UPPP - ECOLI - GREMLIN Contacts

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UPPP - Undecaprenyl-diphosphatase

UniProt:	P60932	Sequences: MSDMHSLLIAAILGVVEGLTEFLPVSSTGHMIIVGHLLGFEGDTAKTFEVVIQLGSILAVVVMFWRRLFGLIGIHFGRPLQHEGESKGRLTLIHILLGMIPAVVLGLLFHDTIKSLFNPINVMYALVVGGLLLIAAECLKPKEPRAPGLDDMTYRQAFMIGCFQCLALWPGFSRSGATISGGMLMGVSRYAASEFSFLLAVPMMMGATALDLYKSWGFLTSGDIPMFAVGFITAFVVALIAIKTFLQLIKRISFIPFAIYRFIVAAAVYVVFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11665
Length:	273 (257)
Sequences:	4128 (2713)
Seq/√Len:	169.3

ECOLI - UPPP
BACSU - UPPP
SULSO - UPPP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_R	194_E	3.589	1.00
98_G	195_F	3.419	1.00
163_F	181_G	3.076	1.00
16_V	34_V	2.879	1.00
6_S	9_I	2.745	1.00
68_L	201_V	2.742	1.00
103_V	206_G	2.697	1.00
127_V	265_A	2.591	1.00
11_A	233_T	2.530	1.00
138_C	255_I	2.521	1.00
131_L	135_A	2.358	1.00
188_S	191_A	2.343	1.00
99_M	203_M	2.329	1.00
182_G	187_V	2.328	1.00
17_E	56_S	2.295	1.00
130_G	262_F	2.242	1.00
247_Q	251_R	2.225	1.00
114_K	211_D	2.203	1.00
209_A	213_Y	2.178	1.00
102_A	203_M	2.057	1.00
15_V	237_V	2.037	1.00
210_L	214_K	1.947	1.00
158_F	162_C	1.942	1.00
110_H	211_D	1.923	1.00
123_M	265_A	1.881	1.00
65_W	69_F	1.843	1.00
60_V	242_I	1.837	1.00
14_G	233_T	1.807	1.00
7_L	229_V	1.790	1.00
102_A	165_C	1.772	1.00
124_Y	128_V	1.753	1.00
10_A	14_G	1.749	1.00
31_M	49_E	1.746	1.00
265_A	269_Y	1.744	1.00
97_L	154_Y	1.731	1.00
105_L	165_C	1.717	1.00
247_Q	250_K	1.703	1.00
98_G	199_L	1.697	1.00
118_N	121_N	1.694	1.00
58_L	235_F	1.677	1.00
56_S	238_A	1.671	1.00
29_G	122_V	1.670	1.00
190_Y	250_K	1.655	1.00
206_G	210_L	1.650	1.00
259_I	263_I	1.639	1.00
233_T	237_V	1.622	1.00
33_I	268_V	1.613	1.00
123_M	268_V	1.595	1.00
135_A	139_L	1.583	1.00
155_R	159_M	1.583	1.00
70_G	88_G	1.580	1.00
153_T	156_Q	1.573	1.00
63_M	243_K	1.563	1.00
125_A	169_W	1.554	1.00
54_L	208_T	1.553	1.00
109_F	112_T	1.543	1.00
13_L	31_M	1.526	1.00
13_L	34_V	1.513	1.00
266_A	270_V	1.508	1.00
123_M	269_Y	1.498	1.00
134_I	255_I	1.458	1.00
267_A	271_V	1.441	1.00
147_P	151_D	1.439	1.00
255_I	259_I	1.431	1.00
110_H	114_K	1.426	1.00
90_L	94_H	1.424	1.00
205_M	209_A	1.410	1.00
71_L	92_L	1.409	1.00
103_V	107_L	1.374	1.00
69_F	73_G	1.373	1.00
73_G	77_G	1.364	1.00
5_H	9_I	1.351	1.00
62_V	235_F	1.321	1.00
96_L	100_I	1.320	1.00
132_L	180_S	1.315	1.00
134_I	258_A	1.315	1.00
45_A	49_E	1.314	1.00
10_A	48_F	1.312	1.00
125_A	128_V	1.311	1.00
109_F	113_I	1.308	1.00
20_T	25_V	1.294	1.00
