TCDA - ECOLI - GREMLIN Contacts

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TCDA - tRNA threonylcarbamoyladenosine dehydratase

UniProt:	Q46927	Sequences: MSVVISDAWRQRFGGTARLYGEKALQLFADAHICVVGIGGVGSWAAEALARTGIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKAEVMAERIRQINPECRVTVVDDFVTPDNVAQYMSVGYSYVIDAIDSVRPKAALIAYCRRNKIPLVTTGGAGGQIDPTQIQVTDLAKTIQDPLAAKLRERLKSDFGVVKNSKGKLGVDCVFSTEALVYPQSDGTVCAMKATAEGPKRMDCASGFGAATMVTATFGFVAVSHALKKMMAKAARQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13084
Length:	268 (239)
Sequences:	4348 (2839)
Seq/√Len:	183.6

ECOLI - TCDA THIF MOEB
BACSU - TCDA THIF MOEB
HALSA - Q9HST5
SULSO - Q980J4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_A	101_R	4.489	1.00
90_A	94_R	3.990	1.00
79_D	95_Q	3.644	1.00
83_L	91_E	3.625	1.00
32_H	58_T	3.603	1.00
56_A	103_T	3.433	1.00
45_A	126_I	3.333	1.00
125_V	142_C	3.220	1.00
255_H	258_K	3.053	1.00
17_A	22_E	2.840	1.00
165_Q	207_T	2.813	1.00
84_A	106_D	2.669	1.00
32_H	56_A	2.656	1.00
35_V	46_A	2.606	1.00
87_E	106_D	2.583	1.00
152_T	252_A	2.496	1.00
46_A	93_I	2.494	1.00
126_I	256_A	2.457	1.00
34_C	122_Y	2.411	1.00
90_A	104_V	2.262	1.00
124_Y	256_A	2.225	1.00
139_I	149_L	2.217	1.00
50_A	93_I	2.185	1.00
83_L	87_E	2.143	1.00
93_I	100_C	2.015	1.00
84_A	87_E	2.001	1.00
58_T	122_Y	1.983	1.00
86_A	104_V	1.974	1.00
16_T	25_L	1.897	1.00
87_E	104_V	1.831	1.00
184_R	188_D	1.830	1.00
28_F	257_L	1.828	1.00
75_H	89_M	1.813	1.00
34_C	60_I	1.743	1.00
120_V	145_N	1.738	1.00
26_Q	30_D	1.708	1.00
139_I	201_V	1.691	1.00
64_D	84_A	1.681	1.00
202_D	255_H	1.670	1.00
183_E	187_S	1.657	1.00
163_Q	207_T	1.654	1.00
129_I	134_P	1.611	1.00
138_L	149_L	1.600	1.00
80_N	83_L	1.585	1.00
38_I	89_M	1.564	1.00
58_T	105_V	1.553	1.00
140_A	144_R	1.552	1.00
14_G	18_R	1.532	1.00
141_Y	145_N	1.510	1.00
198_K	202_D	1.504	1.00
172_T	175_D	1.500	1.00
36_V	60_I	1.499	1.00
167_T	171_K	1.493	1.00
86_A	106_D	1.485	1.00
52_T	242_T	1.481	1.00
93_I	102_V	1.452	1.00
12_R	78_R	1.439	1.00
58_T	103_T	1.413	1.00
63_D	85_K	1.407	1.00
109_V	114_V	1.393	1.00
22_E	26_Q	1.385	1.00
127_D	138_L	1.372	1.00
249_G	253_V	1.360	1.00
31_A	260_M	1.354	1.00
69_N	85_K	1.353	1.00
20_Y	25_L	1.346	1.00
247_T	251_V	1.324	1.00
44_W	47_E	1.319	1.00
70_T	81_V	1.317	1.00
87_E	91_E	1.280	1.00
35_V	49_L	1.244	1.00
43_S	75_H	1.232	1.00
202_D	206_S	1.230	1.00
