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Conserved domains on  [gi|16128427|ref|NP_414976|]
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helix-hairpin-helix 3 family protein [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

helix-hairpin-helix domain-containing protein( domain architecture ID 10015649)

helix-hairpin-helix (HhH) domain-containing protein binds DNA in the major groove; similar to Haemophilus influenzae protein HI_1008

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 55-123 2.73e-33

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


:

Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 110.79  E-value: 2.73e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128427    55 SDEEGTRVSINNASAEELARAMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERNLAVLTL 123
Cdd:TIGR00426   1 SDEEGTRVNINTATAEELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVITL 69
 
Name Accession Description Interval E-value
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 55-123 2.73e-33

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 110.79  E-value: 2.73e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128427    55 SDEEGTRVSINNASAEELARAMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERNLAVLTL 123
Cdd:TIGR00426   1 SDEEGTRVNINTATAEELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVITL 69
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 51-122 4.80e-25

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 89.92  E-value: 4.80e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16128427  51 PAKASDEEGTRVSINNASAEELArAMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERNLAVLT 122
Cdd:COG1555   2 PASASAAAGGKVDINTATAEELQ-TLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEKLKPYLT 72
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 59-117 4.81e-18

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 71.74  E-value: 4.81e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 16128427    59 GTRVSINNASAEELARaMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERN 117
Cdd:pfam12836   1 AVGVDINTASAELLSR-VPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQL 58
polC PRK00448
DNA polymerase III PolC; Validated
 74-121 6.10e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.98  E-value: 6.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 16128427    74 RAMNGVGLKKAQAIVSYREEyGPFKTVEDLKQVPGMGNSLVE--RNLAVL 121
Cdd:PRK00448 1376 NALPGLGENVAKSIVEAREE-GEFLSKEDLRKRTKVSKTLIEklDELGVL 1424
 
Name Accession Description Interval E-value
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 55-123 2.73e-33

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 110.79  E-value: 2.73e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128427    55 SDEEGTRVSINNASAEELARAMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERNLAVLTL 123
Cdd:TIGR00426   1 SDEEGTRVNINTATAEELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVITL 69
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 51-122 4.80e-25

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 89.92  E-value: 4.80e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16128427  51 PAKASDEEGTRVSINNASAEELArAMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERNLAVLT 122
Cdd:COG1555   2 PASASAAAGGKVDINTATAEELQ-TLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEKLKPYLT 72
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 59-117 4.81e-18

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 71.74  E-value: 4.81e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 16128427    59 GTRVSINNASAEELARaMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMGNSLVERN 117
Cdd:pfam12836   1 AVGVDINTASAELLSR-VPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQL 58
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
62-110 3.10e-09

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 53.11  E-value: 3.10e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 16128427  62 VSINNASAEELARaMNGVGLKKAQAIVSYREEYGPFKTVEDLKQVPGMG 110
Cdd:COG2183 487 VDLNTASAPLLSY-VSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLG 534
polC PRK00448
DNA polymerase III PolC; Validated
 74-121 6.10e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 40.98  E-value: 6.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 16128427    74 RAMNGVGLKKAQAIVSYREEyGPFKTVEDLKQVPGMGNSLVE--RNLAVL 121
Cdd:PRK00448 1376 NALPGLGENVAKSIVEAREE-GEFLSKEDLRKRTKVSKTLIEklDELGVL 1424
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
74-103 2.31e-03

DNA polymerase III, alpha subunit [Replication, recombination and repair];


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 36.20  E-value: 2.31e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 16128427   74 RAMNGVGLKKAQAIVSYREEYGPFKTVEDL 103
Cdd:COG0587  818 GAIKGVGEAAAEAIVAAREENGPFTSLFDF 847
RmsH COG0275
16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 64-106 8.73e-03

16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]; 16S rRNA C1402 N4-methylase RsmH is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440044  Cd Length: 312  Bit Score: 34.65  E-value: 8.73e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 16128427  64 INNASAEELARAmngvgLKK----------AQAIVSYREEyGPFKTVEDLKQV 106
Cdd:COG0275 142 LNTYSEEELARI-----LREygeerfarriARAIVEARKE-KPITTTGELAEI 188
 
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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