FPG - ECOLI - GREMLIN Contacts

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FPG - Formamidopyrimidine-DNA glycosylase

UniProt:	P05523	Sequences: MPELPEVETSRRGIEPHLVGATILHAVVRNGRLRWPVSEEIYRLSDQPVLSVQRRAKYLLLELPEGWIIIHLGMSGSLRILPEELPPEKHDHVDLVMSNGKVLRYTDPRRFGAWLWTKELEGHNVLTHLGPEPLSDDFNGEYLHQKCAKKKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKAVLLRSIEQGGTTLKDFLQSDGKPGYFAQELQVYGRKGEPCRVCGTPIVATKHAQRATFYCRQCQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10329
Length:	269 (264)
Sequences:	5432 (3694)
Seq/√Len:	227.3

ECOLI - FPG END8
BACSU - FPG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_Q	62_E	3.857	1.00
185_R	194_E	3.642	1.00
251_I	262_F	3.017	1.00
191_S	194_E	2.933	1.00
167_V	172_A	2.907	1.00
157_W	187_A	2.893	1.00
178_A	208_R	2.860	1.00
154_I	181_I	2.776	1.00
151_K	188_S	2.653	1.00
47_Q	65_E	2.606	1.00
60_L	67_W	2.587	1.00
15_E	19_V	2.584	1.00
235_Q	245_R	2.409	1.00
140_G	199_A	2.384	1.00
147_C	157_W	2.346	1.00
21_A	99_N	2.320	1.00
179_A	201_V	2.246	1.00
27_V	96_V	2.132	1.00
25_H	45_S	2.109	1.00
11_R	59_L	2.093	1.00
239_R	245_R	2.073	1.00
70_I	78_L	2.072	1.00
144_H	195_C	2.001	1.00
70_I	114_W	1.993	1.00
177_F	246_V	1.964	1.00
194_E	197_L	1.945	1.00
185_R	189_S	1.939	1.00
249_T	265_R	1.932	1.00
252_V	265_R	1.908	1.00
11_R	15_E	1.898	1.00
21_A	98_S	1.885	1.00
254_T	263_Y	1.879	1.00
25_H	96_V	1.879	1.00
50_L	64_P	1.861	1.00
15_E	51_S	1.860	1.00
140_G	196_E	1.855	1.00
128_H	162_K	1.839	1.00
184_D	254_T	1.837	1.00
47_Q	64_P	1.815	1.00
215_T	234_L	1.801	1.00
178_A	201_V	1.791	1.00
93_V	114_W	1.788	1.00
144_H	192_L	1.780	1.00
142_Y	146_K	1.733	1.00
152_T	160_D	1.719	1.00
239_R	242_E	1.706	1.00
198_L	202_I	1.705	1.00
51_S	62_E	1.697	1.00
140_G	200_R	1.673	1.00
157_W	163_L	1.669	1.00
21_A	101_K	1.668	1.00
201_V	204_A	1.664	1.00
156_P	257_A	1.644	1.00
30_N	110_R	1.623	1.00
52_V	61_L	1.585	1.00
236_V	251_I	1.579	1.00
23_I	63_L	1.576	1.00
153_A	156_P	1.576	1.00
253_A	260_A	1.571	1.00
24_L	98_S	1.571	1.00
167_V	202_I	1.570	1.00
178_A	235_Q	1.537	1.00
190_L	194_E	1.535	1.00
178_A	205_V	1.533	1.00
249_T	266_Q	1.501	1.00
175_S	202_I	1.494	1.00
147_C	195_C	1.482	1.00
142_Y	145_Q	1.471	1.00
203_K	207_L	1.465	1.00
178_A	204_A	1.459	1.00
8_E	54_R	1.458	1.00
144_H	148_A	1.447	1.00
186_L	189_S	1.438	1.00
208_R	233_E	1.438	1.00
192_L	196_E	1.437	1.00
22_T	48_P	1.431	1.00
167_V	175_S	1.411	1.00
55_R	132_E	1.400	1.00
143_L	199_A	1.400	1.00
152_T	157_W	1.384	1.00
140_G	143_L	1.381	1.00
35_W	113_A	1.378	1.00
62_E	67_W	1.374	1.00
