COXX - SULSO - GREMLIN Contacts

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COXX - Protoheme IX farnesyltransferase

UniProt:	Q9UX46	Sequences: MSLQQKIKAYLKLGKLGVVSLLDLAAIAGAFLAYKHGISLLPIIPMLIGGTLASMGAMIINSGIEINRDKVMSRTSNRPTVVGYVSRKEVIVVGSLLAVLGTALGFIDNALTAFFIALGVIIYVFVYTILLKPRTWLNIVIGGFAGSAAAWAGYTSLTNSLTLEAFLLGFLIFMWTPGHFWSLALKYREDYINAHYPMLPAVVGITTSARAIATSNALMIPIVLLMGYYISLIALIVFSVLSALLLFLSYRLILNPTKEEAMKSFIFSNIYLMLILLSIIIIKLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	285 (272)
Sequences:	9597 (6875)
Seq/√Len:	416.8

ECOLI - CYOE UBIA MENA
BACSU - COXX1 COXX2 MENA
HALSA - DGGGP Q9HQN6 COXX 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
63_G	87_R	4.198	1.00
66_I	87_R	4.092	1.00
9_A	84_Y	3.626	1.00
63_G	91_I	3.434	1.00
86_S	89_E	3.408	1.00
56_G	98_A	3.147	1.00
12_K	84_Y	2.979	1.00
206_T	210_R	2.902	1.00
73_S	76_S	2.734	1.00
30_A	43_I	2.524	1.00
88_K	92_V	2.499	1.00
247_F	251_R	2.470	1.00
53_A	101_G	2.392	1.00
10_Y	89_E	2.306	1.00
188_R	192_I	2.192	1.00
8_K	12_K	2.124	1.00
109_N	112_T	2.091	1.00
19_V	51_T	2.086	1.00
189_E	192_I	2.082	1.00
162_T	165_A	2.069	1.00
104_L	108_D	2.059	1.00
68_R	196_Y	2.025	1.00
262_M	265_F	2.007	1.00
262_M	266_I	2.007	1.00
112_T	155_T	2.006	1.00
110_A	114_F	2.005	1.00
105_G	108_D	1.952	1.00
241_L	244_L	1.944	1.00
45_P	107_I	1.861	1.00
39_S	42_P	1.793	1.00
59_I	97_L	1.793	1.00
207_T	210_R	1.783	1.00
70_K	81_V	1.776	1.00
14_G	59_I	1.775	1.00
244_L	248_L	1.756	1.00
154_Y	158_T	1.753	1.00
80_T	90_V	1.739	1.00
66_I	80_T	1.718	1.00
27_I	47_L	1.709	1.00
240_V	244_L	1.696	1.00
66_I	70_K	1.689	1.00
64_I	129_I	1.680	1.00
92_V	96_L	1.679	1.00
91_I	95_S	1.651	1.00
203_V	207_T	1.636	1.00
210_R	214_T	1.634	1.00
268_S	272_L	1.624	1.00
257_T	260_E	1.622	1.00
180_F	184_A	1.607	1.00
265_F	269_N	1.583	1.00
10_Y	93_V	1.580	1.00
106_F	113_A	1.572	1.00
21_L	179_H	1.571	1.00
13_L	59_I	1.569	1.00
192_I	201_A	1.549	1.00
244_L	247_F	1.539	1.00
95_S	99_V	1.526	1.00
114_F	118_L	1.496	1.00
122_I	145_A	1.477	1.00
200_P	208_S	1.420	1.00
263_K	266_I	1.413	1.00
232_L	236_I	1.397	1.00
53_A	116_I	1.377	1.00
52_L	101_G	1.374	1.00
150_A	153_G	1.372	1.00
11_L	16_L	1.368	1.00
98_A	120_V	1.353	1.00
251_R	254_L	1.351	1.00
59_I	94_G	1.341	1.00
52_L	100_L	1.339	1.00
161_L	165_A	1.338	1.00
217_A	221_P	1.329	1.00
90_V	94_G	1.326	1.00
205_I	209_A	1.325	1.00
14_G	93_V	1.320	1.00
181_W	184_A	1.300	1.00
13_L	85_V	1.275	1.00
85_V	90_V	1.260	1.00
91_I	94_G	1.260	1.00
269_N	273_M	1.259	1.00
248_L	252_L	1.256	1.00
245_L	248_L	1.248	1.00
174_M	215_S	1.247	1.00
261_A	265_F	1.243	1.00
188_R	201_A	1.242	1.00
126_V	141_I	1.242	1.00
