COXX2 - BACSU - GREMLIN Contacts

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COXX2 - Protoheme IX farnesyltransferase 2

UniProt:	P24009	Sequences: MANSRILNDTAIDGQIEETTAWKDFLSLIKIGIVNSNLITTFTGMWLALHISGLSFLGNINTVLLTLIGSSLIIAGSCAINNWYDRDIDHLMERTKVRPTVTGKIQPSQALWSGILLVALGLIMLLMTTVMAAVIGFIGVFTYVVLYTMWTKRRYTINTVVGSVSGAVPPLIGWTAVEGNIGVVAWVLFMILFIWQIPHFLALAIKKTEDYRAANIPMLPVVYGFEVTKRQIIVWVACLMPLPFFLGSLGLPIVILGLLLNIGWLILGLMGFRSKNIMKWATQMFVYSLNYMTIYFVAMVVLTLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	305 (273)
Sequences:	8948 (6348)
Seq/√Len:	384.2

ECOLI - CYOE UBIA MENA
BACSU - COXX2 COXX1 MENA
HALSA - DGGGP COXX Q9HQN6 LYEL
SULSO - COXX Q980Z2 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
83_W	107_P	4.251	1.00
86_R	107_P	3.960	1.00
24_D	104_K	3.656	1.00
83_W	111_L	3.246	1.00
21_A	109_Q	3.210	1.00
106_Q	109_Q	3.191	1.00
76_G	118_V	3.156	1.00
27_S	104_K	2.941	1.00
93_E	96_K	2.695	1.00
226_E	230_R	2.674	1.00
125_L	128_T	2.542	1.00
108_S	112_W	2.484	1.00
266_I	270_M	2.391	1.00
129_T	132_A	2.252	1.00
73_I	121_G	2.249	1.00
45_M	63_V	2.224	1.00
25_F	109_Q	2.200	1.00
182_G	185_A	2.195	1.00
130_V	134_V	2.128	1.00
88_I	216_I	2.111	1.00
34_V	71_S	2.104	1.00
277_I	280_W	2.074	1.00
208_T	212_R	2.002	1.00
79_A	117_L	1.976	1.00
132_A	175_T	1.971	1.00
209_E	212_R	1.968	1.00
90_H	101_V	1.955	1.00
100_T	110_A	1.949	1.00
65_L	127_M	1.933	1.00
112_W	116_L	1.870	1.00
278_M	281_A	1.824	1.00
23_K	27_S	1.799	1.00
42_F	67_L	1.797	1.00
256_L	260_L	1.761	1.00
84_Y	149_M	1.731	1.00
86_R	90_H	1.731	1.00
282_T	286_V	1.723	1.00
59_N	62_T	1.703	1.00
263_G	267_L	1.692	1.00
86_R	100_T	1.690	1.00
230_R	234_V	1.657	1.00
227_V	230_R	1.647	1.00
65_L	124_M	1.636	1.00
280_W	284_M	1.578	1.00
223_Y	227_V	1.575	1.00
126_L	133_A	1.569	1.00
115_I	119_A	1.566	1.00
282_T	285_F	1.561	1.00
259_L	263_G	1.528	1.00
111_L	115_I	1.518	1.00
25_F	113_S	1.517	1.00
134_V	138_I	1.514	1.00
212_R	221_V	1.495	1.00
200_F	203_L	1.485	1.00
200_F	204_A	1.485	1.00
79_A	114_G	1.472	1.00
285_F	289_L	1.462	1.00
28_L	79_A	1.462	1.00
29_I	117_L	1.459	1.00
83_W	110_A	1.457	1.00
199_H	203_L	1.448	1.00
29_I	79_A	1.442	1.00
72_L	120_L	1.413	1.00
142_T	165_S	1.412	1.00
225_F	229_K	1.401	1.00
105_I	110_A	1.397	1.00
174_W	178_E	1.393	1.00
72_L	121_G	1.365	1.00
73_I	136_G	1.354	1.00
118_V	140_V	1.344	1.00
141_F	145_V	1.343	1.00
26_L	31_I	1.340	1.00
111_L	114_G	1.327	1.00
270_M	273_R	1.324	1.00
256_L	298_A	1.322	1.00
288_S	292_M	1.320	1.00
208_T	225_F	1.312	1.00
28_L	105_I	1.311	1.00
186_W	190_M	1.310	1.00
79_A	113_S	1.300	1.00
80_I	114_G	1.295	1.00
262_I	266_I	1.294	1.00
255_I	259_L	1.285	1.00
170_P	173_G	1.283	1.00
29_I	113_S	1.282	1.00
