UPF0126 - PFAM28P - GREMLIN Contacts

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UPF0126 - UPF0126 domain

PFAM:	PF03458	Sequences: LVLDALGLAAFAVSGALKALRLDLFGAVVLGVVTAVGGGTLRDVLLGREVPVVLRRDLYATAALAGALVVFLLAH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (71)
Sequences:	33689 (15644)
Seq/√Len:	1856.6
META:	0.856

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_L	26_G	2.914	1.00
40_T	54_L	2.807	1.00
16_A	27_A	2.307	1.00
17_L	21_R	2.286	1.00
9_A	66_G	2.044	1.00
5_A	8_L	1.853	1.00
63_A	67_A	1.827	1.00
47_G	50_V	1.799	1.00
50_V	55_R	1.787	1.00
23_D	26_G	1.701	1.00
14_S	17_L	1.599	1.00
52_V	55_R	1.549	1.00
24_L	71_F	1.491	1.00
28_V	68_L	1.487	1.00
7_G	11_F	1.481	1.00
18_K	21_R	1.435	1.00
6_L	10_A	1.420	1.00
12_A	63_A	1.420	1.00
12_A	67_A	1.389	1.00
33_V	37_G	1.389	1.00
26_G	30_L	1.381	1.00
12_A	16_A	1.369	1.00
20_L	27_A	1.343	1.00
40_T	53_V	1.328	1.00
52_V	56_R	1.305	1.00
15_G	19_A	1.276	1.00
16_A	31_G	1.268	1.00
58_L	61_T	1.251	1.00
61_T	65_A	1.232	1.00
51_P	54_L	1.218	1.00
44_V	47_G	1.214	1.00
64_L	68_L	1.207	1.00
62_A	66_G	1.174	1.00
32_V	36_V	1.118	1.00
9_A	13_V	1.109	1.00
68_L	72_L	1.105	1.00
15_G	34_T	1.097	1.00
10_A	14_S	1.082	1.00
28_V	67_A	1.068	1.00
4_D	11_F	1.067	1.00
28_V	64_L	1.041	1.00
17_L	70_V	1.033	1.00
16_A	70_V	1.027	1.00
19_A	22_L	1.022	1.00
13_V	70_V	1.018	1.00
19_A	27_A	0.999	1.00
11_F	14_S	0.949	1.00
27_A	71_F	0.944	1.00
31_G	67_A	0.916	1.00
36_V	63_A	0.902	1.00
37_G	41_L	0.901	1.00
16_A	67_A	0.898	1.00
53_V	56_R	0.895	1.00
32_V	60_A	0.848	1.00
28_V	32_V	0.833	1.00
67_A	71_F	0.825	1.00
50_V	54_L	0.820	1.00
48_R	51_P	0.817	1.00
50_V	56_R	0.812	1.00
19_A	30_L	0.808	1.00
58_L	62_A	0.787	1.00
11_F	35_A	0.740	1.00
5_A	58_L	0.728	1.00
47_G	51_P	0.726	1.00
14_S	18_K	0.715	1.00
41_L	45_L	0.715	1.00
30_L	33_V	0.709	1.00
54_L	57_D	0.700	1.00
59_Y	62_A	0.699	1.00
65_A	68_L	0.698	1.00
14_S	34_T	0.696	1.00
70_V	73_L	0.685	1.00
28_V	71_F	0.673	1.00
32_V	63_A	0.667	1.00
52_V	57_D	0.666	1.00
66_G	70_V	0.635	1.00
24_L	28_V	0.634	1.00
25_F	29_V	0.621	1.00
48_R	53_V	0.592	1.00
18_K	30_L	0.589	1.00
41_L	44_V	0.585	1.00
30_L	34_T	0.584	1.00
65_A	69_V	0.566	1.00
60_A	70_V	0.562	1.00
14_S	30_L	0.561	1.00
5_A	62_A	0.553	1.00
6_L	9_A	0.549	1.00
8_L	11_F	0.545	1.00
47_G	52_V	0.545	1.00
8_L	63_A	0.533	1.00
40_T	44_V	0.528	1.00
5_A	9_A	0.526	1.00
59_Y	63_A	0.525	1.00
4_D	59_Y	0.525	1.00
2_V	5_A	0.525	1.00
40_T	52_V	0.523	1.00
62_A	65_A	0.521	1.00
16_A	19_A	0.515	1.00
11_F	18_K	0.511	1.00
22_L	25_F	0.510	1.00
19_A	26_G	0.510	1.00
16_A	20_L	0.508	1.00
48_R	55_R	0.503	1.00
20_L	71_F	0.502	1.00
26_G	29_V	0.501	1.00
4_D	8_L	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
4wbyA	1	0.7067	4.9	0.87	Contact Map
1miwA	2	0.68	4.9	0.87	Contact Map
3wfpA	2	0.7333	3.4	0.879	Contact Map
3orgA	2	0.8	3.2	0.881	Contact Map
4x4wA	2	0.6933	2.7	0.885	Contact Map
3aqlA	2	0.6533	2.4	0.888	Contact Map
3rceA	1	0.9867	2.3	0.889	Contact Map
3h38A	1	0.84	2	0.893	Contact Map
3wfsC	1	0.7333	2	0.893	Contact Map
3wfrE	1	0.7333	1.9	0.894	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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