YAZA - BACSU - GREMLIN Contacts

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YAZA - UPF0213 protein YazA

UniProt:	O31414	Sequences: METNNHFFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELYIEEKRNSKEAVYVKAPNEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	99 (81)
Sequences:	2253 (1721)
Seq/√Len:	191.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_K	32_T	2.869	1.00
20_A	69_F	2.368	1.00
54_E	65_A	2.339	1.00
58_T	61_E	2.312	1.00
10_V	20_A	2.225	1.00
67_Y	71_K	2.188	1.00
6_H	22_Y	2.148	1.00
12_K	49_E	2.139	1.00
22_Y	63_M	2.042	1.00
65_A	68_Y	1.990	1.00
17_S	41_Y	1.929	1.00
26_L	53_A	1.878	1.00
31_K	35_D	1.851	1.00
73_T	76_K	1.760	1.00
60_R	64_Q	1.662	1.00
30_V	34_N	1.654	1.00
11_V	30_V	1.567	1.00
15_D	45_R	1.565	1.00
18_W	78_E	1.562	1.00
12_K	51_I	1.551	1.00
8_F	69_F	1.496	1.00
59_K	63_M	1.474	1.00
39_A	43_K	1.445	1.00
74_R	78_E	1.438	1.00
12_K	16_N	1.431	1.00
6_H	59_K	1.318	1.00
34_N	48_V	1.289	1.00
10_V	69_F	1.287	1.00
72_L	76_K	1.234	1.00
36_G	46_R	1.228	1.00
22_Y	59_K	1.211	1.00
79_L	83_E	1.208	1.00
78_E	82_E	1.164	1.00
64_Q	68_Y	1.162	1.00
30_V	50_L	1.138	1.00
13_C	41_Y	1.077	1.00
56_F	65_A	1.068	1.00
12_K	78_E	1.067	1.00
13_C	47_P	1.064	1.00
42_T	47_P	1.043	1.00
36_G	48_V	1.042	1.00
75_K	79_L	1.036	1.00
76_K	79_L	1.024	1.00
51_I	81_I	1.014	1.00
5_N	55_S	1.009	1.00
26_L	50_L	0.995	0.99
65_A	80_Y	0.993	0.99
8_F	20_A	0.991	0.99
52_F	65_A	0.990	0.99
23_T	26_L	0.970	0.99
60_R	63_M	0.926	0.99
34_N	46_R	0.915	0.99
24_N	28_K	0.909	0.99
56_F	61_E	0.877	0.99
30_V	48_V	0.866	0.99
20_A	77_K	0.865	0.99
13_C	42_T	0.845	0.98
32_T	37_K	0.836	0.98
6_H	24_N	0.834	0.98
69_F	80_Y	0.816	0.98
68_Y	72_L	0.811	0.98
52_F	80_Y	0.801	0.98
10_V	52_F	0.783	0.97
63_M	67_Y	0.774	0.97
25_D	28_K	0.760	0.97
11_V	47_P	0.747	0.96
70_K	77_K	0.747	0.96
13_C	17_S	0.742	0.96
7_F	55_S	0.736	0.96
11_V	34_N	0.731	0.96
15_D	41_Y	0.719	0.96
11_V	42_T	0.687	0.94
17_S	45_R	0.683	0.94
14_K	46_R	0.674	0.94
26_L	30_V	0.672	0.94
32_T	46_R	0.664	0.93
18_W	81_I	0.663	0.93
7_F	53_A	0.662	0.93
24_N	32_T	0.661	0.93
12_K	18_W	0.659	0.93
8_F	80_Y	0.652	0.93
42_T	45_R	0.649	0.92
74_R	81_I	0.645	0.92
57_S	61_E	0.644	0.92
71_K	76_K	0.639	0.92
54_E	80_Y	0.638	0.92
40_K	43_K	0.636	0.92
75_K	78_E	0.634	0.92
82_E	85_R	0.634	0.92
8_F	56_F	0.629	0.91
22_Y	32_T	0.626	0.91
11_V	48_V	0.622	0.91
14_K	34_N	0.615	0.90
73_T	79_L	0.604	0.89
31_K	37_K	0.602	0.89
7_F	59_K	0.602	0.89
38_G	43_K	0.598	0.89
10_V	18_W	0.593	0.89
51_I	80_Y	0.593	0.89
63_M	70_K	0.591	0.88
13_C	45_R	0.589	0.88
6_H	63_M	0.589	0.88
8_F	22_Y	0.581	0.88
20_A	72_L	0.573	0.87
34_N	45_R	0.572	0.87
41_Y	44_V	0.562	0.86
27_H	53_A	0.558	0.85
36_G	43_K	0.553	0.85
42_T	48_V	0.553	0.85
39_A	42_T	0.548	0.84
72_L	80_Y	0.542	0.84
67_Y	70_K	0.542	0.84
27_H	84_K	0.541	0.84
24_N	59_K	0.539	0.83
54_E	68_Y	0.536	0.83
37_K	40_K	0.533	0.83
24_N	63_M	0.529	0.82
14_K	45_R	0.521	0.81
43_K	46_R	0.512	0.80
27_H	55_S	0.509	0.80
68_Y	76_K	0.501	0.79
23_T	28_K	0.500	0.79

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
1zg2A	1	0.9495	100	0.201	Contact Map
1ywlA	1	0.9394	100	0.228	Contact Map
4xlgA	1	0.7778	99.9	0.358	Contact Map
1mk0A	1	0.8586	97.5	0.796	Contact Map
1yd0A	1	0.7879	97.4	0.798	Contact Map
1yd6A	5	0.8485	96.9	0.815	Contact Map
2wshA	4	0.7879	79	0.885	Contact Map
4zcfA	2	0.7576	16.7	0.926	Contact Map
4gbsA	1	0.3939	9.6	0.934	Contact Map
3u22A	4	0.4242	8.3	0.936	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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