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Conserved domains on  [gi|2593605598|ref|WP_316317858|]
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FCD domain-containing protein [Clavibacter michiganensis]

Protein Classification

FadR/GntR family transcriptional regulator( domain architecture ID 11450686)

helix-turn-helix transcriptional regulator belonging to the GntR family, which contains FadR, HutC, MocR, YtrA, AraR, PlmA, and many other subfamilies

CATH:  1.10.10.10
Gene Ontology:  GO:0003677|GO:0003700
PubMed:  2060763
SCOP:  4000155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
29-157 1.03e-22

DNA-binding transcriptional regulator, FadR family [Transcription];


:

Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 89.61  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAGAlvDFLAADIEFHHLILEASGNDMFSALREVITEVLSG 108
Cdd:COG2186    97 LLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGE--AFAEADLAFHRAIAEASGNPLLALLLESLRELLRR 174

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2593605598 109 RTHQGLMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMASLLAEVSSAI 157
Cdd:COG2186   175 SVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERL 223
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
29-157 1.03e-22

DNA-binding transcriptional regulator, FadR family [Transcription];


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 89.61  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAGAlvDFLAADIEFHHLILEASGNDMFSALREVITEVLSG 108
Cdd:COG2186    97 LLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGE--AFAEADLAFHRAIAEASGNPLLALLLESLRELLRR 174

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2593605598 109 RTHQGLMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMASLLAEVSSAI 157
Cdd:COG2186   175 SVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERL 223
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 29-148 1.60e-14

FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).


Pssm-ID: 429623 [Multi-domain]  Cd Length: 121  Bit Score: 65.85  E-value: 1.60e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAGALVDFLAADIEFHHLILEASGNDMFSALREVITEVLSG 108
Cdd:pfam07729   2 LYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLRR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2593605598 109 RTHQGLMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMAS 148
Cdd:pfam07729  82 LRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 29-152 1.04e-13

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 63.53  E-value: 1.04e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598   29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAG-ALVDFLAADIEFHHLILEASGNDMFSALREVITEVLS 107
Cdd:smart00895   2 LYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGdDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLR 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2593605598  108 GRTHqglMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMASLLAE 152
Cdd:smart00895  82 RLRR---LSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 41-154 6.88e-07

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 47.32  E-value: 6.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  41 ASLAARNATAGQRTRIAE-LAVDPRRLGEAGAlvdFLAADIEFHHLILEASGNDMFSA--------LREVITEVLSGRTH 111
Cdd:PRK03837  119 ARYAAEHATDEQIALLRKaLERNSQSLGDNAA---FIRSDMEFHRVIAEIPGNPIFMAihealldwLIEARPEVVILHGH 195

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2593605598 112 QGLmprtprphALDTHEQVAHAIRDGDAATAEAGMASLLAEVS 154
Cdd:PRK03837  196 ENV--------TLQEHIAIVDAIRAHDPDEADRALQSHLNRVS 230
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
29-157 1.03e-22

DNA-binding transcriptional regulator, FadR family [Transcription];


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 89.61  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAGAlvDFLAADIEFHHLILEASGNDMFSALREVITEVLSG 108
Cdd:COG2186    97 LLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGE--AFAEADLAFHRAIAEASGNPLLALLLESLRELLRR 174

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2593605598 109 RTHQGLMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMASLLAEVSSAI 157
Cdd:COG2186   175 SVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERL 223
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
29-157 6.97e-15

DNA-binding transcriptional regulator, GntR family [Transcription];


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 68.80  E-value: 6.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAGALVDFLAADIEFHHLILEASGNDMFSALREVITEVLSG 108
Cdd:COG1802    85 LYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLELDREFHRALVEAAGNPRLAELLRRLRARLRR 164

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2593605598 109 RTHQGLMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMASLLAEVSSAI 157
Cdd:COG1802   165 YRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERL 213
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 29-148 1.60e-14

FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).


Pssm-ID: 429623 [Multi-domain]  Cd Length: 121  Bit Score: 65.85  E-value: 1.60e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAGALVDFLAADIEFHHLILEASGNDMFSALREVITEVLSG 108
Cdd:pfam07729   2 LYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLRR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2593605598 109 RTHQGLMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMAS 148
Cdd:pfam07729  82 LRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 29-152 1.04e-13

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 63.53  E-value: 1.04e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598   29 VTQLCRAVEPVAASLAARNATAGQRTRIAELAVDPRRLGEAG-ALVDFLAADIEFHHLILEASGNDMFSALREVITEVLS 107
Cdd:smart00895   2 LYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGdDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLR 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2593605598  108 GRTHqglMPRTPRPHALDTHEQVAHAIRDGDAATAEAGMASLLAE 152
Cdd:smart00895  82 RLRR---LSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 41-154 6.88e-07

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 47.32  E-value: 6.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2593605598  41 ASLAARNATAGQRTRIAE-LAVDPRRLGEAGAlvdFLAADIEFHHLILEASGNDMFSA--------LREVITEVLSGRTH 111
Cdd:PRK03837  119 ARYAAEHATDEQIALLRKaLERNSQSLGDNAA---FIRSDMEFHRVIAEIPGNPIFMAihealldwLIEARPEVVILHGH 195

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2593605598 112 QGLmprtprphALDTHEQVAHAIRDGDAATAEAGMASLLAEVS 154
Cdd:PRK03837  196 ENV--------TLQEHIAIVDAIRAHDPDEADRALQSHLNRVS 230
 
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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