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Conserved domains on  [gi|521099769|ref|WP_020430660|]
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MULTISPECIES: glycine cleavage system protein R [Vibrio]

Protein Classification

glycine cleavage system protein R( domain architecture ID 11457676)

glycine cleavage system protein R is a transcriptional repressor, binding of glycine leads to activation of specific transcription by disrupting GcvA/GcvR interactions and freeing GcvA to activate the gcvTHP operon

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GcvR COG2716
Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];
2-177 3.02e-63

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


:

Pssm-ID: 442029 [Multi-domain]  Cd Length: 174  Bit Score: 192.74  E-value: 3.02e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769   2 TQHLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRTS 81
Cdd:COG2716    1 MQHLVITAIGPDRPGIVAALARAVSEHGCNILDSRMARLGGEFAGILLVSGPWDAIAKLEAALPALAAELGLLVTVKRTE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769  82 PHAQQANAYTVEVYVESDDKPGLTEKFTQFFADRNIGMASLSAQTIDklKLERETNQFQIAITAHVDSDYNLMQLQEEFD 161
Cdd:COG2716   81 PHEAPPAGLPYVVEVVGNDRPGIVAEVTQFLAERGINIEDLSTKTYP--APMSGTPLFSAQITVHVPAGLDIDALRDALE 158

                        170
                 ....*....|....*.
gi 521099769 162 ALCQTFDVHGSLNFIK 177
Cdd:COG2716  159 DLADELNVDISLEPIK 174
 
Name Accession Description Interval E-value
GcvR COG2716
Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];
2-177 3.02e-63

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


Pssm-ID: 442029 [Multi-domain]  Cd Length: 174  Bit Score: 192.74  E-value: 3.02e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769   2 TQHLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRTS 81
Cdd:COG2716    1 MQHLVITAIGPDRPGIVAALARAVSEHGCNILDSRMARLGGEFAGILLVSGPWDAIAKLEAALPALAAELGLLVTVKRTE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769  82 PHAQQANAYTVEVYVESDDKPGLTEKFTQFFADRNIGMASLSAQTIDklKLERETNQFQIAITAHVDSDYNLMQLQEEFD 161
Cdd:COG2716   81 PHEAPPAGLPYVVEVVGNDRPGIVAEVTQFLAERGINIEDLSTKTYP--APMSGTPLFSAQITVHVPAGLDIDALRDALE 158

                        170
                 ....*....|....*.
gi 521099769 162 ALCQTFDVHGSLNFIK 177
Cdd:COG2716  159 DLADELNVDISLEPIK 174
gcvR PRK11589
glycine cleavage system transcriptional repressor; Provisional
 3-174 7.32e-54

glycine cleavage system transcriptional repressor; Provisional


Pssm-ID: 236935 [Multi-domain]  Cd Length: 190  Bit Score: 169.57  E-value: 7.32e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769   3 QH-LVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRTS 81
Cdd:PRK11589   6 QHyLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMKRTT 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769  82 PHAQQANAYTVEVYVESDDKPGLTEKFTQFFADRNIGMASLSAQTidKLKLERETNQFQIAITAHVDSDYNLMQLQEEFD 161
Cdd:PRK11589  86 ARPRPAMPATVWVQVEVADSPHLIERFTALFDSHHMNIAELVSRT--QPAEGERPAQLHIQITAHSPASQDAANIEQAFK 163

                        170
                 ....*....|...
gi 521099769 162 ALCQTFDVHGSLN 174
Cdd:PRK11589 164 ALCTELNAQGSIN 176
ACT_GcvR_1 cd04893
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
 4-80 6.89e-37

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: 122.43  E-value: 6.89e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 521099769   4 HLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRT 80
Cdd:cd04893    1 HLVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSWDAIAKLEAALPGLARRLDLTLMMKRT 77
ACT_6 pfam13740
ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains.
 3-78 1.01e-22

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


Pssm-ID: 433446 [Multi-domain]  Cd Length: 76  Bit Score: 86.07  E-value: 1.01e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 521099769    3 QHLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMK 78
Cdd:pfam13740   1 EILLITATGPDRPGLTASLTAVLAEHGCNILDSGQAVIHNRLSLGLLVSGPWDALARLEKDLLFLAHELGLTVRFK 76
 
Name Accession Description Interval E-value
GcvR COG2716
Glycine cleavage system regulator GcvR [Amino acid transport and metabolism];
2-177 3.02e-63

