DUF4183 - PFAM28P - GREMLIN Contacts

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DUF4183 - Domain of unknown function (DUF4183)

PFAM:	PF13799	Sequences: PDGTRYFYTNTDELTEYGTLTILAPSFTDDAGAAATAFPALNSYYNLYINGVLQPGGNYTVTTGSLTLNTGDAPLAGTPIILEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	84 (82)
Sequences:	809 (585)
Seq/√Len:	64.5
META:	0.633

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_L	78_T	4.541	1.00
61_V	82_L	3.825	1.00
29_D	33_A	2.795	1.00
47_L	61_V	2.633	1.00
49_I	80_I	2.505	1.00
46_N	83_E	2.498	1.00
60_T	69_N	2.309	1.00
13_E	21_T	2.086	1.00
46_N	53_L	2.046	1.00
48_Y	83_E	1.974	1.00
6_Y	73_A	1.862	1.00
58_N	70_T	1.676	0.99
10_N	80_I	1.555	0.99
29_D	35_A	1.546	0.99
5_R	46_N	1.527	0.99
45_Y	83_E	1.503	0.99
24_A	63_T	1.488	0.98
52_V	79_P	1.447	0.98
62_T	67_T	1.428	0.98
34_A	37_A	1.418	0.98
5_R	56_G	1.383	0.97
22_I	38_F	1.320	0.97
7_F	67_T	1.312	0.97
66_L	69_N	1.283	0.96
58_N	68_L	1.198	0.94
28_T	34_A	1.193	0.94
62_T	65_S	1.178	0.94
33_A	37_A	1.174	0.94
70_T	73_A	1.130	0.92
32_G	43_S	1.123	0.92
2_D	5_R	1.100	0.91
11_T	48_Y	1.096	0.91
31_A	36_T	1.089	0.91
60_T	65_S	1.075	0.90
11_T	24_A	1.056	0.89
7_F	27_F	1.055	0.89
53_L	82_L	1.016	0.87
65_S	68_L	0.991	0.86
55_P	58_N	0.950	0.84
49_I	68_L	0.945	0.83
25_P	38_F	0.943	0.83
24_A	27_F	0.939	0.83
55_P	66_L	0.933	0.83
27_F	63_T	0.927	0.82
28_T	35_A	0.926	0.82
28_T	64_G	0.923	0.82
6_Y	51_G	0.916	0.81
19_T	48_Y	0.915	0.81
20_L	56_G	0.906	0.81
2_D	40_A	0.896	0.80
5_R	30_D	0.884	0.79
31_A	34_A	0.884	0.79
6_Y	45_Y	0.839	0.75
3_G	73_A	0.831	0.75
67_T	82_L	0.818	0.73
52_V	75_L	0.808	0.73
29_D	32_G	0.804	0.72
62_T	83_E	0.800	0.72
49_I	71_G	0.797	0.71
43_S	55_P	0.788	0.71
16_E	48_Y	0.781	0.70
33_A	36_T	0.779	0.70
6_Y	56_G	0.777	0.70
3_G	81_I	0.775	0.69
27_F	56_G	0.760	0.68
30_D	48_Y	0.755	0.67
11_T	57_G	0.755	0.67
15_T	51_G	0.749	0.67
38_F	41_L	0.745	0.66
61_V	83_E	0.731	0.65
11_T	20_L	0.726	0.64
41_L	61_V	0.718	0.63
25_P	36_T	0.715	0.63
75_L	80_I	0.715	0.63
20_L	27_F	0.712	0.63
12_D	35_A	0.711	0.63
22_I	31_A	0.707	0.62
9_T	28_T	0.706	0.62
4_T	56_G	0.706	0.62
47_L	66_L	0.703	0.62
24_A	69_N	0.702	0.62
62_T	71_G	0.702	0.62
24_A	35_A	0.696	0.61
4_T	76_A	0.693	0.61
6_Y	26_S	0.685	0.60
27_F	83_E	0.684	0.60
21_T	45_Y	0.680	0.59
76_A	81_I	0.675	0.59
78_T	83_E	0.667	0.58
21_T	65_S	0.648	0.56
24_A	44_Y	0.637	0.54
71_G	83_E	0.634	0.54
38_F	79_P	0.631	0.54
37_A	64_G	0.629	0.53
8_Y	22_I	0.620	0.52
19_T	69_N	0.615	0.52
20_L	77_G	0.594	0.49
7_F	65_S	0.593	0.49
33_A	41_L	0.591	0.49
46_N	81_I	0.588	0.49
5_R	48_Y	0.582	0.48
25_P	35_A	0.581	0.48
53_L	81_I	0.578	0.47
2_D	51_G	0.577	0.47
19_T	62_T	0.571	0.47
69_N	74_P	0.570	0.47
5_R	83_E	0.566	0.46
27_F	60_T	0.564	0.46
10_N	14_L	0.561	0.45
18_G	28_T	0.553	0.45
15_T	67_T	0.549	0.44
20_L	80_I	0.541	0.43
13_E	20_L	0.540	0.43
51_G	61_V	0.536	0.43
55_P	64_G	0.529	0.42
7_F	75_L	0.529	0.42
23_L	34_A	0.523	0.41
14_L	26_S	0.520	0.41
6_Y	16_E	0.510	0.40
18_G	36_T	0.510	0.40
37_A	41_L	0.507	0.39
43_S	49_I	0.506	0.39
21_T	58_N	0.500	0.39

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
3ffzA	1	0.7619	21.3	0.887	Contact Map
2uvfA	2	0.8095	16.7	0.892	Contact Map
2vxrA	1	0.5833	14.8	0.894	Contact Map
3rsjA	1	0.5833	13.7	0.896	Contact Map
3waiA	1	0.9286	8.5	0.905	Contact Map
2nyyA	1	0.7619	7.6	0.908	Contact Map
3skvA	2	0.8452	7.4	0.908	Contact Map
3pmqA	1	0.9762	7.4	0.908	Contact Map
4qtfA	2	0.7857	7	0.909	Contact Map
4v2xA	2	0.9881	6.4	0.911	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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