DUF721 - PFAM28P - GREMLIN Contacts

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DUF721 - Protein of unknown function (DUF721)

PFAM:	PF05258	Sequences: PLGDLLPRLLKELGLERRGLAEARLLAAWPEIVGPAIAAHTRPVSLRDGTLTVRVDSSAWAQELRLLKPEILERLNEALGEEAVKDIRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (87)
Sequences:	44790 (29743)
Seq/√Len:	3188.7
META:	0.939

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_V	54_R	3.214	1.00
40_H	56_D	2.411	1.00
68_K	86_D	2.210	1.00
49_G	85_K	2.186	1.00
67_L	70_E	2.164	1.00
50_T	86_D	2.155	1.00
28_A	78_A	2.071	1.00
63_E	67_L	2.017	1.00
28_A	31_E	1.946	1.00
29_W	41_T	1.938	1.00
50_T	88_R	1.839	1.00
65_R	68_K	1.821	1.00
40_H	60_W	1.784	1.00
62_Q	66_L	1.762	1.00
31_E	78_A	1.687	1.00
70_E	74_R	1.661	1.00
68_K	72_L	1.558	1.00
45_S	52_T	1.474	1.00
72_L	76_N	1.466	1.00
30_P	38_A	1.465	1.00
69_P	72_L	1.347	1.00
74_R	77_E	1.341	1.00
52_T	88_R	1.308	1.00
24_R	28_A	1.297	1.00
42_R	54_R	1.294	1.00
9_L	13_L	1.269	1.00
30_P	35_P	1.252	1.00
22_E	26_L	1.245	1.00
34_G	38_A	1.229	1.00
41_T	64_L	1.228	1.00
11_K	16_E	1.194	1.00
29_W	33_V	1.188	1.00
73_E	77_E	1.183	1.00
26_L	43_P	1.166	1.00
58_S	61_A	1.165	1.00
55_V	61_A	1.163	1.00
23_A	27_A	1.147	1.00
74_R	78_A	1.123	1.00
76_N	82_E	1.107	1.00
43_P	54_R	1.101	1.00
36_A	40_H	1.087	1.00
35_P	39_A	1.066	1.00
70_E	73_E	1.059	1.00
69_P	73_E	1.055	1.00
33_V	71_I	1.053	1.00
76_N	83_A	1.048	1.00
28_A	32_I	1.040	1.00
26_L	30_P	1.040	1.00
61_A	89_F	1.015	1.00
21_A	81_E	0.956	1.00
62_Q	65_R	0.950	1.00
80_G	83_A	0.945	1.00
32_I	78_A	0.937	1.00
59_A	63_E	0.912	1.00
5_L	9_L	0.907	1.00
57_S	60_W	0.899	1.00
61_A	65_R	0.884	1.00
43_P	51_L	0.873	1.00
55_V	64_L	0.865	1.00
47_R	52_T	0.863	1.00
13_L	16_E	0.852	1.00
82_E	85_K	0.850	1.00
36_A	39_A	0.847	1.00
76_N	81_E	0.843	1.00
46_L	84_V	0.835	1.00
63_E	66_L	0.833	1.00
44_V	52_T	0.832	1.00
19_G	22_E	0.832	1.00
41_T	53_V	0.826	1.00
21_A	24_R	0.824	1.00
37_I	60_W	0.819	1.00
20_L	23_A	0.811	1.00
64_L	89_F	0.810	1.00
35_P	38_A	0.809	1.00
37_I	67_L	0.804	1.00
60_W	63_E	0.789	1.00
3_G	7_P	0.772	1.00
19_G	23_A	0.765	1.00
79_L	82_E	0.763	1.00
36_A	60_W	0.761	1.00
4_D	7_P	0.760	1.00
75_L	78_A	0.753	1.00
67_L	74_R	0.719	1.00
73_E	76_N	0.718	1.00
76_N	79_L	0.715	1.00
68_K	87_I	0.714	1.00
76_N	84_V	0.709	1.00
75_L	79_L	0.705	1.00
64_L	71_I	0.705	1.00
30_P	39_A	0.703	1.00
24_R	27_A	0.700	1.00
29_W	53_V	0.699	1.00
8_R	12_E	0.695	1.00
15_L	19_G	0.688	1.00
79_L	83_A	0.683	1.00
42_R	56_D	0.679	1.00
59_A	62_Q	0.669	1.00
25_L	51_L	0.664	1.00
29_W	43_P	0.662	1.00
7_P	13_L	0.661	1.00
33_V	41_T	0.649	1.00
46_L	51_L	0.645	1.00
32_I	74_R	0.640	1.00
68_K	89_F	0.637	1.00
55_V	60_W	0.623	1.00
72_L	87_I	0.621	1.00
7_P	11_K	0.609	1.00
34_G	37_I	0.606	1.00
23_A	26_L	0.593	1.00
28_A	79_L	0.590	1.00
20_L	24_R	0.588	1.00
22_E	43_P	0.587	1.00
37_I	64_L	0.586	1.00
55_V	89_F	0.580	1.00
9_L	12_E	0.575	1.00
18_R	22_E	0.564	1.00
45_S	54_R	0.556	1.00
49_G	86_D	0.548	1.00
43_P	55_V	0.546	1.00
16_E	20_L	0.545	1.00
65_R	86_D	0.544	1.00
12_E	15_L	0.533	1.00
14_G	18_R	0.531	1.00
40_H	57_S	0.528	1.00
25_L	75_L	0.527	1.00
47_R	50_T	0.519	1.00
72_L	84_V	0.515	1.00
7_P	16_E	0.500	1.00
9_L	15_L	0.500	1.00
37_I	41_T	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
4iqjM	1	0.7303	60.7	0.773	Contact Map
2jmpA	1	0.764	55.4	0.78	Contact Map
4tpsB	1	0.8427	35.9	0.804	Contact Map
2e0gA	1	0.7865	30	0.812	Contact Map
2z4sA	1	0	25.5	0.819	Contact Map
2d28C	1	0.8764	6.7	0.86	Contact Map
4y0xA	1	0.4494	5.2	0.867	Contact Map
3lmmA	1	1	4.7	0.87	Contact Map
4j8zA	2	0.3034	4.6	0.871	Contact Map
1nh2D	1	0.9213	4.6	0.871	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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