DUF1353 - PFAM28P - GREMLIN Contacts

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DUF1353 - Protein of unknown function (DUF1353)

PFAM:	PF07087	Sequences: WRLLEDFVYVDPDGEVITVPAGFVTDGASIPRILWSLIPPDGRYRRAAVVHDYLYGDTQTVTRKEADRIFREAMRALGVPKWKRWLMYAAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (89)
Sequences:	8827 (7069)
Seq/√Len:	749.3
META:	0.949

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_R	67_D	2.663	1.00
75_R	84_R	2.446	1.00
54_L	66_A	2.395	1.00
25_T	49_V	2.382	1.00
28_A	48_A	2.250	1.00
46_R	77_L	1.967	1.00
71_R	84_R	1.896	1.00
23_F	53_Y	1.883	1.00
70_F	87_M	1.878	1.00
20_P	53_Y	1.825	1.00
55_Y	67_D	1.817	1.00
62_T	65_E	1.743	1.00
55_Y	63_R	1.711	1.00
10_V	16_V	1.703	1.00
50_V	73_A	1.671	1.00
27_G	45_R	1.665	1.00
71_R	85_W	1.614	1.00
85_W	89_A	1.604	1.00
41_D	45_R	1.540	1.00
35_W	40_P	1.540	1.00
32_R	35_W	1.534	1.00
33_I	36_S	1.528	1.00
47_A	73_A	1.517	1.00
35_W	39_P	1.506	1.00
8_V	18_T	1.505	1.00
26_D	29_S	1.499	1.00
47_A	77_L	1.443	1.00
11_D	14_G	1.428	1.00
81_K	85_W	1.386	1.00
71_R	75_R	1.362	1.00
30_I	34_L	1.358	1.00
8_V	16_V	1.347	1.00
81_K	84_R	1.307	1.00
6_D	18_T	1.246	1.00
15_E	61_V	1.231	1.00
64_K	68_R	1.170	1.00
25_T	48_A	1.151	1.00
19_V	53_Y	1.133	1.00
54_L	69_I	1.119	1.00
71_R	88_Y	1.094	1.00
50_V	69_I	1.019	1.00
17_I	54_L	1.016	1.00
68_R	88_Y	1.012	1.00
6_D	21_A	1.002	1.00
74_M	79_V	1.000	1.00
19_V	23_F	0.999	1.00
32_R	36_S	0.997	1.00
82_W	86_L	0.980	1.00
28_A	70_F	0.975	1.00
68_R	72_E	0.970	1.00
73_A	76_A	0.966	1.00
48_A	70_F	0.956	1.00
44_Y	87_M	0.944	1.00
56_G	59_Q	0.941	1.00
85_W	88_Y	0.925	1.00
11_D	72_E	0.890	1.00
42_G	45_R	0.889	1.00
65_E	69_I	0.881	1.00
61_V	65_E	0.881	1.00
28_A	44_Y	0.876	1.00
74_M	91_V	0.871	1.00
20_P	23_F	0.870	1.00
10_V	14_G	0.868	1.00
83_K	86_L	0.853	1.00
72_E	76_A	0.845	1.00
9_Y	73_A	0.845	1.00
38_I	87_M	0.839	1.00
69_I	73_A	0.835	1.00
74_M	87_M	0.830	1.00
15_E	65_E	0.828	1.00
38_I	83_K	0.824	1.00
23_F	57_D	0.821	1.00
11_D	15_E	0.808	1.00
27_G	40_P	0.805	1.00
19_V	50_V	0.804	1.00
61_V	66_A	0.803	1.00
75_R	81_K	0.781	1.00
11_D	17_I	0.768	1.00
62_T	66_A	0.766	1.00
12_P	72_E	0.758	1.00
44_Y	74_M	0.751	1.00
7_F	46_R	0.740	1.00
34_L	38_I	0.735	1.00
70_F	74_M	0.722	1.00
19_V	49_V	0.712	1.00
72_E	75_R	0.711	1.00
34_L	90_A	0.706	1.00
79_V	84_R	0.698	1.00
55_Y	66_A	0.693	1.00
56_G	61_V	0.692	1.00
10_V	13_D	0.692	1.00
47_A	74_M	0.690	1.00
83_K	87_M	0.686	1.00
86_L	89_A	0.685	1.00
5_E	21_A	0.683	1.00
79_V	83_K	0.679	1.00
80_P	83_K	0.674	1.00
39_P	44_Y	0.672	1.00
45_R	77_L	0.667	1.00
46_R	73_A	0.666	1.00
41_D	44_Y	0.656	1.00
29_S	52_D	0.655	1.00
53_Y	58_T	0.653	1.00
65_E	68_R	0.653	1.00
57_D	61_V	0.649	1.00
54_L	73_A	0.642	1.00
7_F	50_V	0.640	1.00
34_L	37_L	0.619	1.00
40_P	45_R	0.617	1.00
27_G	49_V	0.597	1.00
44_Y	79_V	0.588	1.00
28_A	87_M	0.587	1.00
3_L	19_V	0.586	1.00
70_F	91_V	0.575	1.00
29_S	48_A	0.568	1.00
12_P	15_E	0.559	1.00
74_M	84_R	0.557	1.00
14_G	17_I	0.555	1.00
35_W	38_I	0.554	1.00
26_D	48_A	0.552	1.00
54_L	61_V	0.551	1.00
64_K	88_Y	0.550	1.00
9_Y	76_A	0.548	1.00
29_S	55_Y	0.546	1.00
17_I	69_I	0.545	1.00
87_M	90_A	0.542	1.00
18_T	21_A	0.540	1.00
5_E	8_V	0.525	1.00
56_G	60_T	0.518	1.00
27_G	41_D	0.506	1.00
69_I	72_E	0.505	1.00
44_Y	47_A	0.504	1.00
54_L	58_T	0.503	1.00
13_D	65_E	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
4aupA	1	0.956	91.1	0.781	Contact Map
1lwbA	1	0.956	88.6	0.792	Contact Map
4iovA	7	0	12.1	0.889	Contact Map
3k1tA	2	0.9451	9.2	0.894	Contact Map
4g0rA	6	0	7.3	0.899	Contact Map
2b7eA	1	0.3297	5.9	0.903	Contact Map
3ng9A	7	0	5.1	0.906	Contact Map
3hhsB	1	0.989	4.1	0.91	Contact Map
3hhsA	1	0.989	3.9	0.912	Contact Map
2jucA	1	0.3187	3.7	0.912	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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