DGGGP - HALSA - GREMLIN Contacts

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DGGGP - Digeranylgeranylglyceryl phosphate synthase

UniProt:	Q9HRP0	Sequences: METGRGLVELARPVNTLAAGALTFIGAFVAGGAVGRPAATGAAVGATWLATAGGNAINDYFDREVDRINDPDRAIPRGAVSPRGALAYSVVLFVGAAALAATLPVLAVCIAALNLAGLLTYTQYLKGRPGAGNALVAYLGGSTFVFGAAAVGSPLAGGVLAALAALSTFAREVIKDVEDLAGDRAAGLRTLPVVVGHQRALAVSAVFVVGAAAASPVPYLVGVFGWWYLVAVCPGVVVMVVAAARSYTDPAAGQRLLKRGQLLAAAAFVVGRLVTP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	276 (266)
Sequences:	10249 (7381)
Seq/√Len:	452.5

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_R	82_P	4.027	1.00
60_Y	82_P	3.914	1.00
6_G	79_A	3.420	1.00
60_Y	86_L	3.406	1.00
81_S	84_G	3.207	1.00
53_G	93_F	3.202	1.00
83_R	87_A	2.995	1.00
9_E	79_A	2.976	1.00
198_Q	202_A	2.969	1.00
27_A	40_T	2.500	1.00
61_F	123_Q	2.497	1.00
241_V	245_R	2.445	1.00
50_A	96_A	2.272	1.00
8_V	13_P	2.232	1.00
7_L	84_G	2.212	1.00
252_A	256_L	2.180	1.00
199_R	202_A	2.079	1.00
251_A	255_R	2.054	1.00
65_V	188_L	2.023	1.00
42_A	102_T	2.012	1.00
181_A	184_R	2.011	1.00
180_L	184_R	2.008	1.00
237_V	241_V	1.986	1.00
87_A	91_V	1.958	1.00
49_L	95_G	1.951	1.00
105_V	109_C	1.913	1.00
104_P	107_A	1.910	1.00
7_L	88_Y	1.908	1.00
42_A	99_L	1.857	1.00
90_V	94_V	1.855	1.00
56_A	92_L	1.842	1.00
240_V	244_A	1.836	1.00
5_R	9_E	1.828	1.00
254_Q	258_K	1.827	1.00
101_A	108_V	1.827	1.00
36_R	39_A	1.760	1.00
260_G	264_A	1.747	1.00
252_A	255_R	1.701	1.00
202_A	206_V	1.682	1.00
11_A	56_A	1.660	1.00
234_P	238_V	1.650	1.00
10_L	56_A	1.640	1.00
63_R	75_I	1.634	1.00
109_C	113_L	1.625	1.00
225_G	228_Y	1.600	1.00
67_R	76_P	1.596	1.00
107_A	149_A	1.590	1.00
75_I	85_A	1.588	1.00
63_R	67_R	1.569	1.00
46_A	99_L	1.554	1.00
192_P	200_A	1.552	1.00
49_L	96_A	1.529	1.00
117_G	139_L	1.525	1.00
80_V	85_A	1.513	1.00
219_Y	229_L	1.505	1.00
49_L	92_L	1.496	1.00
184_R	193_V	1.494	1.00
211_A	215_S	1.469	1.00
86_L	90_V	1.465	1.00
56_A	88_Y	1.463	1.00
23_T	44_V	1.462	1.00
60_Y	85_A	1.438	1.00
255_R	258_K	1.417	1.00
11_A	92_L	1.415	1.00
180_L	197_H	1.406	1.00
60_Y	89_S	1.389	1.00
18_A	171_R	1.384	1.00
234_P	237_V	1.381	1.00
195_V	199_R	1.379	1.00
82_P	86_L	1.365	1.00
125_L	128_R	1.364	1.00
98_A	102_T	1.354	1.00
253_G	260_G	1.337	1.00
125_L	135_L	1.335	1.00
243_A	246_S	1.333	1.00
11_A	52_A	1.332	1.00
242_A	246_S	1.320	1.00
26_G	30_A	1.319	1.00
254_Q	257_L	1.318	1.00
56_A	89_S	1.286	1.00
11_A	88_Y	1.281	1.00
257_L	261_Q	1.251	1.00
202_A	205_A	1.246	1.00
209_V	213_A	1.245	1.00
197_H	201_L	1.241	1.00
138_Y	161_A	1.235	1.00
