COXX1 - BACSU - GREMLIN Contacts

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COXX1 - Protoheme IX farnesyltransferase 1

UniProt:	O31652	Sequences: MENTRDSAAISETKYIKASNRVTIYDFIKLAKPGIIISNSIAAFGGFWIAFASAEKTLTGLAFLMTMVTAMLGTAFVMASGTVYNNYFDRHMDAKMARTRSRASVTGKMPPAMILTYGSVLGIAGLAMLYSLNPLTAFLGLAAFIFYAIIYTVWVKRTSVWSTFVGSFPGAAPPLMGYCAVTGDFSMTAVLLYTIMFLWQPPHFWAIGIRRKEEYRAAGVPLLPVVKGNHVTKIKMMQYIAVLVPVTLLFPFSLGTGHISPFYFLAALVLGGIWIKKSIKGFKTDDDVKWAKDMFVYSLIYFCLLFFIMMIDSFMMFLIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	320 (278)
Sequences:	8141 (5691)
Seq/√Len:	341.3

ECOLI - CYOE UBIA MENA
BACSU - COXX1 COXX2 MENA
HALSA - COXX DGGGP Q9HQN6 LYEL
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
87_Y	111_P	4.279	1.00
90_R	111_P	4.259	1.00
26_D	108_K	3.537	1.00
87_Y	115_L	3.462	1.00
23_T	113_M	3.345	1.00
110_P	113_M	3.109	1.00
80_S	122_G	3.098	1.00
29_K	108_K	2.904	1.00
230_H	234_I	2.893	1.00
97_A	100_R	2.890	1.00
92_M	220_V	2.408	1.00
112_A	116_T	2.375	1.00
136_T	179_C	2.315	1.00
134_P	138_F	2.303	1.00
290_W	294_M	2.282	1.00
27_F	113_M	2.258	1.00
276_K	280_K	2.235	1.00
133_N	136_T	2.213	1.00
212_K	216_R	2.156	1.00
213_E	216_R	2.102	1.00
186_S	189_A	2.098	1.00
36_I	75_A	2.088	1.00
83_V	121_L	2.050	1.00
47_F	67_M	2.046	1.00
77_V	125_G	2.025	1.00
69_T	131_S	1.957	1.00
94_A	105_V	1.924	1.00
44_F	71_M	1.821	1.00
266_A	308_I	1.772	1.00
129_L	132_L	1.764	1.00
251_P	263_Y	1.758	1.00
69_T	128_M	1.754	1.00
25_Y	29_K	1.746	1.00
292_K	296_V	1.724	1.00
138_F	142_A	1.691	1.00
260_S	312_D	1.683	1.00
231_V	234_I	1.666	1.00
116_T	120_V	1.644	1.00
109_M	114_I	1.637	1.00
63_F	66_T	1.629	1.00
216_R	225_V	1.625	1.00
269_V	273_I	1.619	1.00
104_S	114_I	1.606	1.00
227_K	231_V	1.605	1.00
122_G	144_F	1.563	1.00
83_V	117_Y	1.552	1.00
90_R	94_A	1.531	1.00
87_Y	114_I	1.519	1.00
273_I	276_K	1.518	1.00
241_A	245_P	1.518	1.00
119_S	123_I	1.518	1.00
88_F	153_V	1.509	1.00
31_A	83_V	1.500	1.00
76_F	125_G	1.486	1.00
185_F	189_A	1.461	1.00
146_F	169_P	1.458	1.00
130_Y	137_A	1.447	1.00
150_I	165_V	1.418	1.00
83_V	118_G	1.418	1.00
31_A	79_A	1.413	1.00
145_I	149_I	1.410	1.00
126_L	129_L	1.409	1.00
115_L	119_S	1.406	1.00
30_L	109_M	1.406	1.00
178_Y	182_T	1.401	1.00
168_F	193_Y	1.395	1.00
266_A	270_L	1.390	1.00
31_A	121_L	1.389	1.00
292_K	295_F	1.363	1.00
115_L	118_G	1.344	1.00
284_T	287_D	1.333	1.00
28_I	31_A	1.332	1.00
76_F	124_A	1.312	1.00
90_R	104_S	1.297	1.00
289_K	293_D	1.296	1.00
212_K	229_N	1.295	1.00
114_I	118_G	1.289	1.00
155_V	158_T	1.286	1.00
231_V	235_K	1.280	1.00
125_G	129_L	1.273	1.00
229_N	233_K	1.267	1.00
212_K	225_V	1.267	1.00
135_L	179_C	1.261	1.00
265_L	269_V	1.259	1.00
79_A	121_L	1.259	1.00
28_I	33_P	1.259	1.00
