MRED - ECOLI - GREMLIN Contacts

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MRED - Rod shape-determining protein MreD

UniProt:	P0ABH4	Sequences: MASYRSQGRWVIWLSFLIALLLQIMPWPDNLIVFRPNWVLLILLYWILALPHRVNVGTGFVMGAILDLISGSTLGVRVLAMSIIAYLVALKYQLFRNLALWQQALVVMLLSLVVDIIVFWAEFLVINVSFRPEVFWSSVVNGVLWPWIFLLMRKVRQQFAVQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10610
Length:	162 (151)
Sequences:	735 (523)
Seq/√Len:	42.6

ECOLI - MRED

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_I	85_A	5.319	1.00
111_S	141_N	5.195	1.00
108_M	142_G	5.063	1.00
19_A	42_I	3.461	1.00
56_V	82_S	2.964	1.00
43_L	54_V	2.764	1.00
49_A	153_R	2.497	1.00
44_L	107_V	2.380	1.00
11_V	155_V	2.184	1.00
149_F	156_R	2.142	0.99
94_L	98_L	2.114	0.99
49_A	156_R	2.092	0.99
60_F	82_S	2.022	0.99
22_L	38_W	2.002	0.99
96_R	156_R	1.959	0.99
20_L	39_V	1.873	0.99
24_I	72_S	1.863	0.99
34_F	136_W	1.757	0.98
43_L	85_A	1.756	0.98
115_D	138_S	1.750	0.98
45_Y	153_R	1.739	0.98
45_Y	156_R	1.686	0.97
66_L	81_M	1.665	0.97
55_N	85_A	1.657	0.97
40_L	84_I	1.650	0.97
40_L	111_S	1.638	0.97
153_R	156_R	1.603	0.96
137_S	140_V	1.562	0.96
13_W	62_M	1.527	0.95
16_F	62_M	1.490	0.94
87_L	113_V	1.458	0.94
58_T	62_M	1.441	0.93
23_Q	66_L	1.438	0.93
48_L	88_V	1.414	0.93
24_I	69_I	1.402	0.92
13_W	58_T	1.398	0.92
27_W	34_F	1.371	0.91
72_S	79_L	1.347	0.91
99_A	102_Q	1.340	0.90
15_S	46_W	1.337	0.90
77_R	131_R	1.334	0.90
37_N	81_M	1.313	0.89
76_V	119_F	1.309	0.89
38_W	102_Q	1.289	0.89
44_L	88_V	1.271	0.88
15_S	19_A	1.265	0.88
25_M	30_N	1.264	0.88
51_P	55_N	1.262	0.88
47_I	111_S	1.242	0.87
68_L	73_T	1.239	0.87
37_N	98_L	1.234	0.86
80_A	118_V	1.193	0.84
37_N	141_N	1.179	0.84
49_A	149_F	1.176	0.83
45_Y	96_R	1.145	0.82
112_L	141_N	1.137	0.81
29_D	105_L	1.134	0.81
17_L	155_V	1.130	0.81
25_M	34_F	1.117	0.80
8_G	14_L	1.115	0.80
137_S	141_N	1.111	0.80
122_E	126_I	1.105	0.79
10_W	101_W	1.103	0.79
50_L	153_R	1.092	0.79
39_V	62_M	1.062	0.77
15_S	152_M	1.046	0.76
47_I	90_L	1.037	0.75
90_L	135_F	1.025	0.74
86_Y	111_S	1.022	0.74
83_I	117_I	1.019	0.74
96_R	153_R	1.014	0.73
86_Y	121_A	1.013	0.73
79_L	143_V	0.997	0.72
50_L	156_R	0.994	0.72
12_I	15_S	0.975	0.70
74_L	82_S	0.974	0.70
76_V	136_W	0.970	0.70
29_D	32_I	0.953	0.68
60_F	78_V	0.952	0.68
56_V	110_L	0.947	0.68
70_S	77_R	0.934	0.67
94_L	103_Q	0.932	0.67
77_R	129_S	0.922	0.66
14_L	18_I	0.921	0.66
110_L	118_V	0.917	0.65
95_F	111_S	0.915	0.65
149_F	153_R	0.914	0.65
11_V	16_F	0.914	0.65
45_Y	97_N	0.900	0.64
88_V	98_L	0.899	0.64
55_N	89_A	0.894	0.63
48_L	152_M	0.889	0.63
139_V	143_V	0.883	0.63
13_W	23_Q	0.881	0.62
27_W	35_R	0.870	0.61
8_G	15_S	0.870	0.61
17_L	71_G	0.869	0.61
45_Y	49_A	0.863	0.61
50_L	53_R	0.862	0.61
45_Y	149_F	0.850	0.60
23_Q	81_M	0.838	0.58
40_L	55_N	0.836	0.58
49_A	157_Q	0.832	0.58
41_L	106_V	0.830	0.58
120_W	123_F	0.824	0.57
46_W	152_M	0.817	0.57
112_L	115_D	0.812	0.56
115_D	134_V	0.809	0.56
49_A	96_R	0.807	0.56
76_V	97_N	0.799	0.55
113_V	158_Q	0.798	0.55
84_I	114_V	0.794	0.54
70_S	117_I	0.782	0.53
100_L	150_L	0.777	0.53
