Ycf66_N - PFAM28P - GREMLIN Contacts

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Ycf66_N - Ycf66 protein N-terminus

PFAM:	PF07444	Sequences: YLLGIALALGGLALYFLRFFRPELSRDYDIFWSAVGLLYGLILWFQGWRLDPILLFGQVLLVGLLIFFGWETIRLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (75)
Sequences:	600 (322)
Seq/√Len:	37.2
META:	0.747

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_G	36_G	3.426	1.00
50_L	54_L	2.488	1.00
51_D	54_L	2.452	1.00
47_G	51_D	2.314	1.00
12_L	16_F	2.137	0.99
18_R	27_D	2.044	0.99
46_Q	53_I	1.982	0.98
28_Y	31_F	1.911	0.98
48_W	52_P	1.837	0.97
36_G	70_W	1.764	0.97
5_I	23_E	1.744	0.97
48_W	54_L	1.733	0.96
35_V	66_I	1.642	0.95
49_R	52_P	1.614	0.95
42_I	48_W	1.602	0.94
15_Y	22_P	1.599	0.94
48_W	51_D	1.503	0.92
18_R	25_S	1.486	0.92
35_V	60_L	1.448	0.91
6_A	12_L	1.426	0.90
47_G	54_L	1.395	0.89
46_Q	54_L	1.388	0.89
28_Y	68_F	1.376	0.88
8_A	19_F	1.373	0.88
47_G	52_P	1.310	0.86
8_A	40_G	1.305	0.86
61_L	67_F	1.295	0.85
46_Q	51_D	1.275	0.84
53_I	56_F	1.248	0.83
2_L	6_A	1.199	0.80
56_F	60_L	1.192	0.80
49_R	54_L	1.186	0.79
26_R	71_E	1.164	0.78
4_G	40_G	1.118	0.75
55_L	70_W	1.075	0.72
42_I	46_Q	1.039	0.70
68_F	72_T	1.033	0.69
48_W	53_I	1.032	0.69
2_L	74_R	1.023	0.69
65_L	68_F	0.976	0.65
9_L	20_F	0.928	0.61
61_L	65_L	0.925	0.61
37_L	50_L	0.924	0.61
59_V	70_W	0.914	0.60
54_L	58_Q	0.909	0.59
19_F	32_W	0.896	0.58
3_L	58_Q	0.886	0.57
17_L	23_E	0.883	0.57
42_I	51_D	0.878	0.57
7_L	62_V	0.864	0.55
11_G	40_G	0.851	0.54
35_V	63_G	0.849	0.54
39_Y	46_Q	0.843	0.54
3_L	6_A	0.834	0.53
34_A	62_V	0.819	0.51
16_F	40_G	0.817	0.51
4_G	11_G	0.817	0.51
2_L	8_A	0.806	0.50
10_G	24_L	0.787	0.49
4_G	56_F	0.784	0.48
40_G	63_G	0.777	0.48
14_L	21_R	0.770	0.47
11_G	33_S	0.763	0.46
6_A	57_G	0.750	0.45
73_I	76_R	0.746	0.45
61_L	66_I	0.743	0.45
17_L	60_L	0.734	0.44
41_L	50_L	0.720	0.43
16_F	37_L	0.715	0.42
28_Y	67_F	0.714	0.42
67_F	71_E	0.713	0.42
30_I	33_S	0.708	0.42
43_L	58_Q	0.704	0.41
26_R	43_L	0.700	0.41
7_L	31_F	0.679	0.39
33_S	63_G	0.675	0.39
13_A	53_I	0.671	0.39
2_L	5_I	0.671	0.39
9_L	12_L	0.666	0.38
18_R	32_W	0.661	0.38
71_E	75_L	0.660	0.38
33_S	73_I	0.655	0.37
34_A	37_L	0.639	0.36
4_G	66_I	0.627	0.35
53_I	59_V	0.625	0.35
68_F	73_I	0.606	0.33
3_L	44_W	0.603	0.33
42_I	56_F	0.600	0.33
30_I	36_G	0.599	0.33
42_I	52_P	0.599	0.33
45_F	53_I	0.597	0.33
26_R	32_W	0.591	0.32
10_G	69_G	0.589	0.32
40_G	45_F	0.584	0.32
7_L	28_Y	0.581	0.31
35_V	43_L	0.580	0.31
21_R	24_L	0.566	0.30
6_A	11_G	0.565	0.30
40_G	46_Q	0.565	0.30
9_L	16_F	0.565	0.30
7_L	39_Y	0.562	0.30
7_L	10_G	0.555	0.29
55_L	58_Q	0.551	0.29
15_Y	18_R	0.550	0.29
21_R	26_R	0.536	0.28
47_G	58_Q	0.532	0.28
6_A	10_G	0.519	0.27
4_G	18_R	0.517	0.27
47_G	53_I	0.515	0.27
25_S	30_I	0.510	0.26
32_W	64_L	0.507	0.26
30_I	56_F	0.500	0.26

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
3wajA	1	0.9342	8.1	0.891	Contact Map
3rceA	1	0.9211	6.5	0.896	Contact Map
4xnjA	1	0.3158	3.8	0.907	Contact Map
3pjzA	2	0.9868	3.3	0.91	Contact Map
3ne5A	3	0.8947	3.1	0.911	Contact Map
1cd1A	1	0	2.8	0.913	Contact Map
4o9uB	2	0.8947	2.8	0.913	Contact Map
3j1zP	8	0.9474	2.5	0.915	Contact Map
1xioA	2	0.6974	2.4	0.916	Contact Map
4mt1A	3	0.9605	2.2	0.918	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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