Multi_ubiq - PFAM28P - GREMLIN Contacts

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Multi_ubiq - Multiubiquitin

PFAM:	PF14452	Sequences: YTIIVNGRPYEVPKPTITGAEIVALAGPPPPDDPLLLETVTYGPDGTIGDGESVDLKEPGMEFFVTATD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (65)
Sequences:	8502 (6514)
Seq/√Len:	808.0
META:	0.93

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_V	17_I	2.939	1.00
23_V	50_D	2.808	1.00
16_T	53_S	2.399	1.00
49_G	52_E	2.337	1.00
20_A	50_D	2.331	1.00
19_G	48_I	2.294	1.00
2_T	11_E	2.232	1.00
2_T	9_P	2.198	1.00
17_I	56_L	1.967	1.00
16_T	55_D	1.862	1.00
3_I	12_V	1.822	1.00
20_A	24_A	1.748	1.00
14_K	21_E	1.704	1.00
4_I	9_P	1.654	1.00
14_K	17_I	1.605	1.00
46_G	52_E	1.595	1.00
12_V	25_L	1.550	1.00
15_P	57_K	1.491	1.00
18_T	53_S	1.388	1.00
17_I	21_E	1.369	1.00
21_E	24_A	1.367	1.00
19_G	51_G	1.284	1.00
10_Y	25_L	1.257	1.00
5_V	26_A	1.250	1.00
20_A	51_G	1.247	1.00
15_P	55_D	1.225	1.00
6_N	66_T	1.096	1.00
23_V	28_P	1.095	1.00
48_I	52_E	1.090	1.00
48_I	54_V	1.087	1.00
18_T	21_E	1.002	1.00
4_I	62_E	0.990	1.00
24_A	29_P	0.988	1.00
36_L	47_T	0.986	1.00
33_D	36_L	0.984	1.00
6_N	33_D	0.973	1.00
12_V	56_L	0.951	1.00
5_V	22_I	0.948	1.00
16_T	57_K	0.942	1.00
4_I	7_G	0.900	1.00
36_L	39_T	0.881	1.00
3_I	25_L	0.874	1.00
35_L	47_T	0.872	1.00
29_P	32_D	0.870	1.00
56_L	61_M	0.865	1.00
30_P	33_D	0.783	1.00
6_N	28_P	0.782	1.00
6_N	26_A	0.746	1.00
17_I	22_I	0.743	1.00
8_R	27_G	0.737	1.00
19_G	23_V	0.733	1.00
35_L	39_T	0.697	1.00
59_P	62_E	0.688	1.00
55_D	59_P	0.685	1.00
5_V	10_Y	0.670	1.00
38_E	54_V	0.669	1.00
24_A	30_P	0.668	1.00
3_I	10_Y	0.666	1.00
35_L	41_T	0.664	1.00
32_D	35_L	0.664	1.00
2_T	59_P	0.660	1.00
43_G	61_M	0.659	1.00
41_T	64_F	0.654	1.00
35_L	40_V	0.648	1.00
55_D	60_G	0.643	1.00
17_I	25_L	0.641	1.00
10_Y	26_A	0.640	1.00
34_P	47_T	0.640	1.00
4_I	63_F	0.634	1.00
38_E	46_G	0.629	1.00
41_T	44_P	0.624	1.00
45_D	65_V	0.620	1.00
39_T	42_Y	0.614	1.00
20_A	30_P	0.613	1.00
19_G	22_I	0.613	1.00
14_K	56_L	0.603	1.00
37_L	47_T	0.595	1.00
19_G	50_D	0.593	1.00
36_L	40_V	0.578	1.00
10_Y	29_P	0.569	1.00
57_K	61_M	0.560	1.00
21_E	53_S	0.559	1.00
4_I	61_M	0.555	1.00
28_P	31_P	0.545	1.00
40_V	44_P	0.543	1.00
22_I	63_F	0.543	1.00
39_T	43_G	0.542	1.00
37_L	45_D	0.541	1.00
31_P	34_P	0.540	1.00
24_A	27_G	0.535	1.00
37_L	41_T	0.534	1.00
22_I	26_A	0.532	1.00
28_P	66_T	0.529	1.00
24_A	28_P	0.527	1.00
37_L	67_A	0.513	1.00
54_V	63_F	0.509	1.00
43_G	55_D	0.509	1.00
37_L	65_V	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
1tygB	1	0.7971	36.8	0.79	Contact Map
2cu3A	2	0.7971	33.9	0.794	Contact Map
2lekA	1	0.8841	29.4	0.8	Contact Map
1f0zA	1	0.8261	24.6	0.808	Contact Map
2k5pA	1	0.8986	21.3	0.813	Contact Map
1ryjA	1	0.8261	17.6	0.821	Contact Map
4mmhA	1	0.3043	9.8	0.84	Contact Map
2kmmA	1	0.8986	9.4	0.841	Contact Map
1wwtA	1	0.913	8.9	0.843	Contact Map
2zxqA	1	0.913	7.4	0.848	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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