TRUD - SULSO - GREMLIN Contacts

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TRUD - Probable tRNA pseudouridine synthase D

UniProt:	Q980V2	Sequences: MTPHEIDIALGMEKYYYEDWNELDGTIERPNGFKVIEEIDFKPAQDWKGETKGKYAVFLLTKWGIDHFSAISEVQKVLHSKVNYIGIKDANAITSQLVYIPLNEKQELIEKYQSRSFILKFLGFSSKKLNHTGNIFEISLSISDFDIVIERIEQIKKNPYLPAFIGYQRFGTRRPITHLIGKYLLRRDWEKAFYLILTYPFLSESKETIDIRKLIMEGDFKEAVRSIPSKFKQEKLLLKNYMRFNSYYLALKSSFIPISLYLDAYQSYLFNLYLSRKLDEYKNLNDKVNLLIRIPIYFNNCDDVCKEIYLDEGIERNFFKLQEFKISLRDLVRKAFMNIRDLKVNEETKTISFVLERGMYATILLREILRGDPRKFT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	377 (338)
Sequences:	789 (592)
Seq/√Len:	32.2

ECOLI - TRUD
HALSA - TRUD
SULSO - TRUD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
188_D	191_K	6.795	1.00
274_L	335_A	5.429	1.00
276_R	279_D	4.486	1.00
183_Y	188_D	4.415	1.00
265_Y	312_E	4.173	1.00
70_A	117_F	3.938	1.00
277_K	287_K	3.705	1.00
213_K	217_E	3.667	1.00
60_L	98_V	3.383	1.00
57_V	99_Y	3.347	1.00
246_S	249_L	3.296	1.00
272_L	311_D	3.235	1.00
178_H	268_Y	2.991	1.00
219_D	222_E	2.987	1.00
60_L	70_A	2.866	1.00
337_M	356_E	2.811	1.00
71_I	82_V	2.702	1.00
83_N	99_Y	2.604	1.00
99_Y	125_S	2.557	1.00
180_I	192_A	2.458	0.99
190_E	247_Y	2.451	0.99
59_L	97_L	2.371	0.99
57_V	97_L	2.365	0.99
277_K	286_D	2.315	0.99
214_L	226_S	2.279	0.99
353_F	361_A	2.275	0.99
290_L	305_C	2.138	0.99
152_I	368_I	2.119	0.98
85_I	131_H	2.112	0.98
240_N	249_L	2.106	0.98
162_P	274_L	2.103	0.98
70_A	74_V	2.094	0.98
182_K	312_E	2.078	0.98
82_V	98_V	2.052	0.98
291_L	330_D	2.041	0.98
222_E	225_R	2.032	0.98
57_V	125_S	2.015	0.98
35_V	38_E	1.975	0.97
297_Y	305_C	1.961	0.97
86_G	89_D	1.940	0.97
223_A	238_L	1.933	0.97
149_I	153_E	1.926	0.97
65_I	69_S	1.924	0.97
151_R	370_R	1.915	0.97
182_K	186_R	1.891	0.97
211_I	215_I	1.869	0.96
33_F	37_E	1.861	0.96
56_A	124_F	1.844	0.96
343_K	352_S	1.831	0.96
276_R	280_E	1.826	0.96
166_G	367_E	1.815	0.96
214_L	222_E	1.810	0.96
183_Y	191_K	1.807	0.96
181_G	367_E	1.798	0.96
305_C	332_V	1.792	0.95
32_G	35_V	1.790	0.95
341_D	354_V	1.771	0.95
140_L	369_L	1.728	0.94
60_L	71_I	1.710	0.94
82_V	100_I	1.701	0.94
315_E	318_F	1.700	0.94
303_D	307_E	1.698	0.94
153_E	157_K	1.677	0.94
183_Y	195_L	1.654	0.93
170_F	360_Y	1.639	0.93
353_F	364_L	1.611	0.92
182_K	265_Y	1.609	0.92
32_G	37_E	1.591	0.92
240_N	246_S	1.583	0.91
204_E	212_R	1.565	0.91
70_A	98_V	1.562	0.91
241_Y	247_Y	1.561	0.91
31_N	34_K	1.559	0.91
135_I	354_V	1.548	0.90
297_Y	332_V	1.540	0.90
137_E	352_S	1.533	0.90
71_I	98_V	1.533	0.90
221_K	242_M	1.524	0.90
138_I	192_A	1.499	0.89
170_F	271_N	1.498	0.89