211_D	214_K	1.291	1.00
248_L	252_I	1.288	1.00
156_Q	185_M	1.288	1.00
94_H	154_Y	1.286	1.00
210_L	213_Y	1.280	1.00
127_V	269_Y	1.279	1.00
236_V	240_I	1.255	1.00
237_V	241_A	1.250	1.00
148_G	151_D	1.236	1.00
110_H	214_K	1.229	1.00
47_T	215_S	1.227	1.00
47_T	51_V	1.211	1.00
178_T	196_S	1.209	1.00
11_A	15_V	1.187	1.00
103_V	106_G	1.182	1.00
228_A	232_I	1.167	1.00
89_R	93_I	1.166	1.00
147_P	156_Q	1.160	1.00
99_M	103_V	1.159	1.00
235_F	239_L	1.156	1.00
248_L	256_P	1.154	1.00
64_F	246_L	1.153	1.00
243_K	247_Q	1.151	1.00
172_F	177_A	1.140	1.00
10_A	229_V	1.140	1.00
10_A	226_M	1.137	1.00
7_L	225_P	1.137	1.00
137_E	189_R	1.134	1.00
12_I	16_V	1.133	1.00
154_Y	158_F	1.128	1.00
53_Q	204_M	1.128	1.00
206_G	209_A	1.114	1.00
159_M	181_G	1.108	1.00
156_Q	187_V	1.107	1.00
105_L	109_F	1.102	1.00
124_Y	269_Y	1.101	1.00
104_V	108_L	1.098	1.00
121_N	125_A	1.084	1.00
7_L	11_A	1.083	1.00
120_I	269_Y	1.081	1.00
224_I	228_A	1.077	1.00
30_H	260_Y	1.064	1.00
97_L	158_F	1.063	1.00
134_I	138_C	1.060	0.99
94_H	157_A	1.059	0.99
112_T	115_S	1.051	0.99
54_L	204_M	1.050	0.99
159_M	185_M	1.049	0.99
160_I	187_V	1.041	0.99
66_R	70_G	1.032	0.99
193_S	249_I	1.029	0.99
22_F	238_A	1.027	0.99
66_R	69_F	1.027	0.99
193_S	246_L	1.025	0.99
62_V	65_W	1.025	0.99
256_P	259_I	1.020	0.99
34_V	38_L	1.016	0.99
91_T	198_L	1.014	0.99
113_I	168_L	1.012	0.99
33_I	126_L	1.006	0.99
9_I	38_L	1.002	0.99
50_V	211_D	0.995	0.99
245_F	252_I	0.995	0.99
152_M	187_V	0.995	0.99
220_T	223_D	0.987	0.99
61_V	68_L	0.986	0.99
7_L	226_M	0.985	0.99
75_H	93_I	0.984	0.99
63_M	246_L	0.973	0.99
129_G	166_L	0.971	0.99
182_G	192_A	0.971	0.99
223_D	226_M	0.959	0.99
15_V	19_L	0.956	0.99
213_Y	217_G	0.952	0.99
129_G	261_R	0.949	0.99
105_L	168_L	0.946	0.99
107_L	206_G	0.946	0.99
52_I	230_G	0.939	0.99
75_H	92_L	0.938	0.99
36_H	119_P	0.936	0.99
165_C	168_L	0.931	0.99
66_R	73_G	0.927	0.99
32_I	122_V	0.921	0.99
241_A	244_T	0.917	0.99
64_F	194_E	0.910	0.98
50_V	207_A	0.908	0.98
102_A	168_L	0.900	0.98
156_Q	159_M	0.895	0.98
246_L	249_I	0.893	0.98
229_V	233_T	0.893	0.98
148_G	191_A	0.884	0.98
40_F	45_A	0.881	0.98
156_Q	182_G	0.880	0.98
120_I	124_Y	0.880	0.98
10_A	233_T	0.876	0.98
25_V	245_F	0.876	0.98
160_I	199_L	0.872	0.98
55_G	231_F	0.871	0.98
162_C	166_L	0.871	0.98
239_L	243_K	0.865	0.98
121_N	169_W	0.865	0.98
149_L	191_A	0.864	0.98
134_I	262_F	0.862	0.98
74_I	88_G	0.859	0.98
193_S	245_F	0.859	0.98
263_I	267_A	0.855	0.98
262_F	266_A	0.854	0.98
136_A	184_L	0.851	0.98
86_S	89_R	0.843	0.97
