RSMI - ECOLI - GREMLIN Contacts

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RSMI - Ribosomal RNA small subunit methyltransferase I

UniProt:	P67087	Sequences: MKQHQSADNSQGQLYIVPTPIGNLADITQRALEVLQAVDLIAAEDTRHTGLLLQHFGINARLFALHDHNEQQKAETLLAKLQEGQNIALVSDAGTPLINDPGYHLVRTCREAGIRVVPLPGPCAAITALSAAGLPSDRFCYEGFLPAKSKGRRDALKAIEAEPRTLIFYESTHRLLDSLEDIVAVLGESRYVVLARELTKTWETIHGAPVGELLAWVKEDENRRKGEMVLIVEGHKAQEEDLPADALRTLALLQAELPLKKAAALAAEIHGVKKNALYKYALEQQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12777
Length:	286 (269)
Sequences:	3931 (2677)
Seq/√Len:	163.2

ECOLI - RSMI
BACSU - RSMI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_T	90_V	4.526	1.00
25_A	33_E	3.983	1.00
80_K	85_Q	3.537	1.00
191_Y	233_E	3.211	1.00
82_Q	112_A	3.097	1.00
33_E	37_A	2.787	1.00
29_Q	32_L	2.784	1.00
18_P	119_L	2.737	1.00
188_E	211_G	2.646	1.00
152_R	181_D	2.632	1.00
192_V	213_L	2.542	1.00
192_V	210_V	2.457	1.00
110_R	207_G	2.452	1.00
131_A	205_I	2.258	1.00
27_I	32_L	2.185	1.00
50_G	54_Q	2.185	1.00
182_I	210_V	2.172	1.00
32_L	56_F	2.039	1.00
39_D	86_N	1.959	1.00
108_T	111_E	1.933	1.00
145_L	156_L	1.921	1.00
82_Q	114_I	1.889	1.00
196_R	204_T	1.863	1.00
145_L	155_A	1.859	1.00
146_P	155_A	1.858	1.00
124_A	169_Y	1.837	1.00
17_V	31_A	1.827	1.00
140_C	164_R	1.786	1.00
13_Q	117_V	1.767	1.00
18_P	95_T	1.745	1.00
13_Q	115_R	1.745	1.00
40_L	87_I	1.667	1.00
17_V	88_A	1.644	1.00
109_C	114_I	1.642	1.00
118_P	205_I	1.636	1.00
195_A	205_I	1.635	1.00
74_A	108_T	1.625	1.00
66_H	69_N	1.614	1.00
73_K	76_T	1.614	1.00
38_V	88_A	1.589	1.00
208_A	212_E	1.577	1.00
38_V	86_N	1.576	1.00
42_A	77_L	1.556	1.00
248_R	270_H	1.548	1.00
178_S	230_L	1.538	1.00
180_E	218_K	1.537	1.00
193_V	205_I	1.533	1.00
182_I	232_V	1.525	1.00
248_R	269_I	1.524	1.00
142_E	155_A	1.520	1.00
125_A	169_Y	1.520	1.00
258_P	261_K	1.508	1.00
79_A	83_E	1.499	1.00
40_L	80_K	1.495	1.00
16_I	106_V	1.475	1.00
142_E	164_R	1.472	1.00
95_T	130_S	1.467	1.00
252_L	269_I	1.460	1.00
208_A	213_L	1.451	1.00
108_T	112_A	1.449	1.00
168_F	232_V	1.446	1.00
118_P	131_A	1.431	1.00
81_L	114_I	1.431	1.00
42_A	87_I	1.431	1.00
138_R	142_E	1.425	1.00
153_R	181_D	1.424	1.00
43_A	62_L	1.417	1.00
272_V	277_L	1.405	1.00
39_D	85_Q	1.404	1.00
250_L	254_Q	1.404	1.00
118_P	130_S	1.403	1.00
263_A	267_A	1.402	1.00
17_V	34_V	1.399	1.00
99_N	141_Y	1.395	1.00
257_L	265_L	1.394	1.00
14_L	81_L	1.392	1.00
78_L	82_Q	1.386	1.00
140_C	162_E	1.379	1.00
170_E	174_R	1.368	1.00
153_R	157_K	1.362	1.00
123_C	126_I	1.357	1.00
259_L	263_A	1.353	1.00
63_F	73_K	1.351	1.00
206_H	213_L	1.312	1.00
70_E	104_H	1.298	1.00
65_L	74_A	1.297	1.00
