Caa3_CtaG - PFAM28P - GREMLIN Contacts

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Caa3_CtaG - Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)

PFAM:	PF09678	Sequences: ALYLRGVRRLRRRGWPRWRTAAFLAGLALLALALVSPLDALAEYLFSAHMVQHLLLMMVAPPLLVLGAPGTLLLRALPPRLRRLLRALRSRVLRVLTHPLVAWLLFAAVLWAWHLPALYDAALRSPAVHALEHLSFLAAGLLFWWPVLGPDPEPRRLSYGARLLYLFAAMLPHTVLGALLTFSPRPLYPAYALATAPRSPLADQQLAGLIMWVPGGLVYLVAALVLFFRWLRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	233 (227)
Sequences:	19637 (13233)
Seq/√Len:	878.3
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_A	128_V	3.460	1.00
103_W	168_A	3.227	1.00
31_A	35_V	2.897	1.00
30_L	60_A	2.845	1.00
109_V	139_A	2.714	1.00
7_V	20_T	2.644	1.00
4_L	24_L	2.622	1.00
18_W	22_A	2.562	1.00
111_W	172_P	2.548	1.00
199_S	202_A	2.394	1.00
26_G	64_L	2.354	1.00
29_L	55_L	2.291	1.00
109_V	135_S	2.276	1.00
111_W	176_L	2.237	1.00
16_P	19_R	2.180	1.00
17_R	21_A	2.148	1.00
33_A	55_L	2.128	1.00
105_L	139_A	2.114	1.00
120_D	190_A	2.034	1.00
143_F	169_A	1.997	1.00
107_A	172_P	1.958	1.00
29_L	60_A	1.948	1.00
146_P	165_Y	1.928	1.00
26_G	67_G	1.922	1.00
20_T	24_L	1.905	1.00
113_W	135_S	1.866	1.00
22_A	63_L	1.862	1.00
25_A	63_L	1.855	1.00
202_A	205_Q	1.839	1.00
120_D	124_R	1.810	1.00
46_F	207_A	1.804	1.00
112_A	118_L	1.790	1.00
180_L	187_L	1.785	1.00
108_A	112_A	1.740	1.00
103_W	165_Y	1.725	1.00
29_L	59_V	1.688	1.00
39_D	42_A	1.687	1.00
121_A	125_S	1.670	1.00
2_L	6_G	1.624	1.00
22_A	66_L	1.622	1.00
47_S	51_V	1.602	1.00
98_H	101_V	1.600	1.00
120_D	189_P	1.599	1.00
113_W	136_F	1.566	1.00
25_A	29_L	1.538	1.00
60_A	137_L	1.535	1.00
181_T	208_G	1.527	1.00
186_P	201_L	1.519	1.00
194_A	198_R	1.502	1.00
5_R	9_R	1.492	1.00
7_V	11_R	1.462	1.00
105_L	142_L	1.462	1.00
21_A	25_A	1.443	1.00
101_V	105_L	1.419	1.00
123_L	190_A	1.411	1.00
24_L	28_A	1.385	1.00
26_G	60_A	1.373	1.00
124_R	190_A	1.371	1.00
38_L	48_A	1.367	1.00
66_L	148_L	1.362	1.00
177_G	208_G	1.352	1.00
194_A	197_P	1.349	1.00
103_W	169_A	1.339	1.00
41_L	48_A	1.331	1.00
100_L	104_L	1.325	1.00
85_L	89_R	1.316	1.00
8_R	12_R	1.292	1.00
201_L	205_Q	1.290	1.00
101_V	104_L	1.289	1.00
32_L	36_S	1.277	1.00
147_V	166_L	1.266	1.00
15_W	20_T	1.265	1.00
157_L	161_A	1.265	1.00
87_A	92_V	1.248	1.00
22_A	25_A	1.247	1.00
159_Y	229_R	1.246	1.00
126_P	130_A	1.234	1.00
183_S	187_L	1.225	1.00
51_V	210_I	1.222	1.00
61_P	65_V	1.221	1.00
183_S	186_P	1.216	1.00
102_A	146_P	1.207	1.00
127_A	130_A	1.204	1.00
224_L	228_F	1.197	1.00
23_F	67_G	1.191	1.00
185_R	201_L	1.189	1.00
218_V	221_V	1.182	1.00
45_L	48_A	1.181	1.00
65_V	141_L	1.174	1.00
186_P	189_P	1.172	1.00
122_A	132_E	1.148	1.00
143_F	165_Y	1.136	1.00
158_S	161_A	1.132	1.00
217_L	221_V	1.132	1.00
47_S	203_D	1.131	1.00
24_L	27_L	1.122	1.00
195_T	198_R	1.117	1.00
50_M	53_H	1.103	1.00
128_V	131_L	1.098	1.00
39_D	43_E	1.093	1.00
102_A	142_L	1.090	1.00
113_W	132_E	1.081	1.00
47_S	210_I	1.079	1.00
4_L	8_R	1.079	1.00
