MARA - ECOLI - GREMLIN Contacts

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MARA - Multiple antibiotic resistance protein MarA

UniProt:	P0ACH5	Sequences: MSRRNTDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPLNHYNS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11434
Length:	127 (104)
Sequences:	42318 (32468)
Seq/√Len:	3183.8

ECOLI - MARA YIJO YQHC YIDL RHAR YDIP MELR EUTR RHAS RCLR ARAC YPDC CHBR YKGA APPY ROB GADX YEAM SOXS YBCM XYLR ENVY ADIY GADW YDEO FEAR ADA
BACSU - YTDP YESS ADAA YDEC BTR YISR YBFI YFIF YDEE YOBQ YESN YBFP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_A	100_F	2.925	1.00
52_H	60_S	2.510	1.00
75_E	83_R	2.303	1.00
19_E	61_R	2.250	1.00
96_F	107_Y	2.192	1.00
66_I	92_L	2.139	1.00
69_K	83_R	2.098	1.00
29_E	39_K	2.061	1.00
17_W	21_N	1.978	1.00
69_K	84_Y	1.953	1.00
60_S	99_Y	1.952	1.00
14_I	42_L	1.935	1.00
65_E	68_Q	1.878	1.00
21_N	24_S	1.809	1.00
15_L	50_T	1.750	1.00
17_W	34_R	1.686	1.00
102_V	110_T	1.581	1.00
63_M	100_F	1.566	1.00
27_S	30_K	1.561	1.00
89_Q	93_T	1.553	1.00
39_K	43_Q	1.550	1.00
95_T	98_N	1.519	1.00
46_F	57_Y	1.494	1.00
41_H	45_M	1.493	1.00
59_R	95_T	1.438	1.00
69_K	75_E	1.423	1.00
67_A	107_Y	1.420	1.00
55_G	59_R	1.418	1.00
75_E	79_Y	1.407	1.00
22_L	61_R	1.375	1.00
40_W	44_R	1.365	1.00
78_L	89_Q	1.343	1.00
61_R	65_E	1.316	1.00
61_R	64_T	1.313	1.00
76_P	79_Y	1.305	1.00
15_L	19_E	1.289	1.00
52_H	56_Q	1.273	1.00
31_V	54_L	1.227	1.00
68_Q	72_E	1.227	1.00
18_I	58_I	1.226	1.00
91_T	95_T	1.191	1.00
37_Y	41_H	1.186	1.00
17_W	26_L	1.161	1.00
70_L	77_I	1.156	1.00
78_L	82_E	1.108	1.00
43_Q	54_L	1.099	1.00
65_E	69_K	1.095	1.00
79_Y	82_E	1.083	1.00
45_M	49_E	1.072	1.00
30_K	34_R	1.063	1.00
8_A	49_E	1.062	1.00
79_Y	83_R	1.051	1.00
41_H	44_R	1.041	1.00
14_I	35_S	1.033	1.00
59_R	98_N	0.996	1.00
102_V	106_K	0.994	1.00
63_M	99_Y	0.993	1.00
105_H	109_M	0.987	1.00
60_S	64_T	0.977	1.00
16_D	20_D	0.976	1.00
11_I	50_T	0.965	1.00
71_K	111_N	0.947	1.00
90_Q	93_T	0.945	1.00
15_L	57_Y	0.938	1.00
22_L	65_E	0.933	1.00
23_E	83_R	0.929	1.00
28_L	43_Q	0.928	1.00
10_T	37_Y	0.913	1.00
53_S	56_Q	0.913	1.00
66_I	84_Y	0.900	1.00
67_A	71_K	0.899	1.00
103_P	106_K	0.889	1.00
15_L	46_F	0.882	1.00
65_E	84_Y	0.881	1.00
42_L	54_L	0.877	1.00
40_W	43_Q	0.870	1.00
73_S	108_R	0.867	1.00
46_F	54_L	0.859	1.00
75_E	80_L	0.853	1.00
24_S	30_K	0.846	1.00
10_T	45_M	0.826	1.00
56_Q	59_R	0.825	1.00
106_K	110_T	0.823	1.00
95_T	99_Y	0.821	1.00
38_S	41_H	0.816	1.00
59_R	99_Y	0.799	1.00
13_S	35_S	0.777	1.00
56_Q	60_S	0.775	1.00
97_K	103_P	0.773	1.00
29_E	33_E	0.771	1.00
26_L	31_V	0.768	1.00
37_Y	42_L	0.766	1.00
86_F	95_T	0.748	1.00
80_L	84_Y	0.745	1.00
18_I	54_L	0.745	1.00
93_T	97_K	0.744	1.00
54_L	58_I	0.737	1.00
105_H	108_R	0.734	1.00
10_T	35_S	0.731	1.00
102_V	107_Y	0.730	1.00
32_S	39_K	0.722	1.00
28_L	54_L	0.718	1.00
28_L	39_K	0.717	1.00
91_T	94_R	0.717	1.00
22_L	58_I	0.713	1.00
45_M	48_K	0.713	1.00
64_T	67_A	0.708	1.00
81_A	89_Q	0.706	1.00
93_T	105_H	0.687	1.00
90_Q	94_R	0.681	1.00
56_Q	99_Y	0.677	1.00
13_S	16_D	0.671	1.00
14_I	31_V	0.667	1.00
17_W	35_S	0.661	1.00
25_P	87_E	0.647	1.00
12_H	16_D	0.640	1.00
70_L	108_R	0.640	1.00
23_E	65_E	0.638	1.00
77_I	80_L	0.636	1.00
57_Y	61_R	0.630	1.00
70_L	80_L	0.628	1.00
30_K	33_E	0.622	1.00
94_R	98_N	0.621	1.00
106_K	109_M	0.618	1.00
18_I	61_R	0.611	1.00
8_A	12_H	0.609	1.00
52_H	57_Y	0.609	1.00
21_N	34_R	0.606	1.00
11_I	49_E	0.601	1.00
19_E	57_Y	0.598	1.00
14_I	46_F	0.598	1.00
62_K	84_Y	0.595	1.00
67_A	96_F	0.594	1.00
9_I	13_S	0.593	1.00
88_S	91_T	0.585	1.00
82_E	87_E	0.574	1.00
35_S	42_L	0.566	1.00
31_V	34_R	0.564	1.00
73_S	80_L	0.564	1.00
11_I	45_M	0.563	1.00
13_S	34_R	0.563	1.00
43_Q	47_K	0.563	1.00
92_L	96_F	0.562	1.00
93_T	103_P	0.561	1.00
22_L	26_L	0.558	1.00
47_K	53_S	0.545	1.00
46_F	50_T	0.540	1.00
64_T	100_F	0.537	1.00
22_L	84_Y	0.533	1.00
12_H	15_L	0.531	1.00
88_S	94_R	0.530	1.00
55_G	91_T	0.529	1.00
37_Y	45_M	0.521	1.00
17_W	30_K	0.508	1.00
86_F	91_T	0.505	1.00
87_E	91_T	0.500	1.00

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
1bl0A	1	0.9134	100	0.129	Contact Map
3gbgA	1	0.8898	100	0.133	Contact Map
3oouA	1	0.8268	100	0.175	Contact Map
3oioA	1	0.8819	100	0.177	Contact Map
3w6vA	1	0.874	100	0.178	Contact Map
3mklA	1	0.874	100	0.184	Contact Map
3mn2A	1	0.8346	100	0.185	Contact Map
4fe7A	2	0.8898	100	0.189	Contact Map
2k9sA	1	0.8346	100	0.197	Contact Map
3lsgA	2	0.8031	99.9	0.204	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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