60_F	158_Q	0.772	0.52
134_V	140_V	0.772	0.52
79_L	82_S	0.770	0.52
59_G	87_L	0.769	0.52
14_L	41_L	0.768	0.52
28_P	147_W	0.758	0.51
87_L	91_K	0.757	0.51
42_I	148_I	0.755	0.51
127_N	131_R	0.748	0.50
88_V	155_V	0.740	0.49
98_L	130_F	0.738	0.49
89_A	119_F	0.736	0.49
30_N	61_V	0.734	0.49
26_P	156_R	0.727	0.48
151_L	154_K	0.723	0.48
83_I	133_E	0.721	0.47
53_R	85_A	0.711	0.47
115_D	148_I	0.707	0.46
132_P	144_L	0.704	0.46
77_R	123_F	0.702	0.46
76_V	118_V	0.701	0.46
17_L	139_V	0.697	0.45
58_T	61_V	0.692	0.45
19_A	144_L	0.690	0.45
21_L	105_L	0.677	0.43
119_F	122_E	0.676	0.43
44_L	113_V	0.670	0.43
120_W	137_S	0.669	0.43
38_W	50_L	0.667	0.42
82_S	92_Y	0.664	0.42
27_W	69_I	0.664	0.42
135_F	138_S	0.663	0.42
79_L	105_L	0.660	0.42
100_L	121_A	0.657	0.41
114_V	135_F	0.656	0.41
112_L	116_I	0.655	0.41
119_F	130_F	0.654	0.41
49_A	53_R	0.644	0.40
70_S	111_S	0.643	0.40
122_E	131_R	0.638	0.40
84_I	106_V	0.631	0.39
82_S	107_V	0.627	0.39
144_L	147_W	0.624	0.38
48_L	151_L	0.623	0.38
44_L	48_L	0.622	0.38
72_S	147_W	0.620	0.38
123_F	129_S	0.618	0.38
53_R	73_T	0.612	0.37
13_W	18_I	0.612	0.37
49_A	92_Y	0.612	0.37
82_S	109_L	0.611	0.37
83_I	121_A	0.611	0.37
116_I	120_W	0.604	0.37
112_L	143_V	0.603	0.37
88_V	94_L	0.597	0.36
64_A	137_S	0.596	0.36
12_I	108_M	0.594	0.36
21_L	90_L	0.593	0.36
29_D	139_V	0.593	0.36
36_P	63_G	0.591	0.36
41_L	71_G	0.589	0.35
83_I	113_V	0.588	0.35
27_W	62_M	0.587	0.35
64_A	73_T	0.584	0.35
85_A	107_V	0.583	0.35
76_V	126_I	0.582	0.35
67_D	75_G	0.582	0.35
80_A	114_V	0.581	0.35
56_V	85_A	0.575	0.34
43_L	74_L	0.574	0.34
117_I	133_E	0.574	0.34
50_L	155_V	0.574	0.34
18_I	65_I	0.574	0.34
107_V	150_L	0.570	0.34
43_L	110_L	0.568	0.34
74_L	144_L	0.563	0.33
17_L	61_V	0.561	0.33
42_I	95_F	0.560	0.33
11_V	88_V	0.560	0.33
71_G	93_Q	0.558	0.33
73_T	121_A	0.557	0.33
34_F	124_L	0.557	0.33
41_L	61_V	0.555	0.33
112_L	120_W	0.553	0.32
37_N	111_S	0.552	0.32
43_L	65_I	0.550	0.32
98_L	112_L	0.548	0.32
30_N	143_V	0.546	0.32
35_R	102_Q	0.545	0.32
63_G	67_D	0.540	0.31
76_V	130_F	0.535	0.31
73_T	150_L	0.535	0.31
86_Y	89_A	0.534	0.31
21_L	147_W	0.533	0.31
16_F	98_L	0.533	0.31
107_V	143_V	0.524	0.30
77_R	86_Y	0.522	0.30
37_N	135_F	0.522	0.30
59_G	152_M	0.515	0.29
84_I	113_V	0.512	0.29
124_L	129_S	0.511	0.29
61_V	108_M	0.510	0.29
47_I	139_V	0.509	0.29
28_P	38_W	0.508	0.29
107_V	116_I	0.508	0.29
19_A	124_L	0.507	0.29
126_I	154_K	0.505	0.29
42_I	143_V	0.504	0.28
31_L	104_A	0.503	0.28
69_I	143_V	0.502	0.28
32_I	144_L	0.500	0.28
67_D	145_W	0.500	0.28

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
4hzuS	1	0.9568	72	0.911	Contact Map
4rfsS	1	0.9321	47.6	0.923	Contact Map
3p5nA	2	0.9074	32.7	0.93	Contact Map
4z7fA	2	0.9198	20.2	0.937	Contact Map
3rlbA	1	0.9506	18.4	0.938	Contact Map
4tkrA	2	0.9444	14.9	0.94	Contact Map
4huqS	1	0.9136	10.9	0.944	Contact Map
4brcA	2	0.3457	2.8	0.958	Contact Map
4dveA	3	0.963	2.7	0.958	Contact Map
3tx3A	2	0.3333	2.6	0.958	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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