DDG - ECOLI - GREMLIN Contacts

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DDG - Protein Ddg

UniProt:	P0ACV2	Sequences: MFPQCKFSREFLHPRYWLTWFGLGVLWLWVQLPYPVLCFLGTRIGAMARPFLKRRESIARKNLELCFPQHSAEEREKMIAENFRSLGMALVETGMAWFWPDSRVRKWFDVEGLDNLKRAQMQNRGVMVVGVHFMSLELGGRVMGLCQPMMATYRPHNNQLMEWVQTRGRMRSNKAMIGRNNLRGIVGALKKGEAVWFAPDQDYGRKGSSFAPFFAVENVATTNGTYVLSRLSGAAMLTVTMVRKADYSGYRLFITPEMEGYPTDENQAAAYMNKIIEKEIMRAPEQYLWIHRRFKTRPVGESSLYI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12901
Length:	306 (279)
Sequences:	4319 (3101)
Seq/√Len:	185.6

ECOLI - DDG HTRB MSBB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
270_A	274_K	3.926	1.00
111_E	251_R	3.897	1.00
109_D	251_R	3.685	1.00
111_E	253_F	3.296	1.00
244_K	251_R	3.014	1.00
60_R	79_I	2.830	1.00
60_R	76_E	2.775	1.00
81_E	285_E	2.763	1.00
212_P	217_E	2.725	1.00
71_S	74_E	2.722	1.00
115_N	256_P	2.689	1.00
46_A	84_R	2.682	1.00
212_P	270_A	2.649	1.00
113_L	117_K	2.587	1.00
70_H	74_E	2.552	1.00
274_K	277_E	2.490	1.00
63_L	75_R	2.460	1.00
69_Q	281_M	2.366	1.00
64_E	75_R	2.271	1.00
221_T	273_N	2.249	1.00
41_G	87_G	2.200	1.00
117_K	121_M	2.185	1.00
112_G	115_N	2.173	1.00
188_A	193_E	2.125	1.00
33_P	36_V	2.123	1.00
65_L	216_V	2.095	1.00
150_M	193_E	2.087	1.00
114_D	118_R	2.068	1.00
255_T	275_I	2.064	1.00
70_H	78_M	2.056	1.00
115_N	118_R	2.051	1.00
58_I	292_R	1.983	1.00
214_F	277_E	1.975	1.00
238_T	255_T	1.923	1.00
242_V	251_R	1.908	1.00
242_V	283_A	1.907	1.00
61_K	64_E	1.877	1.00
155_P	178_G	1.846	1.00
42_T	84_R	1.810	1.00
64_E	72_A	1.803	1.00
163_W	167_R	1.801	1.00
124_R	235_A	1.788	1.00
210_F	217_E	1.784	1.00
67_F	70_H	1.776	1.00
266_N	270_A	1.757	1.00
238_T	257_E	1.754	1.00
211_A	270_A	1.734	1.00
109_D	249_G	1.716	1.00
264_D	267_Q	1.709	1.00
92_E	243_R	1.707	1.00
59_A	79_I	1.702	1.00
209_S	269_A	1.649	1.00
211_A	273_N	1.634	1.00
131_V	276_I	1.617	1.00
49_R	56_E	1.543	1.00
275_I	278_K	1.542	1.00
119_A	237_L	1.510	1.00
242_V	253_F	1.497	1.00
115_N	237_L	1.494	1.00
118_R	122_Q	1.474	1.00
186_V	190_K	1.472	1.00
74_E	77_K	1.441	1.00
77_K	81_E	1.437	1.00
237_L	254_I	1.429	1.00
150_M	188_A	1.411	1.00
271_Y	275_I	1.405	1.00
185_I	195_V	1.397	1.00
255_T	278_K	1.396	1.00
59_A	82_N	1.381	1.00
60_R	64_E	1.375	1.00
216_V	297_R	1.374	1.00
245_A	249_G	1.357	1.00
27_W	31_Q	1.356	1.00
60_R	75_R	1.354	1.00
99_W	103_R	1.335	1.00
42_T	88_M	1.332	1.00
175_A	184_G	1.326	1.00
277_E	281_M	1.317	1.00
263_T	268_A	1.306	1.00
154_R	157_N	1.300	1.00
74_E	78_M	1.291	1.00
103_R	107_W	1.290	1.00
57_S	61_K	1.287	1.00
49_R	80_A	1.283	1.00
41_G	45_G	1.280	1.00
166_T	170_M	1.279	1.00
37_L	91_V	1.272	1.00
124_R	233_G	1.264	1.00
70_H	75_R	1.264	1.00
47_M	51_F	1.263	1.00
