TRUB - BACSU - GREMLIN Contacts

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TRUB - tRNA pseudouridine synthase B

UniProt:	P32732	Sequences: MVNGVLLLHKPVGMTSHDCVMKIRKLLKTKKVGHTGTLDPEVSGVLPICVGRATKIVEYLTEKSKTYDAEITLGFSTTTEDQTGETVETKPVNHDIDKADVEKVLNSLKGKQEQIPPMYSAVKVNGKKLYEYARAGIEVERPKRMITIEDIALTTEIKHHGETASFRFTVTCSKGTYVRTLAVMIGEKLGYPAHMSHLIRTASGDFSLDECFTFDELEAQAQSGTVEEHTVPIERALNHLPKWIISDTLAKKVENGALLETPEQFSEMTSGDRIAVFTESGTCLAIYFPHPAKKGLLKPAKVLMQKSEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	309 (276)
Sequences:	3904 (2768)
Seq/√Len:	166.6

ECOLI - TRUB
BACSU - TRUB
HALSA - TRUB
SULSO - TRUB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_E	145_M	4.021	1.00
111_K	145_M	3.585	1.00
78_T	85_E	3.389	1.00
9_H	199_I	3.294	1.00
98_K	102_E	3.136	1.00
8_L	19_C	2.865	1.00
111_K	147_T	2.839	1.00
68_D	169_T	2.824	1.00
66_T	169_T	2.782	1.00
7_L	45_V	2.694	1.00
80_E	183_V	2.621	1.00
127_K	131_E	2.611	1.00
107_S	188_K	2.601	1.00
252_K	257_A	2.581	1.00
41_E	83_T	2.520	1.00
66_T	171_T	2.517	1.00
72_T	165_S	2.254	1.00
23_I	32_V	2.155	1.00
122_V	144_R	2.133	1.00
154_T	169_T	2.102	1.00
97_D	100_D	2.082	1.00
152_A	169_T	2.030	1.00
12_V	43_S	2.029	1.00
104_V	185_I	2.027	1.00
150_D	171_T	2.003	1.00
71_I	182_A	1.982	1.00
72_T	196_S	1.974	1.00
115_I	143_K	1.960	1.00
76_S	187_E	1.954	1.00
246_S	249_L	1.953	1.00
73_L	166_F	1.901	1.00
70_E	167_R	1.868	1.00
23_I	48_I	1.844	1.00
71_I	168_F	1.784	1.00
112_Q	146_I	1.769	1.00
118_M	141_R	1.765	1.00
76_S	88_E	1.764	1.00
68_D	167_R	1.762	1.00
43_S	199_I	1.762	1.00
64_S	171_T	1.738	1.00
182_A	195_M	1.730	1.00
29_T	50_V	1.708	1.00
82_Q	194_H	1.707	1.00
108_L	188_K	1.697	1.00
80_E	180_T	1.678	1.00
70_E	165_S	1.673	1.00
49_C	57_V	1.669	1.00
71_I	166_F	1.654	1.00
105_L	151_I	1.647	1.00
100_D	103_K	1.643	1.00
132_Y	137_I	1.624	1.00
105_L	153_L	1.589	1.00
69_A	168_F	1.575	1.00
170_V	181_L	1.572	1.00
129_L	141_R	1.544	1.00
106_N	109_K	1.532	1.00
186_G	193_A	1.530	1.00
35_T	49_C	1.510	1.00
155_T	167_R	1.503	1.00
102_E	153_L	1.489	1.00
8_L	217_L	1.486	1.00
186_G	191_Y	1.482	1.00
76_S	87_V	1.474	1.00
240_L	286_I	1.474	1.00
186_G	192_P	1.470	1.00
113_E	143_K	1.458	1.00
69_A	195_M	1.455	1.00
75_F	89_T	1.443	1.00
7_L	211_C	1.430	1.00
128_K	131_E	1.394	1.00
66_T	202_A	1.386	1.00
45_V	211_C	1.386	1.00
253_V	276_V	1.372	1.00
9_H	43_S	1.372	1.00
123_K	128_K	1.368	1.00
127_K	132_Y	1.352	1.00
17_H	24_R	1.352	1.00
77_T	194_H	1.345	1.00
171_T	202_A	1.345	1.00
180_T	183_V	1.340	1.00
150_D	169_T	1.336	1.00
105_L	168_F	1.332	1.00
72_T	75_F	1.330	1.00
215_D	218_E	1.306	1.00
12_V	41_E	1.294	1.00
17_H	21_M	1.292	1.00
165_S	196_S	1.274	1.00
