RLUC - ECOLI - GREMLIN Contacts

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RLUC - Ribosomal large subunit pseudouridine synthase C

UniProt:	P0AA39	Sequences: MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPHLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRNAR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11118
Length:	319 (280)
Sequences:	9099 (6419)
Seq/√Len:	383.6

ECOLI - RLUC RLUD TRUC RLUA RLUB RLUF RSUA
BACSU - YLYB YHCT 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
96_L	150_V	3.674	1.00
175_D	233_R	3.451	1.00
50_N	64_D	3.451	1.00
219_R	237_V	3.354	1.00
221_K	233_R	2.903	1.00
98_E	155_K	2.837	1.00
286_A	299_R	2.807	1.00
189_K	220_F	2.779	1.00
94_V	106_N	2.775	1.00
177_L	231_L	2.773	1.00
190_S	219_R	2.762	1.00
177_L	285_A	2.755	1.00
288_K	299_R	2.743	1.00
101_H	293_G	2.697	1.00
101_H	156_K	2.637	1.00
193_A	250_Y	2.499	1.00
106_N	302_A	2.426	1.00
190_S	217_E	2.309	1.00
192_Q	217_E	2.242	1.00
173_Q	235_S	2.228	1.00
192_Q	215_P	2.213	1.00
234_C	248_T	2.165	1.00
104_V	300_I	2.157	1.00
288_K	297_V	2.144	1.00
89_A	121_F	2.069	1.00
290_T	297_V	2.052	1.00
175_D	286_A	2.049	1.00
156_K	159_A	2.040	1.00
286_A	301_E	2.004	1.00
187_H	225_R	2.003	1.00
279_R	307_G	1.988	1.00
188_V	221_K	1.972	1.00
178_A	234_C	1.926	1.00
217_E	237_V	1.902	1.00
22_I	54_I	1.901	1.00
222_V	230_T	1.899	1.00
175_D	235_S	1.899	1.00
173_Q	288_K	1.869	1.00
223_E	233_R	1.857	1.00
54_I	58_Y	1.834	1.00
14_T	17_E	1.820	1.00
166_Q	171_G	1.813	1.00
184_W	230_T	1.790	1.00
148_S	283_H	1.782	1.00
89_A	122_G	1.778	1.00
218_T	234_C	1.755	1.00
180_V	232_V	1.678	1.00
165_E	169_E	1.668	1.00
49_V	58_Y	1.652	1.00
234_C	244_I	1.587	1.00
285_A	301_E	1.578	1.00
277_L	281_F	1.570	1.00
143_L	151_L	1.569	1.00
306_E	310_R	1.542	1.00
96_L	300_I	1.540	1.00
113_V	151_L	1.536	1.00
25_F	29_Q	1.522	1.00
127_L	131_R	1.509	1.00
104_V	150_V	1.489	1.00
225_R	230_T	1.487	1.00
104_V	152_L	1.487	1.00
20_Q	28_T	1.486	1.00
182_G	230_T	1.476	1.00
191_V	251_A	1.470	1.00
99_D	291_H	1.469	1.00
232_V	248_T	1.466	1.00
281_F	308_L	1.440	1.00
219_R	235_S	1.418	1.00
146_D	280_L	1.393	1.00
162_S	166_Q	1.367	1.00
183_Q	225_R	1.367	1.00
48_R	67_R	1.366	1.00
109_S	148_S	1.359	1.00
127_L	132_P	1.340	1.00
18_A	62_A	1.316	1.00
49_V	54_I	1.310	1.00
174_K	236_P	1.305	1.00
177_L	233_R	1.303	1.00
184_W	253_H	1.286	1.00
177_L	304_M	1.282	1.00
198_N	204_E	1.276	1.00
90_A	129_A	1.271	1.00
180_V	248_T	1.264	1.00
124_I	151_L	1.259	1.00
17_E	29_Q	1.252	1.00
158_S	293_G	1.251	1.00
127_L	130_L	1.244	1.00
112_A	119_L	1.242	1.00
222_V	225_R	1.241	1.00
229_A	256_A	1.222	1.00
291_H	298_M	1.218	1.00
108_P	111_T	1.212	1.00
195_L	246_V	1.209	1.00
