TRUB - ECOLI - GREMLIN Contacts

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TRUB - tRNA pseudouridine synthase B

UniProt:	P60340	Sequences: MSRPRRRGRDINGVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTYIRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVNLPLTSSVYFKNGNPVRTSGAPLEGLVRVTEGENGKFIGMGEIDDEGRVAPRRLVVEYPA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11177
Length:	314 (286)
Sequences:	3810 (2735)
Seq/√Len:	161.7

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
120_E	152_P	3.965	1.00
118_D	152_P	3.583	1.00
87_D	94_Q	3.474	1.00
18_D	201_R	3.357	1.00
105_A	109_A	3.135	1.00
17_L	28_A	3.011	1.00
77_R	171_E	2.850	1.00
16_L	54_M	2.814	1.00
75_R	171_E	2.780	1.00
118_D	154_T	2.709	1.00
134_K	138_E	2.666	1.00
89_S	185_D	2.622	1.00
263_Y	268_N	2.536	1.00
50_L	92_D	2.532	1.00
114_T	190_K	2.516	1.00
75_R	173_H	2.431	1.00
81_R	167_E	2.303	1.00
32_V	41_A	2.171	1.00
161_I	171_E	2.141	1.00
21_Q	52_T	2.116	1.00
129_L	151_R	2.090	1.00
159_L	171_E	2.069	1.00
111_A	187_L	2.060	1.00
104_S	107_Q	2.033	1.00
157_E	173_H	2.011	1.00
80_A	184_I	1.995	1.00
81_R	198_I	1.976	1.00
85_R	189_E	1.933	1.00
257_P	260_S	1.915	1.00
122_I	150_A	1.907	1.00
82_L	168_L	1.896	1.00
32_V	57_I	1.868	1.00
79_I	169_E	1.835	1.00
119_I	153_I	1.831	1.00
52_T	201_R	1.806	1.00
77_R	169_E	1.800	1.00
125_M	148_R	1.795	1.00
184_I	197_V	1.773	1.00
80_A	170_L	1.760	1.00
58_C	66_S	1.707	1.00
38_A	59_L	1.698	1.00
73_D	173_H	1.695	1.00
80_A	168_L	1.694	1.00
115_F	190_K	1.694	1.00
85_R	97_E	1.681	1.00
79_I	167_E	1.667	1.00
89_S	182_T	1.666	1.00
91_A	196_H	1.657	1.00
139_Y	144_I	1.654	1.00
296_E	306_R	1.651	1.00
112_L	158_L	1.643	1.00
78_V	170_L	1.622	1.00
107_Q	110_A	1.612	1.00
251_Y	294_M	1.610	1.00
44_T	58_C	1.603	1.00
17_L	219_L	1.594	1.00
172_I	183_I	1.591	1.00
188_G	195_A	1.561	1.00
113_D	116_R	1.542	1.00
136_L	148_R	1.541	1.00
188_G	193_C	1.539	1.00
112_L	160_F	1.535	1.00
188_G	194_G	1.523	1.00
109_A	160_F	1.493	1.00
264_F	283_V	1.467	1.00
78_V	197_V	1.464	1.00
245_D	284_T	1.463	1.00
85_R	96_V	1.442	1.00
162_R	169_E	1.434	1.00
16_L	213_M	1.428	1.00
18_D	52_T	1.412	1.00
135_K	138_E	1.410	1.00
54_M	213_M	1.400	1.00
134_K	139_Y	1.393	1.00
84_Q	98_E	1.393	1.00
75_R	204_A	1.385	1.00
120_E	150_A	1.379	1.00
26_N	33_K	1.352	1.00
67_Q	307_R	1.352	1.00
86_T	196_H	1.347	1.00
182_T	185_D	1.346	1.00
157_E	171_E	1.337	1.00
217_E	220_R	1.334	1.00
21_Q	50_L	1.330	1.00
256_L	264_F	1.328	1.00
81_R	84_Q	1.319	1.00
215_T	218_H	1.318	1.00
125_M	136_L	1.311	1.00
31_K	220_R	1.309	1.00
173_H	204_A	1.302	1.00
112_L	170_L	1.300	1.00
26_N	30_Q	1.299	1.00
163_H	168_L	1.292	1.00
223_V	226_A	1.291	1.00
105_A	163_H	1.290	1.00
264_F	293_G	1.290	1.00
220_R	224_E	1.287	1.00
130_K	135_K	1.275	1.00
85_R	194_G	1.273	1.00
14_V	58_C	1.272	1.00
134_K	142_Q	1.269	1.00
210_V	213_M	1.262	1.00
109_A	116_R	1.260	1.00
95_I	98_E	1.259	1.00
131_Y	148_R	1.246	1.00
116_R	158_L	1.241	1.00
167_E	198_I	1.239	1.00
80_A	195_A	1.236	1.00
282_R	291_F	1.224	1.00
79_I	199_Y	1.205	1.00
77_R	161_I	1.201	1.00
84_Q	95_I	1.193	1.00
242_M	246_S	1.182	1.00
73_D	156_Y	1.181	1.00
66_S	70_L	1.179	1.00
160_F	168_L	1.177	1.00
50_L	197_V	1.163	1.00
111_A	114_T	1.163	1.00
305_P	308_L	1.158	1.00
79_I	198_I	1.140	1.00
262_V	266_N	1.136	1.00
32_V	59_L	1.132	1.00
75_R	203_L	1.120	1.00
156_Y	173_H	1.119	1.00
87_D	126_Y	1.103	1.00
286_G	290_K	1.101	1.00
12_N	61_E	1.100	1.00
154_T	175_S	1.100	1.00
82_L	103_F	1.095	1.00
36_Y	59_L	1.094	1.00
172_I	180_I	1.093	1.00
31_K	34_R	1.092	1.00
131_Y	136_L	1.092	1.00
293_G	308_L	1.089	1.00
115_F	186_D	1.088	1.00
283_V	295_G	1.070	0.99
125_M	146_V	1.063	0.99
108_L	168_L	1.058	0.99
15_L	32_V	1.055	0.99
201_R	210_V	1.055	0.99
20_P	217_E	1.050	0.99
209_P	212_R	1.050	0.99
44_T	66_S	1.048	0.99
263_Y	266_N	1.043	0.99
38_A	41_A	1.036	0.99
50_L	91_A	1.036	0.99
111_A	190_K	1.034	0.99
269_P	302_R	1.018	0.99
87_D	92_D	1.001	0.99
105_A	162_R	0.993	0.99
185_D	189_E	0.992	0.99
23_M	31_K	0.986	0.99
126_Y	140_A	0.977	0.99
24_S	27_D	0.969	0.99
218_H	221_E	0.969	0.99
18_D	210_V	0.967	0.99
265_K	290_K	0.967	0.99
158_L	170_L	0.964	0.99
21_Q	199_Y	0.959	0.99
204_A	209_P	0.957	0.99
208_Y	246_S	0.946	0.99
125_M	145_E	0.945	0.99
120_E	149_E	0.944	0.99
84_Q	196_H	0.941	0.99
61_E	64_K	0.936	0.99
72_S	206_S	0.931	0.98
77_R	203_L	0.928	0.98
222_L	240_L	0.925	0.98
223_V	237_L	0.915	0.98
54_M	210_V	0.915	0.98
214_V	219_L	0.907	0.98
71_D	176_K	0.896	0.98
116_R	157_E	0.888	0.98
106_E	110_A	0.888	0.98
256_L	260_S	0.887	0.98
85_R	185_D	0.886	0.98
88_T	126_Y	0.876	0.98
106_E	109_A	0.864	0.97
124_S	182_T	0.863	0.97
253_V	282_R	0.859	0.97
41_A	57_I	0.857	0.97
253_V	284_T	0.857	0.97
183_I	187_L	0.856	0.97
264_F	295_G	0.855	0.97
137_Y	140_A	0.853	0.97
131_Y	149_E	0.850	0.97
158_L	183_I	0.847	0.97
87_D	93_G	0.846	0.97
214_V	240_L	0.845	0.97
51_A	129_L	0.843	0.97
156_Y	175_S	0.841	0.97
82_L	191_L	0.841	0.97
280_L	306_R	0.836	0.97
23_M	28_A	0.832	0.97
14_V	247_P	0.831	0.97
171_E	203_L	0.831	0.97
54_M	205_V	0.831	0.97
158_L	172_I	0.829	0.97
89_S	124_S	0.826	0.97
125_M	140_A	0.822	0.97
78_V	184_I	0.822	0.97
260_S	263_Y	0.819	0.97
99_R	189_E	0.818	0.96
214_V	218_H	0.818	0.96
80_A	197_V	0.816	0.96
148_R	182_T	0.810	0.96
29_L	41_A	0.809	0.96
245_D	282_R	0.808	0.96
14_V	65_F	0.807	0.96
82_L	193_C	0.805	0.96
174_C	178_T	0.804	0.96
158_L	187_L	0.803	0.96
295_G	303_V	0.802	0.96
169_E	199_Y	0.801	0.96
18_D	215_T	0.798	0.96
