Orphan SelD proteins and selenium-dependent molybdenum hydroxylases

Biology Direct

Table 1 Conserved clustering of top Partial Phylogenetic Profiling results

E. coli gene	Putative protein name	PPP rank	E. coli locus	PPP rank	E. faecalis locus	PPP rank	H. maris. locus	PPP rank	C. difficile locus
xdhA	xanthine dehydrogenase, Mo-binding subunit	6	b2866	14	EF_2570			5	CD2087
xdhB	xanthine dehydrogenase, FAD binding subunit	15	b2867						(CD2101)
xdhC	xanthine dehydrogenase, Fe-S binding subunit	17	b2868	14	(EF_2570)				(CD2088)
ygeV	sigma(54)-dependent activator	13	b2869
ygeW	carbamoyl transferase	7	b2870	5	EF_2577
ygeX	diaminopropionate ammonia-lyase	10	b2871	7	EF_2579			7	CD2085
ygeY	hydrolase, peptidase M20 family	4	b2872	3	EF_2578				(CD2084)
ygeZ	phenyl-hydantoinase	19	b2873		(EF_2580)	6	pNG7258
yqeA	carbamate kinase	18	b2874	15	EF_2575
yqeB	SDMH accessory protein TIGR03309	1	b2875	2	EF_2563	1	pNG7241	1	CD3478
yqeC	SDMH accessory protein TIGR03172	2	b2876	1	EF_2564	2	pNG7237	2	CD2071
ygfJ	SDMH accessory protein TIGR03310	5	b2877	21	EF_2569		pNG7236
ygfK	selenate reductase, Fe-S subunit	8	b2878	4	EF_2581
ygfL	selenium metabolism protein SsnA TIGR03314	3	b2879	6	EF_2582	8	pNG7259
ygfM	selenate reductase, FAD-binding subunit		b2880
ygfN	selenate reductase, Mo-binding subunit	14	b2881		(EF_2570)	3	pNG7246	3	( *CD2099* )
						5	(pNG7244)	4	CD2073
								5	(CD2079)
ygfO	xanthine/uracil family permease		b2882		(EF_2573)
	sulfurtransferase-related protein TIGR03527			12	EF_2566		pNG7238		CD3667
selD	selenophosphate synthase		b1764		EF_2567		pNG7239		CD2496
	selenocysteine lyase TIGR01977			11	EF_2568				CD3670

Partial Phylogenetic Profiling results for Escherichia coli, Enterococcus faecalis, Haloarcula marismortui, and Clostridium difficile vs. the profile of the putative SDMH accessory protein family TIGR03309. The first seventeen rows show a contiguous gene region in E. coli, and the last three a region in E. faecalis. The first two columns show E. coli gene symbols and putative protein names. The third, fifth, seventh, and ninth columns represent rank by PPP for E. coli (out of 4243 proteins), E. faecalis (3277 proteins), H. marismortui (4240 proteins – all loci found are on plasmid with 362 proteins), and C. difficile (3873 proteins); missing values show that the protein did not score in the top twenty-five. Locus tags shown in columns 6, 8, and 10 mark genes with bi-directional best hits vs. the corresponding E. coli locus in column 4 and co-clustered in their respective species, so not all of the top 25 hits appear in the table; locus tags in parentheses are unidirectional best hits from the E. coli gene. The row for putative SDMH accessory protein family TIGR03309 is in boldface. The putative C. difficile ortholog to the C. purinolyticum xanthine dehydrogenase molybdenum-binding subunit is in italicized boldface.

ISSN: 1745-6150