RSMA - ECOLI - GREMLIN Contacts

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RSMA - Ribosomal RNA small subunit methyltransferase A

UniProt:	P06992	Sequences: MNNRVHQGHLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENAPLQES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10523
Length:	273 (252)
Sequences:	4687 (2978)
Seq/√Len:	187.6

ECOLI - RSMA
BACSU - RSMA
HALSA - RSMA
SULSO - Q7LXK6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
247_M	251_N	3.634	1.00
56_G	85_L	3.088	1.00
253_S	256_Q	2.989	1.00
247_M	256_Q	2.930	1.00
40_A	63_T	2.756	1.00
61_Q	86_T	2.625	1.00
256_Q	259_Q	2.597	1.00
145_V	190_A	2.588	1.00
72_A	89_Q	2.415	1.00
22_D	180_A	2.406	1.00
28_S	174_L	2.265	1.00
63_T	88_Y	2.260	1.00
116_Y	189_S	2.204	1.00
169_N	195_V	2.189	1.00
146_N	172_P	2.187	1.00
171_I	193_R	2.173	1.00
169_N	197_H	2.124	1.00
142_K	175_E	2.089	1.00
217_A	257_Y	2.081	1.00
171_I	195_V	2.072	1.00
96_N	99_E	2.062	1.00
55_V	111_F	2.033	1.00
54_P	57_E	2.029	1.00
178_P	188_D	2.022	1.00
69_R	89_Q	1.971	1.00
149_V	170_V	1.954	1.00
161_S	165_Q	1.944	1.00
18_N	184_P	1.937	1.00
31_S	58_R	1.905	1.00
177_P	180_A	1.887	1.00
224_T	246_A	1.873	1.00
168_C	194_L	1.859	1.00
235_V	239_T	1.857	1.00
39_Q	109_R	1.836	1.00
252_I	256_Q	1.832	1.00
213_I	261_A	1.832	1.00
27_D	54_P	1.779	1.00
59_L	62_L	1.770	1.00
197_H	201_P	1.766	1.00
46_P	64_V	1.756	1.00
205_K	262_N	1.753	1.00
172_P	175_E	1.734	1.00
173_V	193_R	1.723	1.00
175_E	190_A	1.702	1.00
53_E	78_H	1.652	1.00
109_R	135_D	1.628	1.00
65_I	95_F	1.608	1.00
148_L	164_A	1.596	1.00
162_V	214_T	1.590	1.00
21_N	182_T	1.575	1.00
124_F	163_M	1.566	1.00
92_A	97_F	1.564	1.00
36_Q	39_Q	1.555	1.00
135_D	193_R	1.554	1.00
76_Q	89_Q	1.549	1.00
236_E	240_G	1.548	1.00
172_P	190_A	1.534	1.00
139_M	176_V	1.515	1.00
224_T	227_N	1.515	1.00
107_P	134_A	1.508	1.00
123_M	140_L	1.503	1.00
164_A	170_V	1.503	1.00
55_V	62_L	1.493	1.00
162_V	254_V	1.482	1.00
32_A	173_V	1.473	1.00
65_I	92_A	1.467	1.00
142_K	146_N	1.446	1.00
26_I	54_P	1.418	1.00
11_A	182_T	1.397	1.00
125_H	129_Y	1.389	1.00
137_H	193_R	1.380	1.00
92_A	122_L	1.368	1.00
209_V	261_A	1.353	1.00
12_R	70_D	1.350	1.00
204_V	262_N	1.350	1.00
259_Q	262_N	1.341	1.00
240_G	263_Y	1.331	1.00
35_P	41_M	1.322	1.00
15_F	67_L	1.320	1.00
244_D	247_M	1.317	1.00
178_P	186_K	1.304	1.00
72_A	76_Q	1.304	1.00
243_I	247_M	1.298	1.00
110_V	126_L	1.291	1.00
210_L	214_T	1.287	1.00
