RSMA - BACSU - GREMLIN Contacts

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RSMA - Ribosomal RNA small subunit methyltransferase A

UniProt:	P37468	Sequences: MNKDIATPIRTKEILKKYGFSFKKSLGQNFLIDTNILNRIVDHAEVTEKTGVIEIGPGIGALTEQLAKRAKKVVAFEIDQRLLPILKDTLSPYENVTVIHQDVLKADVKSVIEEQFQDCDEIMVVANLPYYVTTPIIMKLLEEHLPLKGIVVMLQKEVAERMAADPSSKEYGSLSIAVQFYTEAKTVMIVPKTVFVPQPNVDSAVIRLILRDGPAVDVENESFFFQLIKASFAQRRKTLLNNLVNNLPEGKAQKSTIEQVLEETNIDGKRRGESLSIEEFAALSNGLYKALF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	292 (256)
Sequences:	4647 (2940)
Seq/√Len:	183.7

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
270_R	274_S	3.691	1.00
276_S	279_E	3.017	1.00
67_A	96_V	3.013	1.00
270_R	279_E	2.935	1.00
51_G	74_V	2.795	1.00
159_A	204_A	2.646	1.00
72_K	97_T	2.645	1.00
279_E	282_A	2.572	1.00
83_L	100_H	2.375	1.00
33_D	194_V	2.366	1.00
39_R	188_M	2.267	1.00
107_D	110_S	2.254	1.00
160_E	186_T	2.230	1.00
74_V	99_I	2.223	1.00
183_E	209_I	2.218	1.00
185_K	207_R	2.203	1.00
130_Y	203_S	2.167	1.00
183_E	211_R	2.165	1.00
185_K	209_I	2.147	1.00
231_S	280_F	2.120	1.00
156_K	189_I	2.089	1.00
65_Q	68_K	2.085	1.00
192_K	202_D	2.065	1.00
66_L	125_V	2.036	1.00
42_D	69_R	1.980	1.00
80_Q	100_H	1.956	1.00
29_N	198_Q	1.931	1.00
175_S	179_Q	1.928	1.00
163_A	184_A	1.921	1.00
182_T	208_L	1.900	1.00
219_E	285_N	1.895	1.00
238_T	269_K	1.867	1.00
50_T	123_M	1.847	1.00
191_P	194_V	1.835	1.00
275_L	279_E	1.817	1.00
70_A	73_V	1.789	1.00
38_N	65_Q	1.780	1.00
227_L	284_S	1.754	1.00
186_T	189_I	1.700	1.00
187_V	207_R	1.692	1.00
211_R	215_A	1.690	1.00
64_E	89_T	1.675	1.00
57_P	75_A	1.661	1.00
189_I	204_A	1.653	1.00
162_M	178_V	1.643	1.00
123_M	149_G	1.639	1.00
76_F	106_A	1.637	1.00
47_T	50_T	1.598	1.00
176_I	228_I	1.598	1.00
138_M	177_A	1.592	1.00
103_V	108_V	1.570	1.00
87_K	100_H	1.568	1.00
186_T	204_A	1.562	1.00
32_I	196_V	1.557	1.00
238_T	241_N	1.532	1.00
259_Q	263_E	1.531	1.00
149_G	207_R	1.525	1.00
178_V	184_A	1.525	1.00
137_I	154_L	1.513	1.00
23_K	81_R	1.488	1.00
121_E	148_K	1.487	1.00
258_E	262_E	1.487	1.00
153_M	190_V	1.487	1.00
43_H	187_V	1.476	1.00
156_K	160_E	1.469	1.00
76_F	103_V	1.449	1.00
151_V	207_R	1.422	1.00
139_K	143_E	1.417	1.00
37_L	65_Q	1.414	1.00
176_I	277_I	1.414	1.00
66_L	73_V	1.409	1.00
46_V	52_V	1.390	1.00
282_A	285_N	1.390	1.00
22_F	196_V	1.371	1.00
124_V	140_L	1.371	1.00
64_E	90_L	1.344	1.00
192_K	200_N	1.343	1.00
223_F	284_S	1.342	1.00
167_S	274_S	1.326	1.00
267_D	270_R	1.325	1.00
224_F	228_I	1.318	1.00
