DUF411 - PFAM28P - GREMLIN Contacts

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DUF411 - Protein of unknown function, DUF

PFAM:	PF04214	Sequences: VTVHDTDDLAAIKARLGVPAELASCHTAVVGGYVIEGHVPAADIKRLLAERPDAAGLAVPGMPVGSPGM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (69)
Sequences:	11726 (6779)
Seq/√Len:	816.1
META:	0.902

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_L	29_V	3.231	1.00
35_I	47_L	2.573	1.00
14_A	23_A	2.512	1.00
46_R	50_E	2.248	1.00
47_L	54_A	2.171	1.00
13_K	36_E	2.097	1.00
6_T	9_L	1.985	1.00
9_L	13_K	1.878	1.00
45_K	49_A	1.753	1.00
27_T	36_E	1.676	1.00
35_I	57_L	1.572	1.00
8_D	11_A	1.562	1.00
19_P	22_L	1.547	1.00
35_I	39_V	1.492	1.00
12_I	16_L	1.481	1.00
20_A	23_A	1.476	1.00
33_Y	52_P	1.417	1.00
43_D	46_R	1.404	1.00
41_A	45_K	1.378	1.00
11_A	15_R	1.351	1.00
13_K	23_A	1.326	1.00
13_K	27_T	1.318	1.00
30_V	35_I	1.281	1.00
41_A	67_P	1.267	1.00
59_V	64_V	1.226	1.00
59_V	65_G	1.219	1.00
39_V	59_V	1.215	1.00
9_L	12_I	1.202	1.00
33_Y	47_L	1.201	1.00
14_A	20_A	1.182	1.00
28_A	59_V	1.164	1.00
32_G	51_R	1.161	1.00
59_V	66_S	1.160	1.00
31_G	51_R	1.124	1.00
38_H	66_S	1.073	1.00
6_T	12_I	1.071	1.00
15_R	29_V	1.008	1.00
24_S	58_A	0.997	1.00
12_I	15_R	0.994	1.00
47_L	51_R	0.986	1.00
10_A	23_A	0.976	1.00
22_L	58_A	0.955	1.00
25_C	62_M	0.937	1.00
17_G	55_A	0.920	1.00
6_T	11_A	0.908	1.00
16_L	34_V	0.904	1.00
35_I	44_I	0.877	1.00
29_V	32_G	0.871	1.00
18_V	34_V	0.870	1.00
33_Y	53_D	0.860	1.00
24_S	67_P	0.854	1.00
24_S	36_E	0.841	1.00
43_D	47_L	0.840	1.00
10_A	14_A	0.839	1.00
36_E	58_A	0.834	1.00
13_K	24_S	0.770	1.00
34_V	55_A	0.770	1.00
35_I	67_P	0.758	1.00
24_S	38_H	0.757	1.00
29_V	34_V	0.755	1.00
26_H	62_M	0.748	1.00
19_P	23_A	0.747	1.00
6_T	10_A	0.738	1.00
43_D	57_L	0.732	1.00
43_D	59_V	0.728	1.00
10_A	20_A	0.712	1.00
30_V	44_I	0.703	1.00
7_D	11_A	0.698	1.00
30_V	48_L	0.692	1.00
61_G	64_V	0.687	1.00
63_P	66_S	0.672	1.00
40_P	66_S	0.657	1.00
44_I	47_L	0.655	1.00
33_Y	50_E	0.643	1.00
41_A	44_I	0.640	1.00
25_C	69_M	0.626	1.00
42_A	45_K	0.620	1.00
31_G	48_L	0.613	1.00
24_S	40_P	0.613	1.00
33_Y	56_G	0.609	1.00
22_L	55_A	0.600	1.00
54_A	57_L	0.598	1.00
62_M	69_M	0.597	1.00
13_K	18_V	0.588	1.00
26_H	38_H	0.585	1.00
33_Y	57_L	0.584	1.00
18_V	23_A	0.583	1.00
12_I	27_T	0.575	1.00
7_D	10_A	0.575	1.00
61_G	66_S	0.572	1.00
9_L	23_A	0.570	1.00
55_A	59_V	0.563	1.00
11_A	14_A	0.559	1.00
2_T	7_D	0.557	1.00
4_H	7_D	0.555	1.00
57_L	63_P	0.550	1.00
3_V	6_T	0.542	1.00
33_Y	54_A	0.540	1.00
39_V	57_L	0.530	1.00
24_S	28_A	0.526	1.00
21_E	49_A	0.525	1.00
59_V	63_P	0.517	1.00
30_V	43_D	0.501	1.00
18_V	27_T	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
1ttzA	1	0.6812	37.2	0.876	Contact Map
1z6mA	1	0.7246	23.8	0.888	Contact Map
1s4zC	1	0.4348	23	0.889	Contact Map
3ic4A	1	0.6522	16.4	0.896	Contact Map
4ml1A	4	0.6522	15.6	0.897	Contact Map
3fz5A	2	0.7681	14.5	0.898	Contact Map
1t3bA	2	0.6812	13.5	0.9	Contact Map
4c1lA	4	0.8406	13	0.9	Contact Map
4nv5A	1	0.7391	10.1	0.905	Contact Map
1vs1A	4	0.8261	9.8	0.906	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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