UPPS - ECOLI - GREMLIN Contacts

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UPPS - Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)

UniProt:	P60472	Sequences: MMLSATQPLSEKLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRFGGTEPGDETA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13329
Length:	253 (232)
Sequences:	5078 (3259)
Seq/√Len:	214.0

ECOLI - UPPS
BACSU - ISPT
HALSA - UPPS Q9HP67
SULSO - UPPS

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_K	180_H	3.473	1.00
19_R	63_E	3.419	1.00
219_V	228_D	2.746	1.00
161_K	166_N	2.723	1.00
50_V	67_L	2.690	1.00
104_N	136_G	2.609	1.00
29_G	39_R	2.547	1.00
192_V	209_I	2.460	1.00
129_A	132_A	2.456	1.00
101_H	130_L	2.443	1.00
90_V	119_R	2.413	1.00
94_D	123_R	2.388	1.00
37_K	41_F	2.379	1.00
59_N	226_E	2.260	1.00
104_N	135_T	2.212	1.00
40_A	84_A	2.199	1.00
56_F	230_E	2.166	1.00
228_D	231_G	2.116	1.00
49_S	52_R	2.061	1.00
153_Q	182_C	2.058	1.00
51_R	96_E	2.057	1.00
79_A	83_S	2.041	1.00
152_V	177_L	2.017	1.00
101_H	134_N	2.010	1.00
189_V	212_A	1.955	1.00
121_Q	125_R	1.954	1.00
58_A	136_G	1.953	1.00
140_N	186_L	1.943	1.00
112_D	153_Q	1.941	1.00
113_T	125_R	1.938	1.00
225_D	228_D	1.930	1.00
201_I	209_I	1.890	1.00
215_Y	235_A	1.880	1.00
215_Y	232_A	1.863	1.00
57_A	229_F	1.843	1.00
64_A	187_A	1.778	1.00
113_T	128_E	1.777	1.00
148_R	188_P	1.736	1.00
76_N	245_G	1.718	1.00
64_A	186_L	1.707	1.00
109_I	124_I	1.698	1.00
115_R	144_N	1.683	1.00
149_W	153_Q	1.683	1.00
192_V	212_A	1.665	1.00
64_A	140_N	1.655	1.00
60_N	230_E	1.631	1.00
34_K	220_L	1.608	1.00
118_S	122_E	1.600	1.00
168_Q	171_Q	1.585	1.00
45_A	48_K	1.560	1.00
52_R	226_E	1.532	1.00
41_F	44_K	1.531	1.00
150_D	182_C	1.531	1.00
157_Q	180_H	1.530	1.00
108_R	138_T	1.521	1.00
55_S	103_H	1.519	1.00
149_W	182_C	1.502	1.00
64_A	138_T	1.490	1.00
17_G	62_I	1.474	1.00
155_V	177_L	1.465	1.00
104_N	134_N	1.464	1.00
158_L	176_M	1.456	1.00
160_E	164_Q	1.450	1.00
21_V	229_F	1.382	1.00
23_I	53_A	1.378	1.00
113_T	121_Q	1.368	1.00
158_L	180_H	1.367	1.00
158_L	172_I	1.351	1.00
173_D	176_M	1.342	1.00
60_N	233_L	1.341	1.00
55_S	99_S	1.340	1.00
126_K	130_L	1.332	1.00
23_I	65_L	1.331	1.00
125_R	129_A	1.327	1.00
66_T	142_A	1.303	1.00
163_Q	169_P	1.297	1.00
148_R	174_E	1.284	1.00
233_L	237_A	1.283	1.00
56_F	59_N	1.282	1.00
147_G	206_L	1.273	1.00
116_F	143_A	1.272	1.00
112_D	149_W	1.270	1.00
122_E	126_K	1.220	1.00
159_A	162_V	1.193	1.00
178_N	188_P	1.190	1.00
118_S	121_Q	1.174	1.00
110_I	183_M	1.170	1.00
24_I	192_V	1.165	1.00
97_V	127_S	1.165	1.00
150_D	208_Q	1.162	1.00
106_R	138_T	1.159	1.00
235_A	238_N	1.156	1.00
70_F	82_V	1.154	1.00
112_D	115_R	1.150	1.00
90_V	123_R	1.132	1.00
175_E	179_Q	1.132	1.00
67_L	139_L	1.127	1.00
49_S	53_A	1.120	1.00
90_V	120_L	1.112	1.00
110_I	142_A	1.110	1.00
163_Q	168_Q	1.109	1.00
153_Q	157_Q	1.100	1.00
191_L	232_A	1.095	1.00
177_L	180_H	1.087	1.00
38_I	41_F	1.086	1.00
89_F	143_A	1.078	1.00
97_V	130_L	1.071	1.00
108_R	128_E	1.064	1.00
151_I	177_L	1.061	1.00