42_A	63_F	1.295	1.00
27_I	56_F	1.293	1.00
117_V	203_E	1.292	1.00
259_L	281_A	1.290	1.00
150_K	154_D	1.287	1.00
157_K	160_E	1.284	1.00
190_R	234_G	1.268	1.00
155_A	158_A	1.267	1.00
64_A	73_K	1.256	1.00
32_L	36_Q	1.254	1.00
80_K	83_E	1.249	1.00
95_T	118_P	1.237	1.00
265_L	269_I	1.236	1.00
149_S	181_D	1.234	1.00
156_L	182_I	1.227	1.00
209_P	212_E	1.220	1.00
153_R	184_A	1.212	1.00
193_V	231_I	1.208	1.00
27_I	31_A	1.202	1.00
175_L	228_M	1.198	1.00
183_V	214_L	1.187	1.00
182_I	186_L	1.182	1.00
61_R	80_K	1.180	1.00
206_H	216_W	1.179	1.00
215_A	218_K	1.171	1.00
79_A	82_Q	1.156	1.00
183_V	211_G	1.153	1.00
103_Y	135_P	1.152	1.00
252_L	265_L	1.139	1.00
13_Q	81_L	1.131	1.00
75_E	108_T	1.130	1.00
183_V	188_E	1.126	1.00
125_A	167_I	1.124	1.00
194_L	217_V	1.122	1.00
158_A	163_P	1.119	1.00
187_G	210_V	1.111	1.00
107_R	191_Y	1.107	1.00
263_A	281_A	1.102	1.00
183_V	210_V	1.096	1.00
18_P	127_T	1.090	1.00
65_L	70_E	1.090	1.00
216_W	222_N	1.084	1.00
215_A	219_E	1.083	1.00
217_V	224_R	1.074	0.99
253_L	259_L	1.063	0.99
264_A	274_K	1.052	0.99
33_E	36_Q	1.051	0.99
15_Y	34_V	1.036	0.99
193_V	207_G	1.033	0.99
103_Y	107_R	1.031	0.99
24_L	55_H	1.031	0.99
214_L	218_K	1.026	0.99
180_E	214_L	1.025	0.99
40_L	63_F	1.024	0.99
41_I	53_L	1.021	0.99
194_L	228_M	1.018	0.99
196_R	228_M	1.014	0.99
15_Y	38_V	1.010	0.99
123_C	169_Y	1.007	0.99
13_Q	86_N	1.003	0.99
29_Q	36_Q	0.993	0.99
127_T	131_A	0.988	0.99
28_T	122_P	0.983	0.99
107_R	111_E	0.982	0.99
159_I	162_E	0.980	0.99
48_H	51_L	0.956	0.99
51_L	54_Q	0.947	0.99
266_A	277_L	0.945	0.99
175_L	217_V	0.945	0.99
29_Q	56_F	0.944	0.99
118_P	127_T	0.944	0.99
34_V	88_A	0.944	0.99
140_C	166_L	0.940	0.99
78_L	109_C	0.937	0.99
26_D	120_P	0.936	0.99
176_L	214_L	0.932	0.99
166_L	186_L	0.932	0.99
117_V	131_A	0.929	0.98
249_T	253_L	0.928	0.98
64_A	69_N	0.922	0.98
260_K	264_A	0.918	0.98
191_Y	209_P	0.915	0.98
176_L	180_E	0.911	0.98
262_A	266_A	0.911	0.98
76_T	80_K	0.910	0.98
153_R	185_V	0.907	0.98
206_H	217_V	0.901	0.98
149_S	153_R	0.901	0.98
70_E	74_A	0.900	0.98
34_V	119_L	0.898	0.98
162_E	166_L	0.893	0.98
194_L	213_L	0.893	0.98
270_H	277_L	0.879	0.98
40_L	85_Q	0.879	0.98
41_I	60_A	0.874	0.98
28_T	119_L	0.870	0.98
134_L	231_I	0.870	0.98
65_L	73_K	0.868	0.98
176_L	218_K	0.862	0.98
167_I	231_I	0.862	0.98
63_F	77_L	0.860	0.97
165_T	231_I	0.858	0.97
178_S	182_I	0.858	0.97
168_F	178_S	0.858	0.97
263_A	282_L	0.857	0.97
249_T	281_A	0.851	0.97
182_I	185_V	0.849	0.97
233_E	236_K	0.847	0.97
250_L	253_L	0.845	0.97
147_A	174_R	0.843	0.97
252_L	256_E	0.843	0.97
250_L	281_A	0.838	0.97
16_I	130_S	0.833	0.97
179_L	217_V	0.833	0.97
