DUF3718 - PFAM28P - GREMLIN Contacts

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DUF3718 - Protein of unknown function (DUF3718)

PFAM:	PF12514	Sequences: ICEAVAADDKLRLRKKLKDNRLKLRNIYDGIVCNGQSLLRFAAKNGAVKTGEFLAKGKLPIKDLAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (63)
Sequences:	656 (435)
Seq/√Len:	54.8
META:	0.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_S	40_R	4.312	1.00
36_Q	44_K	4.175	1.00
8_D	49_K	4.092	1.00
31_I	38_L	2.945	1.00
5_V	38_L	2.841	1.00
34_N	41_F	2.729	1.00
1_I	13_L	2.276	1.00
8_D	47_A	1.969	1.00
15_K	21_R	1.805	0.99
45_N	50_T	1.371	0.96
8_D	48_V	1.277	0.94
53_F	60_P	1.274	0.93
14_R	23_K	1.270	0.93
3_E	6_A	1.216	0.92
36_Q	41_F	1.194	0.91
5_V	13_L	1.172	0.90
17_L	24_L	1.143	0.89
31_I	51_G	1.129	0.88
16_K	20_N	1.117	0.88
16_K	31_I	1.104	0.87
10_K	13_L	1.103	0.87
50_T	54_L	1.041	0.84
6_A	45_N	1.033	0.84
42_A	47_A	1.016	0.83
48_V	52_E	0.991	0.81
28_Y	37_S	0.974	0.80
35_G	47_A	0.973	0.80
5_V	28_Y	0.956	0.79
42_A	45_N	0.953	0.78
3_E	7_A	0.943	0.78
25_R	47_A	0.915	0.75
28_Y	39_L	0.909	0.75
20_N	49_K	0.899	0.74
18_K	44_K	0.878	0.72
28_Y	53_F	0.877	0.72
13_L	54_L	0.869	0.72
6_A	47_A	0.861	0.71
5_V	59_L	0.856	0.70
8_D	42_A	0.845	0.69
49_K	53_F	0.839	0.69
39_L	54_L	0.837	0.69
9_D	12_R	0.831	0.68
12_R	64_L	0.813	0.66
8_D	50_T	0.801	0.65
9_D	49_K	0.800	0.65
1_I	20_N	0.797	0.65
18_K	36_Q	0.794	0.65
55_A	64_L	0.766	0.62
58_K	61_I	0.761	0.61
24_L	42_A	0.757	0.61
61_I	64_L	0.742	0.59
54_L	62_K	0.728	0.58
24_L	38_L	0.725	0.58
34_N	63_D	0.719	0.57
17_L	20_N	0.718	0.57
29_D	39_L	0.676	0.52
50_T	56_K	0.675	0.52
59_L	63_D	0.662	0.51
25_R	53_F	0.661	0.51
51_G	59_L	0.652	0.50
4_A	8_D	0.649	0.49
27_I	38_L	0.645	0.49
27_I	31_I	0.642	0.49
11_L	14_R	0.640	0.48
38_L	54_L	0.639	0.48
11_L	19_D	0.636	0.48
22_L	29_D	0.633	0.48
18_K	29_D	0.631	0.48
30_G	35_G	0.624	0.47
43_A	46_G	0.620	0.46
24_L	32_V	0.615	0.46
41_F	50_T	0.614	0.46
20_N	27_I	0.609	0.45
28_Y	38_L	0.595	0.44
17_L	27_I	0.592	0.43
58_K	62_K	0.591	0.43
3_E	26_N	0.588	0.43
23_K	27_I	0.586	0.43
6_A	34_N	0.582	0.42
15_K	64_L	0.581	0.42
23_K	28_Y	0.578	0.42
51_G	55_A	0.572	0.41
3_E	39_L	0.571	0.41
28_Y	40_R	0.565	0.41
43_A	54_L	0.564	0.40
44_K	48_V	0.563	0.40
19_D	29_D	0.557	0.40
45_N	62_K	0.545	0.38
54_L	58_K	0.544	0.38
23_K	40_R	0.532	0.37
37_S	43_A	0.521	0.36
5_V	51_G	0.512	0.35
29_D	55_A	0.511	0.35
32_V	64_L	0.500	0.34

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
3mklA	1	1	52.2	0.813	Contact Map
3lsgA	2	1	47.3	0.818	Contact Map
4fe7A	2	1	47.1	0.818	Contact Map
1bl0A	1	1	46.4	0.819	Contact Map
3oioA	1	1	43.4	0.822	Contact Map
3oouA	1	1	43.2	0.823	Contact Map
3ajiA	1	0.9394	41.5	0.824	Contact Map
3mn2A	1	1	40.3	0.826	Contact Map
3gbgA	1	1	39.1	0.827	Contact Map
1wdyA	1	0.9242	38.3	0.828	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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