SIGA - BACSU - GREMLIN Contacts

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SIGA - RNA polymerase sigma factor SigA

UniProt:	P06224	Sequences: MADKQTHETELTFDQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELISENEETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	371 (325)
Sequences:	3102 (1348)
Seq/√Len:	74.8

ECOLI - RPOD RPOS RPOH FLIA
BACSU - SIGA RPSK RPSB RPSG RPSF RPSD RPSE

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
315_E	319_R	4.969	1.00
229_L	233_L	4.894	1.00
235_R	241_E	4.792	1.00
232_D	245_D	4.540	1.00
240_E	250_P	4.165	1.00
222_L	246_M	3.691	1.00
319_R	325_D	3.431	1.00
242_I	253_V	3.164	1.00
339_F	346_I	3.142	1.00
136_R	140_E	2.980	1.00
122_A	126_K	2.964	1.00
276_S	281_F	2.926	1.00
341_V	346_I	2.865	1.00
302_Q	369_F	2.764	1.00
105_Y	120_E	2.723	1.00
145_L	187_S	2.702	1.00
359_H	362_R	2.668	1.00
116_S	119_E	2.661	1.00
314_E	356_K	2.413	1.00
128_E	181_R	2.396	1.00
225_V	246_M	2.381	1.00
128_E	180_Y	2.347	1.00
126_K	131_D	2.236	1.00
333_E	342_T	2.203	1.00
345_R	348_Q	2.170	1.00
229_L	242_I	2.151	1.00
316_N	338_V	2.101	1.00
222_L	242_I	2.036	1.00
344_E	347_R	2.008	1.00
239_P	257_L	2.004	1.00
229_L	237_P	1.992	1.00
114_L	120_E	1.983	1.00
321_R	350_E	1.961	1.00
229_L	235_R	1.953	1.00
105_Y	110_G	1.943	1.00
112_V	141_A	1.837	1.00
135_K	176_E	1.832	1.00
105_Y	168_N	1.820	1.00
100_D	120_E	1.813	1.00
105_Y	109_I	1.780	1.00
308_D	315_E	1.768	1.00
309_T	362_R	1.765	1.00
233_L	241_E	1.755	1.00
137_R	141_A	1.751	1.00
67_N	70_T	1.712	1.00
100_D	105_Y	1.685	1.00
174_A	190_A	1.656	1.00
115_L	120_E	1.633	1.00
119_E	137_R	1.627	1.00
320_L	330_R	1.603	0.99
110_G	120_E	1.599	0.99
332_L	344_E	1.597	0.99
243_A	253_V	1.577	0.99
105_Y	114_L	1.554	0.99
177_K	217_E	1.553	0.99
149_I	191_T	1.547	0.99
179_D	182_K	1.528	0.99
306_V	366_L	1.514	0.99
101_P	120_E	1.511	0.99
322_F	354_L	1.501	0.99
335_V	339_F	1.488	0.99
120_E	124_A	1.486	0.99
47_D	61_V	1.464	0.99
300_K	304_E	1.464	0.99
326_D	330_R	1.462	0.99
105_Y	124_A	1.453	0.99
56_L	60_G	1.448	0.99
344_E	348_Q	1.438	0.99
345_R	349_I	1.434	0.99
138_L	211_I	1.413	0.99
55_F	59_Q	1.409	0.99
64_I	68_E	1.399	0.99
229_L	241_E	1.388	0.98
225_V	245_D	1.384	0.98
117_A	121_I	1.370	0.98
104_M	108_E	1.365	0.98
331_T	342_T	1.358	0.98
145_L	188_T	1.357	0.98
187_S	200_R	1.357	0.98
109_I	147_V	1.333	0.98
316_N	339_F	1.332	0.98
228_Q	245_D	1.314	0.98
121_I	125_Q	1.314	0.98