177_L	223_E	1.208	1.00
123_V	126_G	1.205	1.00
40_R	44_K	1.203	1.00
39_Y	43_R	1.203	1.00
15_A	62_A	1.202	1.00
129_A	132_P	1.181	1.00
214_K	240_R	1.181	1.00
207_V	250_Y	1.177	1.00
99_D	102_I	1.175	1.00
281_F	311_C	1.174	1.00
184_W	232_V	1.172	1.00
167_L	172_M	1.166	1.00
49_V	66_V	1.161	1.00
160_L	164_H	1.161	1.00
220_F	248_T	1.155	1.00
109_S	279_R	1.151	1.00
179_L	229_A	1.148	1.00
146_D	259_D	1.145	1.00
196_L	210_S	1.143	1.00
179_L	231_L	1.139	1.00
186_S	222_V	1.139	1.00
20_Q	24_N	1.130	1.00
25_F	60_L	1.129	1.00
101_H	159_A	1.111	1.00
182_G	253_H	1.111	1.00
178_A	232_V	1.110	1.00
37_M	41_I	1.109	1.00
51_K	67_R	1.109	1.00
165_E	168_R	1.108	1.00
218_T	236_P	1.107	1.00
236_P	244_I	1.094	1.00
201_Q	204_E	1.094	1.00
43_R	56_P	1.083	1.00
178_A	255_I	1.081	1.00
181_R	263_D	1.078	1.00
27_R	35_K	1.055	1.00
102_I	159_A	1.053	1.00
304_M	308_L	1.049	1.00
162_S	165_E	1.049	1.00
231_L	312_L	1.047	1.00
179_L	312_L	1.045	1.00
116_G	119_L	1.040	1.00
306_E	309_K	1.040	1.00
190_S	237_V	1.040	1.00
109_S	307_G	1.040	1.00
183_Q	227_A	1.039	1.00
123_V	151_L	1.032	1.00
128_R	132_P	1.028	1.00
180_V	184_W	1.021	1.00
173_Q	297_V	1.021	1.00
218_T	247_H	1.018	1.00
150_V	300_I	1.017	1.00
179_L	311_C	1.010	1.00
183_Q	228_F	1.009	1.00
101_H	291_H	1.006	1.00
181_R	256_A	1.005	1.00
102_I	289_F	1.001	1.00
139_L	153_V	0.998	1.00
290_T	295_G	0.993	1.00
248_T	255_I	0.987	1.00
303_P	309_K	0.986	1.00
140_V	163_L	0.981	1.00
110_G	148_S	0.980	1.00
158_S	162_S	0.976	1.00
180_V	230_T	0.973	1.00
127_L	153_V	0.962	1.00
37_M	40_R	0.958	1.00
198_N	201_Q	0.953	1.00
140_V	154_A	0.952	1.00
26_L	38_I	0.945	1.00
105_L	124_I	0.944	1.00
161_R	165_E	0.944	1.00
58_Y	64_D	0.938	1.00
184_W	222_V	0.934	1.00
180_V	255_I	0.931	1.00
48_R	69_P	0.930	1.00
17_E	25_F	0.929	1.00
76_R	79_E	0.920	1.00
196_L	212_E	0.911	1.00
39_Y	56_P	0.908	1.00
195_L	205_R	0.902	1.00
154_A	160_L	0.896	1.00
113_V	143_L	0.893	1.00
289_F	300_I	0.891	1.00
103_L	153_V	0.888	1.00
179_L	308_L	0.883	1.00
181_R	229_A	0.880	1.00
18_A	61_E	0.873	1.00
55_K	58_Y	0.871	1.00
184_W	225_R	0.870	1.00
102_I	291_H	0.866	1.00
42_L	56_P	0.866	1.00
233_R	285_A	0.865	1.00
41_I	46_E	0.862	1.00
191_V	248_T	0.862	1.00
157_R	160_L	0.860	1.00
36_S	39_Y	0.860	1.00
42_L	47_V	0.859	1.00
166_Q	290_T	0.853	1.00
186_S	189_K	0.850	1.00
162_S	295_G	0.850	1.00
20_Q	25_F	0.847	1.00
122_G	126_G	0.846	1.00
206_I	210_S	0.846	1.00
167_L	174_K	0.845	1.00
35_K	39_Y	0.843	1.00
77_E	80_A	0.843	1.00
33_V	41_I	0.841	1.00
26_L	47_V	0.838	1.00
47_V	68_I	0.831	1.00
60_L	66_V	0.831	1.00
244_I	255_I	0.830	1.00
97_Y	300_I	0.830	1.00
150_V	302_A	0.830	1.00
277_L	308_L	0.830	1.00
61_E	64_D	0.826	1.00
