RLUB - BACSU - GREMLIN Contacts

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RLUB - Ribosomal large subunit pseudouridine synthase B

UniProt:	P35159	Sequences: MERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREEPVYFLLYKPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANKLMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELTPHEVKRLRALADHGKNAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	244 (218)
Sequences:	15108 (10186)
Seq/√Len:	689.9

ECOLI - RLUB RLUF RSUA RLUD RLUC RLUA TRUC RLUE
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
31_N	46_D	3.958	1.00
131_T	179_Q	3.782	1.00
165_K	179_Q	3.122	1.00
163_K	183_H	2.983	1.00
133_V	177_I	2.900	1.00
29_K	49_E	2.899	1.00
27_K	51_N	2.710	1.00
35_V	40_V	2.672	1.00
58_E	113_N	2.613	1.00
129_D	181_T	2.560	1.00
61_V	114_D	2.397	1.00
131_T	181_T	2.315	1.00
167_L	179_Q	2.227	1.00
180_L	194_F	2.159	1.00
135_K	177_I	2.005	1.00
7_V	42_V	1.987	1.00
133_V	179_Q	1.986	1.00
21_E	25_E	1.916	1.00
134_A	180_L	1.890	1.00
114_D	117_F	1.889	1.00
18_K	21_E	1.816	1.00
7_V	11_A	1.797	1.00
14_A	19_A	1.785	1.00
65_L	87_F	1.771	1.00
71_V	87_F	1.765	1.00
73_S	109_L	1.746	1.00
84_V	109_L	1.739	1.00
139_I	169_L	1.739	1.00
124_P	127_E	1.723	1.00
69_R	106_S	1.707	1.00
30_V	40_V	1.706	1.00
140_P	176_S	1.696	1.00
106_S	203_K	1.648	1.00
161_P	183_H	1.643	1.00
218_H	221_D	1.636	1.00
166_L	176_S	1.612	1.00
4_L	35_V	1.599	1.00
163_K	181_T	1.591	1.00
131_T	208_E	1.577	1.00
8_I	19_A	1.569	1.00
146_R	150_R	1.540	1.00
178_I	194_F	1.528	1.00
29_K	34_V	1.496	1.00
101_L	109_L	1.488	1.00
136_V	194_F	1.477	1.00
136_V	178_I	1.472	1.00
96_Y	118_A	1.442	1.00
180_L	190_V	1.412	1.00
118_A	122_M	1.392	1.00
168_S	177_I	1.388	1.00
64_L	108_L	1.385	1.00
106_S	219_T	1.361	1.00
106_S	205_K	1.359	1.00
134_A	178_I	1.354	1.00
189_Q	193_M	1.349	1.00
30_V	35_V	1.345	1.00
22_L	50_V	1.338	1.00
120_K	124_P	1.333	1.00
162_A	180_L	1.328	1.00
24_K	38_L	1.315	1.00
18_K	22_L	1.307	1.00
138_G	176_S	1.304	1.00
170_D	173_K	1.303	1.00
134_A	201_V	1.287	1.00
5_Q	20_E	1.284	1.00
135_K	175_T	1.278	1.00
37_E	40_V	1.267	1.00
64_L	110_L	1.266	1.00
188_R	191_R	1.263	1.00
133_V	220_G	1.254	1.00
144_L	199_H	1.253	1.00
30_V	48_I	1.252	1.00
137_K	200_E	1.251	1.00
88_F	111_L	1.249	1.00
32_G	49_E	1.232	1.00
43_T	46_D	1.218	1.00
146_R	149_E	1.218	1.00
116_E	120_K	1.216	1.00
14_A	22_L	1.214	1.00
140_P	199_H	1.208	1.00
47_Q	54_K	1.203	1.00
169_L	176_S	1.202	1.00
143_E	169_L	1.200	1.00
138_G	199_H	1.196	1.00
166_L	169_L	1.190	1.00
75_A	85_T	1.181	1.00
83_V	86_D	1.181	1.00
20_E	24_K	1.169	1.00
73_S	97_P	1.159	1.00
63_F	222_A	1.159	1.00
119_N	123_H	1.132	1.00
151_G	154_L	1.109	1.00
112_T	118_A	1.108	1.00
59_E	62_Y	1.098	1.00
68_P	71_V	1.098	1.00
130_K	182_I	1.098	1.00
135_K	203_K	1.098	1.00
82_K	87_F	1.096	1.00
62_Y	117_F	1.092	1.00
