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

Table 3

Statistical analyses of the motifs in the bacteriorhodopsin-like protein families (EDS2). 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 bacteriorhodopsin-like protein families. 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	TMHMM prediction			Prediction on log-odds				F-measures
PG10	105	17	464	103	17	466	0.942	1.0	0.987
LF10	1900	131	1165	2147	214	835	0.864	0.655	0.782
PG9	187	61	395	223	63	357	0.893	0.952	0.944
LF9	1278	164	565	1170	307	530	0.852	0.586	0.842
VF8	739	118	623	796	104	580	0.945	0.928	0.943
LF8	654	168	362	625	209	350	0.916	0.78	0.966
GY8	715	185	1450	881	186	1283	0.876	0.981	0.928
GA7	1581	2013	1963	1618	1877	2062	0.889	0.95	0.935
AG7	1737	722	1347	1653	782	1371	0.919	0.92	0.924
AA7	1887	1618	1455	1936	1530	1494	0.922	0.923	0.907
GG7	1837	562	1939	1760	506	2072	0.946	0.944	0.955
LY6	1868	189	639	1579	333	784	0.823	0.456	0.704
VG6	1642	199	1011	1562	175	1115	0.956	0.898	0.938
SA6	503	1030	579	614	925	573	0.843	0.926	0.92
PG6	316	56	242	301	54	259	0.94	0.982	0.93
AL6	1969	975	1525	1954	982	1533	0.909	0.908	0.917
PG5	247	39	78	284	37	43	0.904	0.974	0.595
GS5	208	302	574	248	272	564	0.899	0.944	0.965
LG5	2287	949	854	2254	805	1031	0.913	0.796	0.858
AG5	1228	766	746	1222	656	862	0.934	0.878	0.889
GN4	34	222	108	33	179	152	0.925	0.878	0.815
IV4	2612	484	532	2066	821	741	0.811	0.651	0.654
IL4	3586	648	611	2735	1153	957	0.817	0.499	0.681
GS4	136	643	497	193	612	471	0.76	0.969	0.915
GG4	2057	768	945	1972	568	1230	0.95	0.814	0.818
SG4	397	836	365	405	783	410	0.895	0.956	0.88
VL4	2621	619	775	1840	1264	911	0.759	0.579	0.81
AS4	378	1584	943	447	1441	1017	0.815	0.95	0.884
GA4	911	1411	1298	869	1372	1379	0.828	0.934	0.9
AG4	1418	1013	1258	1413	833	1443	0.875	0.813	0.826
SA3	522	1301	359	625	1125	432	0.806	0.893	0.781
AA3	2125	3004	1010	2652	1874	1613	0.695	0.687	0.455
GL3	851	528	435	829	339	646	0.751	0.646	0.614