142_E	159_I	0.832	0.97
29_Q	33_E	0.832	0.97
119_L	127_T	0.829	0.97
97_L	103_Y	0.824	0.97
50_G	62_L	0.823	0.97
14_L	89_L	0.820	0.97
128_A	231_I	0.820	0.97
136_S	165_T	0.820	0.97
249_T	266_A	0.819	0.97
67_D	70_E	0.813	0.96
222_N	225_K	0.813	0.96
25_A	29_Q	0.810	0.96
224_R	228_M	0.807	0.96
212_E	215_A	0.806	0.96
252_L	257_L	0.806	0.96
77_L	87_I	0.802	0.96
51_L	55_H	0.801	0.96
175_L	230_L	0.800	0.96
248_R	252_L	0.799	0.96
97_L	106_V	0.799	0.96
74_A	78_L	0.797	0.96
103_Y	137_D	0.791	0.96
129_L	165_T	0.790	0.96
50_G	59_N	0.790	0.96
179_L	214_L	0.783	0.96
152_R	178_S	0.775	0.95
156_L	185_V	0.773	0.95
259_L	282_L	0.771	0.95
279_K	282_L	0.769	0.95
127_T	198_L	0.769	0.95
91_S	97_L	0.766	0.95
48_H	92_D	0.759	0.95
95_T	126_I	0.757	0.95
40_L	61_R	0.757	0.95
74_A	104_H	0.756	0.95
159_I	186_L	0.752	0.95
69_N	75_E	0.751	0.95
175_L	224_R	0.747	0.94
14_L	109_C	0.747	0.94
246_A	280_Y	0.745	0.94
54_Q	59_N	0.745	0.94
216_W	224_R	0.741	0.94
127_T	199_T	0.738	0.94
75_E	79_A	0.736	0.94
272_V	276_A	0.734	0.94
131_A	193_V	0.732	0.94
166_L	232_V	0.731	0.94
266_A	269_I	0.731	0.94
154_D	157_K	0.729	0.94
260_K	275_N	0.724	0.93
273_K	276_A	0.723	0.93
260_K	274_K	0.721	0.93
251_A	254_Q	0.719	0.93
173_H	225_K	0.716	0.93
49_T	62_L	0.714	0.93
210_V	214_L	0.713	0.93
78_L	112_A	0.711	0.93
135_P	165_T	0.708	0.93
18_P	131_A	0.707	0.93
36_Q	57_G	0.706	0.93
159_I	166_L	0.704	0.92
261_K	265_L	0.704	0.92
53_L	60_A	0.704	0.92
65_L	105_L	0.702	0.92
67_D	103_Y	0.702	0.92
175_L	194_L	0.696	0.92
25_A	37_A	0.696	0.92
263_A	273_K	0.695	0.92
120_P	127_T	0.692	0.92
18_P	122_P	0.692	0.92
11_Q	115_R	0.692	0.92
78_L	114_I	0.691	0.92
241_D	245_D	0.689	0.92
190_R	232_V	0.688	0.92
97_L	130_S	0.686	0.91
76_T	79_A	0.683	0.91
248_R	251_A	0.683	0.91
81_L	87_I	0.683	0.91
181_D	184_A	0.682	0.91
15_Y	86_N	0.676	0.91
161_A	235_H	0.673	0.91
194_L	216_W	0.671	0.90
204_T	222_N	0.669	0.90
160_E	185_V	0.669	0.90
89_L	105_L	0.668	0.90
106_V	110_R	0.663	0.90
25_A	56_F	0.662	0.90
242_L	245_D	0.662	0.90
217_V	228_M	0.662	0.90
178_S	181_D	0.661	0.90
15_Y	117_V	0.659	0.90
275_N	279_K	0.658	0.90
168_F	186_L	0.655	0.89
119_L	199_T	0.654	0.89
179_L	210_V	0.652	0.89
204_T	224_R	0.647	0.89
157_K	185_V	0.647	0.89
37_A	86_N	0.646	0.89
18_P	123_C	0.645	0.89
276_A	280_Y	0.645	0.89
67_D	104_H	0.642	0.88
131_A	195_A	0.640	0.88
266_A	270_H	0.639	0.88
128_A	195_A	0.637	0.88
195_A	231_I	0.634	0.88
136_S	167_I	0.633	0.88
268_E	275_N	0.632	0.88
160_E	186_L	0.632	0.88
63_F	80_K	0.631	0.88
56_F	60_A	0.629	0.87
177_D	181_D	0.629	0.87
251_A	255_A	0.629	0.87
276_A	279_K	0.625	0.87
255_A	265_L	0.623	0.87