57_I	89_S	1.227	1.00
232_V	236_V	1.225	1.00
126_K	129_P	1.225	1.00
8_V	11_A	1.224	1.00
158_G	162_A	1.222	1.00
120_T	135_L	1.217	1.00
54_G	118_L	1.216	1.00
258_K	262_L	1.210	1.00
208_V	211_A	1.200	1.00
52_A	92_L	1.188	1.00
231_A	270_V	1.176	1.00
141_G	165_A	1.176	1.00
23_T	47_T	1.172	1.00
253_G	257_L	1.168	1.00
93_F	115_L	1.163	1.00
50_A	111_A	1.163	1.00
199_R	203_V	1.159	1.00
106_L	110_I	1.152	1.00
204_S	208_V	1.147	1.00
83_R	86_L	1.144	1.00
230_V	234_P	1.141	1.00
163_L	214_A	1.137	1.00
10_L	80_V	1.134	1.00
253_G	256_L	1.120	1.00
241_V	244_A	1.113	1.00
41_G	45_G	1.113	1.00
37_P	41_G	1.109	1.00
155_L	158_G	1.089	1.00
177_V	200_A	1.089	1.00
133_N	173_V	1.087	1.00
205_A	209_V	1.082	1.00
19_A	48_W	1.065	1.00
106_L	109_C	1.061	1.00
258_K	264_A	1.054	1.00
243_A	247_Y	1.043	1.00
233_C	237_V	1.041	1.00
198_Q	201_L	1.035	1.00
215_S	218_P	1.030	1.00
231_A	235_G	1.026	1.00
242_A	245_R	1.024	1.00
244_A	247_Y	1.021	1.00
162_A	166_L	1.014	1.00
240_V	243_A	1.014	1.00
239_M	242_A	1.012	1.00
130_G	194_V	1.002	1.00
100_A	111_A	1.002	1.00
233_C	236_V	1.001	1.00
56_A	80_V	0.994	1.00
191_L	195_V	0.994	1.00
255_R	259_R	0.991	1.00
257_L	260_G	0.988	1.00
132_G	190_T	0.988	1.00
173_V	203_V	0.986	1.00
10_L	85_A	0.979	1.00
101_A	105_V	0.976	1.00
251_A	254_Q	0.973	1.00
23_T	27_A	0.970	1.00
97_A	108_V	0.969	1.00
136_V	172_E	0.969	1.00
180_L	193_V	0.964	1.00
238_V	241_V	0.960	1.00
88_Y	92_L	0.959	1.00
72_D	79_A	0.958	1.00
201_L	204_S	0.936	1.00
137_A	169_F	0.936	1.00
13_P	48_W	0.934	1.00
60_Y	75_I	0.933	1.00
251_A	257_L	0.931	1.00
236_V	240_V	0.929	1.00
254_Q	264_A	0.927	1.00
183_D	190_T	0.925	1.00
189_R	194_V	0.924	1.00
62_D	127_G	0.924	1.00
263_L	267_A	0.924	1.00
46_A	100_A	0.923	1.00
45_G	49_L	0.921	1.00
74_A	78_G	0.917	1.00
227_W	231_A	0.906	1.00
203_V	206_V	0.905	1.00
100_A	103_L	0.904	1.00
256_L	264_A	0.903	1.00
65_V	127_G	0.903	1.00
258_K	261_Q	0.902	1.00
235_G	238_V	0.899	1.00
260_G	263_L	0.893	1.00
219_Y	228_Y	0.891	1.00
256_L	260_G	0.889	1.00
45_G	99_L	0.889	1.00
201_L	205_A	0.888	1.00
89_S	93_F	0.887	1.00
116_A	120_T	0.886	1.00
166_L	207_F	0.884	1.00
181_A	185_A	0.881	1.00
18_A	22_L	0.874	1.00
255_R	260_G	0.864	1.00
80_V	88_Y	0.862	1.00
84_G	87_A	0.862	1.00
115_L	119_L	0.861	1.00
133_N	172_E	0.858	1.00
259_R	263_L	0.857	1.00
38_A	42_A	0.857	1.00
257_L	264_A	0.856	1.00
38_A	41_G	0.852	1.00
104_P	110_I	0.848	1.00
69_N	182_G	0.846	1.00
76_P	85_A	0.845	1.00
242_A	259_R	0.844	1.00
86_L	89_S	0.839	1.00
207_F	210_G	0.838	1.00
238_V	242_A	0.836	1.00
249_D	252_A	0.832	1.00
239_M	246_S	0.826	1.00
