YHCT - BACSU - GREMLIN Contacts

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YHCT - Uncharacterized RNA pseudouridine synthase YhcT

UniProt:	P54604	Sequences: MNQKGRGLEILINEKQDGQWLFSVLKTALKASKPVIQDWMSHQQIKVNHESVLNNMIVKKGDRVFIDLQESEASSVIPEYGELDILFEDNHMLIINKPAGIATHPNEDGQTGTLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTAIAEGKLRTKKGTINSPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLVELELETGRTHQIRVHLASLGHPLTGDSLYGGGSKLLNRQALHANKVQAVHPITDELIVAEAPFPADMKNLCRTYFS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	302 (278)
Sequences:	9289 (6474)
Seq/√Len:	388.3

ECOLI - RLUD RLUC RLUA TRUC RLUB RSUA RLUF
BACSU - YHCT YLYB YJBO RLUB YTZG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
169_T	227_E	3.605	1.00
86_L	144_A	3.361	1.00
211_H	231_E	3.344	1.00
48_N	62_D	3.311	1.00
88_E	149_K	2.932	1.00
213_K	227_E	2.920	1.00
84_D	96_N	2.844	1.00
271_K	284_V	2.812	1.00
273_Q	284_V	2.809	1.00
183_G	212_F	2.677	1.00
171_T	225_L	2.676	1.00
171_T	270_N	2.673	1.00
184_T	211_H	2.650	1.00
91_H	278_I	2.586	1.00
91_H	150_H	2.518	1.00
187_S	244_S	2.452	1.00
182_K	213_K	2.392	1.00
228_L	242_L	2.369	1.00
181_K	217_S	2.350	1.00
264_R	292_D	2.303	1.00
96_N	287_A	2.267	1.00
79_E	111_T	2.259	1.00
167_K	229_E	2.258	1.00
186_N	207_T	2.209	1.00
273_Q	282_L	2.140	1.00
184_T	209_V	2.138	1.00
186_N	209_V	2.117	1.00
94_I	285_A	2.104	1.00
114_L	145_I	2.100	1.00
81_G	117_L	2.074	1.00
169_T	271_K	2.065	1.00
150_H	153_A	2.043	1.00
214_V	224_S	2.032	1.00
271_K	286_E	1.991	1.00
167_K	273_Q	1.920	1.00
275_V	282_L	1.892	1.00
160_Q	165_T	1.882	1.00
172_A	228_L	1.870	1.00
209_V	231_E	1.841	1.00
178_L	224_S	1.826	1.00
79_E	112_G	1.823	1.00
21_L	52_V	1.804	1.00
210_T	228_L	1.801	1.00
142_S	268_H	1.793	1.00
215_M	227_E	1.793	1.00
52_V	56_M	1.789	1.00
169_T	229_E	1.778	1.00
174_A	226_V	1.766	1.00
228_L	238_I	1.736	1.00
159_Q	163_K	1.707	1.00
137_L	145_I	1.695	1.00
47_V	56_M	1.685	1.00
94_I	146_V	1.643	1.00
94_I	144_A	1.612	1.00
176_G	224_S	1.567	1.00
262_L	266_A	1.552	1.00
103_T	145_I	1.551	1.00
270_N	286_E	1.541	1.00
89_D	276_H	1.531	1.00
266_A	293_M	1.528	1.00
86_L	285_A	1.513	1.00
211_H	229_E	1.475	1.00
140_D	265_Q	1.453	1.00
118_I	147_F	1.450	1.00
19_Q	27_T	1.446	1.00
80_Y	120_Y	1.445	1.00
226_V	242_L	1.435	1.00
201_V	244_S	1.434	1.00
217_S	224_S	1.428	1.00
291_A	295_N	1.424	1.00
24_V	28_A	1.409	1.00
168_R	230_L	1.403	1.00
112_G	117_L	1.374	1.00
185_I	245_L	1.368	1.00
177_K	217_S	1.365	1.00
46_K	65_F	1.360	1.00
174_A	242_L	1.331	1.00
156_I	160_Q	1.327	1.00
99_A	142_S	1.320	1.00
223_L	250_T	1.313	1.00
276_H	283_I	1.294	1.00
171_T	227_E	1.284	1.00
212_F	242_L	1.283	1.00
178_L	247_H	1.274	1.00
189_I	240_V	1.259	1.00
47_V	52_V	1.255	1.00
