RLMA - ECOLI - GREMLIN Contacts

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RLMA - 23S rRNA (guanine(745)-N(1))-methyltransferase

UniProt:	P36999	Sequences: MSFSCPLCHQPLSREKNSYICPQRHQFDMAKEGYVNLLPVQHKRSRDPGDSAEMMQARRAFLDAGHYQPLRDAIVAQLRERLDDKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSMDAIIRIYAPCKAEELARVVKPGGWVITATPGPRHLMELKGLIYNEVHLHAPHAEQLEGFTLQQSAELCYPMRLRGDEAVALLQMTPFAWRAKPEVWQTLAAKEVFDCQTDFNIHLWQRSY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12207
Length:	269 (258)
Sequences:	1580 (1257)
Seq/√Len:	78.2

ECOLI - RLMA
BACSU - YXJB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_A	229_A	6.041	1.00
150_D	169_K	4.507	1.00
90_L	149_M	4.147	1.00
186_E	257_Q	4.128	1.00
163_E	166_R	3.827	1.00
142_L	167_V	3.806	1.00
94_C	114_G	3.683	1.00
144_F	149_M	3.061	1.00
19_Y	35_V	3.043	1.00
92_I	164_L	2.979	1.00
223_R	226_E	2.753	1.00
175_I	262_I	2.672	1.00
70_L	260_F	2.671	1.00
18_S	26_Q	2.546	1.00
175_I	264_L	2.515	1.00
221_R	255_D	2.491	1.00
92_I	139_S	2.441	1.00
182_R	217_C	2.381	1.00
73_A	214_A	2.330	1.00
168_V	172_G	2.169	1.00
69_P	218_Y	2.134	1.00
219_P	255_D	2.121	1.00
142_L	163_E	2.117	1.00
90_L	167_V	2.064	1.00
152_I	164_L	2.050	1.00
215_E	259_D	1.974	1.00
3_F	135_C	1.970	1.00
66_H	226_E	1.927	1.00
218_Y	258_T	1.923	1.00
32_E	123_K	1.895	1.00
146_D	163_E	1.889	1.00
90_L	144_F	1.866	1.00
103_F	153_I	1.814	1.00
68_Q	72_D	1.809	1.00
100_T	112_T	1.796	1.00
73_A	77_Q	1.766	1.00
20_I	26_Q	1.747	1.00
164_L	168_V	1.745	1.00
101_H	129_Y	1.737	1.00
78_L	151_A	1.729	1.00
122_I	136_V	1.726	1.00
7_L	39_P	1.717	1.00
103_F	107_L	1.709	1.00
164_L	174_V	1.693	1.00
182_R	257_Q	1.665	1.00
64_A	226_E	1.652	1.00
173_W	264_L	1.633	1.00
87_T	150_D	1.625	1.00
146_D	166_R	1.594	1.00
115_L	137_A	1.585	1.00
25_H	28_D	1.561	0.99
45_S	48_P	1.551	0.99
29_M	35_V	1.550	0.99
165_A	208_F	1.542	0.99
220_M	258_T	1.524	0.99
54_M	156_Y	1.524	0.99
71_R	102_A	1.520	0.99
10_Q	23_Q	1.515	0.99
14_R	29_M	1.500	0.99
140_H	160_K	1.495	0.99
55_M	121_A	1.481	0.99
88_A	149_M	1.466	0.99
180_G	261_N	1.444	0.99
226_E	229_A	1.433	0.99
94_C	125_A	1.422	0.99
63_D	128_R	1.420	0.99
163_E	167_V	1.393	0.99
10_Q	22_P	1.364	0.99
122_I	125_A	1.354	0.98
61_F	66_H	1.348	0.98
81_R	173_W	1.338	0.98
149_M	167_V	1.328	0.98
