Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia

Table 5 Protein structure analysis

Gene ID^a	Template ID^b	Function	GMQE^c	Coverage^d	Identity^e
P1	6fu5.1.B	Receptor-interacting Serine/threonine-protein kinase 2	0.34	55%	30.50%
	3sd0.1.A	Glycogen synthase kinase-3 beta	0.35	58%	19.26%
	4xlv.1.A	Insulin receptor	0.32	51%	23.19%
P2		No templates were found matching the sequence
P3	3of6.1.A	T cell receptor beta chain	0.38	70%	19.31%
	5fhx.1.C	Antibody fragment light chain	0.38	72%	14.35%
	6bpc.1.B	Monoclonal antibody 4F7 Fab heavy chain	0.34	69%	15.50%
P4		No templates were found matching the sequence
P5		No templates were found matching the sequence
P6		No templates were found matching the sequence
P7		No templates were found matching the sequence
P8	6e56.1.B	Antibody pn132p2C05	0.49	90%	21.93%
P8	5n4g.1.A	Heavy Chain	0.49	93%	23.08%
P9		No templates were found matching the sequence
P10	1j8i.1.A	Lymphotactin	0.42	60%	30.26%
	1ncv.1.B	Monocyte chemoattractant protein 3	0.41	59%	32.43%
	5eki.5.A	C-C motif chemokine 21	0.40	55%	27.54%
P11	3top.1.A	Maltase-glucoamylase, intestinal	0.45	49%	59.66%
	3lpo.1.A	Sucrase-isomaltase	0.44	48%	57.04%
	5nn3.1.A	Lysosomal alpha-glucosidase	0.38	46%	41.65%
P12		No templates were found matching the sequence

Protein structure analysis using SWISS-MODEL [57]
^aGene ID: P1 to P12 correspond to the symbol used for each predicted protein subjected to bioinformatics analysis
^bTemplate ID: 3D structure found that modeled the zebrafish protein of interest
^cGMQE: Global Model Quality Estimation [58], which is the quality estimation of the model taking account properties from the target–template alignment and the template search method. GMQE is a number between 0 and 1. Higher numbers indicate higher reliability. A cut-off of GMQE> 0.3 was applied
^dCoverage: The percentage of the query’s sequence (P1 to P12) that overlaps the Template sequence
^eIdentity is the percentage of characters (amino acid) within the covered part of the query that are identical. Template ID correspond to the name of the template (Ortholog) in the Protein Data Bank (https://www.rcsb.org/ [59];)

ISSN: 1471-2164