LUXS - BACSU - GREMLIN Contacts

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LUXS - S-ribosylhomocysteine lyase

UniProt:	O34667	Sequences: MPSVESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNKQAMKPDTIHTLEHLLAFTIRSHAEKYDHFDIIDISPMGCQTGYYLVVSGEPTSAEIVDLLEDTMKEAVEITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKEELLKVFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	157 (141)
Sequences:	966 (376)
Seq/√Len:	31.7

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
85_Q	131_L	3.684	1.00
38_I	144_W	3.311	1.00
50_P	131_L	3.211	1.00
67_H	107_D	3.034	1.00
42_Q	45_K	2.842	1.00
10_D	13_A	2.787	1.00
21_H	34_N	2.497	1.00
51_D	131_L	2.356	0.99
19_V	105_L	2.300	0.99
41_C	140_L	2.220	0.99
122_N	125_Q	2.182	0.99
116_T	138_K	2.109	0.98
48_M	140_L	2.081	0.98
50_P	85_Q	2.047	0.98
56_L	141_M	2.028	0.98
18_Y	22_C	2.014	0.98
12_N	123_E	1.917	0.97
49_K	52_T	1.834	0.96
55_T	132_H	1.819	0.96
76_I	92_V	1.797	0.95
56_L	112_A	1.779	0.95
97_T	100_E	1.750	0.95
15_V	42_Q	1.731	0.94
110_K	114_E	1.727	0.94
142_R	146_S	1.717	0.94
33_V	91_V	1.714	0.94
10_D	124_K	1.654	0.93
53_I	88_Y	1.591	0.91
82_M	89_Y	1.590	0.91
60_L	108_T	1.565	0.91
60_L	64_I	1.556	0.90
143_F	147_Q	1.550	0.90
52_T	136_G	1.540	0.90
106_E	110_K	1.517	0.89
118_I	132_H	1.476	0.88
4_V	120_A	1.459	0.87
25_H	95_E	1.455	0.87
48_M	53_I	1.435	0.86
76_I	90_L	1.384	0.84
17_P	42_Q	1.344	0.82
32_V	95_E	1.343	0.82
3_S	125_Q	1.318	0.81
36_F	94_G	1.297	0.80
28_G	31_G	1.296	0.80
55_T	118_I	1.223	0.76
79_I	144_W	1.221	0.76
97_T	103_D	1.194	0.74
90_L	101_I	1.182	0.73
98_S	102_V	1.177	0.73
68_A	104_L	1.148	0.71
52_T	133_D	1.146	0.71
139_R	143_F	1.144	0.71
64_I	76_I	1.136	0.70
46_Q	143_F	1.134	0.70
22_C	35_K	1.126	0.69
112_A	141_M	1.122	0.69
106_E	145_L	1.122	0.69
17_P	41_C	1.118	0.69
102_V	106_E	1.116	0.69
64_I	90_L	1.103	0.68
52_T	140_L	1.100	0.68
27_V	30_D	1.089	0.67
60_L	105_L	1.082	0.66
17_P	140_L	1.072	0.66
113_V	142_R	1.060	0.65
14_V	20_R	1.023	0.62
60_L	79_I	1.016	0.61
107_D	110_K	1.016	0.61
67_H	111_E	1.007	0.61
110_K	142_R	1.006	0.61
28_G	77_I	1.004	0.60
136_G	139_R	1.004	0.60
47_A	133_D	0.984	0.59
63_T	67_H	0.983	0.59
113_V	138_K	0.973	0.58
64_I	104_L	0.968	0.58
14_V	42_Q	0.958	0.57
2_P	5_E	0.956	0.57
41_C	143_F	0.941	0.55
133_D	136_G	0.934	0.55
21_H	98_S	0.924	0.54
18_Y	23_G	0.916	0.53
96_P	100_E	0.903	0.52
56_L	109_M	0.901	0.52
79_I	88_Y	0.893	0.52
5_E	9_L	0.891	0.51
3_S	8_E	0.889	0.51
35_K	82_M	0.888	0.51
139_R	142_R	0.883	0.51
103_D	107_D	0.880	0.50
135_E	142_R	0.874	0.50
108_T	112_A	0.866	0.49
27_V	33_V	0.858	0.49
77_I	91_V	0.851	0.48
19_V	140_L	0.846	0.48
56_L	79_I	0.838	0.47
17_P	20_R	0.834	0.47
36_F	98_S	0.832	0.47
35_K	89_Y	0.823	0.46
22_C	80_S	0.812	0.45
12_N	124_K	0.804	0.44
137_A	141_M	0.798	0.44
27_V	31_G	0.797	0.44
101_I	105_L	0.795	0.44
40_F	45_K	0.792	0.43
68_A	101_I	0.790	0.43
