GLPP - BACSU - GREMLIN Contacts

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GLPP - Glycerol uptake operon antiterminator regulatory protein

UniProt:	P30300	Sequences: MMSFHNQPILPAIRNMKQFDEFLNSSFSYGVILDIHLGQLKGVIKEAQKHGKNMMVHVDLIQGIKHDEYGAEFICQDIKPAGIISTRSNVIAKAKQKKIYAIQRLFLLDTSAMEKSMEFIGKHKPDFIEVLPGIVPSLIQEIKEKTGIPIFAGGFIRTEEDVEQALKAGAVAVTTSNTKLWKKYENFLTESD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	192 (178)
Sequences:	642 (519)
Seq/√Len:	38.9

ECOLI - YGCP
BACSU - GLPP

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_A	54_M	4.066	1.00
141_E	157_R	3.995	1.00
159_E	163_E	3.190	1.00
18_Q	178_T	3.014	1.00
22_F	30_G	3.006	1.00
64_I	70_G	2.878	1.00
11_P	27_F	2.777	1.00
95_K	126_D	2.691	1.00
48_Q	81_A	2.682	1.00
30_G	47_A	2.664	1.00
45_K	49_K	2.554	1.00
20_D	46_E	2.533	1.00
44_I	78_I	2.522	1.00
91_I	101_A	2.447	1.00
85_S	91_I	2.423	1.00
137_S	161_D	2.268	1.00
41_K	77_D	2.209	0.99
74_I	80_P	1.990	0.99
21_E	178_T	1.972	0.99
105_L	116_S	1.940	0.98
93_K	96_Q	1.917	0.98
86_T	153_G	1.892	0.98
15_N	18_Q	1.892	0.98
57_H	153_G	1.861	0.98
142_I	150_I	1.807	0.98
119_F	131_L	1.805	0.98
44_I	54_M	1.788	0.97
19_F	47_A	1.763	0.97
72_E	93_K	1.755	0.97
73_F	77_D	1.726	0.97
13_I	47_A	1.715	0.97
28_S	53_N	1.676	0.96
143_K	150_I	1.641	0.96
16_M	34_D	1.624	0.95
75_C	99_I	1.620	0.95
40_L	78_I	1.606	0.95
40_L	73_F	1.586	0.95
60_L	176_S	1.585	0.95
175_T	180_L	1.547	0.94
104_R	129_E	1.492	0.93
151_F	174_T	1.440	0.91
85_S	90_V	1.408	0.91
61_I	95_K	1.384	0.90
130_V	142_I	1.376	0.89
117_M	142_I	1.372	0.89
71_A	97_K	1.364	0.89
86_T	106_F	1.353	0.89
162_V	180_L	1.353	0.89
40_L	48_Q	1.343	0.88
102_I	127_F	1.325	0.88
61_I	64_I	1.320	0.87
32_I	47_A	1.296	0.86
29_Y	53_N	1.296	0.86
165_A	170_A	1.267	0.85
103_Q	156_I	1.261	0.85
57_H	86_T	1.257	0.85
76_Q	128_I	1.249	0.84
14_R	60_L	1.237	0.84
44_I	81_A	1.233	0.84
32_I	54_M	1.224	0.83
12_A	33_L	1.216	0.83
135_V	138_L	1.214	0.83
160_E	164_Q	1.214	0.83
104_R	153_G	1.211	0.82
114_E	145_K	1.210	0.82
88_S	167_K	1.200	0.82
118_E	171_V	1.190	0.81
68_E	131_L	1.152	0.79
108_L	164_Q	1.136	0.78
140_Q	144_E	1.133	0.78
36_H	72_E	1.129	0.78
33_L	104_R	1.124	0.77
43_V	55_M	1.091	0.75
55_M	82_G	1.069	0.74
94_A	101_A	1.069	0.74
108_L	131_L	1.065	0.73
128_I	146_T	1.054	0.73
85_S	101_A	1.052	0.72
143_K	171_V	1.050	0.72
128_I	148_I	1.050	0.72
