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Conserved domains on  [gi|38704091|ref|NP_311368|]
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transcriptional repressor [Escherichia coli O157:H7 str. Sakai]

Protein Classification

glycine cleavage system transcriptional repressor( domain architecture ID 11485420)

glycine binds to glycine cleavage system transcriptional repressor, leading to activation of specific transcription

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
gcvR PRK11589
glycine cleavage system transcriptional repressor; Provisional
 1-190 9.75e-151

glycine cleavage system transcriptional repressor; Provisional


:

Pssm-ID: 236935 [Multi-domain]  Cd Length: 190  Bit Score: 414.95  E-value: 9.75e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091    1 MTLSSQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIV 80
Cdd:PRK11589   1 MPQSSQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091   81 MKRTTARPRPPMPASVWVQVDVADSPHLIERFTALFDAHHMNIAELVSRTQPAENERAAQLHIQITAHSPASADAANIEQ 160
Cdd:PRK11589  81 MKRTTARPRPAMPATVWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPASQDAANIEQ 160

                        170       180       190
                 ....*....|....*....|....*....|
gi 38704091  161 AFKALCTELNAQGSINVVNYSQHDEQDGVK 190
Cdd:PRK11589 161 AFKALCTELNAQGSINVVNYSQHDEQDGVK 190
 
Name Accession Description Interval E-value
gcvR PRK11589
glycine cleavage system transcriptional repressor; Provisional
 1-190 9.75e-151

glycine cleavage system transcriptional repressor; Provisional


Pssm-ID: 236935 [Multi-domain]  Cd Length: 190  Bit Score: 414.95  E-value: 9.75e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091    1 MTLSSQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIV 80
Cdd:PRK11589   1 MPQSSQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091   81 MKRTTARPRPPMPASVWVQVDVADSPHLIERFTALFDAHHMNIAELVSRTQPAENERAAQLHIQITAHSPASADAANIEQ 160
Cdd:PRK11589  81 MKRTTARPRPAMPATVWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPASQDAANIEQ 160

                        170       180       190
                 ....*....|....*....|....*....|
gi 38704091  161 AFKALCTELNAQGSINVVNYSQHDEQDGVK 190
Cdd:PRK11589 161 AFKALCTELNAQGSINVVNYSQHDEQDGVK 190
GcvR COG2716
Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];
6-179 1.32e-77

Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];


Pssm-ID: 442029 [Multi-domain]  Cd Length: 174  Bit Score: 229.34  E-value: 1.32e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091   6 QHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMKRTT 85
Cdd:COG2716   1 MQHLVITAIGPDRPGIVAALARAVSEHGCNILDSRMARLGGEFAGILLVSGPWDAIAKLEAALPALAAELGLLVTVKRTE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091  86 ARPRPPMPASVWVQVDVADSPHLIERFTALFDAHHMNIAELVSRTQPAENERAAQLHIQITAHSPASADAANIEQAFKAL 165
Cdd:COG2716  81 PHEAPPAGLPYVVEVVGNDRPGIVAEVTQFLAERGINIEDLSTKTYPAPMSGTPLFSAQITVHVPAGLDIDALRDALEDL 160

                       170
                ....*....|....
gi 38704091 166 CTELNAQGSINVVN 179
Cdd:COG2716 161 ADELNVDISLEPIK 174
ACT_GcvR_1 cd04893
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
 8-84 4.75e-36

ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR interacts directly with GcvA rather than binding to DNA to cause repression. Members of this CD belong to the superfamily of ACT regulatory domains.


Pssm-ID: 153165 [Multi-domain]  Cd Length: 77  Bit Score: 120.50  E-value: 4.75e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38704091   8 YLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMKRT 84
Cdd:cd04893   1 HLVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSWDAIAKLEAALPGLARRLDLTLMMKRT 77
ACT_6 pfam13740
ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains.
 7-82 8.61e-27

ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains.


Pssm-ID: 433446 [Multi-domain]  Cd Length: 76  Bit Score: 96.86  E-value: 8.61e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 38704091     7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMK 82
Cdd:pfam13740   1 EILLITATGPDRPGLTASLTAVLAEHGCNILDSGQAVIHNRLSLGLLVSGPWDALARLEKDLLFLAHELGLTVRFK 76
 
Name Accession Description Interval E-value
gcvR PRK11589
glycine cleavage system transcriptional repressor; Provisional
 1-190 9.75e-151

glycine cleavage system transcriptional repressor; Provisional


Pssm-ID: 236935 [Multi-domain]  Cd Length: 190  Bit Score: 414.95  E-value: 9.75e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091    1 MTLSSQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIV 80
Cdd:PRK11589   1 MPQSSQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091   81 MKRTTARPRPPMPASVWVQVDVADSPHLIERFTALFDAHHMNIAELVSRTQPAENERAAQLHIQITAHSPASADAANIEQ 160
Cdd:PRK11589  81 MKRTTARPRPAMPATVWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPASQDAANIEQ 160

