YSGA - BACSU - GREMLIN Contacts

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YSGA - Uncharacterized tRNA/rRNA methyltransferase YsgA

UniProt:	P94538	Sequences: MKQIESAKNQKVKDWKKLHTKKERTKTNTFLIEGEHLVEEALKSPGIVKEILVKDETRIPSDLETGIQCYMLSEDAFSAVTETETPQQIAAVCHMPEEKLATARKVLLIDAVQDPGNLGTMIRTADAAGLDAVVLGDGTADAFNGKTLRSAQGSHFHIPVVRRNLPSYVDELKAEGVKVYGTALQNGAPYQEIPQSESFALIVGNEGAGVDAALLEKTDLNLYVPLYGQAESLNVAVAAAILVYHLRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	248 (221)
Sequences:	8347 (5670)
Seq/√Len:	381.4

ECOLI - YFIF RLMB TRML
BACSU - YSGA YACO TRML

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
203_V	235_V	3.931	1.00
181_G	218_T	3.387	1.00
108_L	200_A	3.160	1.00
212_A	216_E	2.798	1.00
237_V	240_A	2.795	1.00
182_T	242_L	2.671	1.00
121_M	239_A	2.643	1.00
49_K	94_H	2.642	1.00
181_G	210_V	2.396	1.00
203_V	239_A	2.380	1.00
50_E	70_Y	2.207	1.00
170_D	217_K	2.197	1.00
107_L	121_M	2.033	1.00
183_A	215_L	2.027	1.00
38_V	91_A	1.932	1.00
132_A	159_P	1.930	1.00
173_K	219_D	1.909	1.00
110_D	211_D	1.894	1.00
122_I	133_V	1.874	1.00
180_Y	222_L	1.836	1.00
128_A	244_Y	1.807	1.00
77_F	90_A	1.795	1.00
47_I	94_H	1.780	1.00
104_R	198_S	1.780	1.00
126_D	158_I	1.741	1.00
105_K	130_L	1.698	1.00
239_A	243_V	1.680	1.00
151_A	155_H	1.670	1.00
106_V	132_A	1.662	1.00
188_A	220_L	1.660	1.00
107_L	243_V	1.635	1.00
178_K	220_L	1.625	1.00
164_N	167_S	1.621	1.00
126_D	228_G	1.613	1.00
29_T	49_K	1.589	1.00
180_Y	199_F	1.564	1.00
148_L	155_H	1.563	1.00
130_L	243_V	1.515	1.00
201_L	242_L	1.497	1.00
202_I	210_V	1.492	1.00
177_V	198_S	1.488	1.00
56_E	74_E	1.485	1.00
125_A	130_L	1.483	1.00
154_S	230_A	1.473	1.00
127_A	226_L	1.458	1.00
55_D	71_M	1.457	1.00
177_V	200_A	1.443	1.00
180_Y	220_L	1.441	1.00
190_Y	242_L	1.439	1.00
50_E	92_V	1.418	1.00
74_E	78_S	1.402	1.00
107_L	125_A	1.386	1.00
128_A	190_Y	1.381	1.00
32_I	41_A	1.377	1.00
189_P	192_E	1.361	1.00
113_Q	207_G	1.355	1.00
201_L	246_L	1.348	1.00
51_I	91_A	1.344	1.00
126_D	154_S	1.338	1.00
169_V	179_V	1.328	1.00
104_R	131_D	1.323	1.00
128_A	241_I	1.316	1.00
120_T	236_A	1.312	1.00
72_L	77_F	1.296	1.00
107_L	130_L	1.295	1.00
170_D	174_A	1.289	1.00
102_T	131_D	1.278	1.00
172_L	200_A	1.278	1.00
193_I	222_L	1.278	1.00
72_L	76_A	1.277	1.00
126_D	157_H	1.277	1.00
184_L	223_Y	1.268	1.00
112_V	235_V	1.257	1.00
215_L	221_N	1.247	1.00
183_A	221_N	1.237	1.00
205_N	208_A	1.234	1.00
181_G	221_N	1.233	1.00
105_K	131_D	1.224	1.00
178_K	219_D	1.221	1.00
134_V	168_Y	1.218	1.00
106_V	177_V	1.217	1.00
124_T	240_A	1.212	1.00
166_P	217_K	1.198	1.00
202_I	214_L	1.197	1.00
55_D	73_S	1.187	1.00
111_A	138_G	1.186	1.00
126_D	230_A	1.176	1.00
39_E	43_K	1.175	1.00
48_V	91_A	1.169	1.00
76_A	79_A	1.166	1.00
108_L	169_V	1.165	1.00
171_E	175_E	1.159	1.00
203_V	238_A	1.144	1.00
40_E	157_H	1.142	1.00
106_V	134_V	1.140	1.00
48_V	93_C	1.134	1.00
132_A	161_V	1.132	1.00
186_N	223_Y	1.119	1.00
189_P	223_Y	1.106	1.00
