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Conserved domains on  [gi|489842153|ref|WP_003745853|]
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Crp/Fnr family transcriptional regulator [Listeria seeligeri]

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 ...
 24-217 3.34e-24

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: 95.44  E-value: 3.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153  24 EAVLPYKRIR-FRRNQKILTEGEETTYFYVIGDGVVSMSKNTCK-EDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEV 101
Cdd:COG0664   10 EALLAHLELRtLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDgREQILGFLGPGDFFGELSLLGGEPSPATAEALEDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153 102 SVYQFERKYVLGKFLSSPDVFWQMNTLMQSMIQPILER-EAYVNLPSNEKVLAGLIACGERFGriesdgsCLIPYYFTQK 180
Cdd:COG0664   90 ELLRIPREDLEELLERNPELARALLRLLARRLRQLQERlVSLAFLSAEERLARFLLELADRLD-------GRIDLPLTQE 162

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489842153 181 ILGNYLNLARAYVATNLRKLEEEGIITLSPKPWRIND 217
Cdd:COG0664  163 EIASYLGLTRETVSRILKKLEKEGLIELERGRITILD 199
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 24-217 3.34e-24

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: 95.44  E-value: 3.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153  24 EAVLPYKRIR-FRRNQKILTEGEETTYFYVIGDGVVSMSKNTCK-EDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEV 101
Cdd:COG0664   10 EALLAHLELRtLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDgREQILGFLGPGDFFGELSLLGGEPSPATAEALEDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153 102 SVYQFERKYVLGKFLSSPDVFWQMNTLMQSMIQPILER-EAYVNLPSNEKVLAGLIACGERFGriesdgsCLIPYYFTQK 180
Cdd:COG0664   90 ELLRIPREDLEELLERNPELARALLRLLARRLRQLQERlVSLAFLSAEERLARFLLELADRLD-------GRIDLPLTQE 162

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489842153 181 ILGNYLNLARAYVATNLRKLEEEGIITLSPKPWRIND 217
Cdd:COG0664  163 EIASYLGLTRETVSRILKKLEKEGLIELERGRITILD 199
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 31-112 2.58e-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: 2.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153   31 RIRFRRNQKILTEGEETTYFYVIGDGVVSMSKNT-CKEDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEVSVYQFERK 109
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLeDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ...
gi 489842153  110 YVL 112
Cdd:pfam00027  81 DFL 83
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 30-109 1.51e-09

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: 53.87  E-value: 1.51e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153  30 KRIRFRRNQKILTEGEETTYFYVIGDGVVSMSKNTC-KEDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEVSVYQFER 108
Cdd:cd00038   18 EERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPR 97


                 .
gi 489842153 109 K 109
Cdd:cd00038   98 S 98
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 30-99 2.74e-06

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: 45.08  E-value: 2.74e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489842153    30 KRIRFRRNQKILTEGEETTYFYVIGDGVVSMSKNTC-KEDSIITFLGKNDAIGPLTMLGGANSPVNYTTIS 99
Cdd:smart00100  18 EPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEdGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVA 88
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 24-217 3.34e-24

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: 95.44  E-value: 3.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153  24 EAVLPYKRIR-FRRNQKILTEGEETTYFYVIGDGVVSMSKNTCK-EDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEV 101
Cdd:COG0664   10 EALLAHLELRtLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDgREQILGFLGPGDFFGELSLLGGEPSPATAEALEDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153 102 SVYQFERKYVLGKFLSSPDVFWQMNTLMQSMIQPILER-EAYVNLPSNEKVLAGLIACGERFGriesdgsCLIPYYFTQK 180
Cdd:COG0664   90 ELLRIPREDLEELLERNPELARALLRLLARRLRQLQERlVSLAFLSAEERLARFLLELADRLD-------GRIDLPLTQE 162

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489842153 181 ILGNYLNLARAYVATNLRKLEEEGIITLSPKPWRIND 217
Cdd:COG0664  163 EIASYLGLTRETVSRILKKLEKEGLIELERGRITILD 199
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 31-112 2.58e-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: 2.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153   31 RIRFRRNQKILTEGEETTYFYVIGDGVVSMSKNT-CKEDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEVSVYQFERK 109
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLeDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ...
gi 489842153  110 YVL 112
Cdd:pfam00027  81 DFL 83
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 30-109 1.51e-09

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: 53.87  E-value: 1.51e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489842153  30 KRIRFRRNQKILTEGEETTYFYVIGDGVVSMSKNTC-KEDSIITFLGKNDAIGPLTMLGGANSPVNYTTISEVSVYQFER 108
Cdd:cd00038   18 EERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPR 97


                 .
gi 489842153 109 K 109
Cdd:cd00038   98 S 98
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 30-99 2.74e-06

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: 45.08  E-value: 2.74e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489842153    30 KRIRFRRNQKILTEGEETTYFYVIGDGVVSMSKNTC-KEDSIITFLGKNDAIGPLTMLGGANSPVNYTTIS 99
Cdd:smart00100  18 EPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEdGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVA 88
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 166-207 3.66e-03

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: 35.13  E-value: 3.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489842153  166 ESDGSCLIPYYFTQKILGNYLNLARAYVATNLRKLEEEGIIT 207
Cdd:pfam13545  12 ARDGGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLIE 53
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
169-216 4.51e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 34.34  E-value: 4.51e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 489842153   169 GSCLIPYYFTQKILGNYLNLARAYVATNLRKLEEEGIITLSPKPWRIN 216
Cdd:smart00419   1 EGIRVRLPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRIVIL 48
 
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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