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Conserved domains on  [gi|516617427|ref|WP_017992270|]
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MULTISPECIES: Crp/Fnr family transcriptional regulator [Rhizobium]

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

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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 ...
 14-221 3.63e-32

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: 115.85  E-value: 3.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  14 FAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSYA 93
Cdd:COG0664    1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  94 YSARSADGAEVALFALAELLAFADQHPIVHRNVMRIMVRHLLGAMDCIAGDRLLTAAQRVANYLMSRcpasATTSRVTFR 173
Cdd:COG0664   81 ATAEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLEL----ADRLDGRID 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 516617427 174 LPYRKRILAGKLGLAPEALSRAFAALAPSG-VEVRGKVVLVDSVDLLRE 221
Cdd:COG0664  157 LPLTQEEIASYLGLTRETVSRILKKLEKEGlIELERGRITILDREALER 205
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 14-221 3.63e-32

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: 115.85  E-value: 3.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  14 FAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSYA 93
Cdd:COG0664    1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  94 YSARSADGAEVALFALAELLAFADQHPIVHRNVMRIMVRHLLGAMDCIAGDRLLTAAQRVANYLMSRcpasATTSRVTFR 173
Cdd:COG0664   81 ATAEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLEL----ADRLDGRID 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 516617427 174 LPYRKRILAGKLGLAPEALSRAFAALAPSG-VEVRGKVVLVDSVDLLRE 221
Cdd:COG0664  157 LPLTQEEIASYLGLTRETVSRILKKLEKEGlIELERGRITILDREALER 205
ftrB PRK09392
transcriptional activator FtrB; Provisional
 13-222 5.55e-30

transcriptional activator FtrB; Provisional


Pssm-ID: 181817 [Multi-domain]  Cd Length: 236  Bit Score: 111.27  E-value: 5.55e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  13 LFAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSkSESAGREADICVCEPGDTFgeyLLAG---G 89
Cdd:PRK09392  14 LFADMADATFERLMRGAFLQRFPPGTMLITEGEPADFLFVVLDGLVELS-ASSQDRETTLAILRPVSTF---ILAAvvlD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  90 GSYAYSARSADGAEVALFALAELLAFADQHPIVHRNVMRIMVRHLLGAMDCIAGDRLLTAAQRVANYLMSRcpASATTSR 169
Cdd:PRK09392  90 APYLMSARTLTRSRVLMIPAELVREAMSEDPGFMRAVVFELAGCYRGLVKSLKNQKLRSSAERLANYLLKQ--SLRQGGA 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516617427 170 VTFRLPYRKRILAGKLGLAPEALSRAFAALAPSGVEVRG-KVVLVDSVDLLREA 222
Cdd:PRK09392 168 DVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHVDGsAVTITDPAGLARFA 221
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 13-104 4.43e-17

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 73.90  E-value: 4.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  13 LFAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSY 92
Cdd:cd00038    1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPR 80

                         90
                 ....*....|..
gi 516617427  93 AYSARSADGAEV 104
Cdd:cd00038   81 SATVRALTDSEL 92
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 31-104 2.69e-11

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: 58.00  E-value: 2.69e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516617427   31 FRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSYAYSARSADGAEV 104
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSEL 74
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 13-96 1.72e-10

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 56.64  E-value: 1.72e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427    13 LFAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSY 92
Cdd:smart00100   1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRR 80


                   ....
gi 516617427    93 AYSA 96
Cdd:smart00100  81 AASA 84
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 14-221 3.63e-32

