YCFH - ECOLI - GREMLIN Contacts

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YCFH - Uncharacterized deoxyribonuclease YcfH

UniProt:	P0AFQ7	Sequences: MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12303
Length:	265 (249)
Sequences:	7050 (4981)
Seq/√Len:	315.7

ECOLI - YCFH YJJV TATD
BACSU - YABD
SULSO - Q981A2 Q97ZA2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_R	122_E	3.268	1.00
114_I	144_E	3.052	1.00
161_R	194_Y	2.813	1.00
230_Y	233_V	2.729	1.00
99_Y	137_D	2.597	1.00
55_G	86_E	2.459	1.00
28_K	220_Q	2.365	1.00
117_I	127_V	2.350	1.00
152_G	172_F	2.219	1.00
248_D	252_R	2.197	1.00
229_E	239_V	2.157	1.00
143_R	166_K	2.134	1.00
189_R	230_Y	2.031	1.00
110_Q	137_D	1.985	1.00
131_T	138_T	1.944	1.00
118_Q	145_E	1.865	1.00
197_L	245_V	1.859	1.00
84_A	92_L	1.841	1.00
63_S	91_A	1.836	1.00
197_L	235_K	1.834	1.00
19_H	22_V	1.828	1.00
244_Q	248_D	1.821	1.00
237_V	242_L	1.808	1.00
21_D	218_E	1.793	1.00
8_C	37_C	1.793	1.00
114_I	145_E	1.792	1.00
27_A	31_A	1.784	1.00
192_A	231_M	1.770	1.00
99_Y	106_K	1.752	1.00
54_V	62_F	1.732	1.00
36_F	61_V	1.724	1.00
197_L	237_V	1.712	1.00
63_S	128_I	1.701	1.00
143_R	170_L	1.700	1.00
228_A	239_V	1.690	1.00
161_R	165_G	1.690	1.00
136_A	140_A	1.688	1.00
30_A	59_N	1.676	1.00
111_E	115_H	1.667	1.00
36_F	251_A	1.645	1.00
23_D	56_E	1.634	1.00
156_C	177_S	1.627	1.00
48_L	79_D	1.626	1.00
62_F	89_V	1.619	1.00
6_S	250_F	1.618	1.00
166_K	169_D	1.599	1.00
154_L	167_L	1.587	1.00
202_V	228_A	1.573	1.00
95_T	116_H	1.573	1.00
115_H	118_Q	1.542	1.00
95_T	127_V	1.541	1.00
186_E	190_D	1.539	1.00
165_G	169_D	1.533	1.00
176_F	192_A	1.517	1.00
180_V	231_M	1.511	1.00
165_G	194_Y	1.506	1.00
131_T	135_R	1.485	1.00
52_D	56_E	1.466	1.00
77_V	115_H	1.464	1.00
110_Q	140_A	1.444	1.00
113_F	129_V	1.438	1.00
153_V	253_L	1.429	1.00
190_D	193_R	1.420	1.00
160_D	163_T	1.410	1.00
173_Y	199_R	1.403	1.00
4_V	36_F	1.382	1.00
173_Y	252_R	1.375	1.00
229_E	233_V	1.374	1.00
164_A	174_I	1.371	1.00
43_T	46_G	1.371	1.00
225_R	229_E	1.368	1.00
81_R	123_L	1.367	1.00
140_A	144_E	1.360	1.00
139_L	166_K	1.354	1.00
114_I	141_I	1.351	1.00
247_T	251_A	1.344	1.00
186_E	189_R	1.326	1.00
84_A	123_L	1.309	1.00
226_D	229_E	1.295	1.00
4_V	38_L	1.293	1.00
29_A	37_C	1.290	1.00
124_N	151_G	1.289	1.00
110_Q	114_I	1.284	1.00
11_D	46_G	1.282	1.00
189_R	234_L	1.280	1.00
79_D	82_R	1.276	1.00
