DUF3659 - PFAM28P - GREMLIN Contacts

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DUF3659 - Protein of unknown function (DUF3659)

PFAM:	PF12396	Sequences: SILEGLKVNKDGNVVDEDGNVVGRLVEGDAKKLAGKKVDEDGEILDKDGNVIGRAELLPEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (59)
Sequences:	2390 (1338)
Seq/√Len:	174.2
META:	0.631

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_D	43_E	3.531	1.00
16_D	20_N	3.115	1.00
46_D	50_N	2.699	1.00
9_N	13_N	2.370	1.00
13_N	24_R	2.304	1.00
43_E	54_R	2.089	1.00
24_R	56_E	2.021	1.00
23_G	53_G	1.979	1.00
13_N	21_V	1.851	1.00
6_L	22_V	1.824	1.00
43_E	51_V	1.680	1.00
14_V	38_V	1.666	1.00
9_N	15_V	1.611	1.00
29_D	32_K	1.585	1.00
25_L	33_L	1.523	1.00
30_A	33_L	1.417	1.00
39_D	45_L	1.342	1.00
27_E	54_R	1.285	1.00
8_V	38_V	1.263	1.00
2_I	57_L	1.181	1.00
4_E	40_E	1.168	1.00
26_V	54_R	1.159	1.00
7_K	37_K	1.145	1.00
15_V	21_V	1.144	1.00
21_V	58_L	1.130	1.00
37_K	47_K	1.125	1.00
23_G	55_A	1.100	1.00
6_L	17_E	1.044	0.99
14_V	44_I	1.018	0.99
3_L	6_L	0.978	0.99
57_L	60_E	0.970	0.99
38_V	44_I	0.961	0.99
3_L	23_G	0.959	0.99
47_K	50_N	0.909	0.99
6_L	16_D	0.907	0.99
30_A	34_A	0.891	0.98
36_K	52_I	0.880	0.98
21_V	51_V	0.834	0.98
29_D	43_E	0.824	0.97
17_E	20_N	0.774	0.96
8_V	14_V	0.767	0.96
23_G	38_V	0.766	0.96
38_V	55_A	0.758	0.96
10_K	47_K	0.742	0.95
38_V	59_P	0.741	0.95
28_G	44_I	0.737	0.95
23_G	57_L	0.725	0.94
45_L	52_I	0.721	0.94
31_K	34_A	0.711	0.94
40_E	43_E	0.705	0.94
9_N	19_G	0.700	0.93
28_G	53_G	0.699	0.93
45_L	50_N	0.693	0.93
7_K	10_K	0.681	0.92
10_K	49_G	0.677	0.92
26_V	56_E	0.648	0.90
25_L	44_I	0.647	0.90
2_I	60_E	0.634	0.89
51_V	55_A	0.634	0.89
24_R	53_G	0.634	0.89
52_I	57_L	0.633	0.89
24_R	27_E	0.628	0.89
5_G	37_K	0.624	0.89
21_V	60_E	0.619	0.88
18_D	48_D	0.616	0.88
45_L	51_V	0.605	0.87
36_K	50_N	0.594	0.86
22_V	55_A	0.587	0.86
13_N	52_I	0.582	0.85
25_L	30_A	0.578	0.85
5_G	20_N	0.573	0.84
26_V	29_D	0.570	0.84
19_G	49_G	0.560	0.83
48_D	57_L	0.558	0.83
2_I	6_L	0.557	0.83
51_V	54_R	0.554	0.82
48_D	52_I	0.550	0.82
27_E	32_K	0.548	0.82
46_D	52_I	0.546	0.81
8_V	45_L	0.532	0.80
37_K	41_D	0.529	0.79
6_L	46_D	0.523	0.78
35_G	49_G	0.521	0.78
12_G	42_G	0.514	0.77
28_G	34_A	0.511	0.77
35_G	44_I	0.508	0.76
47_K	59_P	0.505	0.76
10_K	13_N	0.500	0.75

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
4qiwA	2	0.7869	9.8	0.83	Contact Map
3rd7A	2	0.5574	5.9	0.846	Contact Map
4r9zA	2	0.541	4.7	0.853	Contact Map
1c8uA	2	0.5738	4.7	0.853	Contact Map
3bbjA	2	0.8197	4.6	0.854	Contact Map
2v2fA	1	0.2459	4.4	0.856	Contact Map
4h5bA	2	0.9836	4	0.858	Contact Map
3cjyA	2	0.541	3.9	0.858	Contact Map
2grgA	1	0.9672	3	0.867	Contact Map
1xi4A	8	0.8525	2.8	0.869	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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