22_L	27_K	1.090	1.00
133_V	167_L	1.084	1.00
159_T	162_A	1.082	1.00
148_L	151_G	1.082	1.00
164_A	194_F	1.077	1.00
85_T	97_P	1.072	1.00
147_K	150_R	1.072	1.00
65_L	88_F	1.071	1.00
136_V	176_S	1.071	1.00
140_P	178_I	1.064	1.00
129_D	183_H	1.062	1.00
175_T	202_I	1.060	1.00
136_V	199_H	1.052	1.00
208_E	213_N	1.044	1.00
142_K	166_L	1.043	1.00
9_A	16_R	1.039	1.00
162_A	193_M	1.038	1.00
26_G	34_V	1.036	1.00
28_V	50_V	1.035	1.00
147_K	151_G	1.035	1.00
60_P	113_N	1.025	1.00
215_R	218_H	1.010	1.00
23_I	38_L	0.995	1.00
144_L	165_K	0.992	1.00
70_G	103_Y	0.987	1.00
133_V	207_E	0.976	1.00
137_K	202_I	0.972	1.00
141_P	144_L	0.966	1.00
139_I	176_S	0.963	1.00
195_E	200_E	0.960	1.00
69_R	203_K	0.958	1.00
72_I	79_K	0.954	1.00
63_F	88_F	0.953	1.00
219_T	222_A	0.950	1.00
23_I	28_V	0.945	1.00
148_L	152_I	0.944	1.00
162_A	182_I	0.942	1.00
64_L	212_L	0.926	1.00
120_K	123_H	0.924	1.00
95_I	111_L	0.921	1.00
129_D	208_E	0.919	1.00
153_R	158_K	0.917	1.00
170_D	174_Q	0.916	1.00
75_A	83_V	0.910	1.00
98_I	112_T	0.909	1.00
139_I	174_Q	0.904	1.00
137_K	209_Y	0.899	1.00
17_R	20_E	0.899	1.00
104_D	205_K	0.898	1.00
145_L	149_E	0.896	1.00
150_R	154_L	0.895	1.00
154_L	192_R	0.889	1.00
16_R	20_E	0.880	1.00
75_A	97_P	0.879	1.00
63_F	111_L	0.877	1.00
42_V	48_I	0.873	1.00
61_V	117_F	0.871	1.00
84_V	111_L	0.867	1.00
104_D	191_R	0.867	1.00
112_T	117_F	0.864	1.00
8_I	11_A	0.861	1.00
119_N	122_M	0.860	1.00
182_I	189_Q	0.855	1.00
149_E	152_I	0.855	1.00
218_H	222_A	0.854	1.00
33_K	40_V	0.848	1.00
182_I	190_V	0.846	1.00
21_E	24_K	0.843	1.00
40_V	46_D	0.842	1.00
137_K	199_H	0.841	1.00
136_V	140_P	0.841	1.00
137_K	175_T	0.840	1.00
49_E	54_K	0.840	1.00
157_G	186_R	0.836	1.00
20_E	38_L	0.818	1.00
117_F	121_L	0.816	1.00
105_T	134_A	0.808	1.00
135_K	170_D	0.806	1.00
165_K	181_T	0.803	1.00
136_V	201_V	0.802	1.00
97_P	111_L	0.787	1.00
141_P	199_H	0.785	1.00
144_L	197_I	0.783	1.00
115_G	119_N	0.783	1.00
179_Q	207_E	0.780	1.00
145_L	151_G	0.778	1.00
194_F	201_V	0.775	1.00
40_V	43_T	0.774	1.00
65_L	84_V	0.774	1.00
160_A	183_H	0.766	1.00
8_I	28_V	0.764	1.00
85_T	111_L	0.762	1.00
158_K	186_R	0.760	1.00
74_A	83_V	0.760	1.00
192_R	195_E	0.760	1.00
161_P	164_A	0.758	1.00
80_G	103_Y	0.749	1.00
8_I	14_A	0.748	1.00
98_I	121_L	0.746	1.00
139_I	173_K	0.743	1.00
73_S	101_L	0.737	1.00
153_R	157_G	0.731	1.00
76_Q	79_K	0.727	1.00
147_K	197_I	0.726	1.00
115_G	118_A	0.724	1.00
209_Y	212_L	0.723	1.00
137_K	174_Q	0.723	1.00
6_K	10_H	0.715	1.00
153_R	196_A	0.715	1.00
170_D	175_T	0.714	1.00
105_T	191_R	0.711	1.00
7_V	48_I	0.710	1.00
131_T	221_D	0.709	1.00
212_L	216_G	0.707	1.00
140_P	166_L	0.697	1.00
144_L	164_A	0.691	1.00
130_K	189_Q	0.690	1.00
157_G	160_A	0.689	1.00
29_K	52_G	0.686	1.00
86_D	89_K	0.684	1.00
145_L	148_L	0.684	1.00
29_K	51_N	0.679	1.00
32_G	47_Q	0.677	1.00
3_R	41_K	0.676	1.00
100_R	185_G	0.675	1.00
