YFIH - ECOLI - GREMLIN Contacts

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YFIH - Laccase domain protein YfiH

UniProt:	P33644	Sequences: MSKLIVPQWPQPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAAHAGWRGLCAGVLEETVSCFADNPENILAWLGPAIGPRAFEVGGEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12097
Length:	243 (228)
Sequences:	3479 (2634)
Seq/√Len:	174.4

ECOLI - YFIH
BACSU - YLMD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
161_A	216_C	3.137	1.00
139_V	149_I	3.093	1.00
161_A	219_T	3.034	1.00
111_L	122_A	2.836	1.00
123_A	138_T	2.712	1.00
49_E	52_K	2.643	1.00
104_T	238_S	2.613	1.00
220_E	223_T	2.559	1.00
90_A	138_T	2.398	1.00
29_P	32_D	2.332	1.00
28_L	46_H	2.318	1.00
112_F	123_A	2.306	1.00
166_G	170_E	2.284	1.00
49_E	53_R	2.245	1.00
160_R	219_T	2.237	1.00
110_V	135_L	2.233	1.00
73_K	137_E	2.226	1.00
116_A	148_N	2.188	1.00
68_E	87_R	2.173	1.00
136_E	201_R	2.166	1.00
108_L	156_A	2.123	1.00
90_A	123_A	2.041	1.00
112_F	151_A	2.041	1.00
196_Q	199_R	2.035	1.00
156_A	195_Y	1.978	1.00
119_E	142_F	1.912	1.00
162_F	192_A	1.897	1.00
43_N	46_H	1.867	1.00
20_S	54_L	1.861	1.00
158_G	161_A	1.811	1.00
34_L	54_L	1.795	1.00
158_G	216_C	1.761	1.00
186_H	189_K	1.759	1.00
215_R	220_E	1.756	1.00
112_F	149_I	1.753	1.00
112_F	138_T	1.742	1.00
130_L	198_A	1.730	1.00
38_A	48_E	1.712	1.00
144_D	149_I	1.676	1.00
108_L	198_A	1.657	1.00
157_I	218_Y	1.652	1.00
215_R	224_F	1.603	1.00
137_E	140_S	1.589	1.00
133_G	136_E	1.573	1.00
151_A	202_L	1.568	1.00
199_R	203_A	1.536	1.00
73_K	132_A	1.522	1.00
114_N	118_T	1.503	1.00
67_L	88_A	1.488	1.00
215_R	223_T	1.466	1.00
139_V	205_V	1.458	1.00
74_D	87_R	1.451	1.00
125_A	198_A	1.447	1.00
165_G	168_V	1.444	1.00
19_S	238_S	1.440	1.00
195_Y	212_G	1.436	1.00
199_R	212_G	1.436	1.00
26_V	46_H	1.433	1.00
26_V	49_E	1.424	1.00
101_A	237_A	1.423	1.00
169_R	173_M	1.404	1.00
115_R	148_N	1.402	1.00
169_R	190_Y	1.397	1.00
122_A	240_I	1.384	1.00
99_V	241_W	1.382	1.00
111_L	238_S	1.364	1.00
91_S	100_C	1.364	1.00
120_V	240_I	1.347	1.00
163_E	189_K	1.340	1.00
115_R	150_L	1.338	1.00
119_E	144_D	1.315	1.00
131_C	172_F	1.311	1.00
76_L	88_A	1.305	1.00
123_A	135_L	1.302	1.00
77_K	94_N	1.287	1.00
44_P	48_E	1.280	1.00
67_L	91_S	1.273	1.00
111_L	240_I	1.269	1.00
33_S	225_F	1.264	1.00
161_A	218_Y	1.252	1.00
70_V	87_R	1.233	1.00
196_Q	200_Q	1.218	1.00
64_P	101_A	1.218	1.00
117_G	144_D	1.217	1.00
80_G	95_T	1.213	1.00
75_V	137_E	1.209	1.00
158_G	219_T	1.207	1.00
109_P	154_G	1.204	1.00
216_C	219_T	1.200	1.00
31_Y	232_T	1.199	1.00
121_A	138_T	1.190	1.00
26_V	53_R	1.188	1.00
92_Y	121_A	1.172	1.00
135_L	198_A	1.171	1.00
60_L	99_V	1.154	1.00
66_W	101_A	1.135	1.00
92_Y	142_F	1.124	1.00
36_L	54_L	1.123	1.00
128_R	132_A	1.121	1.00
195_Y	213_G	1.117	1.00
23_I	223_T	1.111	1.00
115_R	209_Q	1.102	1.00
54_L	239_F	1.096	1.00
114_N	144_D	1.096	1.00
182_A	196_Q	1.084	1.00
78_L	91_S	1.083	1.00
19_S	236_M	1.082	1.00
67_L	102_V	1.071	1.00
