DUF3390 - PFAM28P - GREMLIN Contacts

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DUF3390 - Domain of unknown function (DUF3390)

PFAM:	PF11870	Sequences: RLREEAVPAGEGRQVVVGQGGKRPRAERLAMKAWAWVMSSPRLYRLAGRLARRGRRLLPGPLGAWTRTRDLPAPPKESFREWWRERGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (71)
Sequences:	6495 (4101)
Seq/√Len:	486.7
META:	0.863

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_E	85_E	4.575	1.00
40_S	43_L	2.963	1.00
77_E	82_W	2.541	1.00
78_S	81_E	2.413	1.00
44_Y	48_G	2.381	1.00
35_A	39_S	2.305	1.00
49_R	81_E	2.290	1.00
79_F	83_W	2.230	1.00
36_W	43_L	2.171	1.00
37_V	47_A	2.100	1.00
41_P	45_R	2.042	1.00
36_W	40_S	1.952	1.00
34_W	38_M	1.923	1.00
45_R	80_R	1.765	1.00
55_R	58_L	1.742	1.00
38_M	44_Y	1.551	1.00
25_R	28_R	1.503	1.00
57_L	60_G	1.432	1.00
55_R	60_G	1.271	1.00
33_A	37_V	1.211	1.00
23_R	28_R	1.210	1.00
34_W	44_Y	1.182	1.00
52_R	81_E	1.176	1.00
49_R	53_R	1.127	1.00
82_W	86_R	1.111	1.00
31_M	34_W	1.103	1.00
33_A	36_W	1.057	1.00
42_R	46_L	1.047	1.00
27_E	30_A	0.986	1.00
41_P	44_Y	0.958	1.00
47_A	51_A	0.950	1.00
60_G	63_G	0.927	1.00
45_R	84_R	0.911	1.00
38_M	48_G	0.910	1.00
50_L	54_G	0.909	1.00
64_A	67_R	0.896	1.00
25_R	29_L	0.889	1.00
28_R	32_K	0.881	1.00
57_L	61_P	0.878	1.00
66_T	71_L	0.873	1.00
83_W	86_R	0.855	1.00
19_Q	22_K	0.848	1.00
21_G	24_P	0.842	1.00
77_E	81_E	0.839	1.00
50_L	53_R	0.833	1.00
55_R	59_P	0.826	1.00
16_V	19_Q	0.820	1.00
58_L	63_G	0.813	1.00
46_L	50_L	0.811	1.00
18_G	23_R	0.809	1.00
29_L	33_A	0.802	1.00
80_R	83_W	0.798	1.00
37_V	43_L	0.795	1.00
27_E	31_M	0.782	1.00
30_A	33_A	0.774	1.00
52_R	78_S	0.766	1.00
32_K	35_A	0.754	1.00
24_P	31_M	0.753	1.00
48_G	51_A	0.753	1.00
34_W	75_P	0.747	1.00
75_P	78_S	0.744	1.00
58_L	61_P	0.741	1.00
56_R	59_P	0.716	1.00
32_K	36_W	0.713	1.00
60_G	66_T	0.701	1.00
22_K	25_R	0.695	1.00
48_G	78_S	0.679	1.00
62_L	66_T	0.675	1.00
29_L	32_K	0.668	1.00
51_A	74_P	0.667	1.00
17_V	21_G	0.664	1.00
81_E	84_R	0.662	1.00
38_M	47_A	0.653	1.00
37_V	40_S	0.646	1.00
17_V	20_G	0.630	1.00
18_G	21_G	0.623	1.00
82_W	85_E	0.623	1.00
55_R	73_A	0.622	1.00
69_R	86_R	0.617	0.99
49_R	52_R	0.617	0.99
81_E	86_R	0.609	0.99
26_A	30_A	0.606	0.99
70_D	73_A	0.590	0.99
26_A	29_L	0.586	0.99
48_G	52_R	0.586	0.99
45_R	49_R	0.585	0.99
55_R	61_P	0.584	0.99
56_R	60_G	0.578	0.99
31_M	38_M	0.576	0.99
72_P	75_P	0.568	0.99
43_L	47_A	0.558	0.99
64_A	68_T	0.551	0.99
63_G	66_T	0.546	0.99
81_E	85_E	0.542	0.99
45_R	48_G	0.540	0.99
36_W	46_L	0.540	0.99
28_R	71_L	0.536	0.99
79_F	82_W	0.525	0.98
71_L	75_P	0.515	0.98
59_P	63_G	0.514	0.98
60_G	64_A	0.513	0.98
61_P	64_A	0.512	0.98
42_R	45_R	0.511	0.98
18_G	25_R	0.508	0.98
19_Q	24_P	0.505	0.98
57_L	73_A	0.500	0.98

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
1q2fA	1	0.1932	14.5	0.875	Contact Map
2bn8A	1	0.2727	7.4	0.891	Contact Map
4yz6B	1	0.2045	1.9	0.919	Contact Map
1pm6A	1	0.3295	1.4	0.925	Contact Map
2iskA	2	0.2727	1.2	0.928	Contact Map
3pm0A	1	0.1818	1.1	0.929	Contact Map
1r7cA	1	0.3523	0.9	0.933	Contact Map
4l54A	1	0.3409	0.9	0.933	Contact Map
4ascA	1	0.5341	0.9	0.934	Contact Map
1ro2A	1	0.5455	0.8	0.935	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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