CcmF_C - PFAM28P - GREMLIN Contacts

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CcmF_C - Cytochrome c-type biogenesis protein CcmF C-terminal

PFAM:	PF16327	Sequences: LAFLALVIGGSLALFAWRAPLLRSGGRFSLVSRESALLLNNLLLVVAAATVLLGTLYPLISEALTGGKISVGPPYFNRVFVPLMLPLLLLMGVGPLLAWRRASLASLRRRLLWPAAAALVAALLLALLGGGRSLLALLGLALAAWVIATILLELWRRARESLAGALRRLRRLPRRRYGGYLAHLGVAVFVIGIAGSSAFSTERDVRLKPGESVEVGGYTLTFDGVTEVQGPNYTAVRATFTVSRDGKPVGTLYPEKRFYPVSGQPTTEAAIRSGLLRDLYVVLGEPLDDGAWTVRVYVKPLVRWIWLGGLLMALGGLLALSDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	323 (321)
Sequences:	16982 (11292)
Seq/√Len:	630.3
META:	0.89

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
223_D	241_T	5.137	1.00
214_E	219_T	3.425	1.00
221_T	243_S	3.404	1.00
122_A	141_A	2.948	1.00
237_R	255_E	2.902	1.00
147_I	184_L	2.817	1.00
239_T	253_Y	2.733	1.00
241_T	248_P	2.633	1.00
189_F	193_I	2.608	1.00
212_S	219_T	2.593	1.00
205_V	213_V	2.568	1.00
212_S	221_T	2.445	1.00
273_S	303_R	2.423	1.00
243_S	248_P	2.417	1.00
36_A	97_L	2.389	1.00
208_K	211_E	2.387	1.00
62_E	68_K	2.336	1.00
228_V	235_A	2.330	1.00
13_A	17_W	2.300	1.00
239_T	251_T	2.298	1.00
108_R	112_L	2.269	1.00
121_A	144_A	2.243	1.00
174_R	321_S	2.240	1.00
188_V	311_L	2.232	1.00
226_T	239_T	2.198	1.00
240_F	294_V	2.191	1.00
240_F	281_V	2.137	1.00
195_G	301_L	2.053	1.00
229_Q	234_T	2.021	1.00
228_V	237_R	2.005	1.00
242_V	279_L	1.994	1.00
221_T	241_T	1.990	1.00
160_E	164_G	1.981	1.00
50_T	79_V	1.975	1.00
88_L	190_V	1.965	1.00
252_L	270_A	1.964	1.00
223_D	239_T	1.943	1.00
254_P	270_A	1.934	1.00
47_A	80_F	1.904	1.00
73_P	77_N	1.893	1.00
241_T	251_T	1.889	1.00
213_V	296_V	1.880	1.00
207_L	213_V	1.875	1.00
117_A	148_A	1.867	1.00
207_L	211_E	1.846	1.00
214_E	217_G	1.820	1.00
237_R	253_Y	1.813	1.00
248_P	251_T	1.776	1.00
229_Q	260_P	1.769	1.00
226_T	237_R	1.751	1.00
208_K	291_A	1.744	1.00
139_G	194_A	1.741	1.00
222_F	225_V	1.727	1.00
17_W	20_P	1.725	1.00
39_L	90_L	1.676	1.00
91_M	186_V	1.671	1.00
227_E	236_V	1.639	1.00
272_R	277_R	1.637	1.00
147_I	187_A	1.623	1.00
160_E	165_A	1.617	1.00
161_S	164_G	1.602	1.00
82_P	86_P	1.585	1.00
162_L	165_A	1.575	1.00
219_T	243_S	1.572	1.00
102_A	106_S	1.567	1.00
160_E	163_A	1.562	1.00
136_A	198_A	1.558	1.00
258_F	265_P	1.554	1.00
250_G	272_R	1.549	1.00
220_L	240_F	1.538	1.00
61_S	69_I	1.517	1.00
200_S	299_K	1.510	1.00
281_V	296_V	1.489	1.00
235_A	255_E	1.482	1.00
78_R	82_P	1.478	1.00
159_R	162_L	1.475	1.00
