SIGI - BACSU - GREMLIN Contacts

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SIGI - RNA polymerase sigma factor SigI

UniProt:	O31654	Sequences: MKPVLSLLFKLGKKKQTLEKAVESIQKGNKDLQNELIQQYKPFIAKTVSSVCKRYIDEKDDEFSIGLIAFNEAIEKYSPEKGNSLLAFAELIIKRKVIDYIRKEARSAQNINIDLQEGDDQESSQSLIEAELSIDEYRRQIEQEQRREEILYFQKQLKDYGLSFKELLENSPKHTDARQNAIKVAMTLVEHEELAAILYTKKQLPVKQLEQLVSVSRKTIERNRKYIIAMCIIITGDYIYLKDYLKGVLHS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	251 (227)
Sequences:	300 (256)
Seq/√Len:	17.0

BACSU - SIGI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
198_L	228_I	5.505	1.00
48_V	66_G	4.445	1.00
33_Q	75_E	3.767	1.00
24_S	29_N	3.590	1.00
191_H	212_L	3.401	0.99
33_Q	71_N	3.241	0.99
56_I	63_F	3.102	0.99
162_L	228_I	3.084	0.99
188_L	231_C	2.965	0.98
150_I	164_F	2.903	0.98
21_A	25_I	2.887	0.98
25_I	32_L	2.820	0.98
97_V	101_I	2.803	0.98
206_V	220_I	2.801	0.98
188_L	209_L	2.752	0.98
72_E	96_K	2.713	0.97
82_G	238_Y	2.638	0.97
88_F	95_R	2.614	0.97
160_Y	197_I	2.563	0.96
175_T	179_Q	2.543	0.96
99_D	102_R	2.433	0.95
25_I	29_N	2.224	0.92
230_M	245_L	2.210	0.91
44_I	70_F	2.202	0.91
77_Y	233_I	2.191	0.91
219_T	223_N	2.151	0.90
164_F	233_I	1.953	0.85
54_R	60_D	1.921	0.84
157_L	162_L	1.898	0.84
146_R	244_Y	1.799	0.80
52_C	137_Y	1.670	0.75
25_I	36_L	1.649	0.74
63_F	223_N	1.616	0.72
21_A	32_L	1.613	0.72
33_Q	74_I	1.579	0.70
146_R	240_Y	1.577	0.70
160_Y	199_Y	1.576	0.70
58_E	63_F	1.544	0.69
177_A	195_A	1.544	0.69
221_E	224_R	1.482	0.65
186_M	191_H	1.465	0.64
112_N	116_Q	1.417	0.62
71_N	75_E	1.391	0.60
99_D	224_R	1.381	0.60
43_F	98_I	1.380	0.60
46_K	225_K	1.354	0.58
66_G	97_V	1.339	0.57
60_D	171_S	1.319	0.56
162_L	198_L	1.319	0.56
25_I	37_I	1.313	0.56
217_R	221_E	1.301	0.55
22_V	86_L	1.301	0.55
193_E	208_Q	1.294	0.55
27_K	153_F	1.286	0.54
117_E	230_M	1.284	0.54
32_L	37_I	1.279	0.54
181_A	223_N	1.273	0.53
36_L	177_A	1.269	0.53
181_A	227_I	1.264	0.53
68_I	92_I	1.224	0.50
40_Y	86_L	1.213	0.50
55_Y	77_Y	1.210	0.50
204_L	217_R	1.199	0.49
156_Q	159_D	1.191	0.48
159_D	202_K	1.188	0.48
140_Q	143_Q	1.186	0.48
210_E	217_R	1.174	0.47
65_I	206_V	1.172	0.47
187_T	209_L	1.171	0.47
181_A	216_S	1.145	0.46
156_Q	238_Y	1.134	0.45
37_I	44_I	1.130	0.45
