DUF4115 - PFAM28P - GREMLIN Contacts

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DUF4115 - Domain of unknown function (DUF4115)

PFAM:	PF13464	Sequences: LVLRATEDSWVEVTDADGKVLFEGLLKAGETRTVEAAEPLRLRLGNAGAVEVTVNGKPVGLLGYARGQVARLTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (71)
Sequences:	31292 (21121)
Seq/√Len:	2506.6
META:	0.93

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_T	51_E	2.396	1.00
5_A	26_L	2.351	1.00
8_D	27_K	2.262	1.00
12_E	23_E	2.105	1.00
4_R	31_T	2.058	1.00
51_E	58_P	2.041	1.00
2_V	53_T	1.908	1.00
20_V	23_E	1.830	1.00
7_E	49_A	1.812	1.00
27_K	30_E	1.782	1.00
53_T	58_P	1.778	1.00
2_V	31_T	1.726	1.00
10_W	45_G	1.715	1.00
44_L	50_V	1.679	1.00
24_G	32_R	1.640	1.00
2_V	33_T	1.638	1.00
22_F	26_L	1.622	1.00
46_N	49_A	1.598	1.00
4_R	51_E	1.548	1.00
36_A	40_L	1.537	1.00
5_A	11_V	1.533	1.00
12_E	20_V	1.467	1.00
14_T	41_R	1.440	1.00
7_E	46_N	1.411	1.00
8_D	25_L	1.393	1.00
43_R	71_R	1.376	1.00
22_F	32_R	1.333	1.00
4_R	53_T	1.328	1.00
65_A	68_Q	1.300	1.00
14_T	20_V	1.298	1.00
26_L	32_R	1.293	1.00
9_S	44_L	1.285	1.00
52_V	59_V	1.268	1.00
12_E	43_R	1.128	1.00
3_L	34_V	1.098	1.00
13_V	34_V	1.074	1.00
26_L	30_E	1.059	1.00
15_D	19_K	1.019	1.00
5_A	50_V	1.007	1.00
3_L	52_V	0.994	1.00
9_S	50_V	0.986	1.00
22_F	34_V	0.977	1.00
16_A	21_L	0.942	1.00
43_R	69_V	0.930	1.00
7_E	28_A	0.905	1.00
8_D	28_A	0.884	1.00
24_G	30_E	0.856	1.00
7_E	66_R	0.842	1.00
53_T	56_G	0.821	1.00
9_S	49_A	0.819	1.00
11_V	26_L	0.800	1.00
68_Q	71_R	0.795	1.00
6_T	49_A	0.793	1.00
48_G	68_Q	0.791	1.00
41_R	71_R	0.786	1.00
11_V	44_L	0.777	1.00
17_D	37_A	0.766	1.00
13_V	40_L	0.748	1.00
13_V	42_L	0.743	1.00
21_L	24_G	0.720	1.00
25_L	45_G	0.705	1.00
48_G	63_G	0.695	1.00
44_L	62_L	0.690	1.00
65_A	70_A	0.684	1.00
65_A	69_V	0.681	1.00
5_A	9_S	0.672	1.00
60_G	63_G	0.670	1.00
54_V	59_V	0.662	1.00
67_G	70_A	0.662	1.00
10_W	25_L	0.659	1.00
47_A	69_V	0.657	1.00
35_E	40_L	0.655	1.00
16_A	36_A	0.647	1.00
3_L	11_V	0.643	1.00
66_R	70_A	0.629	1.00
23_E	43_R	0.625	1.00
62_L	72_L	0.625	1.00
69_V	72_L	0.620	1.00
36_A	54_V	0.609	1.00
3_L	50_V	0.604	1.00
10_W	23_E	0.603	1.00
14_T	43_R	0.602	1.00
9_S	45_G	0.600	1.00
40_L	54_V	0.591	1.00
28_A	49_A	0.591	1.00
35_E	55_N	0.587	1.00
13_V	36_A	0.585	1.00
58_P	61_L	0.581	1.00
16_A	34_V	0.555	1.00
47_A	50_V	0.542	1.00
42_L	72_L	0.542	1.00
45_G	69_V	0.531	1.00
18_G	39_P	0.530	1.00
37_A	40_L	0.529	1.00
15_D	18_G	0.529	1.00
36_A	39_P	0.520	1.00
9_S	47_A	0.519	1.00
52_V	62_L	0.513	1.00
18_G	38_E	0.512	1.00
63_G	68_Q	0.511	1.00
47_A	62_L	0.511	1.00
3_L	13_V	0.506	1.00
34_V	38_E	0.504	1.00
34_V	40_L	0.503	1.00
1_L	40_L	0.501	1.00
18_G	41_R	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
1ogoX	1	0.9865	36.9	0.793	Contact Map
1x0cA	2	0.973	34	0.797	Contact Map
3ujzA	2	0.3649	14.7	0.828	Contact Map
1fxzA	3	1	14.2	0.83	Contact Map
3c3vA	5	1	14.1	0.83	Contact Map
4wqoA	1	0.9595	13.6	0.832	Contact Map
3kglA	3	1	12.3	0.835	Contact Map
3fipA	1	0.7973	12.3	0.835	Contact Map
3fz3A	5	1	11.6	0.836	Contact Map
3qacA	3	1	11.1	0.838	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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