280_K	283_K	1.257	1.00
31_A	117_Y	1.251	1.00
273_I	277_K	1.235	1.00
293_D	296_V	1.233	1.00
299_L	303_C	1.232	1.00
84_Y	118_G	1.228	1.00
135_L	139_L	1.226	1.00
198_L	239_Y	1.222	1.00
296_V	299_L	1.215	1.00
295_F	299_L	1.211	1.00
277_K	281_G	1.211	1.00
298_S	302_F	1.208	1.00
43_A	74_T	1.202	1.00
117_Y	121_L	1.200	1.00
234_I	238_Q	1.199	1.00
50_A	178_Y	1.191	1.00
89_D	157_R	1.189	1.00
174_P	177_G	1.177	1.00
209_I	231_V	1.173	1.00
43_A	70_A	1.164	1.00
190_V	194_T	1.161	1.00
65_M	69_T	1.160	1.00
114_I	117_Y	1.158	1.00
291_A	295_F	1.152	1.00
127_A	131_S	1.148	1.00
296_V	300_I	1.142	1.00
77_V	140_G	1.141	1.00
162_S	222_L	1.139	1.00
195_I	246_V	1.137	1.00
209_I	229_N	1.137	1.00
30_L	83_V	1.137	1.00
68_V	72_L	1.135	1.00
291_A	294_M	1.133	1.00
87_Y	118_G	1.129	1.00
38_S	203_H	1.121	1.00
243_L	247_T	1.104	1.00
27_F	117_Y	1.101	1.00
166_G	170_G	1.072	1.00
185_F	190_V	1.068	1.00
237_M	241_A	1.068	1.00
83_V	109_M	1.055	1.00
211_R	215_Y	1.050	1.00
124_A	128_M	1.050	1.00
275_I	278_S	1.049	1.00
308_I	312_D	1.048	1.00
91_H	95_K	1.043	1.00
155_V	165_V	1.042	1.00
171_A	197_F	1.037	1.00
171_A	200_Q	1.032	1.00
286_D	289_K	1.027	1.00
300_I	304_L	1.019	1.00
204_F	207_I	1.016	1.00
109_M	117_Y	1.014	1.00
194_T	198_L	1.011	1.00
264_F	268_L	1.004	1.00
251_P	264_F	1.004	1.00
96_M	214_E	0.999	1.00
221_P	226_V	0.995	1.00
49_I	178_Y	0.992	1.00
187_M	190_V	0.989	1.00
202_P	239_Y	0.988	1.00
302_F	306_F	0.985	1.00
65_M	68_V	0.985	1.00
155_V	159_S	0.980	1.00
223_L	227_K	0.977	1.00
141_L	145_I	0.976	1.00
123_I	127_A	0.973	1.00
62_A	67_M	0.969	1.00
161_W	164_F	0.967	1.00
40_S	71_M	0.967	1.00
186_S	190_V	0.965	1.00
143_A	172_A	0.965	1.00
105_V	114_I	0.964	1.00
87_Y	104_S	0.964	1.00
24_I	28_I	0.964	1.00
129_L	137_A	0.957	1.00
156_K	159_S	0.955	1.00
282_F	285_D	0.955	1.00
95_K	218_A	0.952	1.00
92_M	157_R	0.952	1.00
272_G	276_K	0.942	1.00
305_L	308_I	0.936	1.00
290_W	293_D	0.934	1.00
261_P	265_L	0.930	1.00
172_A	176_M	0.929	1.00
278_S	282_F	0.926	1.00
38_S	42_A	0.925	1.00
89_D	92_M	0.923	1.00
76_F	121_L	0.923	1.00
300_I	303_C	0.919	1.00
121_L	125_G	0.918	1.00
242_V	246_V	0.913	1.00
276_K	279_I	0.907	1.00
129_L	140_G	0.906	1.00
295_F	298_S	0.905	1.00
118_G	122_G	0.902	1.00
266_A	269_V	0.895	1.00
22_V	25_Y	0.893	1.00
277_K	297_Y	0.892	1.00
260_S	270_L	0.889	1.00
79_A	117_Y	0.886	1.00
259_I	309_M	0.877	1.00
260_S	263_Y	0.873	1.00
286_D	290_W	0.870	1.00
146_F	168_F	0.870	1.00
259_I	312_D	0.868	1.00
73_G	129_L	0.867	1.00
230_H	233_K	0.863	1.00
48_W	310_M	0.861	1.00
135_L	138_F	0.861	1.00
129_L	133_N	0.860	1.00
263_Y	270_L	0.856	1.00
203_H	207_I	0.856	1.00
84_Y	88_F	0.852	1.00
208_G	224_P	0.851	1.00
228_G	232_T	0.851	1.00
64_L	68_V	0.850	1.00
196_M	200_Q	0.848	1.00
