NUSA - BACSU - GREMLIN Contacts

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NUSA - Transcription termination/antitermination protein NusA

UniProt:	P32727	Sequences: MSSELLDALTILEKEKGISKEIIIEAIEAALISAYKRNFNQAQNVRVDLNRETGSIRVFARKDVVDEVYDQRLEISIEEAQGIHPEYMVGDVVEIEVTPKDFGRIAAQTAKQVVTQRVREAERGVIYSEFIDREEDIMTGIVQRLDNKFIYVSLGKIEALLPVNEQMPNESYKPHDRIKVYITKVEKTTKGPQIYVSRTHPGLLKRLFEIEVPEIYDGTVELKSVAREAGDRSKISVRTDDPDVDPVGSCVGPKGQRVQAIVNELKGEKIDIVNWSSDPVEFVANALSPSKVLDVIVNEEEKATTVIVPDYQLSLAIGKRGQNARLAAKLTGWKIDIKSETDARELGIYPRELEEDDEPLFTEPETAESDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	371 (348)
Sequences:	2043 (1041)
Seq/√Len:	55.8

ECOLI - NUSA
BACSU - NUSA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
310_D	341_T	5.963	1.00
204_L	233_S	5.254	1.00
46_R	94_E	4.960	1.00
206_R	209_E	4.648	1.00
223_K	238_R	4.403	1.00
182_I	194_I	3.873	1.00
180_V	196_V	3.872	1.00
159_A	196_V	3.695	1.00
57_R	96_E	3.656	1.00
63_D	92_V	3.640	1.00
63_D	74_E	3.420	1.00
276_S	281_E	3.398	1.00
312_Q	315_L	3.397	1.00
134_E	184_K	3.360	1.00
298_N	301_E	3.331	1.00
10_T	20_K	3.106	1.00
67_E	78_E	2.989	1.00
172_Y	178_I	2.950	1.00
219_T	244_V	2.856	1.00
129_E	156_K	2.749	1.00
167_M	170_E	2.682	1.00
183_T	200_H	2.592	1.00
69_Y	74_E	2.559	1.00
258_V	272_I	2.516	1.00
235_I	258_V	2.507	1.00
68_V	76_S	2.506	1.00
62_K	95_I	2.473	1.00
236_S	282_F	2.441	1.00
81_Q	88_M	2.343	1.00
208_F	258_V	2.343	1.00
61_R	94_E	2.279	1.00
24_I	51_R	2.229	1.00
75_I	79_E	2.164	1.00
247_V	251_V	2.059	1.00
150_I	172_Y	2.034	1.00
212_V	258_V	1.992	1.00
98_T	101_D	1.986	1.00
223_K	275_W	1.983	1.00
224_S	282_F	1.931	1.00
140_G	152_V	1.924	1.00
162_P	165_E	1.919	1.00
124_G	128_S	1.903	1.00
70_D	73_L	1.891	1.00
283_V	304_T	1.882	1.00
221_E	240_D	1.835	0.99
68_V	74_E	1.815	0.99
275_W	282_F	1.790	0.99
173_K	176_D	1.788	0.99
28_E	51_R	1.775	0.99
127_Y	131_I	1.774	0.99
278_D	281_E	1.768	0.99
46_R	61_R	1.730	0.99
220_V	244_V	1.717	0.99
87_Y	91_D	1.692	0.99
76_S	79_E	1.692	0.99
133_R	136_D	1.685	0.99
212_V	235_I	1.678	0.99
162_P	195_Y	1.674	0.99
152_V	196_V	1.671	0.99
48_D	57_R	1.667	0.99
29_A	117_R	1.657	0.99
309_P	340_E	1.645	0.99
63_D	90_G	1.579	0.98
153_S	156_K	1.531	0.98
302_K	333_W	1.525	0.98
126_I	157_I	1.519	0.98
225_V	233_S	1.513	0.98
77_I	81_Q	1.505	0.98
87_Y	93_V	1.501	0.98
181_Y	202_G	1.496	0.98
10_T	14_K	1.493	0.97
61_R	92_V	1.492	0.97
165_E	183_T	1.472	0.97
273_V	282_F	1.452	0.97
66_D	89_V	1.442	0.97
32_I	45_V	1.439	0.97
127_Y	185_V	1.416	0.97
29_A	33_S	1.416	0.97
307_I	310_D	1.386	0.96
279_P	333_W	1.379	0.96
282_F	330_L	1.378	0.96
105_I	113_V	1.372	0.96
124_G	187_K	1.366	0.96
