EBRA - BACSU - GREMLIN Contacts

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EBRA - Multidrug resistance protein EbrA

UniProt:	P0CW80	Sequences: MLIGYIFLTIAICSESIGAAMLKVSDGFKKWKPSALVVIGYSLAFYMLSLTLNHIPLSLSYATWSGAGTVLTTVIGVKWFKEDLNAKGLIGILLLLSGVVLLNWP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	105 (100)
Sequences:	4246 (2985)
Seq/√Len:	298.5

ECOLI - EMRE SUGE MDTJ MDTI
BACSU - EBRA YVDR YKKD EBRB YVAE YKKC YVDS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_G	101_L	3.060	1.00
14_S	43_L	2.713	1.00
50_L	53_N	2.570	1.00
77_V	84_L	2.402	1.00
4_G	54_H	2.346	1.00
7_F	50_L	2.339	1.00
21_M	36_L	2.320	1.00
17_I	40_G	2.111	1.00
73_T	92_I	2.058	1.00
75_I	79_W	1.981	1.00
12_I	67_A	1.924	1.00
52_L	60_S	1.807	1.00
32_K	36_L	1.785	1.00
94_L	98_G	1.777	1.00
55_I	60_S	1.739	1.00
18_G	40_G	1.614	1.00
93_L	97_S	1.567	1.00
38_V	42_S	1.536	1.00
17_I	36_L	1.489	1.00
25_S	34_S	1.452	1.00
41_Y	45_F	1.443	1.00
86_A	90_I	1.440	1.00
94_L	97_S	1.432	1.00
20_A	24_V	1.409	1.00
85_N	88_G	1.407	1.00
20_A	75_I	1.396	1.00
46_Y	50_L	1.393	1.00
52_L	57_L	1.379	1.00
28_F	34_S	1.348	1.00
18_G	41_Y	1.334	1.00
95_L	98_G	1.297	1.00
92_I	102_L	1.284	1.00
7_F	47_M	1.281	1.00
91_G	98_G	1.276	1.00
22_L	37_V	1.276	1.00
25_S	28_F	1.266	1.00
14_S	40_G	1.266	1.00
89_L	93_L	1.248	1.00
16_S	71_L	1.246	1.00
24_V	80_F	1.242	1.00
51_T	60_S	1.238	1.00
31_W	34_S	1.219	1.00
5_Y	63_T	1.199	1.00
30_K	33_P	1.191	1.00
91_G	95_L	1.165	1.00
48_L	60_S	1.157	1.00
83_D	88_G	1.143	1.00
32_K	35_A	1.117	1.00
17_I	21_M	1.102	1.00
69_T	73_T	1.101	1.00
84_L	89_L	1.056	1.00
95_L	99_V	1.041	1.00
9_T	67_A	1.017	1.00
88_G	102_L	1.016	1.00
87_K	90_I	1.001	1.00
26_D	30_K	0.987	1.00
23_K	27_G	0.978	1.00
31_W	35_A	0.977	1.00
84_L	88_G	0.961	1.00
42_S	46_Y	0.941	1.00
6_I	10_I	0.935	1.00
74_V	78_K	0.923	1.00
97_S	101_L	0.922	1.00
63_T	67_A	0.908	1.00
58_S	62_A	0.905	1.00
4_G	55_I	0.900	1.00
83_D	86_A	0.898	1.00
82_E	88_G	0.895	1.00
59_L	88_G	0.894	1.00
4_G	7_F	0.882	1.00
91_G	94_L	0.880	1.00
70_V	92_I	0.871	1.00
57_L	72_T	0.863	1.00
10_I	47_M	0.862	1.00
26_D	29_K	0.834	1.00
86_A	89_L	0.831	1.00
96_L	100_V	0.831	1.00
94_L	101_L	0.826	1.00
19_A	72_T	0.825	1.00
21_M	24_V	0.817	1.00
70_V	96_L	0.816	1.00
9_T	12_I	0.815	1.00
20_A	80_F	0.790	0.99
35_A	39_I	0.787	0.99
29_K	53_N	0.781	0.99
16_S	75_I	0.778	0.99
57_L	80_F	0.762	0.99
75_I	80_F	0.756	0.99
90_I	94_L	0.753	0.99
65_S	76_G	0.743	0.99
12_I	44_A	0.741	0.99
29_K	34_S	0.741	0.99
29_K	33_P	0.740	0.99
69_T	96_L	0.734	0.99
62_A	65_S	0.728	0.99
76_G	80_F	0.720	0.99
66_G	99_V	0.704	0.99
35_A	38_V	0.690	0.99
87_K	91_G	0.689	0.99
18_G	37_V	0.688	0.99
21_M	37_V	0.678	0.98
76_G	82_E	0.676	0.98
77_V	83_D	0.665	0.98
15_E	44_A	0.660	0.98
21_M	40_G	0.649	0.98
13_C	71_L	0.632	0.98
77_V	89_L	0.625	0.97
34_S	37_V	0.620	0.97
50_L	54_H	0.619	0.97
13_C	17_I	0.616	0.97
21_M	25_S	0.615	0.97
78_K	81_K	0.613	0.97
62_A	92_I	0.612	0.97
41_Y	65_S	0.610	0.97
39_I	43_L	0.604	0.97
67_A	71_L	0.597	0.96
8_L	60_S	0.593	0.96
11_A	47_M	0.591	0.96
28_F	33_P	0.590	0.96
56_P	59_L	0.590	0.96
20_A	57_L	0.585	0.96
45_F	52_L	0.579	0.96
90_I	93_L	0.578	0.96
73_T	102_L	0.573	0.96
11_A	48_L	0.567	0.95
41_Y	57_L	0.556	0.95
12_I	99_V	0.554	0.95
36_L	40_G	0.550	0.94
76_G	88_G	0.549	0.94
23_K	26_D	0.547	0.94
64_W	95_L	0.547	0.94
27_G	33_P	0.546	0.94
59_L	62_A	0.545	0.94
25_S	29_K	0.541	0.94
91_G	97_S	0.540	0.94
82_E	85_N	0.540	0.94
36_L	39_I	0.540	0.94
18_G	65_S	0.538	0.94
4_G	51_T	0.536	0.94
58_S	88_G	0.534	0.94
8_L	55_I	0.534	0.94
14_S	37_V	0.533	0.94
22_L	64_W	0.525	0.93
45_F	49_S	0.525	0.93
77_V	82_E	0.522	0.93
25_S	30_K	0.521	0.93
7_F	51_T	0.509	0.92
70_V	102_L	0.507	0.92
19_A	41_Y	0.501	0.91
20_A	23_K	0.500	0.91

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
3b5dA	2	0.9619	99.9	0.344	Contact Map
2i68A	2	0.7429	99.9	0.381	Contact Map
4gx0A	3	0.7333	3.6	0.941	Contact Map
4pypA	1	1	3.5	0.941	Contact Map
4f35D	2	0.8762	2.5	0.945	Contact Map
2ls4A	1	0.2286	2.4	0.946	Contact Map
3effK	4	0.7619	2.1	0.947	Contact Map
3rqwA	4	0.4952	1.8	0.949	Contact Map
2c9kA	1	0.3714	1.8	0.949	Contact Map
4xnjA	1	0.9905	1.2	0.954	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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