DUF1844 - PFAM28P - GREMLIN Contacts

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DUF1844 - Domain of unknown function (DUF1844)

PFAM:	PF08899	Sequences: IDFSTLVLSLATQALMHLGEIPDPETGKPEVDLELARQTIDLLAMLEEKTKGNLTPEEERLLENVLYELRMRY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (72)
Sequences:	15131 (8678)
Seq/√Len:	1022.7
META:	0.986

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_E	63_E	2.724	1.00
44_A	70_R	2.672	1.00
59_E	63_E	2.568	1.00
64_N	68_E	2.240	1.00
56_P	60_R	2.230	1.00
20_E	72_R	2.160	1.00
17_H	39_T	1.849	1.00
56_P	59_E	1.815	1.00
22_P	27_G	1.778	1.00
23_D	26_T	1.775	1.00
11_A	65_V	1.769	1.00
32_D	35_L	1.620	1.00
67_Y	71_M	1.575	1.00
60_R	64_N	1.530	1.00
54_L	59_E	1.498	1.00
47_E	51_K	1.484	1.00
35_L	39_T	1.451	1.00
41_D	44_A	1.434	1.00
48_E	51_K	1.424	1.00
17_H	35_L	1.366	1.00
51_K	54_L	1.364	1.00
8_L	12_T	1.352	1.00
47_E	59_E	1.315	1.00
44_A	48_E	1.289	1.00
22_P	29_P	1.266	1.00
9_S	13_Q	1.247	1.00
68_E	72_R	1.210	1.00
6_L	10_L	1.203	1.00
47_E	70_R	1.167	1.00
4_S	61_L	1.153	1.00
14_A	39_T	1.143	1.00
23_D	27_G	1.112	1.00
37_R	41_D	1.105	1.00
2_D	5_T	1.087	1.00
38_Q	42_L	1.049	1.00
23_D	30_E	1.049	1.00
44_A	47_E	1.028	1.00
67_Y	70_R	1.018	1.00
39_T	42_L	1.017	1.00
51_K	59_E	0.993	1.00
6_L	45_M	0.990	1.00
15_L	20_E	0.979	1.00
6_L	42_L	0.946	1.00
43_L	62_L	0.945	1.00
13_Q	39_T	0.943	1.00
26_T	30_E	0.935	1.00
66_L	70_R	0.930	1.00
57_E	60_R	0.921	1.00
13_Q	16_M	0.902	1.00
13_Q	17_H	0.895	1.00
50_T	53_N	0.890	1.00
44_A	66_L	0.885	1.00
5_T	8_L	0.881	1.00
55_T	58_E	0.873	1.00
49_K	58_E	0.873	1.00
11_A	15_L	0.861	1.00
45_M	49_K	0.860	1.00
5_T	9_S	0.830	1.00
15_L	72_R	0.824	1.00
3_F	54_L	0.823	1.00
3_F	7_V	0.821	1.00
35_L	38_Q	0.795	1.00
60_R	63_E	0.793	1.00
12_T	16_M	0.790	1.00
22_P	28_K	0.782	1.00
4_S	8_L	0.743	1.00
10_L	39_T	0.740	1.00
14_A	69_L	0.738	1.00
13_Q	35_L	0.703	1.00
26_T	29_P	0.701	1.00
7_V	43_L	0.692	1.00
50_T	54_L	0.689	1.00
4_S	57_E	0.682	1.00
6_L	46_L	0.674	1.00
18_L	36_A	0.673	1.00
8_L	11_A	0.669	1.00
42_L	45_M	0.664	1.00
14_A	18_L	0.654	1.00
42_L	46_L	0.646	1.00
11_A	68_E	0.641	1.00
63_E	67_Y	0.637	1.00
65_V	68_E	0.629	1.00
22_P	26_T	0.615	1.00
9_S	16_M	0.603	1.00
15_L	21_I	0.592	1.00
7_V	65_V	0.589	1.00
34_E	37_R	0.588	1.00
10_L	42_L	0.584	1.00
12_T	21_I	0.583	1.00
19_G	32_D	0.582	1.00
2_D	6_L	0.579	1.00
25_E	28_K	0.574	1.00
47_E	54_L	0.573	1.00
19_G	36_A	0.563	1.00
5_T	38_Q	0.551	1.00
3_F	62_L	0.546	1.00
61_L	65_V	0.541	1.00
12_T	15_L	0.536	1.00
18_L	33_L	0.532	1.00
54_L	62_L	0.522	1.00
33_L	73_Y	0.521	1.00
47_E	62_L	0.520	1.00
7_V	62_L	0.514	1.00
9_S	12_T	0.509	1.00
43_L	66_L	0.506	1.00
54_L	58_E	0.505	1.00
16_M	25_E	0.505	1.00
13_Q	38_Q	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
3nwzA	3	0.4247	10.9	0.875	Contact Map
3j60S	1	0.9589	9.2	0.878	Contact Map
4ga6A	2	0.9315	9.1	0.879	Contact Map
3kp7A	2	0.8767	8.9	0.879	Contact Map
2wh5A	1	0.6027	8.3	0.881	Contact Map
2h5nA	5	0.7123	6.9	0.885	Contact Map
3u0hA	3	0.6849	6.8	0.885	Contact Map
2ou3A	2	0.863	6.5	0.886	Contact Map
3bddA	2	0.9726	6.2	0.888	Contact Map
3j38S	1	0.8904	6.1	0.888	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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