180_G	259_D	1.320	0.98
125_A	134_F	1.316	0.98
73_A	76_A	1.307	0.98
149_M	152_I	1.295	0.98
145_S	148_S	1.285	0.98
210_L	263_H	1.280	0.98
186_E	256_C	1.272	0.98
70_L	177_A	1.260	0.98
4_S	145_S	1.257	0.98
241_K	245_W	1.255	0.97
113_F	149_M	1.255	0.97
30_A	34_Y	1.243	0.97
80_E	212_Q	1.237	0.97
54_M	183_H	1.237	0.97
71_R	98_Y	1.214	0.97
184_L	230_L	1.186	0.96
156_Y	183_H	1.184	0.96
246_Q	250_A	1.161	0.96
78_L	175_I	1.144	0.96
99_Y	183_H	1.142	0.96
19_Y	29_M	1.137	0.95
135_C	144_F	1.134	0.95
20_I	24_R	1.130	0.95
66_H	222_L	1.125	0.95
102_A	105_D	1.120	0.95
178_T	263_H	1.114	0.95
154_R	164_L	1.109	0.95
152_I	168_V	1.104	0.95
213_S	263_H	1.104	0.95
217_C	259_D	1.102	0.95
54_M	118_S	1.087	0.94
5_C	8_C	1.070	0.94
74_I	175_I	1.063	0.94
217_C	258_T	1.059	0.93
143_P	163_E	1.051	0.93
142_L	166_R	1.050	0.93
101_H	128_R	1.050	0.93
61_F	67_Y	1.049	0.93
93_G	157_A	1.028	0.92
197_L	200_P	1.011	0.92
13_S	16_K	1.011	0.92
50_D	55_M	1.010	0.92
251_K	254_F	1.009	0.92
168_V	174_V	1.007	0.92
62_L	98_Y	0.993	0.91
158_P	179_P	0.988	0.91
68_Q	98_Y	0.983	0.91
243_E	247_T	0.983	0.91
15_E	20_I	0.978	0.90
231_L	245_W	0.978	0.90
188_K	192_Y	0.977	0.90
27_F	30_A	0.977	0.90
14_R	17_N	0.967	0.90
182_R	185_M	0.962	0.90
13_S	22_P	0.961	0.90
104_A	112_T	0.955	0.89
113_F	144_F	0.953	0.89
231_L	240_A	0.936	0.88
30_A	123_K	0.934	0.88
88_A	169_K	0.926	0.88
71_R	75_V	0.916	0.87
256_C	259_D	0.916	0.87
4_S	11_P	0.905	0.87
76_A	106_A	0.901	0.86
202_A	205_L	0.900	0.86
18_S	35_V	0.899	0.86
242_P	246_Q	0.898	0.86
104_A	131_Q	0.895	0.86
155_I	179_P	0.895	0.86
11_P	14_R	0.890	0.86
113_F	135_C	0.887	0.85
225_D	228_V	0.886	0.85
213_S	261_N	0.879	0.85
242_P	245_W	0.879	0.85
87_T	110_I	0.873	0.85
91_D	115_L	0.865	0.84
137_A	143_P	0.855	0.83
54_M	58_R	0.854	0.83
36_N	136_V	0.851	0.83
182_R	186_E	0.850	0.83
99_Y	156_Y	0.845	0.83
147_T	169_K	0.842	0.82
129_Y	134_F	0.839	0.82
41_Q	46_R	0.838	0.82
94_C	134_F	0.837	0.82
145_S	175_I	0.835	0.82
27_F	37_L	0.832	0.82
14_R	18_S	0.831	0.82
67_Y	99_Y	0.829	0.81
74_I	155_I	0.828	0.81
100_T	114_G	0.825	0.81
147_T	170_P	0.823	0.81
3_F	144_F	0.818	0.80
117_V	136_V	0.815	0.80
196_H	199_A	0.809	0.80
88_A	150_D	0.808	0.80
143_P	166_R	0.807	0.80
10_Q	15_E	0.805	0.79
40_V	48_P	0.804	0.79
88_A	111_T	0.803	0.79
7_L	40_V	0.802	0.79