107_L	137_S	1.026	0.71
72_E	97_K	1.024	0.70
34_D	110_T	1.017	0.70
120_I	125_P	1.008	0.69
58_V	71_A	1.006	0.69
141_E	145_K	1.005	0.69
51_G	144_E	0.999	0.69
103_Q	149_P	0.978	0.67
11_P	131_L	0.977	0.67
121_G	173_V	0.976	0.67
57_H	125_P	0.960	0.65
19_F	23_L	0.957	0.65
29_Y	84_I	0.952	0.65
83_I	159_E	0.949	0.64
121_G	145_K	0.941	0.64
65_K	115_K	0.939	0.64
13_I	30_G	0.928	0.63
24_N	179_K	0.922	0.62
33_L	84_I	0.906	0.61
32_I	176_S	0.902	0.60
16_M	176_S	0.888	0.59
32_I	43_V	0.884	0.59
82_G	104_R	0.880	0.59
24_N	50_H	0.879	0.58
139_I	152_A	0.874	0.58
71_A	99_I	0.873	0.58
84_I	131_L	0.869	0.58
13_I	43_V	0.866	0.57
46_E	50_H	0.863	0.57
58_V	74_I	0.859	0.57
91_I	123_H	0.851	0.56
81_A	105_L	0.848	0.56
8_P	159_E	0.847	0.56
44_I	105_L	0.841	0.55
8_P	43_V	0.840	0.55
33_L	59_D	0.830	0.54
17_K	179_K	0.826	0.54
162_V	165_A	0.826	0.54
32_I	107_L	0.820	0.53
115_K	118_E	0.819	0.53
139_I	165_A	0.812	0.53
43_V	176_S	0.810	0.52
36_H	69_Y	0.809	0.52
29_Y	56_V	0.807	0.52
114_E	117_M	0.804	0.52
15_N	22_F	0.794	0.51
65_K	90_V	0.793	0.51
149_P	166_L	0.788	0.50
144_E	178_T	0.785	0.50
127_F	130_V	0.785	0.50
93_K	115_K	0.784	0.50
141_E	144_E	0.781	0.50
88_S	103_Q	0.781	0.50
71_A	83_I	0.778	0.49
12_A	174_T	0.778	0.49
32_I	66_H	0.772	0.49
55_M	180_L	0.770	0.49
137_S	162_V	0.765	0.48
112_A	153_G	0.763	0.48
124_K	148_I	0.762	0.48
87_R	99_I	0.760	0.48
19_F	111_S	0.755	0.47
7_Q	75_C	0.755	0.47
139_I	170_A	0.753	0.47
117_M	120_I	0.752	0.47
34_D	176_S	0.751	0.47
35_I	108_L	0.749	0.47
55_M	177_N	0.745	0.46
40_L	55_M	0.742	0.46
116_S	127_F	0.741	0.46
83_I	164_Q	0.739	0.46
14_R	67_D	0.733	0.45
64_I	72_E	0.729	0.45
11_P	53_N	0.726	0.45
65_K	148_I	0.724	0.45
54_M	81_A	0.723	0.44
75_C	80_P	0.715	0.44
158_T	163_E	0.712	0.44
33_L	86_T	0.710	0.43
57_H	104_R	0.706	0.43
41_K	45_K	0.706	0.43
167_K	171_V	0.702	0.43
157_R	173_V	0.697	0.42
35_I	116_S	0.696	0.42
7_Q	112_A	0.691	0.42
71_A	75_C	0.688	0.41
82_G	129_E	0.681	0.41
85_S	126_D	0.672	0.40
86_T	103_Q	0.672	0.40
25_S	168_A	0.670	0.40
21_E	79_K	0.664	0.39
85_S	142_I	0.663	0.39
113_M	142_I	0.662	0.39
123_H	156_I	0.661	0.39
6_N	28_S	0.661	0.39
8_P	56_V	0.656	0.39
30_G	66_H	0.653	0.38
55_M	151_F	0.650	0.38
104_R	131_L	0.649	0.38
73_F	87_R	0.649	0.38
60_L	131_L	0.648	0.38
37_L	151_F	0.645	0.38
33_L	131_L	0.644	0.38
163_E	167_K	0.641	0.37
133_G	156_I	0.640	0.37
