YJBO - BACSU - GREMLIN Contacts

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YJBO - Uncharacterized RNA pseudouridine synthase YjbO

UniProt:	O31613	Sequences: MTVKEYAGELGISKRLLTDIKFGGGDLQINGEHVTVKYVLKEGDLLIVKFPEEQVSETLLAEPVPLDILYEDEHVLVINKQPYVSSIPSREHPSGSIANGIIDHYQTTGVRATVHLVTRLDRDTSGIMLVAKHRFAHSILSSAQKNGLVKRRYAAVVHGRMAQMEGTVDAPIGRHPDSIIERTVTPDGQKAVTHFYVTCANDDMTSVALQLETGRTHQIRVHMSYLGHPLCGDTLYGGTRQEIGRQALHSEHLSFIHPLTQENMRFHAPLPQDMSKLIKGENH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	283 (262)
Sequences:	9613 (6670)
Seq/√Len:	412.1

ECOLI - RLUD RLUC RLUA TRUC RLUB RSUA RLUF
BACSU - YJBO YHCT YLYB 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
152_R	208_A	3.490	1.00
194_H	212_E	3.359	1.00
69_L	127_I	3.067	1.00
30_N	44_D	3.044	1.00
71_E	132_K	2.905	1.00
252_H	265_R	2.823	1.00
254_S	265_R	2.739	1.00
196_Y	208_A	2.711	1.00
67_D	79_N	2.649	1.00
154_A	251_E	2.630	1.00
154_A	206_S	2.608	1.00
166_G	195_F	2.565	1.00
167_T	194_H	2.536	1.00
74_H	133_H	2.450	1.00
170_A	225_Y	2.430	1.00
74_H	259_L	2.427	1.00
209_L	223_M	2.350	1.00
165_E	196_Y	2.274	1.00
254_S	263_N	2.249	1.00
150_K	210_Q	2.238	1.00
79_N	268_A	2.201	1.00
164_M	200_A	2.150	1.00
169_D	192_V	2.145	1.00
169_D	190_K	2.140	1.00
167_T	192_V	2.139	1.00
245_R	273_D	2.104	1.00
152_R	252_H	2.097	1.00
77_V	266_F	2.080	1.00
133_H	136_A	2.022	1.00
150_K	254_S	1.961	1.00
256_I	263_N	1.954	1.00
197_V	205_T	1.921	1.00
252_H	267_H	1.909	1.00
97_I	128_M	1.902	1.00
64_V	100_G	1.901	1.00
125_S	249_H	1.892	1.00
192_V	212_E	1.882	1.00
155_A	209_L	1.872	1.00
209_L	219_I	1.866	1.00
152_R	210_Q	1.863	1.00
143_A	148_L	1.862	1.00
157_V	207_V	1.817	1.00
62_E	94_S	1.803	1.00
193_T	209_L	1.790	1.00
198_T	208_A	1.787	1.00
34_V	38_Y	1.781	1.00
161_M	205_T	1.734	1.00
142_S	146_N	1.664	1.00
251_E	267_H	1.581	1.00
77_V	129_L	1.534	1.00
29_I	38_Y	1.534	1.00
62_E	95_G	1.530	1.00
243_I	247_A	1.522	1.00
120_L	128_M	1.521	1.00
86_S	128_M	1.517	1.00
159_G	205_T	1.509	1.00
194_H	210_Q	1.508	1.00
72_D	257_H	1.499	1.00
77_V	127_I	1.498	1.00
13_S	18_T	1.482	1.00
123_D	246_Q	1.468	1.00
69_L	266_F	1.446	1.00
272_Q	276_K	1.441	1.00
247_A	274_M	1.417	1.00
15_R	18_T	1.389	1.00
160_R	200_A	1.388	1.00
14_K	18_T	1.378	1.00
139_I	143_A	1.377	1.00
101_I	130_V	1.356	1.00
28_Q	47_I	1.353	1.00
207_V	223_M	1.329	1.00
168_V	226_L	1.324	1.00
157_V	223_M	1.323	1.00
200_A	205_T	1.316	1.00
14_K	20_I	1.315	1.00
161_M	228_H	1.311	1.00
14_K	17_L	1.311	1.00
172_I	221_V	1.309	1.00
63_P	103_D	1.302	1.00
154_A	208_A	1.288	1.00
82_P	125_S	1.286	1.00
