RSME - BACSU - GREMLIN Contacts

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RSME - Ribosomal RNA small subunit methyltransferase E

UniProt:	P54461	Sequences: MQRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLRGDQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	256 (231)
Sequences:	4647 (3549)
Seq/√Len:	233.5

ECOLI - RSME
BACSU - RSME

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
107_A	152_M	3.470	1.00
136_A	151_V	3.452	1.00
54_E	68_I	3.270	1.00
114_A	210_T	3.034	1.00
114_A	212_A	2.807	1.00
54_E	66_L	2.802	1.00
82_Y	109_I	2.780	1.00
56_Q	66_L	2.698	1.00
97_I	136_A	2.517	1.00
170_C	222_G	2.498	1.00
53_C	65_C	2.497	1.00
52_K	69_E	2.469	1.00
80_K	198_S	2.457	1.00
107_A	150_R	2.423	1.00
100_G	108_F	2.403	1.00
49_F	70_W	2.357	1.00
84_A	160_L	2.349	1.00
172_V	214_V	2.316	1.00
84_A	200_L	2.259	1.00
88_P	234_T	2.236	1.00
40_Q	52_K	2.192	1.00
27_H	31_N	2.179	1.00
156_S	159_Q	2.049	1.00
40_Q	54_E	2.040	1.00
115_R	210_T	2.029	1.00
215_E	219_E	2.004	1.00
201_I	241_A	1.980	1.00
18_T	64_S	1.945	1.00
174_Y	214_V	1.927	1.00
57_S	64_S	1.914	1.00
86_G	113_A	1.861	1.00
158_Q	216_R	1.826	1.00
110_P	153_D	1.807	1.00
109_I	152_M	1.766	1.00
25_E	141_E	1.706	1.00
157_F	217_L	1.699	1.00
26_V	63_V	1.663	1.00
85_S	238_P	1.638	1.00
18_T	66_L	1.616	1.00
82_Y	107_A	1.612	1.00
83_I	100_G	1.598	1.00
94_E	131_R	1.585	1.00
80_K	107_A	1.582	1.00
80_K	106_H	1.581	1.00
76_E	147_E	1.563	1.00
113_A	116_S	1.558	1.00
88_P	96_I	1.558	1.00
218_T	224_T	1.537	1.00
81_V	242_L	1.522	1.00
20_S	64_S	1.504	1.00
129_R	133_T	1.479	1.00
41_I	65_C	1.469	1.00
95_W	239_L	1.456	1.00
20_S	62_K	1.448	1.00
172_V	217_L	1.441	1.00
211_E	215_E	1.423	1.00
168_D	198_S	1.417	1.00
35_M	39_D	1.398	1.00
97_I	132_W	1.391	1.00
244_A	247_Y	1.385	1.00
95_W	99_K	1.378	1.00
50_E	146_N	1.371	1.00
42_I	50_E	1.344	1.00
112_Q	154_V	1.340	1.00
105_A	108_F	1.332	1.00
29_I	35_M	1.329	1.00
93_L	110_P	1.325	1.00
202_V	222_G	1.323	1.00
92_K	96_I	1.312	1.00
84_A	111_F	1.292	1.00
35_M	55_L	1.289	1.00
111_F	160_L	1.285	1.00
131_R	135_I	1.283	1.00
40_Q	68_I	1.260	1.00
215_E	218_T	1.255	1.00
55_L	63_V	1.253	1.00
30_V	63_V	1.250	1.00
83_I	105_A	1.250	1.00
140_A	148_V	1.232	1.00
93_L	132_W	1.231	1.00
29_I	41_I	1.231	1.00
55_L	65_C	1.227	1.00
240_Y	243_S	1.198	1.00
169_K	223_V	1.187	1.00
85_S	96_I	1.179	1.00
172_V	209_L	1.178	1.00
168_D	200_L	1.176	1.00
53_C	67_V	1.172	1.00
171_V	225_C	1.164	1.00
103_L	240_Y	1.163	1.00
23_G	26_V	1.157	1.00
95_W	98_Q	1.146	1.00
89_K	117_V	1.145	1.00
18_T	56_Q	1.144	1.00
98_Q	102_E	1.144	1.00
24_E	134_K	1.139	1.00
202_V	217_L	1.139	1.00
55_L	58_V	1.118	1.00
45_S	48_G	1.108	1.00
161_L	216_R	1.100	1.00
59_S	62_K	1.099	1.00
29_I	63_V	1.095	1.00
52_K	68_I	1.094	1.00
126_K	130_E	1.083	1.00
26_V	30_V	1.082	1.00
77_L	246_S	1.076	1.00
38_G	54_E	1.076	1.00
216_R	220_Q	1.063	1.00
100_G	242_L	1.062	1.00
98_Q	135_I	1.062	1.00
76_E	145_R	1.059	1.00
