FADM - ECOLI - GREMLIN Contacts

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FADM - Long-chain acyl-CoA thioesterase FadM

UniProt:	P77712	Sequences: MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLENSDSFQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13251
Length:	132 (124)
Sequences:	6497 (4709)
Seq/√Len:	422.9

ECOLI - FADM YBGC
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
55_N	59_N	3.291	1.00
77_Q	87_S	2.630	1.00
62_R	97_Q	2.412	1.00
27_L	102_A	2.371	1.00
64_A	99_V	2.269	1.00
57_N	103_L	2.248	1.00
110_D	113_T	2.239	1.00
61_R	101_D	2.191	1.00
64_A	70_L	2.131	1.00
22_R	25_E	1.980	1.00
24_L	56_I	1.966	1.00
73_T	89_V	1.945	1.00
78_Q	85_I	1.903	1.00
27_L	100_A	1.892	1.00
73_T	91_T	1.866	1.00
24_L	58_I	1.816	1.00
4_Q	69_L	1.808	1.00
92_L	95_E	1.795	1.00
75_Q	87_S	1.754	1.00
68_D	92_L	1.725	1.00
50_A	111_L	1.721	1.00
91_T	98_V	1.688	1.00
89_V	98_V	1.639	1.00
121_G	125_E	1.637	1.00
4_Q	71_T	1.616	1.00
18_V	26_F	1.567	1.00
6_K	69_L	1.550	1.00
59_N	101_D	1.549	1.00
58_I	100_A	1.533	1.00
27_L	90_I	1.531	1.00
85_I	103_L	1.526	1.00
72_I	90_I	1.496	1.00
88_Q	104_I	1.469	1.00
120_E	123_L	1.457	1.00
63_P	114_Q	1.449	1.00
82_K	116_A	1.446	1.00
92_L	97_Q	1.436	1.00
33_D	37_N	1.416	1.00
87_S	103_L	1.410	1.00
89_V	101_D	1.382	1.00
30_A	74_S	1.380	1.00
80_N	83_S	1.362	1.00
77_Q	103_L	1.358	1.00
124_R	128_E	1.305	1.00
6_K	36_E	1.305	1.00
6_K	33_D	1.291	1.00
92_L	99_V	1.258	1.00
30_A	72_I	1.251	1.00
10_Y	25_E	1.244	1.00
43_W	46_A	1.241	1.00
83_S	105_T	1.231	1.00
54_V	59_N	1.210	1.00
21_A	25_E	1.182	1.00
56_I	104_I	1.179	1.00
8_R	11_H	1.173	1.00
28_E	31_R	1.163	1.00
109_I	114_Q	1.161	1.00
36_E	67_S	1.142	1.00
81_G	118_A	1.121	1.00
40_S	43_W	1.104	1.00
91_T	96_G	1.089	1.00
52_V	109_I	1.086	1.00
11_H	25_E	1.078	1.00
7_V	18_V	1.076	1.00
110_D	117_L	1.073	1.00
55_N	105_T	1.050	1.00
75_Q	89_V	1.041	1.00
77_Q	85_I	1.026	1.00
85_I	105_T	1.021	1.00
20_N	56_I	1.010	1.00
61_R	98_V	0.981	1.00
54_V	105_T	0.965	1.00
82_K	107_V	0.956	1.00
5_I	72_I	0.952	1.00
125_E	128_E	0.942	1.00
98_V	101_D	0.932	1.00
48_N	112_K	0.893	1.00
26_F	70_L	0.891	1.00
122_E	125_E	0.885	1.00
121_G	124_R	0.868	1.00
7_V	26_F	0.866	1.00
74_S	88_Q	0.852	1.00
49_I	108_C	0.849	1.00
36_E	40_S	0.844	1.00
27_L	58_I	0.842	1.00
70_L	99_V	0.829	1.00
8_R	29_E	0.823	1.00
55_N	103_L	0.822	1.00
11_H	26_F	0.816	1.00
20_N	60_Y	0.813	1.00
43_W	47_H	0.811	1.00
87_S	101_D	0.811	1.00
25_E	28_E	0.800	1.00
76_L	86_L	0.798	1.00
42_Q	46_A	0.798	1.00
