. 2006 Nov 17;189(2):561–574. doi: 10.1128/JB.01505-06

TABLE 1.

Proteins used as localization markers for analysis of sucrose density gradient fractions

Locus	Protein^a	PSORTb localization^b	PSORTb score^b	PROFtmb score^c	BOMP score^d	TMB-Hunt score^e	Predicted mass^f	Recombinant mass^g
FTT0842	Pal	OM	10.00				21.0	24.2
FTT1095c	TolC-A	OM	10.00				49.9	52.9
FTT1156c	PilQ	OM	10.00			10.7	65.0	64.7
FTT1258	SilC	OM	10.00				51.9	54.9
FTT1573c	FtaG	OM	10.00	6.2	3	10.7	85.0	88.2
FTT1724c	TolC-B	OM	10.00				55.1	58.3
FTT0583	FopA	OM	9.93	7.3		8.6	39.0	42.2
FTT1043	Mip	OM	9.92				27.1	29.8
FTT0918	YapH-N^h	OM	9.52	8.1	3	7.4	56.8	27.0
FTT0919	YapH-C^h	OM	9.49	7.8		4.2	50.2	25.7
FTL_0439	YapH-LVS^h	OM	9.52	8.3		7.1	55.8	35.1
FTT0715	Cht1	Un	2.00	6.2			81.0	84.1
FTT0025c	SrfA	IM	9.46	7.6	3	4.9	51.6	51.2
FTT0901	Tul4-A	Un	2.00				13.8	16.9
FTT0904	Tul4-B	Un	2.00				15.5	18.6
FTT0223c	LamB	Cyto	8.96				25.8	24.3
FTT0345	SecY	IM	10.00				44.8	20.2
FTT0404	LolC	IM	10.00				48.2	28.1
FTT0137	EF-Tu	Cyto	9.97				43.4	42.8
FTT1359c	IglA	Cyto	8.96				22.3	24.0

Underlined proteins are putative lipoproteins, based upon the LipoP lipoprotein prediction program (http://www.cbs.dtu.dk/services/LipoP/).

PSORTb version 2.0.4 bacterial protein subcellular localization prediction program (http://www.psort.org/psortb/index.html) localization predicted for OM, cytoplasmic membrane (IM), cytoplasm (Cyto), or unknown (Un). Scores of >7.5 were considered significant.

PROFtmb bacterial transmembrane beta-barrel prediction program (http://cubic.bioc.columbia.edu/services/proftmb/). Only significant Z-values (>4.0) are shown.

BOMP beta-barrel integral outer membrane protein prediction program (http://www.bioinfo.no/tools/bomp). Only significant scores (>2) are shown.

TMB-Hunt transmembrane beta-barrel prediction program (http://www.bioinformatics.leeds.ac.uk/∼andy/betaBarrel/AACompPred/aaTMB_Hunt.cgi). Only significant log probability scores (>2) are shown.

For OMPs and IMPs, the predicted molecular mass (in kDa) of the protein was calculated following cleavage by signal peptidase I or II.

A portion of each coding region was cloned into the pProEX HTb six-histidine fusion vector for recombinant expression and purification in E. coli. Sequence upstream of the predicted signal sequence was excluded to aid in purification.

There are two distinct YapH ORF orthologs in Schu S4. In LVS, the YapH-LVS ORF is the result of an in-frame deletion of the C-terminal end of FTT0918 and the N-terminal end of FTT0919.