83_L	87_K	1.315	1.00
26_L	78_I	1.314	1.00
103_V	136_I	1.301	1.00
263_E	286_G	1.296	1.00
266_I	270_R	1.294	1.00
133_T	154_L	1.286	1.00
162_M	206_I	1.285	1.00
264_T	286_G	1.268	1.00
190_V	205_V	1.228	1.00
22_F	59_I	1.228	1.00
231_S	272_G	1.227	1.00
223_F	287_L	1.220	1.00
160_E	170_E	1.218	1.00
180_F	224_F	1.210	1.00
154_L	159_A	1.205	1.00
213_G	217_D	1.205	1.00
193_T	198_Q	1.196	1.00
51_G	72_K	1.189	1.00
128_L	152_V	1.184	1.00
216_V	281_A	1.178	1.00
99_I	106_A	1.177	1.00
141_L	182_T	1.173	1.00
189_I	202_D	1.169	1.00
236_R	273_E	1.166	1.00
156_K	202_D	1.158	1.00
49_K	71_K	1.157	1.00
101_Q	106_A	1.149	1.00
182_T	210_L	1.138	1.00
36_I	194_V	1.138	1.00
41_V	125_V	1.137	1.00
75_A	98_V	1.134	1.00
233_A	242_N	1.132	1.00
179_Q	184_A	1.130	1.00
151_V	205_V	1.118	1.00
188_M	205_V	1.111	1.00
133_T	158_V	1.106	1.00
90_L	96_V	1.103	1.00
34_T	65_Q	1.083	1.00
267_D	274_S	1.078	1.00
74_V	97_T	1.073	1.00
75_A	96_V	1.067	1.00
88_D	91_S	1.058	1.00
231_S	239_L	1.055	1.00
231_S	242_N	1.053	1.00
259_Q	262_E	1.052	1.00
149_G	209_I	1.049	1.00
169_K	273_E	1.047	1.00
165_D	168_S	1.042	1.00
265_N	282_A	1.039	1.00
163_A	186_T	1.030	1.00
162_M	184_A	1.025	1.00
144_H	221_E	1.024	1.00
46_V	70_A	1.021	1.00
44_A	126_A	1.020	1.00
53_I	76_F	1.016	0.99
44_A	125_V	1.009	0.99
102_D	105_K	1.001	0.99
67_A	95_N	1.000	0.99
260_V	287_L	0.999	0.99
63_T	73_V	0.999	0.99
44_A	52_V	0.989	0.99
53_I	112_I	0.983	0.99
76_F	111_V	0.982	0.99
51_G	71_K	0.980	0.99
262_E	268_G	0.980	0.99
46_V	50_T	0.975	0.99
35_N	38_N	0.968	0.99
26_L	81_R	0.965	0.99
83_L	98_V	0.961	0.99
55_I	124_V	0.958	0.99
182_T	211_R	0.957	0.99
38_N	42_D	0.956	0.99
101_Q	105_K	0.953	0.99
35_N	194_V	0.950	0.99
126_A	152_V	0.950	0.99
278_E	282_A	0.949	0.99
41_V	46_V	0.944	0.99
242_N	272_G	0.943	0.99
59_I	82_L	0.939	0.99
217_D	285_N	0.939	0.99
181_Y	225_F	0.934	0.99
27_G	131_Y	0.934	0.99
211_R	214_P	0.926	0.99
156_K	204_A	0.920	0.99
34_T	64_E	0.915	0.99
180_F	221_E	0.910	0.99
37_L	61_A	0.908	0.99
180_F	277_I	0.899	0.99
59_I	85_I	0.894	0.99
18_Y	88_D	0.894	0.99
258_E	268_G	0.890	0.99
84_P	87_K	0.888	0.99
104_L	132_V	0.885	0.99
44_A	151_V	0.884	0.99
43_H	188_M	0.880	0.99
137_I	162_M	0.878	0.99
57_P	86_L	0.877	0.99
281_A	285_N	0.872	0.98
240_L	258_E	0.868	0.98
221_E	225_F	0.866	0.98
51_G	120_D	0.856	0.98
192_K	198_Q	0.845	0.98
52_V	70_A	0.844	0.98
230_A	272_G	0.833	0.98
156_K	186_T	0.820	0.98
227_L	231_S	0.818	0.98
86_L	98_V	0.811	0.98
171_Y	280_F	0.807	0.97
132_V	136_I	0.807	0.97