192_D	198_R	1.251	1.00
102_A	109_G	1.250	1.00
173_I	223_L	1.232	1.00
16_Q	28_A	1.231	1.00
17_D	60_K	1.223	1.00
113_T	116_N	1.222	1.00
171_T	289_F	1.220	1.00
37_Q	41_S	1.214	1.00
89_D	92_M	1.211	1.00
210_T	230_L	1.181	1.00
206_Q	234_R	1.179	1.00
98_P	101_I	1.159	1.00
99_A	264_R	1.156	1.00
161_L	166_L	1.149	1.00
214_V	217_S	1.138	1.00
266_A	296_L	1.133	1.00
171_T	215_M	1.133	1.00
230_L	238_I	1.133	1.00
172_A	226_V	1.125	1.00
154_H	158_D	1.119	1.00
140_D	253_S	1.114	1.00
152_L	278_I	1.114	1.00
95_I	114_L	1.112	1.00
190_G	202_S	1.109	1.00
176_G	247_H	1.107	1.00
19_Q	23_S	1.104	1.00
47_V	64_V	1.103	1.00
159_Q	162_E	1.100	1.00
24_V	58_V	1.095	1.00
178_L	226_V	1.082	1.00
173_I	225_L	1.081	1.00
91_H	153_A	1.077	1.00
101_I	117_L	1.072	1.00
26_K	33_K	1.071	1.00
99_A	292_D	1.070	1.00
174_A	178_L	1.067	1.00
156_I	159_Q	1.059	1.00
49_H	65_F	1.054	1.00
291_A	294_K	1.053	1.00
35_V	39_W	1.045	1.00
91_H	276_H	1.037	1.00
173_I	296_L	1.035	1.00
38_D	42_H	1.035	1.00
184_T	231_E	1.035	1.00
175_E	257_G	1.031	1.00
134_V	148_A	1.028	1.00
177_K	222_R	1.020	1.00
167_K	282_L	1.009	1.00
134_V	157_L	1.002	1.00
210_T	241_H	1.001	1.00
133_H	147_F	0.999	1.00
180_T	214_V	0.998	1.00
218_N	221_E	0.993	1.00
25_L	36_I	0.990	1.00
289_F	293_M	0.990	1.00
101_I	114_L	0.987	1.00
175_E	250_T	0.983	1.00
195_H	198_R	0.982	1.00
155_A	159_Q	0.981	1.00
106_N	109_G	0.979	1.00
144_A	285_A	0.974	1.00
92_M	274_A	0.973	1.00
92_M	276_H	0.965	1.00
178_L	217_S	0.960	1.00
172_A	249_L	0.958	1.00
275_V	280_D	0.958	1.00
238_I	249_L	0.952	1.00
144_A	287_A	0.939	1.00
56_M	62_D	0.937	1.00
93_L	122_Y	0.936	1.00
92_M	153_A	0.935	1.00
242_L	249_L	0.931	1.00
178_L	214_V	0.930	1.00
197_T	254_L	0.929	1.00
262_L	293_M	0.922	1.00
35_V	38_D	0.920	1.00
148_A	154_H	0.916	1.00
180_T	183_G	0.916	1.00
174_A	224_S	0.916	1.00
175_E	223_L	0.914	1.00
31_A	39_W	0.913	1.00
173_I	293_M	0.912	1.00
16_Q	24_V	0.903	1.00
288_P	294_K	0.898	1.00
74_S	128_T	0.897	1.00
174_A	249_L	0.893	1.00
46_K	67_D	0.891	1.00
34_P	37_Q	0.889	1.00
192_D	195_H	0.887	1.00
151_R	154_H	0.884	1.00
274_A	285_A	0.881	1.00
189_I	199_R	0.881	1.00
276_H	279_T	0.879	1.00
152_L	156_I	0.875	1.00
160_Q	275_V	0.874	1.00
180_T	212_F	0.873	1.00
93_L	118_I	0.872	1.00
31_A	36_I	0.866	1.00
93_L	147_F	0.866	1.00
103_T	137_L	0.860	1.00
58_V	64_V	0.858	1.00
86_L	288_P	0.857	1.00
161_L	168_R	0.855	1.00
174_A	247_H	0.851	1.00
185_I	241_H	0.848	1.00
83_L	117_L	0.847	1.00
216_A	225_L	0.844	1.00
169_T	270_N	0.844	1.00
268_H	287_A	0.839	1.00
218_N	222_R	0.838	1.00
177_K	221_E	0.833	1.00
182_K	211_H	0.828	1.00
25_L	45_I	0.825	1.00
161_L	230_L	0.824	1.00
264_R	293_M	0.822	1.00
190_G	204_G	0.822	1.00
17_D	59_K	0.821	1.00
266_A	292_D	0.821	1.00
