RLMB - ECOLI - GREMLIN Contacts

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RLMB - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB

UniProt:	P63177	Sequences: MSEMIYGIHAVQALLERAPERFQEVFILKGREDKRLLPLIHALESQGVVIQLANRQYLDEKSDGAVHQGIIARVKPGRQYQENDLPDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVGTAGEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12483
Length:	243 (230)
Sequences:	8406 (5831)
Seq/√Len:	384.5

ECOLI - RLMB YFIF TRML TRMH
BACSU - YACO YSGA 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
195_M	227_V	4.085	1.00
173_G	210_C	3.501	1.00
99_I	192_A	3.250	1.00
204_R	208_E	2.881	1.00
229_V	232_G	2.878	1.00
174_T	234_C	2.753	1.00
23_Q	75_K	2.718	1.00
112_C	231_T	2.701	1.00
195_M	231_T	2.471	1.00
173_G	202_M	2.441	1.00
24_E	51_Q	2.354	1.00
237_E	240_R	2.348	1.00
162_R	209_H	2.230	1.00
175_A	207_R	2.097	1.00
98_L	112_C	2.069	1.00
165_Q	211_D	2.047	1.00
11_V	72_A	1.971	1.00
101_D	203_R	1.961	1.00
172_V	214_I	1.951	1.00
123_A	150_P	1.904	1.00
58_L	71_I	1.862	1.00
113_L	124_V	1.852	1.00
95_P	190_R	1.837	1.00
21_R	75_K	1.809	1.00
119_A	236_F	1.781	1.00
156_N	159_R	1.747	1.00
142_A	146_A	1.742	1.00
117_D	220_G	1.716	1.00
98_L	235_L	1.715	1.00
117_D	149_V	1.715	1.00
96_F	121_V	1.705	1.00
97_L	123_A	1.704	1.00
170_W	212_E	1.691	1.00
231_T	235_L	1.682	1.00
172_V	191_L	1.647	1.00
180_H	212_E	1.584	1.00
145_A	222_V	1.553	1.00
182_L	234_C	1.546	1.00
139_K	146_A	1.531	1.00
121_V	235_L	1.508	1.00
172_V	212_E	1.489	1.00
193_L	238_A	1.488	1.00
169_I	192_A	1.486	1.00
193_L	234_C	1.478	1.00
194_V	202_M	1.473	1.00
30_G	55_R	1.465	1.00
24_E	73_R	1.454	1.00
118_A	218_M	1.450	1.00
169_I	190_R	1.448	1.00
29_K	52_L	1.447	1.00
55_R	59_D	1.441	1.00
116_A	121_V	1.436	1.00
98_L	116_A	1.430	1.00
119_A	182_L	1.362	1.00
117_D	145_A	1.360	1.00
179_D	215_S	1.352	1.00
185_S	214_I	1.350	1.00
111_A	228_S	1.341	1.00
161_M	171_I	1.340	1.00
5_I	14_L	1.328	1.00
181_T	184_Q	1.326	1.00
176_G	215_S	1.309	1.00
53_A	57_Y	1.308	1.00
104_T	199_G	1.301	1.00
197_A	200_E	1.290	1.00
95_P	122_H	1.288	1.00
175_A	213_L	1.286	1.00
98_L	121_V	1.284	1.00
103_V	227_V	1.276	1.00
162_R	166_E	1.274	1.00
93_D	122_H	1.273	1.00
207_R	213_L	1.273	1.00
219_A	239_V	1.272	1.00
97_L	169_I	1.268	1.00
163_M	167_E	1.263	1.00
102_G	129_D	1.261	1.00
119_A	233_I	1.260	1.00
53_A	58_L	1.259	1.00
117_D	148_S	1.254	1.00
115_S	232_G	1.243	1.00
117_D	222_V	1.240	1.00
12_Q	16_E	1.238	1.00
25_V	72_A	1.236	1.00
194_V	206_T	1.235	1.00
170_W	211_D	1.227	1.00
81_Q	84_D	1.223	1.00
99_I	161_M	1.206	1.00
96_F	122_H	1.192	1.00
173_G	213_L	1.188	1.00
12_Q	38_P	1.186	1.00
22_F	72_A	1.184	1.00
158_A	209_H	1.174	1.00
195_M	230_A	1.170	1.00
97_L	125_I	1.160	1.00
171_I	192_A	1.156	1.00
181_T	215_S	1.154	1.00
164_L	192_A	1.152	1.00
96_F	238_A	1.146	1.00
57_Y	60_E	1.145	1.00
29_K	54_N	1.140	1.00
183_Y	240_R	1.139	1.00
98_L	195_M	1.139	1.00
187_M	238_A	1.138	1.00
125_I	160_T	1.135	1.00
119_A	239_V	1.132	1.00
116_A	124_V	1.105	1.00
