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Conserved domains on  [gi|2024563503|gb|QTQ92283|]
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DUF536 domain-containing protein (plasmid) [Enterococcus faecium]

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 ...
 4-42 4.73e-04

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 pfam08279:

Pssm-ID: 481199 [Multi-domain]  Cd Length: 52  Bit Score: 36.64  E-value: 4.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2024563503   4 QETFTIKELSELFKMSRQAISKHIQKLDSSMI---AKNERGY 42
Cdd:pfam08279  11 RGPISGQELAEKLGVSRRTIRRDIKILEELGVpieAEPGRGY 52
rep_pAB02_ORF2 super family cl45742
plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal ...
 7-170 7.87e-03

plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal DNA-binding helix-turn-helix domain, occurs in replication regions of a large number of Acinetobacter plasmids. The founding members of this family, AAR00518.1 and WP_000839337.1 from plasmids pAB02 and pMAC, are referred to as ORF2 there, sitting adjacent to RepM, which in turn is adjacent to the DNA repeat region at each plasmid's origin of replication.


The actual alignment was detected with superfamily member NF038291:

Pssm-ID: 468456  Cd Length: 172  Bit Score: 35.38  E-value: 7.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024563503   7 FTIKELSELFKMSRQAISKHIQKLDssmIAKNERGykvvlRSGVLQLARNLGNQMlldrlhEYEQDNDKNVNIPSKNVVT 86
Cdd:NF038291    3 LSVSEASKLFNISRSTIYKAIKKGD---LSKDSDG-----LIDLSEAIRVFGEPS------KKSTDVNTSQSINSQKSTE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024563503  87 nklLDQLREENEFLREQLALREQNNSHIqklldqqqqltlqaNKQIEKLQekLQLTYteEAPENDSTTLSEATETIDKQI 166
Cdd:NF038291   69 ---VELLKQQVDMLKKQLEQAKERESFY--------------QKQIDDLQ--LLLEY--KAPKPNMTTFTDQPEANDTAT 127


                  ....
gi 2024563503 167 DTEK 170
Cdd:NF038291  128 DPQP 131
 
Name Accession Description Interval E-value
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 4-42 4.73e-04

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 36.64  E-value: 4.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2024563503   4 QETFTIKELSELFKMSRQAISKHIQKLDSSMI---AKNERGY 42
Cdd:pfam08279  11 RGPISGQELAEKLGVSRRTIRRDIKILEELGVpieAEPGRGY 52
BirA COG1654
Biotin operon repressor [Transcription];
11-44 4.59e-03

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 36.50  E-value: 4.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2024563503  11 ELSELFKMSRQAISKHIQKLDssmiaknERGYKV 44
Cdd:COG1654    23 ELAEELGVSRAAVWKHIKALR-------ELGYEI 49
rep_pAB02_ORF2 NF038291
plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal ...
 7-170 7.87e-03

plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal DNA-binding helix-turn-helix domain, occurs in replication regions of a large number of Acinetobacter plasmids. The founding members of this family, AAR00518.1 and WP_000839337.1 from plasmids pAB02 and pMAC, are referred to as ORF2 there, sitting adjacent to RepM, which in turn is adjacent to the DNA repeat region at each plasmid's origin of replication.


Pssm-ID: 468456  Cd Length: 172  Bit Score: 35.38  E-value: 7.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024563503   7 FTIKELSELFKMSRQAISKHIQKLDssmIAKNERGykvvlRSGVLQLARNLGNQMlldrlhEYEQDNDKNVNIPSKNVVT 86
Cdd:NF038291    3 LSVSEASKLFNISRSTIYKAIKKGD---LSKDSDG-----LIDLSEAIRVFGEPS------KKSTDVNTSQSINSQKSTE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024563503  87 nklLDQLREENEFLREQLALREQNNSHIqklldqqqqltlqaNKQIEKLQekLQLTYteEAPENDSTTLSEATETIDKQI 166
Cdd:NF038291   69 ---VELLKQQVDMLKKQLEQAKERESFY--------------QKQIDDLQ--LLLEY--KAPKPNMTTFTDQPEANDTAT 127


                  ....
gi 2024563503 167 DTEK 170
Cdd:NF038291  128 DPQP 131
 
Name Accession Description Interval E-value
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 4-42 4.73e-04

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 36.64  E-value: 4.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2024563503   4 QETFTIKELSELFKMSRQAISKHIQKLDSSMI---AKNERGY 42
Cdd:pfam08279  11 RGPISGQELAEKLGVSRRTIRRDIKILEELGVpieAEPGRGY 52
BirA COG1654
Biotin operon repressor [Transcription];
11-44 4.59e-03

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 36.50  E-value: 4.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2024563503  11 ELSELFKMSRQAISKHIQKLDssmiaknERGYKV 44
Cdd:COG1654    23 ELAEELGVSRAAVWKHIKALR-------ELGYEI 49
rep_pAB02_ORF2 NF038291
plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal ...
 7-170 7.87e-03

plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal DNA-binding helix-turn-helix domain, occurs in replication regions of a large number of Acinetobacter plasmids. The founding members of this family, AAR00518.1 and WP_000839337.1 from plasmids pAB02 and pMAC, are referred to as ORF2 there, sitting adjacent to RepM, which in turn is adjacent to the DNA repeat region at each plasmid's origin of replication.


Pssm-ID: 468456  Cd Length: 172  Bit Score: 35.38  E-value: 7.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024563503   7 FTIKELSELFKMSRQAISKHIQKLDssmIAKNERGykvvlRSGVLQLARNLGNQMlldrlhEYEQDNDKNVNIPSKNVVT 86
Cdd:NF038291    3 LSVSEASKLFNISRSTIYKAIKKGD---LSKDSDG-----LIDLSEAIRVFGEPS------KKSTDVNTSQSINSQKSTE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024563503  87 nklLDQLREENEFLREQLALREQNNSHIqklldqqqqltlqaNKQIEKLQekLQLTYteEAPENDSTTLSEATETIDKQI 166
Cdd:NF038291   69 ---VELLKQQVDMLKKQLEQAKERESFY--------------QKQIDDLQ--LLLEY--KAPKPNMTTFTDQPEANDTAT 127


                  ....
gi 2024563503 167 DTEK 170
Cdd:NF038291  128 DPQP 131
 
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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