DUF2794 - PFAM28P - GREMLIN Contacts

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DUF2794 - Protein of unknown function (DUF2794)

PFAM:	PF10984	Sequences: VFFDRRELNRILNLYGRMVAAGEWRDYAIDFLRDRAVFSVFRRASERPLYRIEKRPKLARRQGAYAVIGAGGQILKRGHDLAQVL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (85)
Sequences:	4350 (1607)
Seq/√Len:	174.3
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_N	13_N	3.480	1.00
35_R	55_R	3.378	1.00
30_D	39_S	3.187	1.00
59_A	64_A	2.560	1.00
40_V	52_I	2.419	1.00
2_F	31_F	2.419	1.00
35_R	53_E	2.383	1.00
18_M	21_A	2.205	1.00
67_V	84_V	2.197	1.00
18_M	23_E	2.100	1.00
6_R	9_N	2.069	1.00
42_R	46_E	2.036	1.00
10_R	82_A	2.007	1.00
37_V	51_R	1.837	1.00
69_G	73_Q	1.762	1.00
32_L	37_V	1.755	1.00
17_R	21_A	1.735	1.00
55_R	66_A	1.706	1.00
18_M	24_W	1.695	1.00
80_D	83_Q	1.674	1.00
8_L	12_L	1.633	1.00
19_V	24_W	1.623	1.00
16_G	20_A	1.453	1.00
47_R	70_A	1.452	1.00
56_P	63_G	1.412	1.00
24_W	40_V	1.403	1.00
40_V	49_L	1.401	1.00
25_R	43_R	1.316	1.00
10_R	13_N	1.312	1.00
4_D	9_N	1.276	1.00
58_L	62_Q	1.228	1.00
23_E	49_L	1.159	1.00
25_R	46_E	1.106	1.00
5_R	9_N	1.094	1.00
24_W	50_Y	1.064	1.00
40_V	67_V	1.063	1.00
32_L	39_S	1.032	0.99
6_R	10_R	1.023	0.99
40_V	50_Y	0.995	0.99
15_Y	54_K	0.978	0.99
79_H	83_Q	0.962	0.99
70_A	73_Q	0.961	0.99
32_L	35_R	0.918	0.99
55_R	58_L	0.912	0.99
41_F	45_S	0.872	0.98
30_D	37_V	0.864	0.98
2_F	36_A	0.859	0.98
4_D	18_M	0.820	0.97
15_Y	22_G	0.816	0.97
56_P	62_Q	0.813	0.97
78_G	84_V	0.803	0.97
75_L	79_H	0.802	0.97
63_G	79_H	0.790	0.97
74_I	77_R	0.790	0.97
58_L	64_A	0.788	0.97
22_G	54_K	0.775	0.96
4_D	10_R	0.774	0.96
58_L	63_G	0.773	0.96
20_A	43_R	0.765	0.96
15_Y	19_V	0.764	0.96
31_F	36_A	0.761	0.96
62_Q	67_V	0.735	0.95
67_V	83_Q	0.729	0.95
52_I	67_V	0.729	0.95
3_F	11_I	0.722	0.94
3_F	7_E	0.717	0.94
28_A	31_F	0.712	0.94
50_Y	67_V	0.706	0.94
4_D	11_I	0.703	0.94
49_L	70_A	0.701	0.93
32_L	60_R	0.696	0.93
28_A	36_A	0.696	0.93
10_R	14_L	0.690	0.93
55_R	68_I	0.669	0.92
10_R	81_L	0.668	0.92
60_R	64_A	0.667	0.92
11_I	56_P	0.667	0.92
31_F	50_Y	0.665	0.92
40_V	46_E	0.663	0.91
62_Q	75_L	0.658	0.91
2_F	13_N	0.658	0.91
39_S	51_R	0.658	0.91
16_G	29_I	0.649	0.91
2_F	8_L	0.646	0.90
37_V	53_E	0.637	0.90
60_R	63_G	0.636	0.90
14_L	18_M	0.636	0.90
13_N	31_F	0.626	0.89
7_E	54_K	0.626	0.89
7_E	15_Y	0.621	0.89
31_F	60_R	0.616	0.88
49_L	52_I	0.615	0.88
52_I	62_Q	0.611	0.88
42_R	51_R	0.606	0.87
79_H	82_A	0.604	0.87
53_E	56_P	0.603	0.87
9_N	34_D	0.603	0.87
36_A	39_S	0.601	0.87
11_I	52_I	0.597	0.87
16_G	72_G	0.595	0.86
46_E	53_E	0.591	0.86
35_R	74_I	0.590	0.86
73_Q	83_Q	0.590	0.86
27_Y	38_F	0.588	0.86
13_N	25_R	0.587	0.86
23_E	50_Y	0.587	0.86
12_L	29_I	0.584	0.85
11_I	18_M	0.581	0.85
16_G	42_R	0.562	0.83
33_R	64_A	0.554	0.82
62_Q	79_H	0.552	0.82
2_F	17_R	0.551	0.82
26_D	44_A	0.550	0.82
82_A	85_L	0.550	0.82
47_R	51_R	0.545	0.81
34_D	42_R	0.543	0.81
10_R	33_R	0.543	0.81
59_A	62_Q	0.536	0.80
19_V	54_K	0.535	0.80
45_S	60_R	0.532	0.80
36_A	43_R	0.526	0.79
51_R	68_I	0.526	0.79
64_A	77_R	0.524	0.79
72_G	80_D	0.514	0.77
28_A	47_R	0.506	0.76
39_S	44_A	0.504	0.76
23_E	48_P	0.502	0.76
75_L	78_G	0.500	0.75

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
2k8eA	1	0.4353	27.8	0.901	Contact Map
4o0aA	1	0.7412	19.6	0.908	Contact Map
3j20F	1	0.6	11.4	0.917	Contact Map
3l4gA	2	0.9882	10.9	0.918	Contact Map
1ofdA	1	0.9765	9	0.921	Contact Map
3gd5A	4	0.8	7.4	0.924	Contact Map
1vlvA	6	0.9647	7.3	0.924	Contact Map
3r7fA	3	0.9176	6.4	0.926	Contact Map
1q98A	2	0.9647	6.4	0.926	Contact Map
3grfA	3	0.8353	6.3	0.926	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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