225_V	229_R	1.077	1.00
82_R	85_L	1.073	1.00
61_P	140_G	1.072	1.00
55_L	60_A	1.071	1.00
37_P	41_L	1.070	1.00
78_P	81_L	1.069	1.00
125_S	128_V	1.061	1.00
6_G	9_R	1.054	1.00
8_R	11_R	1.042	1.00
162_R	226_L	1.025	1.00
34_L	56_L	1.025	1.00
114_H	211_M	1.023	1.00
224_L	227_F	1.016	1.00
30_L	137_L	1.012	1.00
134_L	138_A	1.009	1.00
157_L	165_Y	1.009	1.00
30_L	64_L	1.009	1.00
41_L	45_L	1.006	1.00
6_G	10_L	1.004	1.00
202_A	206_L	1.003	1.00
221_V	225_V	1.000	1.00
159_Y	162_R	0.994	1.00
9_R	13_R	0.990	1.00
11_R	14_G	0.981	1.00
11_R	20_T	0.979	1.00
18_W	21_A	0.973	1.00
7_V	15_W	0.971	1.00
107_A	169_A	0.969	1.00
49_H	53_H	0.965	1.00
53_H	129_H	0.964	1.00
127_A	131_L	0.961	1.00
132_E	136_F	0.958	1.00
95_V	101_V	0.952	1.00
135_S	139_A	0.949	1.00
2_L	5_R	0.944	1.00
61_P	137_L	0.938	1.00
45_L	203_D	0.925	1.00
68_A	71_T	0.924	1.00
84_L	88_L	0.919	1.00
115_L	118_L	0.916	1.00
92_V	96_L	0.915	1.00
144_W	222_A	0.907	1.00
131_L	135_S	0.905	1.00
55_L	59_V	0.896	1.00
172_P	176_L	0.895	1.00
225_V	228_F	0.893	1.00
178_A	181_T	0.889	1.00
159_Y	226_L	0.887	1.00
87_A	90_S	0.886	1.00
118_L	121_A	0.883	1.00
103_W	107_A	0.877	1.00
11_R	15_W	0.876	1.00
92_V	95_V	0.874	1.00
106_F	140_G	0.873	1.00
60_A	64_L	0.873	1.00
166_L	226_L	0.871	1.00
57_M	140_G	0.867	1.00
7_V	24_L	0.855	1.00
47_S	206_L	0.853	1.00
160_G	230_W	0.852	1.00
52_Q	133_H	0.846	1.00
42_A	45_L	0.842	1.00
33_A	60_A	0.842	1.00
110_L	173_H	0.840	1.00
58_M	106_F	0.836	1.00
74_L	78_P	0.836	1.00
109_V	112_A	0.832	1.00
43_E	133_H	0.828	1.00
7_V	72_L	0.827	1.00
49_H	129_H	0.819	1.00
30_L	56_L	0.819	1.00
174_T	177_G	0.816	1.00
122_A	128_V	0.816	1.00
75_R	78_P	0.808	1.00
210_I	214_P	0.805	1.00
106_F	139_A	0.799	1.00
90_S	94_R	0.798	1.00
84_L	91_R	0.795	1.00
72_L	76_A	0.786	1.00
135_S	138_A	0.785	1.00
170_M	173_H	0.780	1.00
15_W	72_L	0.777	1.00
120_D	191_Y	0.774	1.00
50_M	211_M	0.774	1.00
85_L	88_L	0.768	1.00
186_P	200_P	0.763	1.00
186_P	194_A	0.761	1.00
149_G	155_R	0.758	1.00
156_R	162_R	0.756	1.00
68_A	150_P	0.755	1.00
96_L	99_P	0.753	1.00
5_R	8_R	0.748	1.00
121_A	124_R	0.745	1.00
88_L	91_R	0.744	1.00
104_L	108_A	0.744	1.00
44_Y	47_S	0.744	1.00
54_L	210_I	0.738	1.00
62_P	140_G	0.736	1.00
16_P	21_A	0.735	1.00
175_V	178_A	0.729	1.00
177_G	212_W	0.727	1.00
218_V	222_A	0.723	1.00
172_P	175_V	0.723	1.00
23_F	27_L	0.720	1.00
53_H	133_H	0.720	1.00
27_L	64_L	0.711	1.00
91_R	94_R	0.708	1.00
72_L	75_R	0.706	1.00
168_A	172_P	0.705	1.00
29_L	33_A	0.704	1.00
61_P	141_L	0.703	1.00
49_H	114_H	0.703	1.00
104_L	107_A	0.703	1.00
64_L	141_L	0.702	1.00
181_T	212_W	0.702	1.00
45_L	199_S	0.701	1.00
58_M	218_V	0.700	1.00
86_R	90_S	0.697	1.00
50_M	114_H	0.696	1.00
163_L	223_A	0.696	1.00
64_L	67_G	0.690	1.00
71_T	75_R	0.689	1.00
117_A	121_A	0.688	1.00
188_Y	191_Y	0.686	1.00
129_H	133_H	0.685	1.00
113_W	118_L	0.685	1.00
84_L	87_A	0.677	1.00
186_P	204_Q	0.674	1.00
89_R	94_R	0.670	1.00
137_L	141_L	0.670	1.00
