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Conserved domains on  [gi|1092228486|gb|AOY86824|]
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homoprotocatechuate degradation operon regulator, HpaR [Marinobacter salinus]

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 ...
 7-123 4.69e-45

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 TIGR02337:

Pssm-ID: 481199 [Multi-domain]  Cd Length: 118  Bit Score: 142.91  E-value: 4.69e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   7 SLPLRLLKAREAAMAFFRPLLQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSED 86
Cdd:TIGR02337   1 SLPLALLQAREAAMSFFRPILAQHGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASND 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1092228486  87 QRRILISLTDKSKEMFARMSPLLEARYLEMTERFSPE 123
Cdd:TIGR02337  81 QRRVYISLTPKGQALYASLSPQIEEIYAAIEERLGEE 117
 
Name Accession Description Interval E-value
HpaR TIGR02337
homoprotocatechuate degradation operon regulator, HpaR; This Helix-Turn-Helix transcriptional ...
 7-123 4.69e-45

homoprotocatechuate degradation operon regulator, HpaR; This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.


Pssm-ID: 188209 [Multi-domain]  Cd Length: 118  Bit Score: 142.91  E-value: 4.69e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   7 SLPLRLLKAREAAMAFFRPLLQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSED 86
Cdd:TIGR02337   1 SLPLALLQAREAAMSFFRPILAQHGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASND 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1092228486  87 QRRILISLTDKSKEMFARMSPLLEARYLEMTERFSPE 123
Cdd:TIGR02337  81 QRRVYISLTPKGQALYASLSPQIEEIYAAIEERLGEE 117
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
6-135 2.56e-28

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 101.20  E-value: 2.56e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   6 DSLPLRLLKAREAAMAFFRPLLQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSE 85
Cdd:COG1846    10 ERLGLLLRRLARALRRALDRALAELGLTPAQFRVLAALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVEREPDPE 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1092228486  86 DQRRILISLTDKSKEMFARMSPLLEARYLEMTERFSPEDMKKLEELLNKL 135
Cdd:COG1846    90 DRRAVLVRLTEKGRALLEEARPALEALLAELLAGLSEEELEALLRLLRRL 139
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
27-125 1.40e-22

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 85.34  E-value: 1.40e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   27 LQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRILISLTDKSKEMFARMS 106
Cdd:smart00347   3 LKPLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLVRREPSPEDRRSVLVSLTEEGRELIEQLL 82

                           90
                   ....*....|....*....
gi 1092228486  107 PLLEARYLEMTERFSPEDM 125
Cdd:smart00347  83 EARSETLAELLAGLTAEEQ 101
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 32-90 8.96e-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: 53.71  E-value: 8.96e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1092228486  32 LTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRI 90
Cdd:pfam01047   1 LTLTQFHILRILYEHGPLTVSELAEKLGVSKSTVTRVLDRLEKKGLIERSRSPEDRREV 59
PRK03573 PRK03573
transcriptional regulator SlyA; Provisional
 27-135 1.92e-08

transcriptional regulator SlyA; Provisional


Pssm-ID: 179596  Cd Length: 144  Bit Score: 49.62  E-value: 1.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486  27 LQEIPLTEQQWRVIRALNEFEELESK-QLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRILISLTDKSKEMFARM 105
Cdd:PRK03573   24 LKPLELTQTHWVTLHNIHQLPPEQSQiQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV 103

                          90       100       110
                  ....*....|....*....|....*....|
gi 1092228486 106 SPLLEARYLEMTERFSPEDMKKLEELLNKL 135
Cdd:PRK03573  104 EAVINKTRAEILHGISAEEIEQLITLIAKL 133
 
Name Accession Description Interval E-value
HpaR TIGR02337
homoprotocatechuate degradation operon regulator, HpaR; This Helix-Turn-Helix transcriptional ...
 7-123 4.69e-45

homoprotocatechuate degradation operon regulator, HpaR; This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.


Pssm-ID: 188209 [Multi-domain]  Cd Length: 118  Bit Score: 142.91  E-value: 4.69e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   7 SLPLRLLKAREAAMAFFRPLLQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSED 86
Cdd:TIGR02337   1 SLPLALLQAREAAMSFFRPILAQHGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASND 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1092228486  87 QRRILISLTDKSKEMFARMSPLLEARYLEMTERFSPE 123
Cdd:TIGR02337  81 QRRVYISLTPKGQALYASLSPQIEEIYAAIEERLGEE 117
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
6-135 2.56e-28

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 101.20  E-value: 2.56e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   6 DSLPLRLLKAREAAMAFFRPLLQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSE 85
Cdd:COG1846    10 ERLGLLLRRLARALRRALDRALAELGLTPAQFRVLAALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVEREPDPE 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1092228486  86 DQRRILISLTDKSKEMFARMSPLLEARYLEMTERFSPEDMKKLEELLNKL 135
Cdd:COG1846    90 DRRAVLVRLTEKGRALLEEARPALEALLAELLAGLSEEELEALLRLLRRL 139
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
27-125 1.40e-22

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 85.34  E-value: 1.40e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   27 LQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRILISLTDKSKEMFARMS 106
Cdd:smart00347   3 LKPLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLVRREPSPEDRRSVLVSLTEEGRELIEQLL 82

