CYOE - ECOLI - GREMLIN Contacts

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CYOE - Protoheme IX farnesyltransferase

UniProt:	P0AEA5	Sequences: MMFKQYLQVTKPGIIFGNLISVIGGFLLASKGSIDYPLFIYTLVGVSLVVASGCVFNNYIDRDIDRKMERTKNRVLVKGLISPAVSLVYATLLGIAGFMLLWFGANPLACWLGVMGFVVYVGVYSLYMKRHSVYGTLIGSLSGAAPPVIGYCAVTGEFDSGAAILLAIFSLWQMPHSYAIAIFRFKDYQAANIPVLPVVKGISVAKNHITLYIIAFAVATLMLSLGGYAGYKYLVVAAAVSVWWLGMALRGYKVADDRIWARKLFGFSIIAITALSVMMSVDFMVPDSHTLLAAVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10182
Length:	296 (274)
Sequences:	6778 (4582)
Seq/√Len:	276.8

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_R	83_P	4.476	1.00
59_Y	83_P	4.304	1.00
6_Y	10_T	4.237	1.00
59_Y	87_L	3.566	1.00
52_S	94_G	3.160	1.00
5_Q	80_L	3.134	1.00
69_E	72_K	3.069	1.00
82_S	85_V	2.932	1.00
106_N	109_A	2.738	1.00
64_I	193_I	2.614	1.00
55_V	93_L	2.495	1.00
203_S	207_N	2.442	1.00
109_A	152_C	2.402	1.00
107_P	111_W	2.337	1.00
236_V	278_M	2.315	1.00
186_K	189_Q	2.293	1.00
41_Y	104_G	2.233	1.00
66_R	77_V	2.185	1.00
15_I	47_S	2.130	1.00
84_A	88_V	2.058	1.00
185_F	189_Q	2.055	1.00
49_V	97_G	2.052	1.00
230_G	282_D	2.032	1.00
23_I	43_L	1.983	1.00
5_Q	10_T	1.980	1.00
41_Y	100_L	1.932	1.00
7_L	10_T	1.891	1.00
6_Y	85_V	1.786	1.00
60_I	127_Y	1.763	1.00
103_F	110_C	1.758	1.00
260_W	264_L	1.757	1.00
243_W	246_G	1.748	1.00
159_D	162_A	1.748	1.00
59_Y	86_S	1.713	1.00
94_G	117_F	1.699	1.00
55_V	89_Y	1.650	1.00
182_I	204_V	1.648	1.00
189_Q	198_V	1.643	1.00
239_A	243_W	1.614	1.00
141_L	166_L	1.606	1.00
35_D	38_L	1.579	1.00
119_V	142_S	1.573	1.00
108_L	152_C	1.548	1.00
118_V	122_G	1.532	1.00
250_R	253_K	1.521	1.00
48_L	96_A	1.520	1.00
128_M	131_H	1.519	1.00
8_Q	80_L	1.518	1.00
76_L	86_S	1.512	1.00
67_K	191_A	1.511	1.00
214_I	218_V	1.510	1.00
62_R	66_R	1.508	1.00
123_V	138_I	1.506	1.00
185_F	202_I	1.493	1.00
81_I	86_S	1.491	1.00
128_M	138_I	1.464	1.00
55_V	90_A	1.456	1.00
223_L	233_Y	1.454	1.00
135_G	195_V	1.451	1.00
246_G	250_R	1.451	1.00
88_V	92_L	1.449	1.00
61_D	130_R	1.427	1.00
26_F	39_F	1.423	1.00
243_W	247_M	1.405	1.00
111_W	115_M	1.399	1.00
51_A	93_L	1.388	1.00
91_T	95_I	1.360	1.00
249_L	252_Y	1.356	1.00
163_A	167_A	1.352	1.00
55_V	81_I	1.352	1.00
244_W	247_M	1.350	1.00
242_V	246_G	1.349	1.00
158_F	162_A	1.337	1.00
185_F	198_V	1.333	1.00
68_M	187_D	1.324	1.00
10_T	93_L	1.317	1.00
204_V	208_H	1.316	1.00
29_A	151_Y	1.316	1.00
22_V	46_V	1.310	1.00
207_N	211_L	1.305	1.00
171_L	214_I	1.303	1.00
240_V	275_L	1.295	1.00
158_F	163_A	1.294	1.00
224_S	234_L	1.287	1.00
49_V	113_G	1.268	1.00
40_I	44_V	1.264	1.00
19_L	23_I	1.253	1.00
48_L	97_G	1.244	1.00
61_D	64_I	1.238	1.00
