NUSG - BACSU - GREMLIN Contacts

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NUSG - Transcription termination/antitermination protein NusG

UniProt:	Q06795	Sequences: MEKNWYVVHTYSGYENKVKANLEKRVESMGMQDKIFRVVVPEEEETDIKNGKKKVVKKKVFPGYVLVEIVMTDDSWYVVRNTPGVTGFVGSAGSGSKPTPLLPGEAETILKRMGMDERKTDIDFELKETVKVIDGPFANFTGSIEEIDYDKSKVKVFVNMFGRETPVELEFTQIDKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	177 (171)
Sequences:	2372 (1216)
Seq/√Len:	93.0

ECOLI - NUSG RFAH
BACSU - NUSG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_K	23_E	5.003	1.00
34_K	72_T	4.242	1.00
154_V	174_I	3.998	1.00
37_R	68_E	3.816	1.00
103_P	107_E	3.721	1.00
27_E	32_Q	3.697	1.00
44_E	55_V	3.481	1.00
153_K	168_E	3.347	1.00
146_E	155_K	3.263	1.00
36_F	68_E	3.139	1.00
3_K	68_E	2.788	1.00
131_K	175_D	2.756	1.00
44_E	57_K	2.300	1.00
3_K	36_F	2.121	1.00
101_L	106_A	2.074	1.00
18_V	85_V	2.056	1.00
42_E	57_K	2.032	1.00
72_T	75_S	2.021	1.00
128_E	176_K	2.011	1.00
69_I	75_S	1.982	1.00
9_H	86_T	1.833	1.00
14_Y	84_G	1.792	1.00
148_D	151_K	1.785	1.00
43_E	58_K	1.771	1.00
153_K	170_E	1.758	1.00
69_I	79_V	1.756	1.00
156_V	169_L	1.687	1.00
47_D	58_K	1.669	1.00
149_Y	171_F	1.648	1.00
134_D	173_Q	1.642	1.00
129_T	141_T	1.564	1.00
73_D	97_K	1.548	1.00
145_E	157_F	1.524	1.00
66_L	109_I	1.520	1.00
157_F	166_P	1.504	1.00
17_K	20_A	1.494	1.00
61_F	66_L	1.492	1.00
169_L	173_Q	1.487	1.00
157_F	164_E	1.482	1.00
91_S	96_S	1.464	1.00
48_I	53_K	1.451	1.00
142_G	156_V	1.434	0.99
77_Y	81_N	1.431	0.99
3_K	70_V	1.413	0.99
25_R	82_T	1.391	0.99
8_V	67_V	1.375	0.99
22_L	85_V	1.353	0.99
46_T	55_V	1.326	0.99
131_K	139_N	1.290	0.99
125_E	128_E	1.290	0.99
75_S	79_V	1.279	0.99
169_L	174_I	1.265	0.99
126_L	147_I	1.236	0.98
45_E	58_K	1.198	0.98
22_L	79_V	1.198	0.98
130_V	156_V	1.157	0.98
16_N	42_E	1.154	0.98
23_E	38_V	1.126	0.97
60_V	66_L	1.122	0.97
25_R	29_M	1.114	0.97
160_M	163_R	1.104	0.97
61_F	109_I	1.098	0.97
155_K	166_P	1.091	0.97
23_E	37_R	1.083	0.96
11_Y	84_G	1.076	0.96
80_R	87_G	1.074	0.96
37_R	110_L	1.071	0.96
149_Y	152_S	1.068	0.96
49_K	54_K	1.065	0.96
170_E	173_Q	1.057	0.96
156_V	162_G	1.044	0.96
45_E	160_M	1.042	0.96
131_K	141_T	1.041	0.96
31_M	75_S	1.039	0.95
9_H	87_G	1.021	0.95
35_I	38_V	1.005	0.95
22_L	26_V	1.000	0.94