199_L	203_V	1.239	1.00
59_I	93_V	1.234	1.00
121_I	125_F	1.232	1.00
156_S	159_N	1.225	1.00
263_K	267_F	1.220	1.00
14_G	55_M	1.220	1.00
188_R	205_I	1.220	1.00
180_F	183_L	1.214	1.00
111_L	115_F	1.210	1.00
14_G	97_L	1.206	1.00
207_T	211_A	1.198	1.00
219_M	223_V	1.196	1.00
171_L	222_I	1.189	1.00
63_G	94_G	1.184	1.00
63_G	90_V	1.178	1.00
269_N	272_L	1.155	1.00
44_I	48_I	1.144	1.00
243_A	247_F	1.144	1.00
94_G	98_A	1.143	1.00
183_L	187_Y	1.139	1.00
131_L	134_R	1.132	1.00
210_R	213_A	1.130	1.00
267_F	271_Y	1.125	1.00
104_L	107_I	1.124	1.00
90_V	97_L	1.120	1.00
55_M	97_L	1.116	1.00
11_L	14_G	1.114	1.00
90_V	93_V	1.114	1.00
65_E	133_P	1.110	1.00
131_L	141_I	1.104	1.00
26_A	50_G	1.101	1.00
144_F	169_G	1.099	1.00
233_I	237_V	1.096	1.00
187_Y	191_Y	1.086	1.00
87_R	91_I	1.084	1.00
7_I	11_L	1.083	1.00
52_L	97_L	1.065	1.00
57_A	124_V	1.063	1.00
147_S	173_F	1.061	1.00
179_H	183_L	1.058	1.00
166_F	170_F	1.055	1.00
260_E	264_S	1.050	1.00
60_I	94_G	1.047	1.00
184_A	187_Y	1.045	1.00
138_N	198_M	1.035	1.00
132_K	135_T	1.034	1.00
249_S	253_I	1.032	1.00
199_L	202_V	1.030	1.00
197_P	202_V	1.029	1.00
224_L	227_G	1.029	1.00
250_Y	253_I	1.028	1.00
59_I	85_V	1.026	1.00
266_I	270_I	1.024	1.00
231_S	234_A	1.022	1.00
102_T	105_G	1.020	1.00
111_L	114_F	1.018	1.00
224_L	228_Y	1.007	1.00
112_T	152_A	1.007	1.00
235_L	238_F	1.004	1.00
154_Y	157_L	0.991	1.00
33_A	154_Y	0.989	1.00
105_G	110_A	0.988	1.00
247_F	250_Y	0.986	1.00
117_A	121_I	0.983	1.00
142_G	146_G	0.982	1.00
243_A	246_L	0.975	1.00
103_A	107_I	0.972	1.00
119_G	148_A	0.964	1.00
40_L	44_I	0.964	1.00
246_L	249_S	0.963	1.00
41_L	44_I	0.963	1.00
55_M	93_V	0.962	1.00
270_I	274_L	0.961	1.00
227_G	235_L	0.956	1.00
81_V	90_V	0.949	1.00
131_L	135_T	0.946	1.00
206_T	209_A	0.944	1.00
148_A	152_A	0.939	1.00
242_S	245_L	0.937	1.00
255_N	258_K	0.936	1.00
268_S	271_Y	0.934	1.00
269_N	276_L	0.930	1.00
93_V	97_L	0.924	1.00
38_I	43_I	0.922	1.00
161_L	166_F	0.920	1.00
170_F	174_M	0.920	1.00
213_A	217_A	0.919	1.00
237_V	241_L	0.917	1.00
63_G	80_T	0.910	1.00
185_L	207_T	0.910	1.00
231_S	236_I	0.909	1.00
189_E	193_N	0.903	1.00
262_M	269_N	0.901	1.00
77_N	84_Y	0.898	1.00
183_L	186_K	0.895	1.00
237_V	278_S	0.895	1.00
184_A	200_P	0.893	1.00
261_A	264_S	0.888	1.00
97_L	101_G	0.883	1.00
259_E	263_K	0.880	1.00
265_F	268_S	0.878	1.00
136_W	202_V	0.870	1.00
220_I	242_S	0.868	1.00
111_L	155_T	0.867	1.00
41_L	45_P	0.867	1.00
138_N	142_G	0.860	1.00
32_L	154_Y	0.859	1.00
241_L	245_L	0.855	1.00
79_P	83_G	0.852	1.00
26_A	46_M	0.851	1.00
223_V	226_M	0.851	1.00
178_G	215_S	0.847	1.00
54_S	58_M	0.847	1.00
68_R	133_P	0.841	1.00
265_F	278_S	0.835	1.00