193_D	196_Q	1.056	1.00
150_L	209_Q	1.055	1.00
36_L	237_A	1.047	1.00
99_V	239_F	1.046	1.00
114_N	142_F	1.046	1.00
144_D	148_N	1.045	0.99
100_C	120_V	1.044	0.99
90_A	134_V	1.043	0.99
139_V	207_V	1.042	0.99
93_S	98_T	1.040	0.99
227_Y	233_T	1.039	0.99
170_E	174_A	1.036	0.99
114_N	119_E	1.029	0.99
218_Y	229_R	1.019	0.99
140_S	205_V	1.010	0.99
102_V	122_A	1.005	0.99
55_F	64_P	1.005	0.99
125_A	130_L	0.999	0.99
159_P	193_D	0.993	0.99
108_L	153_L	0.984	0.99
113_C	150_L	0.982	0.99
151_A	207_V	0.978	0.99
20_S	239_F	0.975	0.99
40_C	233_T	0.966	0.99
117_G	148_N	0.965	0.99
131_C	171_A	0.965	0.99
230_D	233_T	0.960	0.99
110_V	123_A	0.956	0.99
92_Y	141_C	0.951	0.99
93_S	100_C	0.941	0.99
39_H	68_E	0.931	0.99
131_C	168_V	0.930	0.99
77_K	92_Y	0.924	0.99
74_D	88_A	0.923	0.99
65_V	98_T	0.923	0.99
145_N	148_N	0.923	0.99
108_L	194_I	0.921	0.99
178_K	200_Q	0.921	0.99
14_G	113_C	0.897	0.98
24_G	27_S	0.893	0.98
34_L	53_R	0.888	0.98
79_T	95_T	0.866	0.98
96_P	118_T	0.862	0.98
194_I	218_Y	0.852	0.98
221_N	229_R	0.851	0.98
182_A	200_Q	0.851	0.98
19_S	152_W	0.841	0.98
179_A	197_L	0.840	0.98
103_M	237_A	0.840	0.98
166_G	190_Y	0.838	0.98
79_T	82_P	0.836	0.98
133_G	201_R	0.834	0.98
77_K	141_C	0.830	0.97
104_T	122_A	0.830	0.97
92_Y	119_E	0.821	0.97
168_V	171_A	0.814	0.97
94_N	119_E	0.812	0.97
65_V	82_P	0.806	0.97
75_V	138_T	0.803	0.97
112_F	135_L	0.798	0.97
163_E	191_L	0.796	0.97
198_A	201_R	0.796	0.97
78_L	98_T	0.792	0.97
95_T	98_T	0.791	0.97
39_H	103_M	0.790	0.97
151_A	205_V	0.787	0.96
159_P	184_I	0.786	0.96
78_L	100_C	0.784	0.96
75_V	92_Y	0.784	0.96
134_V	137_E	0.784	0.96
66_W	103_M	0.778	0.96
119_E	149_I	0.778	0.96
200_Q	204_N	0.775	0.96
18_C	239_F	0.775	0.96
130_L	197_L	0.771	0.96
37_G	40_C	0.769	0.96
15_V	113_C	0.768	0.96
52_K	56_A	0.766	0.96
114_N	117_G	0.762	0.96
92_Y	138_T	0.761	0.96
221_N	230_D	0.760	0.96
172_F	176_D	0.756	0.96
24_G	33_S	0.756	0.96
113_C	118_T	0.756	0.96
67_L	103_M	0.749	0.95
157_I	162_F	0.748	0.95
169_R	183_F	0.744	0.95
63_K	83_Y	0.742	0.95
160_R	184_I	0.737	0.95
128_R	171_A	0.735	0.95
25_G	42_D	0.733	0.95
192_A	197_L	0.732	0.95
110_V	151_A	0.730	0.95
114_N	143_A	0.726	0.95
133_G	204_N	0.726	0.95
227_Y	230_D	0.725	0.94
195_Y	215_R	0.724	0.94
220_E	224_F	0.723	0.94
168_V	192_A	0.721	0.94
60_L	241_W	0.721	0.94
61_P	99_V	0.720	0.94
199_R	210_I	0.719	0.94
162_F	218_Y	0.717	0.94
46_H	49_E	0.712	0.94
72_G	132_A	0.709	0.94
133_G	175_V	0.704	0.94
212_G	215_R	0.704	0.94
136_E	140_S	0.700	0.93
40_C	235_R	0.698	0.93
164_V	168_V	0.696	0.93
40_C	47_V	0.693	0.93
159_P	195_Y	0.692	0.93
27_S	50_N	0.690	0.93
203_A	210_I	0.689	0.93
104_T	236_M	0.685	0.93
125_A	134_V	0.683	0.93
114_N	148_N	0.680	0.92
20_S	36_L	0.678	0.92
157_I	164_V	0.676	0.92
73_K	134_V	0.675	0.92
23_I	33_S	0.673	0.92
179_A	201_R	0.672	0.92
165_G	190_Y	0.663	0.91
19_S	155_P	0.662	0.91
100_C	121_A	0.662	0.91
200_Q	203_A	0.662	0.91
68_E	86_K	0.661	0.91
225_F	233_T	0.661	0.91
