TRUB - SULSO - GREMLIN Contacts

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TRUB - Probable tRNA pseudouridine synthase B

UniProt:	Q980C3	Sequences: MLPIGIENATKIMNYISKGGKEYVCVMQVHCEYNKEELAKIISSFKGEIYQRPPVRSSVKRRLRIRRIYDIEILDMDKKLVLLRVNCDSGTYMRKLCHDIGIIYGCGAHMRELRRTRSGIFTESTNLVKLHELSEAIYLYKNCKDETELRRVLIPMEFATCEIPKIVIEDSAVNALAYGAQLAVPGVVAYQNFKKNDTVAVLTLKGELVATGNALMDSEELENAKKGIVVNLSRVFMQRDIYPKAWKKHES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	251 (203)
Sequences:	3219 (2394)
Seq/√Len:	168.0

ECOLI - TRUB
BACSU - TRUB
HALSA - TRUB
SULSO - TRUB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_Y	65_I	4.024	1.00
48_E	65_I	3.778	1.00
24_V	84_R	2.899	1.00
48_E	67_R	2.814	1.00
36_E	98_H	2.800	1.00
22_E	84_R	2.787	1.00
44_S	103_I	2.685	1.00
175_A	180_A	2.560	1.00
28_Q	80_L	2.539	1.00
22_E	86_N	2.517	1.00
28_Q	111_R	2.202	1.00
70_D	86_N	2.167	1.00
74_L	84_R	2.159	1.00
41_I	100_I	2.148	1.00
27_M	97_C	2.109	1.00
55_V	61_R	2.107	1.00
59_V	64_R	2.104	1.00
97_C	110_M	2.079	1.00
52_R	63_L	1.957	1.00
29_V	81_V	1.952	1.00
27_M	81_V	1.920	1.00
42_I	71_I	1.913	1.00
32_E	102_I	1.909	1.00
45_F	103_I	1.886	1.00
5_G	13_M	1.880	1.00
169_E	172_A	1.872	1.00
24_V	82_L	1.871	1.00
72_E	84_R	1.859	1.00
27_M	83_L	1.851	1.00
26_V	82_L	1.806	1.00
49_I	66_R	1.788	1.00
36_E	95_K	1.739	1.00
43_S	46_K	1.726	1.00
20_G	86_N	1.708	1.00
85_V	96_L	1.705	1.00
25_C	83_L	1.702	1.00
101_G	108_A	1.686	1.00
26_V	80_L	1.663	1.00
101_G	107_G	1.605	1.00
101_G	106_C	1.578	1.00
42_I	73_I	1.529	1.00
25_C	110_M	1.516	1.00
39_A	73_I	1.509	1.00
129_K	132_E	1.507	1.00
76_M	81_V	1.505	1.00
75_D	82_L	1.487	1.00
32_E	107_G	1.478	1.00
154_I	158_F	1.469	1.00
134_S	138_Y	1.461	1.00
86_N	117_R	1.447	1.00
176_L	201_V	1.447	1.00
168_I	176_L	1.445	1.00
50_Y	63_L	1.436	1.00
33_Y	109_H	1.419	1.00
46_K	71_I	1.415	1.00
13_M	17_S	1.414	1.00
95_K	98_H	1.408	1.00
22_E	117_R	1.405	1.00
80_L	111_R	1.404	1.00
123_E	127_L	1.400	1.00
148_E	151_R	1.392	1.00
38_L	81_V	1.378	1.00
26_V	112_E	1.351	1.00
8_N	11_K	1.341	1.00
24_V	74_L	1.337	1.00
34_N	56_R	1.332	1.00
26_V	111_R	1.330	1.00
27_M	108_A	1.327	1.00
163_I	211_T	1.321	1.00
42_I	83_L	1.316	1.00
39_A	46_K	1.307	1.00
131_H	134_S	1.304	1.00
176_L	210_A	1.287	1.00
20_G	69_Y	1.270	1.00
157_E	202_L	1.269	1.00
70_D	84_R	1.268	1.00
174_N	178_Y	1.264	1.00
28_Q	31_C	1.256	1.00
114_R	123_E	1.249	1.00
41_I	44_S	1.248	1.00
122_T	126_N	1.235	1.00
73_I	81_V	1.212	1.00
85_V	93_M	1.210	1.00
69_Y	86_N	1.205	1.00
77_D	82_L	1.198	1.00
121_F	158_F	1.185	1.00
98_H	102_I	1.180	1.00
45_F	99_D	1.180	1.00
41_I	103_I	1.178	1.00
200_A	208_L	1.159	1.00
18_K	89_S	1.154	1.00