142_E	166_L	0.622	0.87
263_A	277_L	0.621	0.87
43_A	49_T	0.620	0.87
134_L	165_T	0.620	0.87
176_L	224_R	0.619	0.87
175_L	216_W	0.618	0.87
126_I	130_S	0.617	0.86
34_V	37_A	0.616	0.86
17_V	41_I	0.615	0.86
129_L	136_S	0.612	0.86
147_A	151_G	0.607	0.86
138_R	165_T	0.599	0.85
148_K	151_G	0.599	0.85
249_T	252_L	0.596	0.85
71_Q	104_H	0.594	0.84
146_P	151_G	0.593	0.84
134_L	193_V	0.590	0.84
95_T	123_C	0.586	0.84
256_E	261_K	0.586	0.84
244_A	247_L	0.585	0.83
206_H	223_R	0.585	0.83
198_L	205_I	0.584	0.83
247_L	280_Y	0.584	0.83
67_D	97_L	0.580	0.83
242_L	246_A	0.580	0.83
39_D	60_A	0.577	0.83
217_V	223_R	0.577	0.83
259_L	275_N	0.577	0.83
110_R	133_G	0.576	0.82
175_L	196_R	0.576	0.82
97_L	136_S	0.573	0.82
195_A	198_L	0.561	0.81
173_H	228_M	0.560	0.81
156_L	186_L	0.560	0.81
50_G	53_L	0.560	0.81
18_P	199_T	0.552	0.80
188_E	209_P	0.550	0.80
128_A	229_V	0.547	0.79
107_R	110_R	0.546	0.79
243_P	246_A	0.545	0.79
236_K	241_D	0.544	0.79
138_R	164_R	0.544	0.79
142_E	162_E	0.543	0.79
15_Y	88_A	0.541	0.78
194_L	230_L	0.540	0.78
103_Y	136_S	0.540	0.78
249_T	269_I	0.538	0.78
95_T	127_T	0.538	0.78
190_R	233_E	0.538	0.78
125_A	139_F	0.537	0.78
141_Y	169_Y	0.537	0.78
104_H	108_T	0.536	0.78
12_G	81_L	0.536	0.78
194_L	206_H	0.535	0.78
243_P	247_L	0.533	0.77
210_V	232_V	0.533	0.77
162_E	234_G	0.532	0.77
119_L	131_A	0.532	0.77
163_P	237_A	0.531	0.77
151_G	154_D	0.530	0.77
69_N	73_K	0.529	0.77
17_V	119_L	0.528	0.77
219_E	222_N	0.526	0.76
46_T	64_A	0.525	0.76
181_D	185_V	0.525	0.76
180_E	184_A	0.524	0.76
126_I	169_Y	0.523	0.76
240_E	244_A	0.523	0.76
159_I	168_F	0.523	0.76
257_L	262_A	0.520	0.76
210_V	213_L	0.519	0.76
260_K	268_E	0.518	0.75
48_H	90_V	0.518	0.75
77_L	81_L	0.517	0.75
263_A	266_A	0.516	0.75
118_P	193_V	0.515	0.75
249_T	262_A	0.514	0.75
211_G	215_A	0.514	0.75
225_K	228_M	0.509	0.74
216_W	219_E	0.505	0.74
175_L	179_L	0.504	0.73
258_P	263_A	0.504	0.73
255_A	261_K	0.503	0.73
187_G	190_R	0.503	0.73
26_D	95_T	0.502	0.73
264_A	275_N	0.502	0.73
89_L	97_L	0.502	0.73
72_Q	75_E	0.501	0.73
186_L	210_V	0.501	0.73
246_A	250_L	0.500	0.73

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
3kwpA	2	0.7972	100	0.334	Contact Map
1wyzA	2	0.7517	100	0.594	Contact Map
1cbfA	2	0.8042	100	0.612	Contact Map
4e16A	2	0.7762	100	0.619	Contact Map
3ndcA	2	0.8112	100	0.63	Contact Map
1s4dA	4	0.8776	100	0.631	Contact Map
2yboA	2	0.8357	100	0.632	Contact Map
1pjqA	2	0.8392	100	0.638	Contact Map
1va0A	2	0.7692	100	0.642	Contact Map
1ve2A	2	0.7692	100	0.644	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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