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Conserved domains on  [gi|1009369165|ref|WP_061892277|]
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MULTISPECIES: YdaS family helix-turn-helix protein [Escherichia]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 366238)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family; HTH domain binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cro super family cl46781
Cro; Members of this family are involved in the repression of transcription by binding as a ...
 14-64 2.90e-11

Cro; Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.


The actual alignment was detected with superfamily member COG4197:

Pssm-ID: 481121  Cd Length: 68  Bit Score: 53.76  E-value: 2.90e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1009369165 14 QLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVTNFEVTPHELRPDIY 64
Cdd:COG4197   11 QSALARALGVSQQAVSQWLNGKRRVPAERCLAIERATGGAVTREELRPDLD 61
 
Name Accession Description Interval E-value
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
14-64 2.90e-11

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 53.76  E-value: 2.90e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1009369165 14 QLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVTNFEVTPHELRPDIY 64
Cdd:COG4197   11 QSALARALGVSQQAVSQWLNGKRRVPAERCLAIERATGGAVTREELRPDLD 61
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 13-64 1.09e-10

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 51.96  E-value: 1.09e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1009369165 13 TQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVTNFEVTPHELRPDIY 64
Cdd:pfam15943 10 GQKALAEALGVTQQAVSQWLHGKKGIPAEYCPAIERATSGKVTREELRPDVD 61
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 2-59 6.13e-09

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 47.55  E-value: 6.13e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1009369165  2 NLRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKA--LGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
2-59 3.20e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.59  E-value: 3.20e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1009369165   2 NLRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKA--LGVSLDEL 56
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 3-56 4.90e-04

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 35.29  E-value: 4.90e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1009369165  3 LRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTP 56
Cdd:TIGR02607 10 LEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKA--LGTSP 61
 
Name Accession Description Interval E-value
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
14-64 2.90e-11

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 53.76  E-value: 2.90e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1009369165 14 QLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVTNFEVTPHELRPDIY 64
Cdd:COG4197   11 QSALARALGVSQQAVSQWLNGKRRVPAERCLAIERATGGAVTREELRPDLD 61
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 13-64 1.09e-10

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 51.96  E-value: 1.09e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1009369165 13 TQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVTNFEVTPHELRPDIY 64
Cdd:pfam15943 10 GQKALAEALGVTQQAVSQWLHGKKGIPAEYCPAIERATSGKVTREELRPDVD 61
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 2-59 6.13e-09

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 47.55  E-value: 6.13e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1009369165  2 NLRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKA--LGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
2-59 3.20e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.59  E-value: 3.20e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1009369165   2 NLRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKA--LGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-59 9.73e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.99  E-value: 9.73e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1009369165  2 NLRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:COG1396   11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKA--LGVSLDEL 66
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 3-57 1.56e-07

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 44.41  E-value: 1.56e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1009369165  3 LRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPH 57
Cdd:COG3093   14 REEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARA--FGTSAE 66
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
2-59 1.60e-07

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 44.07  E-value: 1.60e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1009369165  2 NLRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARA--LGVSLEEL 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 3-59 1.20e-06

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 41.37  E-value: 1.20e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1009369165  3 LRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTPHEL 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEA--LGVSLDEL 55
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 3-56 4.90e-04

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 35.29  E-value: 4.90e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1009369165  3 LRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVtnFEVTP 56
Cdd:TIGR02607 10 LEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKA--LGTSP 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-54 1.26e-03

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 34.61  E-value: 1.26e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1009369165  3 LRDYLKEKHITQLQFGKLTGLSQVHVSRVLGGYERFSPEKALRVAEVTNFEV 54
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKEL 73
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 10-32 2.41e-03

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 34.89  E-value: 2.41e-03
                          10        20
                  ....*....|....*....|...
gi 1009369165  10 KHITQLQFGKLTGLSQVHVSRVL 32
Cdd:TIGR02980 193 EDKTQSEIAERLGISQMHVSRLL 215
 
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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