62_L	156_Y	0.800	0.79
91_D	94_C	0.796	0.79
17_N	29_M	0.796	0.79
18_S	29_M	0.795	0.79
73_A	262_I	0.793	0.78
112_T	129_Y	0.789	0.78
26_Q	29_M	0.786	0.78
258_T	263_H	0.786	0.78
122_I	134_F	0.782	0.77
58_R	118_S	0.780	0.77
86_A	150_D	0.779	0.77
169_K	247_T	0.779	0.77
11_P	145_S	0.778	0.77
17_N	31_K	0.776	0.77
179_P	233_M	0.776	0.77
182_R	259_D	0.774	0.77
100_T	132_V	0.772	0.77
182_R	197_L	0.767	0.76
13_S	255_D	0.766	0.76
139_S	154_R	0.766	0.76
72_D	76_A	0.765	0.76
100_T	153_I	0.761	0.75
28_D	34_Y	0.761	0.75
8_C	157_A	0.760	0.75
18_S	223_R	0.758	0.75
13_S	76_A	0.757	0.75
14_R	35_V	0.754	0.75
183_H	235_P	0.753	0.75
69_P	216_L	0.753	0.75
93_G	154_R	0.753	0.75
158_P	163_E	0.752	0.75
62_L	99_Y	0.749	0.74
54_M	187_L	0.748	0.74
3_F	133_T	0.748	0.74
116_D	156_Y	0.744	0.74
137_A	142_L	0.743	0.74
254_F	257_Q	0.743	0.74
58_R	67_Y	0.742	0.74
3_F	12_L	0.737	0.73
220_M	256_C	0.733	0.73
91_D	117_V	0.725	0.72
4_S	9_H	0.723	0.72
119_K	136_V	0.722	0.72
58_R	156_Y	0.719	0.71
112_T	132_V	0.715	0.71
165_A	171_G	0.715	0.71
8_C	158_P	0.715	0.71
159_C	176_T	0.712	0.71
61_F	222_L	0.711	0.70
78_L	122_I	0.710	0.70
236_F	256_C	0.710	0.70
60_A	68_Q	0.709	0.70
27_F	126_A	0.708	0.70
91_D	97_G	0.704	0.70
84_D	87_T	0.702	0.69
92_I	154_R	0.701	0.69
245_W	248_L	0.699	0.69
62_L	65_G	0.698	0.69
241_K	244_V	0.697	0.69
50_D	156_Y	0.693	0.68
173_W	211_Q	0.692	0.68
53_E	79_R	0.692	0.68
32_E	127_K	0.690	0.68
247_T	251_K	0.687	0.68
62_L	67_Y	0.687	0.68
194_E	238_W	0.687	0.68
224_G	251_K	0.683	0.67
222_L	226_E	0.683	0.67
55_M	91_D	0.682	0.67
154_R	157_A	0.679	0.67
236_F	260_F	0.679	0.67
58_R	233_M	0.678	0.67
245_W	249_A	0.678	0.67
74_I	77_Q	0.678	0.67
183_H	233_M	0.677	0.67
231_L	237_A	0.673	0.66
59_R	124_A	0.673	0.66
76_A	79_R	0.667	0.66
7_L	27_F	0.666	0.65
147_T	162_E	0.662	0.65
156_Y	179_P	0.657	0.64
10_Q	13_S	0.654	0.64
230_L	234_T	0.653	0.64
9_H	14_R	0.650	0.64
158_P	183_H	0.649	0.63
152_I	167_V	0.647	0.63
227_A	253_V	0.646	0.63
73_A	216_L	0.644	0.63
128_R	132_V	0.643	0.63
8_C	179_P	0.641	0.62
14_R	20_I	0.641	0.62
152_I	174_V	0.639	0.62
134_F	236_F	0.638	0.62
228_V	249_A	0.637	0.62
138_S	234_T	0.635	0.62
50_D	183_H	0.633	0.62
68_Q	71_R	0.632	0.61
36_N	117_V	0.631	0.61
58_R	183_H	0.629	0.61
3_F	261_N	0.629	0.61
26_Q	35_V	0.629	0.61
