DGGGP - SULSO - GREMLIN Contacts

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DGGGP - Digeranylgeranylglyceryl phosphate synthase

UniProt:	Q9UWY6	Sequences: MSLKSYMQLVRIHNVIGAALGAIMGFLVSSQWYLELKGILLSALVVGLIAAGGYVINDVYDVEIDKINKPYRPIPSGKISVNKAKALSIALFIIGIALSILLNIYALVIALVTAIGLIYYAKDLKKTGFYGNLLVATTTALSIFYGGLAFFSDNWLLRIIIPTLYAFFLTLIREIVKGIEDYNGDSLNNVKTLATTLGINKSWRIAKILLVLLLIISPLPFFIGFNLIYLILLILVFIPFTILSIIQKETIEGASKARTYLKISAISGIIAFLLGSLPFFKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	282 (270)
Sequences:	10210 (7408)
Seq/√Len:	450.8

ECOLI - CYOE UBIA MENA
BACSU - COXX2 COXX1 MENA
HALSA - DGGGP Q9HQN6 LYEL COXX
SULSO - DGGGP COXX Q980Z2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_V	81_V	3.887	1.00
62_V	81_V	3.876	1.00
59_V	85_K	3.432	1.00
5_S	78_K	3.305	1.00
52_G	92_F	3.169	1.00
80_S	83_K	2.995	1.00
82_N	86_A	2.995	1.00
200_N	204_R	2.877	1.00
238_I	242_I	2.846	1.00
238_I	241_T	2.841	1.00
8_Q	78_K	2.820	1.00
26_F	39_I	2.491	1.00
49_I	95_G	2.260	1.00
6_Y	83_K	2.212	1.00
239_P	242_I	2.141	1.00
183_N	186_S	2.112	1.00
103_N	106_A	2.103	1.00
201_K	204_R	2.085	1.00
7_M	12_I	2.063	1.00
100_I	107_L	1.988	1.00
104_I	108_V	1.960	1.00
100_I	104_I	1.951	1.00
48_L	94_I	1.950	1.00
55_V	91_L	1.933	1.00
182_Y	186_S	1.904	1.00
41_L	98_L	1.878	1.00
86_A	90_A	1.873	1.00
89_I	93_I	1.844	1.00
6_Y	87_L	1.841	1.00
64_I	190_V	1.828	1.00
258_R	262_K	1.806	1.00
250_T	253_G	1.797	1.00
62_V	66_K	1.787	1.00
237_F	241_T	1.737	1.00
244_S	247_Q	1.716	1.00
243_L	246_I	1.699	1.00
204_R	208_I	1.675	1.00
106_A	148_L	1.672	1.00
194_A	202_S	1.667	1.00
186_S	195_T	1.666	1.00
10_V	55_V	1.651	1.00
9_L	55_V	1.645	1.00
74_I	84_A	1.641	1.00
4_K	8_Q	1.620	1.00
62_V	74_I	1.599	1.00
41_L	101_L	1.586	1.00
197_L	201_K	1.581	1.00
35_E	38_G	1.573	1.00
97_A	101_L	1.553	1.00
229_Y	233_L	1.552	1.00
66_K	75_P	1.548	1.00
48_L	91_L	1.522	1.00
214_L	235_L	1.521	1.00
261_L	265_A	1.515	1.00
79_I	84_A	1.512	1.00
156_L	159_I	1.504	1.00
108_V	112_V	1.501	1.00
116_G	138_T	1.495	1.00
182_Y	199_I	1.492	1.00
48_L	95_G	1.470	1.00
259_T	263_I	1.465	1.00
55_V	87_L	1.459	1.00
85_K	89_I	1.440	1.00
10_V	51_A	1.439	1.00
271_A	275_G	1.415	1.00
259_T	262_K	1.409	1.00
59_V	84_A	1.403	1.00
45_V	98_L	1.393	1.00
243_L	247_Q	1.391	1.00
59_V	88_S	1.390	1.00
22_A	43_A	1.385	1.00
82_N	85_K	1.384	1.00
253_G	257_A	1.372	1.00
55_V	88_S	1.370	1.00
105_Y	109_I	1.366	1.00
263_I	267_S	1.365	1.00
211_V	215_I	1.353	1.00
10_V	91_L	1.353	1.00
237_F	240_F	1.334	1.00
199_I	203_W	1.322	1.00
10_V	87_L	1.318	1.00
17_G	173_R	1.314	1.00
155_W	159_I	1.311	1.00
124_L	134_L	1.303	1.00