151_T	161_V	1.272	1.00
29_I	75_A	1.256	1.00
263_G	266_I	1.255	1.00
146_L	161_V	1.249	1.00
113_S	117_L	1.231	1.00
251_L	255_I	1.229	1.00
182_G	186_W	1.227	1.00
41_T	70_S	1.225	1.00
151_T	154_R	1.224	1.00
283_Q	286_V	1.221	1.00
26_L	29_I	1.220	1.00
237_A	241_P	1.219	1.00
267_L	271_G	1.215	1.00
123_I	127_M	1.206	1.00
265_L	268_G	1.204	1.00
131_M	135_I	1.201	1.00
289_L	293_T	1.198	1.00
181_I	185_A	1.197	1.00
122_L	125_L	1.187	1.00
227_V	231_Q	1.176	1.00
75_A	117_L	1.154	1.00
36_S	199_H	1.153	1.00
252_P	256_L	1.144	1.00
230_R	233_I	1.141	1.00
69_G	124_M	1.132	1.00
162_G	166_G	1.131	1.00
191_I	242_L	1.123	1.00
268_G	272_F	1.120	1.00
47_L	174_W	1.120	1.00
220_P	228_T	1.119	1.00
194_I	235_W	1.119	1.00
83_W	100_T	1.117	1.00
110_A	114_G	1.114	1.00
64_L	68_I	1.112	1.00
53_G	58_G	1.106	1.00
243_P	246_L	1.105	1.00
139_G	168_V	1.103	1.00
260_L	263_G	1.102	1.00
279_K	283_Q	1.096	1.00
83_W	114_G	1.095	1.00
110_A	117_L	1.092	1.00
162_G	167_A	1.081	1.00
290_N	294_I	1.077	1.00
277_I	281_A	1.077	1.00
79_A	105_I	1.074	1.00
201_L	204_A	1.066	1.00
121_G	125_L	1.065	1.00
48_A	174_W	1.063	1.00
85_D	153_R	1.049	1.00
101_V	110_A	1.048	1.00
120_L	124_M	1.046	1.00
219_L	223_Y	1.045	1.00
204_A	207_K	1.045	1.00
131_M	175_T	1.038	1.00
22_W	26_L	1.036	1.00
61_N	65_L	1.031	1.00
272_F	275_K	1.030	1.00
264_W	267_L	1.030	1.00
167_A	193_F	1.026	1.00
217_P	222_V	1.023	1.00
152_K	155_Y	1.018	1.00
72_L	117_L	1.014	1.00
224_G	228_T	1.014	1.00
203_L	207_K	1.013	1.00
286_V	290_N	1.001	1.00
60_I	64_L	0.994	1.00
190_M	194_I	0.991	1.00
219_L	222_V	0.983	1.00
54_L	58_G	0.975	1.00
205_I	227_V	0.972	1.00
254_V	258_L	0.966	1.00
287_Y	291_Y	0.962	1.00
88_I	153_R	0.962	1.00
61_N	64_L	0.957	1.00
269_L	272_F	0.951	1.00
142_T	164_V	0.947	1.00
207_K	211_Y	0.937	1.00
208_T	221_V	0.937	1.00
158_N	218_M	0.933	1.00
41_T	66_T	0.933	1.00
119_A	123_I	0.933	1.00
77_S	144_V	0.932	1.00
164_V	189_F	0.929	1.00
248_S	251_L	0.928	1.00
97_V	104_K	0.926	1.00
157_I	160_V	0.917	1.00
137_F	141_F	0.916	1.00
266_I	269_L	0.915	1.00
250_G	253_I	0.912	1.00
233_I	237_A	0.910	1.00
87_D	91_L	0.909	1.00
286_V	289_L	0.906	1.00
131_M	134_V	0.902	1.00
107_P	111_L	0.898	1.00
289_L	296_F	0.898	1.00
132_A	172_I	0.891	1.00
235_W	239_L	0.888	1.00
181_I	186_W	0.888	1.00
270_M	274_S	0.884	1.00
110_A	113_S	0.878	1.00
278_M	285_F	0.873	1.00
290_N	293_T	0.869	1.00
280_W	287_Y	0.866	1.00
204_A	220_P	0.863	1.00
262_I	265_L	0.862	1.00
125_L	136_G	0.859	1.00
203_L	206_K	0.858	1.00
105_I	113_S	0.858	1.00
99_P	103_G	0.853	1.00
91_L	214_A	0.850	1.00
44_G	48_A	0.849	1.00
168_V	172_I	0.847	1.00
285_F	288_S	0.847	1.00
114_G	118_V	0.844	1.00
256_L	259_L	0.838	1.00
100_T	105_I	0.838	1.00
