YKKC - BACSU - GREMLIN Contacts

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YKKC - Multidrug resistance protein YkkC

UniProt:	P49856	Sequences: MKWGLVVLAAVFEVVWVIGLKHADSALTWSGTAIGIIFSFYLLMKATHSLPVGTVYAVFTGLGTAGTVLSEIVLFHEPVGWPKLLLIGVLLIGVIGLKLVTQDETEEKGGEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	112 (100)
Sequences:	4313 (3046)
Seq/√Len:	304.6

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_L	96_G	3.082	1.00
12_F	38_F	2.709	1.00
45_K	48_H	2.683	1.00
72_I	79_V	2.473	1.00
19_G	31_G	2.454	1.00
5_L	45_K	2.426	1.00
2_K	49_S	2.296	1.00
15_V	35_G	2.150	1.00
10_A	62_L	2.083	1.00
68_V	87_I	2.047	1.00
70_S	74_L	1.913	1.00
47_T	55_V	1.851	1.00
89_V	93_G	1.815	1.00
50_L	55_V	1.765	1.00
88_G	92_I	1.613	1.00
33_A	37_I	1.569	1.00
16_W	35_G	1.562	1.00
15_V	31_G	1.554	1.00
89_V	92_I	1.537	1.00
23_A	26_A	1.536	1.00
81_W	85_L	1.491	1.00
41_Y	45_K	1.456	1.00
36_I	40_F	1.446	1.00
18_I	22_H	1.439	1.00
47_T	52_V	1.430	1.00
16_W	36_I	1.408	1.00
24_D	28_T	1.344	1.00
18_I	70_S	1.326	1.00
86_L	93_G	1.326	1.00
90_L	93_G	1.323	1.00
86_L	100_V	1.319	1.00
20_L	32_T	1.300	1.00
84_L	88_G	1.299	1.00
64_T	68_V	1.295	1.00
14_V	66_G	1.293	1.00
5_L	42_L	1.281	1.00
12_F	35_G	1.266	1.00
22_H	75_F	1.260	1.00
46_A	55_V	1.198	1.00
43_L	55_V	1.183	1.00
95_I	99_L	1.176	1.00
86_L	90_L	1.176	1.00
80_G	83_K	1.169	1.00
3_W	58_V	1.155	1.00
87_I	97_L	1.151	1.00
82_P	100_V	1.115	1.00
15_V	19_G	1.079	1.00
79_V	84_L	1.058	1.00
82_P	85_L	1.057	1.00
78_P	83_K	1.051	1.00
37_I	41_Y	1.037	1.00
79_V	83_K	1.032	1.00
71_E	77_E	1.025	1.00
53_G	57_A	1.011	1.00
4_G	8_L	0.997	1.00
7_V	62_L	0.994	1.00
23_A	28_T	0.991	1.00
90_L	94_V	0.975	1.00
92_I	96_G	0.974	1.00
57_A	60_T	0.962	1.00
77_E	83_K	0.929	1.00
54_T	83_K	0.905	1.00
81_W	84_L	0.902	1.00
69_L	73_V	0.901	1.00
65_A	87_I	0.900	1.00
86_L	89_V	0.898	1.00
83_K	97_L	0.896	1.00
21_K	25_S	0.887	1.00
7_V	10_A	0.877	1.00
52_V	67_T	0.868	1.00
19_G	22_H	0.846	1.00
2_K	50_L	0.841	1.00
19_G	32_T	0.836	1.00
8_L	42_L	0.834	1.00
91_L	95_I	0.832	1.00
30_S	34_I	0.831	1.00
64_T	91_L	0.822	1.00
65_A	91_L	0.819	1.00
10_A	39_S	0.815	1.00
14_V	70_S	0.813	1.00
16_W	32_T	0.805	1.00
61_G	94_V	0.804	1.00
58_V	62_L	0.788	1.00
82_P	86_L	0.779	0.99
9_A	42_L	0.775	0.99
78_P	81_W	0.771	0.99
17_V	67_T	0.761	0.99
27_L	48_H	0.757	0.99
71_E	75_F	0.748	0.99
51_P	54_T	0.734	0.99
18_I	75_F	0.731	0.99
70_S	75_F	0.729	0.99
13_E	39_S	0.723	0.99
24_D	27_L	0.719	0.99
89_V	96_G	0.713	0.99
6_V	55_V	0.689	0.99
2_K	5_L	0.689	0.99
31_G	35_G	0.688	0.99
72_I	84_L	0.682	0.99
54_T	57_A	0.676	0.98
19_G	35_G	0.673	0.98
30_S	33_A	0.670	0.98
62_L	66_G	0.667	0.98
96_G	100_V	0.665	0.98
11_V	66_G	0.661	0.98
85_L	89_V	0.661	0.98
60_T	71_E	0.659	0.98
36_I	60_T	0.656	0.98
45_K	49_S	0.651	0.98
61_G	64_T	0.642	0.98
20_L	59_F	0.632	0.98
52_V	75_F	0.626	0.98
32_T	35_G	0.620	0.97
34_I	38_F	0.617	0.97
21_K	24_D	0.612	0.97
26_A	29_W	0.610	0.97
20_L	39_S	0.608	0.97
73_V	76_H	0.606	0.97
19_G	23_A	0.604	0.97
18_I	71_E	0.601	0.97
11_V	15_V	0.595	0.97
71_E	83_K	0.591	0.96
23_A	27_L	0.588	0.96
5_L	46_A	0.586	0.96
57_A	97_L	0.577	0.96
68_V	97_L	0.577	0.96
9_A	43_L	0.570	0.96
60_T	98_K	0.568	0.96
40_F	47_T	0.566	0.96
72_I	78_P	0.565	0.95
6_V	50_L	0.562	0.95
40_F	44_M	0.551	0.95
6_V	46_A	0.540	0.94
10_A	94_V	0.538	0.94
19_G	33_A	0.534	0.94
34_I	37_I	0.531	0.94
16_W	64_T	0.529	0.94
57_A	87_I	0.527	0.94
66_G	70_S	0.526	0.93
77_E	80_G	0.525	0.93
25_S	28_T	0.523	0.93
36_I	52_V	0.522	0.93
25_S	44_M	0.518	0.93
12_F	32_T	0.518	0.93
86_L	92_I	0.515	0.93
46_A	50_L	0.508	0.92
64_T	100_V	0.504	0.92
31_G	34_I	0.503	0.92
18_I	52_V	0.500	0.92
38_F	42_L	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	0.8839	99.9	0.395	Contact Map
2i68A	2	0.6964	99.9	0.421	Contact Map
1pw4A	1	1	9.2	0.932	Contact Map
4dx5A	3	0.9732	9.2	0.932	Contact Map
1l1yA	1	0.0982	4.5	0.941	Contact Map
4k0jA	3	0.8571	4.2	0.942	Contact Map
3w9iA	3	0.9554	4.1	0.942	Contact Map
4o9uB	2	0.7411	4	0.942	Contact Map
4xnjA	1	0.9196	3.9	0.942	Contact Map
3effK	4	0.7857	3.7	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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