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Conserved domains on  [gi|2030565372|gb|QUK52376|]
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cyclic nucleotide-binding domain-containing protein [Treponema pallidum]

Protein Classification

HATPase_c and CAP_ED domain-containing protein( domain architecture ID 10209475)

HATPase_c and CAP_ED domain-containing protein

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 ...
 307-406 5.48e-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: 73.90  E-value: 5.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 307 SILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEG 381
Cdd:cd00038    12 ELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDedgreQIVGFLGPGDLF-GELALLGNGPRSATVRALTDS 90

                          90       100
                  ....*....|....*....|....*
gi 2030565372 382 TLVKISKMKFISLIEDHPHYGIYLA 406
Cdd:cd00038    91 ELLVLPRSDFRRLLQEYPELARRLL 115
RsbW COG2172
Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];
182-295 1.99e-06

Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];


:

Pssm-ID: 441775 [Multi-domain]  Cd Length: 127  Bit Score: 46.83  E-value: 1.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 182 AMMELLLNALEHGNcgisydektewleqrkdifdlialrkqdPRISAKKIYISYDITLQRTRITIRDEGTGFDWKSRMAS 261
Cdd:COG2172    38 AVSEAVTNAVRHAY----------------------------GGDPDGPVEVELELDPDGLEIEVRDEGPGFDPEDLPDP 89

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030565372 262 ACKPGLHGMGIKMTEIFVKRLSYN--DVGNEVTFEI 295
Cdd:COG2172    90 YSTLAEGGRGLFLIRRLMDEVEYEsdPGGTTVRLVK 125
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 307-406 5.48e-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: 73.90  E-value: 5.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 307 SILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEG 381
Cdd:cd00038    12 ELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDedgreQIVGFLGPGDLF-GELALLGNGPRSATVRALTDS 90

                          90       100
                  ....*....|....*....|....*
gi 2030565372 382 TLVKISKMKFISLIEDHPHYGIYLA 406
Cdd:cd00038    91 ELLVLPRSDFRRLLQEYPELARRLL 115
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 308-436 2.56e-14

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: 71.56  E-value: 2.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 308 ILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEGT 382
Cdd:COG0664    12 LLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISedgreQILGFLGPGDFF-GELSLLGGEPSPATAEALEDSE 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2030565372 383 LVKISKMKFISLIEDHPHYGIYLARLLAGRLAHqsresakLKNTLTLLGQRTPD 436
Cdd:COG0664    91 LLRIPREDLEELLERNPELARALLRLLARRLRQ-------LQERLVSLAFLSAE 137
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 314-398 8.42e-14

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: 66.48  E-value: 8.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 314 VLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEGTLVKISK 388
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLedgreQILAVLGPGDFF-GELALLGGEPRSATVVALTDSELLVIPR 79

                          90
                  ....*....|
gi 2030565372 389 MKFISLIEDH 398
Cdd:pfam00027  80 EDFLELLERD 89
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 307-409 1.48e-11

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: 61.26  E-value: 1.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372  307 SILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRR--SATIVSVG 379
Cdd:smart00100  12 ELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLedgeeQIVGTLGPGDFF-GELALLTNSRRaaSAAAVALE 90

                           90       100       110
                   ....*....|....*....|....*....|
gi 2030565372  380 EGTLVKISKMKFISLIEDHPHYGIYLARLL 409
Cdd:smart00100  91 LATLLRIDFRDFLQLLPELPQLLLELLLEL 120
PRK11753 PRK11753
cAMP-activated global transcriptional regulator CRP;
325-423 1.08e-08

cAMP-activated global transcriptional regulator CRP;


Pssm-ID: 236969 [Multi-domain]  Cd Length: 211  Bit Score: 54.99  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 325 YQNEESSSLFYISSGKFAVYVDNK-----FMSMLTPSDiFIGEMS-FLLNNRRSATIVSVGEGTLVKISKMKFISLIEDH 398
Cdd:PRK11753   33 HAGEKAETLYYIVKGSVAVLIKDEegkemILSYLNQGD-FIGELGlFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVN 111

                          90       100
                  ....*....|....*....|....*
gi 2030565372 399 PHYGIYLARLLAGRLAHQSRESAKL 423
Cdd:PRK11753  112 PDILMALSAQMARRLQNTSRKVGDL 136
RsbW COG2172
Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];
182-295 1.99e-06

Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];


Pssm-ID: 441775 [Multi-domain]  Cd Length: 127  Bit Score: 46.83  E-value: 1.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 182 AMMELLLNALEHGNcgisydektewleqrkdifdlialrkqdPRISAKKIYISYDITLQRTRITIRDEGTGFDWKSRMAS 261
Cdd:COG2172    38 AVSEAVTNAVRHAY----------------------------GGDPDGPVEVELELDPDGLEIEVRDEGPGFDPEDLPDP 89

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030565372 262 ACKPGLHGMGIKMTEIFVKRLSYN--DVGNEVTFEI 295
Cdd:COG2172    90 YSTLAEGGRGLFLIRRLMDEVEYEsdPGGTTVRLVK 125
HATPase_c_2 pfam13581
Histidine kinase-like ATPase domain;
185-293 4.27e-03

Histidine kinase-like ATPase domain;


