UPF0180 - PFAM28P - GREMLIN Contacts

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UPF0180 - Uncharacterised protein family (UPF0180)

PFAM:	PF03698	Sequences: KKIAVEEGLTNVKEALEEKGYEVVELDEESDAQGVDAIVVSGQDSNVMGMQDTSTKAPVINASGKTAEEVVQEVENR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (76)
Sequences:	1116 (882)
Seq/√Len:	101.1
META:	0.667

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_A	74_V	3.331	1.00
2_K	22_E	2.868	1.00
65_K	73_E	2.754	1.00
15_A	71_V	2.706	1.00
13_K	17_E	2.660	1.00
40_V	45_S	2.397	1.00
24_V	35_V	2.389	1.00
19_K	71_V	2.215	1.00
5_V	12_V	1.980	1.00
65_K	70_V	1.899	1.00
73_E	77_R	1.871	1.00
2_K	34_G	1.843	1.00
19_K	75_E	1.834	1.00
13_K	25_E	1.824	1.00
11_N	67_A	1.810	1.00
39_V	62_A	1.748	1.00
71_V	75_E	1.704	1.00
3_I	21_Y	1.686	1.00
15_A	68_E	1.615	1.00
40_V	59_V	1.505	1.00
15_A	19_K	1.468	1.00
7_E	25_E	1.418	1.00
15_A	67_A	1.401	1.00
7_E	27_D	1.401	1.00
69_E	72_Q	1.341	0.99
39_V	60_I	1.329	0.99
12_V	70_V	1.245	0.99
43_Q	47_V	1.189	0.98
53_T	56_K	1.116	0.98
73_E	76_N	1.078	0.97
14_E	17_E	1.014	0.96
5_V	16_L	1.008	0.96
63_S	75_E	1.001	0.96
67_A	70_V	0.986	0.95
6_E	41_S	0.966	0.95
27_D	32_A	0.962	0.95
66_T	69_E	0.952	0.94
72_Q	76_N	0.944	0.94
4_A	36_D	0.936	0.94
26_L	38_I	0.926	0.93
34_G	57_A	0.917	0.93
39_V	74_V	0.911	0.93
19_K	39_V	0.908	0.93
37_A	58_P	0.899	0.92
49_G	64_G	0.894	0.92
5_V	13_K	0.890	0.92
22_E	30_S	0.880	0.91
49_G	52_D	0.877	0.91
46_N	49_G	0.798	0.87
12_V	74_V	0.794	0.87
24_V	29_E	0.792	0.87
65_K	69_E	0.783	0.86
18_E	74_V	0.780	0.86
30_S	56_K	0.765	0.85
68_E	71_V	0.764	0.85
5_V	25_E	0.746	0.83
4_A	35_V	0.739	0.83
41_S	47_V	0.726	0.81
42_G	46_N	0.722	0.81
68_E	72_Q	0.721	0.81
33_Q	56_K	0.713	0.80
42_G	64_G	0.711	0.80
30_S	54_S	0.708	0.80
4_A	24_V	0.698	0.79
71_V	74_V	0.695	0.79
45_S	61_N	0.692	0.78
40_V	58_P	0.689	0.78
21_Y	75_E	0.686	0.78
6_E	11_N	0.684	0.77
35_V	71_V	0.674	0.76
72_Q	75_E	0.667	0.76
40_V	61_N	0.664	0.75
34_G	56_K	0.662	0.75
45_S	63_S	0.660	0.75
3_I	71_V	0.654	0.74
32_A	55_T	0.648	0.74
33_Q	54_S	0.644	0.73
11_N	17_E	0.638	0.72
40_V	56_K	0.637	0.72
2_K	35_V	0.632	0.72
16_L	66_T	0.631	0.72
46_N	51_Q	0.631	0.72
70_V	76_N	0.621	0.70
43_Q	63_S	0.620	0.70
12_V	67_A	0.618	0.70
65_K	75_E	0.612	0.69
54_S	63_S	0.603	0.68
41_S	61_N	0.592	0.67
35_V	38_I	0.592	0.67
39_V	66_T	0.587	0.66
27_D	31_D	0.586	0.66
48_M	52_D	0.584	0.66
44_D	49_G	0.569	0.64
7_E	10_T	0.566	0.63
14_E	18_E	0.559	0.62
66_T	76_N	0.556	0.62
2_K	57_A	0.556	0.62
8_G	11_N	0.549	0.61
7_E	30_S	0.547	0.61
13_K	30_S	0.543	0.60
3_I	20_G	0.542	0.60
44_D	48_M	0.535	0.59
9_L	62_A	0.535	0.59
67_A	74_V	0.528	0.58
43_Q	61_N	0.520	0.57
35_V	57_A	0.511	0.56
38_I	57_A	0.510	0.55
45_S	49_G	0.507	0.55
39_V	58_P	0.505	0.55
41_S	49_G	0.504	0.55
43_Q	46_N	0.503	0.54
29_E	35_V	0.501	0.54
4_A	27_D	0.500	0.54
18_E	22_E	0.500	0.54

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
2ywdA	1	0.8831	62.3	0.812	Contact Map
2issD	1	0.8831	61.4	0.814	Contact Map
4fccA	5	0.6494	59.7	0.816	Contact Map
1q7rA	1	0.8831	58.9	0.816	Contact Map
1jvnA	1	0.8831	57.8	0.817	Contact Map
4gudA	1	0.8442	55.5	0.82	Contact Map
4jc0A	1	0.9091	53.9	0.822	Contact Map
1ka9H	1	0.8701	52	0.824	Contact Map
2nv0A	1	0.8831	48.7	0.827	Contact Map
2abwA	1	0.8961	48.5	0.827	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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