154_V	160_T	1.099	1.00
180_H	184_Q	1.097	1.00
13_A	16_E	1.092	1.00
113_L	151_L	1.091	1.00
25_V	43_L	1.087	1.00
123_A	152_I	1.072	1.00
99_I	157_L	1.070	1.00
126_V	151_L	1.062	1.00
203_R	206_T	1.057	1.00
11_V	70_I	1.046	1.00
109_L	131_S	1.042	1.00
115_S	229_V	1.037	1.00
109_L	126_V	1.031	1.00
20_E	77_G	1.030	1.00
125_I	154_V	1.020	1.00
161_M	206_T	1.018	1.00
16_E	42_A	1.017	1.00
56_Q	59_D	1.006	1.00
13_A	148_S	0.998	1.00
62_S	71_I	0.992	1.00
28_L	55_R	0.991	1.00
22_F	74_V	0.990	1.00
158_A	162_R	0.988	1.00
115_S	235_L	0.987	1.00
180_H	185_S	0.979	1.00
113_L	138_A	0.964	1.00
194_V	210_C	0.957	1.00
162_R	165_Q	0.954	1.00
187_M	191_L	0.948	1.00
210_C	213_L	0.940	1.00
158_A	205_L	0.936	1.00
96_F	235_L	0.933	1.00
214_I	234_C	0.930	1.00
159_R	162_R	0.930	1.00
27_I	52_L	0.928	1.00
100_L	195_M	0.924	1.00
126_V	130_R	0.921	1.00
148_S	221_S	0.921	1.00
107_H	141_V	0.916	1.00
157_L	206_T	0.916	1.00
100_L	112_C	0.913	1.00
27_I	70_I	0.912	1.00
28_L	31_R	0.907	1.00
117_D	221_S	0.905	1.00
174_T	195_M	0.903	1.00
5_I	10_A	0.902	1.00
191_L	238_A	0.900	1.00
5_I	74_V	0.895	1.00
128_K	155_T	0.892	1.00
182_L	187_M	0.891	1.00
86_P	167_E	0.888	1.00
12_Q	42_A	0.882	1.00
120_G	219_A	0.879	1.00
115_S	119_A	0.872	1.00
54_N	57_Y	0.871	1.00
101_D	206_T	0.871	1.00
170_W	189_G	0.870	1.00
163_M	166_E	0.868	1.00
63_D	136_A	0.861	1.00
94_Q	122_H	0.852	1.00
77_G	134_L	0.851	1.00
118_A	222_V	0.845	1.00
173_G	207_R	0.840	1.00
177_E	207_R	0.839	1.00
97_L	164_L	0.838	1.00
4_M	71_I	0.836	1.00
96_F	191_L	0.836	1.00
177_E	213_L	0.835	1.00
100_L	109_L	0.834	1.00
178_A	215_S	0.831	1.00
27_I	50_I	0.831	1.00
99_I	164_L	0.830	1.00
164_L	169_I	0.829	1.00
101_D	202_M	0.825	1.00
24_E	49_V	0.818	1.00
159_R	163_M	0.810	1.00
99_I	194_V	0.807	1.00
82_E	152_I	0.807	1.00
107_H	111_A	0.804	1.00
102_G	200_E	0.800	1.00
102_G	127_P	0.799	1.00
20_E	147_E	0.798	1.00
95_P	169_I	0.794	1.00
205_L	208_E	0.793	1.00
26_F	61_K	0.791	1.00
83_N	163_M	0.787	1.00
17_R	148_S	0.785	1.00
38_P	42_A	0.783	1.00
172_V	185_S	0.780	1.00
82_E	85_L	0.777	1.00
42_A	45_S	0.777	1.00
131_S	135_N	0.776	1.00
205_L	209_H	0.774	1.00
165_Q	209_H	0.771	1.00
4_M	73_R	0.761	1.00
174_T	202_M	0.759	1.00
119_A	183_Y	0.759	1.00
28_L	58_L	0.757	1.00
14_L	74_V	0.756	1.00
14_L	147_E	0.754	1.00
170_W	191_L	0.754	1.00
161_M	192_A	0.754	1.00
183_Y	237_E	0.753	1.00
161_M	209_H	0.752	1.00
6_Y	64_G	0.751	1.00
139_K	147_E	0.748	1.00
103_V	109_L	0.747	1.00
102_G	197_A	0.742	1.00
102_G	203_R	0.742	1.00
155_T	159_R	0.736	1.00
9_H	143_C	0.735	1.00
26_F	53_A	0.731	1.00
158_A	206_T	0.729	1.00
94_Q	189_G	0.728	1.00
113_L	146_A	0.726	1.00
165_Q	171_I	0.725	1.00
185_S	212_E	0.723	1.00
23_Q	73_R	0.718	1.00
202_M	210_C	0.718	1.00
53_A	71_I	0.717	1.00
177_E	215_S	0.714	1.00
124_V	149_V	0.711	1.00
171_I	194_V	0.709	1.00
204_R	207_R	0.708	1.00
175_A	215_S	0.706	1.00
100_L	103_V	0.705	1.00
112_C	227_V	0.703	1.00
179_D	212_E	0.702	1.00
103_V	112_C	0.700	1.00
175_A	178_A	0.700	1.00
