Table 2.

Summary of the predicted and experimental topology data for the 34 inner membrane proteins included in the study (protein names are from the Colibri database at http://genolist.pasteur.fr/Colibri (Rudd 2000)

Protein	Length	TMHMM	HMMTOP	MEMSAT	PHD	TOPPRED	Consensus prediction	S3 Score	Accuracy	Expression	Experimentally determined C terminus	TMHMM C term fix	S3 Score C-term fix	Accuracy C-term fix
SdhC	129	3P	3P	2C	3P	3P	P(4:1)	0.94	0.95		P	3P	1.00	1.00
CysW	291	6C	6C	5P	6C	5P	C(3:2)	0.91	0.93		C	6C	0.98	0.98
YhjW	563	5P	5P	6C	5P	5P	P(4:1)	0.27	0.42		P	5P	0.94	0.96
YjiG	153	3P	4C	4C	4C	3P	C(3:2)	0.70	0.76		P	3P	0.91	0.93
PotC	264	6C	6C	6C	7P	6C	C(4:1)	0.88	0.90	F	C	6C	0.90	0.93
YfbV	151	2C	2C	2C	1P	2C	C(4:1)	0.67	0.74		C	2C	0.88	0.92
TauC	275	6C	6C	7P	7P	6C	C(3:2)	0.85	0.88	F	C	6C	0.87	0.91
YagU	204	3P	3P	3P	4C	3P	P(4:1)	0.39	0.51		C	4C	0.86	0.90
YcdT	452	8C	7P	8C	8C	8C	C(4:1)	0.81	0.85		C	8C	0.85	0.90
CcmF	647	15C	15C	15C	14P	15C	C(4:1)	0.81	0.85	G	C	15C	0.81	0.87
YhjV	423	11P	11P	11P	12C	11P	P(4:1)	0.78	0.82	G	P	11P	0.78	0.85
YbjO	162	4C	4C	3P	3P	4C	C(3:2)	0.60	0.68		C	4C	0.78	0.85
YcdU	328	8C	8C	8C	8C	8C	C(5:0)	0.72	0.77		C	8C	0.72	0.80
YejM	586	5P	5P	5P	5P	6C	P(4:1)	0.70	0.76		P	5P	0.70	0.79
YcfT	357	8C	9P	8C	9P	8C	C(3:2)	0.59	0.67		C	8C	0.69	0.78
PsiE	136	4C	4C	4C	4C	3P	C(4:1)	0.49	0.59		C	4C	0.49	0.64
SrlA	187	3C	3C	3C	4P	3C	C(4:1)	0.44	0.55		C	3C	0.48	0.64
YjeM	500	12C	12C	12C	13P	12C	C(4:1)	0.47	0.58	G,F	C	12C	0.48	0.63
YddG	293	10C	10C	10C	9P	9P	C(3:2)	0.42	0.54	F	C	10C	0.43	0.60
MenA	308	9P	9P	9P	8C	8C	P(3:2)	0.27	0.42		P	9P	0.42	0.60
YgdQ	237	7C	7C	7C	7C	7C	C(5:0)	0.39	0.51		C	7C	0.41	0.59
YdgG	344	8C	8C	8C	8C	8C	C(5:0)	0.23	0.39		C	8C	0.38	0.57
NarU	462	12C	12C	12C	13P	12C	C(4:1)	0.38	0.50		C	12C	0.38	0.56
YegH	527	7C	7C	7C	7C	7C	C(5:0)	0.27	0.42		C	7C	0.36	0.55
TsgA	393	12C	12C	12C	11P	12C	C(4:1)	0.27	0.42	F	C	12C	0.27	0.49
YebS	427	8C	8C	7P	8C	8C	C(4:1)	0.19	0.35	F	C	8C	0.23	0.46
ZitB*	313	5P	5P	6C	6C	5P	P(3:2)	0.37	0.49		C	6C	0.19	0.43
HcaT	379	12C	12C	12C	11P	11P	C(3:2)	0.14	0.31	G	C	12C	0.17	0.42
YkgB	197	3P	4C	3P	4C	4C	C(3:2)	0.24	0.39		C	3C	0.11	0.38
BtuC	326	9P	9P	9P	9P	9P	P(5:0)	0.13	0.30		C	8C	0.08	0.35
YjcD	449	13P	13P	13P	13P	13P	P(5:0)	0.04	0.23		P	13P	0.05	0.33
PotH	317	6C	6C	6C	7P	6C	C(4:1)	0.85	0.88		?
YahN	223	6P	6P	6P	6P	5C	P(4:1)	0.56	0.65	F	?
TdcC	443	11P	11P	10C	11P	11P	P(4:1)	0.27	0.41	G,F	?

The topologies predicted by five commonly used prediction programs are summarized by indicating the predicted cytoplasmic (C) or periplasmic (P) location of the C terminus together with the predicted number of transmembrane helices (columns 3–7). The consensus topology prediction is summarized by the location of the C terminus followed by the majority level (5 : 0 means that all five methods give the same prediction, 4 : 1, that four methods agree, etc.; column 8). The reliability score (S3 score) and the estimated prediction accuracy calculated by TMHMM with no inclusion of information on the location of the C-terminus are given in columns 9 and 10. Fusions for which only a fragment corresponding in size to the PhoA or GFP reporter moieties, but no full-length protein was visible on Western blots are indicated by F and G, respectively (column 11). The experimentally determined location of the C terminus is given in column 12 (c.f., Fig. 2B ▶). The topology, S3 score, and estimated accuracy predicted by TMHMM with information on the experimentally determined C-terminal location included are given in columns 13–15.