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Conserved domains on  [gi|515410324|ref|WP_016899346|]
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MULTISPECIES: TraR/DksA C4-type zinc finger protein [Pseudoalteromonas]

Protein Classification

TraR/DksA family transcriptional regulator( domain architecture ID 10004441)

TraR/DksA family transcriptional regulator similar to Bacillus subtilis general stress protein 16O (GSP16O) and Agrobacterium tumefaciens DnaK suppressor protein

CATH:  1.10.287.3960
Gene Ontology:  GO:0008270
PubMed:  15294157|12665246|17210253|15963892|15718139|10529348|15333933
SCOP:  4003090

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
5-121 1.03e-14

RNA polymerase-binding transcription factor DksA [Transcription];


:

Pssm-ID: 441340  Cd Length: 119  Bit Score: 65.31  E-value: 1.03e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515410324   5 LKTDQLGHIINQVNDEISMLKNALNEPINKNV---ESNVLADILDRAALEEERKQQY--ISRYRKGLQL--KALQRVkfr 77
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELLsgdLSAYDPDPADRATEEEERELELalRDRERKLLRKidAALERI--- 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 515410324  78 lqkEPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIEVQNR 121
Cdd:COG1734   78 ---EEGTYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
 
Name Accession Description Interval E-value
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
5-121 1.03e-14

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 65.31  E-value: 1.03e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515410324   5 LKTDQLGHIINQVNDEISMLKNALNEPINKNV---ESNVLADILDRAALEEERKQQY--ISRYRKGLQL--KALQRVkfr 77
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELLsgdLSAYDPDPADRATEEEERELELalRDRERKLLRKidAALERI--- 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 515410324  78 lqkEPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIEVQNR 121
Cdd:COG1734   78 ---EEGTYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 37-114 9.94e-14

RNA polymerase-binding protein DksA; The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage. [Transcription, Transcription factors, Regulatory functions, Small molecule interactions]


Pssm-ID: 274124  Cd Length: 110  Bit Score: 62.65  E-value: 9.94e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515410324   37 ESNVLADILDRAALEEERKQQYISRYRkglQLKALQRVKFRLQK-EPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQS 114
Cdd:TIGR02420  34 ESENFPDPADRATQEEERALELRTRDR---ERKLIKKIDEALKRiEDGEYGYCEECGEEIGLRRLEARPTATLCIDCKT 109
dksA PRK10778
RNA polymerase-binding protein DksA;
3-121 2.59e-12

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 60.15  E-value: 2.59e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515410324   3 EFLKTDQLGHII-------NQVNDEISMLKNALNEpinknvESNVLADILDRAALEEERKQQYISRYRkglQLKALQRVK 75
Cdd:PRK10778  30 EYMNEAQLAHFKrileawrNQLRDEVDRTVTHMQD------EAANFPDPVDRAAQEEEFSLELRNRDR---ERKLIKKIE 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 515410324  76 FRLQK-EPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIEVQNR 121
Cdd:PRK10778 101 KTLKKvEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
83-117 1.95e-06

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 41.89  E-value: 1.95e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 515410324   83 GEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIE 117
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYE 35
 
Name Accession Description Interval E-value
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
5-121 1.03e-14

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 65.31  E-value: 1.03e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515410324   5 LKTDQLGHIINQVNDEISMLKNALNEPINKNV---ESNVLADILDRAALEEERKQQY--ISRYRKGLQL--KALQRVkfr 77
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELLsgdLSAYDPDPADRATEEEERELELalRDRERKLLRKidAALERI--- 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 515410324  78 lqkEPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIEVQNR 121
Cdd:COG1734   78 ---EEGTYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 37-114 9.94e-14

RNA polymerase-binding protein DksA; The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage. [Transcription, Transcription factors, Regulatory functions, Small molecule interactions]


Pssm-ID: 274124  Cd Length: 110  Bit Score: 62.65  E-value: 9.94e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515410324   37 ESNVLADILDRAALEEERKQQYISRYRkglQLKALQRVKFRLQK-EPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQS 114
Cdd:TIGR02420  34 ESENFPDPADRATQEEERALELRTRDR---ERKLIKKIDEALKRiEDGEYGYCEECGEEIGLRRLEARPTATLCIDCKT 109
dksA PRK10778
RNA polymerase-binding protein DksA;
3-121 2.59e-12

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 60.15  E-value: 2.59e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515410324   3 EFLKTDQLGHII-------NQVNDEISMLKNALNEpinknvESNVLADILDRAALEEERKQQYISRYRkglQLKALQRVK 75
Cdd:PRK10778  30 EYMNEAQLAHFKrileawrNQLRDEVDRTVTHMQD------EAANFPDPVDRAAQEEEFSLELRNRDR---ERKLIKKIE 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 515410324  76 FRLQK-EPGEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIEVQNR 121
Cdd:PRK10778 101 KTLKKvEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 43-117 1.68e-08

phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 274123  Cd Length: 63  Bit Score: 47.78  E-value: 1.68e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515410324   43 DILDRA-ALEEERKQQYISRYRKglqlkalqrvkfrlQKEPGEYGY-CETCGIEIQFKRLVTVPTAENCCDCQSIIE 117
Cdd:TIGR02419   1 DEFDRAqELEEELLERALAAARA--------------KKVIGPSLReCEDCGEPIPEARREALPGVTRCVSCQEILE 63
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
83-117 1.95e-06

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 41.89  E-value: 1.95e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 515410324   83 GEYGYCETCGIEIQFKRLVTVPTAENCCDCQSIIE 117
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYE 35
PHA00080 PHA00080
DksA-like zinc finger domain containing protein
 42-126 4.09e-05

DksA-like zinc finger domain containing protein


Pssm-ID: 222775  Cd Length: 72  Bit Score: 39.35  E-value: 4.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515410324  42 ADILDRAA-LEEERKQQYISRYRkglqlkalqrvkfrlQKEPGEYGY-CETCGIEIQFKRLVTVPTAENCCDCQSIIEVQ 119
Cdd:PHA00080   1 ADIIDRAAeIEELQRERALANRR---------------NKYQAPSAThCEECGDPIPEARREAVPGCRTCVSCQEILELK 65


                 ....*..
gi 515410324 120 NRYKCRR 126
Cdd:PHA00080  66 SYQRGAK 72
PRK11019 PRK11019
DksA/TraR family C4-type zinc finger protein;
70-121 6.53e-03

DksA/TraR family C4-type zinc finger protein;


Pssm-ID: 182903  Cd Length: 88  Bit Score: 33.69  E-value: 6.53e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 515410324  70 ALQRVKFRLQKEPGEYgYCETCGIEIQFKRLVTVPTAENCCDCQSIIEVQNR 121
Cdd:PRK11019  22 AIARARSELPRGESLT-ECEECGEPIPEARRKAIPGVRLCVACQQEKDLQQA 72
 
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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