119_L	123_Q	0.823	1.00
239_M	244_A	0.822	1.00
262_L	266_A	0.821	1.00
26_G	29_V	0.821	1.00
191_L	194_V	0.817	1.00
170_A	207_F	0.803	1.00
179_D	183_D	0.802	1.00
117_G	135_L	0.801	1.00
253_G	258_K	0.800	1.00
112_A	116_A	0.798	1.00
16_T	48_W	0.796	1.00
64_E	68_I	0.795	1.00
176_D	192_P	0.794	1.00
27_A	44_V	0.794	1.00
87_A	90_V	0.794	1.00
125_L	129_P	0.792	1.00
51_T	55_N	0.785	1.00
97_A	100_A	0.785	1.00
9_E	14_V	0.783	1.00
260_G	268_F	0.780	1.00
226_W	230_V	0.778	1.00
145_V	161_A	0.776	1.00
131_A	134_A	0.774	1.00
188_L	194_V	0.772	1.00
192_P	195_V	0.771	1.00
35_G	40_T	0.771	1.00
52_A	88_Y	0.770	1.00
91_V	95_G	0.769	1.00
107_A	146_F	0.767	1.00
141_G	168_T	0.764	1.00
231_A	234_P	0.763	1.00
133_N	176_D	0.756	1.00
177_V	199_R	0.755	1.00
216_P	219_Y	0.754	1.00
84_G	88_Y	0.754	1.00
225_G	229_L	0.752	1.00
120_T	125_L	0.751	1.00
259_R	262_L	0.747	1.00
68_I	186_A	0.746	1.00
56_A	85_A	0.746	1.00
39_A	103_L	0.746	1.00
141_G	164_A	0.743	1.00
18_A	21_A	0.743	1.00
105_V	108_V	0.740	1.00
106_L	149_A	0.739	1.00
149_A	157_G	0.738	1.00
60_Y	63_R	0.737	1.00
219_Y	222_G	0.734	1.00
62_D	65_V	0.733	1.00
261_Q	265_A	0.732	1.00
147_G	151_V	0.730	1.00
156_A	159_V	0.728	1.00
203_V	207_F	0.726	1.00
148_A	152_G	0.726	1.00
206_V	210_G	0.722	1.00
95_G	99_L	0.716	1.00
180_L	192_P	0.714	1.00
210_G	214_A	0.704	1.00
261_Q	264_A	0.699	1.00
237_V	244_A	0.693	1.00
230_V	233_C	0.690	1.00
228_Y	235_G	0.690	1.00
260_G	267_A	0.689	1.00
140_G	168_T	0.686	1.00
224_F	228_Y	0.686	1.00
149_A	153_S	0.686	1.00
265_A	268_F	0.685	1.00
177_V	197_H	0.682	1.00
23_T	43_A	0.682	1.00
13_P	52_A	0.682	1.00
170_A	208_V	0.682	1.00
62_D	122_T	0.680	1.00
74_A	79_A	0.678	1.00
254_Q	261_Q	0.676	1.00
172_E	175_K	0.676	1.00
181_A	197_H	0.675	1.00
43_A	150_A	0.671	1.00
25_I	160_L	0.670	1.00
237_V	240_V	0.667	1.00
25_I	29_V	0.666	1.00
53_G	92_L	0.666	1.00
252_A	259_R	0.666	1.00
229_L	233_C	0.664	1.00
207_F	214_A	0.664	1.00
65_V	68_I	0.663	1.00
261_Q	268_F	0.660	1.00
162_A	214_A	0.659	1.00
212_A	215_S	0.658	1.00
64_E	67_R	0.656	1.00
5_R	8_V	0.652	1.00
31_G	35_G	0.651	1.00
52_A	56_A	0.648	1.00
7_L	80_V	0.646	1.00
65_V	186_A	0.646	1.00
164_A	168_T	0.646	1.00
93_F	96_A	0.646	1.00
136_V	171_R	0.646	1.00
99_L	103_L	0.643	1.00
235_G	267_A	0.639	0.99
49_L	99_L	0.638	0.99
108_V	112_A	0.638	0.99
254_Q	260_G	0.637	0.99
137_A	168_T	0.633	0.99
94_V	98_A	0.628	0.99
228_Y	231_A	0.628	0.99
97_A	101_A	0.623	0.99
53_G	119_L	0.620	0.99
214_A	217_V	0.620	0.99
75_I	80_V	0.620	0.99
228_Y	232_V	0.618	0.99
107_A	150_A	0.618	0.99
