DUF4389 - PFAM28P - GREMLIN Contacts

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DUF4389 - Domain of unknown function (DUF4389)

PFAM:	PF14333	Sequences: RLTVLFRWLLAIPHLIVLAFLGIAAFVVAIIAWFAILFTGRYPRGLFDFVVGVLRWSARVYAYLLLLTDRYPPFFS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (71)
Sequences:	28187 (14623)
Seq/√Len:	1735.4
META:	0.976

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_A	42_Y	3.622	1.00
36_I	42_Y	2.283	1.00
11_A	64_L	2.256	1.00
31_I	46_L	2.179	1.00
25_A	50_V	2.145	1.00
44_R	48_D	2.126	1.00
28_V	46_L	2.122	1.00
22_G	57_S	2.046	1.00
14_H	56_W	1.903	1.00
32_A	43_P	1.860	1.00
30_I	34_F	1.833	1.00
24_A	49_F	1.830	1.00
19_A	23_I	1.674	1.00
57_S	61_Y	1.655	1.00
11_A	15_L	1.608	1.00
28_V	50_V	1.602	1.00
21_L	53_V	1.544	1.00
25_A	53_V	1.512	1.00
42_Y	47_F	1.469	1.00
35_A	43_P	1.459	1.00
58_A	62_A	1.434	1.00
47_F	51_V	1.291	1.00
27_V	31_I	1.229	1.00
19_A	22_G	1.190	1.00
29_A	50_V	1.175	1.00
42_Y	50_V	1.154	1.00
6_F	10_L	1.142	1.00
22_G	53_V	1.124	1.00
14_H	18_L	1.111	1.00
18_L	57_S	1.074	1.00
8_W	33_W	1.062	1.00
58_A	61_Y	1.060	1.00
18_L	22_G	1.051	1.00
14_H	60_V	1.010	1.00
61_Y	65_L	1.004	1.00
17_V	56_W	0.994	1.00
51_V	55_R	0.978	1.00
17_V	20_F	0.971	1.00
71_Y	74_F	0.969	1.00
20_F	24_A	0.957	1.00
62_A	67_L	0.940	1.00
50_V	54_L	0.936	1.00
54_L	58_A	0.922	1.00
22_G	26_F	0.921	1.00
11_A	60_V	0.901	1.00
36_I	39_T	0.892	1.00
7_R	69_D	0.882	1.00
15_L	60_V	0.848	1.00
29_A	33_W	0.844	1.00
44_R	47_F	0.821	1.00
16_I	20_F	0.816	1.00
58_A	67_L	0.796	1.00
34_F	38_F	0.795	1.00
7_R	66_L	0.795	1.00
5_L	8_W	0.787	1.00
21_L	52_G	0.780	1.00
21_L	56_W	0.773	1.00
26_F	30_I	0.766	1.00
49_F	53_V	0.765	1.00
56_W	60_V	0.758	1.00
4_V	66_L	0.738	1.00
53_V	57_S	0.738	1.00
18_L	60_V	0.731	1.00
62_A	68_T	0.728	1.00
45_G	48_D	0.724	1.00
35_A	39_T	0.715	1.00
8_W	64_L	0.710	1.00
48_D	52_G	0.708	1.00
52_G	56_W	0.705	1.00
62_A	65_L	0.696	1.00
19_A	26_F	0.691	1.00
54_L	57_S	0.685	1.00
31_I	35_A	0.680	1.00
33_W	66_L	0.675	1.00
14_H	71_Y	0.675	1.00
14_H	63_Y	0.671	1.00
41_R	44_R	0.664	1.00
14_H	17_V	0.642	1.00
63_Y	66_L	0.638	1.00
23_I	27_V	0.637	1.00
32_A	46_L	0.633	1.00
36_I	47_F	0.631	1.00
24_A	27_V	0.630	1.00
50_V	53_V	0.627	1.00
51_V	54_L	0.618	1.00
63_Y	68_T	0.614	1.00
20_F	23_I	0.604	1.00
62_A	66_L	0.604	1.00
51_V	62_A	0.599	1.00
34_F	37_L	0.595	1.00
56_W	73_P	0.591	1.00
25_A	29_A	0.575	1.00
59_R	68_T	0.567	1.00
48_D	51_V	0.554	1.00
10_L	14_H	0.548	1.00
49_F	52_G	0.545	1.00
55_R	59_R	0.539	1.00
39_T	45_G	0.535	1.00
18_L	53_V	0.534	1.00
21_L	49_F	0.518	1.00
14_H	73_P	0.512	1.00
32_A	36_I	0.511	1.00
15_L	19_A	0.511	1.00
33_W	40_G	0.506	1.00
10_L	63_Y	0.506	1.00
6_F	9_L	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
3k1tA	2	0.5921	2.4	0.896	Contact Map
3rvyA	3	0.9211	2	0.899	Contact Map
2kogA	1	0.3816	1.5	0.906	Contact Map
3fymA	1	0	1.5	0.906	Contact Map
3j08A	2	1	1.4	0.908	Contact Map
1j7mA	1	0.2368	1.3	0.91	Contact Map
3wvoA	2	0.8684	1.3	0.911	Contact Map
2r2nA	2	0.6447	1.2	0.913	Contact Map
3dl8C	1	0.4342	1.2	0.913	Contact Map
4bgnA	3	0.8553	1.1	0.914	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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