UPF0016 - PFAM28P - GREMLIN Contacts

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UPF0016 - Uncharacterized protein family UPF0016

PFAM:	PF01169	Sequences: LTSFGAVFLAELGDKTQLATLALAARYRPLPVFLGATLALLLAHALAVLLGAALARRLPPRLLRLVAAALFLAFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (74)
Sequences:	32477 (16676)
Seq/√Len:	1938.5
META:	0.909

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_L	65_L	3.047	1.00
61_R	65_L	2.898	1.00
20_T	36_A	2.502	1.00
53_A	57_R	2.461	1.00
28_R	31_P	2.403	1.00
37_T	41_L	2.176	1.00
59_P	62_L	2.131	1.00
60_P	64_R	2.127	1.00
69_A	73_A	2.054	1.00
62_L	66_V	2.049	1.00
52_A	56_R	2.001	1.00
50_L	53_A	1.977	1.00
65_L	69_A	1.888	1.00
43_A	47_A	1.877	1.00
40_L	44_H	1.522	1.00
68_A	72_L	1.522	1.00
53_A	56_R	1.478	1.00
49_L	53_A	1.405	1.00
30_L	34_L	1.401	1.00
36_A	40_L	1.378	1.00
2_T	6_A	1.344	1.00
31_P	35_G	1.326	1.00
13_G	17_Q	1.313	1.00
5_G	9_L	1.296	1.00
23_L	35_G	1.203	1.00
45_A	49_L	1.195	1.00
11_E	14_D	1.115	1.00
49_L	52_A	1.111	1.00
34_L	38_L	1.088	1.00
8_F	12_L	1.088	1.00
46_L	49_L	1.065	1.00
61_R	64_R	1.050	1.00
63_L	67_A	1.046	1.00
39_A	43_A	1.035	1.00
18_L	22_A	1.006	1.00
67_A	70_L	1.002	1.00
38_L	41_L	1.000	1.00
70_L	74_F	0.995	1.00
38_L	42_L	0.975	1.00
65_L	68_A	0.964	1.00
60_P	63_L	0.958	1.00
66_V	70_L	0.958	1.00
52_A	55_A	0.934	1.00
19_A	22_A	0.930	1.00
66_V	69_A	0.930	1.00
28_R	32_V	0.928	1.00
33_F	37_T	0.918	1.00
12_L	15_K	0.908	1.00
2_T	5_G	0.899	1.00
11_E	16_T	0.893	1.00
5_G	8_F	0.886	1.00
31_P	34_L	0.883	1.00
3_S	23_L	0.874	1.00
50_L	54_L	0.869	1.00
72_L	75_G	0.866	1.00
4_F	8_F	0.865	1.00
12_L	21_L	0.849	1.00
27_Y	32_V	0.834	1.00
3_S	7_V	0.805	1.00
20_T	24_A	0.787	1.00
63_L	66_V	0.765	1.00
42_L	45_A	0.756	1.00
12_L	17_Q	0.741	1.00
55_A	59_P	0.726	1.00
64_R	67_A	0.713	1.00
32_V	35_G	0.703	1.00
23_L	32_V	0.689	1.00
43_A	46_L	0.682	1.00
35_G	39_A	0.676	1.00
32_V	36_A	0.666	1.00
42_L	46_L	0.661	1.00
67_A	71_F	0.656	1.00
29_P	33_F	0.648	1.00
41_L	44_H	0.648	1.00
54_L	58_L	0.647	1.00
30_L	33_F	0.640	1.00
58_L	62_L	0.635	1.00
6_A	10_A	0.624	1.00
24_A	27_Y	0.620	1.00
26_R	29_P	0.610	1.00
55_A	63_L	0.605	1.00
57_R	62_L	0.604	1.00
12_L	16_T	0.604	1.00
54_L	57_R	0.600	1.00
22_A	26_R	0.596	1.00
55_A	60_P	0.592	1.00
17_Q	33_F	0.589	1.00
50_L	55_A	0.587	1.00
46_L	50_L	0.587	1.00
64_R	71_F	0.583	1.00
21_L	43_A	0.579	1.00
48_V	52_A	0.577	1.00
15_K	19_A	0.574	1.00
59_P	63_L	0.571	1.00
23_L	26_R	0.559	1.00
3_S	6_A	0.556	1.00
46_L	74_F	0.546	1.00
71_F	74_F	0.545	1.00
20_T	23_L	0.544	1.00
19_A	71_F	0.537	1.00
47_A	50_L	0.536	1.00
18_L	44_H	0.535	1.00
7_V	44_H	0.530	1.00
4_F	7_V	0.524	1.00
15_K	18_L	0.522	1.00
52_A	60_P	0.513	1.00
15_K	24_A	0.510	1.00
7_V	11_E	0.502	1.00
22_A	25_A	0.502	1.00
20_T	40_L	0.501	1.00
33_F	36_A	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
4ymuD	2	0.7867	3.1	0.882	Contact Map
1q90G	1	0.4	1.1	0.908	Contact Map
4oh3A	2	0.9867	1.1	0.909	Contact Map
1rh1A	1	0.8533	1	0.91	Contact Map
4hlsA	2	0.2267	1	0.911	Contact Map
4j05A	3	1	0.9	0.912	Contact Map
4uvmA	1	0.9867	0.9	0.913	Contact Map
4k0jA	3	0.32	0.9	0.915	Contact Map
4tphA	2	1	0.8	0.916	Contact Map
3tuiA	2	0.7867	0.8	0.916	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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