119_S	140_L	1.271	1.00
217_A	249_A	1.269	1.00
153_N	251_N	1.267	1.00
204_V	258_C	1.241	1.00
241_M	263_Y	1.237	1.00
146_N	156_A	1.237	1.00
148_L	192_V	1.225	1.00
64_V	87_I	1.217	1.00
140_L	145_V	1.211	1.00
142_K	188_D	1.209	1.00
88_Y	95_F	1.205	1.00
114_L	138_F	1.196	1.00
209_V	264_L	1.196	1.00
176_V	191_V	1.193	1.00
166_Y	210_L	1.189	1.00
11_A	48_L	1.188	1.00
175_E	188_D	1.179	1.00
40_A	61_Q	1.167	1.00
127_F	168_C	1.164	1.00
179_S	184_P	1.154	1.00
25_V	180_A	1.143	1.00
137_H	191_V	1.138	1.00
219_N	228_S	1.138	1.00
90_Q	95_F	1.135	1.00
38_G	60_D	1.128	1.00
168_C	196_P	1.113	1.00
226_R	235_V	1.107	1.00
165_Q	170_V	1.107	1.00
23_Q	54_P	1.106	1.00
222_R	250_E	1.103	1.00
119_S	144_V	1.095	1.00
174_L	191_V	1.094	1.00
236_E	239_T	1.090	1.00
91_D	94_T	1.089	1.00
63_T	86_T	1.087	1.00
244_D	251_N	1.078	1.00
64_V	85_L	1.069	1.00
155_K	250_E	1.042	1.00
151_G	154_S	1.041	1.00
33_I	112_G	1.040	1.00
239_T	245_P	1.035	1.00
148_L	170_V	1.035	1.00
24_F	180_A	1.032	1.00
217_A	225_I	1.030	1.00
135_D	195_V	1.026	1.00
149_V	172_P	1.019	1.00
242_G	259_Q	1.018	1.00
30_V	111_F	1.016	1.00
217_A	228_S	1.010	1.00
52_T	62_L	1.008	1.00
35_P	59_L	1.006	0.99
24_F	27_D	1.003	0.99
33_I	111_F	0.993	0.99
72_A	87_I	0.991	0.99
235_V	245_P	0.986	0.99
16_G	117_N	0.983	0.99
15_F	70_D	0.981	0.99
42_V	101_A	0.980	0.99
197_H	200_M	0.979	0.99
30_V	35_P	0.977	0.99
168_C	197_H	0.976	0.99
167_Y	211_S	0.971	0.99
27_D	31_S	0.968	0.99
56_G	84_K	0.960	0.99
33_I	41_M	0.959	0.99
79_P	82_G	0.956	0.99
90_Q	94_T	0.956	0.99
35_P	39_Q	0.955	0.99
112_G	138_F	0.951	0.99
255_A	259_Q	0.946	0.99
130_T	207_V	0.945	0.99
166_Y	207_V	0.936	0.99
40_A	60_D	0.934	0.99
142_K	190_A	0.932	0.99
42_V	65_I	0.930	0.99
73_A	76_Q	0.926	0.99
93_M	118_I	0.912	0.99
44_I	110_V	0.909	0.99
48_L	71_L	0.907	0.99
23_Q	53_E	0.906	0.99
228_S	249_A	0.906	0.99
26_I	50_A	0.901	0.99
32_A	174_L	0.898	0.99
48_L	74_R	0.898	0.99
237_V	264_L	0.897	0.99
206_D	262_N	0.892	0.99
46_P	75_L	0.890	0.99
166_Y	254_V	0.880	0.99
79_P	84_K	0.875	0.99
123_M	148_L	0.866	0.98
33_I	137_H	0.865	0.98
207_V	211_S	0.864	0.98
200_M	258_C	0.859	0.98
258_C	262_N	0.859	0.98
206_D	209_V	0.855	0.98
150_A	154_S	0.851	0.98
40_A	106_Q	0.846	0.98
26_I	30_V	0.831	0.98
216_E	249_A	0.822	0.98
118_I	122_L	0.815	0.98
64_V	75_L	0.814	0.98
41_M	59_L	0.813	0.98
24_F	28_S	0.813	0.98
209_V	213_I	0.812	0.98
159_R	215_T	0.811	0.98