9_L	13_E	1.359	0.96
343_A	347_G	1.353	0.95
88_M	91_D	1.349	0.95
310_D	339_S	1.342	0.95
79_E	82_G	1.336	0.95
149_F	160_L	1.327	0.95
136_D	206_R	1.323	0.95
228_E	329_K	1.310	0.95
25_E	29_A	1.307	0.95
150_I	166_Q	1.307	0.95
13_E	19_S	1.302	0.94
64_V	80_A	1.274	0.94
84_H	91_D	1.274	0.94
293_L	340_E	1.273	0.94
208_F	222_L	1.261	0.93
138_M	182_I	1.248	0.93
130_F	134_E	1.245	0.93
205_K	209_E	1.239	0.93
143_Q	153_S	1.225	0.92
60_A	95_I	1.224	0.92
103_G	106_A	1.222	0.92
251_V	262_V	1.215	0.92
306_V	335_I	1.212	0.92
202_G	205_K	1.211	0.92
161_L	180_V	1.204	0.92
304_T	331_T	1.199	0.92
228_E	325_R	1.190	0.91
287_L	306_V	1.184	0.91
26_A	117_R	1.184	0.91
276_S	285_N	1.181	0.91
340_E	344_R	1.177	0.91
34_A	120_E	1.172	0.91
181_Y	200_H	1.165	0.90
254_K	259_Q	1.155	0.90
75_I	80_A	1.153	0.90
8_A	12_L	1.151	0.90
64_V	87_Y	1.149	0.90
11_I	15_E	1.148	0.90
6_L	54_G	1.147	0.90
290_S	327_A	1.134	0.89
81_Q	85_P	1.131	0.89
145_L	150_I	1.118	0.88
6_L	49_L	1.118	0.88
141_I	177_R	1.117	0.88
67_E	76_S	1.114	0.88
316_A	327_A	1.112	0.88
66_D	69_Y	1.104	0.88
140_G	180_V	1.103	0.88
306_V	324_A	1.102	0.88
294_D	343_A	1.101	0.88
33_S	36_K	1.100	0.88
47_V	58_V	1.093	0.87
21_E	51_R	1.092	0.87
68_V	71_Q	1.078	0.87
23_I	27_I	1.078	0.87
55_S	233_S	1.077	0.87
142_V	172_Y	1.074	0.86
18_I	276_S	1.066	0.86
277_S	282_F	1.061	0.86
133_R	182_I	1.056	0.85
105_I	108_Q	1.050	0.85
24_I	49_L	1.042	0.85
9_L	24_I	1.041	0.85
77_I	89_V	1.036	0.84
27_I	282_F	1.035	0.84
251_V	258_V	1.033	0.84
19_S	249_S	1.033	0.84
5_L	27_I	1.030	0.84
109_T	113_V	1.018	0.83
127_Y	251_V	1.017	0.83
129_E	155_G	1.013	0.83
284_A	295_V	1.006	0.83
139_T	179_K	1.000	0.82
304_T	333_W	0.996	0.82
83_I	87_Y	0.995	0.82
200_H	205_K	0.994	0.82
85_P	88_M	0.994	0.82
309_P	312_Q	0.990	0.81
170_E	198_R	0.990	0.81
247_V	262_V	0.989	0.81
117_R	120_E	0.987	0.81
183_T	195_Y	0.984	0.81
204_L	225_V	0.981	0.81
70_D	74_E	0.980	0.81
161_L	196_V	0.977	0.81
138_M	180_V	0.972	0.80
314_S	325_R	0.960	0.79
58_V	98_T	0.954	0.79
84_H	87_Y	0.952	0.79
28_E	48_D	0.949	0.79
6_L	51_R	0.948	0.79
165_E	200_H	0.947	0.79
224_S	275_W	0.940	0.78
145_L	174_P	0.932	0.77
21_E	25_E	0.927	0.77
157_I	194_I	0.926	0.77
121_A	124_G	0.924	0.77
238_R	277_S	0.924	0.77
80_A	83_I	0.922	0.77
80_A	93_V	0.919	0.76
343_A	348_I	0.917	0.76
30_A	113_V	0.916	0.76
166_Q	172_Y	0.916	0.76
22_I	26_A	0.912	0.76
5_L	38_N	0.912	0.76
342_D	345_E	0.907	0.75
20_K	24_I	0.902	0.75
256_Q	260_A	0.901	0.75
84_H	88_M	0.899	0.75
119_R	272_I	0.897	0.75
44_N	61_R	0.892	0.74
236_S	330_L	0.891	0.74
338_K	346_L	0.890	0.74
309_P	341_T	0.889	0.74
345_E	348_I	0.882	0.73
119_R	122_E	0.874	0.73
253_P	259_Q	0.873	0.73