85_S	234_T	1.056	1.00
7_E	11_Q	1.045	1.00
157_F	161_L	1.042	1.00
52_K	71_T	1.035	1.00
212_A	215_E	1.032	1.00
102_E	236_T	1.030	1.00
105_A	242_L	1.030	1.00
167_F	200_L	1.030	1.00
202_V	209_L	1.012	1.00
134_K	138_E	1.002	1.00
169_K	199_L	0.997	1.00
99_K	235_E	0.985	1.00
85_S	203_F	0.978	1.00
158_Q	212_A	0.968	1.00
216_R	219_E	0.960	1.00
83_I	96_I	0.956	1.00
51_A	70_W	0.949	1.00
27_H	32_V	0.946	1.00
164_M	170_C	0.945	1.00
170_C	200_L	0.941	1.00
4_Y	33_M	0.940	1.00
44_C	50_E	0.934	1.00
37_E	57_S	0.930	1.00
108_F	149_P	0.923	1.00
17_P	66_L	0.914	1.00
173_A	241_A	0.907	1.00
101_T	149_P	0.906	1.00
30_V	58_V	0.904	1.00
155_H	163_R	0.903	1.00
159_Q	162_Q	0.902	1.00
87_L	112_Q	0.899	0.99
25_E	137_K	0.896	0.99
99_K	102_E	0.893	0.99
98_Q	138_E	0.893	0.99
95_W	235_E	0.892	0.99
160_L	200_L	0.887	0.99
26_V	58_V	0.886	0.99
175_E	231_I	0.886	0.99
44_C	146_N	0.881	0.99
103_L	243_S	0.880	0.99
4_Y	29_I	0.879	0.99
240_Y	246_S	0.871	0.99
97_I	108_F	0.871	0.99
152_M	163_R	0.871	0.99
199_L	245_I	0.870	0.99
92_K	98_Q	0.868	0.99
3_R	42_I	0.866	0.99
203_F	238_P	0.866	0.99
162_Q	165_Q	0.864	0.99
92_K	235_E	0.860	0.99
75_R	146_N	0.858	0.99
14_E	17_P	0.855	0.99
21_I	29_I	0.853	0.99
155_H	159_Q	0.853	0.99
240_Y	244_A	0.852	0.99
129_R	151_V	0.850	0.99
19_F	65_C	0.846	0.99
50_E	73_E	0.837	0.99
167_F	198_S	0.828	0.99
133_T	150_R	0.826	0.99
36_N	39_D	0.826	0.99
28_H	141_E	0.823	0.99
203_F	234_T	0.823	0.99
22_T	26_V	0.821	0.99
43_C	65_C	0.816	0.99
42_I	52_K	0.814	0.99
155_H	160_L	0.808	0.99
84_A	109_I	0.808	0.99
45_S	49_F	0.806	0.99
99_K	239_L	0.806	0.99
160_L	202_V	0.801	0.99
49_F	72_N	0.794	0.99
158_Q	162_Q	0.793	0.99
76_E	230_R	0.782	0.99
41_I	53_C	0.773	0.98
43_C	53_C	0.765	0.98
21_I	26_V	0.762	0.98
165_Q	168_D	0.757	0.98
22_T	25_E	0.756	0.98
4_Y	28_H	0.756	0.98
175_E	208_G	0.754	0.98
82_Y	200_L	0.750	0.98
73_E	146_N	0.750	0.98
101_T	136_A	0.745	0.98
169_K	197_S	0.742	0.98
103_L	236_T	0.741	0.98
88_P	93_L	0.736	0.98
137_K	141_E	0.735	0.98
168_D	197_S	0.733	0.98
109_I	155_H	0.733	0.98
113_A	209_L	0.731	0.98
174_Y	224_T	0.731	0.98
209_L	214_V	0.728	0.98
94_E	135_I	0.727	0.98
133_T	137_K	0.723	0.98
177_S	180_Q	0.720	0.98
97_I	151_V	0.717	0.98
140_A	149_P	0.715	0.97
4_Y	25_E	0.714	0.97
85_S	108_F	0.710	0.97
56_Q	64_S	0.707	0.97
50_E	71_T	0.705	0.97
93_L	97_I	0.702	0.97
142_Q	233_R	0.702	0.97
110_P	154_V	0.699	0.97
30_V	55_L	0.693	0.97
100_G	105_A	0.691	0.97
110_P	155_H	0.689	0.97
50_E	75_R	0.681	0.97
111_F	202_V	0.677	0.96
160_L	217_L	0.677	0.96
4_Y	43_C	0.672	0.96
85_S	93_L	0.669	0.96
176_E	211_E	0.668	0.96
145_R	230_R	0.665	0.96
6_I	43_C	0.661	0.96
3_R	50_E	0.660	0.96
7_E	133_T	0.660	0.96
4_Y	141_E	0.658	0.96
51_A	67_V	0.658	0.96
194_P	197_S	0.656	0.96
86_G	209_L	0.653	0.96
128_K	135_I	0.645	0.95
58_V	63_V	0.641	0.95
126_K	153_D	0.640	0.95
90_G	118_V	0.636	0.95
126_K	129_R	0.633	0.95
42_I	71_T	0.631	0.95
29_I	55_L	0.631	0.95
83_I	242_L	0.630	0.95