107_A	111_W	0.667	1.00
4_L	20_T	0.666	1.00
178_A	182_F	0.664	1.00
10_L	13_R	0.663	1.00
33_A	38_L	0.660	1.00
48_A	51_V	0.659	1.00
28_A	32_L	0.659	1.00
71_T	74_L	0.652	1.00
3_Y	67_G	0.651	1.00
160_G	164_L	0.649	1.00
50_M	136_F	0.647	1.00
43_E	129_H	0.646	1.00
212_W	216_G	0.643	1.00
73_L	76_A	0.639	1.00
53_H	211_M	0.639	1.00
138_A	141_L	0.638	1.00
64_L	137_L	0.637	1.00
96_L	142_L	0.636	1.00
161_A	164_L	0.633	1.00
130_A	134_L	0.633	1.00
124_R	127_A	0.632	1.00
199_S	203_D	0.628	1.00
54_L	215_G	0.628	1.00
222_A	226_L	0.627	1.00
93_L	97_T	0.624	1.00
87_A	91_R	0.624	1.00
113_W	122_A	0.621	1.00
98_H	157_L	0.620	1.00
95_V	98_H	0.620	1.00
111_W	115_L	0.619	1.00
179_L	183_S	0.614	1.00
216_G	220_L	0.612	1.00
54_L	214_P	0.612	1.00
7_V	10_L	0.611	1.00
110_L	176_L	0.608	1.00
96_L	101_V	0.604	1.00
213_V	217_L	0.604	1.00
39_D	52_Q	0.603	1.00
57_M	61_P	0.603	1.00
226_L	229_R	0.602	1.00
33_A	56_L	0.601	1.00
151_D	154_P	0.599	1.00
138_A	142_L	0.597	1.00
22_A	67_G	0.594	1.00
97_T	142_L	0.591	1.00
167_F	170_M	0.586	1.00
21_A	24_L	0.584	1.00
65_V	148_L	0.584	1.00
40_A	43_E	0.583	1.00
174_T	216_G	0.583	1.00
36_S	40_A	0.582	1.00
70_G	74_L	0.579	1.00
170_M	212_W	0.579	1.00
169_A	219_Y	0.578	1.00
169_A	173_H	0.576	1.00
123_L	129_H	0.576	1.00
149_G	162_R	0.574	1.00
106_F	110_L	0.572	1.00
15_W	19_R	0.571	1.00
170_M	174_T	0.571	1.00
119_Y	191_Y	0.568	1.00
119_Y	133_H	0.568	1.00
119_Y	123_L	0.566	1.00
223_A	227_F	0.566	1.00
120_D	188_Y	0.564	1.00
23_F	64_L	0.563	1.00
209_L	213_V	0.563	1.00
46_F	180_L	0.559	1.00
228_F	231_L	0.558	1.00
181_T	209_L	0.558	1.00
177_G	181_T	0.558	1.00
173_H	215_G	0.557	1.00
37_P	40_A	0.557	1.00
32_L	37_P	0.557	1.00
132_E	135_S	0.556	1.00
54_L	132_E	0.554	1.00
77_L	81_L	0.551	1.00
105_L	109_V	0.550	1.00
88_L	92_V	0.549	1.00
38_L	55_L	0.548	1.00
29_L	63_L	0.548	1.00
167_F	171_L	0.548	1.00
17_R	20_T	0.545	1.00
97_T	102_A	0.544	1.00
115_L	179_L	0.543	1.00
179_L	187_L	0.539	1.00
180_L	183_S	0.536	1.00
5_R	10_L	0.531	1.00
169_A	172_P	0.529	1.00
74_L	153_E	0.529	1.00
65_V	146_P	0.527	1.00
85_L	91_R	0.525	1.00
206_L	210_I	0.523	1.00
171_L	174_T	0.523	1.00
9_R	12_R	0.521	1.00
27_L	30_L	0.520	1.00
213_V	216_G	0.519	1.00
209_L	216_G	0.518	1.00
153_E	156_R	0.515	1.00
41_L	44_Y	0.514	1.00
118_L	132_E	0.513	1.00
113_W	116_P	0.511	1.00
82_R	87_A	0.506	1.00
114_H	132_E	0.504	1.00
27_L	31_A	0.503	1.00
35_V	39_D	0.500	1.00

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
2kncB	1	0.1588	3.9	0.955	Contact Map
3pjzA	2	0.5665	3.6	0.956	Contact Map
2m20A	2	0.1245	2.8	0.959	Contact Map
1kf6D	2	0.3519	2.4	0.96	Contact Map
4mt1A	3	0.3047	2.2	0.961	Contact Map
2l6wA	2	0.1502	2.1	0.961	Contact Map
2l2tA	2	0.1545	1.6	0.964	Contact Map
4b19A	1	0.1116	1.6	0.964	Contact Map
2kluA	1	0.1545	1.6	0.964	Contact Map
4o6yA	2	0.5966	1.6	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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