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Conserved domains on  [gi|1101771196|gb|OIR52007|]
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transcriptional regulator [Lelliottia nimipressuralis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rep_pAB02_ORF2 super family cl45742
plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal ...
 2-115 1.45e-20

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: 81.61  E-value: 1.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1101771196   2 AKISISEAARLTGKSRTTLHRLIKTGELStchgaRNAR-LVDVSELIRVFGpleyrpfEHVSAQVLEQPGTGISQQSEQV 80
Cdd:NF038291    1 AKLSVSEASKLFNISRSTIYKAIKKGDLS-----KDSDgLIDLSEAIRVFG-------EPSKKSTDVNTSQSINSQKSTE 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1101771196  81 IAQLRQEVEHLKTLV-SAKD------SHIDSLKqamLLIEHK 115
Cdd:NF038291   69 VELLKQQVDMLKKQLeQAKEresfyqKQIDDLQ---LLLEYK 107
 
Name Accession Description Interval E-value
rep_pAB02_ORF2 NF038291
plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal ...
 2-115 1.45e-20

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: 81.61  E-value: 1.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1101771196   2 AKISISEAARLTGKSRTTLHRLIKTGELStchgaRNAR-LVDVSELIRVFGpleyrpfEHVSAQVLEQPGTGISQQSEQV 80
Cdd:NF038291    1 AKLSVSEASKLFNISRSTIYKAIKKGDLS-----KDSDgLIDLSEAIRVFG-------EPSKKSTDVNTSQSINSQKSTE 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1101771196  81 IAQLRQEVEHLKTLV-SAKD------SHIDSLKqamLLIEHK 115
Cdd:NF038291   69 VELLKQQVDMLKKQLeQAKEresfyqKQIDDLQ---LLLEYK 107
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 5-48 9.58e-05

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 37.44  E-value: 9.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1101771196   5 SISEAARLTGKSRTTLHRLIKTGELStCHGARNARLVDVSELIR 48
Cdd:pfam12728   3 TVEEAAELLGVSRRTVYRLIRSGELP-AAKIGRRWRIRKSDLEE 45
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
4-29 4.03e-04

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 36.45  E-value: 4.03e-04
                          10        20
                  ....*....|....*....|....*.
gi 1101771196   4 ISISEAARLTGKSRTTLHRLIKTGEL 29
Cdd:COG3311     9 LRLKEVAELLGVSRSTIYRLIKKGEF 34
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 5-51 2.73e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 33.71  E-value: 2.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1101771196   5 SISEAARLTGKSRTTLHRLIKTGELSTCHGARNARLVDVSELIRVFG 51
Cdd:cd04762     2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLLG 48
 
Name Accession Description Interval E-value
rep_pAB02_ORF2 NF038291
plasmid replication DNA-binding protein; This uncharacterized protein, with an N-terminal ...
 2-115 1.45e-20

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: 81.61  E-value: 1.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1101771196   2 AKISISEAARLTGKSRTTLHRLIKTGELStchgaRNAR-LVDVSELIRVFGpleyrpfEHVSAQVLEQPGTGISQQSEQV 80
Cdd:NF038291    1 AKLSVSEASKLFNISRSTIYKAIKKGDLS-----KDSDgLIDLSEAIRVFG-------EPSKKSTDVNTSQSINSQKSTE 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1101771196  81 IAQLRQEVEHLKTLV-SAKD------SHIDSLKqamLLIEHK 115
Cdd:NF038291   69 VELLKQQVDMLKKQLeQAKEresfyqKQIDDLQ---LLLEYK 107
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 5-48 9.58e-05

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 37.44  E-value: 9.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1101771196   5 SISEAARLTGKSRTTLHRLIKTGELStCHGARNARLVDVSELIR 48
Cdd:pfam12728   3 TVEEAAELLGVSRRTVYRLIRSGELP-AAKIGRRWRIRKSDLEE 45
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
4-29 4.03e-04

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 36.45  E-value: 4.03e-04
                          10        20
                  ....*....|....*....|....*.
gi 1101771196   4 ISISEAARLTGKSRTTLHRLIKTGEL 29
Cdd:COG3311     9 LRLKEVAELLGVSRSTIYRLIKKGEF 34
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 5-51 2.73e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 33.71  E-value: 2.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1101771196   5 SISEAARLTGKSRTTLHRLIKTGELSTCHGARNARLVDVSELIRVFG 51
Cdd:cd04762     2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLLG 48
 
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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