RLUB - ECOLI - GREMLIN Contacts

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RLUB - Ribosomal large subunit pseudouridine synthase B

UniProt:	P37765	Sequences: MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12433
Length:	291 (231)
Sequences:	9068 (6079)
Seq/√Len:	399.9

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_D	48_L	5.030	1.00
28_R	53_D	3.861	1.00
30_S	51_R	3.775	1.00
173_K	185_N	3.448	1.00
139_E	185_N	3.362	1.00
36_A	40_D	2.854	1.00
72_Y	94_R	2.500	1.00
139_E	214_R	2.415	1.00
141_A	183_W	2.333	1.00
8_V	42_V	2.318	1.00
15_G	20_I	2.280	1.00
143_R	183_W	2.258	1.00
137_E	187_T	2.200	1.00
141_A	185_N	2.186	1.00
22_S	26_A	2.160	1.00
114_C	209_R	2.139	1.00
152_K	205_V	2.008	1.00
19_E	22_S	1.980	1.00
154_R	158_R	1.978	1.00
114_C	211_I	1.968	1.00
78_E	94_R	1.961	1.00
225_P	228_G	1.945	1.00
23_I	52_I	1.944	1.00
175_S	185_N	1.938	1.00
139_E	187_T	1.928	1.00
171_T	189_T	1.853	1.00
30_S	35_I	1.852	1.00
195_E	199_L	1.849	1.00
9_L	20_I	1.835	1.00
234_L	238_N	1.811	1.00
104_I	126_A	1.789	1.00
230_T	236_Q	1.779	1.00
49_K	56_L	1.778	1.00
70_L	231_E	1.770	1.00
6_Q	21_E	1.764	1.00
3_E	11_R	1.755	1.00
194_R	197_R	1.734	1.00
31_V	40_D	1.713	1.00
114_C	226_R	1.707	1.00
88_R	111_V	1.693	1.00
76_E	114_C	1.659	1.00
91_V	117_L	1.652	1.00
154_R	157_S	1.638	1.00
68_R	122_D	1.637	1.00
186_V	200_W	1.610	1.00
145_F	206_Q	1.603	1.00
184_Y	200_W	1.602	1.00
51_R	56_L	1.528	1.00
142_V	184_Y	1.510	1.00
82_R	92_F	1.500	1.00
167_A	170_K	1.489	1.00
37_K	40_D	1.484	1.00
71_A	218_I	1.481	1.00
148_V	182_Q	1.475	1.00
137_E	189_T	1.474	1.00
3_E	41_R	1.466	1.00
80_C	117_L	1.450	1.00
8_V	12_A	1.384	1.00
143_R	209_R	1.366	1.00
149_D	152_K	1.364	1.00
3_E	8_V	1.360	1.00
137_E	214_R	1.358	1.00
214_R	219_P	1.356	1.00
162_L	198_R	1.352	1.00
126_A	130_M	1.347	1.00
176_G	183_W	1.300	1.00
161_Q	166_P	1.286	1.00
70_L	229_W	1.283	1.00
71_A	116_L	1.272	1.00
68_R	231_E	1.261	1.00
144_V	200_W	1.251	1.00
146_G	182_Q	1.246	1.00
82_R	105_A	1.245	1.00
5_L	36_A	1.232	1.00
29_V	52_I	1.218	1.00
217_D	239_Y	1.212	1.00
141_A	213_V	1.197	1.00
201_E	206_Q	1.196	1.00
80_C	105_A	1.188	1.00
146_G	205_V	1.186	1.00
69_V	125_L	1.170	1.00
144_V	205_V	1.169	1.00
155_D	203_V	1.161	1.00
25_E	38_L	1.151	1.00
147_Q	182_Q	1.139	1.00
124_E	128_R	1.138	1.00
92_F	105_A	1.135	1.00
144_V	184_Y	1.134	1.00
76_E	209_R	1.130	1.00
72_Y	95_L	1.128	1.00
31_V	50_I	1.126	1.00
165_G	192_R	1.126	1.00
150_D	174_F	1.123	1.00
153_L	157_S	1.114	1.00
145_F	205_V	1.114	1.00
174_F	182_Q	1.113	1.00
171_T	187_T	1.112	1.00
33_G	51_R	1.110	1.00
77_G	111_V	1.103	1.00
22_S	25_E	1.095	1.00
128_R	134_R	1.093	1.00
24_I	29_V	1.086	1.00
15_G	23_I	1.085	1.00
112_N	197_R	1.083	1.00
21_E	25_E	1.078	1.00
109_L	117_L	1.070	1.00
233_D	236_Q	1.069	1.00
45_T	48_L	1.069	1.00
8_V	50_I	1.068	1.00
130_M	215_Y	1.068	1.00
9_L	15_G	1.063	1.00
169_F	172_I	1.054	1.00
129_L	215_Y	1.046	1.00
30_S	54_G	1.043	1.00
9_L	57_I	1.030	1.00
42_V	50_I	1.013	1.00
141_A	175_S	1.013	1.00
144_V	182_Q	1.006	1.00
81_T	90_T	1.001	1.00
142_V	186_V	0.997	1.00
152_K	203_V	0.993	1.00
95_L	119_F	0.991	1.00
113_T	142_V	0.989	1.00
188_L	195_E	0.985	1.00
4_K	41_R	0.985	1.00
122_D	125_L	0.984	1.00
23_I	28_R	0.980	1.00
127_N	131_H	0.976	1.00
137_E	171_T	0.973	1.00
103_W	119_F	0.969	1.00
185_N	213_V	0.968	1.00
125_L	129_L	0.964	1.00
168_A	189_T	0.955	1.00
161_Q	202_A	0.952	1.00
156_L	203_V	0.945	1.00
80_C	92_F	0.941	1.00
142_V	207_V	0.939	1.00
113_T	197_R	0.928	1.00
156_L	159_G	0.924	1.00
3_E	7_K	0.921	1.00
186_V	196_V	0.921	1.00
155_D	158_R	0.910	1.00
92_F	119_F	0.904	1.00
170_K	188_L	0.900	1.00
90_T	93_D	0.900	1.00
148_V	205_V	0.898	1.00
34_K	40_D	0.897	1.00
27_G	35_I	0.893	1.00
79_L	86_E	0.892	1.00
132_P	135_E	0.891	1.00
162_L	165_G	0.888	1.00
120_T	126_A	0.885	1.00
113_T	196_V	0.884	1.00
148_V	184_Y	0.878	1.00
147_Q	177_G	0.876	1.00
143_R	181_N	0.871	1.00
19_E	23_I	0.865	1.00
31_V	36_A	0.863	1.00
14_H	52_I	0.863	1.00
24_I	38_L	0.862	1.00
235_A	238_N	0.861	1.00
198_R	201_E	0.854	1.00
70_L	95_L	0.848	1.00
165_G	198_R	0.847	1.00
127_N	130_M	0.845	1.00
224_L	228_G	0.842	1.00
172_I	200_W	0.838	1.00
141_A	209_R	0.837	1.00
5_L	24_I	0.831	1.00
138_R	188_L	0.827	1.00
21_E	38_L	0.825	1.00
5_L	31_V	0.824	1.00
108_R	191_G	0.818	1.00
96_P	100_G	0.818	1.00
156_L	160_V	0.817	1.00
151_A	177_G	0.816	1.00
15_G	19_E	0.812	1.00
69_V	122_D	0.812	1.00
145_F	208_S	0.811	1.00
170_K	186_V	0.810	1.00
235_A	239_Y	0.803	1.00
67_C	121_T	0.799	1.00
82_R	90_T	0.788	1.00
153_L	156_L	0.784	1.00
148_V	152_K	0.784	1.00
144_V	148_V	0.781	1.00
73_Y	225_P	0.780	1.00
72_Y	78_E	0.778	1.00
10_A	17_R	0.775	1.00
71_A	221_P	0.773	1.00
6_Q	39_G	0.768	1.00
230_T	233_D	0.767	1.00
163_E	166_P	0.767	1.00
146_G	206_Q	0.758	1.00
156_L	172_I	0.757	1.00
78_E	89_P	0.753	1.00
73_Y	226_R	0.753	1.00
152_K	155_D	0.748	1.00
155_D	159_G	0.747	1.00
232_L	236_Q	0.747	1.00
172_I	186_V	0.747	1.00
138_R	195_E	0.745	1.00
128_R	132_P	0.738	1.00
59_V	62_S	0.737	1.00
173_K	187_T	0.737	1.00
157_S	160_V	0.727	1.00
232_L	237_T	0.720	1.00
156_L	199_L	0.718	1.00
170_K	189_T	0.716	1.00
160_V	203_V	0.710	1.00
224_L	230_T	0.709	1.00
18_R	21_E	0.706	1.00
79_L	88_R	0.701	1.00
165_G	170_K	0.697	1.00
5_L	50_I	0.695	1.00
200_W	203_V	0.689	1.00
9_L	14_H	0.685	1.00
125_L	240_L	0.685	1.00
170_K	195_E	0.685	1.00
9_L	29_V	0.683	0.99
223_G	226_R	0.682	0.99
190_E	195_E	0.681	0.99
224_L	227_G	0.676	0.99
169_F	189_T	0.669	0.99
91_V	119_F	0.667	0.99
106_V	120_T	0.667	0.99
79_L	84_D	0.664	0.99
71_A	230_T	0.663	0.99
150_D	154_R	0.662	0.99
127_N	133_S	0.660	0.99
177_G	182_Q	0.658	0.99
183_W	209_R	0.657	0.99
228_G	231_E	0.656	0.99
170_K	199_L	0.652	0.99
161_Q	165_G	0.651	0.99
149_D	205_V	0.650	0.99
5_L	40_D	0.650	0.99
187_T	214_R	0.649	0.99
81_T	85_P	0.649	0.99
14_H	23_I	0.644	0.99
147_Q	179_G	0.644	0.99