109_K	145_L	0.806	0.97
163_A	204_A	0.805	0.97
123_M	148_K	0.804	0.97
173_S	229_K	0.801	0.97
103_V	128_L	0.801	0.97
123_M	151_V	0.800	0.97
37_L	41_V	0.798	0.97
35_N	39_R	0.792	0.97
150_I	210_L	0.790	0.97
37_L	153_M	0.787	0.97
164_A	168_S	0.784	0.97
34_T	38_N	0.782	0.97
142_E	225_F	0.781	0.97
90_L	93_Y	0.778	0.97
224_F	284_S	0.777	0.97
40_I	205_V	0.775	0.97
75_A	86_L	0.771	0.97
171_Y	175_S	0.765	0.96
223_F	227_L	0.763	0.96
221_E	224_F	0.762	0.96
222_S	226_Q	0.759	0.96
44_A	123_M	0.758	0.96
23_K	26_L	0.756	0.96
39_R	193_T	0.756	0.96
40_I	153_M	0.755	0.96
112_I	122_I	0.754	0.96
226_Q	246_N	0.749	0.96
223_F	226_Q	0.747	0.96
282_A	286_G	0.745	0.96
48_E	71_K	0.743	0.96
108_V	136_I	0.738	0.96
46_V	123_M	0.736	0.96
53_I	122_I	0.735	0.96
50_T	148_K	0.734	0.96
20_F	81_R	0.728	0.95
103_V	132_V	0.728	0.95
183_E	215_A	0.727	0.95
77_E	83_L	0.726	0.95
128_L	136_I	0.723	0.95
147_L	150_I	0.721	0.95
176_I	280_F	0.719	0.95
260_V	286_G	0.717	0.95
180_F	218_V	0.716	0.95
172_G	273_E	0.716	0.95
65_Q	69_R	0.715	0.95
226_Q	230_A	0.713	0.95
124_V	147_L	0.712	0.95
214_P	281_A	0.711	0.95
22_F	30_F	0.710	0.95
137_I	178_V	0.709	0.95
239_L	243_L	0.709	0.95
51_G	119_C	0.709	0.95
180_F	225_F	0.701	0.94
173_S	177_A	0.699	0.94
128_L	133_T	0.696	0.94
227_L	246_N	0.694	0.94
261_L	268_G	0.693	0.94
191_P	202_D	0.690	0.94
143_E	147_L	0.686	0.94
177_A	225_F	0.683	0.93
21_S	81_R	0.679	0.93
218_V	285_N	0.678	0.93
130_Y	153_M	0.675	0.93
180_F	281_A	0.674	0.93
103_V	139_K	0.673	0.93
138_M	142_E	0.672	0.93
188_M	204_A	0.670	0.93
262_E	265_N	0.669	0.93
192_K	201_V	0.667	0.93
190_V	201_V	0.664	0.92
212_D	215_A	0.664	0.92
59_I	89_T	0.660	0.92
234_Q	242_N	0.655	0.92
121_E	212_D	0.650	0.92
142_E	222_S	0.650	0.92
138_M	173_S	0.647	0.92
261_L	265_N	0.645	0.91
109_K	143_E	0.645	0.91
181_Y	221_E	0.643	0.91
73_V	126_A	0.642	0.91
163_A	206_I	0.640	0.91
108_V	139_K	0.639	0.91
218_V	281_A	0.636	0.91
36_I	188_M	0.634	0.91
22_F	82_L	0.631	0.90
239_L	275_L	0.629	0.90
19_G	22_F	0.628	0.90
124_V	152_V	0.625	0.90
160_E	189_I	0.624	0.90
36_I	190_V	0.623	0.90
20_F	85_I	0.623	0.90
236_R	271_R	0.623	0.90
85_I	88_D	0.620	0.90
39_R	42_D	0.619	0.90
66_L	70_A	0.618	0.90
41_V	69_R	0.615	0.89
61_A	65_Q	0.614	0.89
93_Y	96_V	0.612	0.89
53_I	108_V	0.609	0.89
240_L	244_V	0.607	0.89
29_N	200_N	0.607	0.89
272_G	280_F	0.606	0.89
183_E	212_D	0.605	0.89
161_R	164_A	0.604	0.88
153_M	203_S	0.602	0.88
43_H	207_R	0.601	0.88
41_V	65_Q	0.598	0.88
154_L	178_V	0.597	0.88
