DUF4190 - PFAM28P - GREMLIN Contacts

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DUF4190 - Domain of unknown function (DUF4190)

PFAM:	PF13828	Sequences: LAIASLVLGILGLVLLLLLGILAIILGHIALRQIRRSGLGGRGLAIAGLVLGYIGLVLLVLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (61)
Sequences:	28522 (20741)
Seq/√Len:	2655.6
META:	0.91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_H	53_Y	3.751	1.00
31_L	42_R	2.181	1.00
43_G	47_A	2.113	1.00
22_L	26_L	1.987	1.00
25_I	29_I	1.975	1.00
31_L	46_I	1.808	1.00
1_L	33_Q	1.753	1.00
23_A	52_G	1.700	1.00
35_R	42_R	1.694	1.00
32_R	36_R	1.538	1.00
42_R	46_I	1.466	1.00
46_I	50_V	1.454	1.00
6_L	44_L	1.438	1.00
4_A	8_L	1.438	1.00
5_S	27_G	1.397	1.00
3_I	44_L	1.362	1.00
33_Q	39_L	1.333	1.00
47_A	51_L	1.318	1.00
49_L	53_Y	1.294	1.00
20_G	55_G	1.261	1.00
4_A	26_L	1.251	1.00
24_I	28_H	1.241	1.00
28_H	32_R	1.238	1.00
34_I	39_L	1.225	1.00
31_L	49_L	1.221	1.00
6_L	10_I	1.193	1.00
30_A	34_I	1.187	1.00
12_G	55_G	1.175	1.00
31_L	35_R	1.171	1.00
28_H	49_L	1.141	1.00
9_G	51_L	1.122	1.00
3_I	7_V	1.120	1.00
34_I	37_S	1.097	1.00
13_L	55_G	1.096	1.00
5_S	48_G	1.079	1.00
7_V	11_L	1.013	1.00
53_Y	57_V	1.007	1.00
50_V	54_I	1.006	1.00
27_G	49_L	0.986	1.00
27_G	48_G	0.978	1.00
55_G	59_L	0.953	1.00
8_L	22_L	0.950	1.00
24_I	49_L	0.934	1.00
12_G	15_L	0.920	1.00
24_I	53_Y	0.918	1.00
30_A	45_A	0.852	1.00
18_L	22_L	0.843	1.00
21_I	25_I	0.842	1.00
2_A	41_G	0.804	1.00
29_I	33_Q	0.803	1.00
8_L	26_L	0.803	1.00
18_L	21_I	0.800	1.00
6_L	47_A	0.793	1.00
20_G	52_G	0.779	1.00
51_L	55_G	0.767	1.00
34_I	41_G	0.746	1.00
1_L	26_L	0.743	1.00
46_I	49_L	0.733	1.00
33_Q	37_S	0.728	1.00
21_I	56_L	0.724	1.00
20_G	56_L	0.710	1.00
29_I	32_R	0.699	1.00
54_I	58_L	0.669	1.00
28_H	31_L	0.667	1.00
17_L	59_L	0.662	1.00
8_L	19_L	0.660	1.00
24_I	56_L	0.651	1.00
11_L	15_L	0.650	1.00
19_L	22_L	0.648	1.00
34_I	40_G	0.631	1.00
30_A	37_S	0.620	1.00
32_R	35_R	0.612	1.00
1_L	29_I	0.611	1.00
9_G	48_G	0.610	1.00
27_G	53_Y	0.599	1.00
4_A	22_L	0.584	1.00
34_I	42_R	0.578	1.00
9_G	23_A	0.560	1.00
12_G	20_G	0.552	1.00
22_L	25_I	0.546	1.00
16_L	19_L	0.545	1.00
11_L	14_V	0.542	1.00
15_L	59_L	0.532	1.00
44_L	47_A	0.530	1.00
4_A	7_V	0.526	1.00
13_L	19_L	0.520	1.00
2_A	9_G	0.519	1.00
26_L	30_A	0.512	1.00
6_L	51_L	0.508	1.00
24_I	52_G	0.503	1.00
53_Y	56_L	0.501	1.00
26_L	29_I	0.500	1.00

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
2xq2A	2	0.5645	6.2	0.831	Contact Map
3w4tA	1	1	6	0.832	Contact Map
4us3A	1	0.3871	5.9	0.833	Contact Map
4humA	1	1	5.4	0.836	Contact Map
4lz6A	1	1	5.2	0.837	Contact Map
3mktA	1	1	5	0.838	Contact Map
4tq3A	1	1	3.7	0.848	Contact Map
2kluA	1	0.4032	3.3	0.852	Contact Map
4o9uB	2	0.8387	2.6	0.86	Contact Map
3ojoA	2	0.3065	2.2	0.865	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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