                        170       180       190
                 ....*....|....*....|....*....|
gi 38704091  161 AFKALCTELNAQGSINVVNYSQHDEQDGVK 190
Cdd:PRK11589 161 AFKALCTELNAQGSINVVNYSQHDEQDGVK 190
GcvR COG2716
Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];
6-179 1.32e-77

Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];


Pssm-ID: 442029 [Multi-domain]  Cd Length: 174  Bit Score: 229.34  E-value: 1.32e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091   6 QHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMKRTT 85
Cdd:COG2716   1 MQHLVITAIGPDRPGIVAALARAVSEHGCNILDSRMARLGGEFAGILLVSGPWDAIAKLEAALPALAAELGLLVTVKRTE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091  86 ARPRPPMPASVWVQVDVADSPHLIERFTALFDAHHMNIAELVSRTQPAENERAAQLHIQITAHSPASADAANIEQAFKAL 165
Cdd:COG2716  81 PHEAPPAGLPYVVEVVGNDRPGIVAEVTQFLAERGINIEDLSTKTYPAPMSGTPLFSAQITVHVPAGLDIDALRDALEDL 160

                       170
                ....*....|....
gi 38704091 166 CTELNAQGSINVVN 179
Cdd:COG2716 161 ADELNVDISLEPIK 174
ACT_GcvR_1 cd04893
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
 8-84 4.75e-36

ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR interacts directly with GcvA rather than binding to DNA to cause repression. Members of this CD belong to the superfamily of ACT regulatory domains.


Pssm-ID: 153165 [Multi-domain]  Cd Length: 77  Bit Score: 120.50  E-value: 4.75e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38704091   8 YLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMKRT 84
Cdd:cd04893   1 HLVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSWDAIAKLEAALPGLARRLDLTLMMKRT 77
ACT_6 pfam13740
ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains.
 7-82 8.61e-27

ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains.


Pssm-ID: 433446 [Multi-domain]  Cd Length: 76  Bit Score: 96.86  E-value: 8.61e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 38704091     7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMK 82
Cdd:pfam13740   1 EILLITATGPDRPGLTASLTAVLAEHGCNILDSGQAVIHNRLSLGLLVSGPWDALARLEKDLLFLAHELGLTVRFK 76
ACT_GcvR_2 cd04869
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
 99-176 4.20e-14

ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR interacts directly with GcvA rather than binding to DNA to cause repression. Members of this CD belong to the superfamily of ACT regulatory domains.


Pssm-ID: 153141 [Multi-domain]  Cd Length: 81  Bit Score: 64.55  E-value: 4.20e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38704091  99 QVDV--ADSPHLIERFTALFDAHHMNIAELVSRTQPAENERAAQLHIQITAHSPASADAANIEQAFKALCTELNAQGSIN 176
Cdd:cd04869   1 VVEVvgNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPAGTDLDALREELEELCDDLNVDISLE 80
ACT_UUR-ACR-like cd04873
ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) ...
 9-69 6.66e-07

ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.


Pssm-ID: 153145 [Multi-domain]  Cd Length: 70  Bit Score: 44.85  E-value: 6.66e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38704091   9 LVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWN------AITLIESTLP 69
Cdd:cd04873   1 TVVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSDGrpldpeRIARLEEALE 67
ACT COG3830
ACT domain, binds amino acids and other small ligands [Signal transduction mechanisms];
9-77 8.76e-06

ACT domain, binds amino acids and other small ligands [Signal transduction mechanisms];


Pssm-ID: 443042 [Multi-domain]  Cd Length: 212  Bit Score: 44.31  E-value: 8.76e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38704091   9 LVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIML--LSGSWNAITLIESTLPLKGAELDL 77
Cdd:COG3830   5 ALITVTGKDRPGITAAVSGVLAEHGVNILDISQTVIHGYFTMGMLvdLPESSASFEELQKDLEAAGEELGV 75
ACT_1ZPV cd04872
ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain ...
 10-55 5.22e-05

ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.


Pssm-ID: 153144 [Multi-domain]  Cd Length: 88  Bit Score: 40.29  E-value: 5.22e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 38704091  10 VITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLS 55
Cdd:cd04872   3 VITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVD 48
PRK00194 PRK00194
ACT domain-containing protein;
10-55 5.93e-04

ACT domain-containing protein;


Pssm-ID: 178923 [Multi-domain]  Cd Length: 90  Bit Score: 37.48  E-value: 5.93e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 38704091   10 VITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLS 55
Cdd:PRK00194   5 IITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVD 50
ACT_F4HF-DF cd04875
N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate ...
 10-39 3.77e-03

N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.


Pssm-ID: 153147 [Multi-domain]  Cd Length: 74  Bit Score: 34.84  E-value: 3.77e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 38704091  10 VITALGADRPGIVNTITRHVSSCGCNIEDS 39
Cdd:cd04875   1 ILTLSCPDRPGIVAAVSGFLAEHGGNIVES 30
ACT cd02116
ACT domains are commonly involved in specifically binding an amino acid or other small ligand ...
 11-54 5.40e-03

ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times.


Pssm-ID: 153139 [Multi-domain]  Cd Length: 60  Bit Score: 34.19  E-value: 5.40e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 38704091  11 ITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLL 54
Cdd:cd02116   1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFI 44
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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