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

Table 2

Statistical analyses of the motifs in the protein families with domains of unknown functions (EDS1). The results are split into three subtables. The “TMHMM prediction,” the “Prediction on log-odds,” and the “F-measures”-table. Thereby the “TMHMM prediction”-table represents the absolute occurrences of a motif in all investigated protein families with domains of unknown functions. The “Prediction on log-odds”-table represents the topology state winners (see (6)) followed by the “F-measures”-table which indicates how good or bad a motif can be separated and assigned to a topology state.

Motif	TMHMM prediction			Prediction on log-odds			F-measures
PG10	430	1556	900	429	1556	901	0.997	1.0	0.998
LF10	2838	1535	2860	2840	1536	2857	0.998	0.998	0.999
PG9	572	1596	896	577	1590	897	0.99	0.998	0.995
LF9	3271	1392	2425	3272	1392	2424	0.998	0.997	0.999
VF8	1936	1065	1116	1933	1065	1119	0.998	0.999	0.996
LF8	3589	1446	2185	3583	1447	2190	0.998	0.998	0.997
GY8	775	863	685	771	860	692	0.995	0.998	0.995
GA7	3035	2907	1943	3047	2889	1949	0.996	0.996	0.993
AG7	3009	2939	2104	3016	2926	2110	0.995	0.997	0.992
AA7	5100	4623	2883	5124	4592	2890	0.993	0.995	0.99
GG7	2380	3171	1463	2373	3175	1466	0.99	0.997	0.987
LY6	1861	1315	1263	1873	1305	1261	0.993	0.995	0.989
VG6	2518	2331	1317	2536	2324	1306	0.987	0.993	0.981
SA6	1747	2683	1269	1757	2674	1268	0.987	0.997	0.985
PG6	566	1756	681	583	1745	675	0.983	0.997	0.982
AL6	6974	3789	2931	7155	3680	2859	0.981	0.98	0.969
PG5	640	1576	696	682	1542	688	0.955	0.989	0.957
GS5	1041	2161	763	1115	2097	753	0.951	0.98	0.959
LG5	4775	3050	1959	5071	2879	1834	0.951	0.952	0.919
AG5	3464	3092	1433	3761	2895	1333	0.942	0.958	0.908
GN4	228	952	271	276	891	284	0.869	0.96	0.919
IV4	3285	1562	723	3568	1339	663	0.905	0.861	0.765
IL4	5700	2244	1282	6209	1889	1128	0.879	0.773	0.699
GS4	1080	2356	651	1381	2063	643	0.807	0.905	0.791
GG4	2302	3822	893	2758	3387	872	0.814	0.89	0.714
SG4	1125	2542	723	1457	2228	705	0.796	0.908	0.789
VL4	6680	3046	1592	7202	2498	1618	0.847	0.737	0.634
AS4	1903	2807	946	2423	2311	922	0.795	0.854	0.769
GA4	3769	3300	1253	4463	2664	1195	0.823	0.807	0.698
AG4	3594	3456	1214	4381	2661	1222	0.813	0.795	0.695
SA3	2005	2965	728	2603	1901	1194	0.65	0.674	0.452
AA3	6719	5358	1327	7855	3199	2350	0.747	0.596	0.386
GL3	5758	3252	1343	6026	2066	2261	0.767	0.597	0.452