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Conserved domains on  [gi|1080407005|gb|OFL93288|]
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hypothetical protein HMPREF2742_00390 [Enterococcus sp. HMSC072H05]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10657338)

helix-turn-helix (HTH) domain-containing protein may bind DNA and function as a transcriptional regulator

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Trans_reg_C smart00862
Transcriptional regulatory protein, C terminal; This domain is almost always found associated ...
 142-213 1.78e-10

Transcriptional regulatory protein, C terminal; This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.


:

Pssm-ID: 214866 [Multi-domain]  Cd Length: 76  Bit Score: 55.25  E-value: 1.78e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080407005  142 LKLKQKE--IVYYLIQAGDRTVPREEISRQIWEKDPTKSVlASLSKVVSKVNEKIGNEFGEEAIQTVWGQGYRL 213
Cdd:smart00862   4 IKLTPKEfrLLELLLRNPGRVVSREELLEAVWGDDEDVDD-NTLDVHISRLRKKLEDDGDPRLIETVRGVGYRL 76
 
Name Accession Description Interval E-value
Trans_reg_C smart00862
Transcriptional regulatory protein, C terminal; This domain is almost always found associated ...
 142-213 1.78e-10

Transcriptional regulatory protein, C terminal; This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.


Pssm-ID: 214866 [Multi-domain]  Cd Length: 76  Bit Score: 55.25  E-value: 1.78e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080407005  142 LKLKQKE--IVYYLIQAGDRTVPREEISRQIWEKDPTKSVlASLSKVVSKVNEKIGNEFGEEAIQTVWGQGYRL 213
Cdd:smart00862   4 IKLTPKEfrLLELLLRNPGRVVSREELLEAVWGDDEDVDD-NTLDVHISRLRKKLEDDGDPRLIETVRGVGYRL 76
trans_reg_C cd00383
DNA-binding effector domain of two-component system response regulators; Bacteria and some ...
 129-213 4.06e-09

DNA-binding effector domain of two-component system response regulators; Bacteria and some eukaryotes use two-component signal transduction systems to detect and respond to changes in the environment. The systems consists of a sensor histidine kinase and a response regulator. The former autophosphorylates a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. This C-terminal effector domain belongs to the winged helix-turn-helix family of transcriptional regulators and contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunit of RNA polymerase.


Pssm-ID: 294013 [Multi-domain]  Cd Length: 89  Bit Score: 52.10  E-value: 4.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080407005 129 QQVSVKQKlsdlNLKLKQKE--IVYYLIQAGDRTVPREEISRQIW--EKDPTKSVLASLskvVSKVNEKIGNEFGEEAIQ 204
Cdd:cd00383     8 REVTVDGE----EVELTPKEfeLLELLARNPGRVVSREELLEAVWgyDYEVDDRTVDVH---ISRLRKKLEDDPEPRLIK 80


                  ....*....
gi 1080407005 205 TVWGQGYRL 213
Cdd:cd00383    81 TVRGVGYRL 89
CadC1 COG3710
DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];
145-214 6.27e-08

DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];


Pssm-ID: 442924 [Multi-domain]  Cd Length: 106  Bit Score: 49.13  E-value: 6.27e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080407005 145 KQKEIVYYLIQAGDRTVPREEISRQIWEKdpTKSVLASLSKVVSKVNEKIG-NEFGEEAIQTVWGQGYRLN 214
Cdd:COG3710    29 RAFDLLLLLLEHPGRVVSRDELLAAVWPG--RVVSDNSLTQAISRLRKALGdDGLEPRLIRTVPRRGYRLV 97
Trans_reg_C pfam00486
Transcriptional regulatory protein, C terminal;
139-213 1.25e-07

Transcriptional regulatory protein, C terminal;


Pssm-ID: 425712 [Multi-domain]  Cd Length: 77  Bit Score: 47.51  E-value: 1.25e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080407005 139 DLNLKLKQKEIVYYLIQAGDRTVPREEISRQIWEKDPTkSVLASLSKVVSKVNEKIG-NEFGEEAIQTVWGQGYRL 213
Cdd:pfam00486   3 EVELTPKEFKLLELLAENPGRVVSREQLLEEVWGEDYD-VDDNTVDVHISRLRKKLEdDPRDPRLIKTVRGVGYRL 77
PRK09836 PRK09836
DNA-binding transcriptional activator CusR; Provisional
 128-213 2.79e-03

DNA-binding transcriptional activator CusR; Provisional


Pssm-ID: 182102 [Multi-domain]  Cd Length: 227  Bit Score: 37.98  E-value: 2.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080407005 128 VQQVSVKQKLSDLNLKLKQKE--IVYYLIQAGDRTVPREEISRQIWEKDpTKSVLASLSKVVSKVNEKIGNEFGEEAIQT 205
Cdd:PRK09836  135 VDLVSRKVTRSGTRITLTSKEftLLEFFLRHQGEVLPRSLIASQVWDMN-FDSDTNAIDVAVKRLRGKIDNDFEPKLIQT 213


                  ....*...
gi 1080407005 206 VWGQGYRL 213
Cdd:PRK09836  214 VRGVGYML 221
 
Name Accession Description Interval E-value
Trans_reg_C smart00862
Transcriptional regulatory protein, C terminal; This domain is almost always found associated ...
 142-213 1.78e-10

Transcriptional regulatory protein, C terminal; This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.