166_G	169_R	0.656	0.91
16_A	241_W	0.656	0.91
18_C	58_G	0.656	0.91
30_P	232_T	0.655	0.91
201_R	205_V	0.653	0.91
55_F	60_L	0.651	0.91
156_A	212_G	0.647	0.90
125_A	129_G	0.646	0.90
79_T	94_N	0.646	0.90
176_D	201_R	0.645	0.90
153_L	212_G	0.643	0.90
171_A	174_A	0.643	0.90
166_G	188_D	0.640	0.90
53_R	56_A	0.640	0.90
158_G	218_Y	0.639	0.90
35_N	42_D	0.636	0.90
39_H	51_R	0.636	0.90
66_W	237_A	0.636	0.90
25_G	50_N	0.632	0.89
38_A	68_E	0.631	0.89
136_E	204_N	0.628	0.89
130_L	135_L	0.626	0.89
155_P	217_T	0.624	0.89
38_A	44_P	0.622	0.89
42_D	47_V	0.619	0.88
55_F	63_K	0.619	0.88
102_V	238_S	0.616	0.88
72_G	87_R	0.615	0.88
159_P	162_F	0.615	0.88
152_W	211_F	0.614	0.88
159_P	191_L	0.612	0.88
48_E	52_K	0.611	0.88
119_E	143_A	0.609	0.88
17_A	152_W	0.609	0.88
127_W	168_V	0.607	0.87
166_G	187_G	0.606	0.87
136_E	205_V	0.605	0.87
108_L	130_L	0.602	0.87
153_L	195_Y	0.598	0.87
185_Q	188_D	0.595	0.86
64_P	99_V	0.591	0.86
65_V	78_L	0.587	0.86
165_G	189_K	0.585	0.85
178_K	204_N	0.584	0.85
167_E	171_A	0.580	0.85
142_F	149_I	0.578	0.85
122_A	238_S	0.576	0.85
90_A	104_T	0.575	0.84
54_L	237_A	0.575	0.84
51_R	235_R	0.574	0.84
111_L	236_M	0.574	0.84
101_A	239_F	0.573	0.84
160_R	191_L	0.570	0.84
207_V	210_I	0.569	0.84
179_A	200_Q	0.568	0.84
75_V	90_A	0.568	0.84
132_A	171_A	0.567	0.84
85_S	88_A	0.565	0.83
104_T	109_P	0.562	0.83
158_G	212_G	0.561	0.83
185_Q	190_Y	0.561	0.83
173_M	179_A	0.559	0.83
168_V	172_F	0.558	0.83
28_L	43_N	0.558	0.83
139_V	146_P	0.558	0.83
70_V	74_D	0.555	0.82
30_P	233_T	0.554	0.82
172_F	192_A	0.549	0.82
77_K	119_E	0.548	0.82
21_T	224_F	0.546	0.81
19_S	34_L	0.544	0.81
112_F	121_A	0.540	0.81
93_S	120_V	0.540	0.81
90_A	137_E	0.537	0.80
125_A	194_I	0.537	0.80
162_F	189_K	0.535	0.80
162_F	191_L	0.534	0.80
153_L	199_R	0.534	0.80
187_G	191_L	0.534	0.80
77_K	95_T	0.532	0.80
196_Q	203_A	0.531	0.79
24_G	50_N	0.530	0.79
167_E	172_F	0.528	0.79
74_D	77_K	0.522	0.78
60_L	63_K	0.522	0.78
25_G	33_S	0.521	0.78
127_W	191_L	0.521	0.78
58_G	239_F	0.519	0.78
163_E	187_G	0.517	0.78
160_R	218_Y	0.515	0.77
150_L	211_F	0.514	0.77
127_W	189_K	0.513	0.77
51_R	66_W	0.511	0.77
146_P	207_V	0.510	0.77
55_F	239_F	0.510	0.77
114_N	150_L	0.509	0.77
162_F	165_G	0.509	0.77
38_A	51_R	0.508	0.76
60_L	239_F	0.504	0.76
45_D	49_E	0.504	0.76
169_R	192_A	0.503	0.76
13_K	16_A	0.503	0.76
23_I	222_E	0.502	0.76
218_Y	230_D	0.502	0.76
20_S	58_G	0.501	0.75
173_M	178_K	0.500	0.75

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
1z9tA	1	0.9877	100	0.028	Contact Map
1rv9A	1	0.9877	100	0.055	Contact Map
1t8hA	1	1	100	0.075	Contact Map
1xfjA	1	1	100	0.081	Contact Map
2f9zC	1	0.5391	30.7	0.962	Contact Map
1np7A	1	0.642	21	0.965	Contact Map
4h31A	3	0.7572	15.3	0.967	Contact Map
1jaeA	1	0.2881	14.5	0.967	Contact Map
4x9yA	1	0.284	13.8	0.968	Contact Map
1g94A	1	0.2551	12.8	0.968	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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