332_L	348_Q	1.311	0.98
147_V	272_E	1.306	0.98
139_A	175_V	1.301	0.98
332_L	347_R	1.301	0.98
50_D	53_Y	1.293	0.98
226_Q	257_L	1.292	0.98
330_R	338_V	1.288	0.98
243_A	250_P	1.271	0.97
75_I	79_A	1.260	0.97
65_S	69_E	1.252	0.97
46_S	66_E	1.251	0.97
126_K	137_R	1.246	0.97
336_G	342_T	1.243	0.97
304_E	325_D	1.233	0.97
320_L	338_V	1.228	0.97
173_K	177_K	1.225	0.97
106_L	109_I	1.221	0.97
332_L	336_G	1.216	0.97
68_E	80_K	1.215	0.96
237_P	241_E	1.214	0.96
60_G	64_I	1.211	0.96
83_E	86_D	1.208	0.96
169_M	172_M	1.201	0.96
312_D	315_E	1.194	0.96
49_M	52_Y	1.190	0.96
60_G	68_E	1.187	0.96
73_P	77_Q	1.177	0.96
101_P	105_Y	1.165	0.96
48_Q	55_F	1.158	0.95
53_Y	63_L	1.153	0.95
196_Q	214_H	1.135	0.95
211_I	259_I	1.126	0.95
125_Q	180_Y	1.125	0.95
200_R	217_E	1.113	0.94
51_E	65_S	1.111	0.94
122_A	129_E	1.107	0.94
186_F	190_A	1.107	0.94
188_T	191_T	1.103	0.94
298_L	302_Q	1.095	0.94
225_V	228_Q	1.094	0.94
53_Y	56_L	1.094	0.94
146_V	167_G	1.093	0.94
63_L	66_E	1.089	0.94
216_V	220_N	1.083	0.93
100_D	110_G	1.083	0.93
317_V	353_A	1.080	0.93
332_L	350_E	1.074	0.93
156_R	220_N	1.072	0.93
114_L	144_R	1.069	0.93
45_E	59_Q	1.069	0.93
200_R	214_H	1.064	0.93
45_E	49_M	1.061	0.93
64_I	71_E	1.061	0.93
106_L	110_G	1.054	0.92
100_D	114_L	1.052	0.92
211_I	215_M	1.050	0.92
331_T	343_R	1.050	0.92
238_T	241_E	1.041	0.92
223_I	253_V	1.035	0.92
45_E	54_E	1.033	0.92
139_A	172_M	1.027	0.91
45_E	48_Q	1.017	0.91
123_Y	127_I	1.012	0.91
218_T	252_K	1.010	0.91
65_S	71_E	1.008	0.91
99_N	102_V	1.005	0.91
48_Q	59_Q	1.004	0.90
321_R	332_L	1.001	0.90
318_L	353_A	1.001	0.90
298_L	301_E	1.001	0.90
67_N	72_D	1.000	0.90
297_E	301_E	0.996	0.90
295_A	298_L	0.991	0.90
51_E	55_F	0.991	0.90
71_E	75_I	0.990	0.90
343_R	348_Q	0.990	0.90
123_Y	134_S	0.990	0.90
51_E	57_G	0.989	0.90
113_N	116_S	0.973	0.89
101_P	115_L	0.973	0.89
336_G	348_Q	0.970	0.89
48_Q	66_E	0.964	0.89
219_I	341_V	0.963	0.89
100_D	104_M	0.963	0.89
220_N	227_R	0.961	0.88
233_L	237_P	0.961	0.88
239_P	254_R	0.960	0.88
57_G	60_G	0.958	0.88
68_E	71_E	0.954	0.88
188_T	200_R	0.944	0.88
200_R	213_V	0.944	0.88
49_M	61_V	0.944	0.88
114_L	124_A	0.936	0.87
355_R	360_P	0.934	0.87
100_D	115_L	0.922	0.86
65_S	68_E	0.922	0.86
56_L	61_V	0.919	0.86
55_F	58_E	0.915	0.86
317_V	339_F	0.910	0.86
110_G	124_A	0.909	0.86
212_P	323_G	0.909	0.86
148_S	151_K	0.908	0.85
341_V	352_K	0.908	0.85
48_Q	58_E	0.905	0.85
51_E	58_E	0.898	0.85
54_E	57_G	0.898	0.85
