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Conserved domains on  [gi|4559397|gb|AAD23057|]
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putative cyclic nucleotide-regulated ion channel protein [Arabidopsis thaliana]

Protein Classification

cyclic nucleotide-binding domain-containing protein( domain architecture ID 10034975)

cyclic nucleotide-binding domain-containing protein binds cyclic nucleotides (cAMP or cGMP) where binding of the effector leads to conformational changes; may be involved in regulating transcription, be present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK), or be part of vertebrate cyclic nucleotide-gated ion-channels.

CATH:  2.60.120.10
Gene Ontology:  GO:0030552|GO:0030551
PubMed:  6280140|12087135|17601606|11734894
SCOP:  4000272

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 404-531 6.62e-15

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: 71.20  E-value: 6.62e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397  404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDLltwALYSL 482
Cdd:cd00038   3 SGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVeVYKLDEDGREQIVGF--LGPGDLFGEL---ALLGN 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 4559397  483 SSqfpiSSRTVQALTEVEGFVISADDLkfvatqyRRLHSKQLQHMFRFY 531
Cdd:cd00038  78 GP----RSATVRALTDSELLVLPRSDF-------RRLLQEYPELARRLL 115
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 404-531 6.62e-15

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: 71.20  E-value: 6.62e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397  404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDLltwALYSL 482
Cdd:cd00038   3 SGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVeVYKLDEDGREQIVGF--LGPGDLFGEL---ALLGN 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 4559397  483 SSqfpiSSRTVQALTEVEGFVISADDLkfvatqyRRLHSKQLQHMFRFY 531
Cdd:cd00038  78 GP----RSATVRALTDSELLVLPRSDF-------RRLLQEYPELARRLL 115
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 404-530 1.71e-09

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: 55.87  E-value: 1.71e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397     404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDlltwalysL 482
Cdd:smart00100   3 KNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVeVYKVLEDGEEQIVGT--LGPGDFFGE--------L 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 4559397     483 SSQFPISSRTVQALTEVEGFVISADDLKFVATQYRRLHSKQLQHMFRF 530
Cdd:smart00100  73 ALLTNSRRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 404-529 3.19e-08

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: 54.22  E-value: 3.19e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397  404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGR---TGFFNsvdliAGDSCGDlltwal 479
Cdd:COG0664   2 AGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVkLYRISEDGReqiLGFLG-----PGDFFGE------ 70

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 4559397  480 YSLSSQFPiSSRTVQALTEVEGFVISADDLKFVATQYRRLHSKQLQHMFR 529
Cdd:COG0664  71 LSLLGGEP-SPATAEALEDSELLRIPREDLEELLERNPELARALLRLLAR 119
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 421-509 5.94e-06

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: 44.91  E-value: 5.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397    421 VHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDLltwalySLSSQFPISSrTVQALTEV 499
Cdd:pfam00027   2 RSYKAGEVIFREGDPADSLYIVLSGKVkVYRTLEDGREQILAV--LGPGDFFGEL------ALLGGEPRSA-TVVALTDS 72

                          90
                  ....*....|
gi 4559397    500 EGFVISADDL 509
Cdd:pfam00027  73 ELLVIPREDF 82
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 404-531 6.62e-15

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: 71.20  E-value: 6.62e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397  404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDLltwALYSL 482
Cdd:cd00038   3 SGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVeVYKLDEDGREQIVGF--LGPGDLFGEL---ALLGN 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 4559397  483 SSqfpiSSRTVQALTEVEGFVISADDLkfvatqyRRLHSKQLQHMFRFY 531
Cdd:cd00038  78 GP----RSATVRALTDSELLVLPRSDF-------RRLLQEYPELARRLL 115
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 404-530 1.71e-09

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: 55.87  E-value: 1.71e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397     404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDlltwalysL 482
Cdd:smart00100   3 KNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVeVYKVLEDGEEQIVGT--LGPGDFFGE--------L 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 4559397     483 SSQFPISSRTVQALTEVEGFVISADDLKFVATQYRRLHSKQLQHMFRF 530
Cdd:smart00100  73 ALLTNSRRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 404-529 3.19e-08

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: 54.22  E-value: 3.19e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397  404 QAMDDQLLDALCARLKTVHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGR---TGFFNsvdliAGDSCGDlltwal 479
Cdd:COG0664   2 AGLSDEELEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVkLYRISEDGReqiLGFLG-----PGDFFGE------ 70

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 4559397  480 YSLSSQFPiSSRTVQALTEVEGFVISADDLKFVATQYRRLHSKQLQHMFR 529
Cdd:COG0664  71 LSLLGGEP-SPATAEALEDSELLRIPREDLEELLERNPELARALLRLLAR 119
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 421-509 5.94e-06

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: 44.91  E-value: 5.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4559397    421 VHYTEKSYIVREGEPVEDMLFIMRGNL-ISTTTYGGRTGFFNSvdLIAGDSCGDLltwalySLSSQFPISSrTVQALTEV 499
Cdd:pfam00027   2 RSYKAGEVIFREGDPADSLYIVLSGKVkVYRTLEDGREQILAV--LGPGDFFGEL------ALLGGEPRSA-TVVALTDS 72

                          90
                  ....*....|
gi 4559397    500 EGFVISADDL 509
Cdd:pfam00027  73 ELLVIPREDF 82
 
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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