Difference between revisions of "Part:BBa K5246021"
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===Usage and Biology===
 
===Usage and Biology===
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Gene from Hirschia baltica that codes a paralogous protein of 435 amino acids of HfsC pollysaccharide polymerase.
+
Gene from Hirschia baltica codes a paralogous protein of 435 amino acids of HfsC polysaccharide polymerase.
  
 
===Sequence and Features===
 
===Sequence and Features===
 
<partinfo>BBa_K5246021 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5246021 SequenceAndFeatures</partinfo>
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−
===Functional Parameters===
 
−
<partinfo>BBa_K5246021 parameters</partinfo>
 
  
 
===Experimental characterization===
 
===Experimental characterization===
 +
 +
====Bioinformatic analysis====
 +
 +
CDD analysis showed that HfsI, analogous to HfsC, has a domain similar to that of O-antigen ligase family proteins. Proteins of this family are responsible for outer membrane lipopolysaccharide synthesis in E. Coli.
 +
 +
Protein BLAST also showed partial similarities with E.Coli O-antigen ligases suggested by the CDD analysis.
 +
 +
DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold3, which shows 12 helices. A pTM score above 0.5 suggests that the predicted overall structure may closely resemble the true protein fold, while ipTM indicates the accuracy of the subunit positioning within the complex. Values higher than 0.8 represent confident, high-quality predictions (Fig.1).
 +
 +
Considering our findings with information present in the literature. We predict that HfsI is a paralogous gene to HfsC with the same functionality in the organism. [1][2][3]
 +
 +
===References===
 +
1. Toh, E., Kurtz, Harry D. and Brun, Y.V. (2008) ‘Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps’, Journal of Bacteriology, 190(21), pp. 7219–7231. doi:10.1128/jb.01003-08.
 +
<br>
 +
2. Chepkwony, N.K., Hardy, G.G. and Brun, Y.V. (2022) ‘HFAE is a component of the holdfast anchor complex that tethers the holdfast adhesin to the cell envelope’, Journal of Bacteriology, 204(11). doi:10.1128/jb.00273-22.
 +
<br>
 +
3. Chepkwony, N.K., Berne, C. and Brun, Y.V. (2019b) ‘Comparative analysis of ionic strength tolerance between freshwater and marine Caulobacterales adhesins’, Journal of Bacteriology, 201(18). doi:10.1128/jb.00061-19.

Revision as of 11:32, 28 September 2024


HB HfsI Polysaccharide polymerase

Introduction

Strain description

Usage and Biology

Gene from Hirschia baltica codes a paralogous protein of 435 amino acids of HfsC polysaccharide polymerase.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal XbaI site found at 48
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1282
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal XbaI site found at 48
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal XbaI site found at 48
    Illegal AgeI site found at 847
  • 1000
    COMPATIBLE WITH RFC[1000]

Experimental characterization

Bioinformatic analysis

CDD analysis showed that HfsI, analogous to HfsC, has a domain similar to that of O-antigen ligase family proteins. Proteins of this family are responsible for outer membrane lipopolysaccharide synthesis in E. Coli.

Protein BLAST also showed partial similarities with E.Coli O-antigen ligases suggested by the CDD analysis.

DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold3, which shows 12 helices. A pTM score above 0.5 suggests that the predicted overall structure may closely resemble the true protein fold, while ipTM indicates the accuracy of the subunit positioning within the complex. Values higher than 0.8 represent confident, high-quality predictions (Fig.1).

Considering our findings with information present in the literature. We predict that HfsI is a paralogous gene to HfsC with the same functionality in the organism. [1][2][3]

References

1. Toh, E., Kurtz, Harry D. and Brun, Y.V. (2008) ‘Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps’, Journal of Bacteriology, 190(21), pp. 7219–7231. doi:10.1128/jb.01003-08.
2. Chepkwony, N.K., Hardy, G.G. and Brun, Y.V. (2022) ‘HFAE is a component of the holdfast anchor complex that tethers the holdfast adhesin to the cell envelope’, Journal of Bacteriology, 204(11). doi:10.1128/jb.00273-22.
3. Chepkwony, N.K., Berne, C. and Brun, Y.V. (2019b) ‘Comparative analysis of ionic strength tolerance between freshwater and marine Caulobacterales adhesins’, Journal of Bacteriology, 201(18). doi:10.1128/jb.00061-19.