YLYB - BACSU - GREMLIN Contacts

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YLYB - Uncharacterized RNA pseudouridine synthase YlyB

UniProt:	Q45480	Sequences: MNQIDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDFNGQALHAGVLGFDHPRTGEYVEFEAPLPEDMAELIENLRKNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	303 (278)
Sequences:	9189 (6375)
Seq/√Len:	382.4

ECOLI - RLUC RLUD RLUA TRUC RLUB RSUA RLUF
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
169_K	225_E	3.503	1.00
83_Y	144_L	3.469	1.00
211_H	229_E	3.415	1.00
45_N	59_D	3.236	1.00
270_V	283_E	2.925	1.00
85_E	149_K	2.896	1.00
213_H	225_E	2.855	1.00
272_G	283_E	2.804	1.00
171_T	223_L	2.794	1.00
171_T	269_G	2.764	1.00
81_D	93_N	2.716	1.00
184_T	211_H	2.703	1.00
88_D	277_R	2.654	1.00
183_G	212_F	2.591	1.00
88_D	150_N	2.564	1.00
187_A	242_Y	2.543	1.00
93_N	286_A	2.383	1.00
182_D	213_H	2.298	1.00
186_D	209_V	2.283	1.00
226_C	240_M	2.273	1.00
181_D	217_R	2.253	1.00
167_T	227_Q	2.249	1.00
272_G	281_Y	2.241	1.00
186_D	207_N	2.240	1.00
184_T	209_V	2.210	1.00
91_V	284_F	2.134	1.00
169_K	270_V	2.092	1.00
263_G	291_D	2.087	1.00
150_N	153_A	2.051	1.00
78_M	114_G	2.046	1.00
76_E	108_T	2.044	1.00
274_D	281_Y	2.039	1.00
270_V	285_E	1.988	1.00
214_V	222_T	1.985	1.00
111_L	145_L	1.970	1.00
169_K	227_Q	1.961	1.00
209_V	229_E	1.938	1.00
172_A	226_C	1.921	1.00
167_T	272_G	1.907	1.00
49_V	53_Y	1.856	1.00
17_I	49_V	1.843	1.00
215_L	225_E	1.839	1.00
160_Q	165_T	1.828	1.00
142_S	267_H	1.806	1.00
178_I	222_T	1.803	1.00
210_T	226_C	1.797	1.00
174_V	224_V	1.752	1.00
76_E	109_G	1.748	1.00
159_N	163_N	1.715	1.00
226_C	236_I	1.649	1.00
269_G	285_E	1.620	1.00
44_V	53_Y	1.590	1.00
137_I	145_L	1.584	1.00
100_V	145_L	1.564	1.00
91_V	144_L	1.562	1.00
91_V	146_M	1.554	1.00
261_F	265_A	1.551	1.00
15_E	23_S	1.541	1.00
176_G	222_T	1.540	1.00
83_Y	284_F	1.515	1.00
20_F	24_T	1.497	1.00
290_E	294_E	1.491	1.00
86_D	275_H	1.469	1.00
217_R	222_T	1.461	1.00
77_P	117_A	1.450	1.00
211_H	227_Q	1.434	1.00
265_A	292_M	1.431	1.00
140_D	264_Q	1.431	1.00
185_I	243_I	1.417	1.00
177_L	217_R	1.413	1.00
156_S	160_Q	1.399	1.00
224_V	240_M	1.389	1.00
115_L	147_V	1.379	1.00
43_V	62_T	1.367	1.00
12_Q	24_T	1.334	1.00
96_R	142_S	1.334	1.00
171_T	225_E	1.317	1.00
174_V	240_M	1.308	1.00
44_V	49_V	1.306	1.00
201_V	242_Y	1.302	1.00
13_K	57_P	1.294	1.00
189_I	238_V	1.274	1.00
212_F	240_M	1.265	1.00
171_T	288_L	1.263	1.00
99_V	106_H	1.257	1.00
168_R	228_L	1.247	1.00
171_T	215_L	1.241	1.00
221_F	248_A	1.233	1.00
206_K	232_R	1.233	1.00
275_H	282_V	1.230	1.00
110_T	113_N	1.229	1.00
178_I	245_F	1.229	1.00
109_G	114_G	1.222	1.00