145_L	175_H	0.871	0.72
128_S	131_I	0.870	0.72
212_V	261_I	0.869	0.72
312_Q	337_I	0.866	0.72
341_T	345_E	0.866	0.72
307_I	338_K	0.865	0.72
77_I	80_A	0.862	0.72
247_V	274_N	0.861	0.72
79_E	85_P	0.856	0.71
259_Q	263_N	0.856	0.71
91_D	138_M	0.855	0.71
167_M	233_S	0.853	0.71
295_V	304_T	0.852	0.71
65_V	89_V	0.849	0.70
16_K	122_E	0.847	0.70
292_V	308_V	0.846	0.70
152_V	178_I	0.845	0.70
196_V	223_K	0.843	0.70
39_F	44_N	0.843	0.70
121_A	193_Q	0.840	0.70
142_V	145_L	0.837	0.69
215_I	222_L	0.837	0.69
31_L	47_V	0.835	0.69
129_E	133_R	0.834	0.69
165_E	195_Y	0.834	0.69
12_L	157_I	0.828	0.69
212_V	272_I	0.828	0.69
235_I	261_I	0.826	0.68
116_Q	122_E	0.823	0.68
293_L	309_P	0.822	0.68
173_K	299_E	0.822	0.68
204_L	270_I	0.821	0.68
29_A	112_Q	0.817	0.68
149_F	161_L	0.814	0.67
152_V	180_V	0.814	0.67
231_D	322_Q	0.813	0.67
201_P	329_K	0.813	0.67
315_L	336_D	0.809	0.67
307_I	339_S	0.805	0.66
205_K	225_V	0.803	0.66
13_E	20_K	0.800	0.66
31_L	275_W	0.800	0.66
33_S	113_V	0.796	0.66
180_V	203_L	0.795	0.65
131_I	134_E	0.792	0.65
313_L	339_S	0.784	0.64
127_Y	130_F	0.775	0.63
75_I	93_V	0.774	0.63
267_G	295_V	0.771	0.63
77_I	84_H	0.770	0.63
229_A	233_S	0.767	0.63
313_L	328_A	0.763	0.62
290_S	316_A	0.761	0.62
127_Y	187_K	0.760	0.62
83_I	95_I	0.757	0.62
283_V	331_T	0.757	0.62
198_R	207_L	0.756	0.61
228_E	322_Q	0.745	0.60
27_I	114_V	0.742	0.60
281_E	284_A	0.741	0.60
219_T	241_D	0.740	0.60
155_G	191_G	0.739	0.60
80_A	87_Y	0.736	0.59
304_T	320_R	0.730	0.59
114_V	267_G	0.730	0.59
113_V	121_A	0.729	0.59
37_R	109_T	0.729	0.59
9_L	20_K	0.727	0.58
29_A	109_T	0.726	0.58
281_E	285_N	0.725	0.58
328_A	334_K	0.725	0.58
179_K	304_T	0.724	0.58
79_E	83_I	0.723	0.58
215_I	250_C	0.722	0.58
157_I	175_H	0.721	0.58
77_I	83_I	0.720	0.58
54_G	112_Q	0.720	0.58
167_M	204_L	0.716	0.57
25_E	28_E	0.711	0.57
28_E	31_L	0.710	0.57
6_L	53_T	0.709	0.57
152_V	194_I	0.709	0.57
249_S	269_K	0.708	0.56
294_D	307_I	0.705	0.56
204_L	231_D	0.704	0.56
296_I	305_T	0.703	0.56
64_V	77_I	0.701	0.56
290_S	324_A	0.699	0.56
35_Y	99_P	0.696	0.55
67_E	233_S	0.696	0.55
126_I	156_K	0.695	0.55
77_I	93_V	0.692	0.55
201_P	258_V	0.691	0.55
17_G	171_S	0.690	0.55
13_E	229_A	0.689	0.54
123_R	232_R	0.688	0.54
221_E	292_V	0.688	0.54
347_G	350_P	0.686	0.54
167_M	256_Q	0.686	0.54
144_R	151_Y	0.686	0.54
303_A	334_K	0.685	0.54
20_K	229_A	0.684	0.54
259_Q	290_S	0.684	0.54
13_E	324_A	0.683	0.54
33_S	109_T	0.682	0.54
239_T	244_V	0.681	0.54
180_V	251_V	0.680	0.53
31_L	56_I	0.676	0.53
154_L	159_A	0.676	0.53
70_D	185_V	0.673	0.53
78_E	81_Q	0.673	0.53
226_A	265_L	0.670	0.52
132_D	157_I	0.669	0.52
19_S	22_I	0.666	0.52
123_R	203_L	0.665	0.52
