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Conserved domains on  [gi|2278571769|ref|WP_255475416|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Micrococcus]

Protein Classification

winged helix-turn-helix domain-containing protein( domain architecture ID 10582168)

winged helix-turn-helix (wHTH) domain-containing protein binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|10473770|8831795
SCOP:  3000034

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_20 pfam12840
Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in ...
 21-71 1.11e-08

Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins.


:

Pssm-ID: 432824 [Multi-domain]  Cd Length: 61  Bit Score: 49.85  E-value: 1.11e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2278571769  21 AITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEH 71
Cdd:pfam12840   6 ALADPTRLRILRALVGDEPLTASELARRLDISRNTLSYHLRKLEEAGLVEV 56
COG2345 super family cl39134
Predicted transcriptional regulator, ArsR family [Transcription];
14-117 1.47e-04

Predicted transcriptional regulator, ArsR family [Transcription];


The actual alignment was detected with superfamily member COG2345:

Pssm-ID: 441914 [Multi-domain]  Cd Length: 217  Bit Score: 41.06  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278571769  14 TDPKAVAAITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQASDNGFH 93
Cdd:COG2345     2 TDTPALAALADPTRRRILELLKRAGPVTAAELAEALGLTPNAVRRHLDALEEEGLVERETERRGRGRPAKLYRLTEAGRA 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2278571769  94 ID-----------LEAIRVQDGGEAAVATLRRVAE 117
Cdd:COG2345    82 RFprayddlavalLDALRELLGEDAVERLARARGR 116
 
Name Accession Description Interval E-value
HTH_20 pfam12840
Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in ...
 21-71 1.11e-08

Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins.


Pssm-ID: 432824 [Multi-domain]  Cd Length: 61  Bit Score: 49.85  E-value: 1.11e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2278571769  21 AITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEH 71
Cdd:pfam12840   6 ALADPTRLRILRALVGDEPLTASELARRLDISRNTLSYHLRKLEEAGLVEV 56
COG4189 COG4189
Predicted transcriptional regulator, ArsR family [Transcription];
12-89 2.61e-07

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 443343 [Multi-domain]  Cd Length: 97  Bit Score: 47.26  E-value: 2.61e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2278571769  12 RITDPKAVAAITHPVRMRLLGELARRGsARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQASD 89
Cdd:COG4189     6 DEESLEVLKALASETRLRILRLLAEEP-LNVNELAEALGLPKSTVSYHIRKLEEAGLIRTEYKPGKRGRQKICYLRVD 82
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 20-75 4.39e-07

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 46.14  E-value: 4.39e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2278571769  20 AAITHPVRMRLLGELARRGsARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDH 75
Cdd:cd00090     2 KALSDPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56
HTH_metalloreg NF033788
metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense ...
 20-74 6.40e-06

metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense toxic heavy metals such as arsenic or cadmium, and are released from DNA so that resistance factors will be expressed, include ArsR, SmtB, ZiaR, CadC, CadX, KmtR, etc. However, some members of this family, including the sporulation delaying system autorepressor SdpR and its family (see NF033789), may lack metal-binding cites and instead regulate other cellular processes.


Pssm-ID: 411368 [Multi-domain]  Cd Length: 76  Bit Score: 42.83  E-value: 6.40e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2278571769  20 AAITHPVRMRLLGELaRRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPD 74
Cdd:NF033788    6 KALADPTRLRILELL-AEGELCVCELAEALGLSQSAVSQHLKVLRDAGLVTSRRE 59
COG2345 COG2345
Predicted transcriptional regulator, ArsR family [Transcription];
14-117 1.47e-04

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441914 [Multi-domain]  Cd Length: 217  Bit Score: 41.06  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278571769  14 TDPKAVAAITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQASDNGFH 93
Cdd:COG2345     2 TDTPALAALADPTRRRILELLKRAGPVTAAELAEALGLTPNAVRRHLDALEEEGLVERETERRGRGRPAKLYRLTEAGRA 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2278571769  94 ID-----------LEAIRVQDGGEAAVATLRRVAE 117
Cdd:COG2345    82 RFprayddlavalLDALRELLGEDAVERLARARGR 116
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
28-70 3.21e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 34.88  E-value: 3.21e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2278571769   28 MRLLgelaRRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIE 70
Cdd:smart00418   3 LKLL----AEGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41
 
Name Accession Description Interval E-value
HTH_20 pfam12840
Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in ...
 21-71 1.11e-08

Helix-turn-helix domain; This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins.