156_K	336_F	1.493	0.89
276_R	307_E	1.469	0.88
155_I	364_L	1.460	0.88
330_D	367_E	1.453	0.87
166_G	181_G	1.451	0.87
337_M	359_M	1.419	0.86
31_N	37_E	1.410	0.86
177_T	181_G	1.385	0.85
64_G	91_N	1.382	0.85
32_G	38_E	1.377	0.84
269_L	312_E	1.369	0.84
59_L	120_K	1.350	0.83
309_Y	319_F	1.344	0.83
166_G	366_R	1.330	0.82
288_V	332_V	1.301	0.81
161_L	337_M	1.297	0.80
32_G	36_I	1.294	0.80
64_G	90_A	1.280	0.80
89_D	96_Q	1.277	0.79
62_K	70_A	1.271	0.79
161_L	364_L	1.260	0.78
54_K	101_P	1.250	0.78
277_K	332_V	1.237	0.77
60_L	119_L	1.236	0.77
356_E	359_M	1.226	0.77
122_L	129_L	1.220	0.76
227_I	238_L	1.214	0.76
190_E	194_Y	1.205	0.75
141_S	164_F	1.197	0.75
127_K	130_N	1.195	0.75
303_D	306_K	1.182	0.74
233_Q	254_S	1.182	0.74
119_L	122_L	1.175	0.73
281_Y	284_L	1.169	0.73
145_F	346_E	1.168	0.73
178_H	264_A	1.168	0.73
167_Y	363_I	1.164	0.73
209_I	351_I	1.158	0.72
211_I	227_I	1.150	0.72
321_L	324_F	1.142	0.71
162_P	278_L	1.136	0.71
59_L	121_F	1.124	0.70
67_H	71_I	1.123	0.70
280_E	300_N	1.119	0.70
181_G	330_D	1.113	0.69
31_N	63_W	1.104	0.69
176_I	212_R	1.099	0.68
86_G	168_Q	1.084	0.67
89_D	168_Q	1.083	0.67
196_I	233_Q	1.081	0.67
165_I	248_Y	1.076	0.67
180_I	213_K	1.074	0.66
178_H	181_G	1.068	0.66
87_I	260_L	1.065	0.66
67_H	170_F	1.057	0.65
61_T	118_I	1.055	0.65
196_I	237_L	1.045	0.64
226_S	235_K	1.039	0.64
73_E	114_S	1.029	0.63
168_Q	360_Y	1.026	0.63
290_L	296_I	1.022	0.63
204_E	208_T	1.018	0.62
86_G	96_Q	1.015	0.62
86_G	360_Y	1.011	0.62
153_E	156_K	1.006	0.61
206_K	210_D	0.996	0.60
290_L	297_Y	0.989	0.60
138_I	345_N	0.987	0.60
136_F	168_Q	0.985	0.60
184_L	192_A	0.983	0.59
74_V	82_V	0.982	0.59
139_S	350_T	0.979	0.59
254_S	305_C	0.977	0.59
228_P	231_F	0.961	0.58
238_L	255_F	0.953	0.57
166_G	177_T	0.942	0.56
193_F	251_L	0.939	0.56
239_K	243_R	0.937	0.56
260_L	315_E	0.936	0.56
36_I	135_I	0.935	0.56
164_F	360_Y	0.933	0.55
270_F	328_L	0.932	0.55
233_Q	261_Y	0.928	0.55
128_K	142_I	0.928	0.55
263_D	277_K	0.923	0.55
103_N	106_Q	0.922	0.55
86_G	169_R	0.921	0.54
196_I	261_Y	0.921	0.54
236_L	254_S	0.915	0.54
193_F	196_I	0.914	0.54
106_Q	124_F	0.910	0.54
30_P	37_E	0.904	0.53
309_Y	315_E	0.899	0.53
218_G	352_S	0.898	0.53
235_K	239_K	0.897	0.52
172_T	175_P	0.896	0.52
265_Y	327_S	0.890	0.52
181_G	366_R	0.890	0.52
207_E	217_E	0.888	0.52
259_S	270_F	0.885	0.52
106_Q	110_E	0.883	0.51
148_V	349_K	0.883	0.51
145_F	209_I	0.881	0.51
66_D	69_S	0.876	0.51
30_P	33_F	0.876	0.51
99_Y	197_L	0.871	0.50
91_N	366_R	0.870	0.50
148_V	155_I	0.864	0.50
287_K	332_V	0.862	0.50
281_Y	344_V	0.862	0.50
184_L	326_I	0.860	0.49
91_N	263_D	0.860	0.49
33_F	38_E	0.857	0.49