22_K	218_E	1.272	1.00
86_T	89_T	1.268	1.00
234_E	277_F	1.268	1.00
213_T	216_E	1.267	1.00
93_N	96_I	1.267	1.00
245_I	253_V	1.264	1.00
118_M	129_L	1.249	1.00
127_K	135_A	1.247	1.00
70_E	197_H	1.240	1.00
104_V	107_S	1.234	1.00
102_E	109_K	1.234	1.00
208_L	211_C	1.229	1.00
76_S	192_P	1.223	1.00
253_V	285_A	1.218	1.00
231_V	235_R	1.217	1.00
5_V	49_C	1.217	1.00
153_L	166_F	1.213	1.00
68_D	154_T	1.201	1.00
218_E	222_Q	1.199	1.00
109_K	151_I	1.194	1.00
278_T	282_T	1.192	1.00
64_S	149_E	1.191	1.00
75_F	86_T	1.190	1.00
57_V	61_T	1.184	1.00
124_V	141_R	1.179	1.00
3_N	52_R	1.174	1.00
41_E	195_M	1.160	1.00
78_T	119_Y	1.154	1.00
275_A	283_C	1.154	1.00
251_K	255_N	1.149	1.00
124_V	129_L	1.148	1.00
276_V	287_Y	1.146	1.00
23_I	50_V	1.145	1.00
170_V	178_V	1.141	1.00
71_I	193_A	1.140	1.00
6_L	23_I	1.133	1.00
22_K	25_K	1.131	1.00
70_E	196_S	1.127	1.00
149_E	171_T	1.121	1.00
252_K	255_N	1.111	1.00
29_T	32_V	1.098	1.00
199_I	208_L	1.087	1.00
225_T	228_E	1.083	1.00
118_M	139_V	1.080	1.00
66_T	201_T	1.076	1.00
27_L	50_V	1.069	0.99
41_E	82_Q	1.069	0.99
108_L	184_M	1.063	0.99
11_P	215_D	1.055	0.99
207_S	210_E	1.045	0.99
104_V	188_K	1.043	0.99
35_T	57_V	1.040	0.99
101_V	166_F	1.039	0.99
202_A	207_S	1.029	0.99
9_H	208_L	1.021	0.99
52_R	55_K	1.021	0.99
78_T	83_T	1.017	0.99
12_V	197_H	1.013	0.99
147_T	173_S	1.010	0.99
216_E	219_A	1.005	0.99
73_L	96_I	0.993	0.99
151_I	168_F	0.985	0.99
118_M	138_E	0.982	0.99
183_V	187_E	0.978	0.99
15_T	18_D	0.975	0.99
14_M	22_K	0.968	0.99
99_A	103_K	0.960	0.99
75_F	194_H	0.958	0.99
62_E	174_K	0.952	0.99
98_K	155_T	0.952	0.99
119_Y	133_A	0.949	0.99
220_Q	229_H	0.936	0.99
68_D	201_T	0.928	0.99
45_V	208_L	0.927	0.99
206_F	235_R	0.923	0.99
254_E	282_T	0.921	0.98
245_I	249_L	0.920	0.98
113_E	142_P	0.912	0.98
241_P	272_D	0.903	0.98
76_S	183_V	0.901	0.98
63_K	204_G	0.899	0.98
151_I	170_V	0.894	0.98
161_G	164_A	0.892	0.98
72_T	164_A	0.890	0.98
151_I	181_L	0.887	0.98
79_T	119_Y	0.880	0.98
5_V	236_A	0.875	0.98
149_E	173_S	0.875	0.98
109_K	150_D	0.874	0.98
130_Y	133_A	0.873	0.98
32_V	48_I	0.873	0.98
124_V	142_P	0.865	0.98
250_A	278_T	0.864	0.98
169_T	201_T	0.864	0.98
5_V	56_I	0.857	0.98
117_P	180_T	0.855	0.98
249_L	252_K	0.853	0.98
14_M	19_C	0.851	0.97
242_K	277_F	0.850	0.97
118_M	133_A	0.849	0.97
9_H	213_T	0.849	0.97
99_A	102_E	0.849	0.97
17_H	20_V	0.840	0.97
103_K	106_N	0.828	0.97
78_T	84_G	0.827	0.97
42_V	122_V	0.824	0.97
69_A	151_I	0.819	0.97
73_L	189_L	0.816	0.97
80_E	117_P	0.815	0.97
212_F	217_L	0.812	0.97
6_L	27_L	0.810	0.97
244_I	278_T	0.809	0.97
221_A	226_V	0.803	0.96
167_R	197_H	0.800	0.96
77_T	86_T	0.798	0.96
232_P	235_R	0.795	0.96
181_L	185_I	0.795	0.96
