NDUFA12 - PFAM28P - GREMLIN Contacts

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NDUFA12 - NADH ubiquinone oxidoreductase subunit NDUFA12

PFAM:	PF05071	Sequences: GELVGEDEFGNRYYESKKKIDRERRWVIYNDGEAEASRVPPEWHGWLHHTVDEPPTEEPLLKPRPWQKPHQPNLTGTPAAYRPPGSLRKKYEAWTP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (94)
Sequences:	8365 (4217)
Seq/√Len:	435.0
META:	0.865

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_L	12_R	5.276	1.00
15_E	23_E	3.991	1.00
3_L	6_E	3.726	1.00
2_E	15_E	3.592	1.00
39_V	47_L	3.141	1.00
44_H	48_H	2.674	1.00
74_L	79_A	2.589	1.00
45_G	51_V	2.243	1.00
16_S	23_E	2.236	1.00
13_Y	40_P	2.066	1.00
71_Q	74_L	2.023	1.00
30_N	38_R	1.876	1.00
16_S	21_D	1.869	1.00
8_E	69_P	1.799	1.00
9_F	38_R	1.777	1.00
6_E	12_R	1.600	1.00
1_G	26_W	1.527	1.00
71_Q	79_A	1.511	1.00
34_A	38_R	1.404	1.00
82_R	86_S	1.391	1.00
44_H	50_T	1.375	1.00
82_R	88_R	1.305	1.00
45_G	50_T	1.297	1.00
8_E	42_E	1.286	1.00
64_R	67_Q	1.234	1.00
54_P	57_E	1.191	1.00
68_K	71_Q	1.175	1.00
16_S	22_R	1.168	1.00
23_E	49_H	1.155	1.00
38_R	72_P	1.141	1.00
56_T	59_P	1.141	1.00
53_E	57_E	1.126	1.00
24_R	49_H	1.122	1.00
8_E	40_P	1.120	1.00
19_K	23_E	1.118	1.00
32_G	38_R	1.107	1.00
59_P	62_K	1.088	1.00
2_E	17_K	1.043	1.00
42_E	50_T	1.019	1.00
86_S	90_K	1.016	1.00
43_W	54_P	0.990	1.00
18_K	22_R	0.984	1.00
18_K	21_D	0.951	1.00
63_P	67_Q	0.946	1.00
41_P	44_H	0.945	1.00
36_A	39_V	0.945	1.00
41_P	70_H	0.939	1.00
73_N	76_G	0.935	1.00
84_P	87_L	0.930	1.00
79_A	84_P	0.924	1.00
53_E	58_E	0.922	1.00
53_E	61_L	0.916	1.00
42_E	63_P	0.909	1.00
58_E	61_L	0.901	1.00
9_F	40_P	0.898	1.00
84_P	90_K	0.895	1.00
33_E	38_R	0.894	1.00
36_A	48_H	0.893	1.00
22_R	49_H	0.885	1.00
49_H	52_D	0.885	1.00
77_T	80_A	0.850	1.00
4_V	54_P	0.846	1.00
42_E	61_L	0.831	1.00
9_F	70_H	0.828	1.00
51_V	61_L	0.809	1.00
61_L	64_R	0.797	1.00
15_E	49_H	0.792	1.00
18_K	23_E	0.791	1.00
39_V	44_H	0.783	1.00
51_V	54_P	0.782	1.00
4_V	15_E	0.781	1.00
61_L	67_Q	0.763	1.00
91_Y	94_W	0.760	1.00
30_N	33_E	0.748	1.00
16_S	19_K	0.742	1.00
5_G	43_W	0.735	1.00
55_P	87_L	0.721	1.00
36_A	44_H	0.720	1.00
82_R	85_G	0.717	1.00
74_L	77_T	0.716	1.00
3_L	14_Y	0.716	1.00
87_L	92_E	0.711	1.00
61_L	65_P	0.693	1.00
35_E	73_N	0.680	1.00
47_L	50_T	0.679	1.00
58_E	62_K	0.676	1.00
14_Y	28_I	0.670	1.00
53_E	59_P	0.660	1.00
51_V	55_P	0.651	0.99
37_S	70_H	0.637	0.99
93_A	96_P	0.634	0.99
17_K	23_E	0.634	0.99
84_P	88_R	0.630	0.99
81_Y	84_P	0.628	0.99
84_P	89_K	0.626	0.99
77_T	83_P	0.625	0.99
73_N	77_T	0.623	0.99
16_S	20_I	0.619	0.99
37_S	75_T	0.615	0.99
6_E	30_N	0.604	0.99
66_W	72_P	0.598	0.99
45_G	48_H	0.597	0.99
2_E	16_S	0.597	0.99
63_P	69_P	0.595	0.99
87_L	90_K	0.591	0.99
37_S	73_N	0.590	0.99
11_N	27_V	0.589	0.99
86_S	92_E	0.589	0.99
54_P	59_P	0.582	0.99
29_Y	37_S	0.579	0.99
8_E	57_E	0.578	0.99
88_R	95_T	0.569	0.99
33_E	78_P	0.565	0.99
53_E	56_T	0.562	0.98
45_G	55_P	0.560	0.98
78_P	82_R	0.558	0.98
66_W	75_T	0.557	0.98
19_K	22_R	0.555	0.98
27_V	39_V	0.554	0.98
29_Y	49_H	0.550	0.98
77_T	81_Y	0.543	0.98
7_D	46_W	0.542	0.98
84_P	95_T	0.541	0.98
12_R	17_K	0.536	0.98
82_R	87_L	0.534	0.98
66_W	73_N	0.532	0.98
80_A	83_P	0.531	0.98
16_S	26_W	0.525	0.98
76_G	80_A	0.522	0.98
39_V	70_H	0.520	0.97
42_E	67_Q	0.518	0.97
78_P	84_P	0.516	0.97
58_E	63_P	0.516	0.97
86_S	89_K	0.513	0.97
16_S	24_R	0.512	0.97
43_W	46_W	0.510	0.97
15_E	57_E	0.508	0.97
38_R	79_A	0.504	0.97
36_A	70_H	0.504	0.97
66_W	70_H	0.502	0.97
85_G	93_A	0.500	0.97

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
2f5kA	3	0.6354	5.6	0.922	Contact Map
4op0A	1	0.3229	5.2	0.923	Contact Map
3bfmA	2	0.3229	4.6	0.925	Contact Map
4emkA	1	0.4479	4.5	0.925	Contact Map
4c92E	1	0.4688	4.1	0.927	Contact Map
1mgqA	3	0.4271	3.9	0.928	Contact Map
2jxwA	1	0.3021	3.9	0.928	Contact Map
2lrqA	1	0.5625	3.8	0.928	Contact Map
2dwvA	2	0.3438	3.6	0.929	Contact Map
1ywiA	1	0.2812	3.2	0.93	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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