22_E	116_T	1.152	1.00
132_E	135_E	1.135	1.00
31_C	109_H	1.135	1.00
117_R	122_T	1.127	1.00
68_I	96_L	1.100	1.00
203_T	207_E	1.087	1.00
175_A	178_Y	1.048	0.99
29_V	104_Y	1.035	0.99
128_V	133_L	1.035	0.99
136_A	152_V	1.028	0.99
67_R	88_D	1.024	0.99
177_A	207_E	1.010	0.99
19_G	119_G	1.008	0.99
61_R	95_K	1.001	0.99
46_K	70_D	0.997	0.99
1_M	127_L	0.983	0.99
35_K	56_R	0.979	0.99
168_I	172_A	0.971	0.99
137_I	149_L	0.967	0.99
82_L	112_E	0.958	0.99
27_M	110_M	0.956	0.99
54_P	95_K	0.955	0.99
25_C	97_C	0.954	0.99
128_V	132_E	0.952	0.99
128_V	152_V	0.952	0.99
201_V	212_G	0.951	0.99
28_Q	79_K	0.950	0.99
71_I	83_L	0.948	0.99
87_C	91_T	0.947	0.99
160_T	163_I	0.940	0.99
11_K	14_N	0.931	0.99
50_Y	62_R	0.926	0.99
45_F	96_L	0.925	0.99
173_V	203_T	0.917	0.98
36_E	54_P	0.908	0.98
29_V	106_C	0.899	0.98
172_A	175_A	0.898	0.98
25_C	71_I	0.892	0.98
32_E	98_H	0.889	0.98
160_T	208_L	0.880	0.98
38_L	76_M	0.873	0.98
155_P	158_F	0.866	0.98
73_I	76_M	0.864	0.98
171_S	174_N	0.859	0.98
164_P	197_D	0.859	0.98
71_I	96_L	0.852	0.98
42_I	100_I	0.849	0.98
157_E	200_A	0.829	0.97
32_E	106_C	0.828	0.97
12_I	159_A	0.828	0.97
3_P	118_S	0.827	0.97
121_F	159_A	0.827	0.97
40_K	43_S	0.826	0.97
99_D	102_I	0.820	0.97
19_G	118_S	0.817	0.97
158_F	161_C	0.813	0.97
136_A	148_E	0.809	0.97
55_V	95_K	0.803	0.97
77_D	80_L	0.801	0.96
14_N	17_S	0.791	0.96
1_M	123_E	0.786	0.96
6_I	153_L	0.784	0.96
76_M	79_K	0.779	0.96
49_I	68_I	0.777	0.96
25_C	93_M	0.775	0.96
84_R	116_T	0.773	0.96
68_I	87_C	0.769	0.96
69_Y	88_D	0.769	0.96
29_V	108_A	0.766	0.95
46_K	49_I	0.762	0.95
61_R	98_H	0.760	0.95
71_I	100_I	0.758	0.95
39_A	72_E	0.756	0.95
157_E	208_L	0.754	0.95
171_S	175_A	0.753	0.95
165_K	200_A	0.750	0.95
24_V	116_T	0.749	0.95
96_L	100_I	0.748	0.95
17_S	59_V	0.748	0.95
12_I	156_M	0.746	0.95
1_M	118_S	0.738	0.94
101_G	104_Y	0.728	0.94
137_I	148_E	0.724	0.94
176_L	212_G	0.719	0.94
83_L	93_M	0.719	0.94
172_A	180_A	0.718	0.94
16_I	19_G	0.716	0.94
173_V	204_L	0.716	0.94
173_V	177_A	0.708	0.93
14_N	18_K	0.706	0.93
12_I	160_T	0.702	0.93
33_Y	37_E	0.687	0.92
52_R	55_V	0.687	0.92
28_Q	109_H	0.686	0.92
156_M	159_A	0.685	0.92
170_D	205_K	0.683	0.92
170_D	204_L	0.680	0.92
68_I	91_T	0.679	0.92
176_L	209_V	0.671	0.91
165_K	206_G	0.671	0.91
166_I	172_A	0.669	0.91
42_I	46_K	0.662	0.91
53_P	61_R	0.661	0.90
71_I	85_V	0.661	0.90
39_A	43_S	0.659	0.90
126_N	154_I	0.659	0.90
184_V	187_V	0.656	0.90
182_L	212_G	0.653	0.90
40_K	44_S	0.652	0.90
147_T	150_R	0.652	0.90
149_L	152_V	0.649	0.90
173_V	209_V	0.649	0.90
9_A	156_M	0.646	0.89
133_L	152_V	0.643	0.89
74_L	82_L	0.643	0.89
52_R	61_R	0.643	0.89
53_P	63_L	0.641	0.89
160_T	165_K	0.641	0.89
