DUF965 - PFAM28P - GREMLIN Contacts

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DUF965 - Bacterial protein of unknown function (DUF965)

PFAM:	PF06135	Sequences: DETMKFSVEKEKENEVKEILKEVYEALKEKGYNPINQIVGYLLSGDPTYITSHNNARSLIRKLERDELLEELVKSYLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	78 (78)
Sequences:	3427 (1785)
Seq/√Len:	202.1
META:	0.834

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_E	59_L	3.800	1.00
29_E	54_N	3.226	1.00
55_N	58_S	3.009	1.00
26_A	54_N	2.354	1.00
29_E	53_H	2.188	1.00
19_I	63_L	2.048	1.00
17_K	21_K	1.988	1.00
28_K	34_P	1.984	1.00
19_I	23_V	1.854	1.00
14_N	18_E	1.831	1.00
39_V	69_L	1.741	1.00
17_K	75_S	1.721	1.00
18_E	22_E	1.716	1.00
45_G	70_E	1.700	1.00
15_E	18_E	1.622	1.00
19_I	59_L	1.514	1.00
48_T	51_T	1.480	1.00
38_I	42_L	1.444	1.00
35_I	74_K	1.433	1.00
25_E	28_K	1.421	1.00
2_E	5_K	1.411	1.00
33_N	36_N	1.404	1.00
16_V	68_L	1.363	1.00
75_S	78_E	1.360	1.00
23_V	27_L	1.321	1.00
26_A	30_K	1.277	1.00
39_V	73_V	1.269	1.00
42_L	69_L	1.255	1.00
38_I	73_V	1.252	1.00
2_E	10_K	1.240	1.00
72_L	75_S	1.197	1.00
71_E	75_S	1.189	1.00
41_Y	44_S	1.098	1.00
18_E	21_K	1.081	1.00
20_L	38_I	1.075	1.00
20_L	72_L	1.063	1.00
25_E	54_N	1.034	1.00
40_G	46_D	1.031	1.00
42_L	48_T	1.015	1.00
45_G	64_E	1.010	1.00
42_L	61_R	0.945	0.99
55_N	59_L	0.944	0.99
13_E	71_E	0.941	0.99
64_E	70_E	0.924	0.99
7_S	11_E	0.923	0.99
52_S	70_E	0.922	0.99
22_E	26_A	0.918	0.99
15_E	62_K	0.916	0.99
16_V	19_I	0.911	0.99
69_L	73_V	0.904	0.99
23_V	60_I	0.846	0.99
5_K	10_K	0.845	0.99
27_L	50_I	0.843	0.99
22_E	25_E	0.840	0.99
32_Y	36_N	0.835	0.99
48_T	66_D	0.824	0.98
11_E	14_N	0.823	0.98
21_K	25_E	0.823	0.98
63_L	68_L	0.821	0.98
68_L	72_L	0.820	0.98
30_K	53_H	0.819	0.98
1_D	42_L	0.819	0.98
24_Y	34_P	0.808	0.98
25_E	29_E	0.782	0.98
18_E	62_K	0.765	0.97
27_L	58_S	0.740	0.97
71_E	76_Y	0.715	0.96
53_H	56_A	0.706	0.96
36_N	39_V	0.702	0.96
15_E	33_N	0.689	0.95
43_L	61_R	0.683	0.95
42_L	68_L	0.681	0.95
69_L	72_L	0.678	0.95
7_S	10_K	0.674	0.95
32_Y	46_D	0.669	0.94
47_P	61_R	0.666	0.94
20_L	24_Y	0.649	0.93
22_E	54_N	0.641	0.93
38_I	60_I	0.640	0.93
60_I	68_L	0.640	0.93
43_L	48_T	0.635	0.93
58_S	62_K	0.634	0.93
24_Y	77_L	0.633	0.93
12_K	18_E	0.626	0.92
45_G	52_S	0.621	0.92
48_T	58_S	0.621	0.92
14_N	17_K	0.614	0.91
24_Y	38_I	0.609	0.91
5_K	9_E	0.609	0.91
23_V	56_A	0.607	0.91
8_V	15_E	0.607	0.91
35_I	39_V	0.606	0.91
21_K	75_S	0.604	0.91
10_K	14_N	0.600	0.90
16_V	63_L	0.599	0.90
51_T	56_A	0.598	0.90
2_E	12_K	0.595	0.90
9_E	12_K	0.577	0.89
9_E	14_N	0.577	0.89
71_E	74_K	0.577	0.89
9_E	13_E	0.565	0.88
4_M	9_E	0.562	0.87
14_N	21_K	0.554	0.87
15_E	19_I	0.553	0.87
41_Y	60_I	0.552	0.86
67_E	76_Y	0.547	0.86
8_V	11_E	0.543	0.86
1_D	4_M	0.541	0.85
26_A	56_A	0.536	0.85
20_L	42_L	0.534	0.85
74_K	78_E	0.531	0.84
24_Y	28_K	0.528	0.84
49_Y	67_E	0.520	0.83
33_N	67_E	0.516	0.83
39_V	66_D	0.509	0.82
13_E	17_K	0.509	0.82
40_G	49_Y	0.500	0.81

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
3va9A	2	0.7949	70.8	0.863	Contact Map
3lhqA	2	0.859	17.2	0.905	Contact Map
1ujpA	1	0.6923	16.5	0.906	Contact Map
2iaiA	2	0.8333	13.3	0.91	Contact Map
4pjwA	1	0.8846	12.8	0.91	Contact Map
4bejA	2	0.7821	11.6	0.912	Contact Map
3ccyA	2	0.7436	10.9	0.913	Contact Map
3ih6A	5	0.9487	10.9	0.913	Contact Map
2fd5A	2	0.7949	10	0.915	Contact Map
3qkxA	2	0.7821	9.2	0.916	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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