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Conserved domains on  [gi|1677275736|emb|VTM71551|]
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Multiple antibiotic resistance protein marR [Raoultella planticola]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 229396)

helix-turn-helix domain-containing protein may bind DNA and be involved in the regulation of gene expression

Gene Ontology:  GO:0003677|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 1-143 1.58e-36

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member PRK11512:

Pssm-ID: 481199  Cd Length: 144  Bit Score: 122.70  E-value: 1.58e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736   1 MNNHPGIINNKFHLGLLIHLANQFKDQLISQHFSGMDITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVK 79
Cdd:PRK11512    1 MKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRcAACITPVELKKVLSVDLGALTRMLDRLVC 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1677275736  80 RELISRSPNPQDKRQVILALTDKGLLICERFVNEALVSIISELTARLTPDESRQLVDLMTKMLP 143
Cdd:PRK11512   81 KGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDLHQELTKNLTADEVATLEHLLKKVLP 144
 
Name Accession Description Interval E-value
PRK11512 PRK11512
multiple antibiotic resistance transcriptional regulator MarR;
1-143 1.58e-36

multiple antibiotic resistance transcriptional regulator MarR;


Pssm-ID: 183170  Cd Length: 144  Bit Score: 122.70  E-value: 1.58e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736   1 MNNHPGIINNKFHLGLLIHLANQFKDQLISQHFSGMDITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVK 79
Cdd:PRK11512    1 MKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRcAACITPVELKKVLSVDLGALTRMLDRLVC 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1677275736  80 RELISRSPNPQDKRQVILALTDKGLLICERFVNEALVSIISELTARLTPDESRQLVDLMTKMLP 143
Cdd:PRK11512   81 KGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDLHQELTKNLTADEVATLEHLLKKVLP 144
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
14-142 7.55e-28

DNA-binding transcriptional regulator, MarR family [Transcription];


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 100.43  E-value: 7.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736  14 LGLLIHLANQFKDQLISQHFSGMDITAAQFKVLISIYK-GFNSPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDK 92
Cdd:COG1846    12 LGLLLRRLARALRRALDRALAELGLTPAQFRVLAALAEaGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVEREPDPEDR 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1677275736  93 RQVILALTDKGLLICERfVNEALVSIISELTARLTPDESRQLVDLMTKML 142
Cdd:COG1846    92 RAVLVRLTEKGRALLEE-ARPALEALLAELLAGLSEEELEALLRLLRRLA 140
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
31-130 8.36e-22

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 83.80  E-value: 8.36e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736   31 QHFSGMDITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQVILALTDKGLLICER 109
Cdd:smart00347   1 EELKPLGLTPTQFLVLRILYeEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLVRREPSPEDRRSVLVSLTEEGRELIEQ 80

                           90       100
                   ....*....|....*....|.
gi 1677275736  110 fVNEALVSIISELTARLTPDE 130
Cdd:smart00347  81 -LLEARSETLAELLAGLTAEE 100
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 38-95 1.71e-11

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 426012 [Multi-domain]  Cd Length: 59  Bit Score: 56.02  E-value: 1.71e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1677275736  38 ITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQV 95
Cdd:pfam01047   1 LTLTQFHILRILYeHGPLTVSELAEKLGVSKSTVTRVLDRLEKKGLIERSRSPEDRREV 59
 
Name Accession Description Interval E-value
PRK11512 PRK11512
multiple antibiotic resistance transcriptional regulator MarR;
1-143 1.58e-36

multiple antibiotic resistance transcriptional regulator MarR;


Pssm-ID: 183170  Cd Length: 144  Bit Score: 122.70  E-value: 1.58e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736   1 MNNHPGIINNKFHLGLLIHLANQFKDQLISQHFSGMDITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVK 79
Cdd:PRK11512    1 MKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRcAACITPVELKKVLSVDLGALTRMLDRLVC 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1677275736  80 RELISRSPNPQDKRQVILALTDKGLLICERFVNEALVSIISELTARLTPDESRQLVDLMTKMLP 143
Cdd:PRK11512   81 KGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDLHQELTKNLTADEVATLEHLLKKVLP 144
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
14-142 7.55e-28

DNA-binding transcriptional regulator, MarR family [Transcription];


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 100.43  E-value: 7.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736  14 LGLLIHLANQFKDQLISQHFSGMDITAAQFKVLISIYK-GFNSPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDK 92
Cdd:COG1846    12 LGLLLRRLARALRRALDRALAELGLTPAQFRVLAALAEaGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVEREPDPEDR 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1677275736  93 RQVILALTDKGLLICERfVNEALVSIISELTARLTPDESRQLVDLMTKML 142
Cdd:COG1846    92 RAVLVRLTEKGRALLEE-ARPALEALLAELLAGLSEEELEALLRLLRRLA 140
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
31-130 8.36e-22

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 83.80  E-value: 8.36e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736   31 QHFSGMDITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQVILALTDKGLLICER 109
Cdd:smart00347   1 EELKPLGLTPTQFLVLRILYeEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLVRREPSPEDRRSVLVSLTEEGRELIEQ 80

                           90       100
                   ....*....|....*....|.
gi 1677275736  110 fVNEALVSIISELTARLTPDE 130
Cdd:smart00347  81 -LLEARSETLAELLAGLTAEE 100
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 38-95 1.71e-11

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 426012 [Multi-domain]  Cd Length: 59  Bit Score: 56.02  E-value: 1.71e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1677275736  38 ITAAQFKVLISIY-KGFNSPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQV 95
Cdd:pfam01047   1 LTLTQFHILRILYeHGPLTVSELAEKLGVSKSTVTRVLDRLEKKGLIERSRSPEDRREV 59
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 37-94 6.69e-11

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 54.52  E-value: 6.69e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1677275736  37 DITAAQFKVLISIYKGFN-SPVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQ 94
Cdd:pfam12802   2 GLTPAQFRVLLALARNPGlTVAELARRLGISKQTVSRLVKRLEAKGLVEREPSPADRRA 60
HTH_27 pfam13463
Winged helix DNA-binding domain;
58-103 1.46e-06

Winged helix DNA-binding domain;


Pssm-ID: 433228 [Multi-domain]  Cd Length: 68  Bit Score: 43.43  E-value: 1.46e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1677275736  58 EISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQVILALTDKG 103
Cdd:pfam13463  23 DICFRLNVEDSHVSYSLKKLTEAGLVEREGSEEDGRETRVRLTAKG 68
PRK10870 PRK10870
transcriptional repressor MprA; Provisional
 56-142 1.34e-03

transcriptional repressor MprA; Provisional


Pssm-ID: 182795  Cd Length: 176  Bit Score: 37.03  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1677275736  56 PVEISKNLVMDAGAMSRMVDRMVKRELISRSPNPQDKRQVILALTDKGllicERFVNEALVS---IISELTARLTPDESR 132
Cdd:PRK10870   74 PSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKG----HEFLREVLPPqhnCLHQLWSALSTTEKD 149

                          90
                  ....*....|
gi 1677275736 133 QLVDLMTKML 142
Cdd:PRK10870  150 QLEQITRKLL 159
 
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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