Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Bengtsson-Palme, Johan; Alm Rosenblad, Magnus; Molin, Mikael; Blomberg, Anders

doi:10.1186/1471-2164-15-749

BMC Genomics

Table 1 Detoxification protein families investigated in this work, divided into functional categories

From: Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Protein family	Pfam name	Number of reads GOS Initial	Number of reads GOS Reciprocal	GOS Reciprocal (%)	Genomes average (genes/genome)	Genomes CV (%)
Metal resistance
Arsenate reductase	ArsC	993	853	85.9	1.1	108
Divalent ion tolerance protein	CutA1	511	511	100	0.4	127
Copper resistance protein CopC	CopC	472	426	90.3	0.3	206
Multicopper oxidase	Cu-oxidase_3	435	313	72	0.7	154
Copper transporter	CutC	258	258	100	0.2	182
Tellurite resistance protein	TehB	2956	244	8.3	0.2	206
Arsenical pump membrane protein	ArsB	177	19	10.7	0.3	218
Cadmium binding protein	YodA	1	0	0	0.0	492
Transporters
Major facilitator family	MFS_1	22627	19301	85.3	23.1	108
ACR transporter	ACR_tran	10591	10337	97.6	4.4	126
Multi antimicrobial extrusion protein	MatE	5164	4308	83.4	2.2	120
Efflux pump	HlyD	4048	2693	66.5	6.9	121
Small Multidrug Resistance protein	Multi_Drug_Res	2194	2097	95.6	1.0	134
C4-dicarboxylate transporter	C4dic_mal_tran	71	71	100	0.3	173
Oxidative stress
Peroxiredoxin	AhpC-TSA	14009	7397	52.8	3.5	91
Thioredoxin	Thioredoxin	8221	4668	56.8	2.7	67
Redoxin	Redoxin	13178	4410	33.5	1.7	108
Peroxidase	peroxidase	3067	3065	99.9	0.4	154
Glutathione peroxidase	GSHPx	2380	2218	93.2	0.6	131
Superoxide dismutase	Sod_Fe_C	935	796	85.1	0.9	78
Catalase	Catalase	91	88	96.7	0.8	146
Other detoxification systems
Bacitracin resistance protein	BacA	2803	2799	99.9	0.8	73
Organic solvent tolerance protein	OstA_C	1094	1086	99.3	0.4	121
Fusaric acid resistance protein	FUSC	67	65	97	0.8	205
Di-haem cytochrome c peroxidase	CCP_MauG	606	582	96	0.5	211
Beta-lactamase	Beta-lactamase	5196	4985	95.9	2.6	149
NADH oxidase	Oxidored_FMN	2598	2349	90.4	1.9	130
Penicillin binding transpeptidase	Transpeptidase	9702	8379	86.4	2.1	72
Multiple antibiotic resistance operon repressor	MarR	2949	2078	70.5	5.8	128
MAATS-type multidrug transcriptional repressor	TetR_C_2	21	12	57.1	0.1	343
NADPH-dependent FMN reductase	FMN_red	2222	1076	48.4	2.5	110
Control protein families
Elongation factor TS	EF_TS	2780	2734	98.3	0.8	49
DNA polymerase A	DNA_pol_A	5372	4973	92.6	0.9	55
RNA polymerase rpoB	RNA_pol_Rpb2_6	5847	5106	87.3	1.0	9

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ISSN: 1471-2164

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