121_R	145_E	1.264	1.00
52_D	55_G	1.260	1.00
241_E	244_Q	1.258	1.00
196_P	199_R	1.258	1.00
50_M	62_F	1.246	1.00
174_I	195_V	1.242	1.00
4_V	247_T	1.241	1.00
99_Y	110_Q	1.235	1.00
3_L	228_A	1.229	1.00
113_F	138_T	1.224	1.00
38_L	90_V	1.221	1.00
69_L	101_Y	1.214	1.00
3_L	243_A	1.211	1.00
110_Q	141_I	1.208	1.00
231_M	242_L	1.196	1.00
8_C	206_S	1.196	1.00
51_R	62_F	1.191	1.00
214_H	223_M	1.191	1.00
41_A	47_Y	1.184	1.00
237_V	241_E	1.181	1.00
238_A	241_E	1.177	1.00
168_L	199_R	1.164	1.00
105_T	108_R	1.162	1.00
247_T	250_F	1.159	1.00
228_A	246_T	1.150	1.00
214_H	226_D	1.149	1.00
176_F	200_L	1.148	1.00
106_K	110_Q	1.143	1.00
201_L	253_L	1.127	1.00
44_L	47_Y	1.127	1.00
39_A	50_M	1.124	1.00
214_H	217_K	1.124	1.00
102_T	106_K	1.122	1.00
21_D	24_D	1.104	1.00
246_T	250_F	1.100	1.00
162_E	165_G	1.098	1.00
24_D	28_K	1.086	1.00
82_R	85_A	1.077	1.00
40_V	128_I	1.068	1.00
23_D	27_A	1.065	1.00
118_Q	122_E	1.063	1.00
230_Y	234_L	1.063	1.00
55_G	88_G	1.063	1.00
219_N	223_M	1.059	1.00
135_R	163_T	1.058	1.00
37_C	60_V	1.049	1.00
81_R	85_A	1.046	1.00
3_L	224_V	1.044	1.00
136_A	166_K	1.041	1.00
69_L	104_E	1.041	1.00
71_Q	112_S	1.041	1.00
39_A	60_V	1.036	1.00
173_Y	253_L	1.032	1.00
107_V	111_E	1.031	1.00
136_A	163_T	1.030	1.00
4_V	250_F	1.024	1.00
70_N	73_D	1.023	1.00
202_V	224_V	1.019	1.00
190_D	194_Y	1.016	1.00
28_K	222_A	1.010	1.00
161_R	191_A	1.000	1.00
48_L	52_D	0.998	1.00
24_D	27_A	0.994	1.00
202_V	231_M	0.989	1.00
51_R	86_E	0.988	1.00
182_F	210_A	0.987	1.00
192_A	235_K	0.985	1.00
180_V	192_A	0.977	1.00
44_L	79_D	0.967	1.00
49_H	52_D	0.964	1.00
108_R	111_E	0.959	1.00
245_V	248_D	0.958	1.00
51_R	64_C	0.958	1.00
107_V	110_Q	0.952	1.00
159_E	163_T	0.950	1.00
23_D	57_R	0.947	1.00
38_L	250_F	0.945	1.00
202_V	246_T	0.942	1.00
183_R	212_V	0.940	1.00
48_L	83_L	0.937	1.00
161_R	190_D	0.933	1.00
228_A	243_A	0.932	1.00
15_Y	218_E	0.931	1.00
6_S	201_L	0.924	1.00
243_A	247_T	0.920	1.00
220_Q	223_M	0.917	1.00
192_A	234_L	0.917	1.00
54_V	60_V	0.911	1.00
176_F	195_V	0.908	1.00
153_V	254_F	0.898	1.00
10_L	221_P	0.898	1.00
241_E	245_V	0.896	1.00
85_A	123_L	0.893	1.00
242_L	246_T	0.886	1.00
78_E	82_R	0.885	1.00
79_D	83_L	0.882	1.00
152_G	253_L	0.879	1.00
139_L	167_L	0.878	1.00
51_R	55_G	0.877	1.00
106_K	137_D	0.876	1.00
77_V	81_R	0.873	1.00
225_R	239_V	0.872	1.00
235_K	242_L	0.864	1.00
228_A	242_L	0.863	1.00