77_L	106_H	0.628	0.95
200_L	222_G	0.624	0.94
26_V	29_I	0.621	0.94
19_F	43_C	0.620	0.94
135_I	138_E	0.620	0.94
53_C	68_I	0.619	0.94
82_Y	152_M	0.618	0.94
125_A	129_R	0.617	0.94
3_R	44_C	0.617	0.94
84_A	202_V	0.616	0.94
92_K	95_W	0.614	0.94
115_R	207_G	0.613	0.94
112_Q	125_A	0.612	0.94
161_L	220_Q	0.610	0.94
176_E	214_V	0.610	0.94
37_E	58_V	0.610	0.94
161_L	164_M	0.609	0.94
160_L	164_M	0.608	0.94
57_S	62_K	0.607	0.94
127_K	132_W	0.605	0.94
42_I	144_Y	0.603	0.93
88_P	92_K	0.603	0.93
100_G	239_L	0.603	0.93
99_K	236_T	0.602	0.93
139_A	143_S	0.600	0.93
162_Q	220_Q	0.598	0.93
169_K	196_G	0.593	0.93
232_L	237_A	0.591	0.93
86_G	116_S	0.589	0.93
159_Q	163_R	0.588	0.93
161_L	217_L	0.586	0.92
103_L	239_L	0.584	0.92
88_P	118_V	0.583	0.92
87_L	110_P	0.582	0.92
174_Y	211_E	0.578	0.92
38_G	56_Q	0.578	0.92
133_T	151_V	0.577	0.92
234_T	238_P	0.575	0.92
209_L	213_E	0.574	0.92
209_L	217_L	0.571	0.91
203_F	241_A	0.569	0.91
173_A	225_C	0.568	0.91
174_Y	226_G	0.568	0.91
143_S	146_N	0.567	0.91
109_I	160_L	0.565	0.91
102_E	139_A	0.564	0.91
27_H	30_V	0.563	0.91
144_Y	176_E	0.563	0.91
3_R	144_Y	0.560	0.91
116_S	205_P	0.559	0.91
217_L	222_G	0.558	0.91
112_Q	156_S	0.557	0.90
172_V	224_T	0.557	0.90
98_Q	236_T	0.555	0.90
245_I	248_Q	0.555	0.90
82_Y	106_H	0.555	0.90
125_A	154_V	0.554	0.90
132_W	154_V	0.552	0.90
242_L	246_S	0.550	0.90
101_T	139_A	0.550	0.90
164_M	222_G	0.548	0.90
163_R	166_D	0.547	0.90
133_T	148_V	0.546	0.90
25_E	43_C	0.544	0.89
21_I	65_C	0.544	0.89
140_A	145_R	0.543	0.89
13_I	45_S	0.543	0.89
81_V	245_I	0.543	0.89
193_L	196_G	0.542	0.89
107_A	163_R	0.539	0.89
110_P	132_W	0.539	0.89
119_K	128_K	0.537	0.89
92_K	99_K	0.536	0.89
129_R	136_A	0.536	0.89
59_S	64_S	0.534	0.89
130_E	134_K	0.533	0.88
83_I	203_F	0.532	0.88
244_A	248_Q	0.532	0.88
25_E	28_H	0.530	0.88
82_Y	167_F	0.529	0.88
96_I	100_G	0.529	0.88
74_N	146_N	0.528	0.88
21_I	63_V	0.526	0.88
131_R	138_E	0.524	0.88
28_H	32_V	0.523	0.88
89_K	116_S	0.522	0.87
112_Q	116_S	0.522	0.87
101_T	138_E	0.522	0.87
81_V	199_L	0.522	0.87
129_R	153_D	0.521	0.87
12_Q	47_D	0.518	0.87
111_F	209_L	0.517	0.87
13_I	51_A	0.516	0.87
132_W	136_A	0.515	0.87
179_K	223_V	0.515	0.87
69_E	219_E	0.513	0.87
92_K	234_T	0.512	0.86
87_L	154_V	0.512	0.86
173_A	226_G	0.507	0.86
15_E	68_I	0.506	0.86
170_C	202_V	0.504	0.86
95_W	234_T	0.503	0.85
180_Q	186_F	0.502	0.85
26_V	62_K	0.500	0.85
33_M	231_I	0.500	0.85

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
1vhkA	3	0.9531	100	0.063	Contact Map
1vhyA	2	0.9492	100	0.081	Contact Map
4e8bA	2	0.9453	100	0.087	Contact Map
4l69A	2	0.9336	100	0.094	Contact Map
4j3cA	2	0.9219	100	0.105	Contact Map
3kw2A	2	0.9258	100	0.121	Contact Map
2egvA	2	0.8867	100	0.128	Contact Map
1v6zA	2	0.8828	100	0.134	Contact Map
1z85A	2	0.8438	100	0.161	Contact Map
2qmmA	2	0.7266	99.9	0.677	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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