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Conserved domains on  [gi|1063706987|ref|NP_001324486|]
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cyclic nucleotide-gated channel 12 [Arabidopsis thaliana]

Protein Classification

cyclic nucleotide-gated ion channel( domain architecture ID 13585844)

cyclic nucleotide-gated ion channel is a nonselective channel that is opened by the direct binding of cyclic nucleotides, cAMP and cGMP

Gene Ontology:  GO:0016020|GO:0030551|GO:0005216
PubMed:  12087135|17601606

Graphical summary

 Zoom to residue level

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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 ...
 435-560 1.31e-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: 64.65  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 435 WLNIMDDGwLLEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTGSHEmGVRNNCCDLQDGDICGEL-LFNGS 513
Cdd:cd00038     1 LFSGLDDE-ELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDED-GREQIVGFLGPGDLFGELaLLGNG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1063706987 514 RlptSTRTVMTLTEVEGFILLpddikfiASHLNVFQRQKLQRTFRLY 560
Cdd:cd00038    79 P---RSATVRALTDSELLVLP-------RSDFRRLLQEYPELARRLL 115
Ion_trans super family cl37996
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 302-362 9.70e-03

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


The actual alignment was detected with superfamily member pfam00520:

Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 38.02  E-value: 9.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063706987 302 RKFVYCFWWGLRNISALGQN-------LETSNSAGEIFFAIIICVSGLLLFAVLIGNVQKYLQSSTTR 362
Cdd:pfam00520 169 DNFPNAFLWLFQTMTTEGWGdimydtiDGKGEFWAYIYFVSFIILGGFLLLNLFIAVIIDNFQELTER 236
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 435-560 1.31e-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: 64.65  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 435 WLNIMDDGwLLEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTGSHEmGVRNNCCDLQDGDICGEL-LFNGS 513
Cdd:cd00038     1 LFSGLDDE-ELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDED-GREQIVGFLGPGDLFGELaLLGNG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1063706987 514 RlptSTRTVMTLTEVEGFILLpddikfiASHLNVFQRQKLQRTFRLY 560
Cdd:cd00038    79 P---RSATVRALTDSELLVLP-------RSDFRRLLQEYPELARRLL 115
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 441-559 4.92e-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: 48.94  E-value: 4.92e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987  441 DGWLLEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTgSHEMGVRNNCCDLQDGDICGEL-LFNGSRLPTST 519
Cdd:smart00100   6 DAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYK-VLEDGEEQIVGTLGPGDFFGELaLLTNSRRAASA 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1063706987  520 RTVmTLTEVEgfiLLPDDIKFIASHLNVFQRQKLQRTFRL 559
Cdd:smart00100  85 AAV-ALELAT---LLRIDFRDFLQLLPELPQLLLELLLEL 120
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 455-529 6.22e-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: 6.22e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063706987 455 VFYLANSFIVREGHPVEEMLIVTRGKLKSTTgSHEMGVRNNCCDLQDGDICGEL-LFNGSRLPTstrTVMTLTEVE 529
Cdd:pfam00027   2 RSYKAGEVIFREGDPADSLYIVLSGKVKVYR-TLEDGREQILAVLGPGDFFGELaLLGGEPRSA---TVVALTDSE 73
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 445-621 1.54e-05

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: 46.52  E-value: 1.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 445 LEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTGSHEmGVRNNCCDLQDGDICGEL-LFNGSRlptSTRTVM 523
Cdd:COG0664     9 LEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISED-GREQILGFLGPGDFFGELsLLGGEP---SPATAE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 524 TLTEVEGFILLPDDIKFIASHLNVFQRQKLQRTFRLYSQQwRSWAAFFIQ-------AAWRKHckrkLSKTRDNENIPQG 596
Cdd:COG0664    85 ALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQL-QERLVSLAFlsaeerlARFLLE----LADRLDGRIDLPL 159

                         170       180
                  ....*....|....*....|....*.
gi 1063706987 597 TQLNLASTLYVSR-FVSKALQNRRKD 621
Cdd:COG0664   160 TQEEIASYLGLTReTVSRILKKLEKE 185
Ion_trans pfam00520
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 302-362 9.70e-03

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 38.02  E-value: 9.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063706987 302 RKFVYCFWWGLRNISALGQN-------LETSNSAGEIFFAIIICVSGLLLFAVLIGNVQKYLQSSTTR 362
Cdd:pfam00520 169 DNFPNAFLWLFQTMTTEGWGdimydtiDGKGEFWAYIYFVSFIILGGFLLLNLFIAVIIDNFQELTER 236
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 435-560 1.31e-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: 64.65  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 435 WLNIMDDGwLLEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTGSHEmGVRNNCCDLQDGDICGEL-LFNGS 513
Cdd:cd00038     1 LFSGLDDE-ELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDED-GREQIVGFLGPGDLFGELaLLGNG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1063706987 514 RlptSTRTVMTLTEVEGFILLpddikfiASHLNVFQRQKLQRTFRLY 560
Cdd:cd00038    79 P---RSATVRALTDSELLVLP-------RSDFRRLLQEYPELARRLL 115
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 441-559 4.92e-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: 48.94  E-value: 4.92e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987  441 DGWLLEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTgSHEMGVRNNCCDLQDGDICGEL-LFNGSRLPTST 519
Cdd:smart00100   6 DAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYK-VLEDGEEQIVGTLGPGDFFGELaLLTNSRRAASA 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1063706987  520 RTVmTLTEVEgfiLLPDDIKFIASHLNVFQRQKLQRTFRL 559
Cdd:smart00100  85 AAV-ALELAT---LLRIDFRDFLQLLPELPQLLLELLLEL 120
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 455-529 6.22e-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: 6.22e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063706987 455 VFYLANSFIVREGHPVEEMLIVTRGKLKSTTgSHEMGVRNNCCDLQDGDICGEL-LFNGSRLPTstrTVMTLTEVE 529
Cdd:pfam00027   2 RSYKAGEVIFREGDPADSLYIVLSGKVKVYR-TLEDGREQILAVLGPGDFFGELaLLGGEPRSA---TVVALTDSE 73
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 445-621 1.54e-05

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: 46.52  E-value: 1.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 445 LEAVCDRVKSVFYLANSFIVREGHPVEEMLIVTRGKLKSTTGSHEmGVRNNCCDLQDGDICGEL-LFNGSRlptSTRTVM 523
Cdd:COG0664     9 LEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISED-GREQILGFLGPGDFFGELsLLGGEP---SPATAE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706987 524 TLTEVEGFILLPDDIKFIASHLNVFQRQKLQRTFRLYSQQwRSWAAFFIQ-------AAWRKHckrkLSKTRDNENIPQG 596
Cdd:COG0664    85 ALEDSELLRIPREDLEELLERNPELARALLRLLARRLRQL-QERLVSLAFlsaeerlARFLLE----LADRLDGRIDLPL 159

                         170       180
                  ....*....|....*....|....*.
gi 1063706987 597 TQLNLASTLYVSR-FVSKALQNRRKD 621
Cdd:COG0664   160 TQEEIASYLGLTReTVSRILKKLEKE 185
Ion_trans pfam00520
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 302-362 9.70e-03

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 38.02  E-value: 9.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063706987 302 RKFVYCFWWGLRNISALGQN-------LETSNSAGEIFFAIIICVSGLLLFAVLIGNVQKYLQSSTTR 362
Cdd:pfam00520 169 DNFPNAFLWLFQTMTTEGWGdimydtiDGKGEFWAYIYFVSFIILGGFLLLNLFIAVIIDNFQELTER 236
 
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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