Ubiq_cyt_C_chap - PFAM28P - GREMLIN Contacts

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Ubiq_cyt_C_chap - Ubiquinol-cytochrome C chaperone

PFAM:	PF03981	Sequences: EDLGVPDTVDGRFDMLVLHLFLVLRRLRAEGEAGRALAQALFDAFFADMDDNLREMGVGDLSVGKRMKKMAEAFYGRLAAYDAALAADDAALAAALARNVYGGALAPDAAAAAALAAYVRAAAAALAAQPLAALLAGRVRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	141 (137)
Sequences:	6468 (4711)
Seq/√Len:	402.5
META:	0.853

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
89_D	120_R	3.587	1.00
30_E	131_L	2.812	1.00
133_A	138_R	2.721	1.00
25_R	123_A	2.616	1.00
39_Q	43_D	2.556	1.00
25_R	82_D	2.534	1.00
18_L	119_V	2.447	1.00
28_R	82_D	2.409	1.00
13_F	17_V	2.230	1.00
59_G	62_S	2.201	1.00
123_A	127_A	2.129	1.00
66_R	69_K	2.029	1.00
89_D	117_A	2.007	1.00
5_V	15_M	1.924	1.00
93_A	116_A	1.884	1.00
130_P	133_A	1.869	1.00
62_S	66_R	1.866	1.00
19_H	118_Y	1.804	1.00
96_L	119_V	1.766	1.00
20_L	45_F	1.753	1.00
76_G	99_N	1.670	1.00
21_F	78_L	1.614	1.00
26_R	30_E	1.613	1.00
93_A	113_A	1.594	1.00
14_D	77_R	1.553	1.00
100_V	115_L	1.543	1.00
68_K	72_E	1.529	1.00
122_A	125_A	1.518	1.00
81_Y	95_A	1.515	1.00
124_A	128_A	1.482	1.00
89_D	93_A	1.477	1.00
45_F	49_M	1.477	1.00
29_A	127_A	1.477	1.00
79_A	83_A	1.472	1.00
77_R	81_Y	1.444	1.00
76_G	98_R	1.441	1.00
21_F	82_D	1.429	1.00
62_S	65_K	1.418	1.00
67_M	70_M	1.407	1.00
107_P	112_A	1.374	1.00
4_G	111_A	1.364	1.00
21_F	25_R	1.327	1.00
8_T	11_G	1.301	1.00
88_D	91_A	1.293	1.00
93_A	112_A	1.270	1.00
47_A	51_D	1.259	1.00
48_D	52_N	1.258	1.00
9_V	56_M	1.238	1.00
108_D	111_A	1.186	1.00
18_L	23_V	1.175	1.00
39_Q	42_F	1.174	1.00
28_R	78_L	1.167	1.00
32_E	35_R	1.167	1.00
83_A	87_A	1.154	1.00
25_R	86_A	1.152	1.00
76_G	80_A	1.145	1.00
22_L	126_L	1.138	1.00
58_V	66_R	1.132	1.00
125_A	128_A	1.122	1.00
49_M	70_M	1.116	1.00
133_A	136_A	1.093	1.00
118_Y	122_A	1.088	1.00
129_Q	139_V	1.088	1.00
20_L	24_L	1.057	1.00
90_A	113_A	1.046	1.00
125_A	129_Q	1.045	1.00
31_G	34_G	1.040	1.00
24_L	38_A	1.036	1.00
121_A	124_A	1.032	1.00
46_F	74_F	1.028	1.00
82_D	86_A	1.025	1.00
93_A	97_A	1.022	1.00
23_V	41_L	1.020	1.00
44_A	47_A	1.018	1.00
131_L	135_L	1.017	1.00
117_A	121_A	1.013	1.00
64_G	67_M	1.006	1.00
90_A	94_A	0.995	1.00
30_E	34_G	0.981	1.00
71_A	75_Y	0.979	1.00
45_F	48_D	0.977	1.00
31_G	35_R	0.974	1.00
22_L	123_A	0.962	1.00
42_F	75_Y	0.945	1.00
54_R	60_D	0.943	1.00
10_D	102_G	0.936	1.00
87_A	91_A	0.923	1.00
132_A	136_A	0.891	1.00
5_V	11_G	0.887	1.00
73_A	77_R	0.886	1.00
10_D	70_M	0.882	1.00
48_D	51_D	0.874	1.00
46_F	71_A	0.863	1.00
40_A	43_D	0.861	1.00
94_A	97_A	0.854	1.00
74_F	78_L	0.851	1.00
34_G	131_L	0.849	1.00
78_L	82_D	0.846	1.00
112_A	116_A	0.846	1.00
30_E	33_A	0.838	1.00
65_K	69_K	0.825	1.00
34_G	37_L	0.823	1.00
111_A	114_A	0.821	1.00
