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Conserved domains on  [gi|1197221387|ref|WP_086471380|]
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CopG family ribbon-helix-helix protein [Devosia lucknowensis]

Protein Classification

CopG family ribbon-helix-helix protein( domain architecture ID 10008124)

CopG family ribbon-helix-helix protein may bind DNA and function as a transcriptional regulator, similar to Caulobacter vibrioides orphan antitoxin ParD2, the antitoxin component of a non-functional type II toxin-antitoxin

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PutA1 COG3905
Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription] ...
 3-70 1.84e-18

Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription];


:

Pssm-ID: 443111  Cd Length: 69  Bit Score: 71.78  E-value: 1.84e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1197221387  3 ASTTMTIRLAPEVKEKLDRIATDTRRSKSFLAGEAVAAYVDRELEIIDGIKRGLGDAAAGRLVPHDEA 70
Cdd:COG3905    1 STTTTTVRLDDELKERLDALAAALDRSRSWLIKEAIAQYVEREEWREALIQEGLAAADAGEFVSHEEV 68
 
Name Accession Description Interval E-value
PutA1 COG3905
Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription] ...
 3-70 1.84e-18

Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription];


Pssm-ID: 443111  Cd Length: 69  Bit Score: 71.78  E-value: 1.84e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1197221387  3 ASTTMTIRLAPEVKEKLDRIATDTRRSKSFLAGEAVAAYVDRELEIIDGIKRGLGDAAAGRLVPHDEA 70
Cdd:COG3905    1 STTTTTVRLDDELKERLDALAAALDRSRSWLIKEAIAQYVEREEWREALIQEGLAAADAGEFVSHEEV 68
RHH_CopAso-like cd22233
ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar ...
 5-45 1.93e-09

ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar proteins; This family includes the N-terminal ribbon-helix-helix (RHH) domain of Shewanella oneidensis CopA(SO), a newly identified type II antitoxin, as well as the N-terminal RHH domain of Escherichia coli PutA flavoprotein, among other similar proteins, many of which are as yet uncharacterized. CopA(SO) is a typical RHH antitoxin that includes an ordered N-terminal domain (CopA(SO)-N) and a disordered C-terminal domain (CopA(SO)-C). Biophysical investigation indicates allosteric effects of CopA(SO)-N on CopA(SO)-C; DNA binding of CopA(SO)-N appears to induce CopA(SO)-C to fold and self-associate the C-terminal domain. The multifunctional E. coli proline utilization A (PutA) flavoprotein functions as a membrane-associated proline catabolic enzyme as well as a transcriptional repressor of the proline utilization genes putA and putP. The N-terminal domain of PutA is a transcriptional regulator with an RHH fold; structure studies show that it forms a homodimer to bind one DNA duplex. This family also includes orphan antitoxin ParD2, an antitoxin component of a non-functional type II toxin-antitoxin (TA system); it does not neutralize the effect of any of the RelE or ParE toxins.


Pssm-ID: 409023  Cd Length: 44  Bit Score: 48.14  E-value: 1.93e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1197221387  5 TTMTIRLAPEVKEKLDRIATDTRRSKSFLAGEAVAAYVDRE 45
Cdd:cd22233    1 TTLSVRLDDDLKERLDRLAAATDRSRSWIIKEAIEEYLERE 41
 
Name Accession Description Interval E-value
PutA1 COG3905
Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription] ...
 3-70 1.84e-18

Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription];


Pssm-ID: 443111  Cd Length: 69  Bit Score: 71.78  E-value: 1.84e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1197221387  3 ASTTMTIRLAPEVKEKLDRIATDTRRSKSFLAGEAVAAYVDRELEIIDGIKRGLGDAAAGRLVPHDEA 70
Cdd:COG3905    1 STTTTTVRLDDELKERLDALAAALDRSRSWLIKEAIAQYVEREEWREALIQEGLAAADAGEFVSHEEV 68
RHH_CopAso-like cd22233
ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar ...
 5-45 1.93e-09

ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar proteins; This family includes the N-terminal ribbon-helix-helix (RHH) domain of Shewanella oneidensis CopA(SO), a newly identified type II antitoxin, as well as the N-terminal RHH domain of Escherichia coli PutA flavoprotein, among other similar proteins, many of which are as yet uncharacterized. CopA(SO) is a typical RHH antitoxin that includes an ordered N-terminal domain (CopA(SO)-N) and a disordered C-terminal domain (CopA(SO)-C). Biophysical investigation indicates allosteric effects of CopA(SO)-N on CopA(SO)-C; DNA binding of CopA(SO)-N appears to induce CopA(SO)-C to fold and self-associate the C-terminal domain. The multifunctional E. coli proline utilization A (PutA) flavoprotein functions as a membrane-associated proline catabolic enzyme as well as a transcriptional repressor of the proline utilization genes putA and putP. The N-terminal domain of PutA is a transcriptional regulator with an RHH fold; structure studies show that it forms a homodimer to bind one DNA duplex. This family also includes orphan antitoxin ParD2, an antitoxin component of a non-functional type II toxin-antitoxin (TA system); it does not neutralize the effect of any of the RelE or ParE toxins.


Pssm-ID: 409023  Cd Length: 44  Bit Score: 48.14  E-value: 1.93e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1197221387  5 TTMTIRLAPEVKEKLDRIATDTRRSKSFLAGEAVAAYVDRE 45
Cdd:cd22233    1 TTLSVRLDDDLKERLDRLAAATDRSRSWIIKEAIEEYLERE 41
COG4710 COG4710
Predicted DNA-binding protein with an HTH domain [General function prediction only];
5-69 6.60e-07

Predicted DNA-binding protein with an HTH domain [General function prediction only];


Pssm-ID: 443745  Cd Length: 76  Bit Score: 42.58  E-value: 6.60e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1197221387  5 TTMTIRLAPEVKEKLDRIATDTRRSKSFLAGEAVAAYVDrELEIIDGIKRGLGDAAAGRL--VPHDE 69
Cdd:COG4710    2 KMLSIRLPEELEARLDALAKRTGRSKSFYVREAIEEYLD-DLEDYYLAEERLERVRAGREktYSLEE 67
 
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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