279_I	282_F	0.842	1.00
46_G	50_A	0.840	1.00
210_R	292_K	0.840	1.00
262_F	266_A	0.836	1.00
134_P	137_A	0.835	1.00
121_L	129_L	0.834	1.00
175_L	193_Y	0.834	1.00
184_D	188_T	0.833	1.00
244_V	247_T	0.833	1.00
289_K	296_V	0.832	1.00
104_S	109_M	0.826	1.00
136_T	176_M	0.825	1.00
204_F	208_G	0.822	1.00
234_I	237_M	0.814	1.00
61_L	65_M	0.814	1.00
236_M	240_I	0.811	1.00
142_A	145_I	0.811	1.00
122_G	125_G	0.810	1.00
178_Y	181_V	0.809	1.00
40_S	44_F	0.807	1.00
111_P	115_L	0.804	1.00
270_L	305_L	0.800	1.00
274_W	278_S	0.800	1.00
130_Y	134_P	0.796	1.00
60_G	63_F	0.795	1.00
122_G	126_L	0.794	1.00
238_Q	242_V	0.793	1.00
72_L	76_F	0.790	1.00
294_M	297_Y	0.790	1.00
198_L	241_A	0.789	1.00
23_T	26_D	0.789	1.00
291_A	296_V	0.789	1.00
171_A	177_G	0.784	1.00
50_A	181_V	0.784	1.00
244_V	271_G	0.781	1.00
114_I	121_L	0.781	1.00
103_A	107_G	0.779	1.00
239_Y	243_L	0.778	1.00
224_P	232_T	0.775	1.00
140_G	176_M	0.774	1.00
149_I	153_V	0.769	1.00
63_F	181_V	0.769	1.00
293_D	297_Y	0.764	1.00
294_M	298_S	0.764	1.00
266_A	271_G	0.760	1.00
146_F	150_I	0.756	1.00
213_E	217_A	0.754	1.00
48_W	51_F	0.753	1.00
78_M	82_T	0.751	1.00
47_F	181_V	0.748	1.00
296_V	302_F	0.745	1.00
273_I	280_K	0.745	1.00
298_S	303_C	0.741	0.99
81_G	148_A	0.740	0.99
96_M	99_T	0.739	0.99
163_T	166_G	0.734	0.99
171_A	196_M	0.732	0.99
83_V	114_I	0.732	0.99
233_K	236_M	0.727	0.99
128_M	132_L	0.727	0.99
283_K	286_D	0.726	0.99
27_F	109_M	0.725	0.99
170_G	174_P	0.725	0.99
165_V	170_G	0.725	0.99
304_L	308_I	0.724	0.99
128_M	131_S	0.718	0.99
223_L	226_V	0.717	0.99
194_T	246_V	0.715	0.99
207_I	210_R	0.714	0.99
133_N	139_L	0.710	0.99
263_Y	267_A	0.706	0.99
163_T	204_F	0.705	0.99
160_V	226_V	0.705	0.99
103_A	108_K	0.704	0.99
163_T	205_W	0.702	0.99
290_W	297_Y	0.698	0.99
289_K	294_M	0.695	0.99
47_F	70_A	0.690	0.99
91_H	94_A	0.689	0.99
92_M	218_A	0.688	0.99
155_V	162_S	0.686	0.99
145_I	150_I	0.682	0.99
270_L	273_I	0.680	0.99
212_K	224_P	0.679	0.99
101_S	108_K	0.676	0.99
299_L	306_F	0.668	0.99
87_Y	90_R	0.666	0.99
80_S	84_Y	0.665	0.99
306_F	310_M	0.664	0.99
69_T	132_L	0.663	0.99
109_M	113_M	0.662	0.99
163_T	201_P	0.661	0.99
126_L	137_A	0.656	0.99
207_I	211_R	0.656	0.99
30_L	114_I	0.655	0.99
126_L	130_Y	0.652	0.99
253_S	257_G	0.652	0.99
73_G	128_M	0.650	0.99
294_M	302_F	0.650	0.99
187_M	191_L	0.649	0.99
43_A	173_P	0.648	0.99
84_Y	149_I	0.647	0.99
48_W	306_F	0.644	0.99
268_L	271_G	0.643	0.99
39_N	45_G	0.642	0.99
220_V	225_V	0.640	0.99
160_V	221_P	0.639	0.99
295_F	302_F	0.638	0.98
307_F	311_I	0.637	0.98
89_D	220_V	0.636	0.98
294_M	299_L	0.629	0.98
168_F	197_F	0.628	0.98
166_G	171_A	0.627	0.98
53_S	60_G	0.626	0.98
215_Y	222_L	0.626	0.98
132_L	136_T	0.625	0.98
208_G	211_R	0.625	0.98
112_A	115_L	0.623	0.98
