DUF2180 - PFAM28P - GREMLIN Contacts

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DUF2180 - Uncharacterized protein conserved in archaea (DUF2180)

PFAM:	PF09947	Sequences: MKCYDCAKEGKDTDAVAICIVCGMGLCMEHAIREELPVWEGGYPFPSKKLPKKLPRILCPTCHAALK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (66)
Sequences:	708 (424)
Seq/√Len:	52.2
META:	0.85

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_K	14_D	3.684	1.00
2_K	12_D	2.934	1.00
5_D	24_M	2.303	1.00
16_V	28_M	2.059	1.00
31_A	57_I	2.032	1.00
20_I	23_G	2.006	1.00
42_G	46_P	1.993	1.00
24_M	55_P	1.656	0.98
7_A	28_M	1.562	0.98
5_D	61_T	1.550	0.98
17_A	31_A	1.541	0.97
17_A	57_I	1.526	0.97
16_V	31_A	1.497	0.97
11_K	29_E	1.449	0.96
59_C	62_C	1.412	0.96
25_G	47_S	1.406	0.96
3_C	6_C	1.338	0.94
8_K	28_M	1.321	0.94
41_G	45_F	1.273	0.93
43_Y	46_P	1.239	0.92
8_K	61_T	1.226	0.91
5_D	55_P	1.226	0.91
14_D	63_H	1.223	0.91
41_G	46_P	1.222	0.91
15_A	24_M	1.209	0.91
32_I	63_H	1.182	0.89
6_C	13_T	1.178	0.89
10_G	33_R	1.174	0.89
6_C	19_C	1.174	0.89
26_L	60_P	1.173	0.89
26_L	31_A	1.142	0.88
4_Y	9_E	1.091	0.85
13_T	25_G	1.078	0.85
33_R	57_I	1.066	0.84
54_L	65_A	1.057	0.83
41_G	44_P	1.034	0.82
39_W	64_A	0.997	0.80
16_V	26_L	0.991	0.79
54_L	61_T	0.990	0.79
45_F	48_K	0.955	0.77
55_P	61_T	0.952	0.76
9_E	35_E	0.938	0.75
18_I	25_G	0.917	0.74
34_E	60_P	0.911	0.73
7_A	41_G	0.897	0.72
21_V	58_L	0.895	0.72
52_K	64_A	0.871	0.70
37_P	44_P	0.858	0.69
19_C	30_H	0.850	0.68
17_A	24_M	0.833	0.66
11_K	66_L	0.816	0.65
56_R	62_C	0.808	0.64
26_L	57_I	0.794	0.63
31_A	60_P	0.791	0.62
10_G	14_D	0.777	0.61
13_T	29_E	0.776	0.61
12_D	17_A	0.769	0.60
27_C	62_C	0.766	0.60
16_V	60_P	0.754	0.59
40_E	44_P	0.753	0.59
24_M	33_R	0.745	0.58
28_M	31_A	0.725	0.56
7_A	53_K	0.716	0.55
25_G	64_A	0.706	0.54
21_V	24_M	0.703	0.53
12_D	29_E	0.690	0.52
43_Y	48_K	0.689	0.52
49_K	57_I	0.684	0.51
37_P	66_L	0.683	0.51
2_K	17_A	0.674	0.50
19_C	22_C	0.673	0.50
2_K	24_M	0.665	0.49
37_P	52_K	0.661	0.49
27_C	59_C	0.656	0.48
22_C	27_C	0.656	0.48
17_A	33_R	0.654	0.48
25_G	37_P	0.648	0.48
15_A	26_L	0.644	0.47
18_I	26_L	0.642	0.47
35_E	56_R	0.618	0.44
25_G	52_K	0.612	0.44
1_M	49_K	0.605	0.43
22_C	59_C	0.599	0.43
61_T	65_A	0.598	0.42
12_D	66_L	0.594	0.42
51_P	55_P	0.575	0.40
40_E	43_Y	0.573	0.40
7_A	16_V	0.572	0.40
9_E	32_I	0.562	0.39
25_G	34_E	0.545	0.37
25_G	28_M	0.543	0.37
51_P	54_L	0.542	0.37
2_K	7_A	0.538	0.36
10_G	64_A	0.535	0.36
13_T	18_I	0.535	0.36
7_A	17_A	0.521	0.35
44_P	47_S	0.517	0.34
20_I	54_L	0.510	0.34
41_G	50_L	0.500	0.33

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
3mpxA	1	0	64	0.805	Contact Map
3zyqA	1	0.8507	60.8	0.809	Contact Map
1dvpA	2	0.8507	55.5	0.815	Contact Map
1vfyA	1	0.8507	46	0.825	Contact Map
1wfkA	1	0.8358	45.9	0.825	Contact Map
1x4uA	1	0.9403	45	0.826	Contact Map
2yw8A	1	0.8209	44.3	0.827	Contact Map
1z2qA	1	0.8507	43.3	0.828	Contact Map
1jocA	2	0.8209	42.5	0.829	Contact Map
1y02A	1	0.6716	39.6	0.832	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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