DUF4278 - PFAM28P - GREMLIN Contacts

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DUF4278 - Domain of unknown function (DUF4278)

PFAM:	PF14105	Sequences: MTLTYRGVSYEQHKEAVEKTEVEILTYRGNHYRTRRAKAAPELQPSVELTYRGVAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (56)
Sequences:	1801 (1348)
Seq/√Len:	180.1
META:	0.832

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_L	32_Y	3.932	1.00
50_T	55_A	3.654	1.00
49_L	56_Y	2.190	1.00
17_V	20_T	1.689	1.00
21_E	33_R	1.644	1.00
2_T	11_E	1.614	1.00
27_Y	30_N	1.604	1.00
19_K	37_A	1.601	1.00
36_R	39_A	1.550	1.00
2_T	9_S	1.545	1.00
6_R	28_R	1.539	1.00
16_A	19_K	1.538	1.00
1_M	4_T	1.468	1.00
18_E	21_E	1.368	1.00
25_L	34_T	1.313	1.00
20_T	23_E	1.305	1.00
19_K	35_R	1.298	1.00
11_E	14_K	1.290	1.00
3_L	10_Y	1.281	1.00
26_T	31_H	1.265	1.00
32_Y	36_R	1.216	1.00
19_K	23_E	1.207	1.00
5_Y	8_V	1.201	1.00
2_T	10_Y	1.156	1.00
1_M	29_G	1.153	1.00
41_P	44_Q	1.150	1.00
17_V	21_E	1.105	1.00
31_H	36_R	1.020	0.99
37_A	41_P	0.982	0.99
42_E	45_P	0.974	0.99
27_Y	51_Y	0.947	0.99
24_I	32_Y	0.941	0.99
8_V	11_E	0.937	0.99
45_P	54_V	0.926	0.99
28_R	53_G	0.920	0.99
39_A	42_E	0.904	0.99
43_L	46_S	0.902	0.99
48_E	55_A	0.884	0.98
4_T	8_V	0.883	0.98
8_V	30_N	0.866	0.98
36_R	40_A	0.861	0.98
31_H	35_R	0.855	0.98
9_S	14_K	0.834	0.98
23_E	34_T	0.832	0.98
32_Y	37_A	0.821	0.98
19_K	24_I	0.819	0.98
28_R	52_R	0.788	0.97
19_K	22_V	0.763	0.96
4_T	21_E	0.755	0.96
6_R	27_Y	0.755	0.96
12_Q	47_V	0.746	0.96
2_T	8_V	0.740	0.95
8_V	54_V	0.732	0.95
40_A	43_L	0.731	0.95
53_G	56_Y	0.719	0.95
4_T	9_S	0.691	0.94
31_H	34_T	0.680	0.93
18_E	39_A	0.676	0.93
38_K	41_P	0.665	0.92
24_I	47_V	0.663	0.92
33_R	43_L	0.662	0.92
16_A	20_T	0.662	0.92
4_T	13_H	0.645	0.91
37_A	54_V	0.643	0.91
15_E	24_I	0.641	0.91
43_L	54_V	0.639	0.91
2_T	28_R	0.621	0.89
29_G	38_K	0.620	0.89
29_G	36_R	0.618	0.89
37_A	44_Q	0.602	0.88
11_E	35_R	0.589	0.87
1_M	25_L	0.583	0.86
3_L	9_S	0.572	0.85
21_E	54_V	0.568	0.85
10_Y	52_R	0.559	0.84
44_Q	47_V	0.555	0.83
6_R	52_R	0.546	0.82
3_L	56_Y	0.545	0.82
3_L	49_L	0.527	0.80
48_E	56_Y	0.511	0.78
25_L	28_R	0.502	0.77
9_S	38_K	0.502	0.77
8_V	17_V	0.501	0.77
33_R	36_R	0.500	0.77

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
1ea5A	2	0.5714	13.6	0.815	Contact Map
2h7cA	4	0.625	10.6	0.823	Contact Map
4fnmA	2	0.8571	10.1	0.825	Contact Map
1p0iA	2	0.5357	9.2	0.828	Contact Map
1thgA	1	0.5	9.2	0.828	Contact Map
1qe3A	1	0.5	9.1	0.829	Contact Map
4m0eA	2	0.6071	8.4	0.831	Contact Map
1llfA	2	0.4821	8.1	0.832	Contact Map
2ogtA	1	0.4821	8	0.833	Contact Map
4qwwA	2	0.5893	7.6	0.835	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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