40_F	118_I	0.787	0.43
92_V	104_L	0.786	0.43
14_V	18_Y	0.781	0.42
128_Q	131_L	0.780	0.42
9_L	14_V	0.779	0.42
110_K	113_V	0.778	0.42
36_F	96_P	0.778	0.42
55_T	130_K	0.778	0.42
117_E	125_Q	0.768	0.41
14_V	35_K	0.764	0.41
10_D	123_E	0.750	0.40
49_K	136_G	0.748	0.40
85_Q	129_A	0.746	0.40
38_I	104_L	0.736	0.39
22_C	82_M	0.734	0.39
35_K	120_A	0.728	0.38
18_Y	21_H	0.724	0.38
20_R	80_S	0.724	0.38
1_M	66_S	0.721	0.38
13_A	124_K	0.719	0.38
9_L	42_Q	0.717	0.37
24_V	29_T	0.703	0.36
35_K	78_D	0.696	0.36
7_F	61_A	0.689	0.35
101_I	146_S	0.687	0.35
8_E	62_F	0.685	0.35
41_C	53_I	0.685	0.35
59_L	63_T	0.684	0.35
63_T	115_I	0.682	0.35
61_A	65_R	0.682	0.35
47_A	128_Q	0.678	0.35
64_I	105_L	0.677	0.34
92_V	95_E	0.677	0.34
115_I	138_K	0.675	0.34
24_V	32_V	0.672	0.34
22_C	89_Y	0.664	0.33
3_S	9_L	0.662	0.33
109_M	141_M	0.662	0.33
79_I	85_Q	0.655	0.33
109_M	113_V	0.653	0.33
101_I	135_E	0.649	0.32
23_G	104_L	0.647	0.32
40_F	48_M	0.647	0.32
121_A	132_H	0.646	0.32
40_F	53_I	0.642	0.32
62_F	66_S	0.640	0.32
17_P	147_Q	0.638	0.32
33_V	77_I	0.636	0.31
75_D	96_P	0.634	0.31
4_V	35_K	0.630	0.31
66_S	104_L	0.628	0.31
32_V	97_T	0.622	0.30
20_R	78_D	0.617	0.30
101_I	104_L	0.615	0.30
92_V	141_M	0.610	0.30
27_V	48_M	0.609	0.30
9_L	18_Y	0.608	0.30
40_F	109_M	0.606	0.29
116_T	142_R	0.601	0.29
69_E	107_D	0.598	0.29
63_T	107_D	0.597	0.29
4_V	91_V	0.597	0.29
15_V	147_Q	0.590	0.28
61_A	120_A	0.586	0.28
59_L	109_M	0.586	0.28
133_D	139_R	0.583	0.28
55_T	131_L	0.582	0.28
47_A	131_L	0.580	0.28
31_G	77_I	0.577	0.27
36_F	102_V	0.572	0.27
18_Y	53_I	0.567	0.27
9_L	105_L	0.564	0.27
34_N	94_G	0.563	0.27
110_K	146_S	0.557	0.26
2_P	66_S	0.557	0.26
99_A	103_D	0.557	0.26
45_K	123_E	0.557	0.26
32_V	91_V	0.555	0.26
92_V	101_I	0.555	0.26
40_F	113_V	0.554	0.26
14_V	80_S	0.553	0.26
135_E	139_R	0.552	0.26
34_N	92_V	0.552	0.26
59_L	115_I	0.551	0.26
49_K	139_R	0.549	0.26
60_L	109_M	0.545	0.25
85_Q	128_Q	0.544	0.25
59_L	119_P	0.543	0.25
41_C	46_Q	0.540	0.25
19_V	144_W	0.537	0.25
36_F	101_I	0.536	0.25
12_N	132_H	0.533	0.25
109_M	145_L	0.532	0.25
113_V	116_T	0.529	0.24
92_V	96_P	0.524	0.24
4_V	18_Y	0.523	0.24
99_A	102_V	0.522	0.24
29_T	77_I	0.515	0.24
25_H	32_V	0.510	0.23
15_V	143_F	0.509	0.23
32_V	93_S	0.508	0.23
9_L	132_H	0.505	0.23
20_R	23_G	0.504	0.23
110_K	145_L	0.503	0.23
100_E	103_D	0.502	0.23
21_H	36_F	0.500	0.23

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
1j98A	2	0.9745	100	0.059	Contact Map
1vjeA	2	0.9363	100	0.08	Contact Map
1j6xA	2	0.9554	100	0.085	Contact Map
1j6wA	2	0.9682	100	0.087	Contact Map
4xchA	4	0.9045	100	0.095	Contact Map
2kvoA	1	0.5924	36	0.952	Contact Map
1ihkA	2	0.5605	16.2	0.96	Contact Map
2q7aA	2	0.4777	15.5	0.96	Contact Map
3bw6A	1	0.5541	12.4	0.962	Contact Map
3emuA	1	0.7389	12.2	0.962	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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