37_P	41_Y	1.211	1.00
270_I	274_A	1.207	1.00
181_A	197_P	1.192	1.00
101_L	113_G	1.191	1.00
204_V	207_N	1.188	1.00
81_I	89_Y	1.186	1.00
256_D	259_I	1.184	1.00
175_P	212_Y	1.170	1.00
259_I	263_K	1.170	1.00
229_A	279_M	1.169	1.00
240_V	271_A	1.167	1.00
22_V	42_T	1.166	1.00
119_V	141_L	1.162	1.00
83_P	87_L	1.160	1.00
60_I	125_S	1.151	1.00
48_L	93_L	1.149	1.00
45_G	101_L	1.145	1.00
59_Y	76_L	1.145	1.00
6_Y	9_V	1.142	1.00
168_I	219_A	1.142	1.00
114_V	118_V	1.141	1.00
99_M	104_G	1.131	1.00
89_Y	93_L	1.125	1.00
10_T	51_A	1.124	1.00
19_L	43_L	1.124	1.00
196_L	200_K	1.122	1.00
247_M	267_F	1.121	1.00
87_L	91_T	1.121	1.00
59_Y	90_A	1.119	1.00
64_I	130_R	1.119	1.00
76_L	81_I	1.118	1.00
62_R	76_L	1.104	1.00
81_I	85_V	1.101	1.00
200_K	204_V	1.100	1.00
258_R	261_A	1.088	1.00
262_R	266_G	1.085	1.00
144_A	170_S	1.082	1.00
269_I	273_T	1.082	1.00
98_F	114_V	1.082	1.00
144_A	173_Q	1.079	1.00
216_F	220_T	1.078	1.00
29_A	154_V	1.074	1.00
229_A	282_D	1.064	1.00
148_V	166_L	1.059	1.00
243_W	267_F	1.057	1.00
224_S	227_G	1.049	1.00
26_F	42_T	1.049	1.00
244_W	248_A	1.039	1.00
211_L	215_A	1.032	1.00
56_F	90_A	1.026	1.00
144_A	169_F	1.025	1.00
108_L	112_L	1.020	1.00
232_K	236_V	1.019	1.00
183_F	262_R	1.011	1.00
55_V	86_S	1.010	1.00
184_R	188_Y	1.008	1.00
101_L	105_A	1.007	1.00
263_K	266_G	1.000	1.00
109_A	149_I	0.999	1.00
119_V	123_V	0.997	1.00
221_L	225_L	0.994	1.00
63_D	67_K	0.989	1.00
186_K	190_A	0.984	1.00
160_S	163_A	0.983	1.00
116_G	145_A	0.980	1.00
35_D	154_V	0.980	1.00
128_M	132_S	0.975	1.00
108_L	111_W	0.970	1.00
98_F	110_C	0.969	1.00
61_D	125_S	0.968	1.00
266_G	269_I	0.967	1.00
77_V	86_S	0.964	1.00
16_F	269_I	0.963	1.00
41_Y	105_A	0.960	1.00
169_F	173_Q	0.958	1.00
95_I	99_M	0.954	1.00
220_T	224_S	0.951	1.00
246_G	249_L	0.940	1.00
234_L	238_A	0.934	1.00
107_P	110_C	0.933	1.00
182_I	202_I	0.930	1.00
248_A	252_Y	0.929	1.00
103_F	107_P	0.923	1.00
245_L	248_A	0.922	1.00
27_L	280_S	0.918	1.00
56_F	60_I	0.917	1.00
167_A	171_L	0.916	1.00
104_G	107_P	0.916	1.00
278_M	282_D	0.915	1.00
133_V	194_P	0.913	1.00
7_L	12_P	0.913	1.00
171_L	212_Y	0.907	1.00
251_G	254_V	0.906	1.00
24_G	280_S	0.904	1.00
118_V	123_V	0.899	1.00
177_S	180_I	0.895	1.00
148_V	162_A	0.894	1.00
34_I	39_F	0.894	1.00
143_G	173_Q	0.889	1.00
157_E	161_G	0.888	1.00
210_T	214_I	0.888	1.00
106_N	112_L	0.885	1.00
213_I	248_A	0.885	1.00
145_A	149_I	0.883	1.00
144_A	150_G	0.880	1.00
194_P	199_V	0.876	1.00
108_L	156_G	0.874	1.00
231_Y	235_V	0.864	1.00
69_E	186_K	0.862	1.00
256_D	260_W	0.861	1.00
217_A	241_S	0.859	1.00
37_P	40_I	0.855	1.00
236_V	240_V	0.848	1.00
22_V	146_P	0.847	1.00
115_M	118_V	0.846	1.00
