COX4_pro - PFAM28P - GREMLIN Contacts

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COX4_pro - Prokaryotic Cytochrome C oxidase subunit IV

PFAM:	PF03626	Sequences: VIVFAALLVLTALTVAVAYLDLGGLNNVVALLAIAVVKAALVVLFFMHLKYESRLLRLLVLAPLVFLLLLLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (70)
Sequences:	46999 (28164)
Seq/√Len:	3366.2
META:	0.947

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_A	20_L	2.644	1.00
40_A	44_L	2.577	1.00
27_N	31_L	2.200	1.00
38_K	42_V	2.067	1.00
12_A	16_A	1.976	1.00
27_N	30_A	1.876	1.00
24_G	27_N	1.759	1.00
45_F	50_K	1.751	1.00
5_A	9_V	1.663	1.00
16_A	19_Y	1.661	1.00
4_F	8_L	1.660	1.00
14_T	34_I	1.619	1.00
10_L	37_V	1.615	1.00
3_V	41_L	1.475	1.00
43_V	49_L	1.472	1.00
63_P	66_F	1.432	1.00
25_L	28_V	1.429	1.00
7_L	42_V	1.425	1.00
6_A	41_L	1.402	1.00
17_V	30_A	1.391	1.00
54_R	58_L	1.371	1.00
2_I	6_A	1.369	1.00
26_N	30_A	1.323	1.00
25_L	29_V	1.294	1.00
29_V	33_A	1.256	1.00
52_E	56_L	1.251	1.00
54_R	57_R	1.244	1.00
44_L	50_K	1.230	1.00
38_K	46_F	1.230	1.00
7_L	38_K	1.222	1.00
60_V	63_P	1.202	1.00
40_A	61_L	1.186	1.00
26_N	29_V	1.174	1.00
3_V	45_F	1.157	1.00
15_V	19_Y	1.127	1.00
2_I	5_A	1.124	1.00
10_L	34_I	1.092	1.00
53_S	57_R	1.081	1.00
66_F	69_L	1.073	1.00
66_F	70_L	1.066	1.00
5_A	8_L	1.056	1.00
24_G	28_V	1.039	1.00
6_A	10_L	1.037	1.00
10_L	13_L	1.034	1.00
58_L	62_A	0.992	1.00
13_L	34_I	0.988	1.00
62_A	65_V	0.982	1.00
39_A	43_V	0.974	1.00
65_V	69_L	0.973	1.00
64_L	67_L	0.958	1.00
56_L	59_L	0.926	1.00
63_P	67_L	0.924	1.00
41_L	45_F	0.897	1.00
62_A	66_F	0.879	1.00
28_V	32_L	0.798	1.00
57_R	61_L	0.785	1.00
55_L	58_L	0.774	1.00
26_N	31_L	0.772	1.00
14_T	38_K	0.768	1.00
11_T	14_T	0.748	1.00
56_L	63_P	0.746	1.00
57_R	60_V	0.744	1.00
67_L	70_L	0.730	1.00
67_L	71_L	0.710	1.00
64_L	68_L	0.709	1.00
14_T	31_L	0.702	1.00
65_V	68_L	0.701	1.00
28_V	31_L	0.700	1.00
37_V	40_A	0.691	1.00
23_G	26_N	0.681	1.00
36_V	40_A	0.680	1.00
14_T	18_A	0.665	1.00
9_V	12_A	0.649	1.00
3_V	7_L	0.646	1.00
48_H	52_E	0.641	1.00
20_L	23_G	0.638	1.00
61_L	64_L	0.637	1.00
44_L	51_Y	0.633	1.00
6_A	37_V	0.624	1.00
10_L	14_T	0.620	1.00
19_Y	22_L	0.615	1.00
42_V	47_M	0.614	1.00
49_L	60_V	0.607	1.00
10_L	41_L	0.606	1.00
14_T	35_A	0.604	1.00
48_H	51_Y	0.600	1.00
59_L	62_A	0.600	1.00
57_R	64_L	0.597	1.00
58_L	61_L	0.581	1.00
45_F	51_Y	0.567	1.00
32_L	36_V	0.563	1.00
56_L	60_V	0.559	1.00
56_L	66_F	0.553	1.00
57_R	66_F	0.544	1.00
18_A	35_A	0.537	1.00
56_L	67_L	0.537	1.00
60_V	67_L	0.535	1.00
15_V	18_A	0.535	1.00
11_T	38_K	0.534	1.00
62_A	67_L	0.530	1.00
9_V	13_L	0.526	1.00
55_L	59_L	0.517	1.00
18_A	21_D	0.517	1.00
40_A	45_F	0.502	1.00
57_R	62_A	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
3c02A	3	0.2639	4.4	0.843	Contact Map
4p02A	1	0.9167	2.6	0.86	Contact Map
3ug9A	2	0.875	2.1	0.866	Contact Map
1z1nX	1	0	1.7	0.873	Contact Map
3rlfG	1	0.2361	1.7	0.873	Contact Map
4fbzA	3	1	1.6	0.874	Contact Map
2e84A	1	0	1.6	0.875	Contact Map
1rz2A	1	0	1.5	0.876	Contact Map
2wswA	3	0.7361	1.4	0.88	Contact Map
3dmkA	2	0.0139	1.3	0.882	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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