NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|838277193|gb|AKM97401|]
View 

nitrogen regulatory protein, partial [Synechococcus sp. MV0801]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NtcA_cyano super family cl31464
global nitrogen regulator NtcA, cyanobacterial; Members of this protein family, found in the ...
 1-134 6.64e-71

global nitrogen regulator NtcA, cyanobacterial; Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C. [Regulatory functions, DNA interactions]


The actual alignment was detected with superfamily member TIGR03697:

Pssm-ID: 163409 [Multi-domain]  Cd Length: 193  Bit Score: 210.86  E-value: 6.64e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 838277193    1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDRFYHSIAFTRVEMVTAPATSVRQAIEADTSVGLL 80
Cdd:TIGR03697  12 EKVYFLRRGAVKLSRVYESGEEITVALLRENSVFGVLSLITGHRSDRFYHAVAFTRVELLAVPIEQVEKAIEEDPDLSML 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 838277193   81 LLQGLSSRILQTETMIETLTHRDMSSRLVSFLLVLCRDFGVPGQRGITIDLRLS 134
Cdd:TIGR03697  92 LLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLS 145
 
Name Accession Description Interval E-value
NtcA_cyano TIGR03697
global nitrogen regulator NtcA, cyanobacterial; Members of this protein family, found in the ...
 1-134 6.64e-71

global nitrogen regulator NtcA, cyanobacterial; Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C. [Regulatory functions, DNA interactions]


Pssm-ID: 163409 [Multi-domain]  Cd Length: 193  Bit Score: 210.86  E-value: 6.64e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 838277193    1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDRFYHSIAFTRVEMVTAPATSVRQAIEADTSVGLL 80
Cdd:TIGR03697  12 EKVYFLRRGAVKLSRVYESGEEITVALLRENSVFGVLSLITGHRSDRFYHAVAFTRVELLAVPIEQVEKAIEEDPDLSML 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 838277193   81 LLQGLSSRILQTETMIETLTHRDMSSRLVSFLLVLCRDFGVPGQRGITIDLRLS 134
Cdd:TIGR03697  92 LLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLS 145
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 1-120 1.10e-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: 67.32  E-value: 1.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 838277193   1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDrfYHSIAFTRVEMVTAPATSVRQAIEADTSVGLL 80
Cdd:COG0664   35 DHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSP--ATAEALEDSELLRIPREDLEELLERNPELARA 112

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 838277193  81 LLQGLSSRILQTETMIETLTHRDMSSRLVSFLLVLCRDFG 120
Cdd:COG0664  113 LLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLD 152
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 1-74 4.46e-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://0-doi-org.brum.beds.ac.uk/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 52.61  E-value: 4.46e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 838277193    1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRsdRFYHSIAFTRVEMVTAPATSVRQAIEAD 74
Cdd:pfam00027  18 DSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEP--RSATVVALTDSELLVIPREDFLELLERD 89
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 1-77 4.46e-08

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: 48.09  E-value: 4.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 838277193   1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRsdRFYHSIAFTRVEMVTAPATSVRQAIEADTSV 77
Cdd:cd00038   36 DSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGP--RSATVRALTDSELLVLPRSDFRRLLQEYPEL 110
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 1-74 5.01e-08

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: 48.17  E-value: 5.01e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 838277193     1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDRFYHSIAFTRVEMVTAPATSVRQAIEAD 74
Cdd:smart00100  36 DSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVALELATLLRIDFRDFLQLLPEL 109
 
Name Accession Description Interval E-value
NtcA_cyano TIGR03697
global nitrogen regulator NtcA, cyanobacterial; Members of this protein family, found in the ...
 1-134 6.64e-71

global nitrogen regulator NtcA, cyanobacterial; Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C. [Regulatory functions, DNA interactions]


Pssm-ID: 163409 [Multi-domain]  Cd Length: 193  Bit Score: 210.86  E-value: 6.64e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 838277193    1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDRFYHSIAFTRVEMVTAPATSVRQAIEADTSVGLL 80
Cdd:TIGR03697  12 EKVYFLRRGAVKLSRVYESGEEITVALLRENSVFGVLSLITGHRSDRFYHAVAFTRVELLAVPIEQVEKAIEEDPDLSML 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 838277193   81 LLQGLSSRILQTETMIETLTHRDMSSRLVSFLLVLCRDFGVPGQRGITIDLRLS 134
Cdd:TIGR03697  92 LLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLS 145
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 1-120 1.10e-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: 67.32  E-value: 1.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 838277193   1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDrfYHSIAFTRVEMVTAPATSVRQAIEADTSVGLL 80
Cdd:COG0664   35 DHLYFVLSGLVKLYRISEDGREQILGFLGPGDFFGELSLLGGEPSP--ATAEALEDSELLRIPREDLEELLERNPELARA 112

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 838277193  81 LLQGLSSRILQTETMIETLTHRDMSSRLVSFLLVLCRDFG 120
Cdd:COG0664  113 LLRLLARRLRQLQERLVSLAFLSAEERLARFLLELADRLD 152
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 1-74 4.46e-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://0-doi-org.brum.beds.ac.uk/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 52.61  E-value: 4.46e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 838277193    1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRsdRFYHSIAFTRVEMVTAPATSVRQAIEAD 74
Cdd:pfam00027  18 DSLYIVLSGKVKVYRTLEDGREQILAVLGPGDFFGELALLGGEP--RSATVVALTDSELLVIPREDFLELLERD 89
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 1-77 4.46e-08

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: 48.09  E-value: 4.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 838277193   1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRsdRFYHSIAFTRVEMVTAPATSVRQAIEADTSV 77
Cdd:cd00038   36 DSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGP--RSATVRALTDSELLVLPRSDFRRLLQEYPEL 110
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 1-74 5.01e-08

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: 48.17  E-value: 5.01e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 838277193     1 EKVYLIRRGAVRLSRVYESGEEITVALLRENSLFGVLSLLTGHRSDRFYHSIAFTRVEMVTAPATSVRQAIEAD 74
Cdd:smart00100  36 DSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVALELATLLRIDFRDFLQLLPEL 109
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH