NUSG - ECOLI - GREMLIN Contacts

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NUSG - Transcription termination/antitermination protein NusG

UniProt:	P0AFG0	Sequences: MSEAPKKRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVMVPTEEVVEIRGGQRRKSERKFFPGYVLVQMVMNDASWHLVRSVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10667
Length:	181 (171)
Sequences:	2427 (1229)
Seq/√Len:	94.0

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
23_A	27_R	5.186	1.00
38_L	76_N	4.175	1.00
158_L	178_V	4.130	1.00
41_E	72_Q	3.845	1.00
31_K	36_E	3.644	1.00
105_D	109_D	3.631	1.00
48_E	59_K	3.603	1.00
157_R	172_E	3.291	1.00
150_E	159_K	3.284	1.00
40_G	72_Q	3.228	1.00
7_K	72_Q	3.033	1.00
135_R	179_E	2.777	1.00
7_K	40_G	2.294	1.00
48_E	61_E	2.184	1.00
103_I	108_V	2.162	1.00
22_V	89_V	1.985	1.00
73_M	79_S	1.968	1.00
76_N	79_S	1.961	1.00
13_Q	90_M	1.882	1.00
18_F	88_R	1.876	1.00
46_T	61_E	1.871	1.00
95_G	98_D	1.849	1.00
73_M	83_V	1.820	1.00
152_D	155_K	1.769	1.00
47_E	62_R	1.753	1.00
157_R	174_D	1.749	1.00
51_E	62_R	1.731	1.00
160_V	173_L	1.705	1.00
153_Y	175_F	1.659	1.00
138_D	177_Q	1.656	1.00
65_F	70_L	1.572	1.00
70_L	111_I	1.555	1.00
133_M	145_N	1.537	1.00
161_S	170_P	1.490	1.00
173_L	177_Q	1.488	1.00
149_E	161_S	1.486	1.00
132_E	180_K	1.485	1.00
161_S	168_A	1.448	1.00
29_H	86_V	1.430	0.99
21_R	24_T	1.428	0.99
81_H	85_S	1.415	0.99
12_V	71_V	1.405	0.99
77_D	99_R	1.401	0.99
146_G	160_V	1.394	0.99
7_K	74_V	1.374	0.99
50_V	59_K	1.350	0.99
53_R	58_R	1.343	0.99
20_G	46_T	1.342	0.99
130_P	151_V	1.329	0.99
135_R	143_D	1.304	0.99
26_L	89_V	1.296	0.99
129_E	132_E	1.260	0.99
134_V	160_V	1.260	0.99
41_E	112_M	1.230	0.98
159_K	170_P	1.180	0.98
79_S	83_V	1.179	0.98
52_I	57_R	1.162	0.98
135_R	145_N	1.157	0.98
64_F	70_L	1.156	0.98
129_E	180_K	1.139	0.97
173_L	178_V	1.131	0.97
26_L	83_V	1.088	0.97
164_I	167_R	1.082	0.97
27_R	42_V	1.080	0.96
15_F	88_R	1.076	0.96
108_V	112_M	1.051	0.96
84_R	91_G	1.050	0.96
174_D	177_Q	1.045	0.96
153_Y	156_S	1.036	0.96
39_F	42_V	1.036	0.96
13_Q	91_G	1.017	0.95
65_F	111_I	1.013	0.95
106_K	110_A	1.002	0.95
49_V	62_R	0.993	0.94
90_M	94_G	0.987	0.94
49_V	164_I	0.984	0.94
29_H	33_H	0.972	0.94
35_M	79_S	0.964	0.93
24_T	28_E	0.963	0.93
38_L	74_V	0.957	0.93
11_V	103_I	0.957	0.93
160_V	166_G	0.944	0.93
27_R	41_E	0.942	0.93
80_W	84_R	0.941	0.93
148_V	178_V	0.937	0.92
104_S	112_M	0.936	0.92
50_V	57_R	0.933	0.92
165_F	169_T	0.927	0.92
15_F	18_F	0.926	0.92
30_I	39_F	0.926	0.92
26_L	30_I	0.916	0.92
22_V	69_V	0.915	0.92
17_G	22_V	0.913	0.91
40_G	74_V	0.904	0.91
8_R	105_D	0.899	0.91
30_I	36_E	0.898	0.91
29_H	87_P	0.886	0.90
19_E	68_Y	0.886	0.90
38_L	78_A	0.882	0.90
30_I	71_V	0.872	0.89
14_A	137_N	0.870	0.89
72_Q	105_D	0.864	0.89
163_S	168_A	0.863	0.89
7_K	41_E	0.861	0.89
94_G	102_P	0.847	0.88
143_D	171_V	0.843	0.88
100_P	141_F	0.835	0.87
158_L	173_L	0.826	0.87
44_V	69_V	0.823	0.87
18_F	21_R	0.821	0.86
124_P	156_S	0.804	0.85
10_Y	19_E	0.804	0.85
13_Q	18_F	0.802	0.85
42_V	82_L	0.794	0.85
27_R	30_I	0.790	0.84
157_R	177_Q	0.788	0.84
95_G	101_A	0.785	0.84
106_K	109_D	0.783	0.84
155_K	175_F	0.781	0.84
14_A	18_F	0.779	0.83
136_V	140_P	0.776	0.83
162_V	171_V	0.776	0.83
12_V	83_V	0.767	0.82
159_K	172_E	0.762	0.82
157_R	165_F	0.759	0.82
156_S	176_S	0.758	0.82
16_S	22_V	0.758	0.82
144_F	162_V	0.750	0.81
165_F	172_E	0.740	0.80
125_K	156_S	0.738	0.80
140_P	144_F	0.735	0.80
93_I	106_K	0.734	0.80
95_G	99_R	0.726	0.79
28_E	88_R	0.723	0.79
22_V	26_L	0.718	0.78
28_E	95_G	0.715	0.78
43_M	112_M	0.714	0.78
86_V	90_M	0.708	0.77
151_V	158_L	0.704	0.77
109_D	113_N	0.693	0.76
92_F	100_P	0.685	0.75
128_F	148_V	0.683	0.75
18_F	25_S	0.668	0.73
123_R	134_V	0.664	0.73
39_F	79_S	0.663	0.72
110_A	114_R	0.661	0.72
77_D	83_V	0.658	0.72
111_I	116_Q	0.658	0.72
163_S	173_L	0.657	0.72
136_V	176_S	0.656	0.72
39_F	83_V	0.655	0.71
28_E	32_L	0.655	0.71
33_H	82_L	0.653	0.71
20_G	63_K	0.652	0.71
26_L	86_V	0.648	0.71
77_D	97_S	0.647	0.71
144_F	160_V	0.646	0.70
152_D	172_E	0.642	0.70
73_M	80_W	0.641	0.70
133_M	147_V	0.641	0.70
87_P	111_I	0.640	0.70
132_E	148_V	0.640	0.70
128_F	178_V	0.639	0.70
43_M	115_L	0.636	0.69
28_E	31_K	0.636	0.69
160_V	178_V	0.634	0.69
15_F	69_V	0.634	0.69
15_F	90_M	0.629	0.68
13_Q	88_R	0.627	0.68
38_L	79_S	0.625	0.68
135_R	144_F	0.624	0.68
149_E	170_P	0.623	0.68
126_T	175_F	0.623	0.68
137_N	179_E	0.620	0.67
134_V	146_G	0.619	0.67
29_H	42_V	0.619	0.67
17_G	80_W	0.619	0.67
24_T	27_R	0.617	0.67
50_V	109_D	0.617	0.67
76_N	83_V	0.617	0.67
84_R	88_R	0.615	0.67
54_G	58_R	0.614	0.67
140_P	177_Q	0.613	0.66
25_S	104_S	0.613	0.66
104_S	107_E	0.613	0.66
70_L	103_I	0.612	0.66
11_V	88_R	0.609	0.66
129_E	134_V	0.605	0.65
8_R	128_F	0.603	0.65
87_P	93_I	0.599	0.65
49_V	88_R	0.596	0.64
137_N	142_A	0.592	0.64
149_E	160_V	0.591	0.64
160_V	170_P	0.591	0.64
22_V	86_V	0.588	0.63
27_R	31_K	0.588	0.63
12_V	28_E	0.585	0.63
72_Q	116_Q	0.583	0.63
35_M	137_N	0.583	0.63
21_R	25_S	0.581	0.62
21_R	88_R	0.581	0.62
50_V	122_P	0.580	0.62
152_D	157_R	0.579	0.62
40_G	54_G	0.579	0.62
12_V	30_I	0.578	0.62
101_A	115_L	0.576	0.62
152_D	159_K	0.575	0.62
25_S	29_H	0.572	0.61
155_K	174_D	0.569	0.61
114_R	143_D	0.566	0.60
73_M	101_A	0.563	0.60
33_H	87_P	0.561	0.60
136_V	162_V	0.561	0.60
16_S	21_R	0.559	0.59
144_F	163_S	0.559	0.59
104_S	164_I	0.558	0.59
21_R	86_V	0.554	0.59
18_F	93_I	0.554	0.59
33_H	78_A	0.551	0.58
91_G	98_D	0.549	0.58
138_D	149_E	0.548	0.58
64_F	103_I	0.548	0.58
91_G	102_P	0.548	0.58
172_E	175_F	0.544	0.57
162_V	169_T	0.542	0.57
138_D	142_A	0.542	0.57
61_E	159_K	0.539	0.57
53_R	62_R	0.536	0.56
29_H	82_L	0.535	0.56
147_V	168_A	0.533	0.56
145_N	179_E	0.533	0.56
35_M	82_L	0.527	0.55
18_F	63_K	0.523	0.54
128_F	158_L	0.523	0.54
140_P	159_K	0.523	0.54
156_S	175_F	0.520	0.54
123_R	153_Y	0.518	0.54
125_K	153_Y	0.516	0.53
158_L	175_F	0.516	0.53
162_V	170_P	0.515	0.53
62_R	136_V	0.515	0.53
132_E	152_D	0.515	0.53
14_A	20_G	0.515	0.53
21_R	32_L	0.513	0.53
73_M	94_G	0.511	0.53
126_T	153_Y	0.510	0.53
63_K	174_D	0.509	0.52
52_I	176_S	0.509	0.52
148_V	151_V	0.508	0.52
51_E	112_M	0.506	0.52
93_I	98_D	0.505	0.52
103_I	163_S	0.504	0.52
137_N	145_N	0.504	0.52
34_N	37_D	0.502	0.51
80_W	93_I	0.501	0.51
56_Q	59_K	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	0.326	100	0.148	Contact Map
1m1hA	1	0.6188	100	0.182	Contact Map
2lq8A	1	0.9337	100	0.23	Contact Map
2ougA	1	0.7735	100	0.254	Contact Map
2xhcA	1	0.9337	100	0.267	Contact Map
3p8bB	2	0.7956	100	0.365	Contact Map
1nz8A	1	0.6243	100	0.472	Contact Map
3lpeA	1	0.4641	99.9	0.609	Contact Map
2mi6A	1	0.3425	99.5	0.711	Contact Map
1nz9A	1	0.3204	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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