81_V	85_K	1.302	1.00
25_G	29_S	1.297	1.00
140_A	167_F	1.278	1.00
51_A	91_L	1.277	1.00
201_K	205_I	1.271	1.00
119_Y	134_L	1.267	1.00
49_I	110_A	1.256	1.00
56_I	88_S	1.250	1.00
221_F	230_L	1.249	1.00
53_G	117_L	1.236	1.00
9_L	79_I	1.235	1.00
237_F	242_I	1.230	1.00
262_K	266_I	1.226	1.00
22_A	46_V	1.225	1.00
262_K	265_A	1.220	1.00
96_I	100_I	1.212	1.00
226_N	229_Y	1.208	1.00
7_M	10_V	1.177	1.00
226_N	275_G	1.172	1.00
124_L	127_T	1.168	1.00
204_R	207_K	1.154	1.00
99_S	110_A	1.147	1.00
98_L	102_L	1.132	1.00
200_N	203_W	1.131	1.00
193_L	197_L	1.130	1.00
168_F	209_L	1.123	1.00
182_Y	195_T	1.121	1.00
40_L	44_L	1.111	1.00
63_E	67_I	1.110	1.00
191_K	196_T	1.106	1.00
251_I	254_A	1.106	1.00
129_F	196_T	1.099	1.00
258_R	261_L	1.089	1.00
255_S	259_T	1.088	1.00
68_N	71_Y	1.077	1.00
220_P	229_Y	1.077	1.00
203_W	207_K	1.072	1.00
232_L	271_A	1.072	1.00
160_I	164_L	1.067	1.00
165_Y	216_I	1.066	1.00
137_T	163_T	1.063	1.00
67_I	70_P	1.062	1.00
265_A	268_G	1.051	1.00
251_I	255_S	1.050	1.00
268_G	271_A	1.049	1.00
61_D	126_K	1.037	1.00
104_I	107_L	1.034	1.00
59_V	74_I	1.030	1.00
155_W	160_I	1.027	1.00
131_G	192_T	1.026	1.00
105_Y	108_V	1.013	1.00
25_G	28_V	1.010	1.00
17_G	21_G	1.001	1.00
18_A	47_G	0.994	1.00
115_I	119_Y	0.981	1.00
252_E	256_K	0.981	1.00
174_E	178_G	0.977	1.00
73_P	77_G	0.970	1.00
262_K	269_I	0.969	1.00
26_F	43_A	0.963	1.00
60_Y	123_D	0.959	1.00
87_L	91_L	0.956	1.00
36_L	40_L	0.956	1.00
229_Y	232_L	0.952	1.00
75_P	84_A	0.951	1.00
12_I	47_G	0.950	1.00
248_K	251_I	0.949	1.00
265_A	269_I	0.944	1.00
179_I	201_K	0.944	1.00
114_A	118_I	0.933	1.00
55_V	79_I	0.931	1.00
9_L	84_A	0.928	1.00
45_V	99_S	0.928	1.00
44_L	48_L	0.919	1.00
68_N	184_G	0.915	1.00
231_I	235_L	0.913	1.00
44_L	98_L	0.911	1.00
99_S	102_L	0.905	1.00
106_A	145_Y	0.905	1.00
226_N	230_L	0.892	1.00
207_K	211_V	0.888	1.00
185_D	192_T	0.888	1.00
61_D	64_I	0.884	1.00
135_V	174_E	0.880	1.00
183_N	187_L	0.878	1.00
119_Y	123_D	0.878	1.00
179_I	202_S	0.877	1.00
92_F	114_A	0.871	1.00
151_F	154_N	0.869	1.00
83_K	86_A	0.869	1.00
90_A	94_I	0.868	1.00
50_A	54_Y	0.860	1.00
37_K	41_L	0.856	1.00
264_S	268_G	0.855	1.00
148_L	159_I	0.855	1.00
22_A	26_F	0.853	1.00
64_I	126_K	0.845	1.00
147_G	151_F	0.844	1.00
30_S	34_L	0.842	1.00
226_N	233_L	0.839	1.00
172_I	209_L	0.836	1.00
116_G	134_L	0.834	1.00
72_R	75_P	0.833	1.00
123_D	128_G	0.833	1.00
181_D	185_D	0.828	1.00
88_S	92_F	0.827	1.00
156_L	160_I	0.826	1.00
22_A	42_S	0.823	1.00
256_K	260_Y	0.819	1.00
107_L	111_L	0.813	1.00
63_E	66_K	0.811	1.00
61_D	121_A	0.809	1.00
213_L	217_S	0.807	1.00
96_I	107_L	0.806	1.00
37_K	40_L	0.806	1.00
