EMRE - ECOLI - GREMLIN Contacts

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EMRE - Multidrug transporter EmrE

UniProt:	P23895	Sequences: MNPYIYLGGAILAEVIGTTLMKFSEGFTRLWPSVGTIICYCASFWLLAQTLAYIPTGIAYAIWSGVGIVLISLLSWGFFGQRLDLPAIIGMMLICAGVLIINLLSRSTPH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10629
Length:	110 (102)
Sequences:	4499 (3103)
Seq/√Len:	307.2

ECOLI - EMRE MDTJ SUGE MDTI
BACSU - EBRB EBRA YKKD YVDR 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
90_G	100_I	2.873	1.00
13_A	42_A	2.617	1.00
49_Q	52_A	2.531	1.00
6_Y	49_Q	2.345	1.00
20_L	35_G	2.302	1.00
76_W	83_L	2.302	1.00
16_I	39_C	2.126	1.00
74_L	78_F	1.925	1.00
72_S	91_M	1.906	1.00
3_P	53_Y	1.895	1.00
11_I	66_V	1.868	1.00
51_L	59_A	1.758	1.00
54_I	59_A	1.739	1.00
93_L	97_G	1.727	1.00
31_W	35_G	1.621	1.00
17_G	39_C	1.554	1.00
45_W	49_Q	1.534	1.00
92_M	96_A	1.520	1.00
85_L	89_I	1.518	1.00
51_L	56_T	1.494	1.00
40_Y	44_F	1.487	1.00
16_I	35_G	1.470	1.00
37_I	41_C	1.458	1.00
27_F	33_S	1.443	1.00
93_L	96_A	1.436	1.00
19_T	23_F	1.402	1.00
90_G	104_L	1.376	1.00
19_T	74_L	1.360	1.00
15_V	70_L	1.353	1.00
21_M	36_T	1.353	1.00
86_P	104_L	1.333	1.00
17_G	40_Y	1.323	1.00
50_T	59_A	1.319	1.00
84_D	87_A	1.303	1.00
6_Y	46_L	1.294	1.00
24_S	27_F	1.278	1.00
13_A	39_C	1.271	1.00
24_S	33_S	1.265	1.00
23_F	79_F	1.258	1.00
90_G	97_G	1.255	1.00
94_I	97_G	1.228	1.00
99_L	103_L	1.218	1.00
88_I	92_M	1.208	1.00
30_L	33_S	1.201	1.00
94_I	98_V	1.157	1.00
29_R	32_P	1.143	1.00
91_M	101_I	1.141	1.00
87_A	101_I	1.120	1.00
47_L	59_A	1.108	1.00
41_C	45_W	1.095	1.00
68_I	72_S	1.094	1.00
16_I	20_L	1.085	1.00
82_R	87_A	1.035	1.00
86_P	89_I	1.026	1.00
4_Y	62_I	1.022	1.00
31_W	34_V	1.022	1.00
83_L	88_I	1.020	1.00
68_I	95_C	1.015	1.00
90_G	94_I	0.980	1.00
83_L	87_A	0.975	1.00
81_Q	87_A	0.968	1.00
8_G	66_V	0.964	1.00
22_K	26_G	0.942	1.00
30_L	34_V	0.931	1.00
69_V	91_M	0.928	1.00
73_L	77_G	0.918	1.00
75_S	81_Q	0.917	1.00
5_I	9_G	0.915	1.00
57_G	61_A	0.906	1.00
20_L	23_F	0.891	1.00
8_G	11_I	0.891	1.00
28_T	52_A	0.884	1.00
96_A	100_I	0.878	1.00
58_I	87_A	0.872	1.00
62_I	66_V	0.872	1.00
25_E	29_R	0.865	1.00
25_E	28_T	0.865	1.00
34_V	38_I	0.850	1.00
90_G	93_L	0.843	1.00
85_L	88_I	0.839	1.00
74_L	79_F	0.837	1.00
9_G	46_L	0.810	1.00
82_R	85_L	0.807	1.00
28_T	33_S	0.800	1.00
61_A	64_S	0.783	0.99
100_I	104_L	0.771	0.99
69_V	95_C	0.768	0.99
15_V	74_L	0.766	0.99
10_A	46_L	0.765	0.99
18_T	71_I	0.760	0.99
28_T	32_P	0.759	0.99
65_G	98_V	0.756	0.99
20_L	39_C	0.746	0.99
19_T	79_F	0.743	0.99
11_I	43_S	0.742	0.99
55_P	58_I	0.735	0.99
3_P	6_Y	0.734	0.99
56_T	79_F	0.717	0.99
20_L	36_T	0.717	0.99
95_C	99_L	0.715	0.99
56_T	71_I	0.699	0.99
86_P	90_G	0.693	0.99
77_G	80_G	0.691	0.99
40_Y	64_S	0.685	0.99
93_L	100_I	0.679	0.99
33_S	36_T	0.678	0.99
3_P	50_T	0.672	0.98
20_L	24_S	0.670	0.98
19_T	75_S	0.670	0.98
49_Q	53_Y	0.669	0.98
26_G	32_P	0.665	0.98
76_W	88_I	0.665	0.98
21_M	63_W	0.662	0.98
3_P	54_I	0.658	0.98
14_E	43_S	0.658	0.98
27_F	32_P	0.651	0.98
89_I	93_L	0.648	0.98
75_S	79_F	0.646	0.98
50_T	53_Y	0.644	0.98
38_I	42_A	0.634	0.98
44_F	51_L	0.634	0.98
40_Y	56_T	0.624	0.98
17_G	36_T	0.619	0.97
81_Q	84_D	0.617	0.97
24_S	28_T	0.600	0.97
66_V	70_L	0.598	0.97
35_G	39_C	0.592	0.97
61_A	91_M	0.590	0.97
64_S	75_S	0.589	0.97
6_Y	50_T	0.586	0.96
12_L	70_L	0.585	0.96
58_I	61_A	0.582	0.96
76_W	82_R	0.569	0.96
24_S	29_R	0.566	0.96
34_V	37_I	0.565	0.96
72_S	101_I	0.561	0.95
7_L	59_A	0.560	0.95
22_K	25_E	0.558	0.95
18_T	40_Y	0.552	0.95
75_S	87_A	0.548	0.95
89_I	92_M	0.544	0.95
10_A	47_L	0.539	0.94
65_G	68_I	0.525	0.94
21_M	43_S	0.519	0.93
11_I	98_V	0.519	0.93
70_L	74_L	0.518	0.93
12_L	16_I	0.515	0.93
7_L	50_T	0.507	0.92
19_T	56_T	0.507	0.92
19_T	22_K	0.507	0.92
82_R	104_L	0.506	0.92
76_W	81_Q	0.505	0.92
24_S	36_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	0.9273	99.9	0.297	Contact Map
2i68A	2	0.7091	99.9	0.346	Contact Map
4o9uB	2	0.7	10.5	0.927	Contact Map
4o93B	1	0.7	6.2	0.934	Contact Map
4pypA	1	0.9909	3.7	0.941	Contact Map
4gx0A	3	0.7545	3.5	0.942	Contact Map
2ls4A	1	0.2182	2.7	0.945	Contact Map
4xnjA	1	0.9727	2.5	0.946	Contact Map
1pw4A	1	0.9545	2.3	0.947	Contact Map
4uisB	1	0.3818	1.8	0.95	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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