Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics

Microbiome

Table 1 Identification results of protein groups for the 12 target species from the synthetic microbial community using different databases

	BLAST			Kaiju			Kraken2			MetaPA	Meta6FT	UP-S	UP-G	UP-F
Species name	MD1	MD2	MD3	MD1	MD2	MD3	MD1	MD2	MD3	——	——	——	——	——
Bacteroides fragilis	808	805	810	247	786	809	800	809	788	22	4	808	39	410
Citrobacter freundii	1266	1294	1322	214	557	1290	103	113	1309	293	30	1335	361	8
Clostridium butyricum	1078	1057	1000	327	785	1000	1082	1082	1000	226	18	996	1	286
Enterobacter asburiae	1198	1224	1204	85	294	1197	602	1141	1221	233	29	1210	222	1
Enterococcus casseliflavus	80	134	612	133	597	612	136	320	607	81	4	578	158	200
Enterococcus faecalis	490	489	498	137	319	491	476	491	489	134	5	480	286	362
Escherichia coli	1476	1266	1559	208	377	1515	284	486	1495	845	76	1397	571	685
Klebsiella aerogenes	624	564	630	496	696	649	606	791	713	292	91	751	8	10
Klebsiella pneumoniae	1505	891	1488	377	875	2676	183	209	2477	904	591	1756	192	254
Lactobacillus acidophilus	987	954	0	948	991	991	984	991	991	346	20	985	314	359
Morganella morganii	1592	1595	1577	307	1259	1540	1594	1597	1572	470	11	1569	932	999
Pseudomonas aeruginosa	772	770	783	55	102	767	57	182	767	54	9	739	73	94
Target 12 species	11,876	11,043	*11,483*	3534	7638	*13,537*	6907	8212	*13,429*	1734	400	12,604	3157	3668
Other species	869	644	1081	241	259	0	144	45	0	8218	2496	——	2842	2336
Unannotated	1107	2165	1288	10,077	5955	315	6801	5595	423	3900	888	——	——	——
Total	13,852	13,852	13,852	13,852	13,852	13,852	13,852	13,852	13,852	13,852	3784	12,604	5999	6004

ISSN: 2049-2618