234_T	260_P	1.474	1.00
303_R	307_L	1.473	1.00
98_A	102_A	1.470	1.00
143_A	191_I	1.456	1.00
92_G	149_T	1.447	1.00
275_L	307_L	1.440	1.00
277_R	298_V	1.434	1.00
47_A	83_L	1.425	1.00
233_Y	257_R	1.393	1.00
97_L	102_A	1.386	1.00
159_R	163_A	1.383	1.00
3_F	7_V	1.378	1.00
252_L	281_V	1.377	1.00
201_T	298_V	1.366	1.00
109_R	112_L	1.366	1.00
144_A	148_A	1.355	1.00
133_S	136_A	1.349	1.00
57_Y	61_S	1.340	1.00
140_L	195_G	1.330	1.00
224_G	239_T	1.320	1.00
230_G	233_Y	1.319	1.00
178_G	315_G	1.293	1.00
43_L	86_P	1.290	1.00
181_L	318_L	1.289	1.00
9_G	13_A	1.271	1.00
153_E	157_R	1.264	1.00
256_K	267_T	1.264	1.00
2_A	6_L	1.259	1.00
243_S	246_G	1.258	1.00
310_L	314_L	1.258	1.00
151_L	155_W	1.251	1.00
227_E	234_T	1.236	1.00
147_I	191_I	1.236	1.00
206_R	291_A	1.234	1.00
112_L	116_A	1.227	1.00
197_S	200_S	1.224	1.00
105_A	109_R	1.210	1.00
185_G	311_L	1.210	1.00
159_R	164_G	1.199	1.00
220_L	296_V	1.194	1.00
117_A	121_A	1.186	1.00
152_L	156_R	1.179	1.00
201_T	216_G	1.171	1.00
164_G	167_R	1.168	1.00
196_S	200_S	1.163	1.00
217_G	244_R	1.155	1.00
92_G	145_W	1.152	1.00
192_G	308_G	1.136	1.00
274_G	277_R	1.131	1.00
185_G	312_M	1.130	1.00
150_I	153_E	1.129	1.00
202_E	295_R	1.127	1.00
44_L	87_L	1.113	1.00
207_L	212_S	1.110	1.00
163_A	167_R	1.106	1.00
203_R	213_V	1.105	1.00
114_P	152_L	1.096	1.00
80_F	84_M	1.081	1.00
51_V	80_F	1.080	1.00
220_L	242_V	1.076	1.00
16_A	19_A	1.069	1.00
51_V	55_T	1.052	1.00
222_F	238_A	1.051	1.00
161_S	165_A	1.050	1.00
2_A	5_A	1.039	1.00
52_L	56_L	1.036	1.00
209_P	222_F	1.033	1.00
287_L	290_G	1.032	1.00
176_R	180_Y	1.030	1.00
215_V	220_L	1.028	1.00
258_F	263_G	1.025	1.00
118_A	141_A	1.023	1.00
223_D	251_T	1.022	1.00
106_S	110_R	1.015	1.00
84_M	190_V	1.013	1.00
203_R	215_V	1.013	1.00
153_E	176_R	1.012	1.00
160_E	168_R	1.009	1.00
155_W	158_A	1.008	1.00
12_L	16_A	1.005	1.00
164_G	168_R	1.000	1.00
243_S	247_K	0.999	1.00
88_L	146_V	0.997	1.00
207_L	294_V	0.994	1.00
165_A	168_R	0.990	1.00
302_V	305_I	0.990	1.00
132_R	137_L	0.987	1.00
122_A	126_A	0.981	1.00
192_G	305_I	0.981	1.00
120_V	124_L	0.978	1.00
215_V	296_V	0.976	1.00
147_I	151_L	0.973	1.00
61_S	65_T	0.971	1.00
75_Y	79_V	0.965	1.00
47_A	84_M	0.965	1.00
218_Y	279_L	0.961	1.00
91_M	94_G	0.960	1.00
143_A	187_A	0.959	1.00
307_L	311_L	0.955	1.00
103_S	106_S	0.954	1.00
13_A	16_A	0.951	1.00
12_L	15_F	0.947	1.00
219_T	246_G	0.945	1.00
159_R	165_A	0.943	1.00
243_S	249_V	0.940	1.00
4_L	8_I	0.938	1.00
205_V	294_V	0.935	1.00