180_V	253_H	0.822	1.00
224_E	231_L	0.822	1.00
46_E	69_P	0.821	1.00
203_G	260_R	0.819	1.00
283_H	302_A	0.815	1.00
187_H	222_V	0.815	1.00
22_I	42_L	0.812	1.00
78_E	81_V	0.807	1.00
48_R	53_R	0.806	1.00
154_A	159_A	0.798	1.00
185_Q	253_H	0.797	1.00
277_L	311_C	0.797	1.00
281_F	307_G	0.793	1.00
45_G	53_R	0.793	1.00
175_D	285_A	0.788	1.00
105_L	151_L	0.785	1.00
96_L	303_P	0.782	1.00
102_I	298_M	0.778	1.00
183_Q	230_T	0.777	1.00
279_R	308_L	0.771	1.00
58_Y	61_E	0.770	1.00
33_V	38_I	0.760	1.00
157_R	161_R	0.758	1.00
174_K	237_V	0.758	1.00
291_H	294_T	0.757	1.00
167_L	236_P	0.756	1.00
194_P	215_P	0.751	1.00
187_H	221_K	0.750	1.00
289_F	298_M	0.750	1.00
179_L	226_Y	0.750	1.00
290_T	294_T	0.748	1.00
113_V	139_L	0.744	1.00
93_D	105_L	0.744	1.00
193_A	251_A	0.744	1.00
279_R	283_H	0.742	1.00
17_E	20_Q	0.738	1.00
162_S	293_G	0.736	1.00
198_N	206_I	0.732	1.00
277_L	307_G	0.729	1.00
21_R	24_N	0.728	1.00
17_E	28_T	0.720	1.00
156_K	293_G	0.719	1.00
164_H	168_R	0.719	1.00
141_H	167_L	0.718	1.00
151_L	284_A	0.716	1.00
91_L	111_T	0.710	1.00
77_E	82_S	0.708	1.00
277_L	280_L	0.695	0.99
125_E	137_L	0.695	0.99
128_R	131_R	0.692	0.99
194_P	247_H	0.691	0.99
196_L	206_I	0.691	0.99
97_Y	102_I	0.687	0.99
121_F	126_G	0.686	0.99
161_R	164_H	0.684	0.99
308_L	312_L	0.684	0.99
22_I	66_V	0.675	0.99
96_L	302_A	0.668	0.99
112_A	118_G	0.668	0.99
280_L	307_G	0.667	0.99
79_E	82_S	0.666	0.99
194_P	213_G	0.665	0.99
189_K	222_V	0.663	0.99
79_E	134_A	0.662	0.99
30_L	33_V	0.661	0.99
186_S	220_F	0.661	0.99
191_V	220_F	0.659	0.99
77_E	81_V	0.659	0.99
112_A	116_G	0.659	0.99
33_V	37_M	0.656	0.99
189_K	248_T	0.656	0.99
98_E	131_R	0.656	0.99
103_L	155_K	0.655	0.99
210_S	213_G	0.652	0.99
49_V	60_L	0.651	0.99
218_T	244_I	0.649	0.99
30_L	38_I	0.646	0.99
197_K	202_S	0.646	0.99
41_I	68_I	0.645	0.99
188_V	219_R	0.645	0.99
230_T	253_H	0.644	0.99
191_V	247_H	0.643	0.99
207_V	213_G	0.640	0.99
41_I	70_P	0.639	0.99
137_L	153_V	0.638	0.99
220_F	234_C	0.637	0.99
19_G	62_A	0.632	0.99
221_K	235_S	0.631	0.99
263_D	266_F	0.630	0.99
304_M	312_L	0.628	0.99
124_I	153_V	0.624	0.99
197_K	241_T	0.624	0.99
15_A	18_A	0.624	0.99
179_L	256_A	0.624	0.99
207_V	246_V	0.623	0.99
94_V	108_P	0.620	0.99
226_Y	231_L	0.619	0.99
266_F	276_G	0.619	0.99
138_E	160_L	0.618	0.99
259_D	263_D	0.615	0.99
204_E	260_R	0.615	0.99
226_Y	312_L	0.613	0.99
216_S	240_R	0.612	0.99
284_A	287_L	0.611	0.99
122_G	125_E	0.611	0.99
91_L	127_L	0.611	0.99
131_R	155_K	0.610	0.99
256_A	277_L	0.608	0.99
141_H	284_A	0.608	0.99
24_N	28_T	0.606	0.99
166_Q	172_M	0.605	0.99
175_D	288_K	0.601	0.98
154_A	163_L	0.601	0.98
49_V	64_D	0.601	0.98
173_Q	286_A	0.600	0.98
152_L	167_L	0.600	0.98
101_H	158_S	0.599	0.98