269_L	290_L	0.857	0.49
55_Y	128_K	0.857	0.49
169_R	360_Y	0.857	0.49
33_F	39_I	0.848	0.48
291_L	332_V	0.846	0.48
259_S	325_K	0.842	0.48
178_H	330_D	0.841	0.48
214_L	217_E	0.838	0.48
148_V	281_Y	0.837	0.48
186_R	313_G	0.837	0.48
88_K	94_T	0.837	0.48
228_P	234_E	0.833	0.47
108_L	111_K	0.828	0.47
202_L	212_R	0.827	0.47
223_A	227_I	0.824	0.46
171_G	234_E	0.822	0.46
131_H	336_F	0.820	0.46
209_I	213_K	0.816	0.46
58_F	82_V	0.813	0.46
355_L	362_T	0.808	0.45
177_T	360_Y	0.806	0.45
277_K	367_E	0.806	0.45
214_L	219_D	0.804	0.45
224_V	239_K	0.804	0.45
210_D	213_K	0.802	0.45
224_V	291_L	0.802	0.45
265_Y	268_Y	0.801	0.45
319_F	327_S	0.800	0.45
192_A	250_A	0.799	0.44
294_I	336_F	0.798	0.44
74_V	112_Y	0.797	0.44
57_V	123_G	0.792	0.44
300_N	303_D	0.785	0.43
260_L	264_A	0.784	0.43
292_I	320_K	0.784	0.43
65_I	260_L	0.779	0.43
139_S	348_T	0.778	0.43
213_K	245_N	0.778	0.43
214_L	220_F	0.778	0.43
272_L	308_I	0.777	0.43
141_S	339_I	0.777	0.43
48_K	52_K	0.769	0.42
199_Y	208_T	0.764	0.42
58_F	100_I	0.759	0.41
181_G	263_D	0.758	0.41
368_I	372_D	0.757	0.41
85_I	291_L	0.757	0.41
84_Y	262_L	0.757	0.41
233_Q	258_I	0.755	0.41
31_N	35_V	0.754	0.41
166_G	277_K	0.750	0.41
56_A	165_I	0.750	0.41
160_Y	339_I	0.749	0.40
208_T	331_L	0.748	0.40
228_P	235_K	0.748	0.40
198_T	212_R	0.747	0.40
290_L	294_I	0.747	0.40
193_F	262_L	0.746	0.40
147_I	365_L	0.744	0.40
107_E	372_D	0.743	0.40
214_L	223_A	0.742	0.40
149_I	345_N	0.742	0.40
87_I	330_D	0.740	0.40
257_P	273_Y	0.740	0.40
320_K	327_S	0.740	0.40
59_L	123_G	0.739	0.40
183_Y	186_R	0.736	0.39
266_Q	362_T	0.735	0.39
176_I	270_F	0.735	0.39
65_I	87_I	0.734	0.39
88_K	134_N	0.732	0.39
129_L	364_L	0.728	0.39
63_W	93_I	0.726	0.39
161_L	363_I	0.725	0.39
58_F	162_P	0.725	0.39
184_L	189_W	0.724	0.38
181_G	332_V	0.723	0.38
277_K	330_D	0.721	0.38
192_A	251_L	0.721	0.38
73_E	76_K	0.720	0.38
181_G	277_K	0.719	0.38
189_W	248_Y	0.717	0.38
273_Y	304_V	0.717	0.38
270_F	312_E	0.714	0.38
89_D	362_T	0.711	0.37
41_F	45_Q	0.711	0.37
98_V	116_S	0.711	0.37
160_Y	349_K	0.710	0.37
77_V	303_D	0.710	0.37
208_T	212_R	0.710	0.37
66_D	87_I	0.710	0.37
167_Y	172_T	0.710	0.37
316_R	321_L	0.707	0.37
66_D	167_Y	0.705	0.37
104_E	107_E	0.703	0.37
281_Y	354_V	0.703	0.37
299_N	304_V	0.701	0.37
92_A	337_M	0.701	0.37
171_G	261_Y	0.701	0.37
210_D	226_S	0.700	0.37
65_I	196_I	0.699	0.37
292_I	327_S	0.699	0.37
34_K	38_E	0.698	0.36
165_I	329_R	0.698	0.36
234_E	261_Y	0.698	0.36
269_L	358_G	0.696	0.36
71_I	84_Y	0.695	0.36
34_K	37_E	0.694	0.36
108_L	114_S	0.693	0.36
68_F	87_I	0.688	0.36
191_K	195_L	0.688	0.36
66_D	181_G	0.688	0.36
