DUF2382 - PFAM28P - GREMLIN Contacts

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DUF2382 - Domain of unknown function (DUF2382)

PFAM:	PF09557	Sequences: IPLVEEELRVGKREVETGRVRVRKYVVTEPVTVTVPLRREEVVVERRPVDRPVTAADAAAFEEETIEVPLTEEEPVVEKRAVVVEEVRVRKEVVTETETVSDTVRREEVEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	111 (111)
Sequences:	13448 (8548)
Seq/√Len:	811.3
META:	0.914

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_V	108_E	3.351	1.00
43_V	92_E	2.820	1.00
32_T	101_S	2.602	1.00
34_T	97_T	2.470	1.00
38_R	93_V	2.431	1.00
34_T	99_T	2.409	1.00
43_V	90_R	2.196	1.00
47_R	88_R	2.146	1.00
36_P	95_T	2.089	1.00
28_T	103_T	2.041	1.00
25_Y	110_E	2.007	1.00
30_P	103_T	1.985	1.00
39_R	72_E	1.941	1.00
32_T	99_T	1.939	1.00
5_E	106_R	1.879	1.00
41_E	94_V	1.822	1.00
8_L	102_D	1.794	1.00
38_R	95_T	1.787	1.00
3_L	109_V	1.785	1.00
30_P	101_S	1.784	1.00
39_R	96_E	1.757	1.00
9_R	80_R	1.724	1.00
16_E	19_R	1.651	1.00
9_R	78_E	1.586	1.00
14_E	71_T	1.577	1.00
17_T	72_E	1.541	1.00
40_E	91_K	1.508	1.00
41_E	92_E	1.507	1.00
46_R	85_E	1.494	1.00
36_P	97_T	1.442	1.00
45_E	90_R	1.411	1.00
22_V	89_V	1.393	1.00
8_L	104_V	1.388	1.00
29_E	106_R	1.387	1.00
45_E	88_R	1.351	1.00
55_A	58_A	1.349	1.00
74_E	82_V	1.345	1.00
24_K	107_E	1.337	1.00
74_E	80_R	1.289	1.00
16_E	69_P	1.288	1.00
52_P	82_V	1.239	1.00
53_V	58_A	1.218	1.00
47_R	86_E	1.212	1.00
13_R	76_V	1.188	1.00
19_R	67_E	1.147	1.00
76_V	80_R	1.141	1.00
37_L	75_P	1.140	1.00
79_K	102_D	1.111	1.00
48_P	85_E	1.101	1.00
61_F	64_E	1.098	1.00
61_F	66_I	1.082	1.00
72_E	75_P	1.059	1.00
54_T	57_D	1.046	1.00
15_V	74_E	1.035	1.00
39_R	94_V	0.989	1.00
42_V	70_L	0.984	1.00
50_D	53_V	0.972	1.00
13_R	74_E	0.964	1.00
52_P	80_R	0.962	1.00
74_E	84_V	0.962	1.00
53_V	57_D	0.954	1.00
26_V	107_E	0.928	1.00
30_P	34_T	0.926	1.00
23_R	110_E	0.926	1.00
75_P	79_K	0.921	1.00
50_D	82_V	0.893	1.00
87_V	109_V	0.889	1.00
60_A	63_E	0.886	1.00
19_R	69_P	0.877	1.00
78_E	81_A	0.871	1.00
72_E	84_V	0.869	1.00
54_T	58_A	0.869	1.00
7_E	82_V	0.867	1.00
21_R	65_T	0.866	1.00
51_R	54_T	0.860	1.00
21_R	67_E	0.858	1.00
68_V	89_V	0.852	1.00
49_V	83_V	0.848	1.00
58_A	61_F	0.848	1.00
51_R	57_D	0.843	1.00
58_A	62_E	0.841	1.00
40_E	93_V	0.838	1.00
25_Y	108_E	0.834	1.00
23_R	65_T	0.831	1.00