246_A	250_F	1.197	1.00
43_S	74_I	1.192	1.00
183_E	186_K	1.182	1.00
46_A	59_L	1.180	1.00
17_A	25_L	1.179	1.00
23_K	27_L	1.173	1.00
137_A	141_Y	1.171	1.00
160_D	163_Q	1.161	1.00
193_K	200_G	1.159	1.00
150_V	252_A	1.156	1.00
184_R	187_S	1.146	1.00
109_V	137_A	1.127	1.00
141_Y	144_R	1.124	1.00
65_V	75_H	1.118	1.00
77_L	92_R	1.115	1.00
57_I	100_C	1.105	1.00
173_I	207_T	1.104	1.00
181_L	186_K	1.088	1.00
26_Q	29_A	1.077	1.00
20_Y	241_A	1.068	1.00
188_D	192_V	1.059	1.00
83_L	88_V	1.050	1.00
187_S	190_G	1.050	1.00
127_D	130_D	1.048	1.00
50_A	57_I	1.047	1.00
136_A	140_A	1.043	1.00
27_L	31_A	1.039	1.00
32_H	103_T	1.034	1.00
46_A	89_M	1.033	1.00
124_Y	259_K	1.029	1.00
229_P	232_M	1.025	1.00
206_S	210_L	1.025	1.00
217_G	220_C	1.018	0.99
126_I	252_A	1.012	0.99
40_G	245_T	1.008	0.99
45_A	252_A	1.005	0.99
94_R	100_C	1.003	0.99
118_M	147_I	1.000	0.99
201_V	208_E	0.993	0.99
50_A	100_C	0.991	0.99
159_I	241_A	0.984	0.99
97_N	100_C	0.972	0.99
91_E	95_Q	0.965	0.99
36_V	138_L	0.957	0.99
207_T	210_L	0.952	0.99
177_L	180_K	0.941	0.99
38_I	59_L	0.941	0.99
39_G	129_I	0.941	0.99
185_L	190_G	0.937	0.99
186_K	190_G	0.931	0.99
244_V	247_T	0.929	0.99
25_L	29_A	0.929	0.99
94_R	101_R	0.926	0.99
24_A	31_A	0.921	0.99
152_T	248_F	0.916	0.99
193_K	201_V	0.912	0.99
62_M	108_F	0.907	0.99
180_K	183_E	0.907	0.99
162_T	251_V	0.906	0.99
77_L	95_Q	0.906	0.99
65_V	76_A	0.900	0.99
20_Y	159_I	0.900	0.99
200_G	207_T	0.896	0.99
77_L	80_N	0.896	0.99
139_I	151_T	0.895	0.99
181_L	184_R	0.893	0.99
205_F	209_A	0.881	0.99
177_L	182_R	0.879	0.99
78_R	95_Q	0.877	0.99
38_I	86_A	0.876	0.98
33_I	124_Y	0.873	0.98
205_F	208_E	0.865	0.98
114_V	141_Y	0.865	0.98
242_T	245_T	0.863	0.98
57_I	93_I	0.860	0.98
52_T	257_L	0.856	0.98
167_T	205_F	0.850	0.98
230_K	233_D	0.849	0.98
36_V	109_V	0.849	0.98
47_E	51_R	0.847	0.98
200_G	206_S	0.846	0.98
111_P	137_A	0.843	0.98
105_V	117_Y	0.842	0.98
178_A	182_R	0.842	0.98
44_W	74_I	0.840	0.98
131_S	134_P	0.831	0.98
211_V	215_S	0.828	0.98
20_Y	24_A	0.828	0.98
193_K	198_K	0.823	0.98
161_P	254_S	0.821	0.98
67_V	81_V	0.821	0.98
139_I	143_R	0.820	0.98
207_T	211_V	0.820	0.98
39_G	42_G	0.818	0.98
186_K	191_V	0.811	0.98
200_G	208_E	0.806	0.97
39_G	63_D	0.805	0.97
114_V	137_A	0.804	0.97
49_L	57_I	0.803	0.97
118_M	145_N	0.803	0.97
186_K	192_V	0.802	0.97
140_A	188_D	0.800	0.97
80_N	92_R	0.795	0.97