48_I	52_L	0.835	1.00
147_S	176_T	0.833	1.00
223_V	227_G	0.831	1.00
268_S	273_M	0.820	1.00
29_G	33_A	0.817	1.00
46_M	156_S	0.813	1.00
49_G	104_L	0.812	1.00
245_L	249_S	0.812	1.00
265_F	272_L	0.811	1.00
134_R	138_N	0.801	1.00
89_E	92_V	0.801	1.00
162_T	166_F	0.797	1.00
72_M	190_D	0.795	1.00
229_Y	233_I	0.793	1.00
239_S	243_A	0.791	1.00
65_E	68_R	0.788	1.00
220_I	223_V	0.785	1.00
122_I	144_F	0.785	1.00
196_Y	202_V	0.783	1.00
272_L	276_L	0.782	1.00
267_F	270_I	0.777	1.00
211_A	215_S	0.776	1.00
273_M	276_L	0.774	1.00
209_A	213_A	0.771	1.00
267_F	273_M	0.769	1.00
267_F	272_L	0.769	1.00
21_L	25_A	0.769	1.00
266_I	269_N	0.768	1.00
272_L	275_I	0.766	1.00
229_Y	232_L	0.765	1.00
67_N	70_K	0.758	1.00
270_I	273_M	0.756	1.00
23_D	27_I	0.756	1.00
200_P	203_V	0.755	1.00
236_I	239_S	0.753	1.00
105_G	116_I	0.749	1.00
209_A	212_I	0.746	1.00
67_N	71_V	0.741	1.00
261_A	268_S	0.740	1.00
276_L	279_I	0.733	1.00
232_L	235_L	0.730	1.00
13_L	90_V	0.728	1.00
188_R	200_P	0.727	1.00
269_N	275_I	0.727	1.00
196_Y	199_L	0.727	1.00
45_P	104_L	0.724	1.00
163_L	166_F	0.723	1.00
222_I	225_L	0.723	1.00
30_A	38_I	0.722	1.00
10_Y	14_G	0.721	1.00
98_A	101_G	0.720	1.00
103_A	106_F	0.719	1.00
218_L	222_I	0.717	1.00
240_V	243_A	0.717	1.00
80_T	85_V	0.713	1.00
72_M	75_T	0.711	1.00
261_A	266_I	0.711	1.00
254_L	257_T	0.709	1.00
253_I	256_P	0.708	1.00
264_S	268_S	0.708	1.00
179_H	184_A	0.705	1.00
234_A	238_F	0.699	1.00
147_S	150_A	0.698	1.00
219_M	222_I	0.698	1.00
37_G	41_L	0.694	1.00
34_Y	38_I	0.688	1.00
266_I	272_L	0.687	1.00
273_M	277_L	0.686	1.00
248_L	267_F	0.685	1.00
153_G	157_L	0.682	1.00
160_S	164_E	0.682	1.00
264_S	272_L	0.679	1.00
222_I	226_M	0.677	1.00
92_V	95_S	0.677	1.00
139_I	177_P	0.675	1.00
62_S	65_E	0.675	1.00
230_I	236_I	0.674	1.00
55_M	59_I	0.673	1.00
139_I	181_W	0.673	1.00
79_P	84_Y	0.672	1.00
88_K	91_I	0.672	1.00
10_Y	85_V	0.665	0.99
131_L	138_N	0.664	0.99
53_A	120_V	0.662	0.99
22_L	54_S	0.661	0.99
63_G	66_I	0.661	0.99
99_V	103_A	0.661	0.99
250_Y	254_L	0.661	0.99
45_P	108_D	0.661	0.99
215_S	218_L	0.660	0.99
22_L	25_A	0.659	0.99
236_I	240_V	0.658	0.99
181_W	211_A	0.657	0.99
142_G	180_F	0.657	0.99
260_E	263_K	0.656	0.99
255_N	260_E	0.652	0.99
216_N	219_M	0.651	0.99
139_I	180_F	0.649	0.99
81_V	84_Y	0.646	0.99
275_I	278_S	0.645	0.99
137_L	140_V	0.642	0.99
268_S	275_I	0.641	0.99
242_S	271_Y	0.635	0.99
23_D	47_L	0.634	0.99
154_Y	159_N	0.632	0.99
230_I	279_I	0.630	0.99
39_S	157_L	0.626	0.99
165_A	169_G	0.626	0.99
249_S	252_L	0.624	0.99
221_P	225_L	0.621	0.99
234_A	237_V	0.620	0.99
185_L	209_A	0.619	0.99
102_T	113_A	0.619	0.99
251_R	255_N	0.617	0.99
85_V	89_E	0.616	0.99