91_D	106_T	1.369	1.00
40_E	43_R	1.361	1.00
8_E	12_R	1.341	1.00
173_S	262_F	1.322	1.00
180_G	246_V	1.319	1.00
207_L	211_E	1.313	1.00
240_K	253_A	1.274	1.00
182_H	263_Y	1.261	1.00
49_V	63_L	1.259	1.00
147_C	154_I	1.252	1.00
141_E	192_L	1.243	1.00
131_P	135_S	1.240	1.00
118_K	121_E	1.239	1.00
19_V	51_S	1.230	1.00
22_T	98_S	1.217	1.00
139_N	142_Y	1.197	1.00
91_D	94_D	1.176	1.00
29_R	94_D	1.173	1.00
150_K	157_W	1.168	1.00
155_K	172_A	1.167	1.00
240_K	262_F	1.162	1.00
264_C	267_C	1.160	1.00
119_E	122_G	1.157	1.00
8_E	11_R	1.156	1.00
56_A	161_N	1.152	1.00
86_P	104_R	1.149	1.00
252_V	263_Y	1.149	1.00
41_I	114_W	1.137	1.00
208_R	211_E	1.133	1.00
141_E	145_Q	1.123	1.00
158_L	202_I	1.121	1.00
212_Q	233_E	1.119	1.00
18_L	97_M	1.113	1.00
49_V	61_L	1.109	1.00
200_R	204_A	1.105	1.00
244_C	264_C	1.099	1.00
175_S	198_L	1.078	1.00
164_V	167_V	1.077	1.00
244_C	247_C	1.077	1.00
152_T	156_P	1.071	1.00
69_I	117_T	1.069	1.00
138_F	164_V	1.066	1.00
177_F	235_Q	1.065	1.00
197_L	201_V	1.063	1.00
244_C	267_C	1.047	1.00
27_V	94_D	1.044	1.00
199_A	203_K	1.041	1.00
133_P	138_F	1.034	1.00
149_K	188_S	1.028	1.00
49_V	97_M	1.022	1.00
50_L	62_E	1.015	1.00
140_G	144_H	1.013	1.00
34_R	37_V	1.007	1.00
229_Y	232_Q	0.996	1.00
179_A	197_L	0.992	1.00
23_I	95_L	0.991	1.00
63_L	68_I	0.988	1.00
26_A	44_L	0.986	1.00
78_L	105_Y	0.979	1.00
48_P	64_P	0.977	1.00
146_K	163_L	0.976	1.00
58_Y	69_I	0.974	1.00
181_I	198_L	0.964	1.00
256_H	261_T	0.959	1.00
247_C	264_C	0.959	1.00
190_L	195_C	0.957	1.00
129_L	165_V	0.938	1.00
70_I	105_Y	0.933	1.00
172_A	261_T	0.922	1.00
196_E	200_R	0.919	1.00
94_D	102_V	0.910	0.99
214_G	228_G	0.908	0.99
91_D	104_R	0.906	0.99
153_A	184_D	0.906	0.99
105_Y	114_W	0.904	0.99
243_P	250_P	0.892	0.99
18_L	49_V	0.882	0.99
28_V	93_V	0.876	0.99
15_E	52_V	0.875	0.99
92_H	110_R	0.875	0.99
243_P	249_T	0.875	0.99
77_S	108_P	0.872	0.99
227_P	232_Q	0.870	0.99
44_L	63_L	0.866	0.99
95_L	114_W	0.861	0.99
82_P	85_L	0.860	0.99
184_D	256_H	0.858	0.99
144_H	147_C	0.855	0.99
144_H	196_E	0.854	0.99
11_R	52_V	0.852	0.99
96_V	102_V	0.844	0.99
159_M	173_S	0.842	0.99
225_G	228_G	0.840	0.99
13_G	213_G	0.838	0.99
12_R	15_E	0.835	0.99
141_E	196_E	0.834	0.99
231_A	234_L	0.830	0.99
148_A	195_C	0.827	0.99
193_A	197_L	0.825	0.99
75_S	108_P	0.823	0.99
167_V	206_L	0.821	0.99
89_K	92_H	0.814	0.99
150_K	163_L	0.813	0.99
61_L	68_I	0.811	0.99
18_L	61_L	0.808	0.99
75_S	112_G	0.804	0.99
119_E	123_H	0.803	0.99
150_K	187_A	0.802	0.99
124_N	127_T	0.794	0.99
253_A	262_F	0.794	0.99
87_P	94_D	0.789	0.99
191_S	195_C	0.788	0.99