38_L	42_F	0.832	1.00
270_M	275_K	0.831	1.00
236_V	239_L	0.830	1.00
283_Q	287_Y	0.829	1.00
138_I	141_F	0.826	1.00
21_A	24_D	0.821	1.00
75_A	113_S	0.819	1.00
125_L	133_A	0.817	1.00
151_T	155_Y	0.814	1.00
280_W	283_Q	0.814	1.00
167_A	196_Q	0.809	1.00
192_L	196_Q	0.805	1.00
92_M	210_D	0.801	1.00
249_L	299_M	0.798	1.00
87_D	90_H	0.794	1.00
226_E	229_K	0.791	1.00
73_I	140_V	0.788	1.00
234_V	238_C	0.788	1.00
265_L	269_L	0.787	1.00
74_I	78_C	0.780	1.00
21_A	25_F	0.780	1.00
286_V	292_M	0.777	1.00
289_L	292_M	0.776	1.00
68_I	72_L	0.771	1.00
205_I	225_F	0.762	1.00
108_S	111_L	0.761	1.00
199_H	204_A	0.760	1.00
294_I	298_A	0.757	1.00
167_A	173_G	0.756	1.00
118_V	121_G	0.752	1.00
240_M	261_N	0.752	1.00
292_M	295_Y	0.750	1.00
209_E	213_A	0.748	1.00
100_T	103_G	0.747	1.00
126_L	130_V	0.746	1.00
124_M	127_M	0.746	1.00
240_M	243_P	0.744	1.00
293_T	296_F	0.742	1.00
105_I	109_Q	0.742	1.00
229_K	233_I	0.742	1.00
69_G	125_L	0.741	1.00
282_T	289_L	0.740	1.00
278_M	282_T	0.739	1.00
85_D	88_I	0.738	1.00
180_N	184_V	0.736	1.00
191_I	195_W	0.732	1.00
264_W	268_G	0.730	1.00
255_I	258_L	0.727	1.00
199_H	202_A	0.724	1.00
281_A	285_F	0.722	1.00
46_W	300_V	0.718	1.00
145_V	149_M	0.716	1.00
239_L	243_P	0.715	1.00
247_G	254_V	0.713	1.00
183_V	187_V	0.710	1.00
253_I	257_G	0.709	1.00
216_I	222_V	0.702	1.00
183_V	186_W	0.701	1.00
148_T	152_K	0.701	1.00
45_M	177_V	0.701	1.00
268_G	271_G	0.698	0.99
123_I	126_L	0.697	0.99
62_T	128_T	0.694	0.99
161_V	166_G	0.693	0.99
250_G	254_V	0.692	0.99
156_T	159_T	0.689	0.99
185_A	189_F	0.687	0.99
36_S	40_T	0.686	0.99
151_T	158_N	0.685	0.99
166_G	170_P	0.682	0.99
38_L	67_L	0.682	0.99
287_Y	290_N	0.682	0.99
155_Y	161_V	0.680	0.99
229_K	232_I	0.679	0.99
254_V	257_G	0.678	0.99
66_T	176_A	0.677	0.99
238_C	242_L	0.674	0.99
246_L	253_I	0.674	0.99
159_T	197_I	0.671	0.99
25_F	105_I	0.669	0.99
206_K	282_T	0.668	0.99
211_Y	218_M	0.667	0.99
49_L	53_G	0.666	0.99
249_L	252_P	0.662	0.99
76_G	79_A	0.658	0.99
156_T	222_V	0.656	0.99
129_T	135_I	0.653	0.99
167_A	170_P	0.653	0.99
28_L	110_A	0.652	0.99
65_L	128_T	0.651	0.99
173_G	177_V	0.650	0.99
75_A	79_A	0.650	0.99
267_L	287_Y	0.648	0.99
216_I	219_L	0.648	0.99
242_L	246_L	0.643	0.99
49_L	177_V	0.642	0.99
59_N	177_V	0.641	0.99
232_I	236_V	0.640	0.99
79_A	110_A	0.638	0.99
249_L	253_I	0.635	0.99
288_S	293_T	0.633	0.99
253_I	260_L	0.633	0.99
88_I	91_L	0.633	0.99
122_L	126_L	0.633	0.99
219_L	225_F	0.632	0.99
146_L	151_T	0.632	0.99
109_Q	112_W	0.629	0.99
92_M	95_T	0.629	0.99
39_I	46_W	0.628	0.99
271_G	274_S	0.628	0.99
27_S	99_P	0.621	0.99
265_L	272_F	0.620	0.99
99_P	104_K	0.619	0.99
114_G	117_L	0.619	0.99
198_P	235_W	0.617	0.99
83_W	86_R	0.617	0.99
