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Conserved domains on  [gi|1475409042|ref|NP_001352638|]
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cyclic nucleotide-binding domain-containing protein 2 isoform 4 [Homo sapiens]

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 ...
 122-218 2.08e-16

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: 75.44  E-value: 2.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 122 EPLQLLLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLdphpKLLHKGSCFGEMDVLHASVRRS 200
Cdd:cd00038     7 DEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKlDEDGREQIV----GFLGPGDLFGELALLGNGPRSA 82

                          90
                  ....*....|....*...
gi 1475409042 201 TIVCMEETEFLVVDREDF 218
Cdd:cd00038    83 TVRALTDSELLVLPRSDF 100
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 122-218 2.08e-16

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: 75.44  E-value: 2.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 122 EPLQLLLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLdphpKLLHKGSCFGEMDVLHASVRRS 200
Cdd:cd00038     7 DEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKlDEDGREQIV----GFLGPGDLFGELALLGNGPRSA 82

                          90
                  ....*....|....*...
gi 1475409042 201 TIVCMEETEFLVVDREDF 218
Cdd:cd00038    83 TVRALTDSELLVLPRSDF 100
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 134-218 5.77e-15

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: 70.33  E-value: 5.77e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 134 FERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLDphpkLLHKGSCFGEMDVLHASVRRSTIVCMEETEFLV 212
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRtLEDGREQILA----VLGPGDFFGELALLGGEPRSATVVALTDSELLV 76


                  ....*.
gi 1475409042 213 VDREDF 218
Cdd:pfam00027  77 IPREDF 82
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 127-263 1.40e-12

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: 66.93  E-value: 1.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 127 LLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLDphpkLLHKGSCFGEMDVLHASVRRSTIVCM 205
Cdd:COG0664    11 ALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRiSEDGREQILG----FLGPGDFFGELSLLGGEPSPATAEAL 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1475409042 206 EETEFLVVDREDFfanklDQEVQKDAQYRFEFFRKMELFASWSDEKLWQLVAMAKIER 263
Cdd:COG0664    87 EDSELLRIPREDL-----EELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEER 139
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 118-241 1.27e-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: 56.26  E-value: 1.27e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042  118 RNYAEPLQLLLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITKD-EDGSSAFLdphpKLLHKGSCFGEMDVLHAS 196
Cdd:smart00100   3 KNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVlEDGEEQIV----GTLGPGDFFGELALLTNS 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1475409042  197 vRRSTIVCMEETEFLVVDREDFfaNKLDQEVQKDAQYRFEFFRKM 241
Cdd:smart00100  79 -RRAASAAAVALELATLLRIDF--RDFLQLLPELPQLLLELLLEL 120
PLN02868 PLN02868
acyl-CoA thioesterase family protein
 128-216 4.99e-04

acyl-CoA thioesterase family protein


Pssm-ID: 178459 [Multi-domain]  Cd Length: 413  Bit Score: 42.79  E-value: 4.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 128 LAKVMRFERFGRRRVIIKKGQKGNSFYFIYLG--TVAITKDEDGSSAFldphpkLLHKGSCFGemDVLHASVRRSTIVCM 205
Cdd:PLN02868   27 IAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGeaEVSGPAEEESRPEF------LLKRYDYFG--YGLSGSVHSADVVAV 98

                          90
                  ....*....|.
gi 1475409042 206 EETEFLVVDRE 216
Cdd:PLN02868   99 SELTCLVLPHE 109
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 122-218 2.08e-16

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: 75.44  E-value: 2.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 122 EPLQLLLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLdphpKLLHKGSCFGEMDVLHASVRRS 200
Cdd:cd00038     7 DEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKlDEDGREQIV----GFLGPGDLFGELALLGNGPRSA 82

                          90
                  ....*....|....*...
gi 1475409042 201 TIVCMEETEFLVVDREDF 218
Cdd:cd00038    83 TVRALTDSELLVLPRSDF 100
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 134-218 5.77e-15

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: 70.33  E-value: 5.77e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 134 FERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLDphpkLLHKGSCFGEMDVLHASVRRSTIVCMEETEFLV 212
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRtLEDGREQILA----VLGPGDFFGELALLGGEPRSATVVALTDSELLV 76


                  ....*.
gi 1475409042 213 VDREDF 218
Cdd:pfam00027  77 IPREDF 82
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 127-263 1.40e-12

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: 66.93  E-value: 1.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 127 LLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITK-DEDGSSAFLDphpkLLHKGSCFGEMDVLHASVRRSTIVCM 205
Cdd:COG0664    11 ALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRiSEDGREQILG----FLGPGDFFGELSLLGGEPSPATAEAL 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1475409042 206 EETEFLVVDREDFfanklDQEVQKDAQYRFEFFRKMELFASWSDEKLWQLVAMAKIER 263
Cdd:COG0664    87 EDSELLRIPREDL-----EELLERNPELARALLRLLARRLRQLQERLVSLAFLSAEER 139
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 118-241 1.27e-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: 56.26  E-value: 1.27e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042  118 RNYAEPLQLLLAKVMRFERFGRRRVIIKKGQKGNSFYFIYLGTVAITKD-EDGSSAFLdphpKLLHKGSCFGEMDVLHAS 196
Cdd:smart00100   3 KNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVlEDGEEQIV----GTLGPGDFFGELALLTNS 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1475409042  197 vRRSTIVCMEETEFLVVDREDFfaNKLDQEVQKDAQYRFEFFRKM 241
Cdd:smart00100  79 -RRAASAAAVALELATLLRIDF--RDFLQLLPELPQLLLELLLEL 120
PLN02868 PLN02868
acyl-CoA thioesterase family protein
 128-216 4.99e-04

acyl-CoA thioesterase family protein


Pssm-ID: 178459 [Multi-domain]  Cd Length: 413  Bit Score: 42.79  E-value: 4.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 128 LAKVMRFERFGRRRVIIKKGQKGNSFYFIYLG--TVAITKDEDGSSAFldphpkLLHKGSCFGemDVLHASVRRSTIVCM 205
Cdd:PLN02868   27 IAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGeaEVSGPAEEESRPEF------LLKRYDYFG--YGLSGSVHSADVVAV 98

                          90
                  ....*....|.
gi 1475409042 206 EETEFLVVDRE 216
Cdd:PLN02868   99 SELTCLVLPHE 109
PRK11753 PRK11753
cAMP-activated global transcriptional regulator CRP;
124-203 1.02e-03

cAMP-activated global transcriptional regulator CRP;


Pssm-ID: 236969 [Multi-domain]  Cd Length: 211  Bit Score: 40.74  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1475409042 124 LQLLLAKVMRfERFGRRRVIIKKGQKGNSFYFIYLGTVAIT-KDEDGSSAFLDphpkLLHKGSCFGEMDVLHASVRRSTI 202
Cdd:PRK11753   13 LEWFLSHCHI-HKYPAKSTLIHAGEKAETLYYIVKGSVAVLiKDEEGKEMILS----YLNQGDFIGELGLFEEGQERSAW 87


                  .
gi 1475409042 203 V 203
Cdd:PRK11753   88 V 88
 
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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