244_R	247_K	0.934	1.00
169_L	177_Y	0.934	1.00
162_L	166_L	0.934	1.00
216_G	298_V	0.925	1.00
125_L	129_G	0.924	1.00
274_G	304_W	0.924	1.00
238_A	283_L	0.924	1.00
105_A	108_R	0.923	1.00
256_K	265_P	0.915	1.00
15_F	19_A	0.910	1.00
140_L	191_I	0.910	1.00
275_L	303_R	0.906	1.00
5_A	9_G	0.906	1.00
29_S	101_R	0.903	1.00
45_V	48_A	0.901	1.00
150_I	184_L	0.900	1.00
158_A	165_A	0.900	1.00
125_L	144_A	0.888	1.00
166_L	170_R	0.887	1.00
186_V	189_F	0.884	1.00
137_L	141_A	0.884	1.00
167_R	170_R	0.881	1.00
220_L	281_V	0.876	1.00
126_A	132_R	0.874	1.00
204_D	295_R	0.874	1.00
150_I	180_Y	0.873	1.00
304_W	307_L	0.873	1.00
43_L	87_L	0.872	1.00
286_P	289_D	0.868	1.00
57_Y	69_I	0.866	1.00
113_W	116_A	0.863	1.00
119_L	123_L	0.860	1.00
16_A	20_P	0.859	1.00
31_V	35_S	0.857	1.00
104_L	108_R	0.854	1.00
184_L	188_V	0.853	1.00
209_P	224_G	0.853	1.00
145_W	149_T	0.852	1.00
114_P	148_A	0.846	1.00
126_A	137_L	0.845	1.00
30_L	35_S	0.842	1.00
77_N	197_S	0.841	1.00
150_I	187_A	0.840	1.00
36_A	94_G	0.835	1.00
47_A	51_V	0.834	1.00
269_A	282_V	0.830	1.00
147_I	150_I	0.829	1.00
154_L	177_Y	0.828	1.00
282_V	297_Y	0.825	1.00
188_V	307_L	0.824	1.00
186_V	312_M	0.824	1.00
225_V	238_A	0.820	1.00
283_L	292_W	0.818	1.00
84_M	193_I	0.813	1.00
31_V	36_A	0.811	1.00
113_W	117_A	0.811	1.00
240_F	254_P	0.806	1.00
257_R	268_E	0.805	1.00
148_A	151_L	0.801	1.00
191_I	195_G	0.799	1.00
233_Y	255_E	0.797	1.00
126_A	129_G	0.797	1.00
287_L	291_A	0.796	1.00
118_A	122_A	0.795	1.00
195_G	199_F	0.792	1.00
8_I	11_S	0.792	1.00
79_V	82_P	0.791	1.00
8_I	12_L	0.790	1.00
186_V	190_V	0.788	1.00
185_G	308_G	0.787	1.00
152_L	155_W	0.786	1.00
244_R	249_V	0.777	1.00
148_A	152_L	0.774	1.00
220_L	279_L	0.769	1.00
193_I	196_S	0.768	1.00
140_L	144_A	0.766	1.00
219_T	223_D	0.766	1.00
275_L	304_W	0.763	1.00
56_L	60_I	0.756	1.00
247_K	250_G	0.755	1.00
278_D	299_K	0.750	1.00
225_V	236_V	0.749	1.00
173_P	176_R	0.745	1.00
37_L	41_N	0.742	1.00
177_Y	180_Y	0.741	1.00
135_L	138_L	0.741	1.00
154_L	180_Y	0.736	1.00
189_F	305_I	0.732	1.00
146_V	187_A	0.732	1.00
218_Y	244_R	0.732	1.00
115_A	119_L	0.732	1.00
64_L	67_G	0.732	1.00
50_T	83_L	0.729	1.00
222_F	294_V	0.727	1.00
40_N	94_G	0.727	1.00
282_V	295_R	0.721	1.00
280_Y	297_Y	0.721	1.00
118_A	144_A	0.720	1.00
201_T	215_V	0.718	1.00
123_L	127_L	0.716	1.00
283_L	294_V	0.714	1.00
9_G	12_L	0.713	1.00
200_S	297_Y	0.712	1.00
275_L	278_D	0.712	1.00
86_P	89_L	0.711	1.00
196_S	302_V	0.711	1.00
71_V	75_Y	0.710	1.00