204_A	208_R	0.786	0.98
177_F	245_R	0.779	0.98
156_P	256_H	0.775	0.98
69_I	126_L	0.772	0.98
97_M	101_K	0.770	0.98
159_M	259_R	0.767	0.98
170_I	215_T	0.766	0.98
67_W	120_L	0.763	0.98
134_L	203_K	0.762	0.98
55_R	60_L	0.760	0.98
170_I	237_Y	0.760	0.98
154_I	187_A	0.756	0.98
153_A	186_L	0.754	0.98
247_C	267_C	0.754	0.98
29_R	92_H	0.752	0.98
61_L	70_I	0.749	0.98
47_Q	66_G	0.748	0.98
135_S	203_K	0.746	0.98
117_T	125_V	0.746	0.98
26_A	41_I	0.745	0.98
42_Y	45_S	0.742	0.98
115_L	125_V	0.741	0.98
37_V	40_E	0.738	0.98
41_I	70_I	0.737	0.98
37_V	93_V	0.736	0.98
249_T	252_V	0.733	0.98
189_S	194_E	0.732	0.98
12_R	211_E	0.732	0.98
9_T	210_I	0.731	0.98
68_I	95_L	0.730	0.98
151_K	186_L	0.730	0.98
21_A	97_M	0.729	0.98
170_I	175_S	0.728	0.98
98_S	101_K	0.727	0.98
175_S	179_A	0.720	0.97
154_I	195_C	0.720	0.97
208_R	235_Q	0.713	0.97
236_V	239_R	0.713	0.97
153_A	257_A	0.713	0.97
216_T	228_G	0.706	0.97
4_L	8_E	0.705	0.97
87_P	91_D	0.704	0.97
19_V	22_T	0.700	0.97
6_E	170_I	0.698	0.97
208_R	212_Q	0.697	0.97
255_K	260_A	0.690	0.97
146_K	149_K	0.685	0.96
23_I	49_V	0.684	0.96
17_H	80_I	0.683	0.96
120_L	123_H	0.679	0.96
226_K	229_Y	0.673	0.96
156_P	258_Q	0.672	0.96
189_S	252_V	0.669	0.96
81_L	104_R	0.669	0.96
212_Q	232_Q	0.668	0.96
241_G	250_P	0.667	0.96
6_E	214_G	0.666	0.96
23_I	97_M	0.666	0.96
182_H	185_R	0.665	0.96
143_L	147_C	0.664	0.96
195_C	199_A	0.660	0.96
140_G	195_C	0.659	0.96
68_I	114_W	0.655	0.95
47_Q	50_L	0.654	0.95
235_Q	246_V	0.653	0.95
154_I	176_L	0.651	0.95
184_D	252_V	0.651	0.95
158_L	167_V	0.649	0.95
173_S	256_H	0.648	0.95
192_L	195_C	0.648	0.95
130_G	165_V	0.648	0.95
197_L	200_R	0.646	0.95
78_L	95_L	0.646	0.95
177_F	180_G	0.646	0.95
14_I	78_L	0.643	0.95
171_Y	206_L	0.642	0.95
139_N	199_A	0.640	0.95
135_S	138_F	0.640	0.95
57_K	76_G	0.639	0.95
226_K	230_F	0.639	0.95
24_L	99_N	0.638	0.95
88_E	106_T	0.637	0.95
4_L	206_L	0.637	0.95
32_R	110_R	0.633	0.95
215_T	231_A	0.632	0.94
73_G	109_R	0.631	0.94
136_D	203_K	0.630	0.94
13_G	80_I	0.629	0.94
225_G	230_F	0.629	0.94
254_T	260_A	0.627	0.94
44_L	68_I	0.626	0.94
28_V	95_L	0.625	0.94
77_S	221_L	0.625	0.94
131_P	164_V	0.625	0.94
53_Q	67_W	0.623	0.94
255_K	258_Q	0.622	0.94
14_I	52_V	0.620	0.94
229_Y	234_L	0.619	0.94
34_R	73_G	0.616	0.94
8_E	210_I	0.611	0.93
134_L	207_L	0.607	0.93
160_D	163_L	0.607	0.93
73_G	111_F	0.605	0.93
61_L	78_L	0.602	0.93
181_I	194_E	0.602	0.93
37_V	41_I	0.602	0.93
138_F	199_A	0.599	0.93
180_G	197_L	0.598	0.93
145_Q	149_K	0.598	0.93
80_I	101_K	0.596	0.93
240_K	250_P	0.596	0.93
43_R	116_W	0.595	0.92