346_I	361_S	0.895	0.85
158_M	201_A	0.892	0.84
76_Q	79_A	0.891	0.84
270_I	281_F	0.889	0.84
46_S	53_Y	0.886	0.84
45_E	64_I	0.883	0.84
311_T	356_K	0.882	0.84
342_T	345_R	0.882	0.84
174_A	186_F	0.880	0.84
185_K	204_D	0.880	0.84
156_R	207_R	0.879	0.84
267_E	277_H	0.876	0.83
243_A	248_L	0.875	0.83
154_V	159_L	0.874	0.83
51_E	56_L	0.872	0.83
253_V	256_I	0.872	0.83
64_I	69_E	0.870	0.83
215_M	219_I	0.868	0.83
125_Q	181_R	0.867	0.83
57_G	68_E	0.866	0.83
336_G	344_E	0.863	0.82
210_R	214_H	0.859	0.82
55_F	61_V	0.851	0.82
49_M	53_Y	0.848	0.81
316_N	320_L	0.845	0.81
182_K	195_R	0.843	0.81
191_T	342_T	0.842	0.81
46_S	55_F	0.839	0.81
52_Y	66_E	0.838	0.81
211_I	219_I	0.833	0.80
119_E	123_Y	0.832	0.80
152_R	202_I	0.831	0.80
113_N	120_E	0.831	0.80
49_M	54_E	0.830	0.80
105_Y	108_E	0.830	0.80
64_I	67_N	0.827	0.80
219_I	256_I	0.827	0.80
66_E	71_E	0.827	0.80
148_S	165_Q	0.824	0.79
336_G	345_R	0.821	0.79
45_E	71_E	0.820	0.79
328_R	334_E	0.818	0.79
332_L	345_R	0.815	0.79
104_M	120_E	0.814	0.79
126_K	134_S	0.810	0.78
70_T	75_I	0.808	0.78
67_N	73_P	0.807	0.78
84_E	88_N	0.807	0.78
46_S	51_E	0.804	0.78
45_E	51_E	0.804	0.78
65_S	79_A	0.803	0.78
88_N	93_P	0.803	0.78
145_L	200_R	0.803	0.78
67_N	71_E	0.801	0.77
47_D	60_G	0.800	0.77
60_G	69_E	0.796	0.77
47_D	71_E	0.796	0.77
302_Q	305_D	0.796	0.77
177_K	205_Q	0.791	0.77
61_V	71_E	0.790	0.76
86_D	90_L	0.789	0.76
65_S	70_T	0.789	0.76
64_I	77_Q	0.789	0.76
53_Y	59_Q	0.788	0.76
268_T	278_L	0.787	0.76
51_E	72_D	0.785	0.76
349_I	352_K	0.785	0.76
70_T	73_P	0.781	0.76
270_I	277_H	0.778	0.75
85_F	89_D	0.778	0.75
147_V	161_L	0.777	0.75
53_Y	57_G	0.776	0.75
57_G	64_I	0.776	0.75
72_D	77_Q	0.775	0.75
82_E	86_D	0.772	0.75
102_V	110_G	0.770	0.75
75_I	80_K	0.768	0.74
77_Q	80_K	0.767	0.74
53_Y	61_V	0.766	0.74
62_E	71_E	0.764	0.74
59_Q	63_L	0.764	0.74
269_P	279_G	0.763	0.74
88_N	91_S	0.762	0.74
51_E	60_G	0.762	0.74
115_L	123_Y	0.761	0.74
56_L	64_I	0.755	0.73
218_T	256_I	0.754	0.73
336_G	347_R	0.752	0.73
109_I	112_V	0.751	0.73
73_P	80_K	0.750	0.73
135_K	165_Q	0.749	0.73
60_G	120_E	0.744	0.72
246_M	253_V	0.743	0.72
289_S	293_H	0.743	0.72
94_P	97_K	0.743	0.72
46_S	60_G	0.743	0.72
54_E	58_E	0.742	0.72
45_E	55_F	0.739	0.72
66_E	70_T	0.738	0.71
255_E	303_L	0.736	0.71
105_Y	115_L	0.736	0.71
228_Q	232_D	0.735	0.71
342_T	352_K	0.735	0.71
69_E	73_P	0.734	0.71
106_L	120_E	0.733	0.71
61_V	68_E	0.730	0.71
51_E	54_E	0.729	0.71
75_I	78_L	0.727	0.70