39_A	151_V	0.618	0.99
215_S	219_Y	0.617	0.99
206_V	209_V	0.616	0.99
176_D	179_D	0.614	0.99
53_G	96_A	0.610	0.99
9_E	74_A	0.609	0.99
89_S	119_L	0.608	0.99
96_A	100_A	0.606	0.99
7_L	11_A	0.605	0.99
224_F	227_W	0.602	0.99
183_D	187_G	0.602	0.99
241_V	246_S	0.602	0.99
196_G	200_A	0.601	0.99
63_R	66_D	0.600	0.99
114_N	142_S	0.600	0.99
20_G	261_Q	0.597	0.99
13_P	16_T	0.597	0.99
31_G	34_V	0.597	0.99
170_A	211_A	0.596	0.99
100_A	108_V	0.596	0.99
227_W	230_V	0.593	0.99
175_K	178_E	0.592	0.99
43_A	47_T	0.592	0.99
73_R	76_P	0.591	0.99
235_G	263_L	0.591	0.99
163_L	215_S	0.591	0.99
42_A	103_L	0.590	0.99
80_V	84_G	0.590	0.99
232_V	235_G	0.590	0.99
188_L	191_L	0.589	0.99
251_A	261_Q	0.589	0.99
29_V	33_A	0.587	0.99
33_A	149_A	0.585	0.99
57_I	119_L	0.585	0.99
201_L	211_A	0.583	0.99
216_P	220_L	0.582	0.99
177_V	201_L	0.579	0.99
22_L	25_I	0.578	0.99
62_D	188_L	0.577	0.99
36_R	151_V	0.576	0.99
224_F	271_G	0.574	0.99
27_A	43_A	0.573	0.99
148_A	157_G	0.571	0.99
24_F	44_V	0.571	0.99
207_F	211_A	0.570	0.99
256_L	259_R	0.568	0.99
131_A	135_L	0.567	0.99
167_S	211_A	0.565	0.99
22_L	26_G	0.563	0.99
189_R	193_V	0.562	0.99
256_L	261_Q	0.562	0.99
223_V	227_W	0.556	0.99
19_A	51_T	0.551	0.98
184_R	189_R	0.545	0.98
256_L	263_L	0.544	0.98
212_A	234_P	0.543	0.98
27_A	35_G	0.543	0.98
74_A	77_R	0.540	0.98
76_P	79_A	0.539	0.98
172_E	176_D	0.537	0.98
19_A	22_L	0.536	0.98
142_S	161_A	0.536	0.98
59_D	62_D	0.535	0.98
217_V	221_V	0.534	0.98
212_A	216_P	0.532	0.98
223_V	226_W	0.532	0.98
252_A	260_G	0.531	0.98
195_V	203_V	0.530	0.98
137_A	165_A	0.530	0.98
240_V	246_S	0.528	0.98
253_G	264_A	0.527	0.98
238_V	245_R	0.525	0.98
259_R	264_A	0.525	0.98
54_G	122_T	0.524	0.98
61_F	122_T	0.523	0.98
137_A	142_S	0.522	0.98
97_A	112_A	0.521	0.98
142_S	146_F	0.521	0.98
231_A	238_V	0.518	0.98
258_K	268_F	0.516	0.98
213_A	217_V	0.516	0.98
264_A	268_F	0.515	0.98
16_T	51_T	0.515	0.98
71_P	76_P	0.510	0.97
239_M	243_A	0.506	0.97
73_R	78_G	0.505	0.97
129_P	194_V	0.504	0.97
225_G	236_V	0.504	0.97
242_A	247_Y	0.503	0.97
240_V	245_R	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	0.942	100	0.212	Contact Map
4tq3A	1	0.9746	100	0.277	Contact Map
2xq2A	2	0.837	63.3	0.923	Contact Map
3dh4A	3	0.7754	10.7	0.949	Contact Map
3ze3A	4	0.3659	8.8	0.951	Contact Map
1pw4A	1	0.8768	5.2	0.956	Contact Map
3m0gA	2	0.7717	3.8	0.959	Contact Map
4tkrA	2	0.5906	3.4	0.96	Contact Map
2onkC	2	0.2572	2.9	0.961	Contact Map
3wajA	1	0.808	2.9	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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