108_L	165_L	1.102	1.00
107_L	203_V	1.096	1.00
172_L	177_V	1.093	1.00
188_A	192_E	1.092	1.00
179_V	200_A	1.090	1.00
135_L	160_V	1.082	1.00
54_K	74_E	1.078	1.00
169_V	214_L	1.076	1.00
28_N	95_M	1.073	1.00
125_A	133_V	1.069	1.00
105_K	246_L	1.052	1.00
118_L	135_L	1.049	1.00
46_G	96_P	1.039	1.00
122_I	160_V	1.033	1.00
118_L	140_A	1.030	1.00
75_D	78_S	1.027	1.00
166_P	213_A	1.023	1.00
211_D	214_L	1.022	1.00
124_T	237_V	1.022	1.00
195_Q	246_L	1.014	1.00
38_V	89_I	1.009	1.00
54_K	57_T	0.999	1.00
182_T	203_V	0.995	1.00
218_T	221_N	0.991	1.00
166_P	170_D	0.990	1.00
40_E	43_K	0.988	1.00
171_E	174_A	0.985	1.00
124_T	243_V	0.974	1.00
73_S	76_A	0.972	1.00
191_Q	245_H	0.971	1.00
195_Q	199_F	0.966	1.00
105_K	243_V	0.965	1.00
170_D	173_K	0.962	1.00
116_G	150_S	0.959	1.00
190_Y	195_Q	0.957	1.00
122_I	147_T	0.954	1.00
135_L	139_T	0.954	1.00
157_H	229_Q	0.952	1.00
81_T	90_A	0.947	1.00
129_G	227_Y	0.941	1.00
188_A	193_I	0.940	1.00
202_I	218_T	0.938	1.00
32_I	93_C	0.937	1.00
98_E	175_E	0.934	1.00
165_L	214_L	0.929	1.00
109_I	203_V	0.923	1.00
137_D	163_R	0.922	1.00
46_G	156_F	0.919	1.00
126_D	229_Q	0.910	1.00
128_A	191_Q	0.904	1.00
32_I	37_L	0.899	1.00
30_F	93_C	0.896	1.00
222_L	242_L	0.894	1.00
109_I	121_M	0.892	1.00
124_T	128_A	0.892	1.00
96_P	143_F	0.886	1.00
31_L	90_A	0.879	1.00
53_V	71_M	0.878	1.00
109_I	118_L	0.877	1.00
60_P	63_L	0.877	1.00
105_K	199_F	0.875	1.00
41_A	45_P	0.873	1.00
181_G	215_L	0.867	1.00
52_L	80_V	0.864	1.00
178_K	197_E	0.851	1.00
167_S	170_D	0.849	1.00
103_A	131_D	0.849	1.00
110_D	214_L	0.847	1.00
36_H	152_Q	0.841	1.00
167_S	171_E	0.836	1.00
108_L	202_I	0.829	1.00
213_A	216_E	0.828	1.00
53_V	89_I	0.828	1.00
185_Q	221_N	0.827	1.00
116_G	120_T	0.821	1.00
191_Q	225_P	0.816	1.00
31_L	92_V	0.814	1.00
54_K	77_F	0.811	1.00
104_R	177_V	0.809	1.00
106_V	172_L	0.808	1.00
111_A	136_G	0.808	1.00
110_D	210_V	0.807	1.00
199_F	246_L	0.805	1.00
140_A	144_N	0.805	1.00
59_I	62_D	0.803	1.00
111_A	208_A	0.798	1.00
185_Q	215_L	0.795	1.00
134_V	163_R	0.793	1.00
29_T	92_V	0.793	1.00
213_A	217_K	0.792	1.00
103_A	197_E	0.790	1.00
50_E	68_Q	0.788	1.00
53_V	69_C	0.782	1.00
188_A	223_Y	0.782	1.00
82_E	145_G	0.782	1.00
29_T	94_H	0.781	1.00
163_R	167_S	0.778	1.00
182_T	210_V	0.777	1.00
169_V	200_A	0.776	1.00
193_I	220_L	0.773	1.00
122_I	155_H	0.770	1.00
108_L	172_L	0.769	1.00
127_A	230_A	0.768	1.00
169_V	217_K	0.767	1.00
187_G	223_Y	0.767	1.00
137_D	164_N	0.766	1.00
166_P	214_L	0.762	1.00
72_L	90_A	0.761	1.00
128_A	243_V	0.760	1.00
111_A	211_D	0.760	1.00
41_A	93_C	0.760	1.00
111_A	205_N	0.757	1.00
178_K	199_F	0.756	1.00
44_S	157_H	0.755	1.00
212_A	215_L	0.753	1.00
52_L	72_L	0.753	1.00
112_V	118_L	0.752	1.00
179_V	202_I	0.741	1.00
180_Y	193_I	0.740	1.00
41_A	156_F	0.736	1.00
118_L	147_T	0.727	1.00
98_E	101_A	0.726	1.00
49_K	68_Q	0.724	1.00
61_S	64_E	0.721	1.00
112_V	121_M	0.719	1.00
148_L	156_F	0.719	1.00
168_Y	172_L	0.719	1.00
39_E	61_S	0.717	1.00
