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Conserved domains on  [gi|489455712|ref|WP_003360982|]
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Crp/Fnr family transcriptional regulator [Clostridium botulinum]

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 ...
 25-221 1.04e-33

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: 120.09  E-value: 1.04e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  25 KDILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDT 104
Cdd:COG0664   10 EALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPATAEALEDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712 105 YLIAIPSDILRKKYLDNVKFLHHLIDSLSEKLYATINNSSYNFVYPLINRLSSYLVEHIED-KNYIILNSSFLEIAQFLG 183
Cdd:COG0664   90 ELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRlDGRIDLPLTQEEIASYLG 169

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489455712 184 TTYRHLNRTFKELESKSIIKCENKTIYILDENRLRDLS 221
Cdd:COG0664  170 LTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 25-221 1.04e-33

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: 120.09  E-value: 1.04e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  25 KDILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDT 104
Cdd:COG0664   10 EALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPATAEALEDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712 105 YLIAIPSDILRKKYLDNVKFLHHLIDSLSEKLYATINNSSYNFVYPLINRLSSYLVEHIED-KNYIILNSSFLEIAQFLG 183
Cdd:COG0664   90 ELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRlDGRIDLPLTQEEIASYLG 169

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489455712 184 TTYRHLNRTFKELESKSIIKCENKTIYILDENRLRDLS 221
Cdd:COG0664  170 LTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
PRK10402 PRK10402
DNA-binding transcriptional activator YeiL; Provisional
 1-227 4.21e-33

DNA-binding transcriptional activator YeiL; Provisional


Pssm-ID: 236682 [Multi-domain]  Cd Length: 226  Bit Score: 119.06  E-value: 4.21e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712   1 MKKILNNDLLNHYINEHNIESIFDKDILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDF 80
Cdd:PRK10402   1 MKESKNSEEISHYMSESAFKDCFSFDVSADTELFHFLAREYIVQEGQQPSYLFYLTRGRAKLYATLANGKVSLIDFFAAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  81 NTIGDLEFLKNIPILCDVDAVGDTYLIAIPSDILRKKYLDNVKFLHHLIDSLSEKLYATINNSSYNFVYPLINRLSSYLV 160
Cdd:PRK10402  81 CFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFIL 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489455712 161 EHIEDKNYIILNSsflEIAQFLGTTYRHLNRTFKELESKSIIKCENKTIYILDENRLRDLSKNFYIK 227
Cdd:PRK10402 161 LTQEGDLYHEKHT---QAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLALELKPE 224
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 27-129 1.95e-11

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: 59.26  E-value: 1.95e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  27 ILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDTYL 106
Cdd:cd00038   13 LADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSEL 92

                         90       100
                 ....*....|....*....|...
gi 489455712 107 IAIPSDILRKKYLDNVKFLHHLI 129
Cdd:cd00038   93 LVLPRSDFRRLLQEYPELARRLL 115
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 33-121 7.64e-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: 56.85  E-value: 7.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712   33 LHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDTYLIAIPSD 112
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ....*....
gi 489455712  113 ILRKKYLDN 121
Cdd:pfam00027  81 DFLELLERD 89
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 26-110 5.00e-05

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: 41.62  E-value: 5.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712    26 DILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPI--LCDVDAVGD 103
Cdd:smart00100  12 ELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRaaSAAAVALEL 91


                   ....*..
gi 489455712   104 TYLIAIP 110
Cdd:smart00100  92 ATLLRID 98
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 25-221 1.04e-33

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: 120.09  E-value: 1.04e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  25 KDILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDT 104
Cdd:COG0664   10 EALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSPATAEALEDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712 105 YLIAIPSDILRKKYLDNVKFLHHLIDSLSEKLYATINNSSYNFVYPLINRLSSYLVEHIED-KNYIILNSSFLEIAQFLG 183
Cdd:COG0664   90 ELLRIPREDLEELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRlDGRIDLPLTQEEIASYLG 169

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489455712 184 TTYRHLNRTFKELESKSIIKCENKTIYILDENRLRDLS 221
Cdd:COG0664  170 LTRETVSRILKKLEKEGLIELERGRITILDREALERLA 207
PRK10402 PRK10402
DNA-binding transcriptional activator YeiL; Provisional
 1-227 4.21e-33

DNA-binding transcriptional activator YeiL; Provisional


Pssm-ID: 236682 [Multi-domain]  Cd Length: 226  Bit Score: 119.06  E-value: 4.21e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712   1 MKKILNNDLLNHYINEHNIESIFDKDILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDF 80
Cdd:PRK10402   1 MKESKNSEEISHYMSESAFKDCFSFDVSADTELFHFLAREYIVQEGQQPSYLFYLTRGRAKLYATLANGKVSLIDFFAAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  81 NTIGDLEFLKNIPILCDVDAVGDTYLIAIPSDILRKKYLDNVKFLHHLIDSLSEKLYATINNSSYNFVYPLINRLSSYLV 160
Cdd:PRK10402  81 CFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFIL 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489455712 161 EHIEDKNYIILNSsflEIAQFLGTTYRHLNRTFKELESKSIIKCENKTIYILDENRLRDLSKNFYIK 227
Cdd:PRK10402 161 LTQEGDLYHEKHT---QAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLALELKPE 224
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 27-129 1.95e-11

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: 59.26  E-value: 1.95e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712  27 ILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDTYL 106
Cdd:cd00038   13 LADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSEL 92

                         90       100
                 ....*....|....*....|...
gi 489455712 107 IAIPSDILRKKYLDNVKFLHHLI 129
Cdd:cd00038   93 LVLPRSDFRRLLQEYPELARRLL 115
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 33-121 7.64e-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: 56.85  E-value: 7.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712   33 LHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPILCDVDAVGDTYLIAIPSD 112
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80


                  ....*....
gi 489455712  113 ILRKKYLDN 121
Cdd:pfam00027  81 DFLELLERD 89
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 154-220 4.87e-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: 54.00  E-value: 4.87e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489455712  154 RLSSYLVEHIED--KNYIILNSSFLEIAQFLGTTYRHLNRTFKELESKSIIkcENKTIYILDENRLRDL 220
Cdd:pfam13545   2 RLARFLLELAARdgGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLI--ERGRITILDPEALEAL 68
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 26-110 5.00e-05

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: 41.62  E-value: 5.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489455712    26 DILKYAQLHFYEKEEYILKAESNLEYYYLIVDGKIKISYPFENGKPMLLKFYKDFNTIGDLEFLKNIPI--LCDVDAVGD 103
Cdd:smart00100  12 ELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRaaSAAAVALEL 91


                   ....*..
gi 489455712   104 TYLIAIP 110
Cdd:smart00100  92 ATLLRID 98
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
177-212 4.85e-04

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 37.03  E-value: 4.85e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 489455712   177 EIAQFLGTTYRHLNRTFKELESKSIIKCENKTIYIL 212
Cdd:smart00419  13 EIAELLGLTRETVSRTLKRLEKEGLISREGGRIVIL 48
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 152-212 1.66e-03

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: 36.10  E-value: 1.66e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489455712 152 INRLSSYLVEHIEDKNYIILNSSFL---EIAQFLGTTYRHLNRTFKELESKSIIKCENKTIYIL 212
Cdd:cd00092    2 KERLASFLLNLSLRYGAGDLVQLPLtrqEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRV 65
 
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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