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Table 1 Gene annotation and interaction details

From: Interaction networks for identifying coupled molecular processes in microbial communities

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
  1. 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