LUXS - ECOLI - GREMLIN Contacts

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LUXS - S-ribosylhomocysteine lyase

UniProt:	P45578	Sequences: MPLLDSFTVDHTRMEAPAVRVAKTMNTPHGDAITVFDLRFCVPNKEVMPERGIHTLEHLFAGFMRNHLNGNGVEIIDISPMGCRTGFYMSLIGTPDEQRVADAWKAAMEDVLKVQDQNQIPELNVYQCGTYQMHSLQEAQDIARSILERDVRINSNEELALPKEKLQELHI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12712
Length:	171 (146)
Sequences:	991 (401)
Seq/√Len:	33.2

ECOLI - LUXS
BACSU - LUXS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_R	133_M	3.692	1.00
38_L	146_I	3.280	1.00
50_E	133_M	3.253	1.00
67_H	106_A	3.198	1.00
42_V	45_K	3.071	1.00
21_V	34_T	2.771	1.00
10_D	13_R	2.717	1.00
19_V	104_W	2.472	1.00
51_R	133_M	2.239	0.99
41_C	142_I	2.187	0.99
48_M	142_I	2.108	0.99
56_L	143_A	2.092	0.98
124_N	127_Q	2.085	0.98
50_E	84_R	2.036	0.98
96_D	99_R	2.032	0.98
55_T	134_H	1.888	0.97
109_E	113_K	1.877	0.97
12_T	125_V	1.866	0.97
56_L	111_V	1.833	0.96
49_P	52_G	1.821	0.96
75_I	91_L	1.779	0.96
33_I	90_S	1.772	0.96
144_R	148_E	1.737	0.95
15_E	42_V	1.729	0.95
105_K	109_E	1.663	0.94
60_F	107_A	1.630	0.93
120_I	134_H	1.624	0.93
10_D	126_Y	1.608	0.93
52_G	138_E	1.604	0.92
53_I	87_F	1.558	0.91
81_M	88_Y	1.529	0.91
48_M	53_I	1.520	0.90
60_F	64_M	1.505	0.90
145_S	149_R	1.491	0.89
117_Q	140_Q	1.453	0.88
3_L	127_Q	1.421	0.87
4_L	122_E	1.407	0.86
109_E	152_R	1.404	0.86
75_I	89_M	1.377	0.85
27_T	30_G	1.368	0.85
17_P	42_V	1.332	0.83
28_P	76_I	1.322	0.83
32_A	94_T	1.322	0.83
36_F	93_G	1.311	0.82
28_P	31_D	1.302	0.82
24_T	32_A	1.272	0.80
52_G	135_S	1.243	0.79
105_K	147_L	1.238	0.78
64_M	75_I	1.225	0.78
89_M	100_V	1.214	0.77
55_T	120_I	1.185	0.75
22_A	35_V	1.164	0.74
52_G	142_I	1.161	0.74
78_I	146_I	1.119	0.71
68_L	103_A	1.119	0.71
101_A	105_K	1.110	0.70
64_M	89_M	1.097	0.69
60_F	104_W	1.097	0.69
141_D	145_S	1.092	0.69
148_E	152_R	1.088	0.69
141_D	144_R	1.078	0.68
106_A	109_E	1.078	0.68
138_E	141_D	1.073	0.68
97_E	101_A	1.059	0.67
111_V	143_A	1.058	0.66
109_E	144_R	1.037	0.65
67_H	110_D	1.024	0.64
14_M	20_R	1.020	0.64
63_F	67_H	1.015	0.63
5_D	9_V	1.012	0.63
96_D	102_D	1.007	0.63
17_P	41_C	1.005	0.62
76_I	90_S	1.000	0.62
112_L	140_Q	0.986	0.61
19_V	142_I	0.976	0.60
46_E	145_S	0.975	0.60
21_V	97_E	0.975	0.60
60_F	78_I	0.962	0.59
47_V	135_S	0.960	0.59
41_C	145_S	0.958	0.59
118_N	140_Q	0.950	0.58
112_L	144_R	0.945	0.58
25_M	94_T	0.944	0.58
135_S	138_E	0.940	0.57
3_L	8_T	0.930	0.56
78_I	87_F	0.930	0.56
137_Q	144_R	0.926	0.56
2_P	5_D	0.919	0.55
64_M	103_A	0.915	0.55
27_T	33_I	0.912	0.55
95_P	99_R	0.912	0.55
15_E	150_D	0.909	0.55
114_V	118_N	0.908	0.55
22_A	79_S	0.899	0.54
17_P	142_I	0.895	0.54
22_A	81_M	0.881	0.52
14_M	42_V	0.880	0.52
36_F	97_E	0.875	0.52
19_V	100_V	0.872	0.52
40_F	120_I	0.864	0.51
14_M	18_A	0.854	0.50
56_L	108_M	0.852	0.50
107_A	111_V	0.841	0.49
35_V	81_M	0.838	0.49
56_L	78_I	0.831	0.48
49_P	138_E	0.827	0.48
55_T	132_Q	0.823	0.48
68_L	100_V	0.822	0.47
22_A	88_Y	0.815	0.47
12_T	126_Y	0.808	0.46