69_L	94_P	0.793	1.00
71_T	96_G	0.792	1.00
18_V	64_A	0.782	1.00
8_R	25_E	0.781	1.00
82_K	118_A	0.768	1.00
19_N	28_E	0.766	1.00
15_Y	52_V	0.766	1.00
71_T	94_P	0.764	1.00
34_G	74_S	0.761	1.00
54_V	61_R	0.746	1.00
9_G	12_L	0.745	1.00
6_K	67_S	0.741	1.00
47_H	122_E	0.738	1.00
79_L	124_R	0.737	1.00
71_T	91_T	0.734	1.00
72_I	88_Q	0.727	1.00
12_L	16_Q	0.723	1.00
15_Y	19_N	0.717	1.00
74_S	86_L	0.716	1.00
9_G	14_V	0.711	1.00
33_D	36_E	0.711	1.00
56_I	102_A	0.710	1.00
31_R	53_V	0.704	1.00
20_N	24_L	0.694	1.00
5_I	29_E	0.692	1.00
54_V	107_V	0.670	1.00
5_I	8_R	0.668	1.00
122_E	126_K	0.663	0.99
119_L	124_R	0.660	0.99
88_Q	106_F	0.659	0.99
20_N	31_R	0.657	0.99
31_R	88_Q	0.656	0.99
65_V	114_Q	0.652	0.99
5_I	26_F	0.650	0.99
15_Y	20_N	0.643	0.99
42_Q	67_S	0.642	0.99
34_G	76_L	0.639	0.99
17_H	63_P	0.632	0.99
17_H	52_V	0.628	0.99
27_L	88_Q	0.626	0.99
121_G	128_E	0.622	0.99
12_L	66_L	0.618	0.99
17_H	114_Q	0.618	0.99
58_I	102_A	0.617	0.99
9_G	66_L	0.616	0.99
22_R	26_F	0.616	0.99
15_Y	50_A	0.609	0.99
31_R	106_F	0.604	0.99
29_E	33_D	0.599	0.99
84_G	119_L	0.597	0.99
19_N	22_R	0.594	0.99
54_V	83_S	0.581	0.99
59_N	103_L	0.578	0.99
23_Y	64_A	0.575	0.99
111_L	114_Q	0.568	0.98
10_Y	19_N	0.567	0.98
88_Q	102_A	0.566	0.98
31_R	86_L	0.563	0.98
108_C	117_L	0.561	0.98
81_G	124_R	0.555	0.98
10_Y	29_E	0.552	0.98
79_L	127_L	0.551	0.98
12_L	22_R	0.551	0.98
42_Q	45_T	0.549	0.98
53_V	106_F	0.545	0.98
23_Y	100_A	0.539	0.98
118_A	121_G	0.539	0.98
56_I	60_Y	0.538	0.98
5_I	11_H	0.536	0.98
92_L	96_G	0.535	0.98
68_D	99_V	0.532	0.98
49_I	117_L	0.531	0.98
124_R	127_L	0.529	0.98
7_V	70_L	0.528	0.97
90_I	100_A	0.527	0.97
80_N	116_A	0.524	0.97
86_L	106_F	0.524	0.97
68_D	94_P	0.523	0.97
10_Y	21_A	0.522	0.97
80_N	124_R	0.521	0.97
64_A	100_A	0.520	0.97
117_L	123_L	0.518	0.97
30_A	88_Q	0.515	0.97
54_V	82_K	0.513	0.97
79_L	84_G	0.512	0.97
53_V	104_I	0.509	0.97
83_S	124_R	0.508	0.97
11_H	22_R	0.506	0.97
34_G	38_S	0.505	0.97
62_R	92_L	0.504	0.97
83_S	107_V	0.500	0.97

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	0.9621	100	0.244	Contact Map
1njkA	4	1	100	0.252	Contact Map
2ownA	3	0.9924	100	0.256	Contact Map
2hljA	2	0.9773	99.9	0.268	Contact Map
2o5uA	4	0.9924	99.9	0.273	Contact Map
2xemA	4	1	99.9	0.282	Contact Map
3ck1A	4	0.9924	99.9	0.282	Contact Map
3qy3A	4	0.9545	99.9	0.283	Contact Map
2nujA	3	0.9848	99.9	0.284	Contact Map
2w3xA	4	1	99.9	0.289	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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