YKKD - BACSU - GREMLIN Contacts

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YKKD - Multidrug resistance protein YkkD

UniProt:	P49857	Sequences: MLHWISLLCAGCLEMAGVALMNQYAKEKSVKWVLLIIVGFAASFSLLSYAMETTPMGTAYAVWTGIGTAGGALIGILFYKEQKDAKRIFFIALILCSAVGLKILS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	105 (101)
Sequences:	4210 (2891)
Seq/√Len:	287.7

ECOLI - SUGE MDTJ MDTI 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
90_F	100_G	3.049	1.00
13_L	42_A	2.717	1.00
49_Y	52_E	2.626	1.00
76_I	83_K	2.396	1.00
6_S	49_Y	2.377	1.00
20_L	35_L	2.302	1.00
16_A	39_G	2.193	1.00
3_H	53_T	2.146	1.00
74_I	78_F	1.997	1.00
72_A	91_I	1.996	1.00
11_G	66_I	1.979	1.00
93_L	97_S	1.830	1.00
51_M	59_A	1.823	1.00
54_T	59_A	1.788	1.00
31_K	35_L	1.751	1.00
17_G	39_G	1.570	1.00
92_A	96_C	1.558	1.00
93_L	96_C	1.544	1.00
16_A	35_L	1.523	1.00
37_I	41_A	1.520	1.00
40_F	44_F	1.489	1.00
24_Y	33_V	1.456	1.00
85_A	89_F	1.443	1.00
45_S	49_Y	1.433	1.00
19_A	23_Q	1.421	1.00
27_E	33_V	1.392	1.00
51_M	56_M	1.353	1.00
17_G	40_F	1.342	1.00
94_I	97_S	1.324	1.00
24_Y	27_E	1.322	1.00
15_M	70_G	1.301	1.00
90_F	97_S	1.301	1.00
84_D	87_R	1.301	1.00
13_L	39_G	1.287	1.00
6_S	46_L	1.282	1.00
19_A	74_I	1.268	1.00
21_M	36_I	1.268	1.00
23_Q	79_Y	1.267	1.00
99_V	103_I	1.264	1.00
50_A	59_A	1.228	1.00
30_V	33_V	1.227	1.00
88_I	92_A	1.197	1.00
29_S	32_W	1.186	1.00
90_F	94_I	1.175	1.00
82_Q	87_R	1.172	1.00
91_I	101_L	1.152	1.00
68_T	72_A	1.139	1.00
87_R	101_L	1.109	1.00
4_W	62_V	1.107	1.00
31_K	34_L	1.103	1.00
16_A	20_L	1.090	1.00
47_L	59_A	1.077	1.00
83_K	88_I	1.065	1.00
8_L	66_I	1.055	1.00
30_V	34_L	1.040	1.00
86_K	89_F	0.992	1.00
83_K	87_R	0.966	1.00
5_I	9_C	0.966	1.00
41_A	45_S	0.950	1.00
94_I	98_A	0.948	1.00
58_T	87_R	0.940	1.00
96_C	100_G	0.940	1.00
22_N	26_K	0.932	1.00
25_A	29_S	0.921	1.00
73_L	77_L	0.913	1.00
90_F	93_L	0.912	1.00
9_C	46_L	0.906	1.00
69_A	91_I	0.906	1.00
3_H	54_T	0.898	1.00
82_Q	85_A	0.896	1.00
62_V	66_I	0.880	1.00
85_A	88_I	0.873	1.00
56_M	71_G	0.867	1.00
81_E	87_R	0.858	1.00
69_A	95_L	0.857	1.00
18_V	71_G	0.848	1.00
57_G	61_A	0.830	1.00
8_L	11_G	0.814	1.00
20_L	23_Q	0.811	1.00
95_L	99_V	0.804	0.99
28_K	33_V	0.797	0.99
11_G	43_S	0.792	0.99
75_G	79_Y	0.775	0.99
61_A	64_T	0.773	0.99
25_A	28_K	0.770	0.99
74_I	79_Y	0.764	0.99
34_L	38_V	0.758	0.99
75_G	81_E	0.753	0.99
15_M	74_I	0.746	0.99
19_A	79_Y	0.746	0.99
65_G	98_A	0.744	0.99
93_L	100_G	0.742	0.99
28_K	52_E	0.741	0.99
68_T	95_L	0.735	0.99
64_T	75_G	0.721	0.99
89_F	93_L	0.720	0.99
3_H	6_S	0.718	0.99
86_K	90_F	0.710	0.99
72_A	101_L	0.693	0.98
34_L	37_I	0.686	0.98
20_L	39_G	0.676	0.98
20_L	36_I	0.674	0.98
56_M	79_Y	0.672	0.98
17_G	36_I	0.666	0.98
14_E	43_S	0.664	0.98
55_P	58_T	0.649	0.98
61_A	91_I	0.641	0.97
28_K	32_W	0.635	0.97
77_L	80_K	0.634	0.97
76_I	82_Q	0.633	0.97
19_A	56_M	0.632	0.97
76_I	88_I	0.629	0.97
20_L	24_Y	0.626	0.97
38_V	42_A	0.623	0.97
66_I	70_G	0.621	0.97
49_Y	53_T	0.612	0.97
44_F	51_M	0.610	0.97
12_C	70_G	0.610	0.97
33_V	36_I	0.609	0.97
24_Y	28_K	0.608	0.96
10_A	46_L	0.599	0.96
11_G	98_A	0.598	0.96
58_T	61_A	0.598	0.96
22_N	25_A	0.596	0.96
75_G	87_R	0.591	0.96
40_F	64_T	0.588	0.96
40_F	56_M	0.582	0.95
10_A	47_L	0.581	0.95
27_E	32_W	0.576	0.95
26_K	32_W	0.573	0.95
19_A	75_G	0.572	0.95
35_L	39_G	0.570	0.95
24_Y	29_S	0.569	0.95
12_C	16_A	0.568	0.95
81_E	84_D	0.558	0.94
7_L	59_A	0.555	0.94
21_M	43_S	0.554	0.94
89_F	92_A	0.550	0.94
76_I	81_E	0.547	0.94
64_T	102_K	0.544	0.94
44_F	48_S	0.542	0.93
63_W	94_I	0.531	0.93
20_L	37_I	0.521	0.92
6_S	50_A	0.518	0.92
39_G	43_S	0.516	0.92
17_G	64_T	0.515	0.92
21_M	63_W	0.508	0.91
18_V	40_F	0.508	0.91
13_L	36_I	0.507	0.91
36_I	48_S	0.506	0.91
90_F	96_C	0.500	0.90
61_A	103_I	0.500	0.90

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	0.9714	99.9	0.3	Contact Map
2i68A	2	0.7429	99.9	0.34	Contact Map
4pypA	1	1	4.3	0.936	Contact Map
4tphA	2	0.9905	3.2	0.94	Contact Map
4zw9A	1	0.9905	2.7	0.942	Contact Map
4xnjA	1	0.9905	2.7	0.943	Contact Map
2ls4A	1	0.2286	2.6	0.943	Contact Map
1pw4A	1	1	2.5	0.943	Contact Map
4o9uB	2	0.6857	2.4	0.944	Contact Map
4nv5A	1	0.9238	2.3	0.944	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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