58_N	61_D	0.843	1.00
209_I	213_I	0.841	1.00
207_N	210_T	0.837	1.00
187_D	190_A	0.836	1.00
239_A	242_V	0.831	1.00
136_T	177_S	0.826	1.00
268_S	272_I	0.821	0.99
116_G	149_I	0.820	0.99
75_V	79_G	0.818	0.99
113_G	149_I	0.815	0.99
233_Y	237_A	0.813	0.99
244_W	251_G	0.812	0.99
6_Y	89_Y	0.812	0.99
270_I	273_T	0.810	0.99
252_Y	255_A	0.808	0.99
61_D	193_I	0.808	0.99
245_L	249_L	0.805	0.99
176_H	180_I	0.801	0.99
63_D	66_R	0.795	0.99
261_A	265_F	0.788	0.99
99_M	103_F	0.786	0.99
260_W	263_K	0.784	0.99
56_F	91_T	0.783	0.99
164_I	226_G	0.783	0.99
253_K	256_D	0.782	0.99
101_L	110_C	0.777	0.99
132_S	138_I	0.777	0.99
203_S	206_K	0.776	0.99
10_T	89_Y	0.775	0.99
98_F	101_L	0.774	0.99
136_T	178_Y	0.772	0.99
25_G	150_G	0.772	0.99
28_L	151_Y	0.771	0.99
85_V	89_Y	0.766	0.99
236_V	241_S	0.765	0.99
243_W	250_R	0.763	0.99
98_F	103_F	0.762	0.99
85_V	88_V	0.762	0.99
252_Y	256_D	0.759	0.99
56_F	122_G	0.755	0.99
50_V	54_C	0.747	0.99
123_V	128_M	0.743	0.99
100_L	104_G	0.742	0.99
8_Q	75_V	0.742	0.99
267_F	271_A	0.740	0.99
44_V	100_L	0.727	0.99
147_P	153_A	0.727	0.99
139_G	176_H	0.725	0.99
220_T	237_A	0.719	0.99
140_S	174_M	0.718	0.99
59_Y	62_R	0.715	0.99
206_K	209_I	0.715	0.99
151_Y	155_T	0.710	0.98
261_A	264_L	0.710	0.98
230_G	233_Y	0.709	0.98
64_I	191_A	0.704	0.98
277_V	281_V	0.702	0.98
109_A	113_G	0.702	0.98
90_A	94_G	0.699	0.98
160_S	164_I	0.696	0.98
33_S	37_P	0.692	0.98
178_Y	196_L	0.690	0.98
202_I	206_K	0.689	0.98
25_G	29_A	0.686	0.98
54_C	58_N	0.685	0.98
143_G	146_P	0.685	0.98
132_S	196_L	0.684	0.98
27_L	276_S	0.684	0.98
188_Y	195_V	0.682	0.98
51_A	89_Y	0.682	0.98
68_M	188_Y	0.679	0.98
92_L	99_M	0.679	0.98
220_T	241_S	0.679	0.98
136_T	173_Q	0.677	0.98
76_L	79_G	0.677	0.98
105_A	109_A	0.671	0.98
145_A	148_V	0.669	0.98
37_P	44_V	0.666	0.98
215_A	219_A	0.665	0.98
248_A	251_G	0.664	0.98
26_F	154_V	0.663	0.98
48_L	100_L	0.658	0.98
147_P	150_G	0.657	0.98
237_A	241_S	0.654	0.97
232_K	281_V	0.650	0.97
105_A	110_C	0.650	0.97
75_V	80_L	0.647	0.97
265_F	269_I	0.646	0.97
151_Y	162_A	0.645	0.97
275_L	278_M	0.641	0.97
64_I	67_K	0.641	0.97
240_V	243_W	0.639	0.97
217_A	220_T	0.636	0.97
214_I	249_L	0.636	0.97
14_I	54_C	0.632	0.97
237_A	278_M	0.629	0.97
180_I	183_F	0.628	0.97
134_Y	137_L	0.626	0.97
147_P	169_F	0.626	0.97
5_Q	8_Q	0.624	0.97
14_I	17_G	0.623	0.97
51_A	55_V	0.623	0.97
27_L	283_F	0.621	0.97
160_S	225_L	0.621	0.97
139_G	177_S	0.621	0.97
238_A	242_V	0.619	0.96
38_L	154_V	0.619	0.96
147_P	151_Y	0.618	0.96
123_V	127_Y	0.617	0.96
52_S	122_G	0.616	0.96
218_V	221_L	0.615	0.96
213_I	216_F	0.614	0.96
232_K	282_D	0.614	0.96
172_W	176_H	0.614	0.96
235_V	239_A	0.614	0.96
