ATP-synt_I - PFAM28P - GREMLIN Contacts

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ATP-synt_I - ATP synthase I chain

PFAM:	PF03899	Sequences: RILRLQLVLTAVAALAALLLGGWRAALSALLGGLIAVLNFALLARRVFRLAGALAASAGAALRGFYLGEALKLALTAALLYLAFKLVLPLSPLALLAGLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	100 (98)
Sequences:	16975 (12228)
Seq/√Len:	1235.2
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_T	33_G	4.180	1.00
81_Y	85_K	3.315	1.00
91_S	94_A	2.971	1.00
17_A	21_G	2.361	1.00
39_N	76_T	2.273	1.00
25_A	94_A	2.069	1.00
31_L	83_A	2.053	1.00
80_L	95_L	1.970	1.00
84_F	92_P	1.949	1.00
21_G	25_A	1.877	1.00
17_A	20_L	1.858	1.00
24_R	27_L	1.787	1.00
29_A	98_G	1.777	1.00
35_I	79_L	1.771	1.00
23_W	27_L	1.718	1.00
42_L	71_L	1.716	1.00
69_E	73_L	1.669	1.00
35_I	39_N	1.547	1.00
42_L	46_R	1.514	1.00
17_A	29_A	1.494	1.00
82_L	86_L	1.462	1.00
17_A	25_A	1.430	1.00
24_R	28_S	1.421	1.00
14_A	30_L	1.416	1.00
28_S	91_S	1.394	1.00
36_A	99_L	1.370	1.00
80_L	99_L	1.370	1.00
57_S	60_A	1.369	1.00
73_L	77_A	1.349	1.00
13_A	29_A	1.340	1.00
41_A	45_R	1.339	1.00
28_S	90_L	1.309	1.00
51_A	54_L	1.302	1.00
28_S	94_A	1.301	1.00
50_L	53_A	1.263	1.00
83_A	95_L	1.247	1.00
4_R	8_V	1.242	1.00
44_A	47_V	1.178	1.00
36_A	39_N	1.174	1.00
48_F	51_A	1.140	1.00
7_L	37_V	1.130	1.00
25_A	29_A	1.123	1.00
3_L	37_V	1.100	1.00
86_L	89_P	1.095	1.00
22_G	25_A	1.089	1.00
52_G	56_A	1.072	1.00
83_A	88_L	1.050	1.00
68_G	72_K	1.047	1.00
46_R	72_K	1.037	1.00
18_L	26_A	1.031	1.00
53_A	56_A	1.010	1.00
52_G	55_A	0.997	1.00
94_A	98_G	0.978	1.00
66_Y	70_A	0.966	1.00
49_R	52_G	0.959	1.00
93_L	97_A	0.941	1.00
58_A	62_L	0.932	1.00
25_A	91_S	0.929	1.00
45_R	68_G	0.927	1.00
58_A	61_A	0.902	1.00
59_G	63_R	0.896	1.00
46_R	71_L	0.896	1.00
10_T	37_V	0.893	1.00
50_L	54_L	0.875	1.00
5_L	9_L	0.859	1.00
63_R	67_L	0.846	1.00
60_A	63_R	0.823	1.00
84_F	95_L	0.820	1.00
57_S	62_L	0.818	1.00
13_A	98_G	0.814	1.00
85_K	88_L	0.813	1.00
29_A	94_A	0.810	1.00
7_L	11_A	0.808	1.00
69_E	72_K	0.802	1.00
46_R	68_G	0.801	1.00
2_I	6_Q	0.799	1.00
27_L	31_L	0.795	1.00
5_L	8_V	0.793	1.00
35_I	83_A	0.792	1.00
14_A	33_G	0.784	1.00
48_F	52_G	0.777	1.00
57_S	63_R	0.776	1.00
39_N	72_K	0.767	1.00
18_L	21_G	0.767	1.00
18_L	23_W	0.757	1.00
14_A	26_A	0.756	1.00
7_L	10_T	0.751	1.00
39_N	42_L	0.751	1.00
16_A	20_L	0.745	1.00
43_L	65_F	0.730	1.00
59_G	62_L	0.729	1.00
39_N	75_L	0.724	1.00
66_Y	69_E	0.715	1.00
61_A	64_G	0.714	1.00
67_L	71_L	0.701	1.00
62_L	66_Y	0.700	1.00
76_T	80_L	0.698	1.00
29_A	33_G	0.695	1.00
76_T	79_L	0.687	1.00
37_V	41_A	0.684	1.00
26_A	30_L	0.683	1.00
64_G	67_L	0.682	1.00
35_I	80_L	0.679	1.00
84_F	88_L	0.676	1.00
42_L	75_L	0.674	1.00
30_L	34_L	0.666	1.00
81_Y	86_L	0.666	1.00
95_L	98_G	0.663	1.00
43_L	68_G	0.646	1.00
90_L	93_L	0.644	1.00
10_T	14_A	0.640	1.00
51_A	55_A	0.632	1.00
46_R	67_L	0.629	1.00
39_N	43_L	0.621	1.00
77_A	81_Y	0.620	1.00
92_P	96_L	0.618	1.00
15_L	19_L	0.598	1.00
32_G	98_G	0.597	1.00
40_F	46_R	0.580	1.00
71_L	75_L	0.580	1.00
81_Y	84_F	0.569	1.00
83_A	90_L	0.569	1.00
17_A	97_A	0.565	1.00
39_N	69_E	0.561	1.00
56_A	60_A	0.559	1.00
88_L	91_S	0.556	1.00
59_G	66_Y	0.552	1.00
71_L	74_A	0.551	1.00
25_A	97_A	0.549	1.00
50_L	55_A	0.544	1.00
11_A	14_A	0.544	1.00
65_F	68_G	0.544	1.00
6_Q	37_V	0.541	1.00
50_L	60_A	0.537	1.00
94_A	97_A	0.534	1.00
16_A	19_L	0.534	1.00
34_L	39_N	0.531	1.00
83_A	86_L	0.523	1.00
42_L	45_R	0.520	1.00
85_K	89_P	0.513	1.00
13_A	16_A	0.513	1.00
24_R	89_P	0.513	1.00
35_I	95_L	0.511	1.00
14_A	18_L	0.510	1.00
13_A	17_A	0.501	1.00
12_V	16_A	0.500	1.00
17_A	94_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
4av3A	2	1	11.5	0.817	Contact Map
3ne5A	3	0.56	3.5	0.856	Contact Map
4a01A	2	1	2.7	0.865	Contact Map
3ze3A	4	0.9	2.3	0.87	Contact Map
2nq2A	2	0.5	2.2	0.871	Contact Map
4pgrA	1	0.46	2.1	0.873	Contact Map
4hyjA	2	0.97	2	0.873	Contact Map
5ajiA	3	0.78	1.9	0.876	Contact Map
3w4tA	1	0.53	1.6	0.88	Contact Map
4hw9A	3	0.72	1.6	0.88	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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