55_I	140_L	0.596	0.88
78_I	100_H	0.596	0.88
52_V	73_V	0.594	0.88
30_F	82_L	0.594	0.88
81_R	84_P	0.592	0.88
84_P	88_D	0.591	0.87
266_I	279_E	0.590	0.87
109_K	146_P	0.590	0.87
227_L	280_F	0.589	0.87
20_F	59_I	0.587	0.87
231_S	243_L	0.582	0.87
135_P	139_K	0.581	0.87
36_I	191_P	0.580	0.86
49_K	120_D	0.579	0.86
154_L	162_M	0.577	0.86
37_L	62_L	0.577	0.86
122_I	147_L	0.575	0.86
275_L	280_F	0.574	0.86
50_T	120_D	0.574	0.86
134_T	150_I	0.572	0.86
106_A	110_S	0.572	0.86
144_H	147_L	0.571	0.86
133_T	138_M	0.571	0.86
55_I	152_V	0.570	0.85
67_A	90_L	0.570	0.85
18_Y	83_L	0.570	0.85
233_A	272_G	0.567	0.85
192_K	204_A	0.567	0.85
91_S	94_E	0.566	0.85
76_F	242_N	0.562	0.85
37_L	126_A	0.560	0.84
143_E	146_P	0.557	0.84
101_Q	110_S	0.556	0.84
40_I	130_Y	0.556	0.84
46_V	125_V	0.554	0.84
150_I	208_L	0.554	0.84
140_L	150_I	0.553	0.84
257_I	261_L	0.552	0.84
230_A	246_N	0.551	0.84
154_L	173_S	0.550	0.83
173_S	228_I	0.550	0.83
224_F	227_L	0.549	0.83
179_Q	277_I	0.548	0.83
153_M	205_V	0.547	0.83
134_T	173_S	0.547	0.83
23_K	80_Q	0.546	0.83
257_I	287_L	0.545	0.83
52_V	123_M	0.544	0.83
133_T	137_I	0.543	0.83
39_R	43_H	0.542	0.83
171_Y	277_I	0.541	0.82
152_V	210_L	0.536	0.82
22_F	25_S	0.536	0.82
218_V	224_F	0.533	0.81
67_A	93_Y	0.533	0.81
90_L	98_V	0.530	0.81
235_R	273_E	0.530	0.81
246_N	249_E	0.529	0.81
57_P	67_A	0.529	0.81
134_T	138_M	0.528	0.81
180_F	211_R	0.528	0.81
238_T	242_N	0.527	0.81
144_H	210_L	0.527	0.81
29_N	82_L	0.527	0.81
283_L	286_G	0.526	0.81
184_A	206_I	0.526	0.81
173_S	225_F	0.523	0.80
232_F	235_R	0.522	0.80
52_V	69_R	0.520	0.80
190_V	194_V	0.518	0.80
264_T	283_L	0.515	0.79
46_V	71_K	0.515	0.79
264_T	270_R	0.515	0.79
241_N	273_E	0.510	0.79
63_T	96_V	0.509	0.78
60_G	67_A	0.509	0.78
238_T	274_S	0.507	0.78
40_I	158_V	0.506	0.78
71_K	120_D	0.506	0.78
277_I	281_A	0.506	0.78
57_P	78_I	0.505	0.78
35_N	191_P	0.504	0.78
224_F	277_I	0.502	0.78
67_A	98_V	0.500	0.77
249_E	259_Q	0.500	0.77
31_L	36_I	0.500	0.77

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	0.9281	100	0.27	Contact Map
4gc5A	2	0.976	100	0.276	Contact Map
4jxjA	1	0.839	100	0.296	Contact Map
3futA	1	0.911	100	0.314	Contact Map
3tqsA	1	0.8425	100	0.325	Contact Map
3gruA	1	0.8699	100	0.326	Contact Map
3uzuA	1	0.8767	100	0.33	Contact Map
1qyrA	1	0.863	100	0.332	Contact Map
3ftdA	1	0.8185	100	0.371	Contact Map
1zq9A	2	0.863	100	0.386	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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