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Conserved domains on  [gi|2499866917|ref|WP_281042441|]
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replication/maintenance protein RepL [Selenomonas infelix]

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_ARSR super family cl46857
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 1-79 8.13e-25

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.


The actual alignment was detected with superfamily member pfam05732:

Pssm-ID: 481197  Cd Length: 164  Bit Score: 90.77  E-value: 8.13e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYRVNPDVLFKGGKNARMNVLLQYHDAAAEGDGSNDSAAIPEE 79
Cdd:pfam05732  76 ATTREIAEATGISLQTVITTMKALEEGNFLKKKTSGVYMLNPDLLFKGDDQKRLNLLLQFGNFEQEANEKSEPTSEKDE 154
 
Name Accession Description Interval E-value
RepL pfam05732
Firmicute plasmid replication protein (RepL); This family consists of Firmicute RepL proteins ...
 1-79 8.13e-25

Firmicute plasmid replication protein (RepL); This family consists of Firmicute RepL proteins which are involved in plasmid replication.


Pssm-ID: 428608  Cd Length: 164  Bit Score: 90.77  E-value: 8.13e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYRVNPDVLFKGGKNARMNVLLQYHDAAAEGDGSNDSAAIPEE 79
Cdd:pfam05732  76 ATTREIAEATGISLQTVITTMKALEEGNFLKKKTSGVYMLNPDLLFKGDDQKRLNLLLQFGNFEQEANEKSEPTSEKDE 154
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 1-42 1.87e-11

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


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 54.21  E-value: 1.87e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYRVNP 42
Cdd:cd00092   26 LTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRVNP 67
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
1-41 1.56e-08

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 46.28  E-value: 1.56e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLqRINQGAYRVN 41
Cdd:smart00419  9 LTRQEIAELLGLTRETVSRTLKRLEKEGLI-SREGGRIVIL 48
COG4861 COG4861
Uncharacterized conserved protein [Function unknown];
2-46 5.94e-08

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443889 [Multi-domain]  Cd Length: 333  Bit Score: 48.10  E-value: 5.94e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2499866917   2 TQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYR-VNPDVLF 46
Cdd:COG4861   152 PYREIAEAAGVSLGTVGKVLKELRELGYLRKTNKNGRRlENYEELL 197
MarR_EPS TIGR04176
EPS-associated transcriptional regulator, MarR family; Members of this family of MarR-family ...
 1-38 2.99e-03

EPS-associated transcriptional regulator, MarR family; Members of this family of MarR-family transcriptional regulators are associated with long genomic loci consisting of genes encoding enzymes for the biosynthesis of exopolysaccharides. These genes include glycosyl transferases, sugar modifying enzymes (epimerases, isomerases, methyltransferases, aminotransferases, etc.), and exopolysaccharide polymerases (wzx, wzy). In Leptospira interrogans, borgpeterenii and biflexa, this gene is observed first in unidirectional EPS biosynthesis loci as long as 90 genes. MarR genes (pfam01407) are known to bind to DNA regions with palindromic or pseudopalindromic sequences as homodimers, and to bind small molecules as triggers for conformational changes controlling on/off states.


Pssm-ID: 275030  Cd Length: 105  Bit Score: 33.77  E-value: 2.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALID------SNFLQRINQGAY 38
Cdd:TIGR04176  19 LSQRELAKELGISLGKVNYCLKALIDkglikaGNFRNSDNKLAY 62
 
Name Accession Description Interval E-value
RepL pfam05732
Firmicute plasmid replication protein (RepL); This family consists of Firmicute RepL proteins ...
 1-79 8.13e-25

Firmicute plasmid replication protein (RepL); This family consists of Firmicute RepL proteins which are involved in plasmid replication.


Pssm-ID: 428608  Cd Length: 164  Bit Score: 90.77  E-value: 8.13e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYRVNPDVLFKGGKNARMNVLLQYHDAAAEGDGSNDSAAIPEE 79
Cdd:pfam05732  76 ATTREIAEATGISLQTVITTMKALEEGNFLKKKTSGVYMLNPDLLFKGDDQKRLNLLLQFGNFEQEANEKSEPTSEKDE 154
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 1-42 1.87e-11

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


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 54.21  E-value: 1.87e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYRVNP 42
Cdd:cd00092   26 LTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRVNP 67
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
1-41 1.56e-08

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 46.28  E-value: 1.56e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLqRINQGAYRVN 41
Cdd:smart00419  9 LTRQEIAELLGLTRETVSRTLKRLEKEGLI-SREGGRIVIL 48
COG4861 COG4861
Uncharacterized conserved protein [Function unknown];
2-46 5.94e-08

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443889 [Multi-domain]  Cd Length: 333  Bit Score: 48.10  E-value: 5.94e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2499866917   2 TQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGAYR-VNPDVLF 46
Cdd:COG4861   152 PYREIAEAAGVSLGTVGKVLKELRELGYLRKTNKNGRRlENYEELL 197
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 1-36 3.62e-05

Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain [General function prediction only];


Pssm-ID: 442002 [Multi-domain]  Cd Length: 80  Bit Score: 38.36  E-value: 3.62e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQG 36
Cdd:COG2512   31 MTQSEIVKETGWSKSKVSRLLSRLEERGLIEKERVG 66
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 1-32 5.50e-05

