Structure Topology Prediction of Discriminative Sequence Motifs in Membrane Proteins with Domains of Unknown Functions

Table 4

Statistical analyses of the motifs in all known PDBTM protein structures (EDS3). The results are split into three subtables. The “PDBTM prediction,” the “Prediction on log-odds,” and the “F-measures”-table. Thereby the “PDBTM prediction”-table represents the absolute occurrences of a motif in all investigated PDBTM protein structures. The “Prediction on log-odds”-table represents the topology state winners (see (6)) followed by the “F-measures”-table witch indicates how good or bad a motif can be separated and assigned to a topology state.

Motif	PDBTM prediction			Prediction on log-odds			F-measures
	α-helical	Side1	Side2	α-helical	Side1	Side2	α-helical	Side1	Side2
PG10	382	1719	1780	382	1297	2202	1.0	0.86	0.894
LF10	2084	1248	1381	2092	1007	1614	0.998	0.893	0.918
PG9	473	1559	1583	474	1158	1983	0.999	0.852	0.887
LF9	2206	1103	1202	2207	962	1342	0.999	0.93	0.945
VF8	1891	1006	1120	1907	787	1323	0.996	0.878	0.905
LF8	3638	1450	1346	3637	1067	1730	0.998	0.845	0.873
GY8	393	1228	1186	392	930	1485	0.999	0.862	0.888
GA7	2614	2516	2914	2607	1775	3662	0.993	0.817	0.881
AG7	3443	2411	2937	3469	1739	3583	0.995	0.836	0.895
AA7	2870	3288	3650	2870	2280	4658	0.991	0.811	0.873
GG7	2899	2982	3285	2917	2132	4117	0.997	0.834	0.883
LY6	1326	1127	1066	1345	901	1273	0.992	0.888	0.904
VG6	2962	2230	2588	2961	1723	3096	0.996	0.869	0.907
SA6	1499	1984	1947	1497	1551	2382	0.998	0.875	0.899
PG6	347	1697	1558	348	1356	1898	0.999	0.888	0.901
AL6	6110	2672	2947	6140	1951	3638	0.996	0.844	0.889
PG5	971	1651	2095	991	1334	2392	0.985	0.893	0.923
GS5	1101	1609	1708	1154	1131	2133	0.976	0.826	0.874
LG5	5049	3013	3411	5083	2124	4266	0.993	0.826	0.879
AG5	3601	3012	3278	3623	2177	4091	0.986	0.833	0.879
GN4	427	1700	1898	453	1281	2291	0.964	0.857	0.894
IV4	4596	1717	1855	4914	1317	1937	0.947	0.838	0.822
IL4	6972	1827	2344	6956	1299	2888	0.964	0.752	0.842
GS4	1298	1773	1858	1425	1331	2173	0.936	0.854	0.879
GG4	3656	2463	2738	3897	1653	3307	0.93	0.784	0.84
SG4	1493	2141	2419	1629	1349	3075	0.948	0.771	0.86
VL4	6840	2363	3081	7067	1757	3460	0.963	0.821	0.873
AS4	2172	2066	2498	2267	1399	3070	0.934	0.807	0.859
GA4	4397	2954	3845	4685	1883	4628	0.933	0.756	0.85
AG4	3668	3402	3838	3950	2376	4582	0.937	0.807	0.856
SA3	2204	2198	2292	2936	1357	2401	0.773	0.678	0.758
AA3	5085	3463	4144	6342	1865	4485	0.798	0.646	0.733
GL3	5730	3075	3552	6026	2147	4184	0.789	0.591	0.723