192_D	198_S	1.221	1.00
34_Q	38_K	1.205	1.00
152_M	277_R	1.196	1.00
173_V	221_F	1.194	1.00
86_D	89_V	1.193	1.00
214_V	217_R	1.188	1.00
15_E	19_K	1.177	1.00
95_P	98_M	1.166	1.00
265_A	295_L	1.162	1.00
96_R	263_G	1.155	1.00
44_V	61_V	1.148	1.00
161_L	166_V	1.146	1.00
159_N	162_V	1.136	1.00
35_Q	39_D	1.135	1.00
210_T	228_L	1.134	1.00
98_M	114_G	1.130	1.00
140_D	251_P	1.130	1.00
154_H	158_V	1.128	1.00
92_V	111_L	1.120	1.00
20_F	55_I	1.113	1.00
32_Q	36_W	1.111	1.00
178_I	224_V	1.101	1.00
195_D	198_S	1.097	1.00
190_G	202_T	1.094	1.00
172_A	224_V	1.092	1.00
176_G	245_F	1.087	1.00
38_K	51_A	1.084	1.00
175_H	255_P	1.083	1.00
22_A	30_R	1.072	1.00
156_S	159_N	1.071	1.00
173_V	223_L	1.070	1.00
210_T	239_H	1.069	1.00
228_L	236_I	1.059	1.00
174_V	178_I	1.058	1.00
290_E	293_A	1.056	1.00
88_D	153_A	1.056	1.00
172_A	247_L	1.053	1.00
46_G	62_T	1.048	1.00
167_T	281_Y	1.047	1.00
177_L	220_D	1.039	1.00
223_L	296_I	1.034	1.00
134_V	157_L	1.028	1.00
173_V	295_L	1.025	1.00
173_V	296_I	1.023	1.00
96_R	291_D	1.020	1.00
155_E	159_N	1.009	1.00
288_L	292_M	1.003	1.00
32_Q	35_Q	1.003	1.00
240_M	247_L	0.992	1.00
175_H	248_A	0.990	1.00
88_D	275_H	0.987	1.00
174_V	222_T	0.984	1.00
152_M	156_S	0.983	1.00
89_V	273_F	0.980	1.00
184_T	229_E	0.978	1.00
178_I	214_V	0.974	1.00
53_Y	59_D	0.970	1.00
90_L	119_C	0.966	1.00
133_I	147_V	0.966	1.00
287_P	293_A	0.959	1.00
103_A	106_H	0.959	1.00
12_Q	20_F	0.955	1.00
21_L	33_V	0.954	1.00
180_H	183_G	0.954	1.00
134_V	148_A	0.950	1.00
274_D	279_G	0.950	1.00
148_A	154_H	0.947	1.00
144_L	284_F	0.943	1.00
98_M	111_L	0.941	1.00
31_T	34_Q	0.933	1.00
89_V	153_A	0.931	1.00
90_L	115_L	0.927	1.00
192_D	195_D	0.918	1.00
190_G	204_D	0.916	1.00
175_H	221_F	0.912	1.00
56_Q	59_D	0.909	1.00
174_V	247_L	0.896	1.00
37_V	51_A	0.893	1.00
41_Q	64_T	0.885	1.00
13_K	56_Q	0.884	1.00
34_Q	51_A	0.883	1.00
89_V	275_H	0.882	1.00
50_K	53_Y	0.882	1.00
43_V	64_T	0.879	1.00
273_F	284_F	0.873	1.00
180_H	212_F	0.872	1.00
225_E	269_G	0.869	1.00
189_I	199_M	0.868	1.00
178_I	217_R	0.867	1.00
173_V	292_M	0.864	1.00
177_L	219_Q	0.862	1.00
180_H	214_V	0.862	1.00
71_L	128_V	0.860	1.00
261_F	292_M	0.858	1.00
144_L	286_A	0.857	1.00
97_G	142_S	0.852	1.00
28_W	36_W	0.849	1.00
255_P	258_T	0.848	1.00
151_D	154_H	0.846	1.00
185_I	240_M	0.846	1.00
160_Q	274_D	0.843	1.00
181_D	214_V	0.837	1.00
148_A	153_A	0.836	1.00
36_W	41_Q	0.835	1.00
197_Q	252_K	0.830	1.00
169_K	269_G	0.829	1.00
216_E	223_L	0.829	1.00
15_E	20_F	0.827	1.00
100_V	137_I	0.826	1.00
267_H	286_A	0.821	1.00
79_D	114_G	0.818	1.00
90_L	147_V	0.816	1.00
236_I	247_L	0.815	1.00
40_G	48_A	0.811	1.00
174_V	245_F	0.797	1.00
28_W	33_V	0.797	1.00