49_S	225_D	1.061	1.00
70_F	75_W	1.060	1.00
159_A	172_I	1.049	1.00
44_K	91_W	1.042	1.00
66_T	205_L	1.040	1.00
123_R	126_K	1.039	1.00
110_I	140_N	1.036	1.00
47_A	92_A	1.029	1.00
199_H	216_F	1.023	1.00
162_V	167_L	1.018	1.00
157_Q	160_E	1.007	1.00
67_L	141_I	1.004	1.00
167_L	176_M	1.003	1.00
109_I	113_T	1.002	1.00
150_D	153_Q	0.999	1.00
98_K	130_L	0.999	1.00
107_L	127_S	0.987	1.00
22_A	189_V	0.981	1.00
151_I	155_V	0.981	1.00
120_L	123_R	0.961	1.00
56_F	229_F	0.959	1.00
234_N	237_A	0.959	1.00
160_E	163_Q	0.956	1.00
209_I	212_A	0.953	1.00
21_V	62_I	0.951	1.00
162_V	169_P	0.949	1.00
158_L	167_L	0.942	1.00
21_V	233_L	0.935	0.99
94_D	126_K	0.933	0.99
209_I	214_L	0.929	0.99
176_M	180_H	0.922	0.99
44_K	48_K	0.920	0.99
160_E	170_D	0.917	0.99
125_R	128_E	0.917	0.99
162_V	165_G	0.910	0.99
58_A	137_L	0.904	0.99
98_K	102_R	0.899	0.99
229_F	233_L	0.887	0.99
25_M	69_A	0.887	0.99
105_V	137_L	0.883	0.99
53_A	56_F	0.872	0.99
72_S	146_G	0.869	0.99
54_V	139_L	0.868	0.99
108_R	140_N	0.868	0.99
201_I	206_L	0.866	0.99
144_N	245_G	0.863	0.99
54_V	105_V	0.863	0.99
156_R	170_D	0.857	0.99
117_N	120_L	0.844	0.99
152_V	155_V	0.827	0.99
231_G	235_A	0.826	0.99
171_Q	176_M	0.824	0.99
226_E	230_E	0.824	0.99
108_R	186_L	0.820	0.99
65_L	137_L	0.819	0.99
29_G	78_P	0.818	0.99
215_Y	228_D	0.818	0.99
189_V	192_V	0.818	0.99
114_S	121_Q	0.817	0.99
112_D	144_N	0.815	0.99
22_A	192_V	0.812	0.99
217_T	232_A	0.811	0.98
155_V	159_A	0.805	0.98
43_H	81_E	0.797	0.98
17_G	237_A	0.797	0.98
230_E	234_N	0.781	0.98
73_E	203_N	0.780	0.98
177_L	181_V	0.779	0.98
89_F	120_L	0.778	0.98
62_I	233_L	0.773	0.98
41_F	45_A	0.773	0.98
161_K	179_Q	0.773	0.98
196_G	199_H	0.769	0.98
241_R	244_G	0.766	0.98
35_Q	223_D	0.766	0.98
108_R	185_E	0.763	0.98
58_A	103_H	0.761	0.98
109_I	128_E	0.760	0.98
147_G	150_D	0.760	0.98
152_V	172_I	0.759	0.98
75_W	144_N	0.758	0.98
86_M	116_F	0.758	0.98
146_G	203_N	0.757	0.98
52_R	225_D	0.756	0.98
80_Q	83_S	0.753	0.98
195_T	217_T	0.749	0.97
60_N	229_F	0.746	0.97
156_R	159_A	0.744	0.97
82_V	86_M	0.742	0.97
73_E	146_G	0.741	0.97
160_E	169_P	0.740	0.97
21_V	57_A	0.739	0.97
56_F	226_E	0.738	0.97
227_Q	230_E	0.731	0.97
159_A	163_Q	0.728	0.97
51_R	99_S	0.726	0.97
153_Q	156_R	0.726	0.97
91_W	95_S	0.725	0.97
199_H	235_A	0.723	0.97
206_L	210_A	0.721	0.97
158_L	177_L	0.716	0.97
31_W	223_D	0.713	0.97
196_G	242_R	0.709	0.97
53_A	226_E	0.706	0.96
52_R	55_S	0.705	0.96
64_A	189_V	0.704	0.96
152_V	156_R	0.703	0.96
167_L	171_Q	0.700	0.96
89_F	92_A	0.698	0.96
56_F	60_N	0.697	0.96
155_V	158_L	0.696	0.96
178_N	181_V	0.694	0.96
113_T	124_I	0.693	0.96
189_V	209_I	0.688	0.96
172_I	176_M	0.687	0.96
179_Q	185_E	0.685	0.96
156_R	169_P	0.684	0.96
55_S	59_N	0.683	0.96
176_M	179_Q	0.678	0.96
124_I	143_A	0.678	0.96
23_I	193_I	0.675	0.95
220_L	223_D	0.672	0.95
147_G	204_F	0.669	0.95
54_V	137_L	0.668	0.95
109_I	141_I	0.667	0.95
219_V	223_D	0.666	0.95
161_K	164_Q	0.661	0.95
68_Y	203_N	0.661	0.95
45_A	49_S	0.661	0.95
63_E	138_T	0.658	0.95
87_E	119_R	0.654	0.95