240_T	279_E	1.263	1.00
66_C	294_F	1.252	1.00
35_P	39_F	1.249	1.00
118_R	121_M	1.241	1.00
212_P	274_K	1.232	1.00
210_F	220_A	1.227	1.00
127_M	234_A	1.213	1.00
214_F	281_M	1.212	1.00
276_I	280_I	1.211	1.00
128_V	239_V	1.208	1.00
240_T	255_T	1.197	1.00
271_Y	274_K	1.194	1.00
39_F	43_R	1.190	1.00
105_R	145_L	1.186	1.00
210_F	298_P	1.180	1.00
53_K	56_E	1.177	1.00
187_G	191_K	1.173	1.00
101_D	105_R	1.170	1.00
126_V	194_A	1.168	1.00
226_Y	269_A	1.162	1.00
126_V	235_A	1.158	1.00
238_T	258_M	1.149	1.00
162_E	166_T	1.139	1.00
244_K	249_G	1.129	1.00
78_M	285_E	1.127	1.00
253_F	282_R	1.126	1.00
153_Y	176_M	1.117	1.00
49_R	79_I	1.117	1.00
150_M	177_I	1.113	1.00
229_S	236_M	1.112	1.00
245_A	248_S	1.110	1.00
175_A	193_E	1.109	1.00
152_T	185_I	1.105	1.00
56_E	60_R	1.105	1.00
109_D	244_K	1.105	1.00
243_R	286_Q	1.092	1.00
265_E	268_A	1.084	1.00
117_K	120_Q	1.069	1.00
244_K	247_Y	1.064	1.00
202_D	296_T	1.061	1.00
184_G	187_G	1.056	1.00
238_T	275_I	1.056	1.00
43_R	47_M	1.051	1.00
34_Y	38_C	1.049	1.00
128_V	194_A	1.043	1.00
240_T	275_I	1.040	1.00
39_F	42_T	1.038	1.00
129_V	272_M	1.038	1.00
152_T	197_F	1.036	1.00
217_E	298_P	1.034	1.00
201_Q	291_H	1.032	1.00
122_Q	235_A	1.022	1.00
283_A	286_Q	1.014	1.00
278_K	281_M	1.013	1.00
23_L	27_W	1.003	0.99
38_C	88_M	0.998	0.99
63_L	79_I	0.995	0.99
53_K	57_S	0.994	0.99
35_P	38_C	0.993	0.99
59_A	290_I	0.985	0.99
255_T	279_E	0.975	0.99
219_V	293_R	0.972	0.99
56_E	83_F	0.971	0.99
115_N	119_A	0.961	0.99
260_G	263_T	0.948	0.99
67_F	75_R	0.948	0.99
23_L	164_V	0.945	0.99
140_G	151_A	0.944	0.99
199_P	225_T	0.939	0.99
66_C	214_F	0.934	0.99
279_E	282_R	0.927	0.99
156_H	165_Q	0.926	0.99
61_K	65_L	0.925	0.99
274_K	278_K	0.924	0.99
86_L	290_I	0.922	0.99
233_G	262_P	0.921	0.99
46_A	80_A	0.919	0.99
85_S	88_M	0.917	0.99
183_R	186_V	0.916	0.99
50_P	76_E	0.915	0.99
115_N	257_E	0.913	0.99
36_V	39_F	0.898	0.99
125_G	234_A	0.897	0.99
209_S	266_N	0.897	0.99
119_A	122_Q	0.893	0.99
230_R	268_A	0.893	0.99
265_E	269_A	0.882	0.99
37_L	95_M	0.878	0.99
209_S	223_N	0.875	0.99
123_N	192_G	0.873	0.99
27_W	30_V	0.868	0.98
32_L	36_V	0.865	0.98
50_P	80_A	0.860	0.98
82_N	290_I	0.858	0.98
85_S	285_E	0.855	0.98
110_V	113_L	0.853	0.98
33_P	39_F	0.848	0.98
131_V	199_P	0.848	0.98
289_W	293_R	0.844	0.98
235_A	257_E	0.839	0.98
261_Y	268_A	0.838	0.98
210_F	296_T	0.837	0.98
63_L	70_H	0.835	0.98
120_Q	192_G	0.832	0.98
201_Q	289_W	0.823	0.98
55_R	291_H	0.822	0.98
118_R	256_P	0.822	0.98
256_P	259_E	0.820	0.98
133_F	286_Q	0.819	0.98
137_E	169_R	0.808	0.98
209_S	270_A	0.808	0.98
201_Q	288_L	0.806	0.97
102_S	106_K	0.802	0.97
203_Y	222_T	0.802	0.97
150_M	175_A	0.799	0.97
129_V	199_P	0.799	0.97