111_T	124_I	0.599	0.98
113_V	124_I	0.598	0.98
22_I	58_Y	0.596	0.98
200_L	204_E	0.595	0.98
51_K	65_E	0.595	0.98
256_A	281_F	0.594	0.98
198_N	202_S	0.593	0.98
256_A	266_F	0.588	0.98
152_L	287_L	0.586	0.98
204_E	249_Q	0.585	0.98
95_I	103_L	0.583	0.98
150_V	287_L	0.577	0.98
285_A	303_P	0.576	0.98
103_L	131_R	0.575	0.98
200_L	203_G	0.573	0.98
170_K	173_Q	0.570	0.98
223_E	231_L	0.568	0.98
109_S	278_N	0.568	0.98
25_F	66_V	0.568	0.98
123_V	128_R	0.567	0.98
194_P	212_E	0.566	0.98
31_K	38_I	0.566	0.98
98_E	103_L	0.565	0.98
141_H	151_L	0.564	0.98
22_I	49_V	0.564	0.98
42_L	54_I	0.563	0.98
181_R	228_F	0.562	0.98
226_Y	229_A	0.561	0.98
129_A	133_E	0.561	0.98
181_R	264_R	0.560	0.98
184_W	189_K	0.558	0.98
140_V	160_L	0.558	0.98
100_D	155_K	0.553	0.97
183_Q	187_H	0.552	0.97
179_L	281_F	0.552	0.97
181_R	266_F	0.551	0.97
94_V	97_Y	0.549	0.97
193_A	247_H	0.549	0.97
106_N	148_S	0.548	0.97
189_K	251_A	0.547	0.97
181_R	262_G	0.547	0.97
48_R	52_K	0.547	0.97
189_K	234_C	0.546	0.97
229_A	311_C	0.543	0.97
166_Q	293_G	0.543	0.97
246_V	250_Y	0.543	0.97
36_S	40_R	0.541	0.97
46_E	71_V	0.541	0.97
115_G	123_V	0.540	0.97
143_L	170_K	0.540	0.97
127_L	133_E	0.539	0.97
41_I	47_V	0.539	0.97
184_W	248_T	0.539	0.97
34_P	37_M	0.537	0.97
93_D	111_T	0.536	0.97
116_G	203_G	0.535	0.97
257_F	281_F	0.533	0.97
225_R	228_F	0.531	0.97
95_I	98_E	0.531	0.97
202_S	205_R	0.530	0.97
140_V	167_L	0.528	0.97
27_R	38_I	0.528	0.97
304_M	309_K	0.528	0.97
171_G	290_T	0.527	0.97
170_K	237_V	0.527	0.97
114_H	123_V	0.526	0.97
138_E	157_R	0.526	0.97
307_G	311_C	0.523	0.96
19_G	59_K	0.521	0.96
199_I	206_I	0.520	0.96
101_H	294_T	0.520	0.96
159_A	293_G	0.520	0.96
76_R	80_A	0.519	0.96
24_N	35_K	0.518	0.96
163_L	166_Q	0.517	0.96
21_R	57_E	0.515	0.96
236_P	255_I	0.514	0.96
266_F	275_T	0.514	0.96
39_Y	42_L	0.514	0.96
50_N	54_I	0.514	0.96
217_E	238_T	0.513	0.96
174_K	216_S	0.513	0.96
186_S	225_R	0.512	0.96
97_Y	298_M	0.512	0.96
40_R	43_R	0.511	0.96
231_L	308_L	0.510	0.96
60_L	64_D	0.506	0.96
184_W	220_F	0.506	0.96
122_G	127_L	0.504	0.96
30_L	68_I	0.503	0.96
134_A	137_L	0.503	0.96
72_R	77_E	0.501	0.95
292_P	298_M	0.501	0.95
143_L	150_V	0.500	0.95

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	0.7241	100	0.191	Contact Map
1v9kA	1	0.7085	100	0.313	Contact Map
2i82A	1	0.674	100	0.363	Contact Map
4lgtA	1	0.7555	100	0.452	Contact Map
3dh3A	1	0.7461	100	0.46	Contact Map
1vioA	2	0.7147	100	0.464	Contact Map
1kskA	1	0.7241	100	0.473	Contact Map
2olwA	1	0.5517	100	0.512	Contact Map
2omlA	1	0.5204	100	0.519	Contact Map
2gmlA	1	0.5361	100	0.58	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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