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Conserved domains on  [gi|548307011|ref|WP_022497727|]
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Crp/Fnr family transcriptional regulator [Megasphaera elsdenii]

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 ...
 14-220 6.39e-38

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: 130.88  E-value: 6.39e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  14 FCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAFACLPES 93
Cdd:COG0664    1 FAGLSDEELEALLAHLELRT--LKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  94 lATVDVVAASDTVIMQVHVDNVLHAGQvltpAQARFMSNLLALMAEKNRLLTEKIRYLTQRSTRQKIVLYLSDLARKKGk 173
Cdd:COG0664   79 -SPATAEALEDSELLRIPREDLEELLE----RNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLD- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 548307011 174 ATFSLPFNRQQMADFLSVDRSALSAELSKMKKEGLIDYRKDKFTLLQ 220
Cdd:COG0664  153 GRIDLPLTQEEIASYLGLTRETVSRILKKLEKEGLIELERGRITILD 199
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 14-220 6.39e-38

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: 130.88  E-value: 6.39e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  14 FCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAFACLPES 93
Cdd:COG0664    1 FAGLSDEELEALLAHLELRT--LKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  94 lATVDVVAASDTVIMQVHVDNVLHAGQvltpAQARFMSNLLALMAEKNRLLTEKIRYLTQRSTRQKIVLYLSDLARKKGk 173
Cdd:COG0664   79 -SPATAEALEDSELLRIPREDLEELLE----RNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLD- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 548307011 174 ATFSLPFNRQQMADFLSVDRSALSAELSKMKKEGLIDYRKDKFTLLQ 220
Cdd:COG0664  153 GRIDLPLTQEEIASYLGLTRETVSRILKKLEKEGLIELERGRITILD 199
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 13-113 2.94e-12

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: 61.19  E-value: 2.94e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  13 LFCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAfACLPE 92
Cdd:cd00038    1 LFSGLDDEELEELADALEERR--FPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGEL-ALLGN 77

                         90       100
                 ....*....|....*....|.
gi 548307011  93 SLATVDVVAASDTVIMQVHVD 113
Cdd:cd00038   78 GPRSATVRALTDSELLVLPRS 98
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 33-110 2.74e-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: 57.62  E-value: 2.74e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 548307011   33 KKKYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAfACLPESLATVDVVAASDTVIMQV 110
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGEL-ALLGGEPRSATVVALTDSELLVI 77
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 13-133 2.56e-07

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: 47.78  E-value: 2.56e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011    13 LFCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGE-AFACLP 91
Cdd:smart00100   1 LFKNLDAEELRELADALEPVR--YPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGElALLTNS 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 548307011    92 ESLATVDVVAASDTVIMQVHVDNVLHAGQVLTPAQARFMSNL 133
Cdd:smart00100  79 RRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
fixK PRK09391
transcriptional regulator FixK; Provisional
 35-212 5.63e-04

transcriptional regulator FixK; Provisional


Pssm-ID: 236494 [Multi-domain]  Cd Length: 230  Bit Score: 39.64  E-value: 5.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  35 KYQKGEFLFYSGDTVPYIGLVLDGAVHIIQedywgnrnILS----QIPAGFFFGEAFACLPESLATVDVVAASDT---VI 107
Cdd:PRK09391  42 SYKKGEEIYGEGEPADYVYQVESGAVRTYR--------LLSdgrrQIGAFHLPGDVFGLESGSTHRFTAEAIVDTtvrLI 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011 108 MQVHVDNVLHAGQVLTPaqarfmsNLLALMAEKNRLLTEKIRYLTQRSTRQKIVLYLSDLARKKGKA-TFSLPFNRQQMA 186
Cdd:PRK09391 114 KRRSLEQAAATDVDVAR-------ALLSLTAGGLRHAQDHMLLLGRKTAMERVAAFLLEMDERLGGAgMMALPMSRRDIA 186

                        170       180
                 ....*....|....*....|....*.
gi 548307011 187 DFLSVDRSALSAELSKMKKEGLIDYR 212
Cdd:PRK09391 187 DYLGLTIETVSRALSQLQDRGLIGLS 212
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 14-220 6.39e-38

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: 130.88  E-value: 6.39e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  14 FCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAFACLPES 93
Cdd:COG0664    1 FAGLSDEELEALLAHLELRT--LKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  94 lATVDVVAASDTVIMQVHVDNVLHAGQvltpAQARFMSNLLALMAEKNRLLTEKIRYLTQRSTRQKIVLYLSDLARKKGk 173
Cdd:COG0664   79 -SPATAEALEDSELLRIPREDLEELLE----RNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLD- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 548307011 174 ATFSLPFNRQQMADFLSVDRSALSAELSKMKKEGLIDYRKDKFTLLQ 220
Cdd:COG0664  153 GRIDLPLTQEEIASYLGLTRETVSRILKKLEKEGLIELERGRITILD 199
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 13-113 2.94e-12