297_Y	301_Y	0.622	0.98
37_I	299_L	0.619	0.98
175_L	189_A	0.618	0.98
302_F	305_L	0.616	0.98
79_A	83_V	0.614	0.98
274_W	277_K	0.612	0.98
159_S	165_V	0.604	0.98
47_F	51_F	0.603	0.98
252_F	264_F	0.602	0.98
86_N	89_D	0.601	0.98
126_L	141_L	0.599	0.98
299_L	302_F	0.598	0.98
287_D	291_A	0.596	0.98
65_M	72_L	0.596	0.98
113_M	116_T	0.595	0.98
209_I	228_G	0.595	0.98
209_I	233_K	0.593	0.98
25_Y	28_I	0.588	0.97
266_A	304_L	0.588	0.97
265_L	268_L	0.587	0.97
22_V	108_K	0.587	0.97
92_M	95_K	0.585	0.97
39_N	42_A	0.585	0.97
89_D	152_T	0.583	0.97
239_Y	242_V	0.582	0.97
161_W	165_V	0.582	0.97
136_T	139_L	0.581	0.97
131_S	134_P	0.579	0.97
258_H	263_Y	0.579	0.97
29_K	103_A	0.579	0.97
127_A	130_Y	0.579	0.97
177_G	181_V	0.576	0.97
281_G	294_M	0.574	0.97
45_G	196_M	0.573	0.97
278_S	281_G	0.572	0.97
91_H	111_P	0.571	0.97
291_A	299_L	0.570	0.97
280_K	286_D	0.567	0.97
132_L	137_A	0.567	0.97
275_I	301_Y	0.566	0.97
143_A	169_P	0.564	0.97
178_Y	186_S	0.561	0.97
88_F	152_T	0.558	0.97
163_T	170_G	0.558	0.97
262_F	265_L	0.558	0.97
259_I	270_L	0.556	0.96
274_W	297_Y	0.555	0.96
259_I	263_Y	0.555	0.96
66_T	132_L	0.555	0.96
51_F	181_V	0.553	0.96
47_F	50_A	0.552	0.96
201_P	239_Y	0.551	0.96
167_S	200_Q	0.550	0.96
22_V	26_D	0.550	0.96
39_N	143_A	0.550	0.96
166_G	204_F	0.550	0.96
296_V	303_C	0.546	0.96
41_I	48_W	0.545	0.96
299_L	305_L	0.545	0.96
294_M	303_C	0.543	0.96
105_V	108_K	0.543	0.96
167_S	170_G	0.542	0.96
166_G	200_Q	0.540	0.96
162_S	166_G	0.540	0.96
160_V	163_T	0.538	0.96
280_K	284_T	0.537	0.96
298_S	305_L	0.536	0.96
104_S	107_G	0.534	0.96
23_T	27_F	0.533	0.95
80_S	149_I	0.533	0.95
77_V	144_F	0.532	0.95
193_Y	200_Q	0.525	0.95
208_G	214_E	0.523	0.95
227_K	235_K	0.521	0.95
170_G	173_P	0.520	0.95
292_K	298_S	0.519	0.95
46_G	177_G	0.518	0.95
39_N	74_T	0.515	0.95
135_L	183_G	0.513	0.94
82_T	86_N	0.512	0.94
292_K	297_Y	0.512	0.94
97_A	213_E	0.512	0.94
191_L	253_S	0.511	0.94
72_L	128_M	0.510	0.94
289_K	292_K	0.508	0.94
39_N	43_A	0.508	0.94
292_K	303_C	0.507	0.94
281_G	290_W	0.507	0.94
158_T	162_S	0.505	0.94
295_F	308_I	0.505	0.94
97_A	101_S	0.503	0.94
272_G	275_I	0.502	0.94
279_I	283_K	0.501	0.94
120_V	124_A	0.501	0.94
77_V	148_A	0.500	0.94

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	0.8313	100	0.29	Contact Map
4tq3A	1	0.8719	100	0.355	Contact Map
4xnjA	1	0.6188	21.2	0.951	Contact Map
2cfqA	1	0.6344	17.2	0.954	Contact Map
4xp4A	1	0.3031	11	0.957	Contact Map
2xq2A	2	0.7469	10.2	0.958	Contact Map
3ze3A	4	0.3406	10.2	0.958	Contact Map
1pw4A	1	0.6031	9.6	0.959	Contact Map
3o7qA	1	0.5906	9.4	0.959	Contact Map
2kogA	1	0.1688	7.1	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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