166_E	170_N	1.129	0.45
101_I	223_N	1.125	0.45
184_V	215_V	1.119	0.44
94_K	163_S	1.119	0.44
240_Y	244_Y	1.111	0.44
101_I	222_R	1.100	0.43
96_K	161_G	1.091	0.43
65_I	133_S	1.090	0.42
77_Y	239_I	1.085	0.42
146_R	178_R	1.077	0.42
56_I	223_N	1.069	0.41
77_Y	136_E	1.056	0.41
53_K	92_I	1.050	0.40
42_P	46_K	1.049	0.40
188_L	194_L	1.048	0.40
76_K	95_R	1.043	0.40
95_R	223_N	1.040	0.40
191_H	194_L	1.037	0.39
149_E	240_Y	1.034	0.39
91_L	95_R	1.034	0.39
35_E	39_Q	1.025	0.39
85_L	92_I	1.025	0.39
194_L	209_L	1.020	0.38
164_F	222_R	1.019	0.38
160_Y	209_L	1.016	0.38
91_L	232_I	1.009	0.38
133_S	178_R	1.006	0.38
51_V	97_V	1.005	0.38
49_S	55_Y	1.003	0.37
113_I	153_F	0.998	0.37
149_E	222_R	0.994	0.37
177_A	181_A	0.989	0.37
36_L	128_I	0.981	0.36
166_E	234_I	0.979	0.36
133_S	146_R	0.974	0.36
188_L	195_A	0.972	0.36
204_L	216_S	0.971	0.36
176_D	219_T	0.967	0.35
175_T	220_I	0.965	0.35
133_S	226_Y	0.964	0.35
81_K	192_E	0.963	0.35
99_D	221_E	0.954	0.35
92_I	167_L	0.953	0.35
21_A	39_Q	0.951	0.35
48_V	68_I	0.948	0.34
61_D	68_I	0.947	0.34
20_K	120_D	0.944	0.34
22_V	226_Y	0.942	0.34
77_Y	116_Q	0.931	0.34
71_N	176_D	0.929	0.33
66_G	239_I	0.923	0.33
189_V	233_I	0.919	0.33
106_R	143_Q	0.917	0.33
59_K	233_I	0.916	0.33
144_E	184_V	0.915	0.33
220_I	230_M	0.912	0.33
58_E	168_L	0.909	0.32
228_I	231_C	0.907	0.32
77_Y	90_E	0.906	0.32
34_N	236_G	0.904	0.32
77_Y	208_Q	0.903	0.32
37_I	90_E	0.901	0.32
62_E	65_I	0.896	0.32
223_N	226_Y	0.889	0.31
199_Y	232_I	0.876	0.31
140_Q	160_Y	0.875	0.31
28_G	71_N	0.870	0.30
153_F	238_Y	0.869	0.30
110_N	175_T	0.868	0.30
37_I	48_V	0.867	0.30
198_L	231_C	0.866	0.30
27_K	175_T	0.864	0.30
174_H	178_R	0.862	0.30
40_Y	219_T	0.859	0.30
147_R	243_D	0.851	0.29
40_Y	46_K	0.851	0.29
104_E	107_S	0.850	0.29
99_D	244_Y	0.849	0.29
177_A	219_T	0.843	0.29
58_E	133_S	0.843	0.29
96_K	228_I	0.841	0.29
42_P	88_F	0.839	0.29
113_I	238_Y	0.835	0.29
157_L	187_T	0.829	0.28
68_I	240_Y	0.828	0.28
177_A	180_N	0.826	0.28
27_K	103_K	0.819	0.28
178_R	216_S	0.810	0.27
20_K	119_D	0.809	0.27
177_A	231_C	0.809	0.27
206_V	218_K	0.803	0.27
28_G	185_A	0.801	0.27
45_A	63_F	0.799	0.27
97_V	213_V	0.799	0.27
20_K	24_S	0.796	0.27
226_Y	235_T	0.796	0.27
237_D	243_D	0.793	0.27