30_P	36_P	0.827	1.00
56_A	59_A	0.818	1.00
66_I	69_P	0.807	1.00
7_E	80_R	0.802	1.00
14_E	38_R	0.798	1.00
35_V	75_P	0.795	1.00
11_G	76_V	0.788	1.00
53_V	56_A	0.777	1.00
10_V	33_V	0.774	1.00
11_G	14_E	0.774	1.00
55_A	59_A	0.756	1.00
12_K	35_V	0.731	1.00
51_R	86_E	0.726	1.00
69_P	75_P	0.721	1.00
12_K	73_E	0.719	1.00
84_V	87_V	0.709	1.00
60_A	64_E	0.704	1.00
98_E	101_S	0.703	1.00
57_D	71_T	0.699	1.00
28_T	105_R	0.693	1.00
31_V	104_V	0.689	1.00
42_V	68_V	0.686	1.00
17_T	70_L	0.681	1.00
11_G	78_E	0.671	1.00
16_E	71_T	0.660	1.00
53_V	83_V	0.656	1.00
49_V	53_V	0.654	1.00
27_V	30_P	0.651	1.00
98_E	102_D	0.648	1.00
75_P	78_E	0.643	1.00
74_E	78_E	0.639	1.00
4_V	83_V	0.636	1.00
20_V	42_V	0.630	1.00
70_L	107_E	0.629	1.00
5_E	84_V	0.629	1.00
83_V	86_E	0.627	1.00
8_L	11_G	0.618	1.00
65_T	68_V	0.607	1.00
37_L	98_E	0.594	1.00
97_T	100_V	0.593	1.00
49_V	85_E	0.588	1.00
48_P	52_P	0.583	1.00
44_V	89_V	0.579	1.00
24_K	70_L	0.579	1.00
9_R	13_R	0.576	1.00
59_A	62_E	0.576	1.00
49_V	52_P	0.574	1.00
59_A	66_I	0.571	1.00
51_R	55_A	0.568	1.00
90_R	93_V	0.566	1.00
54_T	59_A	0.564	1.00
30_P	102_D	0.563	1.00
71_T	81_A	0.561	1.00
53_V	60_A	0.559	1.00
64_E	68_V	0.557	1.00
3_L	27_V	0.557	1.00
93_V	96_E	0.556	1.00
33_V	36_P	0.553	1.00
26_V	61_F	0.553	1.00
3_L	7_E	0.552	1.00
4_V	81_A	0.551	1.00
7_E	84_V	0.549	1.00
20_V	70_L	0.543	1.00
96_E	99_T	0.540	1.00
12_K	37_L	0.540	1.00
62_E	65_T	0.538	1.00
16_E	24_K	0.537	1.00
77_V	102_D	0.534	1.00
14_E	19_R	0.521	1.00
4_V	7_E	0.519	1.00
108_E	111_V	0.517	1.00
42_V	91_K	0.517	1.00
2_P	83_V	0.515	1.00
67_E	88_R	0.511	1.00
18_G	42_V	0.509	1.00
21_R	25_Y	0.509	1.00
4_V	107_E	0.505	1.00
27_V	106_R	0.504	1.00
39_R	43_V	0.502	1.00
15_V	72_E	0.500	1.00
31_V	35_V	0.500	1.00
3_L	84_V	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
4fx5A	1	0.3694	2.2	0.918	Contact Map
4pkyB	2	0.1712	0.8	0.937	Contact Map
1pybA	2	0.3333	0.7	0.939	Contact Map
4a8xB	1	0.0901	0.7	0.941	Contact Map
1tr8A	4	0.2973	0.6	0.942	Contact Map
1m3wA	3	0.0991	0.6	0.943	Contact Map
3n40P	1	0.5135	0.5	0.946	Contact Map
4k0dA	3	0.3063	0.5	0.947	Contact Map
3ibjA	2	0.3063	0.4	0.949	Contact Map
2i4lA	2	0.3604	0.4	0.95	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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