212_F	229_H	0.793	0.96
90_K	192_P	0.791	0.96
32_V	50_V	0.791	0.96
172_C	176_T	0.790	0.96
108_L	181_L	0.787	0.96
90_K	191_Y	0.785	0.96
12_V	83_T	0.782	0.96
69_A	182_A	0.780	0.96
212_F	216_E	0.780	0.96
20_V	32_V	0.779	0.96
73_L	191_Y	0.772	0.96
132_Y	135_A	0.772	0.96
105_L	185_I	0.772	0.96
27_L	217_L	0.771	0.96
71_I	195_M	0.767	0.95
129_L	139_V	0.767	0.95
23_I	217_L	0.766	0.95
45_V	203_S	0.763	0.95
12_V	82_Q	0.762	0.95
235_R	238_N	0.761	0.95
242_K	275_A	0.756	0.95
141_R	180_T	0.756	0.95
154_T	167_R	0.751	0.95
128_K	132_Y	0.751	0.95
151_I	185_I	0.748	0.95
118_M	180_T	0.747	0.95
220_Q	225_T	0.745	0.95
47_P	203_S	0.744	0.95
18_D	22_K	0.744	0.95
118_M	132_Y	0.741	0.94
55_K	58_E	0.739	0.94
221_A	224_G	0.736	0.94
109_K	112_Q	0.735	0.94
250_A	284_L	0.734	0.94
248_T	252_K	0.733	0.94
63_K	203_S	0.733	0.94
88_E	187_E	0.733	0.94
247_D	280_S	0.732	0.94
90_K	187_E	0.732	0.94
253_V	287_Y	0.730	0.94
78_T	87_V	0.730	0.94
58_E	61_T	0.724	0.94
105_L	109_K	0.723	0.94
148_I	181_L	0.723	0.94
233_I	236_A	0.720	0.94
60_L	63_K	0.719	0.94
22_K	26_L	0.718	0.93
116_P	143_K	0.718	0.93
96_I	191_Y	0.716	0.93
101_V	161_G	0.709	0.93
23_I	27_L	0.709	0.93
79_T	84_G	0.703	0.93
112_Q	148_I	0.701	0.93
234_E	275_A	0.701	0.93
56_I	233_I	0.699	0.93
161_G	166_F	0.696	0.92
237_L	240_L	0.695	0.92
79_T	83_T	0.694	0.92
276_V	284_L	0.691	0.92
50_V	230_T	0.690	0.92
249_L	259_L	0.689	0.92
43_S	197_H	0.689	0.92
245_I	250_A	0.688	0.92
98_K	153_L	0.687	0.92
124_V	140_E	0.685	0.92
7_L	210_E	0.681	0.92
131_E	135_A	0.680	0.91
18_D	25_K	0.677	0.91
26_L	218_E	0.677	0.91
184_M	187_E	0.675	0.91
114_Q	184_M	0.674	0.91
102_E	152_A	0.669	0.91
7_L	208_L	0.665	0.91
25_K	28_K	0.665	0.91
237_L	283_C	0.663	0.90
274_I	287_Y	0.662	0.90
148_I	172_C	0.662	0.90
69_A	178_V	0.660	0.90
7_L	43_S	0.659	0.90
96_I	101_V	0.658	0.90
17_H	128_K	0.657	0.90
251_K	254_E	0.656	0.90
20_V	50_V	0.656	0.90
88_E	192_P	0.655	0.90
129_L	132_Y	0.653	0.90
19_C	46_L	0.651	0.90
119_Y	128_K	0.651	0.90
73_L	193_A	0.644	0.89
248_T	251_K	0.642	0.89
6_L	50_V	0.634	0.88
98_K	161_G	0.634	0.88
92_V	191_Y	0.634	0.88
124_V	128_K	0.633	0.88
77_T	87_V	0.628	0.88
58_E	62_E	0.626	0.88
253_V	284_L	0.625	0.88
243_W	249_L	0.623	0.88
77_T	89_T	0.622	0.87
182_A	193_A	0.621	0.87
250_A	279_E	0.620	0.87
226_V	229_H	0.616	0.87
148_I	170_V	0.615	0.87
250_A	254_E	0.614	0.87
244_I	279_E	0.613	0.87
56_I	237_L	0.613	0.87
76_S	191_Y	0.613	0.87
23_I	26_L	0.613	0.87
70_E	166_F	0.613	0.87
6_L	229_H	0.611	0.87
100_D	104_V	0.610	0.86
26_L	217_L	0.608	0.86
104_V	189_L	0.605	0.86
42_V	203_S	0.603	0.86
202_A	205_D	0.602	0.86
101_V	164_A	0.602	0.86
247_D	279_E	0.601	0.86
56_I	236_A	0.598	0.85
