DUF4345 - PFAM28P - GREMLIN Contacts

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DUF4345 - Domain of unknown function (DUF4345)

PFAM:	PF14248	Sequences: ILRILLALAALIFLAIGLLGLLAPAALAALLLGITLASPDLDSELRALYGGLLGLGLLLLLAAFRPERRRTALLLLALAVLGGGLGRLLSLALDGSPSPLLLGALALELVLAPLLLLWQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (114)
Sequences:	7648 (5884)
Seq/√Len:	551.1
META:	0.901

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_L	112_A	4.134	1.00
40_D	98_S	2.594	1.00
46_R	94_D	2.562	1.00
21_L	86_G	2.296	1.00
62_A	72_A	2.271	1.00
14_L	56_G	2.255	1.00
42_D	94_D	2.253	1.00
23_A	26_A	2.069	1.00
70_R	74_L	1.986	1.00
65_R	68_R	1.975	1.00
65_R	69_R	1.932	1.00
91_L	105_L	1.873	1.00
7_A	63_A	1.835	1.00
77_A	115_L	1.826	1.00
89_L	93_L	1.810	1.00
77_A	116_L	1.763	1.00
46_R	93_L	1.727	1.00
85_L	89_L	1.712	1.00
99_P	103_G	1.707	1.00
100_L	104_A	1.664	1.00
57_L	61_L	1.647	1.00
17_G	53_L	1.636	1.00
10_A	60_L	1.588	1.00
84_G	109_L	1.576	1.00
102_L	106_A	1.547	1.00
5_L	115_L	1.542	1.00
43_S	90_S	1.509	1.00
72_A	75_L	1.468	1.00
91_L	96_S	1.460	1.00
16_I	52_L	1.452	1.00
48_L	83_G	1.388	1.00
11_L	15_A	1.377	1.00
10_A	63_A	1.305	1.00
107_L	111_L	1.297	1.00
77_A	112_A	1.296	1.00
19_L	23_A	1.228	1.00
47_A	83_G	1.185	1.00
90_S	94_D	1.179	1.00
36_L	41_L	1.174	1.00
4_I	7_A	1.171	1.00
20_G	49_Y	1.158	1.00
44_E	49_Y	1.153	1.00
17_G	56_G	1.147	1.00
25_A	42_D	1.133	1.00
98_S	101_L	1.128	1.00
58_L	62_A	1.121	1.00
87_R	108_E	1.091	1.00
61_L	72_A	1.086	1.00
46_R	90_S	1.081	1.00
19_L	27_L	1.078	1.00
88_L	92_A	1.078	1.00
68_R	71_T	1.076	1.00
81_L	85_L	1.073	1.00
61_L	68_R	1.070	1.00
10_A	56_G	1.068	1.00
80_V	111_L	1.047	1.00
15_A	19_L	1.043	1.00
4_I	8_L	1.036	1.00
101_L	104_A	1.016	1.00
97_P	102_L	1.010	1.00
78_L	82_G	1.009	1.00
84_G	105_L	0.995	1.00
103_G	107_L	0.993	1.00
113_P	117_L	0.982	1.00
59_L	76_L	0.980	1.00
61_L	65_R	0.961	1.00
91_L	97_P	0.954	1.00
7_A	64_F	0.951	1.00
20_G	44_E	0.946	1.00
26_A	29_A	0.943	1.00
55_L	79_A	0.936	1.00
88_L	109_L	0.928	1.00
7_A	11_L	0.926	1.00
14_L	53_L	0.926	1.00
9_A	111_L	0.919	1.00
10_A	14_L	0.912	1.00
84_G	112_A	0.908	1.00
69_R	72_A	0.907	1.00
38_S	41_L	0.900	1.00
88_L	105_L	0.898	1.00
103_G	106_A	0.893	1.00
36_L	45_L	0.892	1.00
48_L	51_G	0.865	1.00
54_G	82_G	0.864	1.00
62_A	69_R	0.862	1.00
43_S	101_L	0.860	1.00
28_A	45_L	0.853	1.00