274_A	283_I	0.819	1.00
45_I	66_I	0.818	1.00
227_E	270_N	0.815	1.00
44_Q	67_D	0.815	1.00
53_L	56_M	0.808	1.00
264_R	268_H	0.806	1.00
181_K	214_V	0.805	1.00
192_D	200_R	0.805	1.00
100_G	142_S	0.805	1.00
183_G	214_V	0.804	1.00
262_L	296_L	0.803	1.00
82_E	117_L	0.803	1.00
182_K	214_V	0.801	1.00
19_Q	24_V	0.799	1.00
39_W	44_Q	0.797	1.00
179_R	247_H	0.797	1.00
33_K	37_Q	0.789	1.00
257_G	261_L	0.786	1.00
148_A	153_A	0.780	1.00
56_M	59_K	0.779	1.00
43_Q	51_S	0.777	1.00
262_L	292_D	0.777	1.00
190_G	200_R	0.772	1.00
177_K	224_S	0.770	1.00
168_R	231_E	0.768	1.00
115_A	133_H	0.765	1.00
187_S	245_L	0.763	1.00
114_L	147_F	0.758	1.00
87_F	92_M	0.755	1.00
185_I	242_L	0.755	1.00
213_K	229_E	0.754	1.00
188_P	241_H	0.749	1.00
59_K	62_D	0.749	1.00
105_P	113_T	0.748	1.00
210_T	238_I	0.747	1.00
188_P	207_T	0.745	1.00
31_A	35_V	0.744	1.00
87_F	285_A	0.740	1.00
46_K	51_S	0.735	1.00
156_I	278_I	0.735	1.00
262_L	265_Q	0.729	1.00
198_R	243_A	0.728	1.00
131_V	147_F	0.725	1.00
191_R	235_T	0.723	1.00
103_T	114_L	0.717	1.00
115_A	131_V	0.715	1.00
188_P	205_G	0.715	1.00
275_V	279_T	0.714	1.00
95_I	145_I	0.714	1.00
20_W	23_S	0.710	1.00
40_M	45_I	0.706	1.00
83_L	95_I	0.706	1.00
156_I	280_D	0.706	1.00
103_T	133_H	0.703	1.00
29_L	36_I	0.701	1.00
16_Q	27_T	0.700	1.00
151_R	155_A	0.695	1.00
122_Y	149_K	0.695	1.00
135_H	269_A	0.695	1.00
135_H	145_I	0.693	0.99
145_I	269_A	0.693	0.99
135_H	161_L	0.692	0.99
116_N	119_A	0.691	0.99
92_M	283_I	0.684	0.99
185_I	212_F	0.683	0.99
253_S	257_G	0.680	0.99
41_S	54_N	0.680	0.99
112_G	116_N	0.678	0.99
269_A	272_V	0.674	0.99
18_G	60_K	0.672	0.99
158_D	162_E	0.672	0.99
86_L	287_A	0.670	0.99
102_A	108_D	0.668	0.99
39_W	68_L	0.667	0.99
265_Q	292_D	0.666	0.99
187_S	201_V	0.662	0.99
106_N	197_T	0.661	0.99
132_R	154_H	0.659	0.99
104_H	113_T	0.659	0.99
88_E	122_Y	0.656	0.99
201_V	205_G	0.654	0.99
83_L	121_H	0.654	0.99
111_T	116_N	0.654	0.99
39_W	66_I	0.653	0.99
88_E	121_H	0.646	0.99
80_Y	117_L	0.646	0.99
40_M	54_N	0.639	0.99
119_A	131_V	0.638	0.99
218_N	223_L	0.636	0.99
16_Q	19_Q	0.635	0.99
187_S	241_H	0.634	0.99
155_A	158_D	0.632	0.99
123_Q	129_C	0.631	0.99
257_G	260_K	0.631	0.99
144_A	272_V	0.628	0.99
81_G	101_I	0.626	0.99
169_T	273_Q	0.625	0.99
208_A	234_R	0.617	0.99
116_N	120_Y	0.616	0.99
21_L	40_M	0.614	0.99
167_K	271_K	0.612	0.99
215_M	225_L	0.609	0.99
173_I	266_A	0.608	0.99
217_S	222_R	0.608	0.99
93_L	149_K	0.607	0.99
150_H	278_I	0.603	0.99
250_T	260_K	0.602	0.99
250_T	266_A	0.599	0.99
183_G	242_L	0.598	0.99
202_S	205_G	0.598	0.99
148_A	157_L	0.598	0.99
85_I	88_E	0.597	0.98
173_I	250_T	0.597	0.98
30_K	36_I	0.596	0.98
102_A	106_N	0.596	0.98
183_G	245_L	0.593	0.98
146_V	272_V	0.592	0.98
224_S	247_H	0.591	0.98
