DUF1376 - PFAM28P - GREMLIN Contacts

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DUF1376 - Protein of unknown function (DUF1376)

PFAM:	PF07120	Sequences: PYYPFYIGDYLADTAHLTLEEHGAYLRLLDHYWLTEGPLPDDDRRLARIAGASTKEWRKAVEAVLAEFFTLTDGGWRNKRLDEEIAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (84)
Sequences:	11254 (9445)
Seq/√Len:	1030.5
META:	0.963

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_H	27_R	4.285	1.00
10_Y	22_H	3.345	1.00
26_L	30_D	2.874	1.00
5_F	26_L	2.565	1.00
19_L	23_G	2.072	1.00
5_F	30_D	1.961	1.00
7_I	30_D	1.858	1.00
21_E	63_A	1.843	1.00
77_R	82_D	1.725	1.00
18_T	21_E	1.711	1.00
12_A	34_L	1.675	1.00
32_Y	81_L	1.638	1.00
8_G	34_L	1.637	1.00
61_V	65_L	1.632	1.00
32_Y	82_D	1.618	1.00
8_G	12_A	1.573	1.00
80_R	84_E	1.544	1.00
6_Y	9_D	1.529	1.00
72_T	77_R	1.473	1.00
31_H	35_T	1.465	1.00
57_W	61_V	1.454	1.00
41_D	71_L	1.442	1.00
38_P	75_G	1.438	1.00
20_E	56_E	1.395	1.00
15_A	51_G	1.354	1.00
19_L	52_A	1.296	1.00
3_Y	30_D	1.292	1.00
19_L	27_R	1.283	1.00
19_L	24_A	1.257	1.00
29_L	81_L	1.243	1.00
11_L	30_D	1.229	1.00
9_D	80_R	1.211	1.00
43_D	61_V	1.187	1.00
3_Y	7_I	1.174	1.00
54_T	58_R	1.168	1.00
33_W	81_L	1.134	1.00
20_E	60_A	1.076	1.00
22_H	51_G	1.073	1.00
11_L	15_A	1.061	1.00
10_Y	27_R	1.013	1.00
22_H	26_L	1.008	1.00
43_D	62_E	0.996	1.00
45_R	49_I	0.990	1.00
72_T	75_G	0.980	1.00
16_H	67_E	0.970	1.00
78_N	81_L	0.966	1.00
45_R	63_A	0.960	1.00
31_H	49_I	0.951	1.00
5_F	10_Y	0.933	1.00
15_A	31_H	0.920	1.00
32_Y	68_F	0.911	1.00
24_A	60_A	0.881	1.00
4_P	84_E	0.872	1.00
19_L	22_H	0.867	1.00
16_H	45_R	0.866	1.00
21_E	60_A	0.842	1.00
7_I	34_L	0.838	1.00
19_L	50_A	0.833	1.00
47_A	54_T	0.819	1.00
10_Y	26_L	0.816	1.00
10_Y	14_T	0.812	1.00
13_D	34_L	0.805	1.00
32_Y	77_R	0.796	1.00
70_T	79_K	0.792	1.00
62_E	66_A	0.788	1.00
63_A	67_E	0.783	1.00
71_L	76_W	0.774	1.00
43_D	47_A	0.773	1.00
41_D	76_W	0.763	1.00
20_E	23_G	0.759	1.00
64_V	68_F	0.758	1.00
7_I	11_L	0.754	1.00
53_S	56_E	0.752	1.00
65_L	68_F	0.751	1.00
7_I	33_W	0.749	1.00
42_D	45_R	0.743	1.00
29_L	33_W	0.741	1.00
55_K	59_K	0.741	1.00
70_T	76_W	0.736	1.00
65_L	76_W	0.726	1.00
79_K	83_E	0.726	1.00
16_H	31_H	0.722	1.00
28_L	50_A	0.715	1.00
16_H	35_T	0.712	1.00
32_Y	38_P	0.707	1.00
3_Y	33_W	0.706	1.00
11_L	34_L	0.704	1.00
43_D	57_W	0.698	1.00
33_W	85_I	0.688	1.00
43_D	58_R	0.682	1.00
25_Y	29_L	0.677	1.00
10_Y	29_L	0.675	1.00
39_L	46_L	0.667	1.00
47_A	50_A	0.654	1.00
17_L	67_E	0.654	1.00
15_A	27_R	0.652	1.00
47_A	62_E	0.647	1.00
50_A	57_W	0.620	1.00
44_R	54_T	0.603	1.00
27_R	51_G	0.600	1.00
11_L	27_R	0.598	1.00
24_A	50_A	0.597	1.00
13_D	79_K	0.593	1.00
22_H	30_D	0.591	1.00
38_P	82_D	0.588	1.00
44_R	48_R	0.586	1.00
16_H	48_R	0.578	1.00
82_D	85_I	0.576	1.00
47_A	52_A	0.570	1.00
23_G	26_L	0.566	1.00
28_L	39_L	0.562	1.00
60_A	63_A	0.553	1.00
64_V	67_E	0.550	1.00
11_L	51_G	0.528	1.00
24_A	52_A	0.522	1.00
62_E	65_L	0.520	1.00
55_K	58_R	0.519	1.00
81_L	85_I	0.519	1.00
29_L	78_N	0.514	1.00
47_A	57_W	0.513	1.00
32_Y	76_W	0.512	1.00
47_A	58_R	0.508	1.00
14_T	27_R	0.506	1.00
37_G	82_D	0.505	1.00
32_Y	78_N	0.503	1.00
23_G	27_R	0.500	1.00

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
2w48A	3	0.7586	41.2	0.847	Contact Map
4pt7A	3	0.977	31.1	0.856	Contact Map
2v79A	4	0.977	30.7	0.857	Contact Map
3dv8A	2	1	30.1	0.858	Contact Map
2pjpA	1	0.7701	29.3	0.858	Contact Map
2wteA	2	0.9195	27.4	0.86	Contact Map
4ev0A	2	1	22.5	0.866	Contact Map
2g9wA	2	0.7816	20.7	0.868	Contact Map
3b02A	2	1	20.1	0.869	Contact Map
2b0lA	4	0.9655	20	0.869	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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