DUF3880 - PFAM28P - GREMLIN Contacts

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DUF3880 - DUF based on E. rectale Gene description (DUF3880)

PFAM:	PF12996	Sequences: WFVDDPLHFLYSLEIAPLYDYVFTFDRDCVEELRALGAKNVHYLPLAADPEIHRPLELSPEERKRYGSDVSFVGSLYT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	78 (77)
Sequences:	7009 (5266)
Seq/√Len:	600.2
META:	0.874

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_Y	42_H	3.074	1.00
23_F	42_H	2.817	1.00
25_F	46_L	2.593	1.00
48_A	53_H	2.410	1.00
31_E	35_A	2.222	1.00
23_F	44_L	2.094	1.00
68_S	71_S	2.059	1.00
21_Y	40_N	2.035	1.00
31_E	34_R	2.028	1.00
58_L	62_E	1.937	1.00
24_T	29_C	1.934	1.00
63_R	67_G	1.855	1.00
32_E	35_A	1.850	1.00
27_R	43_Y	1.755	1.00
26_D	29_C	1.694	1.00
30_V	34_R	1.620	1.00
49_D	52_I	1.565	1.00
50_P	53_H	1.547	1.00
30_V	41_V	1.547	1.00
24_T	33_L	1.497	1.00
60_P	63_R	1.328	1.00
65_R	68_S	1.325	1.00
32_E	36_L	1.307	1.00
61_E	64_K	1.288	1.00
25_F	77_Y	1.266	1.00
59_S	62_E	1.246	1.00
3_V	46_L	1.226	1.00
14_E	17_P	1.142	1.00
60_P	64_K	1.141	1.00
62_E	66_Y	1.092	1.00
61_E	65_R	1.074	1.00
25_F	43_Y	1.074	1.00
29_C	32_E	1.061	1.00
38_A	41_V	1.048	1.00
2_F	7_L	1.047	1.00
4_D	25_F	0.993	1.00
16_A	36_L	0.989	1.00
11_Y	15_I	0.983	1.00
3_V	8_H	0.969	1.00
66_Y	69_D	0.957	1.00
62_E	65_R	0.944	1.00
26_D	43_Y	0.939	1.00
8_H	11_Y	0.936	1.00
15_I	18_L	0.923	1.00
5_D	24_T	0.902	1.00
57_E	63_R	0.887	1.00
58_L	67_G	0.885	1.00
7_L	12_S	0.883	1.00
58_L	63_R	0.879	1.00
26_D	46_L	0.879	1.00
59_S	63_R	0.877	1.00
27_R	30_V	0.874	1.00
57_E	65_R	0.873	1.00
24_T	30_V	0.870	1.00
9_F	12_S	0.866	1.00
5_D	12_S	0.859	1.00
8_H	12_S	0.834	1.00
26_D	71_S	0.833	1.00
2_F	12_S	0.830	1.00
4_D	12_S	0.819	1.00
2_F	8_H	0.815	1.00
25_F	29_C	0.805	1.00
24_T	41_V	0.790	1.00
62_E	67_G	0.786	1.00
15_I	19_Y	0.784	1.00
59_S	67_G	0.780	1.00
6_P	26_D	0.778	1.00
50_P	54_R	0.777	1.00
64_K	67_G	0.771	1.00
43_Y	48_A	0.761	1.00
5_D	9_F	0.753	1.00
4_D	8_H	0.749	1.00
34_R	40_N	0.745	1.00
60_P	66_Y	0.741	1.00
22_V	25_F	0.731	1.00
59_S	66_Y	0.729	1.00
26_D	48_A	0.727	1.00
5_D	8_H	0.698	1.00
37_G	40_N	0.696	1.00
1_W	47_A	0.690	1.00
34_R	63_R	0.685	1.00
26_D	77_Y	0.683	1.00
15_I	22_V	0.663	1.00
29_C	46_L	0.662	1.00
3_V	7_L	0.659	1.00
29_C	33_L	0.658	1.00
25_F	76_L	0.655	1.00
46_L	49_D	0.651	1.00
1_W	44_L	0.634	1.00
26_D	33_L	0.615	1.00
49_D	53_H	0.608	1.00
34_R	41_V	0.589	1.00
2_F	5_D	0.583	1.00
58_L	66_Y	0.575	1.00
60_P	65_R	0.574	1.00
18_L	39_K	0.565	1.00
55_P	58_L	0.558	1.00
49_D	66_Y	0.544	0.99
5_D	29_C	0.544	0.99
22_V	41_V	0.543	0.99
3_V	43_Y	0.543	0.99
2_F	24_T	0.540	0.99
39_K	42_H	0.539	0.99
54_R	58_L	0.538	0.99
4_D	73_V	0.537	0.99
59_S	65_R	0.532	0.99
55_P	65_R	0.532	0.99
7_L	11_Y	0.522	0.99
51_E	54_R	0.521	0.99
6_P	46_L	0.519	0.99
20_D	77_Y	0.514	0.99
49_D	54_R	0.513	0.99
16_A	20_D	0.509	0.99
34_R	39_K	0.507	0.99
58_L	61_E	0.502	0.99
28_D	31_E	0.500	0.99

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
4w6qA	4	0.9231	86.4	0.758	Contact Map
3okpA	1	1	86.4	0.758	Contact Map
2jjmA	4	0.9487	85	0.763	Contact Map
2hy7A	1	0.9231	81.9	0.771	Contact Map
2x0dA	2	0.9487	80.2	0.775	Contact Map
3c48A	2	1	77.7	0.78	Contact Map
4hlnA	1	1	76.7	0.782	Contact Map
3vueA	1	1	75.2	0.785	Contact Map
3oy2A	2	0.9872	74.8	0.786	Contact Map
2r60A	1	1	71.9	0.79	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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