224_V	295_P	0.687	0.36
112_Y	122_L	0.684	0.35
150_E	303_D	0.684	0.35
61_T	120_K	0.682	0.35
99_Y	129_L	0.679	0.35
205_S	208_T	0.678	0.35
304_V	307_E	0.677	0.35
270_F	274_L	0.674	0.35
306_K	310_L	0.671	0.34
266_Q	275_S	0.671	0.34
141_S	349_K	0.671	0.34
55_Y	264_A	0.671	0.34
36_I	149_I	0.671	0.34
177_T	234_E	0.668	0.34
222_E	346_E	0.666	0.34
240_N	253_S	0.664	0.34
255_F	291_L	0.661	0.34
111_K	345_N	0.661	0.34
266_Q	330_D	0.660	0.34
62_K	68_F	0.659	0.34
135_I	308_I	0.659	0.34
139_S	262_L	0.658	0.33
92_A	224_V	0.655	0.33
56_A	106_Q	0.654	0.33
165_I	262_L	0.654	0.33
292_I	329_R	0.652	0.33
259_S	265_Y	0.652	0.33
138_I	365_L	0.651	0.33
166_G	348_T	0.651	0.33
135_I	352_S	0.649	0.33
165_I	207_E	0.649	0.33
134_N	168_Q	0.649	0.33
60_L	117_F	0.649	0.33
211_I	223_A	0.648	0.33
162_P	270_F	0.647	0.33
166_G	330_D	0.646	0.33
175_P	179_L	0.645	0.33
76_K	119_L	0.645	0.33
55_Y	152_I	0.644	0.32
152_I	239_K	0.643	0.32
88_K	136_F	0.640	0.32
165_I	359_M	0.640	0.32
220_F	238_L	0.640	0.32
92_A	174_R	0.640	0.32
180_I	191_K	0.639	0.32
224_V	235_K	0.639	0.32
259_S	361_A	0.637	0.32
194_Y	215_I	0.635	0.32
133_G	366_R	0.634	0.32
304_V	308_I	0.633	0.32
58_F	70_A	0.633	0.32
285_N	298_F	0.631	0.32
335_A	369_L	0.630	0.31
69_S	73_E	0.629	0.31
91_N	277_K	0.628	0.31
215_I	218_G	0.624	0.31
184_L	268_Y	0.624	0.31
343_K	346_E	0.623	0.31
55_Y	148_V	0.623	0.31
286_D	297_Y	0.622	0.31
167_Y	274_L	0.622	0.31
203_S	219_D	0.621	0.31
137_E	350_T	0.617	0.31
208_T	211_I	0.616	0.30
260_L	268_Y	0.616	0.30
148_V	151_R	0.611	0.30
237_L	245_N	0.610	0.30
263_D	271_N	0.609	0.30
167_Y	312_E	0.609	0.30
245_N	255_F	0.608	0.30
128_K	218_G	0.604	0.30
131_H	330_D	0.603	0.30
83_N	101_P	0.603	0.30
92_A	99_Y	0.602	0.29
187_R	249_L	0.601	0.29
224_V	228_P	0.594	0.29
147_I	207_E	0.594	0.29
307_E	311_D	0.592	0.29
88_K	96_Q	0.592	0.29
291_L	370_R	0.591	0.29
146_D	303_D	0.590	0.29
302_D	306_K	0.588	0.29
87_I	257_P	0.586	0.28
87_I	256_I	0.585	0.28
183_Y	254_S	0.584	0.28
87_I	91_N	0.583	0.28
175_P	180_I	0.583	0.28
277_K	291_L	0.583	0.28
142_I	372_D	0.581	0.28
184_L	283_N	0.580	0.28
87_I	266_Q	0.579	0.28
155_I	326_I	0.577	0.28
168_Q	171_G	0.575	0.28
89_D	92_A	0.573	0.28
152_I	351_I	0.571	0.27
119_L	243_R	0.571	0.27
342_L	364_L	0.571	0.27
255_F	258_I	0.571	0.27
128_K	338_N	0.571	0.27
156_K	184_L	0.570	0.27
31_N	45_Q	0.570	0.27
160_Y	282_K	0.569	0.27
163_A	359_M	0.569	0.27
133_G	166_G	0.569	0.27
102_L	187_R	0.569	0.27
151_R	332_V	0.567	0.27
48_K	53_G	0.566	0.27
109_I	372_D	0.566	0.27
353_F	368_I	0.565	0.27
256_I	261_Y	0.564	0.27
57_V	65_I	0.563	0.27
58_F	120_K	0.563	0.27