176_D	182_I	0.792	0.27
111_I	166_E	0.791	0.27
26_Q	63_F	0.787	0.26
77_Y	134_I	0.786	0.26
101_I	166_E	0.781	0.26
98_I	102_R	0.778	0.26
158_K	161_G	0.778	0.26
181_A	213_V	0.771	0.26
104_E	113_I	0.770	0.26
92_I	96_K	0.770	0.26
143_Q	196_A	0.770	0.26
42_P	86_L	0.767	0.25
72_E	92_I	0.765	0.25
216_S	226_Y	0.764	0.25
55_Y	82_G	0.762	0.25
23_E	77_Y	0.761	0.25
65_I	220_I	0.761	0.25
238_Y	242_K	0.760	0.25
184_V	220_I	0.760	0.25
105_A	171_S	0.755	0.25
184_V	202_K	0.754	0.25
26_Q	239_I	0.753	0.25
52_C	239_I	0.753	0.25
41_K	223_N	0.750	0.25
44_I	238_Y	0.747	0.25
169_E	215_V	0.745	0.24
60_D	89_A	0.743	0.24
43_F	70_F	0.742	0.24
45_A	137_Y	0.739	0.24
39_Q	75_E	0.737	0.24
57_D	108_A	0.735	0.24
97_V	125_Q	0.733	0.24
76_K	88_F	0.727	0.24
134_I	194_L	0.723	0.23
17_T	35_E	0.720	0.23
41_K	217_R	0.719	0.23
90_E	94_K	0.718	0.23
37_I	70_F	0.717	0.23
80_E	209_L	0.714	0.23
36_L	181_A	0.712	0.23
56_I	216_S	0.710	0.23
146_R	217_R	0.707	0.23
234_I	237_D	0.706	0.23
83_N	241_L	0.706	0.23
25_I	223_N	0.699	0.22
195_A	231_C	0.699	0.22
61_D	198_L	0.698	0.22
26_Q	78_S	0.696	0.22
215_V	222_R	0.695	0.22
64_S	71_N	0.692	0.22
17_T	37_I	0.689	0.22
45_A	223_N	0.688	0.22
113_I	232_I	0.688	0.22
169_E	194_L	0.685	0.22
105_A	154_Q	0.682	0.22
153_F	162_L	0.682	0.22
107_S	202_K	0.680	0.22
171_S	234_I	0.679	0.22
168_L	171_S	0.678	0.22
196_A	200_T	0.678	0.22
191_H	228_I	0.677	0.22
87_A	100_Y	0.674	0.21
194_L	225_K	0.674	0.21
214_S	220_I	0.670	0.21
63_F	174_H	0.666	0.21
205_P	225_K	0.665	0.21
63_F	100_Y	0.660	0.21
64_S	67_L	0.654	0.21
61_D	153_F	0.653	0.21
171_S	217_R	0.647	0.20
29_N	48_V	0.647	0.20
176_D	223_N	0.645	0.20
35_E	135_D	0.641	0.20
48_V	97_V	0.639	0.20
19_E	26_Q	0.635	0.20
136_E	193_E	0.633	0.20
79_P	242_K	0.632	0.20
195_A	235_T	0.632	0.20
20_K	191_H	0.629	0.20
34_N	83_N	0.629	0.20
46_K	219_T	0.625	0.20
129_E	211_Q	0.621	0.19
47_T	71_N	0.620	0.19
52_C	181_A	0.620	0.19
33_Q	162_L	0.619	0.19
23_E	44_I	0.616	0.19
90_E	95_R	0.616	0.19
161_G	168_L	0.616	0.19
98_I	244_Y	0.615	0.19
200_T	245_L	0.613	0.19
36_L	143_Q	0.611	0.19
163_S	187_T	0.611	0.19
100_Y	188_L	0.604	0.19
37_I	244_Y	0.603	0.19
33_Q	243_D	0.602	0.19
50_S	94_K	0.601	0.19
120_D	134_I	0.598	0.19
136_E	208_Q	0.598	0.19
