EBRB - BACSU - GREMLIN Contacts

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EBRB - Multidrug resistance protein EbrB

UniProt:	P0CW82	Sequences: MRGLLYLALAIVSEVFGSTMLKLSEGFTQAWPIAGVIVGFLSAFTFLSFSLKTIDLSSAYATWSGVGTALTAIVGFLLFGETISLKGVFGLTLVIAGVVVLNQSKAHAEDKKQTACE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	117 (103)
Sequences:	4648 (3227)
Seq/√Len:	317.9

ECOLI - EMRE MDTJ SUGE MDTI
BACSU - EBRB YVAE YKKD EBRA YVDR 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
90_G	100_V	2.810	1.00
13_S	42_S	2.642	1.00
49_F	52_K	2.482	1.00
20_M	35_G	2.294	1.00
76_F	83_I	2.289	1.00
6_Y	49_F	2.255	1.00
3_G	53_T	2.207	1.00
16_F	39_G	2.074	1.00
74_V	78_L	1.986	1.00
72_A	91_L	1.884	1.00
11_I	66_V	1.858	1.00
51_L	59_A	1.715	1.00
93_L	97_G	1.667	1.00
54_I	59_A	1.659	1.00
17_G	39_G	1.598	1.00
45_T	49_F	1.556	1.00
31_W	35_G	1.542	1.00
92_T	96_A	1.522	1.00
40_F	44_F	1.516	1.00
37_I	41_L	1.477	1.00
85_L	89_F	1.476	1.00
51_L	56_L	1.469	1.00
27_F	33_I	1.462	1.00
19_T	23_L	1.451	1.00
93_L	96_A	1.430	1.00
16_F	35_G	1.411	1.00
29_Q	32_P	1.407	1.00
21_L	36_V	1.401	1.00
19_T	74_V	1.379	1.00
15_V	70_L	1.362	1.00
24_S	33_I	1.345	1.00
17_G	40_F	1.338	1.00
24_S	27_F	1.332	1.00
6_Y	46_F	1.313	1.00
50_S	59_A	1.311	1.00
23_L	79_F	1.275	1.00
99_V	103_Q	1.264	1.00
90_G	104_S	1.260	1.00
90_G	97_G	1.256	1.00
13_S	39_G	1.244	1.00
88_V	92_T	1.239	1.00
94_V	97_G	1.221	1.00
30_A	33_I	1.211	1.00
84_S	87_G	1.194	1.00
86_K	104_S	1.159	1.00
94_V	98_V	1.144	1.00
41_L	45_T	1.120	1.00
91_L	101_L	1.116	1.00
87_G	101_L	1.115	1.00
16_F	20_M	1.103	1.00
82_T	87_G	1.082	1.00
68_T	72_A	1.080	1.00
86_K	89_F	1.073	1.00
47_L	59_A	1.067	1.00
31_W	34_A	1.061	1.00
83_I	88_V	1.026	1.00
90_G	94_V	1.022	1.00
25_E	29_Q	1.009	1.00
75_G	81_E	1.008	1.00
68_T	95_I	0.995	1.00
81_E	87_G	0.992	1.00
4_L	62_T	0.986	1.00
8_A	66_V	0.941	1.00
5_L	9_L	0.929	1.00
22_K	26_G	0.903	1.00
3_G	6_Y	0.902	1.00
20_M	23_L	0.895	1.00
34_A	38_V	0.895	1.00
73_I	77_L	0.890	1.00
83_I	87_G	0.883	1.00
57_S	61_A	0.879	1.00
85_L	88_V	0.878	1.00
8_A	11_I	0.876	1.00
25_E	28_T	0.875	1.00
69_A	91_L	0.871	1.00
30_A	34_A	0.865	1.00
9_L	46_F	0.864	1.00
58_S	87_G	0.851	1.00
90_G	93_L	0.836	1.00
62_T	66_V	0.828	1.00
96_A	100_V	0.809	1.00
61_A	64_S	0.807	1.00
74_V	79_F	0.806	1.00
11_I	43_A	0.803	1.00
28_T	52_K	0.790	1.00
56_L	71_T	0.788	1.00
20_M	39_G	0.785	1.00
3_G	54_I	0.781	1.00
102_N	105_K	0.777	1.00
28_T	33_I	0.767	0.99
10_A	46_F	0.767	0.99
18_S	71_T	0.759	0.99
65_G	98_V	0.755	0.99
15_V	74_V	0.754	0.99
82_T	85_L	0.743	0.99
28_T	32_P	0.738	0.99
33_I	36_V	0.737	0.99
55_D	58_S	0.731	0.99
69_A	95_I	0.716	0.99
76_F	88_V	0.711	0.99
19_T	79_F	0.709	0.99
20_M	36_V	0.702	0.99
75_G	79_F	0.699	0.99
86_K	90_G	0.693	0.99
95_I	99_V	0.686	0.99
21_L	63_W	0.686	0.99
77_L	80_G	0.681	0.99
12_V	70_L	0.680	0.99
40_F	64_S	0.679	0.99
93_L	100_V	0.665	0.99
100_V	104_S	0.656	0.98
27_F	32_P	0.656	0.98
49_F	53_T	0.655	0.98
56_L	79_F	0.654	0.98
89_F	93_L	0.653	0.98
38_V	42_S	0.652	0.98
14_E	43_A	0.651	0.98
19_T	75_G	0.643	0.98
20_M	24_S	0.640	0.98
40_F	56_L	0.639	0.98
7_L	50_S	0.637	0.98
35_G	39_G	0.633	0.98
24_S	29_Q	0.629	0.98
6_Y	50_S	0.623	0.98
12_V	16_F	0.623	0.98
66_V	70_L	0.623	0.98
65_G	68_T	0.616	0.98
64_S	71_T	0.610	0.97
58_S	61_A	0.609	0.97
3_G	50_S	0.606	0.97
18_S	40_F	0.604	0.97
24_S	28_T	0.603	0.97
81_E	84_S	0.597	0.97
61_A	91_L	0.596	0.97
10_A	47_L	0.577	0.96
64_S	75_G	0.571	0.96
21_L	44_F	0.566	0.96
17_G	36_V	0.557	0.96
7_L	59_A	0.537	0.95
39_G	43_A	0.533	0.95
34_A	37_I	0.532	0.94
44_F	51_L	0.531	0.94
24_S	36_V	0.528	0.94
61_A	101_L	0.527	0.94
20_M	37_I	0.521	0.94
28_T	82_T	0.521	0.94
19_T	22_K	0.520	0.94
70_L	74_V	0.519	0.94
11_I	98_V	0.519	0.94
27_F	30_A	0.511	0.93
22_K	25_E	0.507	0.93
50_S	53_T	0.507	0.93
75_G	87_G	0.505	0.93
76_F	82_T	0.500	0.92

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	0.8718	99.9	0.373	Contact Map
2i68A	2	0.6667	99.9	0.39	Contact Map
4gx0A	3	0.7692	7.3	0.938	Contact Map
4ikvA	1	0.9231	7.3	0.938	Contact Map
4xnjA	1	0.9145	6.7	0.939	Contact Map
4qtnA	3	0.9145	6.2	0.94	Contact Map
1pw4A	1	0.9829	6.1	0.94	Contact Map
3effK	4	0.7863	6	0.94	Contact Map
4nv5A	1	0.9487	5.2	0.942	Contact Map
2cfqA	1	0.9744	4.8	0.943	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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