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: 115.85  E-value: 3.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  14 FAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSYA 93
Cdd:COG0664    1 FAGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  94 YSARSADGAEVALFALAELLAFADQHPIVHRNVMRIMVRHLLGAMDCIAGDRLLTAAQRVANYLMSRcpasATTSRVTFR 173
Cdd:COG0664   81 ATAEALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLEL----ADRLDGRID 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 516617427 174 LPYRKRILAGKLGLAPEALSRAFAALAPSG-VEVRGKVVLVDSVDLLRE 221
Cdd:COG0664  157 LPLTQEEIASYLGLTRETVSRILKKLEKEGlIELERGRITILDREALER 205
ftrB PRK09392
transcriptional activator FtrB; Provisional
 13-222 5.55e-30

transcriptional activator FtrB; Provisional


Pssm-ID: 181817 [Multi-domain]  Cd Length: 236  Bit Score: 111.27  E-value: 5.55e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  13 LFAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSkSESAGREADICVCEPGDTFgeyLLAG---G 89
Cdd:PRK09392  14 LFADMADATFERLMRGAFLQRFPPGTMLITEGEPADFLFVVLDGLVELS-ASSQDRETTLAILRPVSTF---ILAAvvlD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  90 GSYAYSARSADGAEVALFALAELLAFADQHPIVHRNVMRIMVRHLLGAMDCIAGDRLLTAAQRVANYLMSRcpASATTSR 169
Cdd:PRK09392  90 APYLMSARTLTRSRVLMIPAELVREAMSEDPGFMRAVVFELAGCYRGLVKSLKNQKLRSSAERLANYLLKQ--SLRQGGA 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516617427 170 VTFRLPYRKRILAGKLGLAPEALSRAFAALAPSGVEVRG-KVVLVDSVDLLREA 222
Cdd:PRK09392 168 DVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHVDGsAVTITDPAGLARFA 221
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 13-104 4.43e-17

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 73.90  E-value: 4.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  13 LFAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSY 92
Cdd:cd00038    1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPR 80

                         90
                 ....*....|..
gi 516617427  93 AYSARSADGAEV 104
Cdd:cd00038   81 SATVRALTDSEL 92
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 31-104 2.69e-11

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: 58.00  E-value: 2.69e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516617427   31 FRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSYAYSARSADGAEV 104
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSEL 74
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 13-96 1.72e-10

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 56.64  E-value: 1.72e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427    13 LFAGLDQATVEQFTATAEFRAFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGEYLLAGGGSY 92
Cdd:smart00100   1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRR 80


                   ....
gi 516617427    93 AYSA 96
Cdd:smart00100  81 AASA 84
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 151-221 1.27e-06

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: 44.37  E-value: 1.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516617427  151 QRVANYLMSRCpasATTSRVTFRLPYRKRILAGKLGLAPEALSRAFAALAPSGVEVRGKVVLVDsVDLLRE 221
Cdd:pfam13545   1 QRLARFLLELA---ARDGGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLIERGRITILD-PEALEA 67
fixK PRK09391
transcriptional regulator FixK; Provisional
 29-214 3.70e-06

transcriptional regulator FixK; Provisional


Pssm-ID: 236494 [Multi-domain]  Cd Length: 230  Bit Score: 46.19  E-value: 3.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427  29 AEFRaFAADEKIIAEGQQASFVYCVMNGFVRLSKSESAGREADICVCEPGDTFGeylLAGGGSYAYSARSADGAEVALFA 108
Cdd:PRK09391  39 SEFS-YKKGEEIYGEGEPADYVYQVESGAVRTYRLLSDGRRQIGAFHLPGDVFG---LESGSTHRFTAEAIVDTTVRLIK 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516617427 109 LAELLAFADQHPIVHRNVMRIM---VRHllgamdciAGDRLL-----TAAQRVANYLMSRCPASATTSRvtFRLPYRKRI 180
Cdd:PRK09391 115 RRSLEQAAATDVDVARALLSLTaggLRH--------AQDHMLllgrkTAMERVAAFLLEMDERLGGAGM--MALPMSRRD 184

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 516617427 181 LAGKLGLAPEALSRAFAALAPSGV-EVRG--KVVLVD 214
Cdd:PRK09391 185 IADYLGLTIETVSRALSQLQDRGLiGLSGarQIELRN 221
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
168-213 1.44e-04

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 38.19  E-value: 1.44e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 516617427   168 SRVTFRLPYRKRILAGKLGLAPEALSRAFAALAPSG-VEVRGKVVLV 213
Cdd:smart00419   1 EGIRVRLPLTRQEIAELLGLTRETVSRTLKRLEKEGlISREGGRIVI 47
 
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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