Computational identification of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes

BMC Genomics

Table 3 Receptor-like kinases identified by extracellular domains across the species

Domain class	Domain combinations	Species
Domain class	Domain combinations	CC	GM	MT	PV	VA	VR	VU	VV	AT	SL
LRR	lrr	134	579	324	239	254	249	301	136	180	198
G-lectin: combination of ectodomains	s-locus	2	1	1	1	1	1	3	2	0	0
	b-lectin	7	20	25	12	12	14	15	7	2	7
	b-lectin/pan	2	9	7	12	2	5	17	2	1	5
	s-locus/pan	5	10	4	5	1	0	7	18	2	0
	b-lectin/s-locus	11	24	14	15	14	18	15	7	2	10
	b-lectin/s-locus/pan	31	146	131	41	53	44	96	12	33	42
L-Lectin	l-lectin	24	66	46	38	35	36	42	20	44	22
C-lectin	c-lectin	1	4	1	1	1	1	1	1	1	1
Lectin	lysM	7	27	16	14	11	12	13	5	5	8
Lectin (Feronia)	malectin	29	99	54	82	58	50	60	29	36	22
Thaumatin (Osmotin)	pr5k	0	0	0	0	0	0	0	0	2	0
WAK	wak	11	66	33	41	45	39	46	14	27	17
	egf	1	4	0	1	0	0	1	2	0	2
	wak/egf	5	10	16	6	3	7	8	7	4	7
DUF26 recently renamed	stress_antifung	28	173	66	70	57	58	90	22	45	15
Classically related to G-lectin	pan	5	10	1	2	2	0	1	10	0	0
Combination of different domain ectodomains identified	lrr/malectin	12	63	66	32	30	19	28	26	47	7
	pan/wak	0	0	0	0	0	0	0	1	0	0
	s-locus/wak	0	0	0	0	0	2	0	1	0	0
	b-lectin/pr5k	0	1	3	0	1	0	1	0	0	0
	b-lectin/s-locus/wak	2	0	1	2	3	0	3	0	0	0
	b-lectin/s-locus/pan/wak	0	8	2	2	2	2	5	1	0	1
	pan/s-locus/wak	0	0	0	0	0	0	0	1	0	0
RLK - pkinase	rlk – non-target ectodomain	4	11	6	5	3	5	6	18	8	5
Combination of ectodomains Identified RLCK with/without ectodomains	rlk - not ectodomains	30	180	74	87	93	72	86	80	25	28
	rlck extra domain	8	7	6	6	10	3	5	5	5	9
	rlck only pkinase	91	346	163	128	144	133	142	16	86	70

For each species, the results were merge by present “P” and absent “A” of signal peptide. All possible domain combinations were explored and are reported in the “Domain combinations” column (proteins reported are non-redundant). A. thaliana: AT, C. cajan: CC, G. max: GM, M. truncatula: MT, P. vulgaris: PV, S. lycopersicum: SL, V. angularis: VA, V. radiata: VR, V. unguiculata: VU, and V. vinifera: VV (Table A4). RLCK: Only kinase domain identified. All proteins reported in this table have at least one transmembrane helix. Extra: proteins that have the presence/absence of signal peptide, at least one transmembrane helix, a Pkinase and other extracellular/intracellular domains different than LRR, L/C/G-Lectin, LysM, Pr5k-Thaumatin, WAK, Malectin, EGF or Stress-Antifung were only considered for the combination identification analysis, but other domains reported in Table A7 named as “non-target” domains could be present

ISSN: 1471-2164