78_V	158_L	0.798	0.96
135_K	139_Y	0.797	0.96
298_D	304_A	0.797	0.96
32_V	219_L	0.797	0.96
56_P	205_V	0.795	0.96
15_L	36_Y	0.794	0.96
139_Y	142_Q	0.791	0.96
26_N	29_L	0.790	0.96
36_Y	219_L	0.781	0.95
116_R	119_I	0.779	0.95
99_R	194_G	0.776	0.95
110_A	113_D	0.775	0.95
293_G	303_V	0.775	0.95
258_L	288_N	0.771	0.95
264_F	292_I	0.768	0.95
125_M	182_T	0.765	0.95
81_R	166_N	0.760	0.95
161_I	169_E	0.759	0.95
21_Q	92_D	0.758	0.95
86_T	95_I	0.757	0.95
279_G	296_E	0.756	0.95
115_F	183_I	0.754	0.94
97_E	189_E	0.753	0.94
261_S	292_I	0.753	0.94
52_T	199_Y	0.752	0.94
72_S	205_V	0.750	0.94
259_T	263_Y	0.749	0.94
97_E	194_G	0.748	0.94
255_N	286_G	0.747	0.94
261_S	286_G	0.746	0.94
28_A	55_L	0.742	0.94
136_L	146_V	0.740	0.94
252_P	279_G	0.740	0.94
164_E	167_E	0.739	0.94
35_I	220_R	0.736	0.94
82_L	195_A	0.735	0.94
109_A	159_L	0.734	0.94
119_I	155_V	0.731	0.94
64_K	67_Q	0.731	0.94
87_D	96_V	0.731	0.94
108_L	163_H	0.730	0.93
88_T	93_G	0.728	0.93
27_D	31_K	0.728	0.93
41_A	59_L	0.727	0.93
65_F	247_P	0.727	0.93
164_E	169_E	0.724	0.93
69_L	72_S	0.723	0.93
105_A	165_G	0.721	0.93
123_P	150_A	0.720	0.93
88_T	92_D	0.720	0.93
261_S	287_E	0.717	0.93
26_N	135_K	0.716	0.93
101_V	193_C	0.714	0.93
16_L	52_T	0.714	0.93
15_L	240_L	0.713	0.93
160_F	163_H	0.711	0.93
112_L	116_R	0.711	0.93
112_L	187_L	0.706	0.92
258_L	287_E	0.701	0.92
21_Q	91_A	0.699	0.92
255_N	287_E	0.697	0.92
103_F	108_L	0.688	0.91
155_V	174_C	0.686	0.91
125_M	139_Y	0.685	0.91
186_D	189_E	0.683	0.91
246_S	249_S	0.683	0.91
138_E	142_Q	0.682	0.91
67_Q	70_L	0.682	0.91
65_F	244_M	0.681	0.91
271_R	302_R	0.681	0.91
99_R	193_C	0.679	0.91
16_L	210_V	0.679	0.91
105_A	160_F	0.676	0.91
29_L	59_L	0.670	0.90
103_F	193_C	0.669	0.90
280_L	294_M	0.669	0.90
32_V	36_Y	0.667	0.90
256_L	261_S	0.663	0.90
36_Y	57_I	0.662	0.90
67_Q	71_D	0.659	0.89
85_R	193_C	0.658	0.89
121_Q	186_D	0.657	0.89
208_Y	247_P	0.655	0.89
109_A	113_D	0.654	0.89
276_P	279_G	0.650	0.89
65_F	248_A	0.649	0.89
264_F	303_V	0.648	0.89
155_V	183_I	0.648	0.89
51_A	205_V	0.648	0.89
65_F	293_G	0.647	0.89
248_A	291_F	0.647	0.89
259_T	262_V	0.645	0.88
131_Y	147_P	0.645	0.88
31_K	35_I	0.643	0.88
144_I	148_R	0.641	0.88
16_L	212_R	0.636	0.88
248_A	251_Y	0.635	0.88
79_I	168_L	0.634	0.88
136_L	139_Y	0.634	0.88
244_M	247_P	0.634	0.88
184_I	195_A	0.633	0.88
61_E	307_R	0.632	0.87
155_V	172_I	0.632	0.87
107_Q	111_A	0.632	0.87
27_D	34_R	0.631	0.87
204_A	207_K	0.631	0.87
35_I	215_T	0.629	0.87
62_A	243_P	0.625	0.87
135_K	146_V	0.625	0.87
108_L	191_L	0.620	0.86
284_T	291_F	0.617	0.86
260_S	270_V	0.617	0.86
32_V	35_I	0.617	0.86
253_V	289_G	0.614	0.86
212_R	242_M	0.609	0.85
261_S	265_K	0.608	0.85
15_L	59_L	0.608	0.85
35_I	223_V	0.606	0.85
148_R	185_D	0.604	0.85
