DUF2811 - PFAM28P - GREMLIN Contacts

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DUF2811 - Protein of unknown function (DUF2811)

PFAM:	PF10929	Sequences: SLEAEIPEELHEAMKDFIESHPNWDQYRLIQAALAGFLFQNGCEDRAVTRLYLDNLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (57)
Sequences:	675 (269)
Seq/√Len:	35.6
META:	0.846

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_M	27_Y	2.515	1.00
14_M	29_L	2.488	1.00
51_L	55_N	2.179	0.99
28_R	50_R	2.035	0.99
40_Q	57_F	1.808	0.97
25_D	33_A	1.792	0.97
4_A	30_I	1.625	0.94
34_L	41_N	1.620	0.94
33_A	38_L	1.606	0.94
13_A	49_T	1.559	0.93
6_I	30_I	1.511	0.92
7_P	33_A	1.499	0.91
2_L	45_D	1.469	0.90
17_F	47_A	1.416	0.89
24_W	28_R	1.393	0.88
23_N	48_V	1.384	0.87
12_E	16_D	1.321	0.85
17_F	27_Y	1.273	0.83
5_E	43_C	1.230	0.80
10_L	56_L	1.226	0.80
22_P	25_D	1.210	0.79
6_I	9_E	1.209	0.79
1_S	28_R	1.200	0.79
39_F	55_N	1.186	0.78
8_E	56_L	1.181	0.78
47_A	52_Y	1.138	0.75
34_L	37_F	1.105	0.73
8_E	15_K	1.084	0.71
46_R	57_F	1.084	0.71
26_Q	33_A	1.071	0.70
19_E	30_I	1.040	0.68
39_F	51_L	1.032	0.67
42_G	48_V	1.015	0.66
2_L	6_I	0.989	0.64
45_D	48_V	0.961	0.62
15_K	41_N	0.958	0.62
21_H	49_T	0.958	0.62
6_I	21_H	0.956	0.61
53_L	56_L	0.944	0.60
29_L	39_F	0.909	0.57
3_E	8_E	0.905	0.57
41_N	44_E	0.901	0.57
28_R	36_G	0.896	0.56
36_G	55_N	0.891	0.56
27_Y	35_A	0.878	0.55
35_A	48_V	0.877	0.55
33_A	46_R	0.874	0.54
13_A	28_R	0.816	0.49
13_A	32_A	0.814	0.49
24_W	32_A	0.813	0.49
8_E	12_E	0.812	0.49
25_D	31_Q	0.811	0.49
33_A	42_G	0.798	0.48
19_E	27_Y	0.794	0.48
21_H	42_G	0.793	0.47
50_R	55_N	0.780	0.46
51_L	54_D	0.762	0.45
11_H	32_A	0.759	0.45
31_Q	36_G	0.737	0.43
16_D	19_E	0.730	0.42
3_E	30_I	0.712	0.41
49_T	53_L	0.708	0.40
2_L	9_E	0.705	0.40
54_D	57_F	0.697	0.39
24_W	35_A	0.696	0.39
20_S	34_L	0.687	0.39
29_L	56_L	0.636	0.34
28_R	32_A	0.631	0.34
26_Q	42_G	0.617	0.33
46_R	49_T	0.606	0.32
49_T	52_Y	0.604	0.32
44_E	47_A	0.593	0.31
2_L	56_L	0.582	0.30
15_K	55_N	0.580	0.30
36_G	46_R	0.561	0.29
35_A	39_F	0.555	0.28
7_P	10_L	0.539	0.27
5_E	41_N	0.526	0.26
45_D	55_N	0.523	0.26
50_R	54_D	0.523	0.26
1_S	27_Y	0.521	0.26
19_E	36_G	0.520	0.26
21_H	44_E	0.520	0.26
11_H	51_L	0.518	0.26
16_D	50_R	0.513	0.26
19_E	55_N	0.500	0.25

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
1p94A	2	0.7193	47.4	0.854	Contact Map
2kelA	2	0.7368	40.8	0.86	Contact Map
2k9iA	2	0.7895	39.8	0.86	Contact Map
2mdvA	2	0.6491	36.8	0.863	Contact Map
2cpgA	2	0.7368	34.4	0.865	Contact Map
2k5jA	2	0.8596	27.7	0.871	Contact Map
4me7E	2	0.9825	22.3	0.877	Contact Map
4aybC	1	0.807	21.7	0.878	Contact Map
4ps6A	1	0.4386	20.3	0.879	Contact Map
4f0jA	2	0.3509	18.3	0.882	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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