130_Y	133_L	0.805	1.00
157_L	160_I	0.803	1.00
93_I	97_A	0.802	1.00
259_T	265_A	0.802	1.00
267_S	271_A	0.801	1.00
198_G	202_S	0.801	1.00
261_L	264_S	0.800	1.00
256_K	259_T	0.796	1.00
15_V	47_G	0.796	1.00
32_W	35_E	0.795	1.00
64_I	67_I	0.794	1.00
164_L	168_F	0.793	1.00
248_K	253_G	0.793	1.00
23_I	43_A	0.793	1.00
214_L	217_S	0.792	1.00
136_A	171_L	0.789	1.00
83_K	87_L	0.787	1.00
175_I	205_I	0.782	1.00
236_V	239_P	0.782	1.00
234_I	237_F	0.781	1.00
55_V	84_A	0.781	1.00
221_F	224_G	0.779	1.00
34_L	39_I	0.779	1.00
6_Y	79_I	0.779	1.00
228_I	231_I	0.778	1.00
260_Y	265_A	0.777	1.00
260_Y	264_S	0.776	1.00
190_V	196_T	0.772	1.00
241_T	244_S	0.772	1.00
12_I	51_A	0.771	1.00
242_I	260_Y	0.771	1.00
212_L	216_I	0.770	1.00
228_I	232_L	0.768	1.00
205_I	208_I	0.767	1.00
258_R	264_S	0.763	1.00
85_K	88_S	0.760	1.00
140_A	170_T	0.756	1.00
132_N	178_G	0.755	1.00
178_G	194_A	0.755	1.00
132_N	174_E	0.754	1.00
270_I	274_L	0.754	1.00
261_L	269_I	0.752	1.00
132_N	175_I	0.749	1.00
103_N	109_I	0.746	1.00
86_A	89_I	0.746	1.00
220_P	224_G	0.746	1.00
73_P	78_K	0.745	1.00
253_G	256_K	0.745	1.00
182_Y	194_A	0.745	1.00
79_I	87_L	0.744	1.00
8_Q	13_H	0.743	1.00
249_E	253_G	0.735	1.00
217_S	220_P	0.734	1.00
172_I	210_L	0.734	1.00
96_I	99_S	0.733	1.00
132_N	171_L	0.733	1.00
154_N	158_R	0.733	1.00
255_S	258_R	0.732	1.00
174_E	177_K	0.732	1.00
257_A	261_L	0.730	1.00
119_Y	124_L	0.729	1.00
95_G	99_S	0.728	1.00
124_L	128_G	0.728	1.00
41_L	102_L	0.727	1.00
193_L	196_T	0.727	1.00
254_A	257_A	0.725	1.00
94_I	98_L	0.725	1.00
72_R	77_G	0.723	1.00
42_S	149_A	0.722	1.00
164_L	216_I	0.719	1.00
111_L	115_I	0.718	1.00
257_A	260_Y	0.718	1.00
56_I	118_I	0.714	1.00
227_L	231_I	0.706	1.00
24_M	28_V	0.705	1.00
139_T	143_I	0.701	1.00
51_A	87_L	0.700	1.00
59_V	62_V	0.700	1.00
173_R	177_K	0.691	1.00
214_L	218_P	0.691	1.00
190_V	195_T	0.688	1.00
30_S	33_Y	0.688	1.00
79_I	83_K	0.687	1.00
125_K	128_G	0.685	1.00
113_T	141_L	0.685	1.00
166_A	170_T	0.684	1.00
262_K	268_G	0.684	1.00
254_A	258_R	0.680	1.00
233_L	237_F	0.677	1.00
64_I	188_N	0.677	1.00
51_A	55_V	0.674	1.00
42_S	46_V	0.673	1.00
18_A	50_A	0.673	1.00
105_Y	148_L	0.671	1.00
52_G	91_L	0.669	1.00
261_L	271_A	0.667	1.00
177_K	180_E	0.665	1.00
67_I	188_N	0.664	1.00
183_N	199_I	0.661	1.00
229_Y	235_L	0.658	1.00
261_L	268_G	0.657	1.00
230_L	234_I	0.656	1.00
144_F	163_T	0.655	1.00
258_R	271_A	0.654	1.00
17_G	20_L	0.652	1.00
219_L	223_I	0.650	1.00
218_P	221_F	0.649	1.00
75_P	78_K	0.649	1.00
161_I	223_I	0.647	1.00
130_Y	197_L	0.640	0.99
48_L	98_L	0.636	0.99
210_L	213_L	0.635	0.99
235_L	238_I	0.633	0.99
179_I	199_I	0.629	0.99