29_I	34_V	1.285	1.00
154_A	270_L	1.277	1.00
96_S	99_N	1.244	1.00
151_R	211_L	1.240	1.00
257_H	264_M	1.236	1.00
159_G	228_H	1.216	1.00
16_L	20_I	1.215	1.00
204_M	231_C	1.214	1.00
95_G	100_G	1.210	1.00
13_S	20_I	1.202	1.00
13_S	17_L	1.201	1.00
85_S	92_H	1.181	1.00
189_Q	215_R	1.179	1.00
195_F	223_M	1.174	1.00
156_V	204_M	1.168	1.00
184_V	225_Y	1.165	1.00
72_D	75_V	1.164	1.00
154_A	198_T	1.149	1.00
193_T	222_H	1.147	1.00
197_V	200_A	1.143	1.00
29_I	46_L	1.142	1.00
144_Q	149_V	1.134	1.00
137_H	141_S	1.132	1.00
12_I	20_I	1.123	1.00
142_S	145_K	1.116	1.00
123_D	234_T	1.108	1.00
135_F	259_L	1.101	1.00
175_H	181_E	1.095	1.00
82_P	245_R	1.095	1.00
81_Q	84_V	1.092	1.00
117_V	131_A	1.088	1.00
163_Q	197_V	1.087	1.00
116_L	130_V	1.078	1.00
17_L	20_I	1.073	1.00
127_I	266_F	1.072	1.00
31_G	47_I	1.070	1.00
158_H	238_G	1.062	1.00
178_S	181_E	1.050	1.00
23_G	36_V	1.046	1.00
84_V	100_G	1.042	1.00
272_Q	275_S	1.041	1.00
12_I	17_L	1.038	1.00
211_L	219_I	1.033	1.00
139_I	142_S	1.026	1.00
117_V	140_L	1.024	1.00
193_T	211_L	1.022	1.00
74_H	257_H	1.021	1.00
155_A	207_V	1.017	1.00
16_L	19_D	1.015	1.00
131_A	137_H	1.014	1.00
247_A	277_L	1.012	1.00
74_H	136_A	1.011	1.00
160_R	203_D	1.010	1.00
155_A	230_L	1.010	1.00
161_M	207_V	1.002	1.00
138_S	142_S	1.000	1.00
256_I	261_Q	0.996	1.00
150_K	263_N	0.995	1.00
78_I	97_I	0.991	1.00
173_G	185_T	0.989	1.00
157_V	161_M	0.983	1.00
15_R	19_D	0.973	1.00
156_V	206_S	0.973	1.00
255_F	266_F	0.967	1.00
82_P	273_D	0.959	1.00
270_L	274_M	0.958	1.00
167_T	212_E	0.958	1.00
38_Y	44_D	0.952	1.00
143_A	256_I	0.951	1.00
161_M	197_V	0.950	1.00
75_V	255_F	0.944	1.00
269_P	275_S	0.944	1.00
15_R	20_I	0.943	1.00
156_V	277_L	0.930	1.00
75_V	257_H	0.924	1.00
158_H	204_M	0.924	1.00
238_G	242_E	0.917	1.00
157_V	205_T	0.917	1.00
223_M	230_L	0.908	1.00
75_V	136_A	0.904	1.00
175_H	178_S	0.902	1.00
158_H	231_C	0.890	1.00
208_A	251_E	0.881	1.00
131_A	136_A	0.880	1.00
89_S	92_H	0.877	1.00
86_S	120_L	0.876	1.00
35_T	38_Y	0.875	1.00
13_S	16_L	0.872	1.00
127_I	268_A	0.869	1.00
171_P	222_H	0.868	1.00
160_R	202_D	0.865	1.00
163_Q	166_G	0.864	1.00
76_L	105_Y	0.863	1.00
173_G	187_D	0.860	1.00
135_F	139_I	0.859	1.00
199_C	206_S	0.859	1.00
18_T	23_G	0.858	1.00
156_V	274_M	0.852	1.00
152_R	251_E	0.852	1.00
84_V	97_I	0.851	1.00
257_H	260_T	0.850	1.00
168_V	222_H	0.843	1.00
157_V	230_L	0.838	1.00
12_I	16_L	0.837	1.00
243_I	274_M	0.833	1.00
76_L	130_V	0.830	1.00
38_Y	41_K	0.830	1.00
174_R	216_T	0.830	1.00
165_E	194_H	0.827	1.00
25_G	33_H	0.826	1.00
28_Q	49_K	0.821	1.00
