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Conserved domains on  [gi|727016530|ref|WP_033592480|]
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HTH domain-containing protein [Helicobacter pylori]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HARE-HTH super family cl46430
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 2-302 1.54e-80

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


The actual alignment was detected with superfamily member COG2958:

Pssm-ID: 480770  Cd Length: 301  Bit Score: 247.17  E-value: 1.54e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530   2 TYKELGKKVLEQA-EEPLSVREIWERACEMGL----DKECNGGKILLHSLVSVLGEHDISNDKKQFYVAnKKGRTFFYWL 76
Cdd:COG2958    3 TLKELILEVLEDNpKEPFTAREIAEKIVETYPyecqDKKLNSRGKTPVAEIGAQIYVDAKKNPEVKFIK-VSGRPRLYYL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530  77 KSREREFPpqETPDAKEEDDDGQSEcsdaaEKQKNSLKEKNLHKLLVKFLNEdpNFKLLCKTIRHNECKKSTAGECKWNY 156
Cdd:COG2958   82 KKNEDELE--VDAAEIEEEESKAKK-----KKEKKTYSERDLHPLLSYYLYN--ELNLYTKTIDHERSKNSGKGGNKWLH 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530 157 PDIVGVYFPYNKYfpynryEEETLKFLHHTGQKRHKLFSFELKIRINFSNLKESYFQAVSNSTWANEGYLVVFEEIEDKV 236
Cdd:COG2958  153 PDIVGVYFLDKEW------HNEVRDCVKLGKGNSIKLWSFEVKKEINRSNLRESFFQAVSNSSWANEGYLVAAEISDDDT 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727016530 237 LGELRRLNQSFGIGVIKLESE-ISNSKILLPAKERE-VDIPTLNMLTEQSPkDFKPFMEKINKQIKTG 302
Cdd:COG2958  227 LKELRRLSASFGIGVIKLDTEnPDESQILIPAKEREeIDWDTINRLVEENP-DFKKFIELVKIYYQTG 293
 
Name Accession Description Interval E-value
COG2958 COG2958
Uncharacterized conserved protein [Function unknown];
2-302 1.54e-80

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 442198  Cd Length: 301  Bit Score: 247.17  E-value: 1.54e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530   2 TYKELGKKVLEQA-EEPLSVREIWERACEMGL----DKECNGGKILLHSLVSVLGEHDISNDKKQFYVAnKKGRTFFYWL 76
Cdd:COG2958    3 TLKELILEVLEDNpKEPFTAREIAEKIVETYPyecqDKKLNSRGKTPVAEIGAQIYVDAKKNPEVKFIK-VSGRPRLYYL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530  77 KSREREFPpqETPDAKEEDDDGQSEcsdaaEKQKNSLKEKNLHKLLVKFLNEdpNFKLLCKTIRHNECKKSTAGECKWNY 156
Cdd:COG2958   82 KKNEDELE--VDAAEIEEEESKAKK-----KKEKKTYSERDLHPLLSYYLYN--ELNLYTKTIDHERSKNSGKGGNKWLH 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530 157 PDIVGVYFPYNKYfpynryEEETLKFLHHTGQKRHKLFSFELKIRINFSNLKESYFQAVSNSTWANEGYLVVFEEIEDKV 236
Cdd:COG2958  153 PDIVGVYFLDKEW------HNEVRDCVKLGKGNSIKLWSFEVKKEINRSNLRESFFQAVSNSSWANEGYLVAAEISDDDT 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727016530 237 LGELRRLNQSFGIGVIKLESE-ISNSKILLPAKERE-VDIPTLNMLTEQSPkDFKPFMEKINKQIKTG 302
Cdd:COG2958  227 LKELRRLSASFGIGVIKLDTEnPDESQILIPAKEREeIDWDTINRLVEENP-DFKKFIELVKIYYQTG 293
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 1-58 3.34e-06

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


Pssm-ID: 461541  Cd Length: 71  Bit Score: 44.22  E-value: 3.34e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 727016530    1 MTYKELGKKVLEQAEEPLSVREIWERACEMGLDKEcnGGKILLHSLVSVLGeHDISND 58
Cdd:pfam05066   1 GTLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISL--SGKTPEATLAAQLY-TDIKED 55
 
Name Accession Description Interval E-value
COG2958 COG2958
Uncharacterized conserved protein [Function unknown];
2-302 1.54e-80

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 442198  Cd Length: 301  Bit Score: 247.17  E-value: 1.54e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530   2 TYKELGKKVLEQA-EEPLSVREIWERACEMGL----DKECNGGKILLHSLVSVLGEHDISNDKKQFYVAnKKGRTFFYWL 76
Cdd:COG2958    3 TLKELILEVLEDNpKEPFTAREIAEKIVETYPyecqDKKLNSRGKTPVAEIGAQIYVDAKKNPEVKFIK-VSGRPRLYYL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530  77 KSREREFPpqETPDAKEEDDDGQSEcsdaaEKQKNSLKEKNLHKLLVKFLNEdpNFKLLCKTIRHNECKKSTAGECKWNY 156
Cdd:COG2958   82 KKNEDELE--VDAAEIEEEESKAKK-----KKEKKTYSERDLHPLLSYYLYN--ELNLYTKTIDHERSKNSGKGGNKWLH 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727016530 157 PDIVGVYFPYNKYfpynryEEETLKFLHHTGQKRHKLFSFELKIRINFSNLKESYFQAVSNSTWANEGYLVVFEEIEDKV 236
Cdd:COG2958  153 PDIVGVYFLDKEW------HNEVRDCVKLGKGNSIKLWSFEVKKEINRSNLRESFFQAVSNSSWANEGYLVAAEISDDDT 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727016530 237 LGELRRLNQSFGIGVIKLESE-ISNSKILLPAKERE-VDIPTLNMLTEQSPkDFKPFMEKINKQIKTG 302
Cdd:COG2958  227 LKELRRLSASFGIGVIKLDTEnPDESQILIPAKEREeIDWDTINRLVEENP-DFKKFIELVKIYYQTG 293
HARE-HTH pfam05066
HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in ...
 1-58 3.34e-06

HB1, ASXL, restriction endonuclease HTH domain; A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein.


Pssm-ID: 461541  Cd Length: 71  Bit Score: 44.22  E-value: 3.34e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 727016530    1 MTYKELGKKVLEQAEEPLSVREIWERACEMGLDKEcnGGKILLHSLVSVLGeHDISND 58
Cdd:pfam05066   1 GTLKEAAFQVLEEEGRPLHFKEIAEEIQEKGLISL--SGKTPEATLAAQLY-TDIKED 55
 
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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