NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2308965483|ref|WP_261322693|]
View 

Crp/Fnr family transcriptional regulator [Rhizobium leguminosarum]

Protein Classification

Crp/Fnr family transcriptional regulator( domain architecture ID 11429533)

Crp/Fnr family transcriptional regulator containing a DNA-binding Crp-like helix-turn-helix (HTH) domain, may bind cyclic nucleotides

CATH:  2.60.120.10|1.10.10.10
Gene Ontology:  GO:0003677|GO:0030552
PubMed:  11407111|14638413

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 151-354 2.15e-27

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


:

Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 107.38  E-value: 2.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 151 HLTTPQLLVFERILEPLALPRDFELASIGLPVSHYYFLESGIASMVATSPEGKKAEIGLVGRDGVSPPALTMEAEAFSFD 230
Cdd:COG0664     3 GLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPAT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 231 VMMQVGGAGRRVEARALAGFLFDQPAVRQLLARFLQGFFAQVAHTALSNAVHKIDVRLAKWILMCHDRMDGE-EIELTHE 309
Cdd:COG0664    83 AEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLDGRiDLPLTQE 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2308965483 310 YMATMLGVRRSSVTEALHILEGEHFIYSHRGLVIVRNRTSLEAFA 354
Cdd:COG0664   163 EIASYLGLTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 151-354 2.15e-27

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 107.38  E-value: 2.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 151 HLTTPQLLVFERILEPLALPRDFELASIGLPVSHYYFLESGIASMVATSPEGKKAEIGLVGRDGVSPPALTMEAEAFSFD 230
Cdd:COG0664     3 GLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPAT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 231 VMMQVGGAGRRVEARALAGFLFDQPAVRQLLARFLQGFFAQVAHTALSNAVHKIDVRLAKWILMCHDRMDGE-EIELTHE 309
Cdd:COG0664    83 AEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLDGRiDLPLTQE 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2308965483 310 YMATMLGVRRSSVTEALHILEGEHFIYSHRGLVIVRNRTSLEAFA 354
Cdd:COG0664   163 EIASYLGLTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 287-353 1.16e-09

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 54.00  E-value: 1.16e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2308965483 287 RLAKWILMCHDRMDGEEIEL--THEYMATMLGVRRSSVTEALHILEGEHFIysHRGLVIVRNRTSLEAF 353
Cdd:pfam13545   2 RLARFLLELAARDGGGRIDLplTQEDLADLLGTTRETVSRVLSELRREGLI--ERGRITILDPEALEAL 68
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 311-340 1.72e-03

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 36.66  E-value: 1.72e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2308965483 311 MATMLGVRRSSVTEALHILEGEHFIYSHRG 340
Cdd:cd07377    31 LAEELGVSRTTVREALRELEAEGLVERRPG 60
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
300-345 1.81e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 35.88  E-value: 1.81e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2308965483  300 DGEEIELTHEYMATMLGVRRSSVTEALHILEGEHFIYSHRGLVIVR 345
Cdd:smart00419   3 IRVRLPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRIVIL 48
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 151-354 2.15e-27

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 107.38  E-value: 2.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 151 HLTTPQLLVFERILEPLALPRDFELASIGLPVSHYYFLESGIASMVATSPEGKKAEIGLVGRDGVSPPALTMEAEAFSFD 230
Cdd:COG0664     3 GLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPAT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 231 VMMQVGGAGRRVEARALAGFLFDQPAVRQLLARFLQGFFAQVAHTALSNAVHKIDVRLAKWILMCHDRMDGE-EIELTHE 309
Cdd:COG0664    83 AEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLDGRiDLPLTQE 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2308965483 310 YMATMLGVRRSSVTEALHILEGEHFIYSHRGLVIVRNRTSLEAFA 354
Cdd:COG0664   163 EIASYLGLTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 287-353 1.16e-09

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 54.00  E-value: 1.16e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2308965483 287 RLAKWILMCHDRMDGEEIEL--THEYMATMLGVRRSSVTEALHILEGEHFIysHRGLVIVRNRTSLEAF 353
Cdd:pfam13545   2 RLARFLLELAARDGGGRIDLplTQEDLADLLGTTRETVSRVLSELRREGLI--ERGRITILDPEALEAL 68
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 311-340 1.72e-03

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 36.66  E-value: 1.72e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2308965483 311 MATMLGVRRSSVTEALHILEGEHFIYSHRG 340
Cdd:cd07377    31 LAEELGVSRTTVREALRELEAEGLVERRPG 60
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
300-345 1.81e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 35.88  E-value: 1.81e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2308965483  300 DGEEIELTHEYMATMLGVRRSSVTEALHILEGEHFIYSHRGLVIVR 345
Cdd:smart00419   3 IRVRLPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRIVIL 48
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 179-263 5.64e-03

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 35.66  E-value: 5.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308965483 179 GLPVSHYYFLESGIASMVATSPEGKKAEIGLVGRDGVsppaltmeaeafsFDVMMQVGGAGRRVEARALAG---FLFDQP 255
Cdd:pfam00027  14 GDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDF-------------FGELALLGGEPRSATVVALTDselLVIPRE 80


                  ....*...
gi 2308965483 256 AVRQLLAR 263
Cdd:pfam00027  81 DFLELLER 88
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH