DUF3135 - PFAM28P - GREMLIN Contacts

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DUF3135 - Protein of unknown function (DUF3135)

PFAM:	PF11333	Sequences: ELFDFDEWAELAKEDPEAFEALRRELIEELIASAPEEQQRRLRGLQWRIDMERRRAKNPLAACIRISRMMWDSLAELRGAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (77)
Sequences:	1397 (1083)
Seq/√Len:	123.4
META:	0.862

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_E	14_E	2.787	1.00
28_E	43_R	2.410	1.00
28_E	32_A	2.304	1.00
3_F	8_W	2.289	1.00
15_D	18_A	2.239	1.00
40_R	44_G	2.166	1.00
9_A	13_K	2.100	1.00
44_G	47_W	2.087	1.00
34_A	42_L	2.052	1.00
51_M	55_R	1.973	1.00
46_Q	50_D	1.855	1.00
52_E	65_R	1.835	1.00
7_E	22_L	1.817	1.00
20_E	23_R	1.688	1.00
39_Q	43_R	1.680	1.00
49_I	66_I	1.586	1.00
58_N	61_A	1.580	1.00
4_D	7_E	1.524	1.00
47_W	51_M	1.523	1.00
52_E	55_R	1.454	1.00
30_L	34_A	1.438	1.00
51_M	54_R	1.426	1.00
71_W	74_L	1.417	1.00
8_W	22_L	1.366	1.00
53_R	62_A	1.345	1.00
5_F	9_A	1.342	1.00
18_A	21_A	1.325	1.00
3_F	22_L	1.323	1.00
56_A	61_A	1.292	1.00
26_L	29_E	1.233	0.99
57_K	61_A	1.215	0.99
48_R	52_E	1.214	0.99
41_R	44_G	1.164	0.99
31_I	34_A	1.158	0.99
27_I	46_Q	1.140	0.99
30_L	33_S	1.135	0.99
67_S	70_M	1.128	0.99
60_L	63_C	1.113	0.99
32_A	39_Q	1.098	0.99
8_W	26_L	1.093	0.99
21_A	25_E	1.030	0.98
76_E	79_G	1.027	0.98
19_F	27_I	1.013	0.98
26_L	30_L	1.001	0.98
64_I	67_S	0.991	0.97
70_M	73_S	0.977	0.97
44_G	51_M	0.972	0.97
56_A	65_R	0.970	0.97
63_C	67_S	0.956	0.97
36_E	39_Q	0.917	0.96
24_R	28_E	0.904	0.96
22_L	25_E	0.886	0.95
65_R	68_R	0.882	0.95
23_R	53_R	0.874	0.95
7_E	11_L	0.850	0.94
73_S	76_E	0.844	0.94
11_L	22_L	0.823	0.93
8_W	19_F	0.799	0.92
3_F	19_F	0.766	0.90
35_P	38_Q	0.761	0.90
53_R	66_I	0.750	0.89
61_A	64_I	0.748	0.89
52_E	69_M	0.724	0.87
19_F	30_L	0.719	0.87
56_A	62_A	0.718	0.87
19_F	71_W	0.704	0.86
31_I	46_Q	0.691	0.85
35_P	39_Q	0.682	0.84
40_R	75_A	0.679	0.84
24_R	50_D	0.677	0.83
25_E	29_E	0.674	0.83
60_L	64_I	0.671	0.83
19_F	23_R	0.667	0.83
74_L	78_R	0.665	0.82
27_I	30_L	0.658	0.82
70_M	77_L	0.654	0.81
27_I	31_I	0.638	0.80
19_F	22_L	0.634	0.79
64_I	68_R	0.630	0.79
25_E	28_E	0.629	0.79
62_A	66_I	0.626	0.78
44_G	48_R	0.619	0.78
12_A	19_F	0.611	0.77
47_W	77_L	0.604	0.76
18_A	25_E	0.602	0.76
18_A	22_L	0.601	0.76
27_I	50_D	0.596	0.75
47_W	74_L	0.595	0.75
49_I	63_C	0.590	0.74
6_D	9_A	0.588	0.74
67_S	71_W	0.584	0.74
34_A	38_Q	0.579	0.73
20_E	53_R	0.573	0.72
73_S	77_L	0.569	0.72
47_W	71_W	0.567	0.71
57_K	68_R	0.566	0.71
61_A	65_R	0.565	0.71
46_Q	66_I	0.565	0.71
11_L	15_D	0.563	0.71
63_C	66_I	0.559	0.70
41_R	47_W	0.556	0.70
65_R	69_M	0.553	0.69
26_L	54_R	0.552	0.69
62_A	70_M	0.546	0.68
16_P	59_P	0.541	0.68
38_Q	75_A	0.541	0.68
66_I	70_M	0.532	0.67
34_A	39_Q	0.531	0.66
26_L	56_A	0.531	0.66
43_R	50_D	0.531	0.66
48_R	69_M	0.528	0.66
38_Q	74_L	0.527	0.66
58_N	64_I	0.523	0.65
14_E	21_A	0.513	0.64
21_A	32_A	0.502	0.62
49_I	53_R	0.500	0.62

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
3iyuX	3	0.6296	12.3	0.882	Contact Map
4uopA	2	0.4568	11.2	0.884	Contact Map
2p0tA	1	0.9383	8.5	0.89	Contact Map
2p22C	2	0.9877	8	0.891	Contact Map
3bboS	1	0.3704	7.8	0.892	Contact Map
1i7kA	1	0.3827	6.9	0.895	Contact Map
3l1nA	2	0.7407	6.1	0.897	Contact Map
1zkrA	2	0.963	5.9	0.898	Contact Map
1yrvA	1	0.3333	5.6	0.899	Contact Map
4nooA	1	0.8642	5.5	0.899	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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