DoxX - PFAM28P - GREMLIN Contacts

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DoxX - DoxX

PFAM:	PF07681	Sequences: ALLLLRLLLGLVFLAHGLQKLFGFGLAGTAGFFASLGLPPPALLAYLAGLAELVGGLLLLLGLLTRLAALLLAGFMLVAIFTVHW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (82)
Sequences:	85565 (51706)
Seq/√Len:	5710.0
META:	0.883

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_L	68_A	3.225	1.00
18_L	22_F	2.388	1.00
55_G	72_L	2.244	1.00
25_G	28_G	1.953	1.00
10_G	56_G	1.931	1.00
64_L	67_L	1.919	1.00
75_F	79_A	1.915	1.00
42_A	46_Y	1.824	1.00
20_K	52_E	1.822	1.00
26_L	46_Y	1.757	1.00
14_L	56_G	1.603	1.00
50_L	54_V	1.591	1.00
10_G	60_L	1.591	1.00
18_L	53_L	1.577	1.00
43_L	46_Y	1.531	1.00
67_L	71_L	1.491	1.00
46_Y	50_L	1.470	1.00
29_T	32_F	1.451	1.00
13_F	72_L	1.430	1.00
48_A	75_F	1.391	1.00
27_A	31_G	1.389	1.00
26_L	30_A	1.376	1.00
30_A	34_A	1.359	1.00
21_L	49_G	1.328	1.00
11_L	15_A	1.293	1.00
32_F	35_S	1.291	1.00
21_L	50_L	1.282	1.00
55_G	68_A	1.274	1.00
28_G	31_G	1.247	1.00
29_T	33_F	1.246	1.00
74_G	78_V	1.234	1.00
17_G	53_L	1.218	1.00
51_A	75_F	1.217	1.00
31_G	34_A	1.207	1.00
70_L	74_G	1.183	1.00
13_F	76_M	1.181	1.00
14_L	57_L	1.176	1.00
57_L	61_L	1.151	1.00
54_V	58_L	1.139	1.00
65_T	69_A	1.137	1.00
76_M	80_I	1.137	1.00
47_L	51_A	1.100	1.00
55_G	71_L	1.081	1.00
14_L	18_L	1.060	1.00
32_F	36_L	1.031	1.00
11_L	60_L	1.009	1.00
51_A	68_A	1.007	1.00
5_L	9_L	0.995	1.00
26_L	49_G	0.993	1.00
26_L	29_T	0.989	1.00
30_A	42_A	0.985	1.00
68_A	71_L	0.936	1.00
21_L	53_L	0.931	1.00
76_M	79_A	0.920	1.00
78_V	82_T	0.913	1.00
20_K	49_G	0.888	1.00
3_L	7_L	0.881	1.00
43_L	47_L	0.879	1.00
40_P	44_L	0.873	1.00
27_A	30_A	0.872	1.00
28_G	32_F	0.863	1.00
15_A	19_Q	0.858	1.00
51_A	71_L	0.849	1.00
29_T	34_A	0.838	1.00
10_G	14_L	0.826	1.00
77_L	81_F	0.817	1.00
15_A	18_L	0.804	1.00
59_L	69_A	0.800	1.00
19_Q	22_F	0.794	1.00
68_A	72_L	0.789	1.00
64_L	68_A	0.784	1.00
37_G	40_P	0.781	1.00
8_L	11_L	0.781	1.00
59_L	72_L	0.771	1.00
14_L	53_L	0.768	1.00
69_A	73_A	0.764	1.00
44_L	82_T	0.754	1.00
25_G	29_T	0.743	1.00
14_L	60_L	0.739	1.00
71_L	75_F	0.737	1.00
12_V	16_H	0.735	1.00
33_F	36_L	0.733	1.00
61_L	65_T	0.730	1.00
53_L	56_G	0.711	1.00
30_A	41_P	0.711	1.00
16_H	19_Q	0.709	1.00
59_L	68_A	0.701	1.00
34_A	37_G	0.697	1.00
20_K	48_A	0.695	1.00
31_G	35_S	0.693	1.00
8_L	12_V	0.686	1.00
73_A	77_L	0.678	1.00
71_L	74_G	0.676	1.00
12_V	15_A	0.671	1.00
26_L	32_F	0.658	1.00
38_L	44_L	0.653	1.00
34_A	41_P	0.644	1.00
67_L	70_L	0.641	1.00
51_A	55_G	0.630	1.00
65_T	68_A	0.627	1.00
35_S	40_P	0.624	1.00
16_H	20_K	0.623	1.00
58_L	63_L	0.608	1.00
40_P	43_L	0.608	1.00
44_L	78_V	0.601	1.00
6_R	62_G	0.600	1.00
78_V	81_F	0.584	1.00
59_L	65_T	0.581	1.00
17_G	49_G	0.581	1.00
61_L	64_L	0.579	1.00
26_L	45_A	0.575	1.00
22_F	25_G	0.571	1.00
17_G	56_G	0.559	1.00
30_A	45_A	0.555	1.00
41_P	45_A	0.550	1.00
19_Q	23_G	0.534	1.00
79_A	84_H	0.532	1.00
25_G	31_G	0.527	1.00
7_L	11_L	0.518	1.00
29_T	45_A	0.515	1.00
30_A	33_F	0.515	1.00
73_A	76_M	0.508	1.00
7_L	60_L	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
3ux4A	3	0.8471	1.3	0.889	Contact Map
4ytpC	1	0.6824	1	0.898	Contact Map
2wzlA	1	0.4353	0.9	0.901	Contact Map
4ezcA	3	0.7765	0.7	0.906	Contact Map
1ofdA	1	0.3647	0.7	0.908	Contact Map
1ea0A	1	0.3647	0.7	0.909	Contact Map
3hc7A	1	0.3882	0.6	0.911	Contact Map
3oa1A	1	0.3882	0.6	0.912	Contact Map
4qi1A	3	0.5882	0.6	0.913	Contact Map
1v54C	1	0.6235	0.6	0.913	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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