Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis

Table 3 Putative new P. falciparum gene family members of variant gene families

Gene family	New member	MP#	MP %	Avg. E-value	Avg. PID (Stddev)	Current annotation/comment
phist	PF14_0744	21	9.9	0.2	27.6(5.6)	Exported protein, unknown function
	PF14_0745	23	10.9	0.3	24.7(4.7)	Probable protein, unknown function
	MAL8P1.205	40	18.9	0.0002	28.2(4.4)	GEXP13
	PF10_0015^a	88	41.5	7e-14	35.0(11.9)	Carries acyl-CoA binding domain
hyp4/hyp6	PFL2560c	2	12.5	3e-15	46.3(14.4)	Probably truncated pseudogene
	PFI0086w	5	31.3	0.002	29.0(3.7)	Alternative start codon 40 aa downstream
	PF14_0760	4	25.0	0.2	35.7(13.2)	Exported protein, unknown function
TSP_1	MAL8P1.45	48	23.3	7e-17	42.7(14.7)	Conserved protein, unknown function
	PF08_0136b	24	11.7	4e-34	35.3(16.3)	Von Willebrand factor A-domain related
msp-7	PF13_0192	14	46.7	0.9	25.7(4.8)	Part of MSP7 gene cluster on chr13
	PF13_0194	3	10	3	28.8(3.3)	Part of MSP7 gene cluster on chr13
msp-3	PF10_0351	4	14.3	4	30.4(3.8)	Part of MSP gene cluster on chr10
etramp	PFL0065w	2	2.8	9e-15	43.7(6.5)	Conserved protein, unknown function
hyp5	PF14_0743	10	100.0	3e-5	31.4(2.5)	Annotated hyp15 protein
hyp15	PFB0950w	3	100.0	3e-18	44.5(13.0)	Exported protein, unknown function
hyp10	PF08_0001	1	50.0	3	34.6(0.0)	Exported protein, unknown function
hyp12	MAL8P1.206	3	100.0	2e-17	47.1(4.9)	Exported protein, unknown function
hyp17	PF14_0741	1	50.0	1e-198	91.2(0.0)	Split gene model; merged in PlasmoDB 9.0

Clusters corresponding to variant gene families were searched for P. falciparum proteins that are currently not annotated as members of these gene families. Only clusters with a Jaccard index of at least 0.6 were considered in this search (Table 1). Annotated pseudogenes and gene fragment not shown. MP # and MP% indicate number and percentage of BLAST match pairs between the putative new member and all other proteins in the cluster representing that gene family. Avg. E-value and Avg. PID denote the average E-value and the average PID of these BLAST match pairs, respectively. ^aUnusual phist gene family member carrying an N-terminal acyl-CoA-binding protein domain (Pfam PF00887).

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