Ion-pumping microbial rhodopsin protein classification by machine learning approach

Selvaraj, Muthu Krishnan; Thakur, Anamika; Kumar, Manoj; Pinnaka, Anil Kumar; Suri, Chander Raman; Siddhardha, Busi; Elumalai, Senthil Prasad

doi:10.1186/s12859-023-05138-x

BMC Bioinformatics

Table 1 Performance of SVM based predictive models for different classes of rhodopsin during tenfold cross validation

From: Ion-pumping microbial rhodopsin protein classification by machine learning approach

Class	Datasets	Type	ACC	MCC	AUC	GC
Overall (902p + 902n)	T^812p+812n	AAC	97.78	0.96	1.00	g:0.001 c:0.1
	V^90p+90n	AAC	98.89	0.98	1.00	g:0.001 c:0.1
	T^812p+812n	DPC	97.84	0.96	1.00	g:0.005 c:0.1
	V^90p+90n	DPC	99.44	0.99	1.00	g:0.005 c:0.1
	T^812p+812n	HYB	97.6	0.95	1.00	g:0.005 c:0.01
	V^90p+90n	HYB	98.89	0.98	1.00	g:0.005 c:0.01
Actinorhodopsin (139p + 763n)	T^125p+687n	AAC	99.88	1	1.00	g:0.01 c:10
	V^14p+76n	AAC	98.89	0.96	1.00	g:0.01 c:10
	T^125p+687n	DPC	99.88	1	1.00	g:0.01 c:10
	V^14p+76n	DPC	98.89	0.96	1.00	g:0.01 c:10
	T^125p+687n	Hybrid	99.63	0.99	1.00	g:0.01 c:10
	V^14p+76n	Hybrid	100	1	1.00	g:0.01 c:10
Bacteriorhodopsin (366p + 536n)	T^330p+482n	AAC	98.15	0.96	1.00	g:0.01 c:50
	V^36p+54n	AAC	98.89	0.98	1.00	g:0.01 c:50
	T^330p+482n	DPC	99.75	0.99	1.00	g:0.01 c:50
	V^36p+54n	DPC	98.89	0.98	1.00	g:0.01 c:50
	T^330p+482n	Hybrid	99.75	0.99	1.00	g:0.01 c:50
	V^36p+54n	Hybrid	98.89	0.98	1.00	g:0.01 c:50
Halorhodopsin (23p + 879n)	T^21p+791n	AAC	99.75	0.95	0.97	g:0.01 c:10
	V^2p+88n	AAC	100	1.00	1.00	g:0.01 c:10
	T^21p+791n	DPC	99.75	0.95	1.00	g:0.01 c:10
	V^2p+88n	DPC	100	1.00	1.00	g:0.01 c:10
	T^21p+791n	Hybrid	99.75	0.95	1.00	g:0.01 c:5
	V^2p+88n	Hybrid	100	1.00	1.00	g:0.01 c:5
Proteorhodopsin (191p + 711n)	T^171p+640n	AAC	98.27	0.95	1.00	g:0.0001 c:50
	V^20p+71n	AAC	98.9	0.97		g:0.0001 c:50
	T^171p+640n	DPC	98.27	0.95	1.00	g:0.001 c:1
	V^20p+71n	DPC	100	1.00	1.00	g:0.001 c:1
	T^171p+640n	Hybrid	98.77	0.96	1.00	g:0.001 c:1
	V^20p+71n	Hybrid	98.9	0.97	1.00	g:0.001 c:1
Sensoryrhodopsin (16p + 886n)	T^14p+798n	AAC	99.38	0.8	0.90	g:0.01 c:5
	V^2p+88n	AAC	98.89	0.7	0.88	g:0.01 c:5
	T^14p+798n	DPC	99.38	0.81	0.97	g:0.001 c:10
	V^2p+88n	DPC	98.89	0.7	0.99	g:0.001 c:10
	T^14p+798n	Hybrid	99.51	0.85	0.93	g:0.01 c:1
	V^2p+88n	Hybrid	98.89	0.7	0.99	g:0.01 c:1
Xanthorhodopsin (167p + 735n)	T^151p+662n	AAC	98.65	0.96	1.00	g:0.05 c:1
	V^16p+73n	AAC	98.88	0.96	1.00	g:0.05 c:1
	T^151p+662n	DPC	99.02	0.97	1.00	g:0.01 c:1
	V^16p+73n	DPC	97.75	0.92	1.00	g:0.01 c:1
	T^151p+662n	Hybrid	99.02	0.97	1.00	g:0.01 c:1
	V^16p+73n	Hybrid	97.75	0.92	1.00	g:0.01 c:1

ACC, accuracy; MCC, Matthew’s correlation coefficient; AUC, area under curve; AAC, amino acid composition; DPC, dipeptide composition; Hybrid, AAC + DPC

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