YMF19 - PFAM28P - GREMLIN Contacts

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YMF19 - Plant ATP synthase F0

PFAM:	PF02326	Sequences: PQLDPSTFASQLFWLAITFVVLYLLLSRVALPRIGGILEERRKRIAGDLAEAERLKEEAEAALAAYEKALADARANAAANYFYSSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	86 (75)
Sequences:	6498 (3578)
Seq/√Len:	413.1
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_K	72_D	2.980	1.00
51_E	54_R	2.732	1.00
54_R	58_E	2.681	1.00
42_R	46_A	2.451	1.00
4_D	7_T	2.114	1.00
53_E	57_E	1.979	1.00
64_A	68_K	1.911	1.00
23_Y	27_S	1.787	1.00
46_A	50_A	1.767	1.00
43_K	47_G	1.749	1.00
26_L	31_L	1.726	1.00
57_E	61_A	1.714	1.00
61_A	65_A	1.685	1.00
40_E	44_R	1.672	1.00
24_L	28_R	1.668	1.00
12_L	16_A	1.648	1.00
63_L	67_E	1.629	1.00
29_V	33_R	1.559	1.00
57_E	60_E	1.495	1.00
56_K	60_E	1.491	1.00
13_F	17_I	1.486	1.00
21_V	25_L	1.484	1.00
59_A	63_L	1.423	1.00
58_E	61_A	1.333	1.00
7_T	10_S	1.287	1.00
39_E	43_K	1.280	1.00
35_G	39_E	1.265	1.00
60_E	64_A	1.230	1.00
56_K	63_L	1.217	1.00
20_V	24_L	1.195	1.00
16_A	20_V	1.187	1.00
54_R	57_E	1.138	1.00
5_P	9_A	1.113	1.00
7_T	11_Q	1.108	1.00
51_E	55_L	1.105	1.00
10_S	13_F	1.089	1.00
44_R	48_D	1.088	1.00
18_T	21_V	1.068	1.00
61_A	64_A	1.045	1.00
36_G	40_E	1.042	1.00
53_E	56_K	1.009	1.00
2_Q	5_P	1.002	1.00
67_E	71_A	0.975	1.00
72_D	75_A	0.969	1.00
25_L	29_V	0.948	1.00
64_A	67_E	0.937	1.00
47_G	51_E	0.936	1.00
50_A	54_R	0.909	1.00
9_A	13_F	0.901	1.00
26_L	30_A	0.900	1.00
68_K	71_A	0.883	1.00
69_A	72_D	0.879	1.00
3_L	8_F	0.848	1.00
65_A	69_A	0.845	1.00
30_A	34_I	0.837	1.00
36_G	43_K	0.814	1.00
50_A	53_E	0.802	1.00
11_Q	15_L	0.796	1.00
63_L	66_Y	0.791	1.00
66_Y	70_L	0.784	1.00
55_L	58_E	0.782	1.00
49_L	56_K	0.779	1.00
24_L	27_S	0.771	1.00
51_E	58_E	0.763	1.00
15_L	18_T	0.758	1.00
52_A	59_A	0.758	1.00
24_L	29_V	0.737	1.00
62_A	66_Y	0.737	1.00
8_F	37_I	0.724	1.00
71_A	74_R	0.722	1.00
19_F	22_L	0.716	1.00
56_K	66_Y	0.686	1.00
30_A	33_R	0.685	1.00
47_G	50_A	0.685	1.00
15_L	33_R	0.668	0.99
53_E	60_E	0.667	0.99
71_A	75_A	0.664	0.99
66_Y	69_A	0.630	0.99
58_E	62_A	0.628	0.99
5_P	8_F	0.616	0.99
43_K	46_A	0.611	0.99
61_A	68_K	0.603	0.99
53_E	69_A	0.597	0.99
62_A	65_A	0.593	0.99
40_E	47_G	0.592	0.99
31_L	34_I	0.580	0.99
49_L	52_A	0.571	0.98
8_F	18_T	0.564	0.98
5_P	10_S	0.564	0.98
35_G	42_R	0.557	0.98
65_A	68_K	0.549	0.98
12_L	19_F	0.549	0.98
9_A	12_L	0.544	0.98
69_A	73_A	0.541	0.98
40_E	43_K	0.541	0.98
47_G	55_L	0.540	0.98
33_R	36_G	0.539	0.98
15_L	23_Y	0.537	0.98
26_L	35_G	0.536	0.98
33_R	37_I	0.532	0.97
52_A	56_K	0.531	0.97
26_L	29_V	0.530	0.97
11_Q	30_A	0.526	0.97
4_D	9_A	0.525	0.97
11_Q	31_L	0.516	0.97
12_L	21_V	0.515	0.97
17_I	20_V	0.514	0.97
56_K	69_A	0.511	0.97
70_L	73_A	0.511	0.97
10_S	19_F	0.509	0.97
23_Y	26_L	0.508	0.97
22_L	30_A	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
1b9uA	1	0.3953	52.8	0.814	Contact Map
2khkA	1	0.593	24.8	0.845	Contact Map
2clyA	1	0.6047	7.8	0.876	Contact Map
2rddB	1	0.4302	7.2	0.879	Contact Map
4gc0A	1	0.5465	2.2	0.906	Contact Map
3qnqA	2	0.5233	2.1	0.907	Contact Map
1fx0A	1	0.7907	1.8	0.91	Contact Map
4hfiA	3	0.314	1.7	0.912	Contact Map
3zilA	1	0.7209	1.7	0.912	Contact Map
1vryA	1	0.407	1.6	0.913	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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