Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome

Table 4 A summary of the numbers of carbohydrate-active proteins identified in P. parasitica and P. infestans in the current study and comparison of these data with those from three previous studies of P. infestans

	P. parasitica(current study)				P. infestans(current study)				P. infestans[31]		P. infestans[29]		P. infestans[149]
CAZymes	CAZyme families	CAZyme modules	CWDE families	CWDE proteins	CAZyme families	CAZyme modules	CWDE families	CWDE proteins	CAZyme families	CAZyme modules	CAZyme families	CAZyme proteins	CAZyme families	CAZyme proteins
CBM	17	85	14	48	16	74	12	53	12	45	na	na	na	19
AA	8	43	4	13	8	42	4	13	na	na	na	na	na	na
CE	12	113	8	46	12	90	8	38	12	81	8	49	na	47
GH	37	293	34	280	36	275	35	265	34	261	34	244	na	216
GT	29	169	na	na	30	158	na	na	27	142	22	83	na	64
PL	4	47	3	44	5	67	3	54	3	57	3	59	na	59

na: data not available.
In the current study, CAZyme families and CAZyme modules were initially identified using dbCAN, BLAST, keyword and domain searches. Subsequent in-depth bioinformatic analyses of individual genes indicated that some CAZymes were unlikely to be true CWDEs, leading to a lower number of CWDE families than CAZyme families. Our data show that the numbers of CWDE families and CWDE proteins in each CAZyme class are remarkably similar in P. parasitica and P. infestans. Comparison of our P. infestans data with those from the other P. infestans studies exemplify the variation in CAZyme annotation achieved following different approaches and conducted at different times.

ISSN: 1471-2164