275_I	279_E	0.797	0.97
62_N	280_I	0.795	0.97
225_T	272_M	0.794	0.97
107_W	249_G	0.793	0.97
38_C	42_T	0.791	0.97
82_N	86_L	0.783	0.97
202_D	210_F	0.781	0.97
49_R	76_E	0.776	0.97
212_P	215_A	0.768	0.97
175_A	188_A	0.766	0.97
55_R	58_I	0.764	0.97
103_R	106_K	0.764	0.97
219_V	294_F	0.764	0.97
255_T	282_R	0.763	0.97
230_R	265_E	0.761	0.96
287_Y	294_F	0.754	0.96
19_T	23_L	0.752	0.96
56_E	79_I	0.751	0.96
243_R	250_Y	0.751	0.96
136_L	198_A	0.748	0.96
119_A	235_A	0.744	0.96
100_P	103_R	0.743	0.96
26_L	94_G	0.742	0.96
43_R	46_A	0.740	0.96
112_G	256_P	0.738	0.96
133_F	279_E	0.738	0.96
201_Q	293_R	0.736	0.96
85_S	243_R	0.728	0.95
211_A	269_A	0.726	0.95
110_V	142_V	0.725	0.95
102_S	105_R	0.722	0.95
81_E	84_R	0.722	0.95
186_V	231_L	0.721	0.95
188_A	191_K	0.721	0.95
135_S	287_Y	0.716	0.95
49_R	60_R	0.713	0.95
65_L	294_F	0.709	0.95
208_S	220_A	0.709	0.95
189_L	195_V	0.705	0.95
63_L	78_M	0.705	0.95
220_A	296_T	0.702	0.94
184_G	188_A	0.702	0.94
268_A	271_Y	0.700	0.94
58_I	62_N	0.693	0.94
205_R	296_T	0.693	0.94
159_Q	163_W	0.693	0.94
52_L	55_R	0.692	0.94
226_Y	230_R	0.692	0.94
62_N	214_F	0.691	0.94
181_N	184_G	0.691	0.94
291_H	295_K	0.689	0.94
61_K	216_V	0.689	0.94
148_P	193_E	0.684	0.94
183_R	227_V	0.683	0.94
49_R	83_F	0.683	0.94
114_D	117_K	0.681	0.94
32_L	35_P	0.677	0.93
185_I	228_L	0.676	0.93
87_G	90_L	0.676	0.93
210_F	297_R	0.674	0.93
177_I	188_A	0.668	0.93
28_L	31_Q	0.664	0.93
143_M	149_M	0.664	0.93
170_M	176_M	0.662	0.93
31_Q	36_V	0.661	0.93
225_T	236_M	0.659	0.92
188_A	195_V	0.658	0.92
58_I	291_H	0.657	0.92
156_H	162_E	0.657	0.92
139_G	196_W	0.656	0.92
244_K	248_S	0.653	0.92
258_M	261_Y	0.653	0.92
136_L	196_W	0.651	0.92
269_A	273_N	0.649	0.92
45_G	84_R	0.647	0.92
131_V	272_M	0.647	0.92
133_F	283_A	0.646	0.92
30_V	98_F	0.645	0.92
125_G	189_L	0.645	0.92
119_A	126_V	0.645	0.92
227_V	231_L	0.644	0.92
86_L	288_L	0.644	0.92
45_G	49_R	0.643	0.91
137_E	196_W	0.642	0.91
72_A	76_E	0.638	0.91
46_A	50_P	0.638	0.91
112_G	254_I	0.638	0.91
278_K	282_R	0.637	0.91
116_L	120_Q	0.635	0.91
76_E	79_I	0.634	0.91
66_C	216_V	0.633	0.91
240_T	282_R	0.632	0.91
208_S	211_A	0.631	0.91
32_L	40_L	0.629	0.91
46_A	49_R	0.629	0.91
127_M	232_S	0.628	0.91
155_P	162_E	0.622	0.90
85_S	286_Q	0.620	0.90
88_M	243_R	0.618	0.90
203_Y	220_A	0.617	0.90
34_Y	95_M	0.617	0.90
153_Y	178_G	0.614	0.90
238_T	279_E	0.613	0.89
131_V	240_T	0.609	0.89
241_M	252_L	0.608	0.89
214_F	280_I	0.607	0.89
199_P	272_M	0.607	0.89
110_V	252_L	0.606	0.89
88_M	92_E	0.604	0.89
20_W	24_G	0.604	0.89
68_P	75_R	0.604	0.89
242_V	282_R	0.601	0.89
28_L	32_L	0.601	0.89
202_D	220_A	0.599	0.88
30_V	33_P	0.599	0.88
216_V	296_T	0.593	0.88
21_F	24_G	0.593	0.88
57_S	60_R	0.590	0.88