82_E	85_F	0.726	0.70
199_T	217_E	0.725	0.70
73_P	79_A	0.723	0.70
215_M	322_F	0.721	0.70
313_R	345_R	0.720	0.70
54_E	72_D	0.718	0.69
52_Y	68_E	0.718	0.69
68_E	79_A	0.718	0.69
193_W	347_R	0.718	0.69
110_G	114_L	0.717	0.69
57_G	71_E	0.714	0.69
252_K	255_E	0.712	0.69
61_V	70_T	0.712	0.69
363_S	367_K	0.710	0.69
70_T	77_Q	0.700	0.67
304_E	319_R	0.697	0.67
138_L	175_V	0.697	0.67
105_Y	112_V	0.693	0.67
351_A	360_P	0.692	0.67
354_L	358_R	0.686	0.66
173_K	216_V	0.685	0.66
81_A	89_D	0.685	0.66
143_L	166_E	0.684	0.66
127_I	131_D	0.682	0.65
143_L	168_N	0.681	0.65
176_E	329_T	0.681	0.65
51_E	59_Q	0.679	0.65
151_K	160_F	0.679	0.65
57_G	70_T	0.677	0.65
49_M	55_F	0.676	0.65
48_Q	60_G	0.674	0.65
214_H	217_E	0.673	0.64
185_K	217_E	0.673	0.64
98_I	102_V	0.673	0.64
46_S	64_I	0.673	0.64
145_L	191_T	0.672	0.64
332_L	342_T	0.672	0.64
298_L	327_G	0.670	0.64
61_V	67_N	0.667	0.64
56_L	67_N	0.663	0.63
47_D	52_Y	0.663	0.63
57_G	61_V	0.661	0.63
53_Y	72_D	0.659	0.63
45_E	57_G	0.658	0.63
332_L	343_R	0.656	0.62
64_I	80_K	0.654	0.62
64_I	70_T	0.654	0.62
52_Y	60_G	0.653	0.62
130_G	133_E	0.649	0.62
105_Y	117_A	0.649	0.62
192_W	196_Q	0.649	0.62
105_Y	113_N	0.648	0.61
222_L	257_L	0.646	0.61
51_E	69_E	0.645	0.61
56_L	66_E	0.644	0.61
121_I	181_R	0.643	0.61
293_H	297_E	0.643	0.61
57_G	63_L	0.642	0.61
187_S	214_H	0.642	0.61
187_S	191_T	0.641	0.61
89_D	92_V	0.638	0.60
46_S	69_E	0.638	0.60
59_Q	72_D	0.638	0.60
191_T	204_D	0.636	0.60
59_Q	68_E	0.636	0.60
68_E	75_I	0.635	0.60
253_V	273_E	0.635	0.60
61_V	64_I	0.635	0.60
45_E	72_D	0.634	0.60
114_L	130_G	0.634	0.60
48_Q	53_Y	0.633	0.60
166_E	205_Q	0.633	0.60
172_M	176_E	0.631	0.59
215_M	256_I	0.631	0.59
69_E	75_I	0.628	0.59
266_L	279_G	0.627	0.59
47_D	73_P	0.625	0.59
84_E	89_D	0.624	0.59
110_G	121_I	0.622	0.58
53_Y	58_E	0.620	0.58
66_E	73_P	0.619	0.58
339_F	352_K	0.617	0.58
76_Q	80_K	0.617	0.58
53_Y	66_E	0.616	0.58
76_Q	86_D	0.614	0.57
54_E	68_E	0.613	0.57
147_V	168_N	0.611	0.57
117_A	127_I	0.607	0.57
184_Y	258_K	0.606	0.56
47_D	58_E	0.605	0.56
199_T	214_H	0.604	0.56
48_Q	54_E	0.604	0.56
62_E	65_S	0.604	0.56
50_D	65_S	0.603	0.56
175_V	272_E	0.600	0.56
46_S	59_Q	0.600	0.56
55_F	60_G	0.600	0.56
46_S	50_D	0.599	0.56
235_R	238_T	0.598	0.55
53_Y	62_E	0.598	0.55
101_P	114_L	0.597	0.55
81_A	84_E	0.597	0.55
175_V	291_S	0.596	0.55
154_V	264_V	0.596	0.55
48_Q	61_V	0.594	0.55
194_I	198_I	0.594	0.55
263_P	279_G	0.592	0.55