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


Pssm-ID: 442029 [Multi-domain]  Cd Length: 174  Bit Score: 192.74  E-value: 3.02e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769   2 TQHLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRTS 81
Cdd:COG2716    1 MQHLVITAIGPDRPGIVAALARAVSEHGCNILDSRMARLGGEFAGILLVSGPWDAIAKLEAALPALAAELGLLVTVKRTE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769  82 PHAQQANAYTVEVYVESDDKPGLTEKFTQFFADRNIGMASLSAQTIDklKLERETNQFQIAITAHVDSDYNLMQLQEEFD 161
Cdd:COG2716   81 PHEAPPAGLPYVVEVVGNDRPGIVAEVTQFLAERGINIEDLSTKTYP--APMSGTPLFSAQITVHVPAGLDIDALRDALE 158

                        170
                 ....*....|....*.
gi 521099769 162 ALCQTFDVHGSLNFIK 177
Cdd:COG2716  159 DLADELNVDISLEPIK 174
gcvR PRK11589
glycine cleavage system transcriptional repressor; Provisional
 3-174 7.32e-54

glycine cleavage system transcriptional repressor; Provisional


Pssm-ID: 236935 [Multi-domain]  Cd Length: 190  Bit Score: 169.57  E-value: 7.32e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769   3 QH-LVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRTS 81
Cdd:PRK11589   6 QHyLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGAELDLLIVMKRTT 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769  82 PHAQQANAYTVEVYVESDDKPGLTEKFTQFFADRNIGMASLSAQTidKLKLERETNQFQIAITAHVDSDYNLMQLQEEFD 161
Cdd:PRK11589  86 ARPRPAMPATVWVQVEVADSPHLIERFTALFDSHHMNIAELVSRT--QPAEGERPAQLHIQITAHSPASQDAANIEQAFK 163

                        170
                 ....*....|...
gi 521099769 162 ALCQTFDVHGSLN 174
Cdd:PRK11589 164 ALCTELNAQGSIN 176
ACT_GcvR_1 cd04893
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
 4-80 6.89e-37

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: 122.43  E-value: 6.89e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 521099769   4 HLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMKRT 80
Cdd:cd04893    1 HLVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSWDAIAKLEAALPGLARRLDLTLMMKRT 77
ACT_6 pfam13740
ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains.
 3-78 1.01e-22

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


Pssm-ID: 433446 [Multi-domain]  Cd Length: 76  Bit Score: 86.07  E-value: 1.01e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 521099769    3 QHLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETLLPLLGQEQDLITMMK 78
Cdd:pfam13740   1 EILLITATGPDRPGLTASLTAVLAEHGCNILDSGQAVIHNRLSLGLLVSGPWDALARLEKDLLFLAHELGLTVRFK 76
ACT_GcvR_2 cd04869
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
 93-175 6.90e-20

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: 79.19  E-value: 6.90e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521099769  93 EVYVESDDKPGLTEKFTQFFADRNIGMASLSAQTIDklKLERETNQFQIAITAHVDSDYNLMQLQEEFDALCQTFDVHGS 172
Cdd:cd04869    1 VVEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS--APMSGTPLFKAQATLALPAGTDLDALREELEELCDDLNVDIS 78


                 ...
gi 521099769 173 LNF 175
Cdd:cd04869   79 LEP 81
ACT_UUR-ACR-like cd04873
ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) ...
 5-63 2.81e-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: 45.62  E-value: 2.81e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 521099769   5 LVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVSGNANSITRVETL 63
Cdd:cd04873    1 TVVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSDGRPLDPERI 59
ACT COG3830
ACT domain, binds amino acids and other small ligands [Signal transduction mechanisms];
1-73 2.94e-06

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


Pssm-ID: 443042 [Multi-domain]  Cd Length: 212  Bit Score: 45.46  E-value: 2.94e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 521099769   1 MTQHLVITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLV--SGNANSITRVETLLPLLGQEQDL 73
Cdd:COG3830    1 MSMKALITVTGKDRPGITAAVSGVLAEHGVNILDISQTVIHGYFTMGMLVdlPESSASFEELQKDLEAAGEELGV 75
ACT_1ZPV cd04872
ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain ...
 6-51 2.24e-04

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: 38.37  E-value: 2.24e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 521099769   6 VITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLVS 51
Cdd:cd04872    3 VITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVD 48
PRK00194 PRK00194
ACT domain-containing protein;
6-71 1.20e-03

ACT domain-containing protein;


Pssm-ID: 178923 [Multi-domain]  Cd Length: 90  Bit Score: 36.33  E-value: 1.20e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 521099769   6 VITAVGTDRPGICNQVVKLVTQAGCNIIDSRIALFGNEFTLIMLV--SGNANSITRVETLLPLLGQEQ 71
Cdd:PRK00194   5 IITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVdiSESKKDFAELKEELEELGKEL 72
 
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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