71_A	118_L	0.642	0.99
91_V	94_R	0.642	0.99
28_R	52_I	0.638	0.99
89_P	111_V	0.635	0.99
151_A	155_D	0.632	0.99
147_Q	180_I	0.631	0.99
234_L	237_T	0.629	0.99
114_C	197_R	0.628	0.99
81_T	88_R	0.628	0.99
174_F	184_Y	0.628	0.99
54_G	57_I	0.626	0.99
69_V	237_T	0.625	0.99
110_D	191_G	0.622	0.99
83_N	86_E	0.620	0.99
221_P	230_T	0.619	0.99
138_R	189_T	0.619	0.99
69_V	232_L	0.617	0.99
68_R	121_T	0.616	0.99
215_Y	218_I	0.616	0.99
143_R	208_S	0.616	0.99
145_F	180_I	0.613	0.99
79_L	85_P	0.612	0.99
148_V	200_W	0.611	0.99
20_I	24_I	0.611	0.99
82_R	91_V	0.607	0.99
106_V	129_L	0.606	0.99
40_D	45_T	0.606	0.99
227_G	230_T	0.606	0.99
108_R	197_R	0.606	0.99
177_G	180_I	0.605	0.99
70_L	119_F	0.604	0.99
33_G	49_K	0.604	0.99
225_P	229_W	0.600	0.99
75_P	78_E	0.599	0.99
139_E	213_V	0.598	0.99
135_E	168_A	0.597	0.99
97_K	229_W	0.596	0.99
79_L	90_T	0.596	0.99
159_G	162_L	0.594	0.99
6_Q	38_L	0.592	0.99
110_D	197_R	0.592	0.99
89_P	94_R	0.588	0.98
167_A	195_E	0.588	0.98
226_R	229_W	0.587	0.98
141_A	211_I	0.585	0.98
31_V	42_V	0.585	0.98
157_S	171_T	0.582	0.98
193_N	197_R	0.581	0.98
99_R	103_W	0.581	0.98
86_E	89_P	0.580	0.98
12_A	15_G	0.577	0.98
188_L	196_V	0.574	0.98
116_L	215_Y	0.572	0.98
231_E	234_L	0.572	0.98
67_C	122_D	0.569	0.98
192_R	195_E	0.568	0.98
138_R	191_G	0.568	0.98
181_N	208_S	0.566	0.98
73_Y	211_I	0.565	0.98
155_D	160_V	0.565	0.98
76_E	197_R	0.565	0.98
147_Q	181_N	0.565	0.98
42_V	48_L	0.564	0.98
18_R	22_S	0.564	0.98
160_V	202_A	0.563	0.98
9_L	12_A	0.563	0.98
148_V	203_V	0.562	0.98
20_I	23_I	0.560	0.98
60_R	231_E	0.559	0.98
200_W	207_V	0.558	0.98
153_L	172_I	0.556	0.98
178_E	181_N	0.554	0.98
72_Y	117_L	0.553	0.98
68_R	101_A	0.553	0.98
21_E	39_G	0.546	0.98
16_S	19_E	0.546	0.98
172_I	184_Y	0.545	0.98
76_E	112_N	0.540	0.97
164_D	198_R	0.538	0.97
113_T	194_R	0.538	0.97
116_L	220_L	0.537	0.97
79_L	111_V	0.535	0.97
72_Y	91_V	0.531	0.97
175_S	183_W	0.530	0.97
135_E	189_T	0.530	0.97
156_L	200_W	0.527	0.97
144_V	207_V	0.524	0.97
84_D	87_G	0.524	0.97
136_V	216_G	0.524	0.97
108_R	138_R	0.521	0.97
123_G	126_A	0.519	0.97
146_G	181_N	0.514	0.96
21_E	24_I	0.511	0.96
142_V	196_V	0.510	0.96
92_F	95_L	0.510	0.96
93_D	96_P	0.509	0.96
94_R	97_K	0.509	0.96
7_K	11_R	0.509	0.96
232_L	240_L	0.507	0.96
200_W	205_V	0.507	0.96
92_F	103_W	0.502	0.96
163_E	198_R	0.502	0.96
132_P	136_V	0.501	0.96
140_Y	191_G	0.500	0.96
211_I	226_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
1vioA	2	0.7869	100	0.219	Contact Map
4lgtA	1	0.8282	100	0.253	Contact Map
3dh3A	1	0.8213	100	0.255	Contact Map
1kskA	1	0.7973	100	0.259	Contact Map
1v9fA	1	0.7182	100	0.284	Contact Map
2gmlA	1	0.6014	100	0.367	Contact Map
2omlA	1	0.5739	100	0.372	Contact Map
2olwA	1	0.5704	100	0.373	Contact Map
2i82A	1	0.6838	100	0.434	Contact Map
1v9kA	1	0.6873	100	0.435	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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