B12D - PFAM28P - GREMLIN Contacts

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B12D - NADH-ubiquinone reductase complex 1 MLRQ subunit

PFAM:	PF06522	Sequences: KHPELIPLFAIVGAAVGGAAFYLVRLALRNPDVVWNKKNNPEPWNVLDPNEQGKFYSVNRDFSKLKKPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (65)
Sequences:	1040 (720)
Seq/√Len:	89.3
META:	0.431

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_A	35_W	3.842	1.00
22_Y	26_L	3.120	1.00
23_L	27_A	2.842	1.00
17_G	21_F	2.581	1.00
10_A	14_A	2.360	1.00
9_F	13_G	2.130	1.00
5_L	8_L	1.894	1.00
26_L	35_W	1.878	1.00
61_D	64_K	1.857	1.00
26_L	30_N	1.835	1.00
12_V	19_A	1.798	1.00
24_V	28_L	1.768	1.00
60_R	63_S	1.734	1.00
16_V	20_A	1.725	1.00
14_A	17_G	1.677	1.00
11_I	15_A	1.650	1.00
18_G	21_F	1.466	0.99
47_L	51_E	1.396	0.99
36_N	39_N	1.371	0.99
16_V	19_A	1.353	0.99
62_F	66_K	1.248	0.98
42_E	45_N	1.245	0.98
11_I	18_G	1.242	0.98
19_A	23_L	1.221	0.98
8_L	11_I	1.194	0.98
48_D	51_E	1.179	0.98
21_F	24_V	1.124	0.97
44_W	49_P	1.058	0.95
21_F	25_R	1.019	0.94
14_A	18_G	1.018	0.94
2_H	5_L	1.004	0.94
47_L	53_G	0.970	0.93
8_L	15_A	0.964	0.93
40_N	44_W	0.964	0.93
28_L	35_W	0.963	0.92
26_L	33_V	0.931	0.91
25_R	30_N	0.927	0.91
6_I	9_F	0.921	0.91
29_R	47_L	0.916	0.90
63_S	66_K	0.889	0.89
2_H	15_A	0.853	0.87
17_G	34_V	0.843	0.86
20_A	45_N	0.839	0.86
5_L	9_F	0.834	0.86
47_L	52_Q	0.825	0.85
46_V	49_P	0.824	0.85
11_I	14_A	0.804	0.84
4_E	7_P	0.788	0.83
23_L	26_L	0.763	0.80
31_P	53_G	0.743	0.79
18_G	36_N	0.742	0.79
59_N	63_S	0.719	0.76
5_L	15_A	0.710	0.75
61_D	65_L	0.710	0.75
22_Y	27_A	0.703	0.75
45_N	48_D	0.702	0.75
49_P	52_Q	0.691	0.73
17_G	20_A	0.671	0.71
22_Y	55_F	0.654	0.69
41_P	55_F	0.650	0.69
52_Q	57_S	0.645	0.68
42_E	49_P	0.635	0.67
17_G	63_S	0.632	0.67
42_E	46_V	0.625	0.66
36_N	46_V	0.623	0.66
58_V	64_K	0.621	0.65
54_K	57_S	0.620	0.65
15_A	32_D	0.616	0.65
62_F	65_L	0.606	0.63
19_A	55_F	0.603	0.63
30_N	53_G	0.600	0.63
36_N	41_P	0.599	0.63
8_L	57_S	0.593	0.62
51_E	54_K	0.588	0.61
46_V	51_E	0.577	0.60
57_S	64_K	0.576	0.60
12_V	17_G	0.571	0.59
31_P	40_N	0.569	0.59
30_N	33_V	0.568	0.59
15_A	20_A	0.565	0.58
35_W	39_N	0.564	0.58
11_I	66_K	0.564	0.58
6_I	56_Y	0.556	0.57
14_A	37_K	0.555	0.57
60_R	65_L	0.552	0.56
29_R	32_D	0.548	0.56
6_I	60_R	0.547	0.56
8_L	30_N	0.544	0.55
40_N	46_V	0.542	0.55
3_P	51_E	0.539	0.55
34_V	46_V	0.538	0.55
17_G	24_V	0.530	0.53
60_R	64_K	0.524	0.53
16_V	50_N	0.516	0.52
32_D	56_Y	0.504	0.50
19_A	61_D	0.503	0.50
6_I	37_K	0.501	0.49
6_I	40_N	0.500	0.49

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
2losA	1	0.4493	9.8	0.871	Contact Map
2y69J	1	0.4348	8.3	0.875	Contact Map
1v54J	1	0.4493	6.6	0.881	Contact Map
4um9B	2	0	6.2	0.882	Contact Map
2j5lA	1	0	5.8	0.883	Contact Map
1xu0A	1	0.6522	5.4	0.885	Contact Map
4kmlA	1	0.7536	4.1	0.892	Contact Map
2looA	1	0.3913	3.9	0.893	Contact Map
1u3mA	1	0.7246	3.4	0.896	Contact Map
1u5lA	1	0.7391	3.3	0.896	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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