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Conserved domains on  [gi|1373515949|ref|WP_107110975|]
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Crp/Fnr family transcriptional regulator [Shewanella algae]

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 ...
 23-193 1.10e-29

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: 108.54  E-value: 1.10e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEFCLLYsSFLSAEPARY 102
Cdd:COG0664     3 GLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGEL-SLLGGEPSPA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949 103 QLEALENSTLVVVPLSLF-----ELGGFQRAELSLLRAQLRYKEQKEAFLLLKSPEQRY----LWLKNHWPHWIS-ALSQ 172
Cdd:COG0664    82 TAEALEDSELLRIPREDLeelleRNPELARALLRLLARRLRQLQERLVSLAFLSAEERLarflLELADRLDGRIDlPLTQ 161

                         170       180
                  ....*....|....*....|.
gi 1373515949 173 VQLANYIGITPESLSRIRRRL 193
Cdd:COG0664   162 EEIASYLGLTRETVSRILKKL 182
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 23-193 1.10e-29

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: 108.54  E-value: 1.10e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEFCLLYsSFLSAEPARY 102
Cdd:COG0664     3 GLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGEL-SLLGGEPSPA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949 103 QLEALENSTLVVVPLSLF-----ELGGFQRAELSLLRAQLRYKEQKEAFLLLKSPEQRY----LWLKNHWPHWIS-ALSQ 172
Cdd:COG0664    82 TAEALEDSELLRIPREDLeelleRNPELARALLRLLARRLRQLQERLVSLAFLSAEERLarflLELADRLDGRIDlPLTQ 161

                         170       180
                  ....*....|....*....|.
gi 1373515949 173 VQLANYIGITPESLSRIRRRL 193
Cdd:COG0664   162 EEIASYLGLTRETVSRILKKL 182
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 23-121 7.25e-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: 56.95  E-value: 7.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGE-FCLLysSFLSAEPAR 101
Cdd:cd00038     4 GLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDlFGEL--ALLGNGPRS 81

                          90       100
                  ....*....|....*....|
gi 1373515949 102 YQLEALENSTLVVVPLSLFE 121
Cdd:cd00038    82 ATVRALTDSELLVLPRSDFR 101
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 38-121 6.38e-10

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: 53.77  E-value: 6.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  38 LKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEFC-LLysSFLSAEPARYQLEALENSTLVVVP 116
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFgEL--ALLGGEPRSATVVALTDSELLVIP 78


                  ....*
gi 1373515949 117 LSLFE 121
Cdd:pfam00027  79 REDFL 83
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 23-87 4.51e-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: 41.23  E-value: 4.51e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1373515949   23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEF 87
Cdd:smart00100   4 NLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDF 68
ftrB PRK09392
transcriptional activator FtrB; Provisional
 24-188 6.60e-03

transcriptional activator FtrB; Provisional


Pssm-ID: 181817 [Multi-domain]  Cd Length: 236  Bit Score: 36.15  E-value: 6.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  24 LEPSALAPLLDKAQLKSCQAGEVLLAQGgkQQSGFL--LLNGL--LRAChylSDGQQRCKEFYFPGE-FCLlySSFLSAE 98
Cdd:PRK09392   18 MADATFERLMRGAFLQRFPPGTMLITEG--EPADFLfvVLDGLveLSAS---SQDRETTLAILRPVStFIL--AAVVLDA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  99 PARYQLEALENSTLVVVPLSLF-----ELGGFQRA---ELSL-LRAQLR-YKEQKeafllLKSPEQRylwLKNhwphWIS 168
Cdd:PRK09392   91 PYLMSARTLTRSRVLMIPAELVreamsEDPGFMRAvvfELAGcYRGLVKsLKNQK-----LRSSAER---LAN----YLL 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1373515949 169 ALSQVQ--------------LANYIGITPESLSR 188
Cdd:PRK09392  159 KQSLRQggadvvtlpyekrvLASYLGMTPENLSR 192
 
Name Accession Description Interval E-value
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 23-193 1.10e-29

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: 108.54  E-value: 1.10e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEFCLLYsSFLSAEPARY 102
Cdd:COG0664     3 GLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGEL-SLLGGEPSPA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949 103 QLEALENSTLVVVPLSLF-----ELGGFQRAELSLLRAQLRYKEQKEAFLLLKSPEQRY----LWLKNHWPHWIS-ALSQ 172
Cdd:COG0664    82 TAEALEDSELLRIPREDLeelleRNPELARALLRLLARRLRQLQERLVSLAFLSAEERLarflLELADRLDGRIDlPLTQ 161

                         170       180
                  ....*....|....*....|.
gi 1373515949 173 VQLANYIGITPESLSRIRRRL 193
Cdd:COG0664   162 EEIASYLGLTRETVSRILKKL 182
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 23-121 7.25e-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: 56.95  E-value: 7.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGE-FCLLysSFLSAEPAR 101
Cdd:cd00038     4 GLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDlFGEL--ALLGNGPRS 81

                          90       100
                  ....*....|....*....|
gi 1373515949 102 YQLEALENSTLVVVPLSLFE 121
Cdd:cd00038    82 ATVRALTDSELLVLPRSDFR 101
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 38-121 6.38e-10

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: 53.77  E-value: 6.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  38 LKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEFC-LLysSFLSAEPARYQLEALENSTLVVVP 116
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFgEL--ALLGGEPRSATVVALTDSELLVIP 78


                  ....*
gi 1373515949 117 LSLFE 121
Cdd:pfam00027  79 REDFL 83
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 23-87 4.51e-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: 41.23  E-value: 4.51e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1373515949   23 GLEPSALAPLLDKAQLKSCQAGEVLLAQGGKQQSGFLLLNGLLRACHYLSDGQQRCKEFYFPGEF 87
Cdd:smart00100   4 NLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDF 68
ftrB PRK09392
transcriptional activator FtrB; Provisional
 24-188 6.60e-03

transcriptional activator FtrB; Provisional


Pssm-ID: 181817 [Multi-domain]  Cd Length: 236  Bit Score: 36.15  E-value: 6.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  24 LEPSALAPLLDKAQLKSCQAGEVLLAQGgkQQSGFL--LLNGL--LRAChylSDGQQRCKEFYFPGE-FCLlySSFLSAE 98
Cdd:PRK09392   18 MADATFERLMRGAFLQRFPPGTMLITEG--EPADFLfvVLDGLveLSAS---SQDRETTLAILRPVStFIL--AAVVLDA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373515949  99 PARYQLEALENSTLVVVPLSLF-----ELGGFQRA---ELSL-LRAQLR-YKEQKeafllLKSPEQRylwLKNhwphWIS 168
Cdd:PRK09392   91 PYLMSARTLTRSRVLMIPAELVreamsEDPGFMRAvvfELAGcYRGLVKsLKNQK-----LRSSAER---LAN----YLL 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1373515949 169 ALSQVQ--------------LANYIGITPESLSR 188
Cdd:PRK09392  159 KQSLRQggadvvtlpyekrvLASYLGMTPENLSR 192
 
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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