156_S	279_G	0.796	1.00
261_F	295_L	0.796	1.00
177_L	222_T	0.796	1.00
84_Y	284_F	0.793	1.00
187_A	243_I	0.791	1.00
43_V	48_A	0.791	1.00
161_L	168_R	0.790	1.00
190_G	200_T	0.789	1.00
265_A	291_D	0.787	1.00
183_G	214_V	0.785	1.00
263_G	292_M	0.782	1.00
42_V	63_V	0.782	1.00
156_S	277_R	0.775	1.00
80_L	114_G	0.774	1.00
274_D	278_T	0.772	1.00
37_V	42_V	0.769	1.00
55_I	61_V	0.764	1.00
53_Y	56_Q	0.764	1.00
182_D	211_H	0.764	1.00
21_L	42_V	0.760	1.00
161_L	228_L	0.760	1.00
151_D	155_E	0.758	1.00
188_P	239_H	0.750	1.00
113_N	116_M	0.748	1.00
83_Y	287_P	0.747	1.00
273_F	282_V	0.747	1.00
187_A	201_V	0.746	1.00
261_F	264_Q	0.745	1.00
213_H	227_Q	0.739	1.00
179_S	245_F	0.736	1.00
158_V	162_V	0.735	1.00
30_R	34_Q	0.733	1.00
89_V	282_V	0.729	1.00
182_D	214_V	0.728	1.00
192_D	200_T	0.727	1.00
131_P	147_V	0.719	1.00
84_Y	89_V	0.718	1.00
85_E	119_C	0.717	1.00
263_G	267_H	0.716	1.00
201_V	205_G	0.716	1.00
188_P	205_G	0.716	1.00
16_R	19_K	0.711	1.00
111_L	147_V	0.711	1.00
275_H	278_T	0.710	1.00
185_I	239_H	0.710	1.00
12_Q	23_S	0.709	1.00
109_G	113_N	0.704	1.00
188_P	207_N	0.703	1.00
112_V	133_I	0.702	1.00
12_Q	15_E	0.700	0.99
145_L	268_A	0.700	0.99
102_P	110_T	0.699	0.99
119_C	149_K	0.697	0.99
292_M	296_I	0.696	0.99
92_V	145_L	0.692	0.99
191_R	233_T	0.690	0.99
100_V	133_I	0.690	0.99
80_L	92_V	0.688	0.99
17_I	37_V	0.687	0.99
173_V	218_F	0.686	0.99
112_V	131_P	0.684	0.99
175_H	258_T	0.684	0.99
261_F	291_D	0.681	0.99
28_W	32_Q	0.678	0.99
185_I	212_F	0.678	0.99
168_R	229_E	0.677	0.99
155_E	158_V	0.677	0.99
25_E	33_V	0.676	0.99
198_S	241_K	0.675	0.99
80_L	118_H	0.672	0.99
90_L	149_K	0.671	0.99
210_T	236_I	0.671	0.99
255_P	259_I	0.666	0.99
175_H	259_I	0.665	0.99
135_H	145_L	0.661	0.99
25_E	28_W	0.655	0.99
83_Y	286_A	0.653	0.99
135_H	161_L	0.652	0.99
268_A	271_L	0.652	0.99
208_A	232_R	0.647	0.99
99_V	105_G	0.645	0.99
74_L	77_P	0.645	0.99
14_S	57_P	0.642	0.99
264_Q	291_D	0.640	0.99
85_E	118_H	0.640	0.99
218_F	296_I	0.638	0.99
167_T	270_V	0.637	0.99
132_G	154_H	0.635	0.99
191_R	196_R	0.634	0.99
116_M	131_P	0.629	0.99
169_K	272_G	0.624	0.99
88_D	152_M	0.611	0.99
135_H	268_A	0.611	0.99
218_F	223_L	0.610	0.99
36_W	65_V	0.610	0.99
115_L	119_C	0.609	0.99
19_K	23_S	0.608	0.99
99_V	103_A	0.605	0.99
36_W	63_V	0.605	0.99
103_A	197_Q	0.602	0.98
288_L	296_I	0.601	0.98
20_F	61_V	0.600	0.98
100_V	111_L	0.599	0.98
146_M	271_L	0.598	0.98
222_T	245_F	0.598	0.98
144_L	271_L	0.596	0.98
248_A	265_A	0.596	0.98
183_G	243_I	0.594	0.98
173_V	265_A	0.594	0.98
218_F	221_F	0.594	0.98
148_A	157_L	0.592	0.98
77_P	114_G	0.589	0.98
215_L	223_L	0.584	0.98
17_I	61_V	0.581	0.98
197_Q	200_T	0.580	0.98