75_L	87_I	0.810	0.98
207_V	210_L	0.809	0.98
178_P	184_P	0.802	0.98
92_A	114_L	0.801	0.97
142_K	172_P	0.799	0.97
65_I	100_L	0.798	0.97
213_I	217_A	0.794	0.97
12_R	15_F	0.790	0.97
136_M	196_P	0.788	0.97
77_T	80_F	0.787	0.97
157_Y	257_Y	0.787	0.97
29_I	139_M	0.784	0.97
210_L	261_A	0.781	0.97
109_R	134_A	0.780	0.97
157_Y	161_S	0.780	0.97
109_R	137_H	0.772	0.97
23_Q	27_D	0.772	0.97
35_P	109_R	0.769	0.97
26_I	139_M	0.764	0.97
259_Q	263_Y	0.752	0.96
159_R	163_M	0.750	0.96
80_F	83_P	0.749	0.96
29_I	191_V	0.749	0.96
128_S	211_S	0.747	0.96
158_G	250_E	0.747	0.96
101_A	108_L	0.746	0.96
114_L	122_L	0.742	0.96
92_A	118_I	0.730	0.96
163_M	211_S	0.730	0.96
9_H	70_D	0.722	0.95
149_V	190_A	0.721	0.95
28_S	179_S	0.720	0.95
237_V	263_Y	0.719	0.95
209_V	212_R	0.719	0.95
162_V	257_Y	0.719	0.95
123_M	164_A	0.717	0.95
33_I	109_R	0.713	0.95
40_A	105_G	0.710	0.95
37_K	60_D	0.709	0.95
212_R	216_E	0.706	0.95
66_E	72_A	0.705	0.95
169_N	201_P	0.705	0.95
48_L	78_H	0.704	0.95
133_I	136_M	0.702	0.95
98_G	131_D	0.697	0.94
166_Y	211_S	0.696	0.94
11_A	19_F	0.696	0.94
92_A	125_H	0.693	0.94
74_R	77_T	0.692	0.94
213_I	232_L	0.691	0.94
97_F	125_H	0.690	0.94
54_P	58_R	0.690	0.94
176_V	187_V	0.684	0.94
212_R	232_L	0.681	0.94
39_Q	134_A	0.678	0.94
10_L	70_D	0.677	0.94
124_F	128_S	0.672	0.93
42_V	108_L	0.672	0.93
208_R	212_R	0.671	0.93
166_Y	204_V	0.671	0.93
129_Y	133_I	0.670	0.93
97_F	122_L	0.666	0.93
177_P	188_D	0.663	0.93
73_A	77_T	0.662	0.93
124_F	159_R	0.659	0.93
98_G	129_Y	0.658	0.93
198_A	201_P	0.657	0.93
167_Y	207_V	0.654	0.92
149_V	192_V	0.654	0.92
90_Q	99_E	0.653	0.92
62_L	112_G	0.647	0.92
107_P	198_A	0.647	0.92
28_S	31_S	0.647	0.92
108_L	133_I	0.641	0.92
9_H	48_L	0.639	0.91
50_A	54_P	0.637	0.91
114_L	119_S	0.637	0.91
110_V	138_F	0.637	0.91
225_I	229_L	0.636	0.91
56_G	82_G	0.636	0.91
222_R	248_R	0.636	0.91
110_V	133_I	0.633	0.91
178_P	187_V	0.633	0.91
120_T	136_M	0.633	0.91
146_N	175_E	0.630	0.91
249_A	257_Y	0.623	0.90
9_H	74_R	0.619	0.90
32_A	193_R	0.617	0.90
166_Y	258_C	0.616	0.90
220_Q	228_S	0.613	0.90
116_Y	139_M	0.611	0.90
238_L	245_P	0.606	0.89
25_V	174_L	0.604	0.89
44_I	126_L	0.603	0.89
30_V	58_R	0.603	0.89
18_N	186_K	0.599	0.89
53_E	79_P	0.599	0.89
81_L	84_K	0.598	0.89
65_I	228_S	0.598	0.89
243_I	251_N	0.596	0.88
147_R	150_A	0.593	0.88
140_L	164_A	0.593	0.88
128_S	208_R	0.593	0.88
157_Y	254_V	0.592	0.88
213_I	257_Y	0.591	0.88
225_I	252_I	0.589	0.88