54_G	75_Y	0.710	1.00
282_V	299_K	0.710	1.00
168_R	171_R	0.709	1.00
10_G	14_L	0.708	1.00
110_R	156_R	0.708	1.00
149_T	153_E	0.704	1.00
249_V	272_R	0.701	1.00
191_I	301_L	0.696	1.00
242_V	252_L	0.696	1.00
97_L	107_L	0.695	1.00
143_A	147_I	0.695	1.00
154_L	157_R	0.695	1.00
112_L	115_A	0.694	1.00
212_S	243_S	0.694	1.00
278_D	303_R	0.694	1.00
62_E	66_G	0.694	1.00
7_V	10_G	0.691	1.00
162_L	167_R	0.689	1.00
108_R	111_L	0.689	1.00
153_E	156_R	0.688	1.00
50_T	82_P	0.688	1.00
86_P	90_L	0.686	1.00
150_I	154_L	0.686	1.00
118_A	148_A	0.684	1.00
162_L	168_R	0.683	1.00
122_A	137_L	0.683	1.00
115_A	118_A	0.680	1.00
85_L	89_L	0.675	1.00
153_E	180_Y	0.674	1.00
88_L	91_M	0.673	1.00
136_A	199_F	0.672	1.00
91_M	95_P	0.670	1.00
29_S	35_S	0.670	1.00
158_A	166_L	0.670	1.00
134_L	138_L	0.669	1.00
49_A	53_L	0.669	1.00
228_V	233_Y	0.668	1.00
210_G	223_D	0.668	1.00
190_V	194_A	0.667	1.00
195_G	198_A	0.666	1.00
35_S	39_L	0.663	1.00
217_G	298_V	0.663	1.00
17_W	21_L	0.661	1.00
3_F	11_S	0.661	1.00
81_V	190_V	0.660	1.00
242_V	250_G	0.658	1.00
149_T	152_L	0.658	1.00
222_F	240_F	0.656	1.00
18_R	22_L	0.656	1.00
89_L	93_V	0.656	1.00
11_S	15_F	0.656	1.00
106_S	109_R	0.655	1.00
245_D	249_V	0.653	1.00
234_T	258_F	0.653	1.00
22_L	25_G	0.652	1.00
146_V	150_I	0.650	1.00
85_L	142_L	0.650	1.00
14_L	18_R	0.649	1.00
143_A	194_A	0.648	1.00
189_F	308_G	0.648	1.00
19_A	22_L	0.647	1.00
226_T	253_Y	0.643	1.00
217_G	245_D	0.643	1.00
163_A	168_R	0.642	1.00
161_S	168_R	0.638	1.00
190_V	193_I	0.638	1.00
88_L	186_V	0.637	1.00
223_D	243_S	0.634	1.00
10_G	13_A	0.633	1.00
118_A	145_W	0.632	1.00
158_A	169_L	0.631	1.00
279_L	298_V	0.631	1.00
139_G	143_A	0.630	1.00
167_R	171_R	0.630	1.00
18_R	21_L	0.630	1.00
121_A	125_L	0.629	1.00
125_L	140_L	0.629	1.00
102_A	107_L	0.629	1.00
116_A	120_V	0.628	1.00
91_M	146_V	0.627	1.00
227_E	235_A	0.627	1.00
252_L	272_R	0.626	1.00
222_F	292_W	0.625	1.00
201_T	217_G	0.625	1.00
257_R	266_T	0.624	1.00
31_V	104_L	0.624	1.00
159_R	168_R	0.623	1.00
61_S	67_G	0.623	1.00
185_G	315_G	0.622	1.00
215_V	298_V	0.620	1.00
46_V	50_T	0.620	1.00
71_V	74_P	0.618	1.00
174_R	318_L	0.617	1.00
84_M	87_L	0.616	1.00
7_V	11_S	0.615	1.00
163_A	166_L	0.613	1.00
200_S	300_P	0.608	1.00
230_G	235_A	0.605	1.00
182_A	312_M	0.605	1.00
269_A	280_Y	0.605	1.00
39_L	43_L	0.603	1.00
193_I	197_S	0.602	1.00
21_L	25_G	0.599	1.00
251_T	254_P	0.597	1.00
189_F	312_M	0.596	1.00
145_W	150_I	0.594	1.00
59_L	68_K	0.593	1.00
