UPF0154 - PFAM28P - GREMLIN Contacts

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UPF0154 - Uncharacterised protein family (UPF0154)

PFAM:	PF03672	Sequences: IILGLIVGAVIGFFIARKYMKKYLKKNPPINEKMIRAMMMQMGRKPSEKQINQMMKSMKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (59)
Sequences:	1183 (550)
Seq/√Len:	71.6
META:	0.678

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_R	50_Q	3.081	1.00
22_K	26_K	2.843	1.00
36_R	48_E	2.349	1.00
48_E	52_N	2.226	1.00
11_I	15_I	2.145	1.00
18_K	21_K	2.048	1.00
8_G	12_G	1.955	1.00
40_M	45_K	1.947	1.00
56_K	59_K	1.806	1.00
15_I	19_Y	1.688	1.00
17_R	21_K	1.661	1.00
33_K	36_R	1.534	0.99
50_Q	53_Q	1.519	0.99
41_Q	57_S	1.465	0.99
35_I	54_M	1.358	0.98
12_G	16_A	1.329	0.98
39_M	51_I	1.294	0.97
36_R	52_N	1.246	0.97
20_M	23_Y	1.234	0.96
15_I	18_K	1.168	0.95
37_A	40_M	1.163	0.95
41_Q	54_M	1.135	0.94
54_M	57_S	1.135	0.94
9_A	15_I	1.104	0.93
35_I	51_I	1.096	0.93
16_A	20_M	1.067	0.92
32_E	52_N	1.066	0.92
7_V	10_V	1.057	0.92
31_N	34_M	1.043	0.91
49_K	53_Q	0.994	0.89
18_K	22_K	0.971	0.88
5_L	12_G	0.949	0.87
39_M	46_P	0.943	0.86
5_L	8_G	0.935	0.86
40_M	51_I	0.921	0.85
3_L	7_V	0.920	0.85
18_K	26_K	0.910	0.84
45_K	49_K	0.905	0.84
33_K	37_A	0.890	0.83
33_K	52_N	0.875	0.82
52_N	56_K	0.867	0.81
11_I	14_F	0.844	0.80
38_M	42_M	0.834	0.79
36_R	45_K	0.802	0.76
10_V	14_F	0.801	0.76
38_M	54_M	0.800	0.76
32_E	55_M	0.799	0.76
47_S	51_I	0.785	0.74
39_M	54_M	0.784	0.74
27_N	31_N	0.780	0.74
35_I	39_M	0.768	0.73
33_K	39_M	0.763	0.72
25_K	59_K	0.762	0.72
23_Y	26_K	0.738	0.70
4_G	8_G	0.735	0.69
56_K	60_K	0.734	0.69
37_A	41_Q	0.711	0.67
34_M	58_M	0.708	0.67
19_Y	23_Y	0.698	0.65
39_M	49_K	0.691	0.65
21_K	25_K	0.683	0.64
39_M	57_S	0.653	0.60
17_R	34_M	0.648	0.60
30_I	34_M	0.648	0.60
39_M	58_M	0.645	0.59
10_V	15_I	0.642	0.59
11_I	18_K	0.636	0.58
9_A	12_G	0.636	0.58
23_Y	49_K	0.636	0.58
53_Q	56_K	0.635	0.58
5_L	11_I	0.634	0.58
4_G	7_V	0.620	0.56
23_Y	39_M	0.619	0.56
5_L	9_A	0.606	0.55
16_A	23_Y	0.594	0.53
19_Y	51_I	0.592	0.53
21_K	24_L	0.590	0.53
16_A	21_K	0.566	0.50
46_P	51_I	0.563	0.49
13_F	19_Y	0.558	0.49
6_I	9_A	0.550	0.48
2_I	5_L	0.543	0.47
31_N	59_K	0.535	0.46
16_A	19_Y	0.527	0.45
14_F	18_K	0.527	0.45
21_K	51_I	0.526	0.45
3_L	18_K	0.508	0.43
28_P	42_M	0.500	0.42

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
4n5xA	1	0.7333	24.8	0.871	Contact Map
4wl1A	3	0	24.6	0.871	Contact Map
2i7aA	2	0.6333	22.9	0.873	Contact Map
2kldA	1	0	22.9	0.873	Contact Map
3zg1A	2	0.45	21.4	0.875	Contact Map
1bu3A	2	0.3333	18.8	0.878	Contact Map
1rroA	1	0.3333	18.6	0.878	Contact Map
5palA	1	0.3333	18.1	0.879	Contact Map
3qnqA	2	0.5833	16.8	0.881	Contact Map
2rsyB	1	0.6333	16	0.882	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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