 -
RNSLREALAKLVSEGVL LLDR_ECOLI 45 -1 -
RATLREALRILEEEHVI YMFC_BACSU 47 -1 -
RPSVREALAALKRKGLV YHCK_ECOLI 69 -1 -
RITVRKAMQALEEEGVV YEGW_ECOLI 61 -1 -
RMTIRKAIDLLVAWGLV YIDP_ECOLI 39 -1 -
RTTVRLALQQLELEGYI O31459 41 -1 -
RTVVREALIMLEIKGLV UXUR_ECOLI 47 -1 -
RETVRKALHMLAQNGYI TRER_BACSU 42 -1 -
RTPVRESLILLAQEGLV YIN1_STRAM 45 -1 -
RVPVREALRTLEAEGFV O50514 40 -1 -
RMTINRALRELTDEGLL HUTC_KLEAE 49 -1 -
RTTLREVLQRLARDGWL FADR_HAEIN 50 -1 -
RVTLRAALAQLEARGVV O50521 50 -1 -
RMTINRALRELTADGLL HUTC_PSEPU 57 -1 -
RVTVRAAVGMLQRQGWL O86331 59 -1 -
RITVRKAILDLVEEGYL YURK_BACSU 47 -1 -
RSAVREALSALKAMGLV O07007 27 -1 -
RHTIRKAIGDLVSQGLL P96711 63 -1 -
RTIVREAMVMLEVEKLV UXUR_HAEIN 62 -1 -
RTTLREVLQRLARDGWL FADR_ECOLI 44 -1 -
RETVRRAIGQLETEGLV O50192 42 -1 -
RTSLRQGLARLQQMGLI YV20_MYCTU 63 -1 -
RMTLRQALLNLEAESKI YIHL_ECOLI 44 -1 -
RPVLREALSSLETLGVI YCBG_BACSU 55 -1 -
RITIRESLAQLESSGLI P96061 47 -1 -
RTVVREAIIMLEVEGYV EXUR_ECOLI 46 -1 -
RVTVRQALRQLVEQQIL FARR_ECOLI 43 -1 -
RTPLREALNRLTTEGFL NTRA_CHEHE 26 -1 -
RITIRKAISDLVADGVL YHFR_ECOLI 49 -1 -
RSTVITALEELMADGLI P96681 51 -1 -
PVTVSRALAQLAAEGLV O88047 29 -1 -
RSPIREAMRLLEKDGLL YDHC_BACSU 48 -1 -
RHTLRRAIDQLVEKGWV PHNF_ECOLI 48 -1 -
RSALREGLTVLRGRGII GLCC_ECOLI 45 -1 -
RMTMKRALDNLVAEGLL O05509 40 -1 -
RGSMRDALKALEVQGLV P96570 63 -1 -
RNTVAAAYKRLITAGLA PTSJ_SALTY 43 -1 -
RSTVTAAIDELTSQGLL O06731 53 -1 -
RSPIREALKILASEKII GNTR_BACLI 55 -1 -
RNTVISTYDALLAEGYL O85775 49 -1 -
RNTVITTYDALLAEGYL MOCR_RHIME 49 -1 -
RQPIRMAFRLLEQEGLL O24839 39 -1 -
RQPVREAFIKLAENGLI YDFH_ECOLI 49 -1 -
RYTLRQALKQLSNMGYT O50196 43 -1 -
RSPVREALKILASEKII GNTR_BACSU 54 -1 -
RPAVRRILLTLQKLGYV O33539 42 -1 -
QTTVERAYEQLAAEGYI P96669 52 -1 -
RNTISKVYQNLEDAGLV P73804 96 -1 -
KSTVIRALQELEKRHLI YCXD_BACSU 40 -1 -
RTTAKLRLDTLLAEGRI O68050 34 -1 -
TATIERAYEQLTAEGYV O07578 52 -1 -
RTYITRACDSLEKFGFI O82887 27 -1 -
RQTAQRYLKLLERTGRA O70004 188 -1 -
RATAQKVITALKAQGLV Q05077 47 -1 -
VITTRRAYQNLEQQGYI O87562 52 -1 -
PNTVSKAYKELEREGII O34712 49 -1 -
TQSVRNHLPTLVAMGLV Q52045 751 -1 -
QATAMKAVAALRADGLV O70026 47 -1 -
LTTVTRALNEAQRRGLV YRDX_RHOSH 50 -1 -
|