46_T	53_K	0.999	0.94
106_A	110_L	0.993	0.94
76_W	80_R	0.978	0.94
4_N	103_P	0.976	0.94
125_E	176_K	0.966	0.93
104_G	108_T	0.960	0.93
161_F	165_T	0.942	0.92
15_E	64_Y	0.936	0.92
86_T	90_G	0.933	0.92
40_V	65_V	0.932	0.92
34_K	70_V	0.931	0.92
11_Y	14_Y	0.925	0.92
102_L	110_L	0.906	0.91
18_V	65_V	0.905	0.91
91_S	97_K	0.886	0.90
10_T	133_I	0.886	0.90
8_V	79_V	0.885	0.90
7_V	101_L	0.885	0.90
25_R	83_P	0.878	0.90
20_A	24_K	0.878	0.90
120_T	152_S	0.875	0.89
158_V	167_V	0.872	0.89
90_G	100_P	0.866	0.89
159_N	164_E	0.862	0.89
154_V	169_L	0.860	0.89
6_Y	15_E	0.859	0.88
161_F	168_E	0.849	0.88
49_K	52_K	0.840	0.87
10_T	14_Y	0.834	0.87
144_I	174_I	0.834	0.87
26_V	35_I	0.834	0.87
153_K	161_F	0.831	0.87
68_E	103_P	0.824	0.86
9_H	14_Y	0.819	0.86
23_E	26_V	0.815	0.86
38_V	78_V	0.813	0.86
13_G	18_V	0.807	0.85
26_V	32_Q	0.801	0.85
39_V	110_L	0.789	0.84
73_D	95_G	0.785	0.84
125_E	130_V	0.783	0.83
36_F	70_V	0.783	0.83
14_Y	17_K	0.780	0.83
139_N	167_V	0.778	0.83
34_K	74_D	0.773	0.83
104_G	107_E	0.767	0.82
24_K	84_G	0.767	0.82
82_T	86_T	0.760	0.82
109_I	114_G	0.758	0.81
151_K	171_F	0.756	0.81
140_F	158_V	0.746	0.80
119_K	130_V	0.745	0.80
132_V	136_P	0.739	0.80
122_I	171_F	0.733	0.79
155_K	168_E	0.730	0.79
132_V	172_T	0.726	0.79
4_N	124_F	0.724	0.78
3_K	37_R	0.724	0.78
12_S	18_V	0.723	0.78
72_T	79_V	0.715	0.77
89_V	104_G	0.710	0.77
88_F	98_P	0.709	0.77
26_V	67_V	0.703	0.76
18_V	22_L	0.700	0.76
124_F	174_I	0.698	0.76
147_I	154_V	0.692	0.75
98_P	137_F	0.687	0.75
46_T	107_E	0.685	0.74
34_K	75_S	0.681	0.74
83_P	91_S	0.681	0.74
152_S	172_T	0.680	0.74
145_E	156_V	0.680	0.74
24_K	28_S	0.679	0.74
83_P	109_I	0.673	0.73
148_D	153_K	0.668	0.73
131_K	140_F	0.658	0.71
136_P	140_F	0.657	0.71
130_V	142_G	0.654	0.71
124_F	144_I	0.650	0.70
153_K	173_Q	0.650	0.70
136_P	173_Q	0.648	0.70
24_K	27_E	0.648	0.70
29_M	74_D	0.641	0.69
11_Y	65_V	0.640	0.69
87_G	96_S	0.638	0.69
35_I	79_V	0.636	0.69
140_F	156_V	0.635	0.69
129_T	143_S	0.635	0.69
128_E	144_I	0.634	0.69
29_M	78_V	0.631	0.68
20_A	23_E	0.631	0.68
69_I	76_W	0.629	0.68
11_Y	86_T	0.628	0.68
48_I	172_T	0.627	0.68
42_E	52_K	0.625	0.67
133_I	175_D	0.624	0.67
47_D	110_L	0.624	0.67
35_I	75_S	0.619	0.67
20_A	54_K	0.618	0.67
87_G	100_P	0.616	0.66
112_R	139_N	0.615	0.66
