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Conserved domains on  [gi|489526441|ref|WP_003431194|]
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TraR/DksA C4-type zinc finger protein [Clostridioides difficile]

Protein Classification

TraR/DksA C4-type zinc finger protein( domain architecture ID 3397)

TraR/DksA C4-type zinc finger protein may function as a transcriptional regulator

CATH:  1.10.287.3960
Gene Ontology:  GO:0008270
PubMed:  15294157
SCOP:  4003090

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-dskA_traR super family cl00755
Prokaryotic dksA/traR C4-type zinc finger;
1-125 3.24e-31

Prokaryotic dksA/traR C4-type zinc finger;


The actual alignment was detected with superfamily member TIGR02890:

Pssm-ID: 445081  Cd Length: 159  Bit Score: 109.74  E-value: 3.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526441    1 MDTKKYKDKLLKERENLTNLVEDMKDNtlFGDTTKHTSekysSGELSSYDNHIGDMGTDLYMQNMQNSLINHEEGRLYQI 80
Cdd:TIGR02890   1 QQLAELKNMLLQEKKELEQRLKQMNKE--DGIASQRES----TGELSQYDNHPADLATELYEREKDIALREHEERELREI 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 489526441   81 DLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDCAKKENN 125
Cdd:TIGR02890  75 EHALQKIENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119
 
Name Accession Description Interval E-value
bacill_yteA TIGR02890
regulatory protein, yteA family; Members of this predicted regulatory protein are found only ...
 1-125 3.24e-31

regulatory protein, yteA family; Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to Pfam family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. Smaller proteins from the proteobacteria with just the N-terminal domain, including DksA and DksA2 are RNA polymerase-binding regulatory proteins even if the Zn-binding site is not conserved. [Unknown function, General]


Pssm-ID: 274340  Cd Length: 159  Bit Score: 109.74  E-value: 3.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526441    1 MDTKKYKDKLLKERENLTNLVEDMKDNtlFGDTTKHTSekysSGELSSYDNHIGDMGTDLYMQNMQNSLINHEEGRLYQI 80
Cdd:TIGR02890   1 QQLAELKNMLLQEKKELEQRLKQMNKE--DGIASQRES----TGELSQYDNHPADLATELYEREKDIALREHEERELREI 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 489526441   81 DLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDCAKKENN 125
Cdd:TIGR02890  75 EHALQKIENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
1-123 2.54e-30

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 106.14  E-value: 2.54e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526441   1 MDTKK---YKDKLLKERENLTNLVEDMKDNTLfgdttkhtsekysSGELSSYDNHIGDMGTDLYMQNMQNSLINHEEGRL 77
Cdd:COG1734    1 MSDEQleeFRERLLEEREELLEELEETEEELL-------------SGDLSAYDPDPADRATEEEERELELALRDRERKLL 67

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489526441  78 YQIDLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDCAKKE 123
Cdd:COG1734   68 RKIDAALERIEEGTYGICEECGEPIPLERLEARPTATLCIECKERQ 113
DksA_like NF033459
RNA polymerase-binding protein DksA;
68-119 4.03e-12

RNA polymerase-binding protein DksA;


Pssm-ID: 380301  Cd Length: 113  Bit Score: 59.17  E-value: 4.03e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489526441  68 SLINHEEGRLYQIDLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDC 119
Cdd:NF033459  54 AISNQQKKELNEIEEALKKIKNGTYGICEMCEEPIGIERLKVKPHAKYCITC 105
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
90-123 5.51e-08

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 46.51  E-value: 5.51e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 489526441   90 GTYGICDLCHNQIDLERLDILPDTSLCNDCAKKE 123
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKY 34
dksA PRK10778
RNA polymerase-binding protein DksA;
71-119 1.26e-03

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 37.42  E-value: 1.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489526441  71 NHEEGRLYQIDLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDC 119
Cdd:PRK10778  90 DRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDC 138
 
Name Accession Description Interval E-value
bacill_yteA TIGR02890
regulatory protein, yteA family; Members of this predicted regulatory protein are found only ...
 1-125 3.24e-31

regulatory protein, yteA family; Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to Pfam family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. Smaller proteins from the proteobacteria with just the N-terminal domain, including DksA and DksA2 are RNA polymerase-binding regulatory proteins even if the Zn-binding site is not conserved. [Unknown function, General]


Pssm-ID: 274340  Cd Length: 159  Bit Score: 109.74  E-value: 3.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526441    1 MDTKKYKDKLLKERENLTNLVEDMKDNtlFGDTTKHTSekysSGELSSYDNHIGDMGTDLYMQNMQNSLINHEEGRLYQI 80
Cdd:TIGR02890   1 QQLAELKNMLLQEKKELEQRLKQMNKE--DGIASQRES----TGELSQYDNHPADLATELYEREKDIALREHEERELREI 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 489526441   81 DLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDCAKKENN 125
Cdd:TIGR02890  75 EHALQKIENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
1-123 2.54e-30

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 106.14  E-value: 2.54e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526441   1 MDTKK---YKDKLLKERENLTNLVEDMKDNTLfgdttkhtsekysSGELSSYDNHIGDMGTDLYMQNMQNSLINHEEGRL 77
Cdd:COG1734    1 MSDEQleeFRERLLEEREELLEELEETEEELL-------------SGDLSAYDPDPADRATEEEERELELALRDRERKLL 67

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489526441  78 YQIDLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDCAKKE 123
Cdd:COG1734   68 RKIDAALERIEEGTYGICEECGEPIPLERLEARPTATLCIECKERQ 113
DksA_like NF033459
RNA polymerase-binding protein DksA;
68-119 4.03e-12

RNA polymerase-binding protein DksA;


Pssm-ID: 380301  Cd Length: 113  Bit Score: 59.17  E-value: 4.03e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489526441  68 SLINHEEGRLYQIDLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDC 119
Cdd:NF033459  54 AISNQQKKELNEIEEALKKIKNGTYGICEMCEEPIGIERLKVKPHAKYCITC 105
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
90-123 5.51e-08

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 46.51  E-value: 5.51e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 489526441   90 GTYGICDLCHNQIDLERLDILPDTSLCNDCAKKE 123
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKY 34
dksA PRK10778
RNA polymerase-binding protein DksA;
71-119 1.26e-03

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 37.42  E-value: 1.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489526441  71 NHEEGRLYQIDLALSKIENGTYGICDLCHNQIDLERLDILPDTSLCNDC 119
Cdd:PRK10778  90 DRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDC 138
 
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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