42_A	46_Q	0.699	1.00
160_T	164_L	0.696	0.99
119_A	235_L	0.696	0.99
85_L	123_A	0.694	0.99
183_Y	217_P	0.693	0.99
109_L	138_A	0.692	0.99
178_A	213_L	0.683	0.99
195_M	234_C	0.683	0.99
61_K	71_I	0.682	0.99
183_Y	239_V	0.675	0.99
174_T	193_L	0.672	0.99
43_L	48_V	0.668	0.99
128_K	156_N	0.666	0.99
104_T	197_A	0.663	0.99
82_E	86_P	0.657	0.99
26_F	73_R	0.654	0.99
107_H	137_T	0.651	0.99
176_G	223_S	0.650	0.99
111_A	229_V	0.648	0.99
17_R	20_E	0.647	0.99
23_Q	49_V	0.646	0.99
37_L	41_H	0.645	0.99
99_I	125_I	0.642	0.99
148_S	222_V	0.641	0.99
58_L	68_Q	0.640	0.99
34_K	37_L	0.638	0.99
27_I	32_E	0.638	0.99
58_L	62_S	0.637	0.99
173_G	194_V	0.636	0.99
216_I	236_F	0.635	0.99
31_R	36_L	0.629	0.99
168_N	190_R	0.629	0.99
119_A	216_I	0.627	0.99
35_R	38_P	0.625	0.99
41_H	44_E	0.623	0.99
116_A	235_L	0.623	0.99
115_S	231_T	0.622	0.99
82_E	125_I	0.620	0.99
126_V	133_Q	0.619	0.99
40_I	44_E	0.619	0.99
118_A	223_S	0.618	0.99
176_G	179_D	0.612	0.99
32_E	52_L	0.611	0.99
113_L	145_A	0.611	0.99
183_Y	236_F	0.607	0.99
59_D	65_A	0.607	0.99
145_A	148_S	0.607	0.99
92_L	122_H	0.606	0.99
38_P	41_H	0.604	0.99
125_I	164_L	0.600	0.98
122_H	169_I	0.598	0.98
187_M	237_E	0.598	0.98
5_I	22_F	0.598	0.98
14_L	18_A	0.597	0.98
6_Y	140_K	0.594	0.98
59_D	67_H	0.593	0.98
97_L	192_A	0.592	0.98
80_Y	152_I	0.589	0.98
107_H	228_S	0.587	0.98
132_A	135_N	0.587	0.98
160_T	163_M	0.586	0.98
9_H	12_Q	0.578	0.98
104_T	200_E	0.577	0.98
6_Y	136_A	0.574	0.98
10_A	139_K	0.571	0.98
58_L	67_H	0.570	0.98
228_S	231_T	0.569	0.98
119_A	218_M	0.567	0.98
8_I	35_R	0.567	0.98
99_I	127_P	0.567	0.98
26_F	51_Q	0.566	0.98
8_I	12_Q	0.563	0.98
9_H	13_A	0.562	0.98
85_L	97_L	0.562	0.98
82_E	160_T	0.554	0.97
41_H	45_S	0.550	0.97
129_D	203_R	0.549	0.97
161_M	165_Q	0.547	0.97
16_E	221_S	0.542	0.97
56_Q	60_E	0.541	0.97
53_A	61_K	0.540	0.97
117_D	219_A	0.538	0.97
68_Q	105_D	0.537	0.97
127_P	157_L	0.534	0.97
202_M	206_T	0.534	0.97
5_I	139_K	0.530	0.97
22_F	75_K	0.529	0.97
86_P	163_M	0.527	0.97
85_L	152_I	0.527	0.97
118_A	236_F	0.525	0.97
121_V	238_A	0.523	0.96
127_P	206_T	0.522	0.96
216_I	233_I	0.521	0.96
197_A	223_S	0.521	0.96
80_Y	84_D	0.520	0.96
8_I	36_L	0.519	0.96
18_A	21_R	0.518	0.96
139_K	142_A	0.515	0.96
206_T	209_H	0.514	0.96
175_A	202_M	0.511	0.96
170_W	188_T	0.510	0.96
154_V	159_R	0.508	0.96
28_L	52_L	0.507	0.96
11_V	25_V	0.505	0.96
118_A	225_L	0.504	0.96
28_L	32_E	0.504	0.96
183_Y	233_I	0.502	0.96
94_Q	190_R	0.501	0.95
39_L	43_L	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
1gz0A	2	0.9877	100	0.127	Contact Map
3nk6A	2	0.9424	100	0.158	Contact Map
1ipaA	1	0.9465	100	0.161	Contact Map
1x7oA	2	0.963	100	0.179	Contact Map
2i6dA	2	0.9136	100	0.198	Contact Map
4kgnA	2	0.6214	100	0.371	Contact Map
1v2xA	2	0.6914	100	0.382	Contact Map
1zjrA	2	0.6872	100	0.383	Contact Map
3n4jA	2	0.6173	100	0.385	Contact Map
3l8uA	2	0.5802	100	0.39	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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