69_R	72_A	0.588	0.88
121_P	125_H	0.587	0.88
79_P	85_L	0.584	0.87
26_I	51_L	0.583	0.87
26_I	111_F	0.583	0.87
25_V	176_V	0.576	0.87
239_T	242_G	0.576	0.87
53_E	82_G	0.576	0.87
226_R	230_G	0.576	0.87
148_L	161_S	0.574	0.86
44_I	138_F	0.573	0.86
238_L	242_G	0.573	0.86
67_L	89_Q	0.573	0.86
200_M	204_V	0.572	0.86
140_L	159_R	0.572	0.86
174_L	190_A	0.569	0.86
216_E	232_L	0.566	0.86
39_Q	106_Q	0.565	0.86
252_I	257_Y	0.562	0.85
79_P	83_P	0.561	0.85
241_M	260_M	0.560	0.85
19_F	71_L	0.559	0.85
38_G	106_Q	0.559	0.85
11_A	71_L	0.558	0.85
238_L	243_I	0.558	0.85
170_V	192_V	0.557	0.85
8_G	11_A	0.557	0.85
169_N	198_A	0.557	0.85
139_M	189_S	0.556	0.85
42_V	97_F	0.554	0.84
126_L	136_M	0.554	0.84
217_A	229_L	0.554	0.84
120_T	124_F	0.553	0.84
159_R	214_T	0.552	0.84
243_I	256_Q	0.552	0.84
140_L	148_L	0.552	0.84
129_Y	132_A	0.551	0.84
30_V	55_V	0.547	0.84
30_V	54_P	0.547	0.84
41_M	62_L	0.546	0.84
46_P	56_G	0.546	0.84
136_M	194_L	0.545	0.84
224_T	228_S	0.544	0.83
221_R	250_E	0.543	0.83
70_D	73_A	0.541	0.83
95_F	99_E	0.540	0.83
159_R	211_S	0.539	0.83
255_A	258_C	0.538	0.83
98_G	132_A	0.535	0.82
139_M	191_V	0.534	0.82
206_D	258_C	0.534	0.82
206_D	210_L	0.534	0.82
119_S	124_F	0.533	0.82
119_S	123_M	0.533	0.82
11_A	14_R	0.532	0.82
241_M	245_P	0.532	0.82
219_N	249_A	0.531	0.82
25_V	177_P	0.529	0.82
41_M	58_R	0.527	0.81
233_F	238_L	0.526	0.81
41_M	109_R	0.526	0.81
243_I	260_M	0.526	0.81
35_P	60_D	0.525	0.81
28_S	32_A	0.525	0.81
20_L	25_V	0.523	0.81
49_A	56_G	0.520	0.81
210_L	213_I	0.519	0.80
55_V	59_L	0.518	0.80
12_R	69_R	0.514	0.80
241_M	259_Q	0.511	0.79
234_S	237_V	0.510	0.79
165_Q	254_V	0.509	0.79
178_P	190_A	0.509	0.79
145_V	194_L	0.508	0.79
113_N	139_M	0.508	0.79
18_N	71_L	0.507	0.79
50_A	112_G	0.507	0.79
254_V	258_C	0.507	0.79
246_A	251_N	0.504	0.79
136_M	140_L	0.500	0.78
213_I	260_M	0.500	0.78
237_V	260_M	0.500	0.78

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
1i4wA	1	0.967	100	0.246	Contact Map
4gc5A	2	0.9963	100	0.261	Contact Map
4jxjA	1	0.8901	100	0.282	Contact Map
3uzuA	1	0.9414	100	0.29	Contact Map
3tqsA	1	0.9011	100	0.294	Contact Map
1qyrA	1	0.9231	100	0.298	Contact Map
3futA	1	0.9267	100	0.319	Contact Map
3gruA	1	0.9048	100	0.322	Contact Map
3ftdA	1	0.8755	100	0.336	Contact Map
1zq9A	2	0.9011	100	0.374	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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