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: 61.19  E-value: 2.94e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  13 LFCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAfACLPE 92
Cdd:cd00038    1 LFSGLDDEELEELADALEERR--FPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGEL-ALLGN 77

                         90       100
                 ....*....|....*....|.
gi 548307011  93 SLATVDVVAASDTVIMQVHVD 113
Cdd:cd00038   78 GPRSATVRALTDSELLVLPRS 98
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 33-110 2.74e-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: 57.62  E-value: 2.74e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 548307011   33 KKKYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGEAfACLPESLATVDVVAASDTVIMQV 110
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGEL-ALLGGEPRSATVVALTDSELLVI 77
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 158-213 7.42e-10

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: 53.23  E-value: 7.42e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 548307011  158 QKIVLYLSDLARKKGKATFSLPFNRQQMADFLSVDRSALSAELSKMKKEGLIDYRK 213
Cdd:pfam13545   1 QRLARFLLELAARDGGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLIERGR 56
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 13-133 2.56e-07

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: 47.78  E-value: 2.56e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011    13 LFCGITEADVLPLLEHLKVRKkkYQKGEFLFYSGDTVPYIGLVLDGAVHIIQEDYWGNRNILSQIPAGFFFGE-AFACLP 91
Cdd:smart00100   1 LFKNLDAEELRELADALEPVR--YPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGElALLTNS 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 548307011    92 ESLATVDVVAASDTVIMQVHVDNVLHAGQVLTPAQARFMSNL 133
Cdd:smart00100  79 RRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
fixK PRK09391
transcriptional regulator FixK; Provisional
 35-212 5.63e-04

transcriptional regulator FixK; Provisional


Pssm-ID: 236494 [Multi-domain]  Cd Length: 230  Bit Score: 39.64  E-value: 5.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011  35 KYQKGEFLFYSGDTVPYIGLVLDGAVHIIQedywgnrnILS----QIPAGFFFGEAFACLPESLATVDVVAASDT---VI 107
Cdd:PRK09391  42 SYKKGEEIYGEGEPADYVYQVESGAVRTYR--------LLSdgrrQIGAFHLPGDVFGLESGSTHRFTAEAIVDTtvrLI 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 548307011 108 MQVHVDNVLHAGQVLTPaqarfmsNLLALMAEKNRLLTEKIRYLTQRSTRQKIVLYLSDLARKKGKA-TFSLPFNRQQMA 186
Cdd:PRK09391 114 KRRSLEQAAATDVDVAR-------ALLSLTAGGLRHAQDHMLLLGRKTAMERVAAFLLEMDERLGGAgMMALPMSRRDIA 186

                        170       180
                 ....*....|....*....|....*.
gi 548307011 187 DFLSVDRSALSAELSKMKKEGLIDYR 212
Cdd:PRK09391 187 DYLGLTIETVSRALSQLQDRGLIGLS 212
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 158-209 7.49e-04

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 36.87  E-value: 7.49e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 548307011 158 QKIVLYLSDLARKKG-KATFSLPFNRQQMADFLSVDRSALSAELSKMKKEGLI 209
Cdd:cd00092    3 ERLASFLLNLSLRYGaGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLI 55
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 155-215 1.47e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 36.51  E-value: 1.47e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 548307011 155 STRQKIVLYLSDlarkkGKATFSlpfnrqQMADFLSVDRSALSAELSKMKKEGLIDYRKDK 215
Cdd:cd00090    7 PTRLRILRLLLE-----GPLTVS------ELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
172-219 2.52e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 34.72  E-value: 2.52e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 548307011   172 GKATFSLPFNRQQMADFLSVDRSALSAELSKMKKEGLIDYRKDKFTLL 219
Cdd:smart00419   1 EGIRVRLPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRIVIL 48
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
159-214 4.77e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 34.49  E-value: 4.77e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 548307011   159 KIVLYLSDlarkkGKATFSlpfnrqQMADFLSVDRSALSAELSKMKKEGLIDYRKD 214
Cdd:smart00418   1 KILKLLAE-----GELCVC------ELAEILGLSQSTVSHHLKKLREAGLVESRRE 45
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
166-215 7.52e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 35.56  E-value: 7.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 548307011 166 DLARKKGKATFSlpfnrqQMADFLSVDRSALSAELSKMKKEGLIDYRKDK 215
Cdd:COG1321   17 ELSEEGGPVRTS------DIAERLGVSPPSVTEMLKKLEEKGLVEYEPYG 60
 
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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