91_E	94_R	0.794	0.97
134_P	137_A	0.784	0.97
200_G	203_C	0.774	0.97
115_A	141_Y	0.770	0.97
203_C	206_S	0.770	0.97
42_G	73_Q	0.770	0.97
62_M	106_D	0.770	0.97
230_K	234_C	0.770	0.97
211_V	214_Q	0.759	0.96
90_A	102_V	0.755	0.96
28_F	261_M	0.753	0.96
214_Q	218_T	0.753	0.96
251_V	254_S	0.752	0.96
141_Y	147_I	0.751	0.96
159_I	248_F	0.747	0.96
109_V	141_Y	0.738	0.96
59_L	104_V	0.736	0.96
162_T	165_Q	0.734	0.96
44_W	246_A	0.731	0.95
11_Q	68_T	0.730	0.95
208_E	212_Y	0.730	0.95
39_G	128_A	0.728	0.95
127_D	135_K	0.726	0.95
187_S	191_V	0.721	0.95
198_K	206_S	0.721	0.95
203_C	207_T	0.719	0.95
87_E	90_A	0.717	0.95
216_D	219_V	0.716	0.95
21_G	24_A	0.715	0.95
216_D	220_C	0.712	0.95
203_C	208_E	0.710	0.95
135_K	151_T	0.707	0.95
31_A	54_I	0.707	0.95
184_R	191_V	0.705	0.94
63_D	68_T	0.705	0.94
43_S	89_M	0.704	0.94
180_K	184_R	0.704	0.94
14_G	17_A	0.704	0.94
202_D	208_E	0.703	0.94
202_D	211_V	0.697	0.94
177_L	181_L	0.697	0.94
203_C	214_Q	0.692	0.94
212_Y	217_G	0.692	0.94
208_E	217_G	0.687	0.94
59_L	89_M	0.687	0.94
24_A	28_F	0.687	0.94
45_A	49_L	0.686	0.94
200_G	204_V	0.686	0.94
227_E	231_R	0.685	0.94
63_D	130_D	0.684	0.94
80_N	91_E	0.683	0.93
11_Q	17_A	0.683	0.93
227_E	232_M	0.680	0.93
70_T	80_N	0.675	0.93
199_L	208_E	0.673	0.93
167_T	170_A	0.673	0.93
206_S	214_Q	0.672	0.93
211_V	217_G	0.670	0.93
13_F	97_N	0.670	0.93
72_R	130_D	0.669	0.93
208_E	211_V	0.669	0.93
69_N	73_Q	0.669	0.93
199_L	203_C	0.668	0.93
78_R	81_V	0.664	0.92
36_V	127_D	0.663	0.92
63_D	69_N	0.660	0.92
115_A	144_R	0.660	0.92
48_A	250_F	0.659	0.92
124_Y	260_M	0.657	0.92
142_C	149_L	0.656	0.92
202_D	205_F	0.655	0.92
150_V	255_H	0.650	0.92
35_V	42_G	0.648	0.92
46_A	75_H	0.648	0.92
28_F	54_I	0.643	0.91
177_L	185_L	0.643	0.91
32_H	121_G	0.643	0.91
35_V	126_I	0.643	0.91
193_K	208_E	0.640	0.91
150_V	166_V	0.638	0.91
229_P	233_D	0.632	0.91
62_M	86_A	0.632	0.91
211_V	216_D	0.631	0.90
166_V	204_V	0.630	0.90
51_R	96_I	0.629	0.90
225_T	229_P	0.627	0.90
39_G	240_A	0.625	0.90
16_T	52_T	0.625	0.90
166_V	251_V	0.624	0.90
177_L	184_R	0.621	0.90
88_V	91_E	0.619	0.90
41_V	45_A	0.619	0.90
45_A	48_A	0.616	0.89
185_L	188_D	0.615	0.89
184_R	190_G	0.612	0.89
135_K	153_G	0.611	0.89
115_A	145_N	0.611	0.89
38_I	46_A	0.609	0.89
14_G	20_Y	0.604	0.88
31_A	123_S	0.602	0.88
225_T	228_G	0.602	0.88
72_R	240_A	0.602	0.88
11_Q	20_Y	0.599	0.88