104_E	253_S	0.562	0.27
184_L	307_E	0.561	0.27
89_D	169_R	0.560	0.27
75_Q	127_K	0.560	0.27
43_P	47_W	0.560	0.27
120_K	123_G	0.558	0.27
85_I	129_L	0.558	0.27
178_H	291_L	0.558	0.27
66_D	72_S	0.557	0.27
210_D	214_L	0.554	0.26
110_E	143_S	0.554	0.26
77_V	190_E	0.553	0.26
66_D	177_T	0.553	0.26
67_H	82_V	0.553	0.26
55_Y	99_Y	0.553	0.26
192_A	368_I	0.552	0.26
228_P	330_D	0.552	0.26
93_I	314_I	0.551	0.26
273_Y	284_L	0.551	0.26
90_A	263_D	0.550	0.26
106_Q	112_Y	0.549	0.26
109_I	336_F	0.549	0.26
286_D	367_E	0.548	0.26
74_V	279_D	0.547	0.26
82_V	357_R	0.545	0.26
71_I	344_V	0.545	0.26
93_I	276_R	0.544	0.26
147_I	310_L	0.544	0.26
190_E	227_I	0.543	0.26
75_Q	79_H	0.543	0.26
215_I	220_F	0.542	0.26
200_P	258_I	0.542	0.26
141_S	163_A	0.540	0.25
58_F	166_G	0.540	0.25
90_A	221_K	0.540	0.25
355_L	360_Y	0.540	0.25
275_S	366_R	0.539	0.25
88_K	362_T	0.538	0.25
86_G	136_F	0.536	0.25
293_R	300_N	0.535	0.25
98_V	300_N	0.535	0.25
87_I	95_S	0.533	0.25
47_W	53_G	0.533	0.25
88_K	168_Q	0.532	0.25
77_V	81_K	0.532	0.25
265_Y	361_A	0.529	0.25
185_L	365_L	0.528	0.25
277_K	281_Y	0.528	0.25
171_G	264_A	0.528	0.25
227_I	308_I	0.527	0.25
62_K	86_G	0.527	0.25
90_A	173_R	0.527	0.25
85_I	330_D	0.526	0.25
139_S	260_L	0.524	0.24
234_E	291_L	0.523	0.24
184_L	288_V	0.523	0.24
171_G	180_I	0.522	0.24
302_D	332_V	0.522	0.24
167_Y	181_G	0.519	0.24
267_S	271_N	0.518	0.24
87_I	263_D	0.518	0.24
58_F	64_G	0.517	0.24
89_D	94_T	0.517	0.24
55_Y	118_I	0.517	0.24
176_I	189_W	0.517	0.24
152_I	342_L	0.517	0.24
87_I	187_R	0.516	0.24
265_Y	270_F	0.516	0.24
285_N	345_N	0.515	0.24
254_S	265_Y	0.515	0.24
39_I	97_L	0.515	0.24
148_V	344_V	0.514	0.24
316_R	319_F	0.514	0.24
117_F	212_R	0.514	0.24
31_N	36_I	0.513	0.24
240_N	244_F	0.512	0.24
329_R	358_G	0.512	0.24
355_L	361_A	0.511	0.24
330_D	362_T	0.511	0.24
139_S	207_E	0.510	0.24
93_I	115_R	0.508	0.23
150_E	154_Q	0.505	0.23
270_F	330_D	0.504	0.23
77_V	162_P	0.504	0.23
87_I	131_H	0.503	0.23
73_E	223_A	0.503	0.23
154_Q	180_I	0.502	0.23
93_I	187_R	0.502	0.23
57_V	162_P	0.501	0.23
367_E	370_R	0.500	0.23

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
1z2zA	1	0.9708	100	0.191	Contact Map
1szwA	1	0.748	100	0.388	Contact Map
3mkqB	1	0.4615	20.6	0.975	Contact Map
2hr2A	4	0.366	18.9	0.975	Contact Map
3iegA	1	0.5332	15.1	0.976	Contact Map
2vsyA	1	0.4138	14.4	0.976	Contact Map
4bzjA	2	0.8249	12.2	0.977	Contact Map
2mc5A	1	0.1857	11.1	0.978	Contact Map
4ui9J	2	0.4881	10.1	0.978	Contact Map
2katA	1	0.2785	9.8	0.978	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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