58_A	105_V	0.654	0.95
17_G	233_L	0.654	0.95
183_M	208_Q	0.654	0.95
213_E	241_R	0.652	0.94
199_H	218_D	0.649	0.94
124_I	141_I	0.648	0.94
239_R	242_R	0.645	0.94
18_C	21_V	0.639	0.94
138_T	186_L	0.638	0.94
178_N	185_E	0.637	0.94
86_M	117_N	0.633	0.94
48_K	95_S	0.632	0.93
123_R	127_S	0.631	0.93
99_S	102_R	0.630	0.93
57_A	65_L	0.629	0.93
191_L	215_Y	0.629	0.93
43_H	88_L	0.628	0.93
89_F	141_I	0.625	0.93
167_L	172_I	0.624	0.93
213_E	239_R	0.623	0.93
16_H	237_A	0.623	0.93
213_E	244_G	0.620	0.93
96_E	99_S	0.618	0.93
147_G	151_I	0.616	0.93
159_A	167_L	0.616	0.93
54_V	65_L	0.612	0.92
83_S	87_E	0.612	0.92
17_G	61_G	0.611	0.92
22_A	204_F	0.611	0.92
66_T	110_I	0.605	0.92
97_V	123_R	0.601	0.92
159_A	169_P	0.600	0.92
217_T	228_D	0.599	0.92
34_K	223_D	0.599	0.92
120_L	124_I	0.597	0.91
211_Y	244_G	0.597	0.91
21_V	193_I	0.594	0.91
198_E	242_R	0.593	0.91
17_G	60_N	0.591	0.91
122_E	125_R	0.590	0.91
110_I	205_L	0.590	0.91
224_F	232_A	0.588	0.91
114_S	144_N	0.585	0.91
201_I	214_L	0.584	0.91
87_E	91_W	0.584	0.91
154_G	177_L	0.578	0.90
217_T	224_F	0.578	0.90
33_K	39_R	0.576	0.90
227_Q	231_G	0.575	0.90
68_Y	150_D	0.575	0.90
166_N	180_H	0.574	0.90
73_E	211_Y	0.572	0.90
211_Y	241_R	0.571	0.90
193_I	232_A	0.570	0.89
156_R	160_E	0.569	0.89
69_A	141_I	0.569	0.89
147_G	201_I	0.569	0.89
158_L	161_K	0.568	0.89
45_A	52_R	0.567	0.89
15_A	237_A	0.566	0.89
97_V	101_H	0.558	0.88
169_P	176_M	0.558	0.88
49_S	56_F	0.556	0.88
239_R	244_G	0.555	0.88
53_A	229_F	0.554	0.88
71_S	146_G	0.553	0.88
221_W	224_F	0.545	0.87
89_F	93_L	0.545	0.87
43_H	85_L	0.543	0.87
52_R	56_F	0.542	0.87
213_E	242_R	0.540	0.87
68_Y	211_Y	0.540	0.87
193_I	224_F	0.538	0.87
196_G	220_L	0.538	0.87
152_V	174_E	0.535	0.86
90_V	94_D	0.534	0.86
56_F	225_D	0.532	0.86
72_S	203_N	0.528	0.86
100_L	105_V	0.525	0.85
195_T	216_F	0.525	0.85
35_Q	39_R	0.524	0.85
215_Y	231_G	0.524	0.85
107_L	141_I	0.522	0.85
163_Q	166_N	0.521	0.85
107_L	139_L	0.521	0.85
18_C	237_A	0.520	0.85
93_L	127_S	0.520	0.85
101_H	133_G	0.519	0.85
234_N	238_N	0.516	0.84
116_F	121_Q	0.515	0.84
217_T	235_A	0.514	0.84
92_A	96_E	0.514	0.84
55_S	58_A	0.513	0.84
179_Q	184_H	0.513	0.84
190_D	243_F	0.511	0.84
192_V	214_L	0.511	0.84
93_L	97_V	0.510	0.84
94_D	98_K	0.508	0.83
35_Q	38_I	0.507	0.83
225_D	231_G	0.505	0.83
169_P	173_D	0.505	0.83
39_R	43_H	0.504	0.83
54_V	58_A	0.504	0.83
162_V	171_Q	0.502	0.83
174_E	178_N	0.502	0.83
68_Y	201_I	0.501	0.83
157_Q	184_H	0.500	0.82
23_I	221_W	0.500	0.82

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
3sgvB	2	0.9012	100	0.087	Contact Map
1f75A	2	0.8577	100	0.093	Contact Map
2vg3A	2	0.9723	100	0.097	Contact Map
4q9mA	2	0.8933	100	0.108	Contact Map
4h8eA	2	0.9289	100	0.114	Contact Map
2d2rA	2	0.8577	100	0.122	Contact Map
3ugsB	2	0.8221	100	0.138	Contact Map
2vg0A	2	0.8775	100	0.142	Contact Map
3wqlA	2	0.9209	97.9	0.908	Contact Map
3bdkA	2	0.9684	57.5	0.959	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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