MRED - BACSU - GREMLIN Contacts

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MRED - Rod shape-determining protein MreD

UniProt:	Q01467	Sequences: MKRFLLPFVMMLVFSAESIFTDLVHFPFVTDDQVLAPRFLMLVLIFMSAFINQKHAMIYGFIFGFLYDMNYTSLLGVYMFGFAGLCYLASKAFKVLHTNAFVVILIAVLAVCLLEFYVFGIQSLIHKDIMTFNGFVLDRFIPTILLNIAAALILVLPFRLFFMSLKKELRDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (162)
Sequences:	442 (375)
Seq/√Len:	29.5

BACSU - 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
38_R	115_E	5.802	1.00
81_G	117_Y	4.307	1.00
63_F	66_L	3.042	1.00
44_L	86_C	2.884	1.00
43_V	158_F	2.745	1.00
46_F	69_M	2.425	0.99
58_I	62_I	2.390	0.99
22_D	121_I	2.373	0.99
5_L	45_I	2.249	0.99
59_Y	119_F	2.170	0.98
60_G	86_C	2.118	0.98
39_F	154_L	2.071	0.97
115_E	135_F	2.007	0.97
116_F	132_F	1.918	0.96
101_F	128_D	1.894	0.96
109_L	133_N	1.873	0.95
39_F	150_A	1.857	0.95
9_V	115_E	1.831	0.95
6_L	47_M	1.818	0.95
73_S	158_F	1.770	0.94
8_F	124_L	1.750	0.93
35_L	146_L	1.680	0.92
18_S	71_Y	1.658	0.91
72_T	75_L	1.647	0.91
37_P	139_R	1.643	0.91
36_A	43_V	1.596	0.90
70_N	164_S	1.587	0.89
67_Y	82_F	1.564	0.89
44_L	82_F	1.552	0.88
100_A	155_V	1.516	0.87
68_D	76_G	1.514	0.87
65_F	75_L	1.508	0.87
36_A	146_L	1.499	0.86
113_L	148_I	1.493	0.86
42_L	89_A	1.492	0.86
146_L	150_A	1.490	0.86
116_F	148_I	1.470	0.85
28_F	126_H	1.430	0.84
78_Y	114_L	1.416	0.83
59_Y	72_T	1.409	0.83
27_P	152_L	1.391	0.82
140_F	147_N	1.357	0.80
21_T	158_F	1.357	0.80
143_T	147_N	1.339	0.79
25_H	82_F	1.323	0.79
88_L	91_K	1.315	0.78
84_G	127_K	1.274	0.76
7_P	72_T	1.273	0.76
41_M	66_L	1.259	0.75
16_A	28_F	1.254	0.75
150_A	154_L	1.251	0.75
17_E	70_N	1.244	0.74
45_I	110_A	1.241	0.74
75_L	136_V	1.235	0.74
42_L	109_L	1.231	0.73
46_F	136_V	1.228	0.73
66_L	71_Y	1.204	0.72
61_F	160_L	1.198	0.71
21_T	42_L	1.184	0.70
74_L	156_L	1.181	0.70
42_L	150_A	1.168	0.69
102_V	162_F	1.163	0.69
60_G	151_A	1.160	0.69
29_V	149_A	1.157	0.69
60_G	66_L	1.156	0.69
105_L	108_V	1.155	0.68
114_L	162_F	1.154	0.68
89_A	110_A	1.137	0.67
107_A	130_M	1.112	0.65
70_N	81_G	1.111	0.65
18_S	26_F	1.095	0.64
67_Y	72_T	1.089	0.64
42_L	152_L	1.085	0.64
20_F	108_V	1.082	0.63
20_F	39_F	1.080	0.63
12_L	153_I	1.059	0.62
21_T	37_P	1.050	0.61
12_L	148_I	1.045	0.61
60_G	112_C	1.043	0.60
93_F	111_V	1.039	0.60
18_S	21_T	1.032	0.60
115_E	139_R	1.024	0.59
4_F	38_R	1.020	0.59
47_M	162_F	1.017	0.58
6_L	43_V	1.002	0.57
111_V	147_N	0.998	0.57
61_F	75_L	0.994	0.57
85_L	154_L	0.987	0.56
112_C	140_F	0.974	0.55
82_F	137_L	0.969	0.55
104_I	151_A	0.965	0.54
41_M	96_L	0.965	0.54
143_T	162_F	0.956	0.54
46_F	146_L	0.952	0.53
17_E	69_M	0.948	0.53
120_G	152_L	0.945	0.53
37_P	78_Y	0.940	0.52
75_L	121_I	0.937	0.52
131_T	138_D	0.937	0.52
104_I	127_K	0.933	0.52
52_N	111_V	0.932	0.52
39_F	97_H	0.920	0.51
113_L	134_G	0.918	0.51
9_V	16_A	0.911	0.50
6_L	10_M	0.911	0.50
106_I	123_S	0.896	0.49
45_I	149_A	0.886	0.48
67_Y	135_F	0.874	0.47
65_F	118_V	0.872	0.47
17_E	53_Q	0.867	0.47
61_F	91_K	0.861	0.46
70_N	73_S	0.859	0.46
96_L	147_N	0.854	0.46
16_A	149_A	0.839	0.45
8_F	160_L	0.831	0.44
60_G	150_A	0.823	0.43
95_V	99_N	0.815	0.43
49_A	103_V	0.815	0.43
19_I	151_A	0.813	0.43
40_L	99_N	0.813	0.43
50_F	63_F	0.811	0.42
25_H	151_A	0.807	0.42
97_H	146_L	0.803	0.42