241_L	248_L	0.615	0.99
233_I	238_F	0.614	0.99
204_G	208_S	0.613	0.99
242_S	246_L	0.611	0.99
94_G	97_L	0.609	0.99
271_Y	275_I	0.607	0.99
144_F	173_F	0.607	0.99
30_A	157_L	0.605	0.99
177_P	215_S	0.604	0.99
30_A	34_Y	0.603	0.99
12_K	79_P	0.603	0.99
191_Y	198_M	0.601	0.99
85_V	93_V	0.592	0.99
177_P	180_F	0.591	0.99
30_A	46_M	0.588	0.99
248_L	253_I	0.588	0.99
261_A	267_F	0.588	0.99
118_L	121_I	0.587	0.99
172_I	176_T	0.587	0.99
19_V	47_L	0.585	0.99
246_L	250_Y	0.585	0.99
147_S	153_G	0.585	0.99
28_A	172_I	0.583	0.99
108_D	112_T	0.583	0.99
185_L	208_S	0.581	0.99
126_V	131_L	0.581	0.99
185_L	205_I	0.580	0.99
90_V	95_S	0.579	0.99
275_I	279_I	0.576	0.98
68_R	194_A	0.575	0.98
220_I	224_L	0.574	0.98
119_G	145_A	0.573	0.98
222_I	227_G	0.570	0.98
9_A	85_V	0.570	0.98
42_P	108_D	0.569	0.98
93_V	101_G	0.568	0.98
28_A	168_L	0.563	0.98
46_M	50_G	0.561	0.98
78_R	83_G	0.561	0.98
137_L	146_G	0.561	0.98
10_Y	13_L	0.560	0.98
226_M	234_A	0.560	0.98
65_E	196_Y	0.560	0.98
177_P	181_W	0.556	0.98
122_I	141_I	0.555	0.98
178_G	216_N	0.553	0.98
110_A	113_A	0.553	0.98
237_V	274_L	0.551	0.98
71_V	194_A	0.550	0.98
41_L	107_I	0.545	0.98
262_M	272_L	0.543	0.98
60_I	125_F	0.542	0.98
265_F	271_Y	0.541	0.98
121_I	126_V	0.541	0.98
128_T	133_P	0.540	0.98
185_L	188_R	0.539	0.98
239_S	247_F	0.539	0.98
218_L	221_P	0.538	0.98
147_S	172_I	0.536	0.98
215_S	219_M	0.536	0.98
100_L	103_A	0.536	0.98
143_G	148_A	0.536	0.98
60_I	64_I	0.535	0.98
139_I	142_G	0.535	0.98
143_G	176_T	0.532	0.97
235_L	239_S	0.532	0.97
98_A	102_T	0.532	0.97
146_G	150_A	0.530	0.97
159_N	162_T	0.530	0.97
78_R	142_G	0.529	0.97
171_L	175_W	0.528	0.97
149_A	153_G	0.528	0.97
16_L	55_M	0.526	0.97
100_L	104_L	0.524	0.97
31_F	34_Y	0.524	0.97
230_I	234_A	0.520	0.97
238_F	242_S	0.520	0.97
135_T	202_V	0.519	0.97
196_Y	201_A	0.519	0.97
67_N	87_R	0.518	0.97
232_L	238_F	0.514	0.97
135_T	141_I	0.513	0.97
186_K	262_M	0.512	0.97
90_V	108_D	0.510	0.97
34_Y	157_L	0.510	0.97
151_W	169_G	0.510	0.97
264_S	269_N	0.508	0.97
272_L	278_S	0.506	0.97
197_P	201_A	0.506	0.97
183_L	191_Y	0.503	0.96
198_M	202_V	0.503	0.96
102_T	106_F	0.500	0.96

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	0.9263	100	0.202	Contact Map
4tq3A	1	0.9544	100	0.277	Contact Map
2xq2A	2	0.814	35.8	0.937	Contact Map
3ze3A	4	0.3684	14.2	0.948	Contact Map
4xnjA	1	0.593	4.1	0.96	Contact Map
3ne5A	3	0.4561	3.6	0.96	Contact Map
2cfqA	1	0.8877	3.6	0.961	Contact Map
3o7qA	1	0.8491	3	0.962	Contact Map
1qleC	1	0.5474	2.6	0.963	Contact Map
1pw4A	1	0.8772	2.5	0.964	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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