Difference between revisions of "Part:BBa K5246021"
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Protein BLAST also showed partial similarities with E.Coli O-antigen ligases suggested by the CDD analysis. | 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 | + | 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. |
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] | 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] | ||
Revision as of 11:33, 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
- 10INCOMPATIBLE WITH RFC[10]Illegal XbaI site found at 48
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 1282
- 21COMPATIBLE WITH RFC[21]
- 23INCOMPATIBLE WITH RFC[23]Illegal XbaI site found at 48
- 25INCOMPATIBLE WITH RFC[25]Illegal XbaI site found at 48
Illegal AgeI site found at 847 - 1000COMPATIBLE 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.
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.