YNEP - BACSU - GREMLIN Contacts

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YNEP - Putative acyl-CoA thioesterase YneP

UniProt:	Q45061	Sequences: MHVSKKEIEVRYAETDQMGIVYHANYLVWMEVGRTALIKDLGFLYSDMEKKGVLSPVVDINISYKKPLHYGETAVVHTWIEDYNGFKTVYGYHIYNPAGELSIKATSSHICVDKESFKPIQFRKAFPDWHTAYEKAKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	138 (128)
Sequences:	6483 (4705)
Seq/√Len:	415.8

ECOLI - YBGC FADM
BACSU - YNEP YSMA
HALSA - Q9HPZ1
SULSO - Q97WD2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_D	63_S	3.179	1.00
81_E	91_G	2.544	1.00
66_K	100_E	2.340	1.00
5_K	75_V	2.325	1.00
30_M	105_A	2.275	1.00
68_L	102_S	2.222	1.00
65_K	104_K	2.208	1.00
61_N	106_T	2.201	1.00
68_L	74_A	2.145	1.00
5_K	77_H	2.120	1.00
25_N	28_V	2.057	1.00
7_E	73_T	2.033	1.00
27_L	60_I	1.976	1.00
30_M	103_I	1.926	1.00
113_D	116_S	1.850	1.00
7_E	75_V	1.821	1.00
82_D	89_V	1.806	1.00
77_H	95_Y	1.789	1.00
77_H	93_H	1.780	1.00
95_Y	101_L	1.660	1.00
79_W	91_G	1.657	1.00
27_L	62_I	1.648	1.00
54_L	114_K	1.633	1.00
124_K	128_D	1.630	1.00
93_H	101_L	1.609	1.00
30_M	94_I	1.552	1.00
63_S	104_K	1.523	1.00
89_V	106_T	1.514	1.00
62_I	103_I	1.485	1.00
92_Y	107_S	1.463	1.00
72_E	96_N	1.457	1.00
91_G	106_T	1.454	1.00
9_E	73_T	1.443	1.00
76_V	94_I	1.419	1.00
93_H	104_K	1.416	1.00
21_V	29_W	1.396	1.00
86_F	119_P	1.382	1.00
9_E	39_K	1.369	1.00
123_R	126_F	1.359	1.00
9_E	36_A	1.343	1.00
96_N	100_E	1.309	1.00
36_A	40_D	1.295	1.00
84_N	87_K	1.291	1.00
67_P	117_F	1.286	1.00
58_V	63_S	1.285	1.00
96_N	102_S	1.282	1.00
81_E	106_T	1.280	1.00
73_T	97_P	1.270	1.00
127_P	131_T	1.270	1.00
33_G	78_T	1.260	1.00
13_A	28_V	1.224	1.00
47_D	50_K	1.220	1.00
87_K	108_S	1.218	1.00
7_E	97_P	1.208	1.00
60_I	107_S	1.207	1.00
44_L	47_D	1.193	1.00
112_V	117_F	1.170	1.00
11_R	14_E	1.161	1.00
10_V	21_V	1.124	1.00
14_E	28_V	1.124	1.00
31_E	34_R	1.117	1.00
33_G	76_V	1.109	1.00
85_G	121_Q	1.089	1.00
95_Y	99_G	1.087	1.00
89_V	108_S	1.084	1.00
39_K	71_G	1.071	1.00
113_D	120_I	1.064	1.00
56_P	112_V	1.047	1.00
65_K	101_L	1.030	1.00
24_A	28_V	1.025	1.00
53_V	111_C	1.023	1.00
86_F	110_I	1.019	1.00
75_V	97_P	1.014	1.00
59_D	108_S	1.013	1.00
79_W	93_H	1.003	1.00
47_D	51_K	0.984	1.00
8_I	76_V	0.964	1.00
101_L	104_K	0.960	1.00
23_H	60_I	0.936	1.00
81_E	89_V	0.933	1.00
124_K	127_P	0.927	1.00
4_S	78_T	0.903	1.00
74_A	102_S	0.896	1.00
58_V	108_S	0.885	1.00
46_S	50_K	0.882	1.00
51_K	125_A	0.868	1.00
125_A	128_D	0.862	1.00
18_M	56_P	0.859	1.00
22_Y	31_E	0.837	1.00
11_R	32_V	0.832	1.00
39_K	44_L	0.831	1.00
4_S	40_D	0.829	1.00
10_V	29_W	0.825	1.00
91_G	104_K	0.820	1.00
14_E	29_W	0.809	1.00
128_D	131_T	0.800	1.00