245_D	248_P	0.592	1.00
50_T	54_G	0.591	1.00
61_S	64_L	0.591	1.00
121_A	148_A	0.589	1.00
47_A	87_L	0.588	1.00
286_P	292_W	0.588	1.00
172_L	177_Y	0.587	1.00
139_G	142_L	0.587	1.00
194_A	198_A	0.586	1.00
256_K	285_E	0.585	1.00
9_G	16_A	0.585	1.00
309_G	313_A	0.585	1.00
133_S	198_A	0.584	1.00
130_G	133_S	0.580	1.00
288_D	291_A	0.578	1.00
266_T	269_A	0.578	1.00
75_Y	80_F	0.578	1.00
92_G	95_P	0.577	1.00
48_A	52_L	0.577	1.00
171_R	174_R	0.576	1.00
36_A	39_L	0.576	1.00
256_K	284_G	0.575	1.00
62_E	65_T	0.573	1.00
87_L	91_M	0.573	1.00
6_L	9_G	0.573	1.00
150_I	157_R	0.572	1.00
31_V	102_A	0.568	1.00
181_L	314_L	0.566	1.00
173_P	177_Y	0.563	1.00
122_A	125_L	0.563	1.00
37_L	40_N	0.563	1.00
218_Y	277_R	0.562	1.00
225_V	292_W	0.561	1.00
154_L	158_A	0.560	1.00
25_G	28_F	0.560	1.00
273_S	278_D	0.559	1.00
125_L	128_L	0.559	1.00
118_A	121_A	0.557	1.00
184_L	311_L	0.557	1.00
168_R	172_L	0.556	1.00
253_Y	270_A	0.556	1.00
203_R	214_E	0.553	1.00
286_P	290_G	0.553	1.00
172_L	176_R	0.552	1.00
124_L	128_L	0.551	1.00
315_G	319_A	0.550	1.00
61_S	66_G	0.549	1.00
98_A	106_S	0.548	1.00
149_T	157_R	0.547	1.00
238_A	294_V	0.547	1.00
217_G	277_R	0.546	1.00
218_Y	242_V	0.546	1.00
46_V	53_L	0.546	1.00
260_P	265_P	0.543	1.00
15_F	18_R	0.541	0.99
60_I	63_A	0.538	0.99
213_V	220_L	0.538	0.99
178_G	319_A	0.537	0.99
139_G	190_V	0.537	0.99
126_A	199_F	0.536	0.99
286_P	291_A	0.534	0.99
206_R	293_T	0.534	0.99
235_A	257_R	0.534	0.99
79_V	84_M	0.533	0.99
53_L	57_Y	0.533	0.99
77_N	81_V	0.530	0.99
28_F	31_V	0.529	0.99
145_W	153_E	0.526	0.99
182_A	186_V	0.525	0.99
153_E	172_L	0.524	0.99
232_N	235_A	0.524	0.99
109_R	113_W	0.522	0.99
303_R	309_G	0.519	0.99
160_E	167_R	0.516	0.99
83_L	86_P	0.515	0.99
46_V	83_L	0.514	0.99
284_G	297_Y	0.514	0.99
176_R	179_G	0.511	0.99
111_L	114_P	0.510	0.99
204_D	293_T	0.507	0.99
133_S	137_L	0.507	0.99
274_G	303_R	0.505	0.99
270_A	281_V	0.503	0.99
5_A	8_I	0.501	0.99
81_V	84_M	0.500	0.99

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
2zy9A	2	0.2693	13.8	0.961	Contact Map
2mgyA	1	0.483	13.7	0.961	Contact Map
3cfuA	1	0.3282	8.1	0.965	Contact Map
3mcbA	1	0.1672	7.6	0.965	Contact Map
4ryoA	1	0.4303	5.6	0.967	Contact Map
3mceA	2	0.1827	5.3	0.968	Contact Map
4uc1A	3	0.4489	5.3	0.968	Contact Map
4p79A	1	0.2848	5	0.968	Contact Map
3mp7B	1	0.1672	4.4	0.969	Contact Map
2lomA	1	0.1579	4.2	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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