DUF4358 - PFAM28P - GREMLIN Contacts

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DUF4358 - Domain of unknown function (DUF4358)

PFAM:	PF14270	Sequences: SSVDFPDEMMELDADYLEDLYGIDADDVEDYVVYYSMSGATADEIAVFKAKDEDDAEAVKEALEARIEDQKESFEGYLPEQYAKLENAVVVTKGNYVALVVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	102 (95)
Sequences:	2358 (2049)
Seq/√Len:	210.2
META:	0.855

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_E	49_K	3.266	1.00
44_E	66_R	2.804	1.00
60_K	92_T	2.777	1.00
60_K	64_E	2.160	1.00
50_A	59_V	2.040	1.00
43_D	84_K	2.035	1.00
30_D	49_K	1.986	1.00
71_K	86_E	1.852	1.00
55_D	58_A	1.815	1.00
91_V	98_A	1.742	1.00
27_D	55_D	1.711	1.00
48_F	59_V	1.695	1.00
29_E	51_K	1.626	1.00
50_A	56_A	1.616	1.00
56_A	92_T	1.585	1.00
24_D	27_D	1.572	1.00
81_Q	84_K	1.558	1.00
13_D	16_Y	1.555	1.00
68_E	72_E	1.545	1.00
52_D	55_D	1.539	1.00
61_E	65_A	1.503	1.00
33_V	46_A	1.503	1.00
57_E	61_E	1.501	1.00
28_V	31_Y	1.483	1.00
49_K	95_N	1.452	1.00
48_F	63_L	1.431	1.00
67_I	88_A	1.407	1.00
42_A	81_Q	1.388	1.00
53_E	95_N	1.378	1.00
27_D	58_A	1.374	1.00
40_A	78_L	1.350	1.00
67_I	71_K	1.321	1.00
11_E	34_Y	1.267	1.00
82_Y	86_E	1.263	1.00
18_E	24_D	1.256	1.00
83_A	86_E	1.250	1.00
21_Y	33_V	1.214	1.00
68_E	71_K	1.212	1.00
70_Q	85_L	1.211	1.00
71_K	85_L	1.206	1.00
21_Y	46_A	1.199	1.00
47_V	98_A	1.175	1.00
46_A	63_L	1.174	1.00
64_E	68_E	1.173	1.00
83_A	87_N	1.164	1.00
28_V	48_F	1.140	1.00
71_K	82_Y	1.139	1.00
49_K	96_Y	1.137	1.00
85_L	101_V	1.125	1.00
57_E	60_K	1.113	1.00
56_A	97_V	1.093	1.00
69_D	73_S	1.059	1.00
51_K	55_D	1.054	1.00
44_E	70_Q	1.046	1.00
61_E	64_E	1.033	1.00
63_L	99_L	1.032	1.00
72_E	75_E	1.012	1.00
27_D	62_A	1.007	1.00
70_Q	73_S	0.991	1.00
65_A	68_E	0.985	1.00
67_I	99_L	0.975	1.00
12_L	33_V	0.945	0.99
12_L	16_Y	0.939	0.99
14_A	31_Y	0.923	0.99
17_L	31_Y	0.920	0.99
74_F	78_L	0.914	0.99
58_A	61_E	0.904	0.99
74_F	85_L	0.894	0.99
64_E	67_I	0.893	0.99
53_E	56_A	0.887	0.99
50_A	95_N	0.883	0.99
23_I	62_A	0.877	0.99
73_S	76_G	0.863	0.99
70_Q	74_F	0.857	0.99
71_K	75_E	0.853	0.99
63_L	90_V	0.831	0.99
40_A	81_Q	0.822	0.99
66_R	70_Q	0.818	0.98
65_A	69_D	0.815	0.98
75_E	82_Y	0.804	0.98
75_E	86_E	0.795	0.98
78_L	81_Q	0.770	0.98
67_I	85_L	0.763	0.98
59_V	97_V	0.756	0.97
70_Q	101_V	0.755	0.97
50_A	97_V	0.740	0.97
28_V	47_V	0.718	0.97
21_Y	44_E	0.708	0.96
12_L	35_Y	0.697	0.96
63_L	97_V	0.695	0.96
15_D	19_D	0.685	0.96
46_A	99_L	0.683	0.95
22_G	65_A	0.676	0.95
43_D	101_V	0.657	0.94
42_A	101_V	0.652	0.94
41_T	78_L	0.647	0.94
73_S	78_L	0.647	0.94
17_L	21_Y	0.647	0.94
38_S	74_F	0.642	0.94
42_A	74_F	0.641	0.94
28_V	55_D	0.631	0.93
92_T	97_V	0.622	0.93
53_E	57_E	0.619	0.92
36_S	41_T	0.607	0.92
23_I	28_V	0.607	0.92
38_S	41_T	0.607	0.92
67_I	90_V	0.601	0.91
54_D	57_E	0.596	0.91
43_D	85_L	0.591	0.91
90_V	100_V	0.587	0.90
63_L	100_V	0.587	0.90
18_E	22_G	0.587	0.90
36_S	39_G	0.578	0.90
56_A	95_N	0.572	0.89
10_M	37_M	0.558	0.88
74_F	81_Q	0.556	0.88
56_A	60_K	0.552	0.87
40_A	77_Y	0.544	0.87
60_K	90_V	0.541	0.86
90_V	97_V	0.538	0.86
41_T	84_K	0.538	0.86
85_L	88_A	0.534	0.86
52_D	56_A	0.533	0.86
42_A	84_K	0.532	0.86
37_M	40_A	0.532	0.86
22_G	53_E	0.530	0.85
10_M	19_D	0.527	0.85
17_L	25_A	0.525	0.85
57_E	92_T	0.523	0.85
80_E	83_A	0.520	0.84
16_Y	19_D	0.519	0.84
90_V	99_L	0.517	0.84
98_A	101_V	0.516	0.84
36_S	43_D	0.516	0.84
96_Y	99_L	0.514	0.84
79_P	82_Y	0.514	0.84
31_Y	48_F	0.513	0.83
10_M	16_Y	0.509	0.83
33_V	44_E	0.505	0.82
67_I	70_Q	0.504	0.82
27_D	30_D	0.504	0.82
50_A	54_D	0.500	0.82

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
3pgwB	1	0.6765	6.8	0.884	Contact Map
1jmtA	1	0.7451	5.3	0.89	Contact Map
2x8rA	1	0.6569	3.7	0.898	Contact Map
4m77A	1	0.6176	3.7	0.898	Contact Map
1q9uA	2	0.549	3.1	0.902	Contact Map
4m7dA	1	0.6275	3.1	0.902	Contact Map
2hgmA	1	0.8137	3	0.903	Contact Map
3p04A	2	0.6078	2.7	0.905	Contact Map
1jfxA	1	0.6667	2.7	0.905	Contact Map
4f7uA	1	0.6863	2.7	0.905	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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