337_K	340_G	0.592	0.55
303_L	306_V	0.590	0.54
106_L	113_N	0.588	0.54
153_Y	157_G	0.586	0.54
193_W	344_E	0.585	0.54
246_M	316_N	0.585	0.54
59_Q	65_S	0.584	0.54
51_E	67_N	0.583	0.54
115_L	124_A	0.582	0.53
67_N	78_L	0.582	0.53
64_I	73_P	0.576	0.53
45_E	61_V	0.575	0.53
55_F	66_E	0.574	0.52
199_T	204_D	0.572	0.52
55_F	62_E	0.572	0.52
130_G	134_S	0.572	0.52
48_Q	63_L	0.571	0.52
342_T	348_Q	0.570	0.52
302_Q	365_R	0.568	0.52
264_V	268_T	0.567	0.52
48_Q	51_E	0.567	0.52
291_S	358_R	0.564	0.51
60_G	73_P	0.563	0.51
72_D	79_A	0.560	0.51
54_E	65_S	0.555	0.50
47_D	57_G	0.554	0.50
58_E	71_E	0.553	0.50
59_Q	70_T	0.553	0.50
52_Y	77_Q	0.552	0.50
313_R	332_L	0.552	0.50
222_L	225_V	0.552	0.50
61_V	72_D	0.550	0.49
45_E	65_S	0.548	0.49
59_Q	71_E	0.548	0.49
60_G	65_S	0.547	0.49
154_V	216_V	0.547	0.49
178_F	227_R	0.546	0.49
246_M	282_I	0.546	0.49
220_N	223_I	0.545	0.49
127_I	285_Q	0.545	0.49
314_E	352_K	0.544	0.49
101_P	158_M	0.544	0.49
49_M	63_L	0.544	0.49
205_Q	220_N	0.544	0.49
61_V	65_S	0.541	0.48
318_L	351_A	0.541	0.48
51_E	61_V	0.540	0.48
112_V	120_E	0.540	0.48
54_E	61_V	0.540	0.48
71_E	78_L	0.540	0.48
83_E	93_P	0.540	0.48
153_Y	290_P	0.539	0.48
70_T	79_A	0.538	0.48
200_R	331_T	0.538	0.48
45_E	53_Y	0.537	0.48
54_E	70_T	0.535	0.48
82_E	87_L	0.534	0.47
57_G	72_D	0.534	0.47
71_E	77_Q	0.534	0.47
156_R	369_F	0.532	0.47
198_I	206_A	0.530	0.47
46_S	57_G	0.528	0.47
239_P	253_V	0.526	0.46
48_Q	72_D	0.526	0.46
267_E	278_L	0.526	0.46
48_Q	118_K	0.524	0.46
148_S	203_A	0.523	0.46
187_S	213_V	0.522	0.46
66_E	69_E	0.522	0.46
52_Y	56_L	0.522	0.46
261_Q	324_L	0.517	0.45
72_D	80_K	0.516	0.45
214_H	343_R	0.515	0.45
69_E	72_D	0.514	0.45
173_K	197_A	0.514	0.45
57_G	340_G	0.509	0.44
81_A	85_F	0.509	0.44
60_G	70_T	0.508	0.44
191_T	214_H	0.507	0.44
267_E	283_E	0.505	0.44
188_T	215_M	0.505	0.44
305_D	325_D	0.500	0.43
185_K	261_Q	0.500	0.43
333_E	337_K	0.500	0.43

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1l9zH	1	0.7116	100	0.355	Contact Map
2a6hF	1	0.7332	100	0.361	Contact Map
4yfkF	1	0.7385	100	0.367	Contact Map
3ugoA	1	0.2965	100	0.633	Contact Map
1l0oC	1	0.1536	100	0.656	Contact Map
1rp3A	1	0.6173	100	0.682	Contact Map
1sigA	1	0.5256	99.9	0.764	Contact Map
4x8kA	1	0.2453	99.9	0.787	Contact Map
4nqwA	1	0.3989	99.9	0.788	Contact Map
1or7A	2	0.496	99.8	0.814	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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