148_L	152_S	0.625	0.99
266_I	270_I	0.625	0.99
141_L	145_Y	0.618	0.99
232_L	235_L	0.616	0.99
61_D	190_V	0.616	0.99
245_I	257_A	0.616	0.99
38_G	102_L	0.614	0.99
180_E	255_S	0.614	0.99
63_E	69_K	0.613	0.99
12_I	15_V	0.611	0.99
62_V	65_D	0.610	0.99
242_I	245_I	0.610	0.99
260_Y	263_I	0.609	0.99
146_G	150_F	0.608	0.99
30_S	35_E	0.608	0.99
15_V	50_A	0.608	0.99
197_L	205_I	0.607	0.99
139_T	170_T	0.606	0.99
185_D	189_N	0.605	0.99
33_Y	37_K	0.605	0.99
236_V	240_F	0.600	0.99
52_G	118_I	0.597	0.99
145_Y	163_T	0.594	0.99
258_R	265_A	0.594	0.99
99_S	107_L	0.594	0.99
261_L	266_I	0.594	0.99
12_I	18_A	0.592	0.99
126_K	190_V	0.592	0.99
38_G	150_F	0.590	0.99
53_G	113_T	0.589	0.99
6_Y	10_V	0.588	0.99
216_I	219_L	0.586	0.99
136_A	141_L	0.585	0.99
60_Y	121_A	0.582	0.99
26_F	42_S	0.581	0.99
261_L	273_L	0.579	0.99
88_S	118_I	0.578	0.99
209_L	212_L	0.577	0.99
96_I	111_L	0.575	0.99
52_G	95_G	0.574	0.99
92_F	96_I	0.571	0.99
26_F	34_L	0.569	0.99
19_A	22_A	0.568	0.99
58_D	61_D	0.568	0.99
53_G	121_A	0.567	0.99
140_A	166_A	0.567	0.99
194_A	197_L	0.565	0.99
191_K	195_T	0.565	0.99
19_A	47_G	0.564	0.99
248_K	254_A	0.563	0.99
263_I	266_I	0.560	0.99
218_P	222_F	0.557	0.99
192_T	196_T	0.557	0.99
13_H	16_I	0.553	0.98
108_V	111_L	0.553	0.98
257_A	264_S	0.551	0.98
73_P	76_S	0.550	0.98
171_L	209_L	0.546	0.98
92_F	95_G	0.545	0.98
158_R	161_I	0.545	0.98
136_A	170_T	0.544	0.98
144_F	159_I	0.543	0.98
63_E	81_V	0.541	0.98
158_R	223_I	0.539	0.98
254_A	261_L	0.539	0.98
154_N	157_L	0.537	0.98
8_Q	73_P	0.537	0.98
31_Q	34_L	0.537	0.98
26_F	151_F	0.536	0.98
49_I	113_T	0.529	0.98
67_I	71_Y	0.529	0.98
157_L	161_I	0.528	0.98
45_V	110_A	0.528	0.98
175_I	178_G	0.525	0.98
52_G	114_A	0.521	0.98
231_I	234_I	0.521	0.98
57_N	121_A	0.519	0.98
259_T	266_I	0.518	0.98
135_V	173_R	0.517	0.98
205_I	209_L	0.516	0.98
52_G	88_S	0.516	0.98
70_P	184_G	0.515	0.98
15_V	54_Y	0.514	0.98
116_G	137_T	0.513	0.98
208_I	212_L	0.511	0.97
257_A	262_K	0.510	0.97
161_I	219_L	0.509	0.97
141_L	163_T	0.507	0.97
33_Y	36_L	0.505	0.97
14_N	50_A	0.505	0.97
163_T	167_F	0.500	0.97
250_T	255_S	0.500	0.97

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
4od4A	1	0.9397	100	0.232	Contact Map
4tq3A	1	0.9645	100	0.298	Contact Map
2xq2A	2	0.805	42	0.934	Contact Map
1v4eA	3	0.8227	5.7	0.956	Contact Map
1rqjA	2	0.8404	4.5	0.958	Contact Map
3ne5A	3	0.4397	4	0.959	Contact Map
4xnjA	1	0.5887	3.8	0.96	Contact Map
3dh4A	3	0.7411	3.4	0.96	Contact Map
3m0gA	2	0.7695	3.2	0.961	Contact Map
4cz8A	2	0.9716	3.2	0.961	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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