Pssm-ID: 214866 [Multi-domain]  Cd Length: 76  Bit Score: 55.25  E-value: 1.78e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080407005  142 LKLKQKE--IVYYLIQAGDRTVPREEISRQIWEKDPTKSVlASLSKVVSKVNEKIGNEFGEEAIQTVWGQGYRL 213
Cdd:smart00862   4 IKLTPKEfrLLELLLRNPGRVVSREELLEAVWGDDEDVDD-NTLDVHISRLRKKLEDDGDPRLIETVRGVGYRL 76
trans_reg_C cd00383
DNA-binding effector domain of two-component system response regulators; Bacteria and some ...
 129-213 4.06e-09

DNA-binding effector domain of two-component system response regulators; Bacteria and some eukaryotes use two-component signal transduction systems to detect and respond to changes in the environment. The systems consists of a sensor histidine kinase and a response regulator. The former autophosphorylates a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. This C-terminal effector domain belongs to the winged helix-turn-helix family of transcriptional regulators and contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunit of RNA polymerase.


Pssm-ID: 294013 [Multi-domain]  Cd Length: 89  Bit Score: 52.10  E-value: 4.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080407005 129 QQVSVKQKlsdlNLKLKQKE--IVYYLIQAGDRTVPREEISRQIW--EKDPTKSVLASLskvVSKVNEKIGNEFGEEAIQ 204
Cdd:cd00383     8 REVTVDGE----EVELTPKEfeLLELLARNPGRVVSREELLEAVWgyDYEVDDRTVDVH---ISRLRKKLEDDPEPRLIK 80


                  ....*....
gi 1080407005 205 TVWGQGYRL 213
Cdd:cd00383    81 TVRGVGYRL 89
CadC1 COG3710
DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];
145-214 6.27e-08

DNA-binding winged helix-turn-helix (wHTH) domain [Transcription];


Pssm-ID: 442924 [Multi-domain]  Cd Length: 106  Bit Score: 49.13  E-value: 6.27e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080407005 145 KQKEIVYYLIQAGDRTVPREEISRQIWEKdpTKSVLASLSKVVSKVNEKIG-NEFGEEAIQTVWGQGYRLN 214
Cdd:COG3710    29 RAFDLLLLLLEHPGRVVSRDELLAAVWPG--RVVSDNSLTQAISRLRKALGdDGLEPRLIRTVPRRGYRLV 97
Trans_reg_C pfam00486
Transcriptional regulatory protein, C terminal;
139-213 1.25e-07

Transcriptional regulatory protein, C terminal;


Pssm-ID: 425712 [Multi-domain]  Cd Length: 77  Bit Score: 47.51  E-value: 1.25e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080407005 139 DLNLKLKQKEIVYYLIQAGDRTVPREEISRQIWEKDPTkSVLASLSKVVSKVNEKIG-NEFGEEAIQTVWGQGYRL 213
Cdd:pfam00486   3 EVELTPKEFKLLELLAENPGRVVSREQLLEEVWGEDYD-VDDNTVDVHISRLRKKLEdDPRDPRLIKTVRGVGYRL 77
DnrI COG3629
DNA-binding transcriptional regulator DnrI/AfsR/EmbR, SARP family, contains BTAD domain ...
 145-214 4.93e-05

DNA-binding transcriptional regulator DnrI/AfsR/EmbR, SARP family, contains BTAD domain [Transcription];


Pssm-ID: 442847 [Multi-domain]  Cd Length: 244  Bit Score: 43.29  E-value: 4.93e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080407005 145 KQKEIVYYLIQAGDRTVPREEISRQIWEKDPTKSVLASLSKVVSKVNEKIGnEFGEEAIQTVwGQGYRLN 214
Cdd:COG3629    25 KQRALLAYLALRAGRPVSRDRLADLLWGDDPPASARANLRTYVSRLRRALG-PAGGDLLVTR-GGGYRLD 92
PRK09836 PRK09836
DNA-binding transcriptional activator CusR; Provisional
 128-213 2.79e-03

DNA-binding transcriptional activator CusR; Provisional


Pssm-ID: 182102 [Multi-domain]  Cd Length: 227  Bit Score: 37.98  E-value: 2.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080407005 128 VQQVSVKQKLSDLNLKLKQKE--IVYYLIQAGDRTVPREEISRQIWEKDpTKSVLASLSKVVSKVNEKIGNEFGEEAIQT 205
Cdd:PRK09836  135 VDLVSRKVTRSGTRITLTSKEftLLEFFLRHQGEVLPRSLIASQVWDMN-FDSDTNAIDVAVKRLRGKIDNDFEPKLIQT 213


                  ....*...
gi 1080407005 206 VWGQGYRL 213
Cdd:PRK09836  214 VRGVGYML 221
 
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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