Pssm-ID: 432824 [Multi-domain]  Cd Length: 61  Bit Score: 49.85  E-value: 1.11e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2278571769  21 AITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEH 71
Cdd:pfam12840   6 ALADPTRLRILRALVGDEPLTASELARRLDISRNTLSYHLRKLEEAGLVEV 56
COG4189 COG4189
Predicted transcriptional regulator, ArsR family [Transcription];
12-89 2.61e-07

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 443343 [Multi-domain]  Cd Length: 97  Bit Score: 47.26  E-value: 2.61e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2278571769  12 RITDPKAVAAITHPVRMRLLGELARRGsARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQASD 89
Cdd:COG4189     6 DEESLEVLKALASETRLRILRLLAEEP-LNVNELAEALGLPKSTVSYHIRKLEEAGLIRTEYKPGKRGRQKICYLRVD 82
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 20-75 4.39e-07

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 46.14  E-value: 4.39e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2278571769  20 AAITHPVRMRLLGELARRGsARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDH 75
Cdd:cd00090     2 KALSDPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56
ArsR COG0640
DNA-binding transcriptional regulator, ArsR family [Transcription];
20-85 5.48e-07

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


Pssm-ID: 440405 [Multi-domain]  Cd Length: 92  Bit Score: 46.04  E-value: 5.48e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2278571769  20 AAITHPVRMRLLGELARrGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPdhasDRRERWWR 85
Cdd:COG0640    15 KALADPTRLRILRLLAE-GELCVGELAEALGLSQSTVSHHLKVLREAGLVTSRR----EGRWVYYR 75
HTH_metalloreg NF033788
metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense ...
 20-74 6.40e-06

metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense toxic heavy metals such as arsenic or cadmium, and are released from DNA so that resistance factors will be expressed, include ArsR, SmtB, ZiaR, CadC, CadX, KmtR, etc. However, some members of this family, including the sporulation delaying system autorepressor SdpR and its family (see NF033789), may lack metal-binding cites and instead regulate other cellular processes.


Pssm-ID: 411368 [Multi-domain]  Cd Length: 76  Bit Score: 42.83  E-value: 6.40e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2278571769  20 AAITHPVRMRLLGELaRRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPD 74
Cdd:NF033788    6 KALADPTRLRILELL-AEGELCVCELAEALGLSQSAVSQHLKVLRDAGLVTSRRE 59
COG1777 COG1777
Predicted transcriptional regulator, ArsR family [Transcription];
20-96 1.71e-05

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441383  Cd Length: 113  Bit Score: 42.33  E-value: 1.71e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2278571769  20 AAITHPVRMRLLGELARRgSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQASDNGFHIDL 96
Cdd:COG1777    12 DALGNPTRRRILALLSEE-PAYVSELARELGVSRQAVYKHLRKLEEAGLVESYREGREDGRARKYYRLSAFRLEVTL 87
COG2345 COG2345
Predicted transcriptional regulator, ArsR family [Transcription];
14-117 1.47e-04

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441914 [Multi-domain]  Cd Length: 217  Bit Score: 41.06  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278571769  14 TDPKAVAAITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQASDNGFH 93
Cdd:COG2345     2 TDTPALAALADPTRRRILELLKRAGPVTAAELAEALGLTPNAVRRHLDALEEEGLVERETERRGRGRPAKLYRLTEAGRA 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2278571769  94 ID-----------LEAIRVQDGGEAAVATLRRVAE 117
Cdd:COG2345    82 RFprayddlavalLDALRELLGEDAVERLARARGR 116
COG4190 COG4190
Predicted transcriptional regulator, contains HTH domain [Transcription];
14-97 1.49e-04

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443344  Cd Length: 121  Bit Score: 39.88  E-value: 1.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278571769  14 TDPKAVAAITHPVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDHASDRRERWWRQasdngFH 93
Cdd:COG4190    41 ESPESLARVLTPKRLELLRAIAEEGPESIRELARRLGRDVKNVHRDLKTLEELGLVELEEDGRAKRPVVPYDE-----IE 115


                  ....
gi 2278571769  94 IDLE 97
Cdd:COG4190   116 IDFP 119
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
25-83 2.03e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 37.26  E-value: 2.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2278571769  25 PVRMRLLGELARRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIEHDPDhASDRRERW 83
Cdd:COG1846    38 PAQFRVLAALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVEREPD-PEDRRAVL 95
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
28-70 3.21e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 34.88  E-value: 3.21e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2278571769   28 MRLLgelaRRGSARVVDLASLVGEPPNSVSFHLRQLARYGLIE 70
Cdd:smart00418   3 LKLL----AEGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41
 
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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