DUF2897 - PFAM28P - GREMLIN Contacts

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DUF2897 - Protein of unknown function (DUF2897)

PFAM:	PF11446	Sequences: MPWYAWLIIVLVLGVIVGGLLLLRYSAKMKMPLSDEVLKRAKKRNREQDAKEKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (52)
Sequences:	685 (470)
Seq/√Len:	65.2
META:	0.699

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_Q	52_E	3.046	1.00
35_D	39_K	2.691	1.00
39_K	43_K	2.540	1.00
6_W	10_V	2.188	1.00
5_A	8_I	2.107	1.00
9_I	13_L	1.861	1.00
17_V	21_L	1.828	1.00
3_W	7_L	1.760	1.00
38_L	42_K	1.707	0.99
44_R	47_E	1.537	0.99
13_L	16_I	1.530	0.99
16_I	19_G	1.386	0.98
45_N	49_D	1.363	0.97
19_G	25_Y	1.295	0.96
26_S	29_M	1.244	0.95
37_V	40_R	1.186	0.94
19_G	22_L	1.171	0.94
5_A	9_I	1.128	0.92
38_L	45_N	1.126	0.92
8_I	15_V	1.116	0.92
13_L	17_V	1.113	0.92
31_M	34_S	1.094	0.91
11_L	14_G	1.064	0.90
41_A	45_N	1.062	0.90
37_V	41_A	1.058	0.90
33_L	37_V	1.030	0.88
18_G	24_R	1.007	0.87
43_K	46_R	0.997	0.87
50_A	53_K	0.989	0.86
48_Q	53_K	0.965	0.85
21_L	25_Y	0.944	0.84
47_E	51_K	0.943	0.84
18_G	25_Y	0.921	0.82
40_R	43_K	0.907	0.81
24_R	30_K	0.891	0.80
9_I	12_V	0.887	0.80
46_R	49_D	0.856	0.77
38_L	44_R	0.850	0.77
36_E	40_R	0.839	0.76
41_A	44_R	0.834	0.75
4_Y	20_L	0.819	0.74
12_V	25_Y	0.785	0.71
14_G	22_L	0.783	0.71
38_L	41_A	0.783	0.71
9_I	16_I	0.777	0.70
7_L	10_V	0.768	0.69
4_Y	7_L	0.761	0.68
2_P	5_A	0.748	0.67
15_V	19_G	0.742	0.66
27_A	30_K	0.741	0.66
47_E	50_A	0.728	0.65
27_A	51_K	0.720	0.64
6_W	26_S	0.713	0.63
48_Q	51_K	0.704	0.62
12_V	19_G	0.686	0.60
20_L	46_R	0.674	0.59
3_W	10_V	0.673	0.59
15_V	25_Y	0.667	0.58
27_A	49_D	0.665	0.58
40_R	44_R	0.662	0.58
22_L	28_K	0.645	0.56
2_P	13_L	0.630	0.54
42_K	45_N	0.629	0.54
43_K	47_E	0.621	0.53
45_N	48_Q	0.601	0.51
8_I	12_V	0.591	0.49
2_P	6_W	0.589	0.49
43_K	49_D	0.589	0.49
23_L	28_K	0.587	0.49
36_E	44_R	0.579	0.48
23_L	41_A	0.558	0.46
11_L	25_Y	0.553	0.45
46_R	52_E	0.552	0.45
18_G	34_S	0.547	0.44
11_L	32_P	0.542	0.44
33_L	41_A	0.514	0.40
34_S	39_K	0.507	0.40
6_W	14_G	0.500	0.39

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
3mk7C	2	0.9074	40.4	0.804	Contact Map
2k21A	1	0.963	27.3	0.821	Contact Map
5a2fA	1	0	26.2	0.822	Contact Map
2mi2A	1	0.9815	22.3	0.828	Contact Map
2l16A	1	0.6481	13	0.846	Contact Map
1scfA	4	0	11.9	0.848	Contact Map
2m8rA	1	0.4074	11.3	0.849	Contact Map
2ls4A	1	0.4444	11	0.85	Contact Map
4ij3C	1	0	10.5	0.852	Contact Map
2m0qA	1	0.9444	9.6	0.854	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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