59_L	241_L	0.600	0.85
35_I	219_L	0.599	0.85
131_Y	135_K	0.598	0.84
12_N	60_G	0.598	0.84
221_E	225_Q	0.595	0.84
119_I	154_T	0.594	0.84
254_V	260_S	0.593	0.84
258_L	261_S	0.591	0.84
149_E	153_I	0.589	0.84
78_V	180_I	0.588	0.83
92_D	196_H	0.585	0.83
122_I	149_E	0.585	0.83
255_N	284_T	0.584	0.83
283_V	292_I	0.584	0.83
237_L	240_L	0.583	0.83
126_Y	135_K	0.582	0.83
34_R	37_N	0.581	0.83
16_L	201_R	0.581	0.83
89_S	188_G	0.579	0.83
122_I	125_M	0.578	0.82
116_R	159_L	0.578	0.82
64_K	308_L	0.575	0.82
243_P	246_S	0.573	0.82
78_V	199_Y	0.573	0.82
111_A	191_L	0.571	0.82
44_T	69_L	0.566	0.81
256_L	283_V	0.565	0.81
46_A	197_V	0.564	0.81
81_R	196_H	0.563	0.81
123_P	148_R	0.559	0.80
270_V	297_I	0.558	0.80
163_H	166_N	0.558	0.80
262_V	265_K	0.558	0.80
269_P	304_A	0.557	0.80
110_A	114_T	0.554	0.80
23_M	216_L	0.553	0.80
176_K	205_V	0.553	0.80
139_Y	146_V	0.552	0.79
80_A	188_G	0.551	0.79
264_F	308_L	0.551	0.79
49_P	137_Y	0.548	0.79
124_S	140_A	0.546	0.79
248_A	253_V	0.542	0.78
70_L	73_D	0.542	0.78
145_E	148_R	0.542	0.78
158_L	180_I	0.540	0.78
20_P	40_R	0.539	0.78
99_R	103_F	0.537	0.78
168_L	187_L	0.537	0.78
86_T	96_V	0.536	0.77
222_L	225_Q	0.533	0.77
155_V	178_T	0.533	0.77
122_I	148_R	0.529	0.77
178_T	183_I	0.528	0.76
22_G	92_D	0.528	0.76
184_I	188_G	0.528	0.76
297_I	301_G	0.528	0.76
31_K	216_L	0.527	0.76
297_I	303_V	0.527	0.76
245_D	291_F	0.526	0.76
64_K	307_R	0.526	0.76
281_V	284_T	0.526	0.76
271_R	274_G	0.525	0.76
260_S	268_N	0.525	0.76
38_A	64_K	0.524	0.76
25_S	55_L	0.523	0.76
12_N	40_R	0.522	0.76
128_A	141_R	0.521	0.75
129_L	148_R	0.519	0.75
16_L	208_Y	0.518	0.75
28_A	216_L	0.517	0.75
170_L	180_I	0.517	0.75
23_M	27_D	0.517	0.75
263_Y	274_G	0.517	0.75
123_P	151_R	0.515	0.75
70_L	129_L	0.515	0.75
248_A	282_R	0.514	0.75
15_L	219_L	0.514	0.75
85_R	89_S	0.514	0.75
20_P	23_M	0.513	0.74
88_T	137_Y	0.510	0.74
147_P	150_A	0.509	0.74
208_Y	213_M	0.508	0.74
68_Y	294_M	0.506	0.73
121_Q	153_I	0.506	0.73
86_T	93_G	0.506	0.73
124_S	248_A	0.505	0.73
42_G	45_G	0.504	0.73
296_E	304_A	0.504	0.73
26_N	38_A	0.503	0.73
30_Q	34_R	0.503	0.73
155_V	180_I	0.503	0.73
255_N	289_G	0.501	0.73
82_L	194_G	0.501	0.73
103_F	107_Q	0.500	0.72

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
1k8wA	1	0.965	100	0.095	Contact Map
1r3eA	1	0.914	100	0.114	Contact Map
1sgvA	1	0.8344	100	0.122	Contact Map
3u28A	1	0.8694	100	0.289	Contact Map
2apoA	1	0.8471	100	0.295	Contact Map
2ausC	1	0.8439	100	0.299	Contact Map
2v9kA	1	0.5541	100	0.741	Contact Map
1kskA	1	0.5541	99.8	0.815	Contact Map
4lgtA	1	0.5764	98.9	0.885	Contact Map
3dh3A	1	0.5701	98.7	0.895	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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