170_D	173_V	0.638	0.89
167_V	203_T	0.638	0.89
117_R	120_I	0.637	0.89
121_F	127_L	0.636	0.89
68_I	85_V	0.632	0.88
54_P	160_T	0.631	0.88
17_S	20_G	0.626	0.88
15_Y	211_T	0.619	0.87
97_C	108_A	0.612	0.87
62_R	66_R	0.612	0.87
167_V	204_L	0.601	0.86
176_L	180_A	0.597	0.85
183_A	186_G	0.595	0.85
174_N	177_A	0.595	0.85
89_S	118_S	0.593	0.85
30_H	37_E	0.592	0.85
32_E	36_E	0.585	0.84
168_I	201_V	0.581	0.84
128_V	136_A	0.579	0.84
110_M	212_G	0.578	0.84
41_I	104_Y	0.578	0.84
165_K	202_L	0.576	0.83
71_I	93_M	0.576	0.83
30_H	33_Y	0.575	0.83
131_H	135_E	0.575	0.83
172_A	182_L	0.575	0.83
5_G	12_I	0.574	0.83
199_V	212_G	0.572	0.83
32_E	109_H	0.571	0.83
36_E	101_G	0.570	0.83
5_G	16_I	0.570	0.83
39_A	76_M	0.568	0.83
198_T	211_T	0.567	0.82
53_P	64_R	0.565	0.82
97_C	101_G	0.565	0.82
81_V	100_I	0.564	0.82
137_I	147_T	0.563	0.82
29_V	107_G	0.563	0.82
168_I	173_V	0.563	0.82
49_I	67_R	0.562	0.82
24_V	114_R	0.562	0.82
38_L	104_Y	0.555	0.81
175_A	186_G	0.555	0.81
5_G	9_A	0.555	0.81
52_R	62_R	0.555	0.81
51_Q	99_D	0.552	0.81
12_I	210_A	0.551	0.81
202_L	208_L	0.548	0.80
36_E	55_V	0.548	0.80
26_V	81_V	0.547	0.80
166_I	184_V	0.547	0.80
98_H	101_G	0.546	0.80
129_K	134_S	0.546	0.80
168_I	182_L	0.545	0.80
27_M	101_G	0.544	0.80
5_G	89_S	0.543	0.80
199_V	202_L	0.541	0.79
83_L	97_C	0.541	0.79
22_E	70_D	0.540	0.79
198_T	213_N	0.539	0.79
195_K	198_T	0.538	0.79
118_S	127_L	0.535	0.79
97_C	111_R	0.533	0.78
12_I	16_I	0.533	0.78
11_K	80_L	0.533	0.78
66_R	91_T	0.530	0.78
12_I	15_Y	0.527	0.78
11_K	121_F	0.525	0.77
42_I	81_V	0.523	0.77
194_K	197_D	0.521	0.77
27_M	100_I	0.520	0.77
147_T	151_R	0.515	0.76
25_C	112_E	0.515	0.76
208_L	212_G	0.515	0.76
66_R	88_D	0.514	0.76
27_M	109_H	0.514	0.76
203_T	206_G	0.514	0.76
87_C	93_M	0.513	0.76
203_T	209_V	0.512	0.76
4_I	9_A	0.512	0.76
13_M	60_K	0.511	0.76
38_L	78_K	0.511	0.76
91_T	96_L	0.510	0.75
132_E	136_A	0.509	0.75
3_P	19_G	0.509	0.75
46_K	72_E	0.509	0.75
40_K	206_G	0.509	0.75
109_H	120_I	0.509	0.75
36_E	110_M	0.509	0.75
102_I	106_C	0.508	0.75
9_A	155_P	0.508	0.75
4_I	212_G	0.507	0.75
56_R	89_S	0.507	0.75
197_D	213_N	0.501	0.74
3_P	7_E	0.500	0.74

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
2apoA	1	0.9283	100	0.175	Contact Map
2ausC	1	0.9283	100	0.192	Contact Map
3u28A	1	0.9562	100	0.201	Contact Map
1sgvA	1	0.757	100	0.253	Contact Map
1r3eA	1	0.8924	100	0.264	Contact Map
1k8wA	1	0.8845	100	0.285	Contact Map
2v9kA	1	0.502	100	0.627	Contact Map
3zv0C	2	0.5339	99.3	0.833	Contact Map
1kskA	1	0.4781	98.6	0.873	Contact Map
3r90A	5	0.6494	97.1	0.91	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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