DUF4177 - PFAM28P - GREMLIN Contacts

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DUF4177 - Domain of unknown function (DUF4177)

PFAM:	PF13783	Sequences: WEYKVVTVKEKGFGGGKFDPEKLEDYQEVLNELGAEGWELVSIFPVDGSGGFGGTEEIVLIFKRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (61)
Sequences:	6522 (4614)
Seq/√Len:	590.7
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_E	63_K	4.824	1.00
4_K	33_L	2.916	1.00
2_E	64_R	2.296	1.00
41_V	63_K	2.108	1.00
40_L	60_L	2.086	1.00
29_V	33_L	1.989	1.00
29_V	32_E	1.945	1.00
40_L	62_F	1.859	1.00
7_T	57_E	1.704	1.00
43_I	61_I	1.614	1.00
32_E	36_E	1.599	1.00
30_L	34_G	1.573	1.00
30_L	60_L	1.475	1.00
33_L	36_E	1.465	1.00
43_I	60_L	1.422	1.00
6_V	33_L	1.402	1.00
1_W	39_E	1.391	1.00
5_V	30_L	1.338	1.00
21_E	25_D	1.269	1.00
20_P	24_E	1.258	1.00
22_K	25_D	1.235	1.00
34_G	63_K	1.211	1.00
34_G	39_E	1.199	1.00
1_W	65_E	1.196	1.00
5_V	31_N	1.087	1.00
40_L	61_I	1.070	1.00
49_S	52_F	1.067	1.00
1_W	63_K	1.057	1.00
40_L	43_I	1.037	1.00
6_V	29_V	1.031	1.00
44_F	59_V	1.000	1.00
6_V	62_F	0.995	1.00
45_P	48_G	0.989	1.00
1_W	42_S	0.939	1.00
50_G	54_G	0.921	1.00
5_V	24_E	0.920	1.00
48_G	51_G	0.910	1.00
32_E	35_A	0.910	1.00
42_S	61_I	0.885	1.00
44_F	61_I	0.877	1.00
10_E	13_F	0.868	1.00
30_L	62_F	0.863	1.00
34_G	40_L	0.855	1.00
44_F	58_I	0.855	1.00
4_K	24_E	0.845	1.00
52_F	55_T	0.841	1.00
52_F	57_E	0.827	1.00
23_L	60_L	0.826	1.00
19_D	22_K	0.824	1.00
51_G	54_G	0.822	1.00
8_V	29_V	0.818	1.00
51_G	55_T	0.793	1.00
9_K	12_G	0.752	1.00
34_G	41_V	0.725	1.00
4_K	36_E	0.720	1.00
49_S	55_T	0.718	1.00
1_W	34_G	0.701	1.00
18_F	21_E	0.696	1.00
3_Y	34_G	0.687	1.00
19_D	23_L	0.670	1.00
54_G	57_E	0.663	1.00
48_G	55_T	0.657	1.00
50_G	56_E	0.635	1.00
31_N	34_G	0.628	1.00
25_D	32_E	0.624	1.00
19_D	24_E	0.622	1.00
47_D	50_G	0.620	1.00
4_K	62_F	0.614	1.00
31_N	35_A	0.604	1.00
8_V	60_L	0.598	1.00
55_T	58_I	0.597	1.00
56_E	59_V	0.587	1.00
30_L	59_V	0.583	1.00
40_L	44_F	0.571	1.00
17_K	20_P	0.567	1.00
33_L	62_F	0.561	0.99
5_V	59_V	0.561	0.99
50_G	53_G	0.560	0.99
14_G	22_K	0.556	0.99
15_G	18_F	0.554	0.99
43_I	59_V	0.553	0.99
50_G	55_T	0.548	0.99
48_G	54_G	0.542	0.99
38_W	65_E	0.538	0.99
2_E	31_N	0.534	0.99
3_Y	63_K	0.523	0.99
5_V	61_I	0.512	0.99
23_L	61_I	0.505	0.99
48_G	56_E	0.503	0.99
1_W	37_G	0.503	0.99
10_E	51_G	0.503	0.99
30_L	33_L	0.500	0.99

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
1jg5A	3	0.6154	37	0.782	Contact Map
1qb3A	2	0.9692	18.4	0.812	Contact Map
3qy2A	4	0.9692	15.4	0.818	Contact Map
1pucA	2	0.9692	14.6	0.82	Contact Map
4yc6B	1	0.8308	7.8	0.841	Contact Map
1cksA	5	0.8308	6.5	0.846	Contact Map
4tvpG	3	0.3385	5	0.854	Contact Map
4ui9E	1	0.7538	4.4	0.858	Contact Map
4kgnA	2	0.9692	4.1	0.86	Contact Map
4hgzA	4	1	4	0.86	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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