TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins

BMC Bioinformatics

Table 5 Proteomes screened.

Organism	Proteins	No. signal peptide	% proteins with signal peptide	No. bbtm protein <E = 1	% of proteins with signal peptide bbtm E<= 1	% bbtm proteins <E = 1
Escherichia coli	5341	1032	19.32	87	8.43	1.63
E. coli ^Ш	4005	782	19.52	69	8.82	1.72
Pseudomonas aeruginosa	5567	1142	20.51	137	12	2.46
P. aeruginosa ^Ш	5567	1412	25.36	137	9.7	2.46
Staphylococcus aureus	2632	409	15.54	18	4.4	0.68
Aquifex aeolicus	1560	187	11.98	16	8.55	1.02
Chlamydia trachomatis	895	145	16.20	17	11.7	1.89
Thermatoga maritima	1858	265	14.26	12	4.53	0.65
Trepanoma pallidum	1036	203	19.59	12	5.91	1.16
Bacteroides thetaiotaomicron	4778	1614	33.78	131	8.12	2.74
Deinococcus radiodurans	3182	689	21.65	25	3.62	0.76
Rhodopirellula baltica	7325	1584	20.66	49	3.09	0.67
Plasmodium falciparum ^Ш	9178	1613	17.57	3	0.18	0.03
Arabidopsis thaliana	28860	5569	19.30	23	0.41	0.07
Caenorhabditis elegans ^Ш	22561	5778	22.60	26	0.45	0.12
Saccharomyces cerevisiae	5866	651	11.09	4	0.61	0.07

Several proteomes were screened, representing the major kingdoms of life. Proteomes were first filtered for sequences with signal peptides. Remaining sequences were then each queried, returning bb scores and E-value statistics. All proteomes were downloaded from the NCBI FTP site except those denoted ^Ш, downloaded from Uniprot/SwissProt for superior annotation.

ISSN: 1471-2105