164_A	180_L	0.674	1.00
52_G	55_V	0.672	1.00
148_L	206_R	0.660	1.00
79_K	82_K	0.653	1.00
14_A	18_K	0.653	1.00
73_S	85_T	0.652	1.00
120_K	126_Y	0.652	1.00
71_V	84_V	0.652	1.00
65_L	71_V	0.651	1.00
140_P	144_L	0.651	1.00
145_L	150_R	0.651	1.00
190_V	201_V	0.650	1.00
19_A	22_L	0.646	1.00
82_K	86_D	0.645	1.00
217_L	221_D	0.642	1.00
153_R	156_E	0.639	1.00
121_L	209_Y	0.639	1.00
15_S	18_K	0.638	1.00
169_L	174_Q	0.634	1.00
30_V	46_D	0.628	1.00
81_R	86_D	0.627	1.00
5_Q	39_G	0.625	1.00
86_D	90_N	0.620	1.00
4_L	23_I	0.618	1.00
157_G	192_R	0.615	1.00
124_P	128_I	0.615	1.00
130_K	183_H	0.612	1.00
212_L	215_R	0.611	1.00
87_F	90_N	0.609	1.00
99_G	109_L	0.609	1.00
57_R	60_P	0.605	1.00
91_I	95_I	0.603	1.00
85_T	95_I	0.601	1.00
119_N	125_K	0.600	1.00
122_M	209_Y	0.596	1.00
152_I	196_A	0.594	1.00
154_L	157_G	0.592	1.00
213_N	216_G	0.591	1.00
89_K	92_P	0.590	1.00
138_G	200_E	0.589	1.00
176_S	199_H	0.589	1.00
12_G	19_A	0.587	1.00
148_L	154_L	0.587	1.00
140_P	194_F	0.585	1.00
4_L	48_I	0.583	1.00
8_I	55_V	0.573	1.00
216_G	219_T	0.572	1.00
166_L	178_I	0.570	1.00
135_K	202_I	0.570	1.00
140_P	169_L	0.570	1.00
133_V	203_K	0.569	1.00
117_F	120_K	0.568	1.00
98_I	118_A	0.567	1.00
72_I	76_Q	0.567	1.00
150_R	153_R	0.566	1.00
70_G	106_S	0.563	1.00
129_D	163_K	0.558	1.00
167_L	177_I	0.557	1.00
72_I	103_Y	0.556	1.00
66_Y	219_T	0.555	1.00
184_E	189_Q	0.554	1.00
105_T	190_V	0.553	1.00
145_L	152_I	0.553	1.00
30_V	42_V	0.553	1.00
209_Y	213_N	0.553	1.00
162_A	183_H	0.551	1.00
219_T	223_R	0.549	1.00
157_G	162_A	0.546	1.00
130_K	185_G	0.544	1.00
73_S	84_V	0.544	1.00
4_L	30_V	0.541	1.00
177_I	203_K	0.541	1.00
13_V	22_L	0.541	1.00
143_E	166_L	0.541	1.00
215_R	222_A	0.541	1.00
193_M	197_I	0.540	1.00
4_L	40_V	0.537	1.00
162_A	189_Q	0.537	1.00
155_E	192_R	0.535	1.00
71_V	82_K	0.534	1.00
72_I	77_D	0.533	1.00
72_I	78_D	0.533	1.00
63_F	113_N	0.532	1.00
170_D	177_I	0.524	1.00
98_I	110_L	0.520	1.00
13_V	50_V	0.519	1.00
215_R	219_T	0.517	0.99
169_L	173_K	0.516	0.99
31_N	48_I	0.515	0.99
144_L	166_L	0.515	0.99
66_Y	218_H	0.511	0.99
23_I	35_V	0.511	0.99
139_I	143_E	0.511	0.99
146_R	151_G	0.511	0.99
70_G	104_D	0.509	0.99
208_E	211_F	0.507	0.99
77_D	80_G	0.507	0.99
163_K	166_L	0.506	0.99
17_R	21_E	0.506	0.99
63_F	66_Y	0.505	0.99
62_Y	114_D	0.502	0.99
129_D	223_R	0.501	0.99
142_K	169_L	0.500	0.99

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	0.9303	100	0.204	Contact Map
1v9fA	1	0.7664	100	0.211	Contact Map
4lgtA	1	0.9754	100	0.24	Contact Map
1kskA	1	0.9385	100	0.244	Contact Map
3dh3A	1	0.959	100	0.245	Contact Map
2omlA	1	0.6926	100	0.333	Contact Map
2olwA	1	0.6885	100	0.335	Contact Map
2i82A	1	0.8115	100	0.356	Contact Map
2gmlA	1	0.7172	100	0.357	Contact Map
1v9kA	1	0.7746	100	0.357	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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