93_N	142_S	0.577	0.98
212_F	226_C	0.576	0.98
137_I	164_K	0.576	0.98
173_V	248_A	0.576	0.98
217_R	220_D	0.574	0.98
251_P	255_P	0.572	0.98
160_Q	166_V	0.568	0.98
160_Q	277_R	0.567	0.98
82_I	90_L	0.566	0.98
134_V	154_H	0.566	0.98
183_G	240_M	0.566	0.98
134_V	161_L	0.565	0.98
17_I	53_Y	0.561	0.98
44_V	55_I	0.559	0.98
92_V	147_V	0.558	0.98
198_S	201_V	0.558	0.98
150_N	277_R	0.557	0.98
35_Q	38_K	0.557	0.98
256_R	259_I	0.557	0.98
175_H	254_G	0.557	0.98
188_P	204_D	0.556	0.97
146_M	161_L	0.555	0.97
117_A	120_T	0.555	0.97
101_H	110_T	0.555	0.97
269_G	287_P	0.554	0.97
132_G	151_D	0.553	0.97
113_N	117_A	0.553	0.97
165_T	274_D	0.552	0.97
256_R	260_D	0.552	0.97
67_E	70_A	0.550	0.97
257_K	260_D	0.550	0.97
188_P	202_T	0.549	0.97
248_A	261_F	0.548	0.97
175_H	220_D	0.548	0.97
108_T	113_N	0.548	0.97
14_S	54_K	0.547	0.97
198_S	252_K	0.546	0.97
202_T	205_G	0.545	0.97
90_L	118_H	0.544	0.97
78_M	98_M	0.541	0.97
81_D	95_P	0.540	0.97
106_H	109_G	0.539	0.97
221_F	295_L	0.537	0.97
183_G	226_C	0.537	0.97
116_M	120_T	0.536	0.97
201_V	238_V	0.536	0.97
45_N	49_V	0.535	0.97
31_T	35_Q	0.534	0.97
157_L	160_Q	0.534	0.97
87_Q	149_K	0.534	0.97
21_L	25_E	0.532	0.97
77_P	80_L	0.532	0.97
187_A	239_H	0.531	0.97
41_Q	66_P	0.531	0.97
153_A	277_R	0.530	0.97
127_G	151_D	0.530	0.97
288_L	293_A	0.530	0.97
17_I	44_V	0.530	0.97
194_K	198_S	0.530	0.97
46_G	60_Q	0.529	0.97
188_P	201_V	0.528	0.97
248_A	258_T	0.528	0.97
167_T	283_E	0.526	0.96
74_L	108_T	0.526	0.96
68_P	71_L	0.525	0.96
89_V	284_F	0.525	0.96
137_I	144_L	0.525	0.96
44_V	59_D	0.524	0.96
225_E	270_V	0.524	0.96
178_I	212_F	0.524	0.96
291_D	295_L	0.522	0.96
96_R	262_N	0.522	0.96
178_I	240_M	0.520	0.96
82_I	85_E	0.517	0.96
34_Q	37_V	0.517	0.96
120_T	129_M	0.516	0.96
75_A	109_G	0.516	0.96
238_V	242_Y	0.514	0.96
189_I	205_G	0.513	0.96
249_G	265_A	0.512	0.96
181_D	213_H	0.512	0.96
43_V	47_S	0.512	0.96
55_I	59_D	0.511	0.96
164_K	167_T	0.510	0.96
36_W	42_V	0.509	0.96
37_V	49_V	0.508	0.96
115_L	131_P	0.506	0.96
93_N	267_H	0.504	0.96
89_V	157_L	0.502	0.95
66_P	69_E	0.502	0.95
54_K	57_P	0.501	0.95
97_G	140_D	0.501	0.95
84_Y	282_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	0.7492	100	0.154	Contact Map
1v9kA	1	0.7162	100	0.306	Contact Map
2i82A	1	0.703	100	0.342	Contact Map
4lgtA	1	0.7723	100	0.43	Contact Map
1vioA	2	0.7525	100	0.434	Contact Map
3dh3A	1	0.7855	100	0.436	Contact Map
1kskA	1	0.7624	100	0.456	Contact Map
2olwA	1	0.5446	100	0.495	Contact Map
2omlA	1	0.5479	100	0.508	Contact Map
2gmlA	1	0.5776	100	0.564	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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