183_A	186_N	0.717	1.00
173_K	217_K	0.710	1.00
210_V	218_T	0.709	1.00
49_K	92_V	0.708	1.00
33_E	83_T	0.706	1.00
52_L	92_V	0.704	1.00
52_L	70_Y	0.704	1.00
203_V	242_L	0.699	0.99
184_L	231_E	0.685	0.99
185_Q	223_Y	0.681	0.99
122_I	154_S	0.680	0.99
173_K	179_V	0.678	0.99
113_Q	205_N	0.678	0.99
121_M	235_V	0.676	0.99
127_A	231_E	0.674	0.99
133_V	158_I	0.671	0.99
109_I	112_V	0.670	0.99
181_G	202_I	0.670	0.99
191_Q	244_Y	0.669	0.99
157_H	230_A	0.669	0.99
33_E	149_R	0.661	0.99
51_I	62_D	0.659	0.99
116_G	146_K	0.658	0.99
176_G	198_S	0.657	0.99
78_S	84_E	0.657	0.99
125_A	243_V	0.654	0.99
80_V	90_A	0.653	0.99
183_A	223_Y	0.652	0.99
128_A	224_V	0.650	0.99
135_L	142_A	0.648	0.99
61_S	65_T	0.646	0.99
195_Q	245_H	0.644	0.99
187_G	221_N	0.643	0.99
163_R	168_Y	0.641	0.99
120_T	237_V	0.635	0.99
77_F	87_Q	0.635	0.99
134_V	172_L	0.634	0.99
141_D	144_N	0.633	0.99
108_L	134_V	0.633	0.99
131_D	177_V	0.627	0.99
124_T	239_A	0.626	0.99
35_E	39_E	0.619	0.99
32_I	48_V	0.612	0.99
191_Q	195_Q	0.611	0.99
128_A	226_L	0.611	0.99
224_V	244_Y	0.610	0.99
186_N	221_N	0.607	0.99
108_L	136_G	0.604	0.99
36_H	39_E	0.603	0.98
182_T	201_L	0.602	0.98
53_V	58_R	0.600	0.98
116_G	236_A	0.591	0.98
128_A	227_Y	0.590	0.98
154_S	157_H	0.590	0.98
38_V	51_I	0.586	0.98
77_F	86_P	0.580	0.98
138_G	211_D	0.579	0.98
106_V	200_A	0.577	0.98
183_A	210_V	0.576	0.98
30_F	46_G	0.570	0.98
77_F	81_T	0.567	0.98
78_S	86_P	0.566	0.98
241_I	244_Y	0.565	0.98
168_Y	171_E	0.563	0.98
113_Q	208_A	0.559	0.98
33_E	145_G	0.559	0.98
136_G	165_L	0.554	0.97
178_K	196_S	0.554	0.97
43_K	229_Q	0.552	0.97
142_A	162_R	0.548	0.97
168_Y	176_G	0.548	0.97
37_L	148_L	0.546	0.97
210_V	214_L	0.545	0.97
33_E	90_A	0.543	0.97
127_A	244_Y	0.541	0.97
54_K	71_M	0.541	0.97
32_I	148_L	0.539	0.97
33_E	84_E	0.537	0.97
236_A	239_A	0.536	0.97
64_E	67_I	0.536	0.97
136_G	214_L	0.532	0.97
191_Q	194_P	0.531	0.97
224_V	238_A	0.531	0.97
75_D	79_A	0.529	0.97
148_L	151_A	0.527	0.97
59_I	63_L	0.526	0.96
72_L	80_V	0.524	0.96
87_Q	114_D	0.524	0.96
205_N	231_E	0.522	0.96
45_P	65_T	0.518	0.96
169_V	173_K	0.518	0.96
127_A	233_L	0.514	0.96
224_V	241_I	0.514	0.96
104_R	132_A	0.512	0.96
108_L	168_Y	0.512	0.96
103_A	198_S	0.510	0.96
143_F	147_T	0.508	0.96
37_L	152_Q	0.506	0.96
214_L	217_K	0.505	0.96
151_A	156_F	0.502	0.95
58_R	71_M	0.501	0.95
111_A	214_L	0.501	0.95
37_L	156_F	0.501	0.95
62_D	67_I	0.500	0.95
83_T	87_Q	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
1ipaA	1	0.9758	100	0.128	Contact Map
3nk6A	2	0.9677	100	0.128	Contact Map
1x7oA	2	0.9718	100	0.144	Contact Map
2i6dA	2	0.9637	100	0.175	Contact Map
1gz0A	2	0.9315	100	0.24	Contact Map
4kgnA	2	0.5927	100	0.428	Contact Map
3n4jA	2	0.5887	100	0.437	Contact Map
1zjrA	2	0.6573	100	0.44	Contact Map
3l8uA	2	0.5524	100	0.453	Contact Map
1v2xA	2	0.6613	100	0.454	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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