52_G	115_E	0.791	1.00
6_K	36_A	0.785	1.00
30_M	62_I	0.775	1.00
36_A	39_K	0.773	1.00
23_H	27_L	0.770	1.00
78_T	90_Y	0.764	1.00
23_H	64_Y	0.758	1.00
34_R	57_V	0.756	1.00
12_Y	15_T	0.755	1.00
86_F	121_Q	0.745	1.00
8_I	32_V	0.744	1.00
37_L	78_T	0.744	1.00
80_I	90_Y	0.744	1.00
34_R	92_Y	0.742	1.00
21_V	68_L	0.741	1.00
6_K	32_V	0.738	1.00
15_T	19_G	0.735	1.00
59_D	106_T	0.735	1.00
23_H	34_R	0.733	1.00
76_V	92_Y	0.731	1.00
60_I	105_A	0.730	1.00
78_T	92_Y	0.729	1.00
75_V	99_G	0.724	1.00
58_V	65_K	0.721	1.00
12_Y	17_Q	0.711	1.00
75_V	95_Y	0.708	1.00
29_W	74_A	0.706	1.00
9_E	71_G	0.703	1.00
8_I	29_W	0.703	1.00
18_M	22_Y	0.703	1.00
83_Y	130_H	0.700	1.00
28_V	31_E	0.699	1.00
11_R	28_V	0.686	1.00
69_H	117_F	0.681	1.00
6_K	33_G	0.675	1.00
92_Y	109_H	0.665	0.99
15_T	70_Y	0.660	0.99
85_G	127_P	0.656	0.99
26_Y	68_L	0.656	0.99
20_I	67_P	0.647	0.99
18_M	23_H	0.645	0.99
32_V	36_A	0.643	0.99
122_F	127_P	0.641	0.99
20_I	117_F	0.636	0.99
46_S	49_E	0.634	0.99
63_S	106_T	0.631	0.99
88_T	122_F	0.630	0.99
20_I	56_P	0.630	0.99
114_K	117_F	0.629	0.99
37_L	80_I	0.628	0.99
83_Y	127_P	0.627	0.99
58_V	110_I	0.627	0.99
18_M	54_L	0.621	0.99
44_L	71_G	0.616	0.99
34_R	109_H	0.614	0.99
125_A	129_W	0.610	0.99
25_N	29_W	0.605	0.99
72_E	102_S	0.601	0.99
94_I	103_I	0.601	0.99
46_S	71_G	0.600	0.99
15_T	25_N	0.594	0.99
30_M	92_Y	0.590	0.99
124_K	131_T	0.590	0.99
13_A	22_Y	0.585	0.99
10_V	74_A	0.585	0.99
13_A	32_V	0.578	0.99
121_Q	124_K	0.576	0.98
12_Y	70_Y	0.575	0.98
127_P	130_H	0.569	0.98
87_K	110_I	0.568	0.98
84_N	127_P	0.566	0.98
37_L	41_L	0.564	0.98
87_K	127_P	0.564	0.98
34_R	90_Y	0.562	0.98
58_V	87_K	0.559	0.98
8_I	14_E	0.558	0.98
22_Y	25_N	0.554	0.98
55_S	111_C	0.554	0.98
14_E	25_N	0.553	0.98
53_V	120_I	0.552	0.98
34_R	107_S	0.544	0.98
57_V	107_S	0.534	0.98
60_I	64_Y	0.534	0.98
83_Y	88_T	0.528	0.97
120_I	126_F	0.527	0.97
111_C	122_F	0.527	0.97
12_Y	35_T	0.526	0.97
62_I	105_A	0.521	0.97
111_C	123_R	0.516	0.97
41_L	130_H	0.510	0.97
55_S	90_Y	0.509	0.97
110_I	119_P	0.505	0.97
82_D	108_S	0.503	0.96
55_S	122_F	0.502	0.96
41_L	129_W	0.501	0.96
90_Y	109_H	0.500	0.96

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
2essA	2	0.971	100	0.227	Contact Map
2ownA	3	1	100	0.237	Contact Map
2hljA	2	0.9783	100	0.26	Contact Map
4k00A	4	0.971	100	0.265	Contact Map
3ck1A	4	1	100	0.266	Contact Map
1njkA	4	0.9565	100	0.268	Contact Map
2w3xA	4	1	100	0.281	Contact Map
2hx5A	4	0.9638	100	0.285	Contact Map
3hm0A	4	0.8913	100	0.287	Contact Map
4gakA	2	0.9928	100	0.29	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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