PMC:5056897 / 7048-8408
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5056897","sourcedb":"PMC","sourceid":"5056897","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5056897","text":"Sub-cellular localization\nThe function of a protein is very well influenced by its location in the cellular space. For instance, proteins of the exoproteomic pool and secretory proteins often play an essential role in virulence related activities such as adherence to host cells. We used an array of tools to carry out the subcellular localization of the HPs. We used PSORTb [25], PSLpred [26], and Cello [27] to predict the location of HPs in the cell. These predictors use experimental data from known proteins to make predictions for query proteins using their fasta sequences. They predict the possible occurrence of protein in diverse cellular or extracellular localities such as cytoplasm, periplasm, inner membrane, outer membrane, or extracellular space. To predict signal peptides in the HPs, we used SignalP [28] prediction platform for the existence of signal peptides in the HPs, which is a characteristic feature of membrane-bound proteins. SecretomeP [29] server was used to find out nonclassical secretory proteins among the HPs. Prediction of TMHs in the proteins helps in the identification of membranous proteins. We used HMMTOP [30] and TMMHMM [31] for this purpose. Both these programs use Hidden Markov Model (HMM) profiles of training data set to predict TMHs in query sequences. The supplementary data are given in Supplementary Table 2.","divisions":[{"label":"Title","span":{"begin":0,"end":25}}],"tracks":[{"project":"2_test","denotations":[{"id":"27729842-20472543-44840760","span":{"begin":376,"end":378},"obj":"20472543"},{"id":"27729842-15699023-44840761","span":{"begin":390,"end":392},"obj":"15699023"},{"id":"27729842-15096640-44840762","span":{"begin":406,"end":408},"obj":"15096640"},{"id":"27729842-21959131-44840763","span":{"begin":819,"end":821},"obj":"21959131"},{"id":"27729842-16212653-44840764","span":{"begin":966,"end":968},"obj":"16212653"},{"id":"27729842-11590105-44840765","span":{"begin":1148,"end":1150},"obj":"11590105"},{"id":"27729842-11152613-44840766","span":{"begin":1164,"end":1166},"obj":"11152613"}],"attributes":[{"subj":"27729842-20472543-44840760","pred":"source","obj":"2_test"},{"subj":"27729842-15699023-44840761","pred":"source","obj":"2_test"},{"subj":"27729842-15096640-44840762","pred":"source","obj":"2_test"},{"subj":"27729842-21959131-44840763","pred":"source","obj":"2_test"},{"subj":"27729842-16212653-44840764","pred":"source","obj":"2_test"},{"subj":"27729842-11590105-44840765","pred":"source","obj":"2_test"},{"subj":"27729842-11152613-44840766","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93e8","default":true}]}]}}