148_A	192_L	0.594	0.92
153_A	183_P	0.592	0.92
155_K	173_S	0.592	0.92
32_R	35_W	0.591	0.92
134_L	206_L	0.591	0.92
14_I	61_L	0.588	0.92
36_P	40_E	0.586	0.92
4_L	9_T	0.585	0.92
52_V	62_E	0.585	0.92
238_G	262_F	0.582	0.92
131_P	165_V	0.582	0.92
172_A	256_H	0.581	0.92
227_P	230_F	0.579	0.91
250_P	265_R	0.579	0.91
234_L	238_G	0.578	0.91
171_Y	209_S	0.576	0.91
123_H	126_L	0.575	0.91
58_Y	115_L	0.575	0.91
90_H	109_R	0.574	0.91
146_K	150_K	0.574	0.91
246_V	249_T	0.573	0.91
193_A	196_E	0.572	0.91
145_Q	192_L	0.571	0.91
77_S	106_T	0.570	0.91
57_K	71_H	0.569	0.91
230_F	234_L	0.568	0.91
240_K	252_V	0.563	0.90
105_Y	112_G	0.561	0.90
28_V	31_G	0.560	0.90
199_A	202_I	0.559	0.90
81_L	87_P	0.558	0.90
9_T	12_R	0.557	0.90
205_V	209_S	0.555	0.90
256_H	260_A	0.555	0.90
74_M	90_H	0.554	0.90
4_L	54_R	0.553	0.90
147_C	187_A	0.552	0.89
209_S	215_T	0.551	0.89
33_L	37_V	0.551	0.89
24_L	96_V	0.550	0.89
43_R	118_K	0.549	0.89
153_A	187_A	0.549	0.89
176_L	187_A	0.548	0.89
30_N	73_G	0.548	0.89
132_E	165_V	0.548	0.89
35_W	115_L	0.547	0.89
19_V	52_V	0.544	0.89
177_F	247_C	0.543	0.89
28_V	37_V	0.543	0.89
56_A	165_V	0.542	0.89
133_P	206_L	0.542	0.89
71_H	76_G	0.539	0.88
131_P	163_L	0.538	0.88
7_V	74_M	0.538	0.88
146_K	164_V	0.532	0.88
109_R	112_G	0.532	0.88
133_P	164_V	0.530	0.87
6_E	112_G	0.530	0.87
216_T	225_G	0.529	0.87
49_V	52_V	0.529	0.87
227_P	231_A	0.527	0.87
26_A	63_L	0.526	0.87
113_A	125_V	0.526	0.87
241_G	252_V	0.525	0.87
73_G	113_A	0.525	0.87
74_M	111_F	0.525	0.87
117_T	120_L	0.524	0.87
206_L	210_I	0.523	0.87
185_R	191_S	0.523	0.87
190_L	198_L	0.522	0.87
108_P	111_F	0.522	0.87
184_D	263_Y	0.522	0.87
209_S	212_Q	0.515	0.86
146_K	157_W	0.515	0.86
107_D	111_F	0.514	0.86
75_S	92_H	0.513	0.86
254_T	261_T	0.511	0.86
105_Y	109_R	0.510	0.85
29_R	87_P	0.509	0.85
7_V	109_R	0.509	0.85
5_P	8_E	0.507	0.85
30_N	33_L	0.505	0.85
141_E	144_H	0.505	0.85
54_R	132_E	0.503	0.85
179_A	205_V	0.501	0.84
47_Q	63_L	0.501	0.84
10_S	79_R	0.501	0.84
14_I	80_I	0.501	0.84
205_V	208_R	0.500	0.84

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
1k82A	1	0.9665	100	0.037	Contact Map
3u6pA	1	0.9182	100	0.051	Contact Map
4pd2A	1	0.9888	100	0.055	Contact Map
3twlA	1	0.9182	100	0.086	Contact Map
1ee8A	2	0.9591	100	0.115	Contact Map
3vk8A	1	0.9405	100	0.124	Contact Map
1k3xA	1	0.9108	100	0.139	Contact Map
4mb7A	2	0.8996	100	0.178	Contact Map
3w0fA	1	0.9033	100	0.224	Contact Map
1tdhA	1	0.8736	100	0.229	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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