Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

Table 2 Summary of the number of lateral gene transfer (LGTs) in relation to their functional annotation^a

Description	Protein counts (LGT)				Fraction (%) from total
	SP^b	TMD 1-3^c	TMD ≥ 4^c	Total
Entries with annotated EC number^d				220 ^g	61.6 ^g
Part of KEGG metabolic pathways	13	8	1	165	46.2
Involved in translation (GIP)	0	0	0	6	1.7
Reactions, enzymes, but not in a pathway	5	0	2	49	13.7
Entries without annotated EC number^e				137 ^g	38.4 ^g
With some established function	1	1	8	14	3.9
Hypothetical proteins^f
Possess known functional conserved region	5	4	3	87	24.4
Possess domain of unknown function	3	3	2	31	8.7
No significant hit with known domains, suggesting a novel protein family	1	0	1	5	1.4
Total	28	16	17	357

EC, Enzyme Classification; GIP, Genetic Information Processing; KEGG, Kyoto Encyclopedia of Genes and Genomes
^aCandidate LGTs supported by at least one node (see Additional file 2; see Additional file 5).
^bSP: Entries with an SP and without TMD are counted here.
^c'TMDs ≥ 4' or 'TMDs 1-3' refers to the number of TMDs predicted on protein sequences. Transporters typically have at least four TMDs (TMDs ≥ 4). Proteins with one to three TMDs represent putative membrane proteins.
^dEC numbers were annotated for each entry based on a significant sequence similarity to either a PRIAM enzyme profile or an enzyme annotated in KEGG (see Materials and methods).
^eEntries without an EC annotation are classified into two major groups: entries with non-enzymatic functions and hypothetical proteins. These may be involved in cellular processes such as membrane transport or signal transduction.
^fHypothetical proteins were further analyzed for the presence of known conserved regions using HHsearch and InterProScan (see Additional file 2; see Additional file 3; see Additional file 4).
^g Total counts and fractions (%) for the two major listed categories

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