228_G	232_M	0.598	0.88
199_L	210_L	0.598	0.88
214_Q	219_V	0.597	0.88
13_F	16_T	0.596	0.88
175_D	181_L	0.596	0.88
70_T	78_R	0.596	0.88
118_M	121_G	0.594	0.88
124_Y	202_D	0.594	0.88
125_V	149_L	0.594	0.88
212_Y	220_C	0.593	0.88
193_K	199_L	0.589	0.87
32_H	122_Y	0.588	0.87
140_A	191_V	0.583	0.87
166_V	255_H	0.583	0.87
64_D	106_D	0.582	0.87
174_Q	209_A	0.582	0.87
171_K	176_P	0.582	0.87
16_T	19_L	0.582	0.87
226_A	230_K	0.580	0.86
41_V	72_R	0.579	0.86
117_Y	122_Y	0.579	0.86
202_D	207_T	0.577	0.86
198_K	203_C	0.577	0.86
243_M	254_S	0.577	0.86
181_L	185_L	0.575	0.86
57_I	102_V	0.571	0.86
33_I	49_L	0.569	0.85
12_R	70_T	0.569	0.85
171_K	175_D	0.568	0.85
200_G	205_F	0.566	0.85
68_T	72_R	0.565	0.85
233_D	237_G	0.564	0.85
178_A	181_L	0.562	0.85
33_I	126_I	0.561	0.85
69_N	72_R	0.561	0.85
209_A	212_Y	0.558	0.84
41_V	152_T	0.558	0.84
182_R	185_L	0.555	0.84
172_T	176_P	0.553	0.84
183_E	188_D	0.553	0.84
170_A	200_G	0.553	0.84
188_D	191_V	0.551	0.84
72_R	245_T	0.545	0.83
203_C	210_L	0.542	0.83
44_W	51_R	0.539	0.82
135_K	160_D	0.539	0.82
34_C	58_T	0.538	0.82
182_R	186_K	0.537	0.82
204_V	208_E	0.537	0.82
123_S	147_I	0.536	0.82
155_A	248_F	0.536	0.82
69_N	130_D	0.534	0.82
177_L	186_K	0.533	0.81
37_G	42_G	0.533	0.81
42_G	85_K	0.532	0.81
39_G	73_Q	0.528	0.81
14_G	67_V	0.527	0.81
25_L	28_F	0.524	0.80
154_G	245_T	0.523	0.80
45_A	128_A	0.522	0.80
33_I	256_A	0.522	0.80
242_T	250_F	0.521	0.80
205_F	210_L	0.515	0.79
213_P	219_V	0.514	0.79
124_Y	150_V	0.513	0.79
11_Q	14_G	0.513	0.79
92_R	95_Q	0.513	0.79
212_Y	215_S	0.512	0.79
65_V	88_V	0.511	0.79
44_W	250_F	0.510	0.79
113_N	116_Q	0.508	0.78
46_A	57_I	0.508	0.78
175_D	178_A	0.508	0.78
200_G	210_L	0.507	0.78
232_M	237_G	0.507	0.78
240_A	245_T	0.507	0.78
231_R	236_S	0.507	0.78
177_L	190_G	0.501	0.77
47_E	74_I	0.500	0.77

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
1y8qA	1	0.9627	100	0.238	Contact Map
4nnjA	2	0.959	100	0.244	Contact Map
4p22A	2	0.9366	100	0.245	Contact Map
4ii2A	1	0.9515	100	0.246	Contact Map
1tt5A	1	0.9851	100	0.254	Contact Map
1y8qB	1	0.9142	100	0.256	Contact Map
1tt5B	1	0.9701	100	0.287	Contact Map
4d79A	2	0.9216	100	0.313	Contact Map
2nvuB	1	0.9701	100	0.317	Contact Map
1zud1	2	0.7799	100	0.355	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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