DUF370 - PFAM28P - GREMLIN Contacts

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DUF370 - Domain of unknown function (DUF370)

PFAM:	PF04025	Sequences: LLHIGFGNVVSADRIIAIVSPDSAPIKRLIQEAREEGRLIDATYGRKTRSVIITDSGHVILSAISPETLAKRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (72)
Sequences:	5916 (3514)
Seq/√Len:	414.1
META:	0.877

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	55_D	4.313	1.00
32_E	36_E	2.815	1.00
54_T	60_I	2.398	1.00
18_I	50_S	2.160	1.00
65_S	68_T	2.019	1.00
29_L	53_I	2.019	1.00
40_I	58_H	1.976	1.00
21_P	51_V	1.931	1.00
26_I	51_V	1.822	1.00
25_P	28_R	1.644	1.00
15_I	52_I	1.588	1.00
38_R	57_G	1.509	1.00
4_I	10_V	1.484	1.00
33_A	59_V	1.470	1.00
24_A	28_R	1.431	1.00
6_F	63_A	1.420	1.00
16_I	54_T	1.407	1.00
21_P	48_T	1.363	1.00
19_V	53_I	1.286	1.00
41_D	45_G	1.281	1.00
68_T	72_R	1.265	1.00
39_L	61_L	1.261	1.00
19_V	26_I	1.255	1.00
4_I	42_A	1.253	1.00
30_I	51_V	1.247	1.00
65_S	71_K	1.241	1.00
19_V	42_A	1.240	1.00
51_V	61_L	1.218	1.00
6_F	46_R	1.204	1.00
31_Q	35_E	1.191	1.00
48_T	61_L	1.183	1.00
8_N	44_Y	1.179	1.00
32_E	35_E	1.173	1.00
9_V	70_A	1.159	1.00
2_L	12_A	1.146	1.00
35_E	38_R	1.135	1.00
26_I	30_I	1.134	1.00
28_R	32_E	1.058	1.00
43_T	46_R	1.048	1.00
3_H	68_T	1.013	1.00
53_I	59_V	0.976	1.00
65_S	69_L	0.965	1.00
3_H	64_I	0.955	1.00
50_S	66_P	0.942	1.00
41_D	61_L	0.936	1.00
19_V	51_V	0.906	1.00
49_R	65_S	0.898	1.00
64_I	72_R	0.895	1.00
62_S	69_L	0.888	1.00
51_V	59_V	0.887	1.00
20_S	44_Y	0.867	1.00
11_S	14_R	0.858	1.00
43_T	48_T	0.856	1.00
68_T	71_K	0.854	1.00
10_V	60_I	0.849	1.00
64_I	68_T	0.846	1.00
14_R	56_S	0.846	1.00
34_R	41_D	0.831	1.00
32_E	38_R	0.826	1.00
16_I	55_D	0.826	1.00
3_H	9_V	0.809	1.00
41_D	48_T	0.789	1.00
34_R	39_L	0.778	1.00
23_S	26_I	0.778	1.00
54_T	57_G	0.769	1.00
18_I	66_P	0.767	1.00
22_D	25_P	0.734	1.00
2_L	69_L	0.731	1.00
29_L	59_V	0.723	1.00
31_Q	34_R	0.715	1.00
43_T	47_K	0.691	1.00
21_P	50_S	0.677	1.00
42_A	60_I	0.677	1.00
4_I	60_I	0.676	1.00
30_I	39_L	0.670	0.99
1_L	9_V	0.652	0.99
38_R	58_H	0.648	0.99
10_V	52_I	0.622	0.99
3_H	16_I	0.620	0.99
1_L	11_S	0.617	0.99
22_D	47_K	0.614	0.99
42_A	62_S	0.611	0.99
8_N	42_A	0.605	0.99
20_S	66_P	0.605	0.99
3_H	65_S	0.594	0.99
22_D	31_Q	0.592	0.99
47_K	67_E	0.570	0.98
50_S	62_S	0.559	0.98
26_I	29_L	0.557	0.98
27_K	34_R	0.551	0.98
7_G	12_A	0.548	0.98
10_V	33_A	0.544	0.98
4_I	62_S	0.542	0.98
12_A	15_I	0.534	0.97
25_P	29_L	0.534	0.97
14_R	57_G	0.532	0.97
34_R	61_L	0.522	0.97
3_H	44_Y	0.519	0.97
4_I	15_I	0.517	0.97
27_K	33_A	0.516	0.97
1_L	42_A	0.515	0.97
17_A	60_I	0.511	0.97
30_I	34_R	0.506	0.97
27_K	31_Q	0.504	0.96
4_I	19_V	0.503	0.96
23_S	30_I	0.502	0.96
38_R	56_S	0.502	0.96
33_A	39_L	0.500	0.96

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
2jwkA	2	0.3973	15.5	0.856	Contact Map
1rypK	2	0.9178	13.6	0.86	Contact Map
4lb6B	2	0.7534	11.4	0.865	Contact Map
2o0mA	1	0.1233	10.8	0.866	Contact Map
1j2qH	5	1	9.4	0.87	Contact Map
3nzjK	1	1	9.3	0.87	Contact Map
3tgnA	2	0.9863	9.2	0.87	Contact Map
1jgsA	2	1	8.8	0.872	Contact Map
4iqzA	4	0.3014	8.6	0.872	Contact Map
3h4pa	5	1	7.9	0.874	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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