19_T	160_L	0.589	0.88
116_L	128_V	0.588	0.87
89_A	130_G	0.587	0.87
68_P	74_E	0.584	0.87
50_P	53_K	0.583	0.87
154_R	289_W	0.582	0.87
86_L	89_A	0.580	0.87
65_L	214_F	0.579	0.87
48_A	83_F	0.578	0.87
229_S	235_A	0.578	0.87
124_R	259_E	0.578	0.87
153_Y	162_E	0.574	0.86
116_L	126_V	0.574	0.86
222_T	225_T	0.573	0.86
239_V	254_I	0.572	0.86
82_N	288_L	0.572	0.86
87_G	91_V	0.570	0.86
127_M	197_F	0.570	0.86
58_I	61_K	0.570	0.86
236_M	268_A	0.569	0.86
43_R	51_F	0.569	0.86
130_G	196_W	0.569	0.86
152_T	224_G	0.568	0.86
137_E	151_A	0.567	0.85
135_S	201_Q	0.567	0.85
33_P	37_L	0.567	0.85
134_M	241_M	0.566	0.85
73_E	77_K	0.566	0.85
110_V	254_I	0.565	0.85
44_I	81_E	0.565	0.85
213_F	280_I	0.564	0.85
177_I	184_G	0.563	0.85
157_N	179_R	0.560	0.85
75_R	78_M	0.560	0.85
42_T	46_A	0.560	0.85
101_D	141_R	0.559	0.85
62_N	169_R	0.557	0.84
163_W	166_T	0.556	0.84
257_E	271_Y	0.554	0.84
130_G	139_G	0.552	0.84
223_N	227_V	0.551	0.84
111_E	244_K	0.551	0.84
101_D	145_L	0.549	0.84
154_R	203_Y	0.549	0.84
204_G	220_A	0.548	0.84
116_L	143_M	0.547	0.83
267_Q	271_Y	0.547	0.83
34_Y	92_E	0.546	0.83
113_L	116_L	0.546	0.83
195_V	228_L	0.546	0.83
83_F	86_L	0.543	0.83
80_A	84_R	0.542	0.83
125_G	195_V	0.542	0.83
88_M	247_Y	0.539	0.83
221_T	293_R	0.539	0.83
151_A	176_M	0.538	0.82
45_G	50_P	0.538	0.82
54_R	58_I	0.537	0.82
170_M	175_A	0.537	0.82
207_G	231_L	0.533	0.82
189_L	234_A	0.533	0.82
125_G	235_A	0.532	0.82
139_G	198_A	0.532	0.82
129_V	225_T	0.531	0.82
295_K	298_P	0.530	0.81
95_M	103_R	0.530	0.81
189_L	228_L	0.529	0.81
40_L	43_R	0.529	0.81
267_Q	270_A	0.529	0.81
258_M	271_Y	0.528	0.81
19_T	164_V	0.527	0.81
52_L	83_F	0.527	0.81
238_T	276_I	0.526	0.81
140_G	176_M	0.525	0.81
202_D	295_K	0.522	0.80
259_E	263_T	0.522	0.80
216_V	294_F	0.521	0.80
20_W	23_L	0.519	0.80
175_A	191_K	0.518	0.80
152_T	162_E	0.517	0.80
212_P	221_T	0.517	0.80
189_L	232_S	0.516	0.80
83_F	290_I	0.515	0.80
69_Q	75_R	0.515	0.80
162_E	241_M	0.511	0.79
226_Y	294_F	0.508	0.79
108_F	252_L	0.508	0.79
211_A	221_T	0.507	0.79
63_L	66_C	0.507	0.79
62_N	66_C	0.506	0.78
126_V	237_L	0.506	0.78
86_L	136_L	0.503	0.78
24_G	28_L	0.503	0.78
203_Y	224_G	0.500	0.78

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
1iuqA	1	0.915	97.7	0.884	Contact Map
2lpmA	1	0.3987	23.5	0.957	Contact Map
4nutA	1	0.3627	14.5	0.961	Contact Map
4nicA	2	0.3725	9.9	0.964	Contact Map
3n0rA	1	0.719	9.9	0.964	Contact Map
4gr2A	2	0.1961	9.4	0.964	Contact Map
5by3A	1	0.366	9.2	0.964	Contact Map
3a10A	1	0.3791	9	0.964	Contact Map
2pw6A	2	0.5654	8.4	0.965	Contact Map
3eodA	1	0.366	7.9	0.965	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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