MDTI - ECOLI - GREMLIN Contacts

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MDTI - Spermidine export protein MdtI

UniProt:	P69210	Sequences: MAQFEWVHAAWLALAIVLEIVANVFLKFSDGFRRKIFGLLSLAAVLAAFSALSQAVKGIDLSVAYALWGGFGIAATLAAGWILFGQRLNRKGWIGLVLLLAGMIMVKLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13926
Length:	109 (102)
Sequences:	4388 (3012)
Seq/√Len:	298.2

ECOLI - MDTI SUGE MDTJ EMRE
BACSU - YKKD YVDR YVAE EBRB EBRA 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
95_G	105_M	3.025	1.00
18_L	47_A	2.686	1.00
54_Q	57_K	2.619	1.00
8_H	58_G	2.597	1.00
81_W	88_L	2.407	1.00
11_W	54_Q	2.316	1.00
25_F	40_L	2.302	1.00
21_V	44_A	2.075	1.00
77_L	96_L	2.019	1.00
79_A	83_L	1.988	1.00
16_I	71_F	1.871	1.00
98_L	102_G	1.833	1.00
56_V	64_A	1.812	1.00
36_I	40_L	1.778	1.00
59_I	64_A	1.705	1.00
97_V	101_A	1.530	1.00
42_L	46_L	1.512	1.00
50_S	54_Q	1.509	1.00
90_R	94_I	1.508	1.00
22_A	44_A	1.506	1.00
21_V	40_L	1.487	1.00
29_S	38_G	1.483	1.00
32_F	38_G	1.461	1.00
24_V	28_F	1.459	1.00
24_V	79_A	1.439	1.00
45_V	49_F	1.430	1.00
98_L	101_A	1.412	1.00
56_V	61_L	1.390	1.00
89_N	92_G	1.387	1.00
22_A	45_V	1.364	1.00
11_W	51_A	1.332	1.00
18_L	44_A	1.324	1.00
20_I	75_A	1.319	1.00
104_I	108_L	1.304	1.00
29_S	32_F	1.298	1.00
28_F	84_F	1.297	1.00
26_L	41_S	1.291	1.00
35_K	38_G	1.287	1.00
95_G	102_G	1.283	1.00
99_L	102_G	1.272	1.00
55_A	64_A	1.229	1.00
95_G	99_L	1.210	1.00
34_R	37_F	1.196	1.00
87_R	92_G	1.177	1.00
93_W	97_V	1.162	1.00
96_L	106_V	1.161	1.00
73_I	77_L	1.151	1.00
52_L	64_A	1.137	1.00
92_G	106_V	1.123	1.00
21_V	25_F	1.107	1.00
36_I	39_L	1.087	1.00
99_L	103_M	1.085	1.00
30_D	34_R	1.044	1.00
86_Q	92_G	1.037	1.00
91_K	94_I	1.034	1.00
88_L	93_W	1.034	1.00
46_L	50_S	1.020	1.00
9_A	67_L	0.984	1.00
13_A	71_F	0.981	1.00
88_L	92_G	0.969	1.00
10_A	14_L	0.938	1.00
78_A	82_I	0.932	1.00
8_H	59_I	0.928	1.00
35_K	39_L	0.923	1.00
27_K	31_G	0.917	1.00
74_A	96_L	0.912	1.00
67_L	71_F	0.895	1.00
14_L	51_A	0.884	1.00
95_G	98_L	0.882	1.00
101_A	105_M	0.878	1.00
25_F	28_F	0.867	1.00
87_R	90_R	0.866	1.00
8_H	11_W	0.858	1.00
13_A	16_I	0.829	1.00
61_L	76_T	0.827	1.00
63_V	92_G	0.817	1.00
90_R	93_W	0.815	1.00
33_R	38_G	0.812	1.00
79_A	84_F	0.798	1.00
62_S	66_A	0.794	0.99
73_I	100_L	0.783	0.99
80_G	84_F	0.780	0.99
23_N	76_T	0.773	0.99
33_R	37_F	0.771	0.99
30_D	33_R	0.770	0.99
16_I	48_A	0.769	0.99
66_A	69_G	0.762	0.99
80_G	86_Q	0.750	0.99
39_L	43_A	0.747	0.99
24_V	84_F	0.740	0.99
74_A	100_L	0.736	0.99
33_R	57_K	0.734	0.99
98_L	105_M	0.731	0.99
25_F	44_A	0.723	0.99
38_G	41_S	0.723	0.99
91_K	95_G	0.705	0.99
94_I	98_L	0.705	0.99
69_G	80_G	0.698	0.99
61_L	84_F	0.692	0.99
100_L	104_I	0.689	0.99
39_L	42_L	0.689	0.99
7_V	10_A	0.685	0.99
82_I	85_G	0.684	0.98
20_I	79_A	0.677	0.98
70_G	103_M	0.675	0.98
43_A	47_A	0.674	0.98
45_V	69_G	0.674	0.98
25_F	41_S	0.673	0.98
66_A	96_L	0.670	0.98
17_V	75_A	0.670	0.98
19_E	48_A	0.654	0.98
77_L	106_V	0.637	0.98
17_V	21_V	0.637	0.98
49_F	56_V	0.633	0.98
25_F	29_S	0.631	0.97
60_D	63_V	0.625	0.97
86_Q	89_N	0.621	0.97
29_S	34_R	0.614	0.97
54_Q	58_G	0.611	0.97
15_A	51_A	0.609	0.97
81_W	87_R	0.609	0.97
66_A	108_L	0.607	0.97
71_F	75_A	0.592	0.96
24_V	80_G	0.590	0.96
27_K	30_D	0.586	0.96
45_V	61_L	0.583	0.96
32_F	37_F	0.576	0.96
81_W	86_Q	0.566	0.95
11_W	55_A	0.561	0.95
94_I	97_V	0.558	0.95
22_A	41_S	0.556	0.95
24_V	27_K	0.555	0.95
26_L	68_W	0.547	0.94
63_V	66_A	0.547	0.94
29_S	33_R	0.546	0.94
47_A	51_A	0.545	0.94
8_H	55_A	0.543	0.94
80_G	92_G	0.537	0.94
33_R	87_R	0.536	0.94
15_A	52_L	0.535	0.94
24_V	61_L	0.531	0.93
68_W	99_L	0.525	0.93
32_F	35_K	0.524	0.93
16_I	103_M	0.521	0.93
38_G	53_S	0.521	0.93
25_F	42_L	0.518	0.93
81_W	93_W	0.516	0.92
29_S	41_S	0.512	0.92
20_I	61_L	0.507	0.92
23_N	45_V	0.507	0.92
26_L	49_F	0.506	0.92
12_L	64_A	0.502	0.91
40_L	44_A	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	0.9266	99.9	0.326	Contact Map
2i68A	2	0.7156	99.9	0.362	Contact Map
4o9uB	2	0.6147	5.6	0.933	Contact Map
4pypA	1	1	3.9	0.938	Contact Map
4o93B	1	0.6147	3.4	0.94	Contact Map
3rqwA	4	0.5046	3.2	0.941	Contact Map
4gx0A	3	0.7064	2.5	0.944	Contact Map
3effK	4	0.7339	2.4	0.944	Contact Map
4q65A	1	0.7064	2.3	0.945	Contact Map
2r9rB	3	0.7706	2.3	0.945	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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