116_L	123_I	0.612	0.99
258_L	262_I	0.610	0.99
284_M	288_S	0.605	0.99
45_M	66_T	0.603	0.99
159_T	200_F	0.601	0.98
263_G	270_M	0.600	0.98
282_T	288_S	0.599	0.98
135_I	175_T	0.599	0.98
287_Y	292_M	0.599	0.98
48_A	177_V	0.597	0.98
158_N	162_G	0.596	0.98
231_Q	235_W	0.596	0.98
188_L	192_L	0.595	0.98
231_Q	234_V	0.594	0.98
283_Q	288_S	0.592	0.98
249_L	256_L	0.592	0.98
133_A	137_F	0.591	0.98
248_S	252_P	0.590	0.98
242_L	245_F	0.587	0.98
235_W	238_C	0.586	0.98
117_L	121_G	0.586	0.98
49_L	58_G	0.584	0.98
154_R	158_N	0.580	0.98
122_L	137_F	0.575	0.98
171_L	189_F	0.575	0.98
251_L	258_L	0.574	0.98
248_S	254_V	0.569	0.98
122_L	133_A	0.569	0.98
220_P	223_Y	0.567	0.98
213_A	216_I	0.566	0.98
267_L	270_M	0.564	0.98
163_S	167_A	0.561	0.98
166_G	169_P	0.558	0.98
45_M	58_G	0.558	0.98
46_W	49_L	0.557	0.98
120_L	123_I	0.556	0.98
128_T	132_A	0.555	0.97
260_L	295_Y	0.555	0.97
163_S	166_G	0.553	0.97
136_G	172_I	0.551	0.97
288_S	291_Y	0.551	0.97
285_F	298_A	0.550	0.97
281_A	286_V	0.550	0.97
296_F	299_M	0.549	0.97
148_T	153_R	0.547	0.97
252_P	255_I	0.547	0.97
281_A	288_S	0.547	0.97
139_G	165_S	0.546	0.97
76_G	140_V	0.545	0.97
58_G	63_V	0.544	0.97
101_V	104_K	0.542	0.97
41_T	169_P	0.540	0.97
194_I	237_A	0.538	0.97
292_M	296_F	0.538	0.97
243_P	261_N	0.537	0.97
269_L	275_K	0.536	0.97
80_I	145_V	0.534	0.97
82_N	85_D	0.534	0.97
295_Y	298_A	0.534	0.97
80_I	84_Y	0.534	0.97
282_T	287_Y	0.533	0.97
157_I	223_Y	0.532	0.97
43_T	192_L	0.532	0.97
205_I	228_T	0.531	0.97
127_M	130_V	0.530	0.97
85_D	216_I	0.529	0.97
88_I	214_A	0.527	0.97
241_P	245_F	0.526	0.97
142_T	161_V	0.526	0.97
265_L	291_Y	0.525	0.97
225_F	228_T	0.524	0.96
196_Q	200_F	0.522	0.96
132_A	135_I	0.520	0.96
87_D	107_P	0.519	0.96
118_V	122_L	0.518	0.96
218_M	222_V	0.517	0.96
296_F	300_V	0.517	0.96
233_I	269_L	0.516	0.96
76_G	145_V	0.516	0.96
293_T	297_V	0.516	0.96
124_M	128_T	0.516	0.96
257_G	261_N	0.514	0.96
76_G	80_I	0.511	0.96
174_W	177_V	0.510	0.96
193_F	197_I	0.510	0.96
257_G	260_L	0.509	0.96
284_M	287_Y	0.506	0.96
73_I	144_V	0.503	0.96
251_L	256_L	0.502	0.96
77_S	140_V	0.502	0.96
61_N	127_M	0.502	0.96
167_A	192_L	0.502	0.96
43_T	47_L	0.500	0.95

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	0.8656	100	0.275	Contact Map
4tq3A	1	0.8951	100	0.353	Contact Map
2xq2A	2	0.7639	9.9	0.956	Contact Map
3ixzA	1	0.6918	9.3	0.957	Contact Map
2h88C	2	0.3869	6.9	0.959	Contact Map
1zoyC	1	0.3869	6.6	0.96	Contact Map
2cfqA	1	0.6656	5.7	0.961	Contact Map
4xnjA	1	0.6328	5.6	0.961	Contact Map
3tx3A	2	0.4557	4.7	0.962	Contact Map
2zxeA	1	0.6918	4.4	0.963	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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