133_G	170_A	0.639	0.37
129_E	153_G	0.638	0.37
61_I	107_L	0.633	0.37
31_V	35_I	0.626	0.36
37_L	90_V	0.622	0.36
85_S	164_Q	0.620	0.36
159_E	162_V	0.619	0.35
91_I	125_P	0.618	0.35
55_M	100_Y	0.617	0.35
27_F	36_H	0.616	0.35
14_R	161_D	0.612	0.35
12_A	108_L	0.612	0.35
87_R	170_A	0.611	0.35
138_L	161_D	0.608	0.35
59_D	133_G	0.607	0.34
99_I	160_E	0.606	0.34
92_A	155_F	0.605	0.34
19_F	46_E	0.603	0.34
44_I	48_Q	0.602	0.34
172_A	180_L	0.602	0.34
12_A	168_A	0.598	0.34
33_L	60_L	0.596	0.34
133_G	139_I	0.595	0.34
35_I	155_F	0.594	0.33
134_I	155_F	0.592	0.33
152_A	161_D	0.589	0.33
143_K	160_E	0.587	0.33
13_I	16_M	0.581	0.32
14_R	111_S	0.581	0.32
58_V	100_Y	0.580	0.32
89_N	103_Q	0.577	0.32
14_R	110_T	0.575	0.32
75_C	97_K	0.574	0.32
33_L	110_T	0.572	0.32
56_V	156_I	0.571	0.32
26_S	123_H	0.570	0.32
164_Q	167_K	0.570	0.32
130_V	166_L	0.567	0.31
49_K	139_I	0.566	0.31
75_C	85_S	0.564	0.31
16_M	43_V	0.564	0.31
9_I	162_V	0.562	0.31
9_I	59_D	0.561	0.31
67_D	78_I	0.561	0.31
56_V	74_I	0.561	0.31
115_K	119_F	0.559	0.31
30_G	118_E	0.557	0.31
8_P	15_N	0.555	0.30
131_L	153_G	0.553	0.30
32_I	98_K	0.553	0.30
5_H	26_S	0.552	0.30
24_N	51_G	0.551	0.30
16_M	167_K	0.550	0.30
17_K	20_D	0.549	0.30
68_E	85_S	0.549	0.30
14_R	74_I	0.545	0.30
7_Q	27_F	0.544	0.30
46_E	98_K	0.543	0.29
110_T	165_A	0.537	0.29
30_G	60_L	0.533	0.29
49_K	160_E	0.531	0.29
48_Q	167_K	0.531	0.29
113_M	146_T	0.530	0.29
72_E	76_Q	0.529	0.28
61_I	102_I	0.528	0.28
103_Q	141_E	0.527	0.28
37_L	70_G	0.526	0.28
32_I	53_N	0.526	0.28
70_G	127_F	0.525	0.28
10_L	69_Y	0.523	0.28
51_G	167_K	0.521	0.28
56_V	143_K	0.517	0.28
36_H	112_A	0.516	0.27
59_D	162_V	0.512	0.27
85_S	105_L	0.510	0.27
44_I	69_Y	0.508	0.27
33_L	175_T	0.506	0.27
113_M	157_R	0.505	0.27
60_L	152_A	0.505	0.27
23_L	52_K	0.504	0.27
80_P	174_T	0.502	0.26
131_L	136_P	0.500	0.26

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
1vkfA	1	0.8906	100	0.218	Contact Map
3ktsA	1	0.9583	100	0.391	Contact Map
1wa3A	3	0.9271	98.7	0.846	Contact Map
4adtA	5	0.9375	98.5	0.857	Contact Map
4jejA	2	0.9479	98.5	0.857	Contact Map
3vcrA	3	0.9271	98.4	0.86	Contact Map
1vhcA	3	0.9271	98.4	0.861	Contact Map
4utuA	2	0.9219	98.4	0.862	Contact Map
3vndA	3	0.9427	98.4	0.863	Contact Map
1mxsA	3	0.9167	98.3	0.864	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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