81_R	119_I	0.862	1.00
50_M	54_V	0.861	1.00
175_S	201_L	0.859	1.00
71_Q	108_R	0.856	1.00
239_V	243_A	0.855	1.00
129_V	154_L	0.850	1.00
40_V	63_S	0.844	1.00
197_L	242_L	0.844	1.00
121_R	148_T	0.843	1.00
100_Y	133_D	0.842	1.00
78_E	81_R	0.838	1.00
42_T	46_G	0.837	1.00
224_V	227_V	0.831	1.00
64_C	89_V	0.820	1.00
26_L	57_R	0.818	1.00
121_R	146_K	0.813	1.00
168_L	196_P	0.809	1.00
129_V	138_T	0.806	1.00
15_Y	19_H	0.805	1.00
6_S	153_V	0.796	1.00
35_K	247_T	0.791	1.00
124_N	150_C	0.783	1.00
119_I	123_L	0.780	1.00
74_P	112_S	0.778	1.00
117_I	121_R	0.778	1.00
141_I	144_E	0.776	1.00
193_R	234_L	0.775	1.00
89_V	125_K	0.774	1.00
135_R	159_E	0.770	0.99
139_L	163_T	0.763	0.99
131_T	159_E	0.762	0.99
137_D	140_A	0.760	0.99
26_L	37_C	0.760	0.99
135_R	167_L	0.760	0.99
143_R	169_D	0.759	0.99
231_M	235_K	0.759	0.99
168_L	174_I	0.759	0.99
92_L	95_T	0.756	0.99
28_K	31_A	0.755	0.99
240_E	244_Q	0.749	0.99
3_L	225_R	0.747	0.99
74_P	77_V	0.747	0.99
141_I	145_E	0.745	0.99
102_T	105_T	0.744	0.99
38_L	63_S	0.742	0.99
121_R	147_V	0.738	0.99
248_D	251_A	0.735	0.99
47_Y	83_L	0.733	0.99
228_A	232_A	0.732	0.99
43_T	73_D	0.731	0.99
11_D	49_H	0.730	0.99
3_L	247_T	0.728	0.99
173_Y	201_L	0.723	0.99
200_L	242_L	0.723	0.99
121_R	150_C	0.717	0.99
193_R	236_G	0.715	0.99
147_V	150_C	0.711	0.99
108_R	112_S	0.705	0.99
12_G	208_Y	0.702	0.99
114_I	118_Q	0.700	0.99
69_L	103_P	0.699	0.99
153_V	175_S	0.697	0.99
200_L	235_K	0.696	0.99
32_R	225_R	0.695	0.99
19_H	49_H	0.694	0.99
196_P	235_K	0.693	0.99
91_A	128_I	0.678	0.99
179_I	209_L	0.678	0.99
237_V	245_V	0.676	0.99
103_P	106_K	0.672	0.99
124_N	255_H	0.664	0.98
164_A	195_V	0.660	0.98
6_S	128_I	0.660	0.98
46_G	50_M	0.659	0.98
26_L	30_A	0.656	0.98
27_A	30_A	0.656	0.98
164_A	168_L	0.655	0.98
41_A	50_M	0.650	0.98
61_V	88_G	0.650	0.98
151_G	255_H	0.647	0.98
131_T	167_L	0.646	0.98
77_V	119_I	0.637	0.98
3_L	202_V	0.636	0.98
3_L	239_V	0.631	0.98
15_Y	21_D	0.631	0.98
117_I	141_I	0.630	0.98
15_Y	22_V	0.630	0.98
139_L	143_R	0.629	0.98
157_F	163_T	0.627	0.98
117_I	145_E	0.627	0.98
188_L	191_A	0.624	0.98
21_D	25_V	0.623	0.98
195_V	200_L	0.622	0.98
30_A	35_K	0.615	0.98
164_A	191_A	0.615	0.98
97_L	134_A	0.613	0.97
47_Y	64_C	0.611	0.97
200_L	246_T	0.611	0.97
167_L	174_I	0.610	0.97
179_I	188_L	0.610	0.97
25_V	218_E	0.609	0.97
210_A	223_M	0.608	0.97
182_F	212_V	0.608	0.97