44_E	48_L	0.849	1.00
35_T	38_S	0.847	1.00
56_G	60_L	0.843	1.00
12_I	16_I	0.835	1.00
91_L	102_L	0.821	1.00
66_P	69_R	0.817	1.00
7_A	60_L	0.815	1.00
54_G	57_L	0.806	1.00
60_L	64_F	0.805	1.00
40_D	101_L	0.804	1.00
16_I	19_L	0.793	1.00
5_L	9_A	0.791	1.00
42_D	46_R	0.778	1.00
13_F	80_V	0.765	1.00
21_L	53_L	0.759	1.00
67_E	70_R	0.755	1.00
19_L	26_A	0.739	1.00
24_P	42_D	0.727	1.00
18_L	22_L	0.722	1.00
33_G	37_A	0.721	1.00
3_R	7_A	0.721	1.00
37_A	41_L	0.718	1.00
44_E	80_V	0.716	1.00
96_S	99_P	0.716	1.00
102_L	105_L	0.709	1.00
91_L	94_D	0.707	1.00
20_G	27_L	0.691	1.00
33_G	40_D	0.687	1.00
16_I	20_G	0.686	1.00
105_L	109_L	0.685	1.00
9_A	76_L	0.670	1.00
96_S	102_L	0.668	1.00
71_T	74_L	0.667	1.00
33_G	36_L	0.666	1.00
17_G	21_L	0.642	1.00
69_R	73_L	0.637	1.00
52_L	79_A	0.634	1.00
109_L	113_P	0.631	1.00
3_R	66_P	0.627	1.00
39_P	95_G	0.624	1.00
86_G	89_L	0.623	1.00
15_A	18_L	0.623	1.00
110_V	114_L	0.621	1.00
50_G	82_G	0.619	1.00
44_E	87_R	0.617	1.00
112_A	116_L	0.615	1.00
82_G	86_G	0.615	1.00
28_A	34_I	0.608	1.00
5_L	76_L	0.604	1.00
20_G	28_A	0.597	1.00
50_G	54_G	0.593	1.00
99_P	102_L	0.588	1.00
26_A	30_L	0.586	1.00
111_L	115_L	0.582	1.00
28_A	36_L	0.581	0.99
16_I	27_L	0.580	0.99
106_A	110_V	0.579	0.99
18_L	53_L	0.579	0.99
54_G	80_V	0.576	0.99
110_V	113_P	0.573	0.99
48_L	52_L	0.571	0.99
81_L	84_G	0.571	0.99
14_L	60_L	0.568	0.99
55_L	76_L	0.564	0.99
58_L	75_L	0.560	0.99
47_A	86_G	0.559	0.99
32_L	35_T	0.556	0.99
6_L	62_A	0.549	0.99
74_L	116_L	0.548	0.99
27_L	30_L	0.545	0.99
16_I	48_L	0.539	0.99
51_G	83_G	0.538	0.99
51_G	82_G	0.538	0.99
42_D	90_S	0.533	0.99
36_L	42_D	0.526	0.99
100_L	103_G	0.517	0.99
34_I	38_S	0.517	0.99
79_A	83_G	0.516	0.99
13_F	20_G	0.509	0.99
58_L	68_R	0.502	0.99
86_G	90_S	0.502	0.99
45_L	48_L	0.502	0.99
47_A	51_G	0.501	0.99
24_P	27_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
4ev6A	3	0.4958	2.6	0.899	Contact Map
4i0uA	4	0.4622	2.4	0.901	Contact Map
4p02A	1	0.8655	1.5	0.912	Contact Map
3wfdB	1	0.5378	1.4	0.914	Contact Map
4humA	1	0.9916	1.3	0.915	Contact Map
4o9uB	2	0.8319	1.1	0.918	Contact Map
3mktA	1	0.9916	1	0.921	Contact Map
4c7rA	3	0.9412	0.9	0.923	Contact Map
4lz6A	1	0.9832	0.9	0.923	Contact Map
4o93B	1	0.605	0.8	0.925	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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