                           90
                   ....*....|....*....
gi 1092228486  107 PLLEARYLEMTERFSPEDM 125
Cdd:smart00347  83 EARSETLAELLAGLTAEEQ 101
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 32-90 8.96e-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: 53.71  E-value: 8.96e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1092228486  32 LTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRI 90
Cdd:pfam01047   1 LTLTQFHILRILYEHGPLTVSELAEKLGVSKSTVTRVLDRLEKKGLIERSRSPEDRREV 59
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 32-89 1.24e-09

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: 50.67  E-value: 1.24e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1092228486  32 LTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRR 89
Cdd:pfam12802   3 LTPAQFRVLLALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVEREPSPADRRA 60
PRK03573 PRK03573
transcriptional regulator SlyA; Provisional
 27-135 1.92e-08

transcriptional regulator SlyA; Provisional


Pssm-ID: 179596  Cd Length: 144  Bit Score: 49.62  E-value: 1.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486  27 LQEIPLTEQQWRVIRALNEFEELESK-QLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRILISLTDKSKEMFARM 105
Cdd:PRK03573   24 LKPLELTQTHWVTLHNIHQLPPEQSQiQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV 103

                          90       100       110
                  ....*....|....*....|....*....|
gi 1092228486 106 SPLLEARYLEMTERFSPEDMKKLEELLNKL 135
Cdd:PRK03573  104 EAVINKTRAEILHGISAEEIEQLITLIAKL 133
PRK10870 PRK10870
transcriptional repressor MprA; Provisional
 45-135 2.29e-05

transcriptional repressor MprA; Provisional


Pssm-ID: 182795  Cd Length: 176  Bit Score: 42.04  E-value: 2.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486  45 EFEELESKQLAELCCILSPSLTG---IINRLEQQGYIKRRKSSEDQRRILISLTDKSKEMFARMSPLLEARYLEMTERFS 121
Cdd:PRK10870   65 ESQENHSIQPSELSCALGSSRTNatrIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQHNCLHQLWSALS 144

                          90
                  ....*....|....
gi 1092228486 122 PEDMKKLEELLNKL 135
Cdd:PRK10870  145 TTEKDQLEQITRKL 158
PRK14165 PRK14165
winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
 42-129 9.86e-04

winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional


Pssm-ID: 184548 [Multi-domain]  Cd Length: 217  Bit Score: 37.74  E-value: 9.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486  42 ALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQrriLISLTDKSKEmfarmspLLEARYLEMTERFS 121
Cdd:PRK14165   15 AVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQ---LITITEKGLD-------VLYNEYADYSRIFS 84


                  ....*...
gi 1092228486 122 PEDMKKLE 129
Cdd:PRK14165   85 IKDNLELE 92
HTH_27 pfam13463
Winged helix DNA-binding domain;
32-97 1.25e-03

Winged helix DNA-binding domain;


Pssm-ID: 433228 [Multi-domain]  Cd Length: 68  Bit Score: 35.34  E-value: 1.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1092228486  32 LTEQQWRVIRALNEfeELESKQLAELCCILSPSLTGIIN---RLEQQGYIKRRKSSEDQRRILISLTDK 97
Cdd:pfam13463   1 LTRLEALILHNIGH--RGDPKTLADICFRLNVEDSHVSYslkKLTEAGLVEREGSEEDGRETRVRLTAK 67
Staph_reg_Sar TIGR01889
staphylococcal accessory regulator family; This model represents a family of transcriptional ...
 52-105 1.69e-03

staphylococcal accessory regulator family; This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam01047. [Regulatory functions, DNA interactions]


Pssm-ID: 130944  Cd Length: 109  Bit Score: 35.69  E-value: 1.69e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1092228486  52 KQLAELCCILSPSLTGIINRLEQQGYIKRRKSSEDQRRILISLTDKSKEMFARM 105
Cdd:TIGR01889  47 KEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESL 100
PRK11512 PRK11512
multiple antibiotic resistance transcriptional regulator MarR;
4-135 2.54e-03

multiple antibiotic resistance transcriptional regulator MarR;


Pssm-ID: 183170  Cd Length: 144  Bit Score: 36.03  E-value: 2.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092228486   4 FNDSLPL-RLLK-AREAAMAFFRPLLQEIPLTEQQWRVIRALNEFEELESKQLAELCCILSPSLTGIINRLEQQGYIKRR 81
Cdd:PRK11512    8 FNEIIPLgRLIHmVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1092228486  82 KSSEDQRRILISLTDKSKEMFARMSPLL-EARYLEMTERFSPEDMKKLEELLNKL 135
Cdd:PRK11512   88 PNPNDKRGVLVKLTTSGAAICEQCHQLVgQDLHQELTKNLTADEVATLEHLLKKV 142
PRK13777 PRK13777
HTH-type transcriptional regulator Hpr;
71-124 8.17e-03

HTH-type transcriptional regulator Hpr;


Pssm-ID: 237501  Cd Length: 185  Bit Score: 34.63  E-value: 8.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1092228486  71 RLEQQGYIKRRKSSEDQRRILISLTDKSKEMFarmspllearyLEMTERFSPED 124
Cdd:PRK13777   82 KLEERGYLTFSKKEDDKRNTYIELTEKGEELL-----------LETMEEYDPEN 124
 
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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