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 37.44  E-value: 5.50e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQR 32
Cdd:pfam13545 23 LTQEDLADLLGTTRETVSRVLSELRREGLIER 54
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 1-32 6.33e-05

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: 37.18  E-value: 6.33e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQR 32
Cdd:pfam12802 20 LTVAELARRLGISKQTVSRLVKRLEAKGLVER 51
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-48 1.77e-04

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.51  E-value: 1.77e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2499866917  1 MTQRQIADKSGISYQTVSR--TLQALIDSNFLQRINQgAYRVNPDVLFKG 48
Cdd:COG1396   21 LTQEELAERLGVSRSTISRieRGRRNPSLETLLKLAK-ALGVSLDELLGG 69
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 1-45 4.17e-04

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 36.89  E-value: 4.17e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLqRINQGAYRV-NPDVL 45
Cdd:COG0664   159 LTQEEIASYLGLTRETVSRILKKLEKEGLI-ELERGRITIlDREAL 203
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
1-32 6.34e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.10  E-value: 6.34e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQR 32
Cdd:COG1846    53 LTQSELAERLGLTKSTVSRLLDRLEEKGLVER 84
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
1-30 1.17e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 33.56  E-value: 1.17e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFL 30
Cdd:pfam13412 16 ISQRELAERLGLSPSTVNRRLKRLEEEGVI 45
HTH_ICLR smart00346
helix_turn_helix isocitrate lyase regulation;
1-45 1.28e-03

helix_turn_helix isocitrate lyase regulation;


Pssm-ID: 214629 [Multi-domain]  Cd Length: 91  Bit Score: 34.48  E-value: 1.28e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQ-GAYRVNPDVL 45
Cdd:smart00346 21 LTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQnGRYRLGPKVL 66
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
1-33 1.75e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 34.49  E-value: 1.75e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2499866917    1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRI 33
Cdd:smart00347  25 LSVSELAKRLGVSPSTVTRVLDRLEKKGLVRRE 57
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 1-32 1.75e-03

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: 33.29  E-value: 1.75e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQR 32
Cdd:pfam01047 18 LTVSELAEKLGVSKSTVTRVLDRLEKKGLIER 49
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 2-32 2.29e-03

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 34.89  E-value: 2.29e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2499866917   2 TQRQIADKSGISYQTVSRTLQALIDSNFLQR 32
Cdd:COG1974    27 SQREIAEALGLSSSAVHRHLKALEKKGYLRR 57
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
1-45 2.94e-03

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 34.47  E-value: 2.94e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQG---AYRVNPDVL 45
Cdd:COG3398   112 ATNKELAEELGISRSTVSWHLKRLEEDGLVERERDGrnvRYYLNPPER 159
MarR_EPS TIGR04176
EPS-associated transcriptional regulator, MarR family; Members of this family of MarR-family ...
 1-38 2.99e-03

EPS-associated transcriptional regulator, MarR family; Members of this family of MarR-family transcriptional regulators are associated with long genomic loci consisting of genes encoding enzymes for the biosynthesis of exopolysaccharides. These genes include glycosyl transferases, sugar modifying enzymes (epimerases, isomerases, methyltransferases, aminotransferases, etc.), and exopolysaccharide polymerases (wzx, wzy). In Leptospira interrogans, borgpeterenii and biflexa, this gene is observed first in unidirectional EPS biosynthesis loci as long as 90 genes. MarR genes (pfam01407) are known to bind to DNA regions with palindromic or pseudopalindromic sequences as homodimers, and to bind small molecules as triggers for conformational changes controlling on/off states.


Pssm-ID: 275030  Cd Length: 105  Bit Score: 33.77  E-value: 2.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALID------SNFLQRINQGAY 38
Cdd:TIGR04176  19 LSQRELAKELGISLGKVNYCLKALIDkglikaGNFRNSDNKLAY 62
IclR COG1414
DNA-binding transcriptional regulator, IclR family [Transcription];
1-45 4.19e-03

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


Pssm-ID: 441024 [Multi-domain]  Cd Length: 253  Bit Score: 34.41  E-value: 4.19e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQR-INQGAYRVNPDVL 45
Cdd:COG1414    25 LSLSELARRLGLPKSTVHRLLATLEEEGYVERdPEGGRYRLGPRLL 70
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
1-31 5.12e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 33.95  E-value: 5.12e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2499866917   1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQ 31
Cdd:COG2390    11 LTQREIAERLGISRRTVSRLLAEAREEGLVR 41
ArsR COG0640
DNA-binding transcriptional regulator, ArsR family [Transcription];
1-45 5.16e-03

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


Pssm-ID: 440405 [Multi-domain]  Cd Length: 92  Bit Score: 32.94  E-value: 5.16e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGA---YRVNPDVL 45
Cdd:COG0640   34 LCVGELAEALGLSQSTVSHHLKVLREAGLVTSRREGRwvyYRLADEAL 81
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 1-43 7.26e-03

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: 32.27  E-value: 7.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2499866917  1 MTQRQIADKSGISYQTVSRTLQALIDSNFLQRINQGA---YRVNPD 43
Cdd:cd00090   21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRrvyYSLTDA 66
 
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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