132_L	136_A	0.839	0.97
162_C	165_C	0.837	0.97
63_M	239_L	0.837	0.97
225_P	228_A	0.833	0.97
225_P	229_V	0.827	0.97
102_A	106_G	0.826	0.97
211_D	215_S	0.824	0.97
92_L	96_L	0.818	0.97
221_S	225_P	0.816	0.97
180_S	258_A	0.812	0.97
105_L	162_C	0.801	0.97
11_A	229_V	0.801	0.97
160_I	182_G	0.796	0.96
240_I	243_K	0.791	0.96
19_L	25_V	0.787	0.96
33_I	264_V	0.786	0.96
136_A	180_S	0.779	0.96
35_G	40_F	0.774	0.96
223_D	227_F	0.774	0.96
20_T	30_H	0.774	0.96
121_N	124_Y	0.764	0.95
105_L	108_L	0.761	0.95
31_M	234_A	0.760	0.95
112_T	116_L	0.760	0.95
133_L	176_G	0.756	0.95
86_S	90_L	0.755	0.95
95_I	198_L	0.754	0.95
126_L	261_R	0.752	0.95
264_V	267_A	0.751	0.95
261_R	268_V	0.747	0.95
61_V	205_M	0.746	0.95
84_G	89_R	0.743	0.95
46_K	49_E	0.736	0.94
127_V	262_F	0.736	0.94
46_K	53_Q	0.733	0.94
75_H	89_R	0.732	0.94
51_V	208_T	0.731	0.94
139_L	143_E	0.729	0.94
133_L	137_E	0.728	0.94
41_E	45_A	0.728	0.94
139_L	142_K	0.728	0.94
137_E	254_F	0.727	0.94
44_T	223_D	0.727	0.94
28_T	53_Q	0.723	0.94
93_I	96_L	0.722	0.94
127_V	131_L	0.720	0.94
28_T	57_I	0.719	0.94
176_G	183_M	0.719	0.94
35_G	45_A	0.719	0.94
138_C	141_P	0.718	0.94
133_L	180_S	0.716	0.94
33_I	119_P	0.715	0.94
122_V	125_A	0.715	0.94
129_G	172_F	0.712	0.93
46_K	114_K	0.712	0.93
152_M	191_A	0.709	0.93
12_I	34_V	0.708	0.93
199_L	203_M	0.707	0.93
90_L	93_I	0.703	0.93
51_V	231_F	0.700	0.93
57_I	201_V	0.690	0.92
94_H	98_G	0.690	0.92
147_P	188_S	0.684	0.92
104_V	107_L	0.679	0.92
213_Y	216_W	0.677	0.92
194_E	198_L	0.677	0.92
28_T	31_M	0.677	0.92
130_G	134_I	0.676	0.92
75_H	96_L	0.675	0.92
264_V	268_V	0.673	0.91
117_F	121_N	0.673	0.91
37_L	271_V	0.671	0.91
77_G	85_E	0.671	0.91
17_E	28_T	0.671	0.91
47_T	50_V	0.671	0.91
103_V	210_L	0.669	0.91
74_I	86_S	0.664	0.91
212_L	216_W	0.663	0.91
159_M	162_C	0.662	0.91
87_K	150_D	0.662	0.91
10_A	230_G	0.662	0.91
195_F	199_L	0.659	0.91
253_S	261_R	0.659	0.91
200_A	204_M	0.656	0.90
253_S	256_P	0.654	0.90
15_V	233_T	0.653	0.90
8_L	12_I	0.651	0.90
72_I	76_F	0.650	0.90
53_Q	56_S	0.647	0.90
87_K	90_L	0.646	0.90
91_T	149_L	0.645	0.90
228_A	231_F	0.644	0.90
117_F	122_V	0.642	0.89
68_L	72_I	0.641	0.89
234_A	237_V	0.641	0.89
137_E	255_I	0.640	0.89
159_M	163_F	0.637	0.89
47_T	211_D	0.637	0.89
128_V	172_F	0.636	0.89
222_G	225_P	0.634	0.89
72_I	75_H	0.632	0.89
62_V	239_L	0.630	0.88
137_E	242_I	0.629	0.88
131_L	262_F	0.628	0.88
92_L	95_I	0.627	0.88
131_L	134_I	0.625	0.88
85_E	88_G	0.622	0.88
148_G	188_S	0.617	0.87
57_I	200_A	0.615	0.87
152_M	156_Q	0.615	0.87
