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Haloarchaeal rhodopsins are Type-I microbial rhodopsin that elicits various light-driven functions like proton pumping, chloride pumping and Phototaxis behaviour. The industrial application of Ion-pumping Haloarchaeal rhodopsins is limited by the lack of full-length rhodopsin sequence-based classifications, which play an important role in Ion-pumping activity. The well-studied <jats:italic>Haloarchaeal<\/jats:italic> rhodopsin is a proton-pumping bacteriorhodopsin that shows promising applications in optogenetics, biosensitized solar cells, security ink, data storage, artificial retinal implant and biohydrogen generation. As a result, a low-cost computational approach is required to identify Ion-pumping <jats:italic>Haloarchaeal<\/jats:italic> rhodopsin sequences and its subtype.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>This study uses a support vector machine (SVM) technique to identify these ion-pumping <jats:italic>Haloarchaeal<\/jats:italic> rhodopsin proteins. The haloarchaeal ion pumping rhodopsins viz., bacteriorhodopsin, halorhodopsin, xanthorhodopsin, sensoryrhodopsin and marine prokaryotic Ion-pumping rhodopsins like actinorhodopsin, proteorhodopsin have been utilized to develop the methods that accurately identified the ion pumping haloarchaeal and other type I microbial rhodopsins. We achieved overall maximum accuracy of 97.78%, 97.84% and 97.60%, respectively, for amino acid composition, dipeptide composition and hybrid approach on tenfold cross validation using SVM. Predictive models for each class of rhodopsin performed equally well on an independent data set. In addition to this, similar results were achieved using another machine learning technique namely random forest. Simultaneously predictive models performed equally well during five-fold cross validation. Apart from this study, we also tested the own, blank, BLAST dataset and annotated whole-genome rhodopsin sequences of PWS haloarchaeal isolates in the developed methods. The developed web server (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/bioinfo.imtech.res.in\/servers\/rhodopred\">https:\/\/bioinfo.imtech.res.in\/servers\/rhodopred<\/jats:ext-link>) can identify the Ion Pumping Haloarchaeal rhodopsin proteins and their subtypes. We expect this web tool would be useful for rhodopsin researchers.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The overall performance of the developed method results show that it accurately identifies the Ionpumping <jats:italic>Haloarchaeal<\/jats:italic> rhodopsin and their subtypes using known and unknown microbial rhodopsin sequences. We expect that this study would be useful for optogenetics, molecular biologists and rhodopsin researchers.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05138-x","type":"journal-article","created":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T09:04:39Z","timestamp":1674810279000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Ion-pumping microbial rhodopsin protein classification by machine learning approach"],"prefix":"10.1186","volume":"24","author":[{"given":"Muthu Krishnan","family":"Selvaraj","sequence":"first","affiliation":[]},{"given":"Anamika","family":"Thakur","sequence":"additional","affiliation":[]},{"given":"Manoj","family":"Kumar","sequence":"additional","affiliation":[]},{"given":"Anil Kumar","family":"Pinnaka","sequence":"additional","affiliation":[]},{"given":"Chander Raman","family":"Suri","sequence":"additional","affiliation":[]},{"given":"Busi","family":"Siddhardha","sequence":"additional","affiliation":[]},{"given":"Senthil Prasad","family":"Elumalai","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,1,27]]},"reference":[{"issue":"1","key":"5138_CR1","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1021\/cr4003769","volume":"114","author":"OP Ernst","year":"2014","unstructured":"Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H. 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