221_E	238_R	0.665	0.52
246_P	274_N	0.663	0.52
208_F	261_I	0.663	0.52
307_I	342_D	0.661	0.51
6_L	26_A	0.661	0.51
169_N	249_S	0.660	0.51
182_I	185_V	0.659	0.51
20_K	51_R	0.658	0.51
208_F	262_V	0.657	0.51
137_I	140_G	0.655	0.51
81_Q	87_Y	0.654	0.51
139_T	291_K	0.653	0.51
274_N	281_E	0.653	0.51
274_N	285_N	0.652	0.50
233_S	292_V	0.649	0.50
220_V	295_V	0.646	0.50
314_S	321_G	0.644	0.50
56_I	115_T	0.643	0.49
132_D	145_L	0.643	0.49
84_H	133_R	0.642	0.49
38_N	45_V	0.642	0.49
32_I	36_K	0.640	0.49
19_S	85_P	0.638	0.49
122_E	155_G	0.637	0.49
198_R	246_P	0.635	0.49
65_V	90_G	0.633	0.48
88_M	92_V	0.633	0.48
54_G	117_R	0.633	0.48
85_P	277_S	0.632	0.48
23_I	26_A	0.630	0.48
233_S	283_V	0.629	0.48
35_Y	45_V	0.626	0.48
262_V	269_K	0.625	0.48
288_S	291_K	0.624	0.47
28_E	54_G	0.623	0.47
185_V	194_I	0.623	0.47
251_V	296_I	0.622	0.47
46_R	224_S	0.621	0.47
8_A	35_Y	0.620	0.47
99_P	278_D	0.619	0.47
114_V	238_R	0.619	0.47
170_E	191_G	0.617	0.47
212_V	335_I	0.617	0.47
285_N	288_S	0.617	0.47
72_R	75_I	0.614	0.46
201_P	229_A	0.614	0.46
158_E	259_Q	0.614	0.46
263_N	267_G	0.613	0.46
17_G	129_E	0.611	0.46
96_E	261_I	0.611	0.46
116_Q	190_K	0.610	0.46
14_K	127_Y	0.609	0.46
267_G	282_F	0.608	0.46
106_A	109_T	0.608	0.46
148_K	212_V	0.608	0.46
40_N	135_E	0.607	0.46
251_V	319_K	0.605	0.45
17_G	125_V	0.603	0.45
313_L	337_I	0.602	0.45
144_R	220_V	0.602	0.45
55_S	89_V	0.601	0.45
54_G	122_E	0.600	0.45
5_L	210_I	0.599	0.45
103_G	110_A	0.598	0.45
228_E	314_S	0.598	0.45
312_Q	322_Q	0.598	0.45
50_N	79_E	0.597	0.45
30_A	120_E	0.596	0.44
152_V	263_N	0.595	0.44
26_A	121_A	0.594	0.44
154_L	345_E	0.593	0.44
185_V	220_V	0.593	0.44
182_I	340_E	0.592	0.44
231_D	263_N	0.589	0.44
5_L	151_Y	0.589	0.44
214_E	257_R	0.587	0.43
217_D	239_T	0.586	0.43
204_L	208_F	0.584	0.43
43_Q	62_K	0.583	0.43
110_A	228_E	0.583	0.43
112_Q	117_R	0.582	0.43
42_A	225_V	0.581	0.43
57_R	274_N	0.581	0.43
5_L	202_G	0.581	0.43
66_D	76_S	0.580	0.43
23_I	279_P	0.580	0.43
17_G	146_D	0.580	0.43
175_H	249_S	0.579	0.43
142_V	176_D	0.579	0.43
110_A	114_V	0.578	0.42
240_D	293_L	0.578	0.42
29_A	32_I	0.576	0.42
305_T	336_D	0.576	0.42
66_D	71_Q	0.576	0.42
346_L	350_P	0.575	0.42
112_Q	278_D	0.575	0.42
339_S	342_D	0.574	0.42
48_D	51_R	0.574	0.42
131_I	185_V	0.574	0.42
307_I	343_A	0.574	0.42
232_R	315_L	0.574	0.42
121_A	258_V	0.572	0.42
299_E	333_W	0.571	0.42
23_I	249_S	0.569	0.42
225_V	261_I	0.569	0.42
167_M	203_L	0.568	0.41
112_Q	258_V	0.568	0.41
284_A	333_W	0.568	0.41
277_S	281_E	0.567	0.41
120_E	259_Q	0.567	0.41
27_I	312_Q	0.566	0.41
231_D	320_R	0.566	0.41
76_S	182_I	0.566	0.41
254_K	273_V	0.563	0.41
18_I	24_I	0.563	0.41