180_N	215_V	0.598	0.19
94_K	98_I	0.597	0.19
118_G	121_Q	0.597	0.19
61_D	224_R	0.597	0.19
67_L	241_L	0.594	0.18
171_S	241_L	0.594	0.18
44_I	82_G	0.594	0.18
125_Q	230_M	0.594	0.18
142_E	147_R	0.592	0.18
153_F	157_L	0.588	0.18
154_Q	238_Y	0.588	0.18
155_K	211_Q	0.587	0.18
65_I	225_K	0.586	0.18
22_V	127_L	0.585	0.18
107_S	110_N	0.582	0.18
176_D	181_A	0.581	0.18
17_T	235_T	0.581	0.18
137_Y	225_K	0.579	0.18
42_P	61_D	0.579	0.18
115_L	128_I	0.576	0.18
33_Q	167_L	0.576	0.18
87_A	238_Y	0.574	0.18
210_E	226_Y	0.573	0.18
156_Q	164_F	0.572	0.18
72_E	215_V	0.568	0.17
165_K	193_E	0.568	0.17
78_S	84_S	0.567	0.17
101_I	243_D	0.563	0.17
26_Q	60_D	0.561	0.17
26_Q	29_N	0.561	0.17
95_R	219_T	0.560	0.17
67_L	129_E	0.559	0.17
91_L	166_E	0.557	0.17
146_R	164_F	0.554	0.17
66_G	163_S	0.554	0.17
177_A	216_S	0.553	0.17
102_R	229_A	0.551	0.17
186_M	190_E	0.550	0.17
65_I	175_T	0.549	0.17
63_F	219_T	0.549	0.17
19_E	66_G	0.546	0.17
40_Y	101_I	0.546	0.17
41_K	226_Y	0.545	0.17
155_K	245_L	0.545	0.17
183_K	192_E	0.543	0.17
52_C	62_E	0.541	0.17
28_G	219_T	0.541	0.17
137_Y	233_I	0.541	0.17
28_G	129_E	0.540	0.17
80_E	215_V	0.539	0.17
105_A	135_D	0.539	0.17
31_D	131_E	0.538	0.16
154_Q	226_Y	0.537	0.16
160_Y	196_A	0.533	0.16
40_Y	84_S	0.532	0.16
58_E	223_N	0.529	0.16
48_V	95_R	0.526	0.16
75_E	232_I	0.524	0.16
121_Q	175_T	0.524	0.16
106_R	152_Y	0.524	0.16
94_K	244_Y	0.516	0.16
184_V	208_Q	0.515	0.16
163_S	168_L	0.515	0.16
184_V	228_I	0.513	0.16
112_N	115_L	0.512	0.16
22_V	28_G	0.512	0.16
97_V	177_A	0.510	0.16
121_Q	136_E	0.508	0.16
154_Q	224_R	0.507	0.15
183_K	191_H	0.506	0.15
125_Q	179_Q	0.505	0.15
98_I	221_E	0.500	0.15
116_Q	119_D	0.500	0.15

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
1l0oC	1	0.1514	99.4	0.838	Contact Map
4yfkF	1	0.9522	99.3	0.849	Contact Map
4nqwA	1	0.5896	99.3	0.85	Contact Map
1rp3A	1	0.8446	99.2	0.855	Contact Map
1l9zH	1	0.9283	99.2	0.856	Contact Map
2a6hF	1	0.9163	99.2	0.857	Contact Map
1or7A	2	0.7251	99.1	0.862	Contact Map
2q1zA	1	0.6972	99	0.867	Contact Map
1sigA	1	0.4104	98.9	0.869	Contact Map
4x8kA	1	0.4143	98.9	0.87	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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