42_L	111_V	0.802	0.42
79_M	125_I	0.799	0.41
4_F	145_L	0.793	0.41
20_F	32_D	0.788	0.41
18_S	75_L	0.786	0.40
7_P	59_Y	0.776	0.40
89_A	144_I	0.774	0.40
17_E	36_A	0.769	0.39
23_L	84_G	0.768	0.39
85_L	98_T	0.766	0.39
74_L	153_I	0.763	0.39
45_I	52_N	0.753	0.38
56_A	60_G	0.746	0.37
114_L	160_L	0.742	0.37
43_V	47_M	0.741	0.37
39_F	42_L	0.740	0.37
24_V	117_Y	0.736	0.37
8_F	151_A	0.736	0.37
69_M	123_S	0.732	0.36
156_L	160_L	0.728	0.36
60_G	80_F	0.727	0.36
41_M	111_V	0.724	0.36
13_V	62_I	0.724	0.36
63_F	74_L	0.723	0.36
59_Y	130_M	0.714	0.35
9_V	43_V	0.711	0.35
123_S	128_D	0.710	0.35
92_A	117_Y	0.709	0.35
78_Y	139_R	0.708	0.35
44_L	56_A	0.705	0.34
106_I	113_L	0.702	0.34
117_Y	141_I	0.700	0.34
69_M	137_L	0.697	0.34
15_S	19_I	0.695	0.34
119_F	128_D	0.690	0.33
32_D	65_F	0.689	0.33
40_L	129_I	0.687	0.33
50_F	71_Y	0.682	0.33
70_N	122_Q	0.677	0.33
108_V	148_I	0.676	0.32
77_V	82_F	0.672	0.32
65_F	156_L	0.671	0.32
92_A	133_N	0.670	0.32
10_M	43_V	0.666	0.32
62_I	96_L	0.659	0.31
13_V	149_A	0.657	0.31
4_F	159_R	0.652	0.31
109_L	132_F	0.648	0.31
98_T	102_V	0.646	0.30
156_L	159_R	0.642	0.30
125_I	153_I	0.642	0.30
107_A	111_V	0.640	0.30
11_M	18_S	0.638	0.30
42_L	154_L	0.636	0.30
56_A	93_F	0.633	0.30
4_F	123_S	0.632	0.29
111_V	115_E	0.632	0.29
60_G	63_F	0.630	0.29
70_N	160_L	0.626	0.29
46_F	151_A	0.625	0.29
17_E	56_A	0.625	0.29
96_L	100_A	0.624	0.29
125_I	139_R	0.620	0.29
100_A	157_P	0.618	0.29
35_L	45_I	0.618	0.29
43_V	157_P	0.616	0.28
59_Y	63_F	0.615	0.28
146_L	157_P	0.613	0.28
21_T	63_F	0.612	0.28
37_P	100_A	0.607	0.28
46_F	150_A	0.607	0.28
23_L	145_L	0.600	0.27
135_F	139_R	0.592	0.27
50_F	160_L	0.591	0.27
8_F	162_F	0.588	0.27
18_S	25_H	0.585	0.27
141_I	154_L	0.583	0.26
80_F	124_L	0.581	0.26
65_F	109_L	0.581	0.26
40_L	74_L	0.580	0.26
41_M	113_L	0.580	0.26
87_Y	119_F	0.579	0.26
11_M	19_I	0.578	0.26
78_Y	115_E	0.578	0.26
108_V	124_L	0.577	0.26
9_V	131_T	0.576	0.26
74_L	109_L	0.576	0.26
53_Q	142_P	0.575	0.26
15_S	75_L	0.570	0.26
38_R	103_V	0.570	0.26
14_F	131_T	0.563	0.25
142_P	159_R	0.560	0.25
112_C	125_I	0.559	0.25
59_Y	117_Y	0.558	0.25
102_V	128_D	0.555	0.25
140_F	162_F	0.549	0.24
5_L	85_L	0.541	0.24
44_L	149_A	0.540	0.24
109_L	141_I	0.537	0.24
104_I	110_A	0.536	0.24
137_L	145_L	0.536	0.24
86_C	151_A	0.535	0.24
39_F	51_I	0.534	0.24
29_V	106_I	0.526	0.23
16_A	43_V	0.522	0.23
79_M	98_T	0.521	0.23
113_L	128_D	0.520	0.23
77_V	151_A	0.519	0.23
135_F	140_F	0.518	0.23
10_M	31_D	0.514	0.22
17_E	39_F	0.514	0.22
78_Y	131_T	0.513	0.22
65_F	125_I	0.513	0.22
44_L	140_F	0.511	0.22
48_S	131_T	0.508	0.22
31_D	113_L	0.508	0.22
37_P	54_K	0.505	0.22
56_A	73_S	0.501	0.22
121_I	124_L	0.501	0.22
135_F	147_N	0.500	0.22

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
4z7fA	2	0.8953	68.6	0.912	Contact Map
3rlbA	1	0.9244	63.9	0.915	Contact Map
4huqS	1	0.8721	56.3	0.919	Contact Map
4rfsS	1	0.8953	55.1	0.919	Contact Map
4tkrA	2	0.907	49.9	0.922	Contact Map
4hzuS	1	0.9012	40.6	0.926	Contact Map
2ksfA	1	0.564	14.2	0.941	Contact Map
3p5nA	2	0.8605	13.7	0.941	Contact Map
4j72A	2	0.2035	12.6	0.942	Contact Map
4dveA	3	0.9477	12.5	0.942	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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