141_L	170_S	0.614	0.96
14_I	177_S	0.612	0.96
45_G	100_L	0.610	0.96
186_K	258_R	0.609	0.96
236_V	282_D	0.609	0.96
182_I	185_F	0.605	0.96
276_S	280_S	0.604	0.96
44_V	48_L	0.603	0.96
112_L	152_C	0.601	0.96
216_F	241_S	0.601	0.96
18_N	116_G	0.599	0.96
210_T	249_L	0.599	0.96
36_Y	40_I	0.598	0.96
181_A	187_D	0.594	0.96
84_A	87_L	0.594	0.96
106_N	153_A	0.594	0.96
23_I	39_F	0.593	0.95
17_G	21_S	0.591	0.95
230_G	234_L	0.589	0.95
151_Y	159_D	0.588	0.95
133_V	199_V	0.587	0.95
230_G	240_V	0.585	0.95
28_L	229_A	0.584	0.95
143_G	147_P	0.582	0.95
159_D	163_A	0.581	0.95
136_T	174_M	0.580	0.95
223_L	234_L	0.577	0.95
87_L	90_A	0.573	0.95
266_G	270_I	0.568	0.94
186_K	259_I	0.567	0.94
134_Y	200_K	0.565	0.94
236_V	274_A	0.562	0.94
219_A	223_L	0.562	0.94
249_L	253_K	0.560	0.94
272_I	276_S	0.559	0.94
14_I	61_D	0.558	0.94
240_V	244_W	0.556	0.94
254_V	260_W	0.555	0.94
15_I	43_L	0.554	0.94
177_S	181_A	0.553	0.93
69_E	73_N	0.553	0.93
139_G	173_Q	0.552	0.93
143_G	176_H	0.551	0.93
242_V	245_L	0.550	0.93
50_V	180_I	0.546	0.93
241_S	245_L	0.546	0.93
247_M	251_G	0.545	0.93
139_G	180_I	0.543	0.93
68_M	176_H	0.543	0.93
135_G	139_G	0.541	0.93
132_S	199_V	0.541	0.93
49_V	117_F	0.540	0.93
221_L	224_S	0.540	0.93
32_G	35_D	0.540	0.93
38_L	42_T	0.539	0.93
43_L	47_S	0.534	0.92
101_L	104_G	0.532	0.92
205_A	248_A	0.532	0.92
279_M	283_F	0.531	0.92
205_A	209_I	0.527	0.92
9_V	86_S	0.525	0.92
137_L	174_M	0.524	0.92
37_P	104_G	0.523	0.91
220_T	234_L	0.522	0.91
60_I	121_V	0.520	0.91
30_S	33_S	0.518	0.91
224_S	233_Y	0.518	0.91
128_M	135_G	0.516	0.91
209_I	264_L	0.515	0.91
210_T	213_I	0.515	0.91
262_R	265_F	0.514	0.91
139_G	143_G	0.512	0.91
108_L	155_T	0.511	0.91
148_V	158_F	0.510	0.90
231_Y	242_V	0.510	0.90
150_G	154_V	0.510	0.90
274_A	278_M	0.509	0.90
58_N	75_V	0.507	0.90
44_V	96_A	0.507	0.90
220_T	223_L	0.506	0.90
18_N	22_V	0.506	0.90
156_G	159_D	0.506	0.90
19_L	22_V	0.505	0.90
7_L	89_Y	0.505	0.90
201_G	205_A	0.505	0.90
38_L	41_Y	0.504	0.90
94_G	98_F	0.503	0.90
233_Y	240_V	0.502	0.90
280_S	283_F	0.501	0.90
238_A	241_S	0.501	0.90
42_T	46_V	0.501	0.90
97_G	113_G	0.500	0.90

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	0.8986	100	0.231	Contact Map
4tq3A	1	0.9358	100	0.303	Contact Map
2xq2A	2	0.7669	16.2	0.952	Contact Map
4wk5A	2	0.3514	3.7	0.964	Contact Map
3ixzA	1	0.6419	3.2	0.965	Contact Map
3ze3A	4	0.3311	2.5	0.967	Contact Map
4llsA	2	0.3818	2.4	0.968	Contact Map
2ls2A	1	0.0845	2.1	0.968	Contact Map
2zxeA	1	0.6385	2.1	0.969	Contact Map
4lfgA	2	0.4155	2.1	0.969	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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