Pssm-ID: 433327 [Multi-domain]  Cd Length: 127  Bit Score: 37.27  E-value: 4.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 185 ELLLNALEHGNCGISydektewleqrkdifdlialrkqdprisAKKIYISYDITLQRTRITIRDEGTGFDWKSRMASACK 264
Cdd:pfam13581  38 EACTNAVEHAYREGP----------------------------EGPVEVRLTSDGGGLVVTVADSGPPFDPLTLPPPDLE 89

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030565372 265 -----PGLHGMGIKMTEIFVKRLSY--NDVGNEVTF 293
Cdd:pfam13581  90 epdedRKEGGRGLALIRGLMDDVEYtrGGEGNTVRM 125
 
Name Accession Description Interval E-value
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 307-406 5.48e-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: 73.90  E-value: 5.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 307 SILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEG 381
Cdd:cd00038    12 ELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDedgreQIVGFLGPGDLF-GELALLGNGPRSATVRALTDS 90

                          90       100
                  ....*....|....*....|....*
gi 2030565372 382 TLVKISKMKFISLIEDHPHYGIYLA 406
Cdd:cd00038    91 ELLVLPRSDFRRLLQEYPELARRLL 115
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 308-436 2.56e-14

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: 71.56  E-value: 2.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 308 ILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEGT 382
Cdd:COG0664    12 LLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRISedgreQILGFLGPGDFF-GELSLLGGEPSPATAEALEDSE 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2030565372 383 LVKISKMKFISLIEDHPHYGIYLARLLAGRLAHqsresakLKNTLTLLGQRTPD 436
Cdd:COG0664    91 LLRIPREDLEELLERNPELARALLRLLARRLRQ-------LQERLVSLAFLSAE 137
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 314-398 8.42e-14

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: 66.48  E-value: 8.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 314 VLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRRSATIVSVGEGTLVKISK 388
Cdd:pfam00027   1 LRSYKAGEVIFREGDPADSLYIVLSGKVKVYRTLedgreQILAVLGPGDFF-GELALLGGEPRSATVVALTDSELLVIPR 79

                          90
                  ....*....|
gi 2030565372 389 MKFISLIEDH 398
Cdd:pfam00027  80 EDFLELLERD 89
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 307-409 1.48e-11

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: 61.26  E-value: 1.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372  307 SILKNQQVLTFRDAQVVCYQNEESSSLFYISSGKFAVYVDN-----KFMSMLTPSDIFiGEMSFLLNNRR--SATIVSVG 379
Cdd:smart00100  12 ELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLedgeeQIVGTLGPGDFF-GELALLTNSRRaaSAAAVALE 90

                           90       100       110
                   ....*....|....*....|....*....|
gi 2030565372  380 EGTLVKISKMKFISLIEDHPHYGIYLARLL 409
Cdd:smart00100  91 LATLLRIDFRDFLQLLPELPQLLLELLLEL 120
PRK11753 PRK11753
cAMP-activated global transcriptional regulator CRP;
325-423 1.08e-08

cAMP-activated global transcriptional regulator CRP;


Pssm-ID: 236969 [Multi-domain]  Cd Length: 211  Bit Score: 54.99  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 325 YQNEESSSLFYISSGKFAVYVDNK-----FMSMLTPSDiFIGEMS-FLLNNRRSATIVSVGEGTLVKISKMKFISLIEDH 398
Cdd:PRK11753   33 HAGEKAETLYYIVKGSVAVLIKDEegkemILSYLNQGD-FIGELGlFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVN 111

                          90       100
                  ....*....|....*....|....*
gi 2030565372 399 PHYGIYLARLLAGRLAHQSRESAKL 423
Cdd:PRK11753  112 PDILMALSAQMARRLQNTSRKVGDL 136
RsbW COG2172
Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];
182-295 1.99e-06

Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms];


Pssm-ID: 441775 [Multi-domain]  Cd Length: 127  Bit Score: 46.83  E-value: 1.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 182 AMMELLLNALEHGNcgisydektewleqrkdifdlialrkqdPRISAKKIYISYDITLQRTRITIRDEGTGFDWKSRMAS 261
Cdd:COG2172    38 AVSEAVTNAVRHAY----------------------------GGDPDGPVEVELELDPDGLEIEVRDEGPGFDPEDLPDP 89

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030565372 262 ACKPGLHGMGIKMTEIFVKRLSYN--DVGNEVTFEI 295
Cdd:COG2172    90 YSTLAEGGRGLFLIRRLMDEVEYEsdPGGTTVRLVK 125
HATPase_c_2 pfam13581
Histidine kinase-like ATPase domain;
185-293 4.27e-03

Histidine kinase-like ATPase domain;


Pssm-ID: 433327 [Multi-domain]  Cd Length: 127  Bit Score: 37.27  E-value: 4.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030565372 185 ELLLNALEHGNCGISydektewleqrkdifdlialrkqdprisAKKIYISYDITLQRTRITIRDEGTGFDWKSRMASACK 264
Cdd:pfam13581  38 EACTNAVEHAYREGP----------------------------EGPVEVRLTSDGGGLVVTVADSGPPFDPLTLPPPDLE 89

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030565372 265 -----PGLHGMGIKMTEIFVKRLSY--NDVGNEVTF 293
Cdd:pfam13581  90 epdedRKEGGRGLALIRGLMDDVEYtrGGEGNTVRM 125
 
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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