Interaction networks for identifying coupled molecular processes in microbial communities

Table 1 Gene annotation and interaction details

Annotation item	source	gene coverage, At. thiooxidans	gene coverage, At. ferrooxidans
A: gene annotation
Gene/protein identifiers
PATRIC database ID	PATRIC	100.00	100.00
RefSeq gene ID	PATRIC	100.00	100.00
Uniprot gene name	PATRIC	88.62	91.43
IMG database ID	IMG	88.62	54.18
RefSeq protein ID	PATRIC	0.00	91.43
Uniprot ID	UniProt	0.97	83.88
Protein name & function
Protein name	PATRIC	100.00	100.00
Protein function	HAMAP	26.17	29.84
Enzyme Commission nomenclature	PATRIC	17.55	19.74
IMG TERM	IMG	19.90	25.90
COG category	IMG	69.25	70.40
COG entry	IMG	69.25	70.40
Protein domains/families
Prosite domain	Prosite	30.92	33.50
FIGfam protein family ID	PATRIC	66.29	99.02
Pfam protein family	IMG	72.79	77.61
Protein similarity (HAMAP)	HAMAP	28.41	33.04
Protein function & location
Interpro database entry	InterPro	4.48	33.11
GO function	HAMAP	3.71	29.07
GO process	HAMAP	25.68	29.49
GO cellular component	HAMAP	17.65	20.26
PSORT subcellular location	PSORT	100.00	100.00
Pathway assignment
KEGG pathway	PATRIC	17.56	19.74
KEGG orthology	IMG	44.90	51.36
KEGG module	IMG	17.13	20.44
Metacyc pathway	IMG	17.04	19.50
IMG pathway	IMG	7.87	9.96
B: interaction information
pathway relations	KEGG	13.00*	16.47
pathway relations	Metacyc	11.05*	12.99
inferred interactions	STRING	51.07*	91.16

Annotation on gene (A) and interaction level (B) for At. ferrooxidans and At. thiooxidans. Data sources are grouped in content categories. Annotation coverage refers to the percentage of protein coding genes holding a valid entry in the respective data sections for gene annotation, and at least one interaction to another gene as derived from interaction sources. *For At. thiooxidans interactions were assigned based on ortholog assignment

ISSN: 1756-0381