204_L	235_I	0.562	0.41
327_A	331_T	0.559	0.40
31_L	35_Y	0.557	0.40
131_I	194_I	0.555	0.40
35_Y	38_N	0.555	0.40
236_S	275_W	0.553	0.40
218_G	240_D	0.553	0.40
81_Q	84_H	0.553	0.40
110_A	113_V	0.552	0.40
118_V	148_K	0.552	0.40
283_V	306_V	0.551	0.40
49_L	93_V	0.549	0.39
145_L	149_F	0.546	0.39
162_P	213_P	0.546	0.39
30_A	107_A	0.545	0.39
136_D	150_I	0.544	0.39
26_A	267_G	0.544	0.39
48_D	94_E	0.543	0.39
134_E	182_I	0.543	0.39
20_K	33_S	0.542	0.39
59_F	96_E	0.541	0.39
130_F	171_S	0.540	0.39
80_A	251_V	0.538	0.38
219_T	239_T	0.538	0.38
187_K	278_D	0.537	0.38
125_V	129_E	0.536	0.38
238_R	282_F	0.536	0.38
133_R	180_V	0.534	0.38
110_A	116_Q	0.533	0.38
36_K	171_S	0.533	0.38
148_K	282_F	0.533	0.38
42_A	81_Q	0.533	0.38
115_T	120_E	0.532	0.38
245_D	254_K	0.531	0.38
30_A	109_T	0.529	0.37
208_F	215_I	0.529	0.37
280_V	296_I	0.529	0.37
49_L	290_S	0.528	0.37
18_I	23_I	0.528	0.37
155_G	159_A	0.527	0.37
31_L	331_T	0.526	0.37
18_I	131_I	0.525	0.37
117_R	130_F	0.524	0.37
261_I	279_P	0.523	0.37
226_A	235_I	0.523	0.37
106_A	110_A	0.523	0.37
317_I	321_G	0.522	0.37
150_I	176_D	0.522	0.37
199_T	265_L	0.522	0.37
64_V	83_I	0.521	0.37
54_G	107_A	0.520	0.36
253_P	256_Q	0.520	0.36
111_K	322_Q	0.520	0.36
124_G	275_W	0.518	0.36
142_V	212_V	0.517	0.36
35_Y	58_V	0.517	0.36
139_T	177_R	0.517	0.36
244_V	249_S	0.516	0.36
14_K	337_I	0.516	0.36
133_R	192_P	0.516	0.36
208_F	272_I	0.515	0.36
75_I	81_Q	0.515	0.36
122_E	207_L	0.515	0.36
224_S	236_S	0.515	0.36
6_L	56_I	0.515	0.36
46_R	59_F	0.514	0.36
287_L	335_I	0.514	0.36
108_Q	144_R	0.514	0.36
138_M	175_H	0.513	0.36
246_P	255_G	0.513	0.36
96_E	167_M	0.513	0.36
33_S	105_I	0.513	0.36
37_R	112_Q	0.512	0.36
144_R	262_V	0.512	0.36
254_K	319_K	0.512	0.36
22_I	121_A	0.511	0.36
161_L	244_V	0.511	0.36
26_A	146_D	0.511	0.36
105_I	110_A	0.510	0.35
251_V	255_G	0.509	0.35
282_F	331_T	0.509	0.35
238_R	275_W	0.509	0.35
12_L	58_V	0.508	0.35
190_K	272_I	0.507	0.35
267_G	302_K	0.506	0.35
9_L	51_R	0.505	0.35
30_A	333_W	0.503	0.35
176_D	266_K	0.503	0.35
344_R	347_G	0.502	0.35
13_E	27_I	0.501	0.35
193_Q	233_S	0.501	0.35
279_P	304_T	0.500	0.35

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
1k0rA	1	0.841	100	0.156	Contact Map
1hh2P	2	0.9245	100	0.181	Contact Map
4mtnA	1	0.9084	100	0.199	Contact Map
2asbA	1	0.5849	100	0.374	Contact Map
2cxcA	1	0.3666	100	0.709	Contact Map
2kwpA	1	0.3477	100	0.725	Contact Map
2mt4A	1	0.3342	100	0.733	Contact Map
2qndA	2	0.3612	99.5	0.875	Contact Map
4q7jD	1	0.4447	99.5	0.876	Contact Map
4aybE	1	0.3827	98.5	0.919	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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