Purine biosynthesis in archaea: variations on a theme

Biology Direct

Table 1 Annotation errors identified, by gene

	pur genes
	F	D	N	T	L^a	S^a	Q^a	M	K	E	C	B	H1^c	P	P2^d	H2	O
Protein name errors
Partial misannotation/over-attribution			3			2			1	^b
Inappropriately vague name						23				1	1			27		1	4
Not justified due to missing features	14	2					1								4
E. C. number errors
One or more missing			6			13			23	35	1
One or more incorrect/unjustified	14	2	2	2						2			1	1	31	2
Gene structure errors
Start codon mis-called	3								1
Pseudogene label unjustified											1
Gene symbol errors
Incorrect gene symbol							2				1					1	1
Number of genes examined	72	60	31	23	58	51	58	58	28	59	63^e	60	13^c	46^e	31	2^f	25

^a The three gene products share an EC number.
^b Naming of PurE is problematic. Some PurEs are not clearly class I or class II, and some organisms lack a PurK, making a class II type name more appropriate even when PurE appears class I. We counted either a class I or class II-type name as correct in this analysis.
^c Halobacteria fusions of PurN and PurH1 are counted under PurN.
^d Separate counts were maintained for PurP-like proteins in cluster II. We preferred generic names and no EC number, given a lack of demonstrated function for proteins in this cluster.
^e A split or frame-shifted gene was counted as one gene.
^f Excludes full-length PurH, counted under PurH1.

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