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Conserved domains on  [gi|1582565598|gb|TBD46276|]
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TraY domain-containing protein [Rhizobium ruizarguesonis]

Protein Classification

COG4710 family protein( domain architecture ID 10008736)

COG4710 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4710 COG4710
Predicted DNA-binding protein with an HTH domain [General function prediction only];
1-74 1.88e-26

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


:

Pssm-ID: 443745  Cd Length: 76  Bit Score: 91.50  E-value: 1.88e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1582565598  1 MLVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGERRLEELRRDEGDTVPLAELTARYGLDD 74
Cdd:COG4710    3 MLSIRLPEELEARLDALAKRTGRSKSFYVREAIEEYLDDLEDYYLAEERLERVRAGREKTYSLEEVERDLGLED 76
 
Name Accession Description Interval E-value
COG4710 COG4710
Predicted DNA-binding protein with an HTH domain [General function prediction only];
1-74 1.88e-26

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


Pssm-ID: 443745  Cd Length: 76  Bit Score: 91.50  E-value: 1.88e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1582565598  1 MLVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGERRLEELRRDEGDTVPLAELTARYGLDD 74
Cdd:COG4710    3 MLSIRLPEELEARLDALAKRTGRSKSFYVREAIEEYLDDLEDYYLAEERLERVRAGREKTYSLEEVERDLGLED 76
TraY pfam05509
TraY domain; This family consists of several enterobacterial TraY proteins. TraY is involved ...
 2-49 6.82e-10

TraY domain; This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid. These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins.


Pssm-ID: 428502  Cd Length: 49  Bit Score: 49.17  E-value: 6.82e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1582565598  2 LVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGERR 49
Cdd:pfam05509  1 VTLQLDEETNKLLEEAAERSGRSKRKEAALRLKDHLDRFPDIYESEKR 48
RHH_CopAso-like cd22233
ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar ...
 4-42 3.45e-06

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: 39.66  E-value: 3.45e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1582565598  4 LQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLED 42
Cdd:cd22233    5 VRLDDDLKERLDRLAAATDRSRSWIIKEAIEEYLEREEW 43
PRK13740 PRK13740
conjugal transfer relaxosome protein TraY;
1-60 1.15e-03

conjugal transfer relaxosome protein TraY;


Pssm-ID: 184292  Cd Length: 70  Bit Score: 33.60  E-value: 1.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582565598  1 MLVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGErrLEELRRDEGDT 60
Cdd:PRK13740  13 KVSLKLDEDTNNKLIEAKERSGRSKTNEVQIRLRDHLKRFPDFYNSE--IFREVAEETES 70
 
Name Accession Description Interval E-value
COG4710 COG4710
Predicted DNA-binding protein with an HTH domain [General function prediction only];
1-74 1.88e-26

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


Pssm-ID: 443745  Cd Length: 76  Bit Score: 91.50  E-value: 1.88e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1582565598  1 MLVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGERRLEELRRDEGDTVPLAELTARYGLDD 74
Cdd:COG4710    3 MLSIRLPEELEARLDALAKRTGRSKSFYVREAIEEYLDDLEDYYLAEERLERVRAGREKTYSLEEVERDLGLED 76
TraY pfam05509
TraY domain; This family consists of several enterobacterial TraY proteins. TraY is involved ...
 2-49 6.82e-10

TraY domain; This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid. These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins.


Pssm-ID: 428502  Cd Length: 49  Bit Score: 49.17  E-value: 6.82e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1582565598  2 LVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGERR 49
Cdd:pfam05509  1 VTLQLDEETNKLLEEAAERSGRSKRKEAALRLKDHLDRFPDIYESEKR 48
RHH_CopAso-like cd22233
ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar ...
 4-42 3.45e-06

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: 39.66  E-value: 3.45e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1582565598  4 LQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLED 42
Cdd:cd22233    5 VRLDDDLKERLDRLAAATDRSRSWIIKEAIEEYLEREEW 43
PutA1 COG3905
Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription] ...
 4-65 8.57e-04

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


Pssm-ID: 443111  Cd Length: 69  Bit Score: 34.03  E-value: 8.57e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1582565598  4 LQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDvylGERRLEELRR--DEGDTVPLAE 65
Cdd:COG3905    7 VRLDDELKERLDALAAALDRSRSWLIKEAIAQYVEREEW---REALIQEGLAaaDAGEFVSHEE 67
PRK13740 PRK13740
conjugal transfer relaxosome protein TraY;
1-60 1.15e-03

conjugal transfer relaxosome protein TraY;


Pssm-ID: 184292  Cd Length: 70  Bit Score: 33.60  E-value: 1.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582565598  1 MLVLQLPPDIEARLIELSKRTGRSKSFYVRQAILAHLDDLEDVYLGErrLEELRRDEGDT 60
Cdd:PRK13740  13 KVSLKLDEDTNNKLIEAKERSGRSKTNEVQIRLRDHLKRFPDFYNSE--IFREVAEETES 70
 
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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