29_M	83_P	0.609	0.66
46_T	118_R	0.608	0.65
13_G	76_W	0.607	0.65
156_V	166_P	0.606	0.65
80_R	84_G	0.604	0.65
8_V	26_V	0.604	0.65
25_R	38_V	0.601	0.64
148_D	168_E	0.598	0.64
159_N	169_L	0.598	0.64
7_V	84_G	0.596	0.64
21_N	102_L	0.596	0.64
145_E	166_P	0.595	0.64
8_V	24_K	0.595	0.64
12_S	17_K	0.595	0.64
14_Y	21_N	0.594	0.64
132_V	158_V	0.590	0.63
120_T	156_V	0.585	0.62
156_V	174_I	0.585	0.62
148_D	155_K	0.585	0.62
12_S	76_W	0.585	0.62
17_K	84_G	0.580	0.62
158_V	165_T	0.578	0.61
58_K	132_V	0.575	0.61
17_K	21_N	0.573	0.61
23_E	27_E	0.572	0.61
16_N	59_K	0.572	0.61
9_H	65_V	0.570	0.60
134_D	138_A	0.566	0.60
66_L	101_L	0.565	0.60
108_T	113_M	0.562	0.59
151_K	170_E	0.562	0.59
39_V	113_M	0.561	0.59
51_G	147_I	0.559	0.59
140_F	159_N	0.558	0.59
91_S	99_T	0.556	0.59
107_E	111_K	0.555	0.58
144_I	147_I	0.553	0.58
22_L	82_T	0.551	0.58
102_L	160_M	0.547	0.57
31_M	133_I	0.547	0.57
89_V	99_T	0.546	0.57
154_V	176_K	0.545	0.57
51_G	132_V	0.543	0.57
143_S	164_E	0.542	0.57
21_N	25_R	0.541	0.56
99_T	113_M	0.540	0.56
152_S	171_F	0.540	0.56
50_N	54_K	0.539	0.56
17_K	82_T	0.538	0.56
18_V	82_T	0.538	0.56
155_K	160_M	0.537	0.56
10_T	87_G	0.533	0.55
128_E	148_D	0.532	0.55
45_E	109_I	0.532	0.55
41_P	147_I	0.527	0.55
109_I	113_M	0.526	0.54
67_V	108_T	0.525	0.54
14_Y	59_K	0.523	0.54
21_N	35_I	0.522	0.54
57_K	155_K	0.521	0.54
9_H	84_G	0.519	0.53
136_P	155_K	0.518	0.53
8_V	85_V	0.515	0.53
111_K	114_G	0.514	0.53
89_V	149_Y	0.514	0.53
45_E	84_G	0.513	0.53
168_E	171_F	0.511	0.52
141_T	175_D	0.510	0.52
59_K	96_S	0.510	0.52
25_R	78_V	0.510	0.52
22_L	29_M	0.508	0.52
6_Y	64_Y	0.507	0.52
30_G	33_D	0.505	0.51
133_I	141_T	0.503	0.51
134_D	145_E	0.502	0.51
10_T	89_V	0.502	0.51
49_K	58_K	0.501	0.51
160_M	167_V	0.500	0.51

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
2jvvA	1	0.3333	100	0.17	Contact Map
1m1hA	1	0.6328	100	0.18	Contact Map
2lq8A	1	0.9435	100	0.222	Contact Map
2xhcA	1	0.9492	100	0.251	Contact Map
2ougA	1	0.791	100	0.258	Contact Map
3p8bB	2	0.8136	100	0.345	Contact Map
1nz8A	1	0.6384	100	0.48	Contact Map
3lpeA	1	0.4746	99.8	0.617	Contact Map
2mi6A	1	0.3503	99.5	0.71	Contact Map
1nz9A	1	0.3277	99.5	0.721	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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