166_L	177_A	0.613	0.87
52_I	234_A	0.611	0.87
190_Y	194_E	0.611	0.87
13_L	38_L	0.610	0.87
103_V	108_L	0.610	0.87
119_P	268_V	0.610	0.87
35_G	38_L	0.608	0.87
180_S	183_M	0.608	0.87
236_V	239_L	0.607	0.87
19_L	245_F	0.607	0.87
57_I	60_V	0.600	0.86
113_I	169_W	0.598	0.86
53_Q	57_I	0.597	0.86
252_I	256_P	0.597	0.86
127_V	266_A	0.597	0.86
71_L	95_I	0.596	0.86
93_I	97_L	0.595	0.86
138_C	142_K	0.594	0.85
18_G	237_V	0.594	0.85
22_F	31_M	0.594	0.85
172_F	261_R	0.586	0.85
17_E	52_I	0.585	0.85
13_L	45_A	0.582	0.84
175_S	197_F	0.582	0.84
128_V	132_L	0.580	0.84
114_K	117_F	0.580	0.84
25_V	126_L	0.577	0.84
176_G	180_S	0.577	0.84
221_S	224_I	0.574	0.83
163_F	166_L	0.573	0.83
58_L	231_F	0.573	0.83
182_G	185_M	0.573	0.83
89_R	92_L	0.570	0.83
25_V	122_V	0.566	0.83
169_W	172_F	0.566	0.83
102_A	113_I	0.563	0.82
168_L	203_M	0.562	0.82
160_I	195_F	0.556	0.81
64_F	67_R	0.556	0.81
244_T	247_Q	0.556	0.81
255_I	258_A	0.554	0.81
152_M	157_A	0.550	0.81
111_D	115_S	0.549	0.81
231_F	234_A	0.546	0.80
12_I	38_L	0.544	0.80
17_E	57_I	0.543	0.80
180_S	199_L	0.543	0.80
248_L	253_S	0.542	0.80
129_G	169_W	0.541	0.80
108_L	112_T	0.539	0.79
36_H	41_E	0.538	0.79
85_E	89_R	0.538	0.79
29_G	33_I	0.537	0.79
258_A	261_R	0.536	0.79
28_T	56_S	0.534	0.79
84_G	87_K	0.534	0.79
17_E	53_Q	0.532	0.79
137_E	253_S	0.532	0.79
177_A	181_G	0.531	0.78
104_V	162_C	0.530	0.78
48_F	230_G	0.528	0.78
99_M	206_G	0.528	0.78
134_I	259_I	0.528	0.78
56_S	176_G	0.527	0.78
208_T	212_L	0.527	0.78
261_R	264_V	0.525	0.78
60_V	201_V	0.520	0.77
69_F	72_I	0.520	0.77
137_E	183_M	0.520	0.77
134_I	137_E	0.519	0.77
35_G	49_E	0.515	0.76
133_L	254_F	0.513	0.76
130_G	258_A	0.512	0.76
32_I	49_E	0.512	0.76
90_L	154_Y	0.511	0.76
52_I	204_M	0.510	0.76
98_G	152_M	0.510	0.76
263_I	266_A	0.510	0.76
165_C	169_W	0.510	0.76
189_R	253_S	0.509	0.76
101_P	106_G	0.508	0.75
136_A	140_K	0.508	0.75
179_I	254_F	0.507	0.75
93_I	154_Y	0.502	0.75
149_L	200_A	0.501	0.74
32_I	36_H	0.500	0.74

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
4w252	1	0.2271	31.4	0.96	Contact Map
3mp7B	1	0.1978	23.4	0.963	Contact Map
2ww9B	1	0.2198	19.2	0.964	Contact Map
3ux4A	3	0.381	15.2	0.966	Contact Map
3j01B	1	0.4103	7.3	0.97	Contact Map
4x5mA	2	0.3407	7.1	0.971	Contact Map
1rh5B	1	0.2051	6.4	0.971	Contact Map
1iflA	10	0.1941	4.6	0.973	Contact Map
1fdmA	1	0.1832	4.2	0.974	Contact Map
1jb0M	1	0.1136	4	0.974	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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