206_F	236_A	0.598	0.85
272_D	288_F	0.597	0.85
210_E	231_V	0.597	0.85
3_N	51_G	0.595	0.85
237_L	242_K	0.595	0.85
109_K	152_A	0.593	0.85
115_I	141_R	0.592	0.85
132_Y	139_V	0.590	0.85
102_E	106_N	0.588	0.84
28_K	221_A	0.584	0.84
19_C	214_F	0.584	0.84
26_L	213_T	0.583	0.84
271_G	288_F	0.582	0.84
128_K	139_V	0.582	0.84
103_K	107_S	0.577	0.83
72_T	194_H	0.576	0.83
166_F	185_I	0.574	0.83
148_I	176_T	0.573	0.83
260_E	263_E	0.572	0.83
141_R	183_V	0.571	0.83
115_I	142_P	0.571	0.83
155_T	162_E	0.568	0.82
278_T	284_L	0.568	0.82
61_T	64_S	0.567	0.82
56_I	285_A	0.566	0.82
277_F	283_C	0.565	0.82
115_I	118_M	0.564	0.82
71_I	186_G	0.563	0.82
83_T	194_H	0.562	0.82
242_K	281_G	0.561	0.82
22_K	214_F	0.560	0.81
249_L	257_A	0.560	0.81
7_L	199_I	0.559	0.81
261_T	264_Q	0.559	0.81
116_P	141_R	0.559	0.81
162_E	165_S	0.557	0.81
137_I	141_R	0.556	0.81
16_S	46_L	0.556	0.81
234_E	283_C	0.554	0.81
21_M	25_K	0.553	0.81
122_V	141_R	0.553	0.81
37_T	195_M	0.553	0.81
40_P	130_Y	0.552	0.80
14_M	18_D	0.550	0.80
29_T	55_K	0.550	0.80
259_L	289_P	0.548	0.80
151_I	178_V	0.547	0.80
11_P	14_M	0.546	0.80
26_L	221_A	0.546	0.80
35_T	60_L	0.545	0.80
80_E	186_G	0.544	0.80
206_F	211_C	0.544	0.80
247_D	250_A	0.543	0.79
288_F	291_P	0.542	0.79
140_E	143_K	0.539	0.79
49_C	174_K	0.538	0.79
244_I	281_G	0.537	0.79
6_L	217_L	0.537	0.79
18_D	21_M	0.536	0.79
27_L	48_I	0.535	0.78
114_Q	146_I	0.533	0.78
117_P	133_A	0.533	0.78
174_K	203_S	0.532	0.78
101_V	189_L	0.528	0.77
244_I	277_F	0.528	0.77
69_A	197_H	0.526	0.77
76_S	80_E	0.524	0.77
183_V	186_G	0.524	0.77
138_E	141_R	0.521	0.77
7_L	206_F	0.521	0.77
142_P	146_I	0.520	0.76
116_P	144_R	0.518	0.76
253_V	257_A	0.517	0.76
17_H	57_V	0.517	0.76
96_I	100_D	0.517	0.76
125_N	132_Y	0.516	0.76
273_R	286_I	0.514	0.76
92_V	96_I	0.513	0.75
146_I	176_T	0.512	0.75
49_C	53_A	0.512	0.75
182_A	196_S	0.510	0.75
11_P	214_F	0.509	0.75
96_I	164_A	0.509	0.75
278_T	281_G	0.508	0.75
176_T	181_L	0.508	0.75
245_I	276_V	0.508	0.75
261_T	289_P	0.507	0.75
259_L	287_Y	0.505	0.74
224_G	227_E	0.504	0.74
8_L	20_V	0.502	0.74
221_A	225_T	0.501	0.74
238_N	242_K	0.500	0.74
14_M	214_F	0.500	0.74

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
1r3eA	1	0.9417	100	0.106	Contact Map
1sgvA	1	0.8576	100	0.12	Contact Map
1k8wA	1	0.9482	100	0.12	Contact Map
3u28A	1	0.8608	100	0.288	Contact Map
2apoA	1	0.8317	100	0.294	Contact Map
2ausC	1	0.8252	100	0.295	Contact Map
2v9kA	1	0.521	100	0.744	Contact Map
1kskA	1	0.534	99.8	0.81	Contact Map
4lgtA	1	0.5728	99	0.885	Contact Map
3dh3A	1	0.5502	98.7	0.897	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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