97_A	107_P	0.810	1.00
23_V	139_V	0.807	1.00
25_R	127_A	0.803	1.00
14_D	102_G	0.802	1.00
96_L	115_L	0.802	1.00
16_L	52_N	0.791	1.00
23_V	27_L	0.784	1.00
121_A	125_A	0.777	1.00
84_A	91_A	0.770	1.00
13_F	73_A	0.766	1.00
60_D	63_V	0.764	1.00
90_A	93_A	0.760	1.00
58_V	62_S	0.759	1.00
79_A	82_D	0.753	1.00
80_A	99_N	0.748	1.00
83_A	91_A	0.748	1.00
120_R	123_A	0.746	1.00
97_A	109_A	0.745	1.00
3_L	114_A	0.745	1.00
84_A	95_A	0.742	1.00
24_L	42_F	0.741	1.00
46_F	99_N	0.740	1.00
24_L	74_F	0.736	1.00
7_D	12_R	0.732	1.00
42_F	45_F	0.728	1.00
67_M	71_A	0.718	1.00
46_F	67_M	0.716	1.00
85_L	123_A	0.708	1.00
94_A	98_R	0.700	1.00
126_L	129_Q	0.700	1.00
52_N	56_M	0.699	1.00
124_A	127_A	0.692	1.00
57_G	60_D	0.690	1.00
91_A	94_A	0.687	1.00
84_A	92_L	0.687	1.00
49_M	52_N	0.687	1.00
85_L	120_R	0.676	0.99
45_F	64_G	0.671	0.99
37_L	135_L	0.669	0.99
20_L	41_L	0.668	0.99
9_V	52_N	0.668	0.99
89_D	116_A	0.666	0.99
53_L	70_M	0.660	0.99
110_A	113_A	0.657	0.99
16_L	49_M	0.654	0.99
58_V	64_G	0.647	0.99
36_A	40_A	0.646	0.99
113_A	117_A	0.643	0.99
95_A	99_N	0.637	0.99
59_G	63_V	0.637	0.99
129_Q	133_A	0.634	0.99
27_L	34_G	0.627	0.99
33_A	36_A	0.627	0.99
17_V	45_F	0.626	0.99
96_L	116_A	0.623	0.99
21_F	28_R	0.622	0.99
15_M	100_V	0.621	0.99
134_L	138_R	0.615	0.99
46_F	52_N	0.613	0.99
114_A	117_A	0.613	0.99
115_L	118_Y	0.610	0.99
72_E	76_G	0.606	0.99
135_L	138_R	0.599	0.99
54_R	57_G	0.597	0.99
4_G	101_Y	0.593	0.99
24_L	41_L	0.593	0.99
9_V	13_F	0.591	0.99
54_R	63_V	0.585	0.98
34_G	38_A	0.583	0.98
58_V	61_L	0.577	0.98
81_Y	92_L	0.569	0.98
110_A	114_A	0.568	0.98
132_A	135_L	0.566	0.98
2_D	114_A	0.562	0.98
89_D	113_A	0.562	0.98
112_A	115_L	0.561	0.98
19_H	122_A	0.550	0.98
69_K	72_E	0.549	0.98
24_L	75_Y	0.547	0.98
12_R	16_L	0.547	0.98
38_A	42_F	0.546	0.98
42_F	71_A	0.542	0.97
33_A	131_L	0.540	0.97
24_L	28_R	0.539	0.97
16_L	20_L	0.537	0.97
20_L	46_F	0.536	0.97
50_D	60_D	0.530	0.97
3_L	101_Y	0.528	0.97
15_M	19_H	0.526	0.97
96_L	100_V	0.521	0.97
42_F	46_F	0.519	0.97
28_R	38_A	0.518	0.97
26_R	126_L	0.517	0.97
92_L	120_R	0.517	0.97
64_G	68_K	0.514	0.97
107_P	111_A	0.512	0.96
50_D	67_M	0.512	0.96
109_A	113_A	0.505	0.96
134_L	139_V	0.504	0.96
17_V	73_A	0.503	0.96
17_V	78_L	0.503	0.96
73_A	102_G	0.500	0.96
42_F	74_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
3lomA	2	0.695	4.5	0.931	Contact Map
3v46A	1	0.3404	3.8	0.934	Contact Map
4b4sA	1	0.5745	3.6	0.935	Contact Map
3kraB	1	0.6454	3.5	0.935	Contact Map
3npkA	2	0.6383	3.1	0.937	Contact Map
1nktA	3	0.4397	3.1	0.937	Contact Map
4f62A	2	0.617	3	0.938	Contact Map
3llwA	2	0.7021	2.9	0.938	Contact Map
1rqjA	2	0.6738	2.8	0.938	Contact Map
4lfgA	2	0.6312	2.8	0.939	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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