DUF3140 - PFAM28P - GREMLIN Contacts

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DUF3140 - Protein of unknown function (DUF3140)

PFAM:	PF11338	Sequences: EFHEAVNMTAAELEDWLETDESRSVGQKGGGGESVGHASGRRIVEILRKKKADLTDDDYAHMRKVVGYVHRHLAQGRPAGDVEDSRWRYSLM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	92 (91)
Sequences:	2263 (1357)
Seq/√Len:	142.3
META:	0.766

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_A	69_V	3.744	1.00
14_E	48_R	3.739	1.00
88_R	92_M	3.589	1.00
39_S	61_H	3.080	1.00
27_Q	35_V	3.074	1.00
66_V	70_H	2.716	1.00
2_F	59_Y	2.439	1.00
80_G	85_S	2.156	1.00
37_H	40_G	2.029	1.00
10_A	47_L	2.006	1.00
5_A	70_H	1.956	1.00
77_R	80_G	1.935	1.00
50_K	53_D	1.849	1.00
11_A	15_D	1.828	1.00
77_R	82_V	1.766	1.00
49_K	53_D	1.705	1.00
61_H	64_K	1.686	1.00
80_G	83_E	1.653	1.00
84_D	89_Y	1.649	1.00
54_L	59_Y	1.581	1.00
42_R	61_H	1.574	1.00
49_K	58_D	1.375	1.00
42_R	45_E	1.362	1.00
29_G	32_G	1.348	1.00
49_K	54_L	1.325	1.00
39_S	43_I	1.309	1.00
14_E	18_E	1.297	1.00
10_A	48_R	1.271	1.00
44_V	48_R	1.212	1.00
80_G	84_D	1.186	1.00
69_V	73_L	1.173	1.00
70_H	73_L	1.153	0.99
63_R	66_V	1.149	0.99
14_E	44_V	1.123	0.99
81_D	84_D	1.122	0.99
38_A	42_R	1.121	0.99
77_R	85_S	1.107	0.99
28_K	31_G	1.097	0.99
25_V	34_S	1.090	0.99
9_T	12_E	1.090	0.99
68_Y	72_H	1.052	0.99
72_H	75_Q	1.045	0.99
12_E	15_D	1.045	0.99
25_V	89_Y	1.026	0.99
77_R	83_E	1.020	0.99
82_V	85_S	1.019	0.99
25_V	28_K	1.019	0.99
1_E	4_E	0.974	0.98
33_E	41_R	0.968	0.98
33_E	37_H	0.926	0.98
78_P	81_D	0.925	0.98
49_K	55_T	0.925	0.98
72_H	90_S	0.872	0.96
73_L	77_R	0.854	0.96
57_D	60_A	0.837	0.96
5_A	8_M	0.826	0.95
52_A	59_Y	0.819	0.95
77_R	84_D	0.797	0.94
61_H	65_V	0.772	0.93
29_G	38_A	0.771	0.93
18_E	45_E	0.769	0.93
13_L	40_G	0.744	0.92
85_S	88_R	0.739	0.92
23_R	50_K	0.730	0.91
60_A	63_R	0.729	0.91
5_A	66_V	0.727	0.91
21_E	24_S	0.726	0.91
59_Y	63_R	0.722	0.91
85_S	89_Y	0.722	0.91
43_I	65_V	0.722	0.91
60_A	64_K	0.720	0.90
28_K	32_G	0.711	0.90
78_P	87_W	0.702	0.89
15_D	18_E	0.696	0.89
2_F	7_N	0.693	0.89
39_S	90_S	0.691	0.89
28_K	38_A	0.691	0.89
13_L	46_I	0.687	0.88
70_H	74_A	0.684	0.88
11_A	51_K	0.679	0.88
47_L	58_D	0.677	0.88
13_L	73_L	0.675	0.87
31_G	38_A	0.667	0.87
27_Q	31_G	0.661	0.86
89_Y	92_M	0.659	0.86
68_Y	71_R	0.658	0.86
45_E	56_D	0.649	0.85
3_H	47_L	0.649	0.85
79_A	83_E	0.645	0.85
22_S	25_V	0.644	0.85
65_V	68_Y	0.641	0.85
17_L	62_M	0.641	0.85
29_G	50_K	0.629	0.84
67_G	72_H	0.626	0.83
81_D	85_S	0.626	0.83
20_D	23_R	0.625	0.83
46_I	54_L	0.624	0.83
68_Y	75_Q	0.617	0.82
39_S	71_R	0.613	0.82
37_H	41_R	0.612	0.82
25_V	86_R	0.608	0.81
35_V	38_A	0.605	0.81
42_R	57_D	0.598	0.80
34_S	86_R	0.595	0.80
54_L	62_M	0.594	0.80
82_V	88_R	0.586	0.79
8_M	79_A	0.583	0.79
4_E	20_D	0.574	0.78
52_A	60_A	0.573	0.77
4_E	70_H	0.566	0.77
2_F	63_R	0.563	0.76
11_A	48_R	0.563	0.76
34_S	37_H	0.561	0.76
56_D	60_A	0.560	0.76
39_S	65_V	0.558	0.76
17_L	40_G	0.556	0.75
31_G	34_S	0.554	0.75
30_G	56_D	0.551	0.75
35_V	64_K	0.547	0.74
3_H	51_K	0.546	0.74
65_V	69_V	0.544	0.74
9_T	57_D	0.544	0.74
47_L	51_K	0.541	0.73
71_R	90_S	0.539	0.73
67_G	70_H	0.538	0.73
3_H	52_A	0.520	0.70
4_E	42_R	0.519	0.70
75_Q	90_S	0.514	0.70
11_A	73_L	0.507	0.69
47_L	79_A	0.505	0.68
71_R	74_A	0.504	0.68
54_L	58_D	0.503	0.68
17_L	43_I	0.503	0.68
8_M	15_D	0.502	0.68
1_E	70_H	0.500	0.67
8_M	92_M	0.500	0.67

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
1lmb3	2	0.6304	11.6	0.916	Contact Map
1jeyA	1	0	10.6	0.918	Contact Map
2ys9A	1	0.3587	10.3	0.918	Contact Map
3zilB	1	0.1196	8.7	0.921	Contact Map
4rcmA	1	0.6087	7.9	0.922	Contact Map
1wurA	6	0.3913	7.4	0.924	Contact Map
4bpeO	1	0.9457	6.9	0.924	Contact Map
3op9A	4	0.7826	6.6	0.925	Contact Map
3j20Q	1	0.9348	6.6	0.925	Contact Map
2vugA	2	0.2065	6.6	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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