12_I	18_T	0.820	1.00
219_I	230_L	0.817	1.00
172_I	182_R	0.812	1.00
66_L	100_G	0.809	1.00
41_K	44_D	0.807	1.00
56_S	111_R	0.805	1.00
161_M	200_A	0.805	1.00
157_V	228_H	0.803	1.00
165_E	197_V	0.803	1.00
27_L	48_V	0.803	1.00
249_H	268_A	0.802	1.00
168_V	223_M	0.801	1.00
255_F	264_M	0.800	1.00
22_F	36_V	0.800	1.00
170_A	226_L	0.797	1.00
134_R	137_H	0.794	1.00
97_I	130_V	0.792	1.00
83_Y	125_S	0.791	1.00
118_T	128_M	0.787	1.00
160_R	205_T	0.784	1.00
144_Q	211_L	0.783	1.00
70_Y	266_F	0.782	1.00
76_L	101_I	0.780	1.00
245_R	249_H	0.779	1.00
243_I	277_L	0.778	1.00
28_Q	33_H	0.775	1.00
40_L	46_L	0.766	1.00
98_A	116_L	0.764	1.00
26_D	49_K	0.763	1.00
69_L	269_P	0.761	1.00
171_P	190_K	0.756	1.00
71_E	105_Y	0.756	1.00
180_I	235_L	0.752	1.00
245_R	274_M	0.751	1.00
134_R	138_S	0.751	1.00
139_I	259_L	0.751	1.00
196_Y	210_Q	0.751	1.00
171_P	188_G	0.748	1.00
70_Y	75_V	0.747	1.00
162_A	228_H	0.742	1.00
247_A	273_D	0.741	1.00
243_I	246_Q	0.739	1.00
66_L	104_H	0.736	1.00
56_S	59_L	0.735	1.00
175_H	183_T	0.732	1.00
256_I	260_T	0.731	1.00
166_G	197_V	0.728	1.00
151_R	212_E	0.726	1.00
173_G	183_T	0.724	1.00
144_Q	151_R	0.718	1.00
250_S	253_L	0.715	1.00
158_H	241_Q	0.712	1.00
141_S	145_K	0.705	1.00
193_T	219_I	0.705	1.00
105_Y	132_K	0.703	1.00
14_K	19_D	0.700	1.00
88_P	96_S	0.700	1.00
163_Q	195_F	0.698	1.00
71_E	104_H	0.696	1.00
86_S	116_L	0.694	1.00
66_L	78_I	0.693	1.00
22_F	27_L	0.688	1.00
18_T	36_V	0.686	1.00
65_P	100_G	0.685	1.00
118_T	144_Q	0.681	1.00
99_N	102_I	0.680	1.00
22_F	34_V	0.676	1.00
166_G	209_L	0.675	1.00
76_L	132_K	0.674	0.99
138_S	141_S	0.673	0.99
168_V	195_F	0.670	0.99
170_A	222_H	0.666	0.99
98_A	114_V	0.663	0.99
191_A	215_R	0.655	0.99
75_V	264_M	0.650	0.99
243_I	273_D	0.649	0.99
114_V	130_V	0.648	0.99
76_L	104_H	0.646	0.99
166_G	223_M	0.645	0.99
234_T	238_G	0.643	0.99
158_H	242_E	0.642	0.99
129_L	253_L	0.640	0.99
152_R	254_S	0.639	0.99
139_I	261_Q	0.639	0.99
19_D	24_G	0.638	0.99
170_A	184_V	0.635	0.99
195_F	209_L	0.634	0.99
117_V	144_Q	0.631	0.99
115_H	137_H	0.628	0.99
128_M	250_S	0.627	0.99
117_V	137_H	0.627	0.99
184_V	188_G	0.627	0.99
181_E	224_S	0.626	0.99
205_T	228_H	0.623	0.99
102_I	114_V	0.621	0.99
131_A	140_L	0.620	0.99
78_I	128_M	0.619	0.99
174_R	179_I	0.619	0.99
231_C	247_A	0.614	0.99
95_G	99_N	0.614	0.99
69_L	268_A	0.613	0.99
102_I	106_Q	0.612	0.99
208_A	252_H	0.611	0.99
246_Q	273_D	0.611	0.99
118_T	250_S	0.611	0.99
148_L	256_I	0.610	0.99
185_T	188_G	0.601	0.99
156_V	247_A	0.599	0.99
140_L	143_A	0.597	0.99
86_S	97_I	0.596	0.99
85_S	89_S	0.596	0.99