168_L	195_V	0.608	0.97
187_Q	190_D	0.608	0.97
72_N	108_R	0.608	0.97
61_V	90_V	0.606	0.97
84_A	89_V	0.606	0.97
29_A	34_V	0.604	0.97
80_L	84_A	0.601	0.97
82_R	86_E	0.599	0.97
72_N	105_T	0.596	0.97
135_R	139_L	0.596	0.97
245_V	252_R	0.596	0.97
128_I	254_F	0.594	0.97
147_V	151_G	0.593	0.97
112_S	116_H	0.592	0.97
47_Y	50_M	0.591	0.97
29_A	220_Q	0.589	0.97
22_V	25_V	0.588	0.97
198_D	252_R	0.587	0.97
198_D	245_V	0.587	0.97
179_I	182_F	0.585	0.97
166_K	170_L	0.582	0.97
47_Y	62_F	0.582	0.97
154_L	175_S	0.577	0.96
95_T	112_S	0.577	0.96
11_D	39_A	0.577	0.96
11_D	42_T	0.574	0.96
26_L	60_V	0.572	0.96
64_C	83_L	0.570	0.96
201_L	250_F	0.567	0.96
168_L	194_Y	0.567	0.96
32_R	222_A	0.566	0.96
85_A	122_E	0.563	0.96
71_Q	104_E	0.563	0.96
173_Y	249_N	0.559	0.96
235_K	245_V	0.558	0.96
186_E	193_R	0.557	0.96
213_P	216_G	0.556	0.96
45_P	49_H	0.556	0.96
69_L	102_T	0.553	0.95
47_Y	80_L	0.552	0.95
139_L	170_L	0.549	0.95
42_T	70_N	0.549	0.95
119_I	122_E	0.546	0.95
180_V	189_R	0.546	0.95
51_R	54_V	0.544	0.95
245_V	249_N	0.544	0.95
135_R	138_T	0.542	0.95
180_V	188_L	0.542	0.95
4_V	251_A	0.541	0.95
180_V	242_L	0.541	0.95
232_A	239_V	0.540	0.95
188_L	192_A	0.536	0.95
29_A	33_D	0.534	0.94
185_A	189_R	0.533	0.94
45_P	73_D	0.531	0.94
115_H	119_I	0.531	0.94
38_L	254_F	0.530	0.94
147_V	172_F	0.527	0.94
72_N	104_E	0.527	0.94
118_Q	121_R	0.526	0.94
100_Y	132_R	0.524	0.94
25_V	28_K	0.523	0.94
175_S	209_L	0.523	0.94
176_F	179_I	0.521	0.94
22_V	218_E	0.519	0.94
65_G	116_H	0.517	0.93
153_V	201_L	0.517	0.93
202_V	242_L	0.517	0.93
177_S	209_L	0.515	0.93
181_T	212_V	0.515	0.93
66_V	74_P	0.514	0.93
58_D	88_G	0.513	0.93
51_R	83_L	0.512	0.93
53_L	60_V	0.510	0.93
40_V	206_S	0.504	0.93
146_K	172_F	0.504	0.93
182_F	185_A	0.503	0.93
163_T	167_L	0.501	0.92
182_F	213_P	0.500	0.92
182_F	216_G	0.500	0.92
97_L	110_Q	0.500	0.92

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
3e2vA	1	0.9547	100	0.197	Contact Map
3ipwA	1	0.9623	100	0.264	Contact Map
2xioA	1	0.9623	100	0.325	Contact Map
1j6oA	1	0.966	100	0.34	Contact Map
3gg7A	1	0.9057	100	0.357	Contact Map
3rcmA	1	0.9698	100	0.385	Contact Map
1xwyA	1	0.9509	100	0.392	Contact Map
2gzxA	1	0.9434	100	0.396	Contact Map
1yixA	1	1	100	0.401	Contact Map
1zzmA	1	0.9547	100	0.408	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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