201_V	240_V	0.589	0.98
160_Q	166_L	0.587	0.98
40_M	52_V	0.586	0.98
175_E	260_K	0.585	0.98
191_R	196_P	0.579	0.98
23_S	27_T	0.578	0.98
212_F	228_L	0.576	0.98
118_I	122_Y	0.575	0.98
212_F	245_L	0.575	0.98
134_V	161_L	0.573	0.98
109_G	112_G	0.572	0.98
39_W	45_I	0.572	0.98
146_V	161_L	0.571	0.98
21_L	64_V	0.569	0.98
91_H	152_L	0.569	0.98
95_I	147_F	0.569	0.98
127_E	151_R	0.568	0.98
160_Q	278_I	0.568	0.98
250_T	262_L	0.566	0.98
175_E	261_L	0.566	0.98
117_L	120_Y	0.565	0.98
198_R	254_L	0.565	0.98
119_A	123_Q	0.564	0.98
153_A	278_I	0.562	0.98
25_L	29_L	0.562	0.98
188_P	204_G	0.561	0.98
178_L	242_L	0.561	0.98
175_E	258_G	0.561	0.98
270_N	288_P	0.560	0.98
37_Q	54_N	0.560	0.98
192_D	196_P	0.560	0.98
100_G	140_D	0.558	0.98
142_S	264_R	0.558	0.98
217_S	221_E	0.557	0.98
78_P	119_A	0.557	0.98
175_E	256_G	0.553	0.98
26_K	36_I	0.552	0.97
134_V	154_H	0.551	0.97
90_N	149_K	0.550	0.97
73_A	76_V	0.549	0.97
223_L	296_L	0.548	0.97
78_P	120_Y	0.548	0.97
168_R	208_A	0.548	0.97
178_L	212_F	0.547	0.97
114_L	121_H	0.546	0.97
183_G	228_L	0.545	0.97
165_T	275_V	0.545	0.97
96_N	142_S	0.544	0.97
92_M	285_A	0.543	0.97
32_S	39_W	0.543	0.97
173_I	218_N	0.543	0.97
132_R	151_R	0.543	0.97
164_K	167_K	0.542	0.97
172_A	242_L	0.542	0.97
289_F	294_K	0.541	0.97
21_L	47_V	0.540	0.97
137_L	164_K	0.540	0.97
157_L	160_Q	0.540	0.97
22_F	26_K	0.539	0.97
70_E	73_A	0.538	0.97
118_I	131_V	0.538	0.97
168_R	211_H	0.534	0.97
102_A	133_H	0.534	0.97
93_L	121_H	0.533	0.97
95_I	118_I	0.531	0.97
193_R	202_S	0.531	0.97
87_F	283_I	0.530	0.97
240_V	244_S	0.530	0.97
21_L	56_M	0.529	0.97
167_K	284_V	0.527	0.97
137_L	144_A	0.526	0.97
18_G	57_I	0.525	0.97
227_E	271_K	0.525	0.97
199_R	206_Q	0.525	0.97
218_N	225_L	0.524	0.97
48_N	52_V	0.522	0.97
228_L	249_L	0.518	0.96
178_L	181_K	0.517	0.96
226_V	249_L	0.515	0.96
47_V	62_D	0.515	0.96
92_M	157_L	0.513	0.96
23_S	33_K	0.512	0.96
85_I	93_L	0.512	0.96
47_V	58_V	0.511	0.96
188_P	201_V	0.510	0.96
209_V	232_T	0.509	0.96
34_P	38_D	0.508	0.96
99_A	263_N	0.507	0.96
120_Y	123_Q	0.507	0.96
90_N	278_I	0.505	0.96
15_K	28_A	0.504	0.96
115_A	132_R	0.503	0.96
32_S	37_Q	0.503	0.96
208_A	240_V	0.502	0.96
196_P	200_R	0.500	0.96

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
1v9fA	1	0.7417	100	0.165	Contact Map
1v9kA	1	0.7086	100	0.321	Contact Map
2i82A	1	0.6987	100	0.343	Contact Map
4lgtA	1	0.7815	100	0.433	Contact Map
1vioA	2	0.7517	100	0.435	Contact Map
3dh3A	1	0.7781	100	0.448	Contact Map
1kskA	1	0.7649	100	0.455	Contact Map
2olwA	1	0.553	100	0.493	Contact Map
2omlA	1	0.5563	100	0.508	Contact Map
2gmlA	1	0.5695	100	0.57	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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