DUF4315 - PFAM28P - GREMLIN Contacts

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DUF4315 - Domain of unknown function (DUF4315)

PFAM:	PF14193	Sequences: KIEKIRAEIEKTKAKIAELQARLRELERQKTELENLEIVALVRSMNLTPEELAALLKALKGGAPPAPTAAKEQEETEDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (73)
Sequences:	1273 (937)
Seq/√Len:	109.7
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_K	27_E	4.483	1.00
12_T	23_L	3.395	1.00
6_R	30_K	3.034	1.00
39_V	43_R	2.664	1.00
9_I	23_L	2.589	1.00
9_I	27_E	2.468	1.00
38_I	42_V	2.455	1.00
5_I	30_K	2.220	1.00
16_I	20_Q	2.043	1.00
31_T	35_N	1.961	1.00
5_I	26_L	1.897	1.00
9_I	30_K	1.867	1.00
5_I	33_L	1.740	1.00
12_T	16_I	1.406	1.00
67_P	70_A	1.381	1.00
16_I	19_L	1.375	1.00
35_N	43_R	1.272	0.99
54_A	57_K	1.264	0.99
16_I	23_L	1.252	0.99
9_I	26_L	1.220	0.99
29_Q	32_E	1.218	0.99
12_T	19_L	1.196	0.99
66_A	70_A	1.188	0.99
67_P	72_E	1.145	0.99
35_N	38_I	1.138	0.98
34_E	43_R	1.086	0.98
17_A	20_Q	1.083	0.98
55_L	59_L	1.074	0.98
23_L	30_K	1.043	0.97
3_E	7_A	1.041	0.97
51_E	54_A	1.034	0.97
45_M	49_P	1.027	0.97
51_E	60_K	1.019	0.97
14_A	18_E	1.006	0.97
66_A	71_K	0.959	0.96
33_L	37_E	0.951	0.95
69_A	72_E	0.949	0.95
6_R	10_E	0.944	0.95
41_L	52_L	0.942	0.95
19_L	23_L	0.939	0.95
21_A	25_E	0.939	0.95
32_E	36_L	0.918	0.94
65_P	68_T	0.914	0.94
68_T	71_K	0.887	0.93
15_K	19_L	0.860	0.92
35_N	39_V	0.858	0.92
10_E	14_A	0.851	0.92
25_E	28_R	0.851	0.92
11_K	24_R	0.837	0.91
47_L	50_E	0.822	0.90
66_A	69_A	0.815	0.90
39_V	45_M	0.800	0.89
44_S	47_L	0.790	0.89
17_A	21_A	0.768	0.87
38_I	41_L	0.763	0.87
67_P	71_K	0.762	0.87
5_I	9_I	0.755	0.86
2_I	53_A	0.755	0.86
15_K	18_E	0.750	0.86
48_T	51_E	0.747	0.86
3_E	56_L	0.746	0.86
19_L	22_R	0.722	0.84
45_M	56_L	0.710	0.83
26_L	29_Q	0.707	0.82
20_Q	39_V	0.707	0.82
40_A	53_A	0.703	0.82
26_L	30_K	0.702	0.82
9_I	13_K	0.691	0.81
68_T	72_E	0.677	0.80
24_R	27_E	0.672	0.79
8_E	15_K	0.669	0.79
32_E	35_N	0.669	0.79
48_T	59_L	0.667	0.79
13_K	23_L	0.657	0.78
66_A	72_E	0.651	0.77
37_E	40_A	0.648	0.77
10_E	13_K	0.647	0.76
8_E	12_T	0.646	0.76
4_K	31_T	0.644	0.76
57_K	60_K	0.641	0.76
40_A	46_N	0.636	0.75
46_N	56_L	0.636	0.75
34_E	39_V	0.625	0.74
13_K	24_R	0.625	0.74
14_A	57_K	0.624	0.74
7_A	14_A	0.623	0.74
2_I	33_L	0.613	0.73
42_V	52_L	0.609	0.72
67_P	73_Q	0.606	0.72
54_A	73_Q	0.594	0.70
64_P	69_A	0.588	0.69
59_L	62_G	0.587	0.69
70_A	73_Q	0.575	0.68
22_R	52_L	0.574	0.68
49_P	56_L	0.574	0.68
10_E	27_E	0.569	0.67
42_V	56_L	0.551	0.64
58_A	63_A	0.546	0.64
9_I	33_L	0.542	0.63
22_R	40_A	0.538	0.63
24_R	28_R	0.537	0.63
63_A	69_A	0.533	0.62
45_M	59_L	0.521	0.60
36_L	40_A	0.520	0.60
64_P	68_T	0.519	0.60
41_L	51_E	0.518	0.60
65_P	71_K	0.515	0.59
9_I	16_I	0.512	0.59
63_A	70_A	0.504	0.58
28_R	32_E	0.500	0.57

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
4y66A	1	0.9747	31	0.818	Contact Map
3nr7A	2	0.6456	24.7	0.827	Contact Map
2akfA	3	0.4051	23.2	0.829	Contact Map
3u59A	2	0.9873	22.9	0.829	Contact Map
2yy0A	6	0.4304	22.5	0.83	Contact Map
4y66B	1	0.9747	21.8	0.831	Contact Map
3u1cA	2	0.9873	20.9	0.832	Contact Map
3hnwA	2	0.5063	18.3	0.837	Contact Map
4q4gX	1	0	18	0.837	Contact Map
3ghgA	2	0.8101	17.7	0.838	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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