100_G	103_D	0.595	0.99
158_H	239_T	0.593	0.99
150_K	252_H	0.592	0.99
136_A	259_L	0.591	0.99
164_M	205_T	0.590	0.99
198_T	206_S	0.587	0.99
29_I	40_L	0.587	0.99
143_A	149_V	0.586	0.99
158_H	237_G	0.582	0.99
180_I	183_T	0.582	0.99
79_N	125_S	0.580	0.99
133_H	259_L	0.578	0.98
143_A	259_L	0.577	0.98
85_S	91_E	0.575	0.98
83_Y	123_D	0.575	0.98
52_E	55_V	0.572	0.98
155_A	223_M	0.571	0.98
64_V	84_V	0.569	0.98
176_P	183_T	0.568	0.98
68_I	76_L	0.564	0.98
68_I	71_E	0.564	0.98
60_L	63_P	0.562	0.98
53_E	56_S	0.562	0.98
171_P	187_D	0.562	0.98
67_D	81_Q	0.562	0.98
164_M	197_V	0.561	0.98
19_D	23_G	0.559	0.98
166_G	226_L	0.558	0.98
200_A	203_D	0.558	0.98
75_V	266_F	0.557	0.98
79_N	249_H	0.555	0.98
201_N	204_M	0.555	0.98
232_G	247_A	0.554	0.98
20_I	24_G	0.552	0.98
127_I	253_L	0.552	0.98
99_N	103_D	0.551	0.98
29_I	44_D	0.549	0.98
97_I	104_H	0.549	0.98
94_S	99_N	0.547	0.98
26_D	33_H	0.547	0.98
270_L	275_S	0.546	0.98
221_V	225_Y	0.545	0.98
238_G	241_Q	0.545	0.98
75_V	140_L	0.544	0.98
110_V	134_R	0.543	0.98
67_D	70_Y	0.542	0.98
78_I	101_I	0.541	0.98
82_P	244_G	0.539	0.98
92_H	95_G	0.538	0.98
120_L	127_I	0.538	0.98
98_A	115_H	0.535	0.97
25_G	28_Q	0.533	0.97
26_D	51_P	0.532	0.97
78_I	130_V	0.531	0.97
60_L	94_S	0.529	0.97
182_R	216_T	0.529	0.97
20_I	50_F	0.529	0.97
177_D	180_I	0.528	0.97
161_M	223_M	0.527	0.97
201_N	206_S	0.526	0.97
115_H	134_R	0.525	0.97
150_K	265_R	0.525	0.97
85_S	122_R	0.525	0.97
74_H	135_F	0.525	0.97
195_F	226_L	0.524	0.97
156_V	231_C	0.523	0.97
231_C	241_Q	0.523	0.97
70_Y	264_M	0.522	0.97
231_C	243_I	0.521	0.97
69_L	79_N	0.521	0.97
63_P	100_G	0.520	0.97
103_D	106_Q	0.520	0.97
177_D	181_E	0.518	0.97
20_I	26_D	0.517	0.97
50_F	53_E	0.516	0.97
89_S	235_L	0.514	0.97
161_M	166_G	0.514	0.97
129_L	144_Q	0.512	0.97
101_I	114_V	0.510	0.97
251_E	269_P	0.509	0.97
31_G	45_L	0.509	0.97
124_T	216_T	0.508	0.97
125_S	245_R	0.508	0.97
191_A	221_V	0.506	0.96
20_I	48_V	0.505	0.96
206_S	274_M	0.504	0.96
174_R	183_T	0.504	0.96
79_N	269_P	0.502	0.96
101_I	105_Y	0.502	0.96
74_H	260_T	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	0.7915	100	0.163	Contact Map
1v9kA	1	0.7562	100	0.281	Contact Map
2i82A	1	0.7491	100	0.311	Contact Map
4lgtA	1	0.8198	100	0.434	Contact Map
1vioA	2	0.7951	100	0.436	Contact Map
3dh3A	1	0.8163	100	0.443	Contact Map
1kskA	1	0.8021	100	0.459	Contact Map
2olwA	1	0.5795	100	0.469	Contact Map
2omlA	1	0.5866	100	0.481	Contact Map
2gmlA	1	0.6184	100	0.546	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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