ATP-synt_8 - PFAM28P - GREMLIN Contacts

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ATP-synt_8 - ATP synthase protein 8

PFAM:	PF00895	Sequences: MPQLNPSPWFAILLFSWLTFLLIIQPKILSHTFPNNPPSKKTKTKKKTTPWNWPW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (55)
Sequences:	3661 (2152)
Seq/√Len:	290.1
META:	0.004

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_F	19_T	2.928	1.00
17_W	54_P	2.324	1.00
25_Q	28_I	2.068	1.00
38_P	41_K	1.920	1.00
6_P	12_I	1.873	1.00
18_L	22_L	1.846	1.00
43_K	46_K	1.615	1.00
7_S	11_A	1.575	1.00
13_L	17_W	1.567	1.00
41_K	46_K	1.510	1.00
12_I	16_S	1.492	1.00
21_L	25_Q	1.484	1.00
18_L	26_P	1.423	1.00
5_N	10_F	1.392	1.00
4_L	17_W	1.354	1.00
26_P	29_L	1.331	1.00
5_N	12_I	1.321	1.00
20_F	25_Q	1.314	1.00
7_S	33_F	1.308	1.00
51_W	54_P	1.259	1.00
11_A	15_F	1.216	1.00
37_P	40_K	1.211	1.00
36_N	41_K	1.209	1.00
8_P	17_W	1.185	1.00
42_T	45_K	1.184	1.00
5_N	8_P	1.161	1.00
8_P	11_A	1.142	1.00
4_L	29_L	1.123	1.00
34_P	40_K	1.120	1.00
44_T	47_K	1.117	1.00
1_M	55_W	1.104	1.00
35_N	41_K	1.095	1.00
7_S	12_I	1.061	1.00
29_L	32_T	0.983	1.00
35_N	38_P	0.969	1.00
34_P	38_P	0.963	1.00
17_W	53_W	0.951	1.00
23_I	48_T	0.903	1.00
37_P	46_K	0.896	1.00
16_S	27_K	0.887	1.00
37_P	41_K	0.860	1.00
4_L	7_S	0.852	1.00
8_P	51_W	0.848	1.00
22_L	25_Q	0.839	1.00
7_S	15_F	0.829	1.00
17_W	21_L	0.825	1.00
4_L	28_I	0.824	1.00
13_L	21_L	0.818	1.00
43_K	52_N	0.798	0.99
39_S	45_K	0.780	0.99
20_F	27_K	0.778	0.99
8_P	19_T	0.768	0.99
34_P	37_P	0.742	0.99
36_N	42_T	0.733	0.99
13_L	25_Q	0.726	0.99
13_L	24_I	0.720	0.99
13_L	16_S	0.696	0.99
27_K	54_P	0.679	0.98
40_K	43_K	0.652	0.98
34_P	42_T	0.640	0.97
8_P	15_F	0.627	0.97
38_P	45_K	0.619	0.97
13_L	20_F	0.613	0.97
31_H	35_N	0.607	0.97
15_F	18_L	0.606	0.96
6_P	10_F	0.598	0.96
15_F	25_Q	0.578	0.95
10_F	27_K	0.562	0.95
17_W	51_W	0.562	0.95
14_L	18_L	0.558	0.94
20_F	31_H	0.555	0.94
22_L	31_H	0.550	0.94
12_I	27_K	0.547	0.94
7_S	16_S	0.535	0.93
41_K	48_T	0.521	0.92
45_K	53_W	0.518	0.92
6_P	53_W	0.514	0.92
47_K	53_W	0.511	0.92
19_T	24_I	0.511	0.92
33_F	42_T	0.508	0.91
7_S	14_L	0.508	0.91
52_N	55_W	0.500	0.91

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
3hb3B	1	0.9818	2.8	0.853	Contact Map
2gsmB	1	0.9818	2.5	0.856	Contact Map
2yevB	1	1	2.3	0.86	Contact Map
2znlB	1	0	1.2	0.88	Contact Map
1fftB	1	1	0.8	0.892	Contact Map
3ppuA	2	0	0.6	0.902	Contact Map
2c9lY	2	0.3455	0.6	0.904	Contact Map
1uwyA	1	0	0.6	0.905	Contact Map
4i0uA	4	0.5818	0.5	0.906	Contact Map
4ev6A	3	0.6182	0.5	0.909	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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