130_T	133_M	0.800	0.46
19_V	146_I	0.796	0.45
98_Q	102_D	0.790	0.45
91_L	103_A	0.783	0.44
9_V	18_A	0.781	0.44
27_T	31_D	0.779	0.44
35_V	88_Y	0.776	0.44
102_D	106_A	0.771	0.43
100_V	104_W	0.769	0.43
9_V	14_M	0.755	0.42
32_A	96_D	0.754	0.42
33_I	76_I	0.753	0.42
19_V	101_A	0.749	0.41
14_M	35_V	0.747	0.41
20_R	79_S	0.746	0.41
105_K	152_R	0.735	0.40
13_R	126_Y	0.733	0.40
41_C	53_I	0.725	0.39
119_Q	127_Q	0.721	0.39
109_E	112_L	0.717	0.39
100_V	148_E	0.712	0.38
35_V	122_E	0.711	0.38
139_A	143_A	0.707	0.38
68_L	96_D	0.707	0.38
32_A	153_I	0.704	0.38
78_I	84_R	0.699	0.37
59_L	63_F	0.694	0.37
63_F	106_A	0.692	0.37
24_T	94_T	0.686	0.36
61_A	65_R	0.680	0.36
45_K	125_V	0.680	0.36
35_V	77_D	0.676	0.36
1_M	66_N	0.675	0.36
36_F	95_P	0.668	0.35
9_V	104_W	0.664	0.35
47_V	130_T	0.662	0.35
100_V	103_A	0.661	0.34
84_R	131_Y	0.660	0.34
20_R	77_D	0.656	0.34
40_F	45_K	0.656	0.34
18_A	22_A	0.653	0.34
10_D	125_V	0.650	0.34
40_F	108_M	0.646	0.33
4_L	18_A	0.645	0.33
18_A	42_V	0.644	0.33
26_N	29_H	0.634	0.32
76_I	117_Q	0.632	0.32
23_K	103_A	0.630	0.32
38_L	103_A	0.627	0.32
87_F	120_I	0.626	0.32
147_L	152_R	0.626	0.32
40_F	53_I	0.624	0.32
4_L	90_S	0.619	0.31
34_T	93_G	0.618	0.31
7_F	61_A	0.614	0.31
18_A	53_I	0.614	0.31
108_M	143_A	0.612	0.31
4_L	35_V	0.610	0.31
40_F	48_M	0.608	0.31
64_M	104_W	0.603	0.30
109_E	148_E	0.601	0.30
17_P	149_R	0.601	0.30
100_V	137_Q	0.599	0.30
3_L	9_V	0.598	0.30
41_C	46_E	0.596	0.30
55_T	133_M	0.596	0.30
62_G	66_N	0.595	0.30
60_F	111_V	0.593	0.30
9_V	42_V	0.593	0.30
64_M	78_I	0.592	0.29
34_T	91_L	0.592	0.29
101_A	151_V	0.591	0.29
8_T	62_G	0.590	0.29
31_D	76_I	0.588	0.29
36_F	100_V	0.587	0.29
75_I	107_A	0.585	0.29
108_M	112_L	0.577	0.28
61_A	122_E	0.574	0.28
123_L	134_H	0.572	0.28
12_T	134_H	0.565	0.28
144_R	152_R	0.563	0.28
21_V	24_T	0.561	0.27
114_V	140_Q	0.561	0.27
66_N	103_A	0.560	0.27
70_G	141_D	0.558	0.27
112_L	152_R	0.557	0.27
59_L	108_M	0.554	0.27
18_A	35_V	0.546	0.26
47_V	133_M	0.542	0.26
34_T	94_T	0.538	0.26
135_S	141_D	0.537	0.26
22_A	77_D	0.537	0.26
21_V	36_F	0.533	0.26
59_L	121_P	0.531	0.25
98_Q	101_A	0.527	0.25
114_V	119_Q	0.523	0.25
46_E	149_R	0.523	0.25
91_L	100_V	0.517	0.25
84_R	130_T	0.516	0.24
23_K	62_G	0.515	0.24
36_F	134_H	0.514	0.24
14_M	79_S	0.514	0.24
27_T	92_I	0.512	0.24
49_P	107_A	0.510	0.24
69_N	106_A	0.509	0.24
24_T	93_G	0.507	0.24
104_W	152_R	0.502	0.24
59_L	114_V	0.501	0.24
61_A	77_D	0.500	0.24

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
1j6wA	2	0.9415	100	0.068	Contact Map
4xchA	4	0.8713	100	0.133	Contact Map
1vjeA	2	0.8713	100	0.136	Contact Map
1j98A	2	0.883	100	0.14	Contact Map
1j6xA	2	0.8772	100	0.157	Contact Map
2q7aA	2	0.4327	21.1	0.96	Contact Map
3iixA	1	0.6842	18.6	0.96	Contact Map
3s4eA	1	0.7076	13.4	0.963	Contact Map
4jmkA	1	0.7485	11.7	0.964	Contact Map
1eexG	1	0.2456	11.2	0.964	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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