158_P	233_M	0.629	0.61
94_C	122_I	0.624	0.60
71_R	99_Y	0.624	0.60
114_G	134_F	0.623	0.60
66_H	220_M	0.622	0.60
17_N	106_A	0.620	0.60
62_L	183_H	0.618	0.60
139_S	157_A	0.611	0.59
96_E	234_T	0.609	0.59
89_V	112_T	0.607	0.58
15_E	76_A	0.606	0.58
50_D	54_M	0.605	0.58
52_A	81_R	0.604	0.58
253_V	256_C	0.603	0.58
231_L	236_F	0.603	0.58
156_Y	235_P	0.603	0.58
81_R	212_Q	0.603	0.58
53_E	56_Q	0.602	0.58
115_L	135_C	0.601	0.58
224_G	227_A	0.601	0.58
40_V	138_S	0.599	0.57
17_N	20_I	0.599	0.57
147_T	209_T	0.598	0.57
177_A	262_I	0.598	0.57
60_A	225_D	0.597	0.57
101_H	105_D	0.596	0.57
13_S	88_A	0.595	0.57
143_P	184_L	0.594	0.57
179_P	184_L	0.594	0.57
55_M	183_H	0.589	0.56
144_F	167_V	0.588	0.56
14_R	22_P	0.586	0.56
250_A	255_D	0.582	0.55
51_S	55_M	0.581	0.55
39_P	48_P	0.581	0.55
21_C	25_H	0.581	0.55
217_C	257_Q	0.578	0.55
58_R	99_Y	0.577	0.55
40_V	49_G	0.576	0.54
96_E	157_A	0.576	0.54
41_Q	45_S	0.576	0.54
129_Y	157_A	0.575	0.54
7_L	10_Q	0.574	0.54
8_C	21_C	0.572	0.54
50_D	184_L	0.572	0.54
41_Q	117_V	0.571	0.54
179_P	235_P	0.570	0.54
220_M	254_F	0.570	0.54
33_G	37_L	0.568	0.53
76_A	214_A	0.568	0.53
24_R	31_K	0.565	0.53
147_T	171_G	0.561	0.52
41_Q	49_G	0.560	0.52
74_I	177_A	0.560	0.52
30_A	37_L	0.559	0.52
9_H	23_Q	0.559	0.52
15_E	18_S	0.559	0.52
25_H	58_R	0.557	0.52
28_D	31_K	0.557	0.52
91_D	191_I	0.556	0.52
179_P	183_H	0.556	0.52
232_Q	245_W	0.554	0.52
134_F	157_A	0.554	0.52
94_C	201_H	0.551	0.51
200_P	205_L	0.551	0.51
118_S	121_A	0.549	0.51
227_A	254_F	0.548	0.51
50_D	58_R	0.544	0.50
180_G	215_E	0.543	0.50
81_R	108_P	0.542	0.50
244_V	247_T	0.539	0.50
8_C	178_T	0.538	0.50
164_L	178_T	0.538	0.50
38_L	117_V	0.536	0.49
10_Q	16_K	0.536	0.49
68_Q	204_Q	0.535	0.49
121_A	156_Y	0.535	0.49
143_P	167_V	0.534	0.49
58_R	177_A	0.534	0.49
77_Q	207_G	0.534	0.49
78_L	103_F	0.532	0.49
34_Y	37_L	0.532	0.49
241_K	246_Q	0.531	0.49
16_K	255_D	0.529	0.48
61_F	235_P	0.528	0.48
107_L	110_I	0.528	0.48
61_F	226_E	0.528	0.48
25_H	33_G	0.528	0.48
187_L	258_T	0.525	0.48
92_I	100_T	0.524	0.48
186_E	219_P	0.521	0.47
232_Q	237_A	0.521	0.47
216_L	262_I	0.520	0.47
198_H	201_H	0.520	0.47
4_S	7_L	0.518	0.47
180_G	217_C	0.515	0.47
261_N	264_L	0.515	0.47
89_V	261_N	0.514	0.46
157_A	200_P	0.514	0.46
214_A	223_R	0.513	0.46
10_Q	14_R	0.512	0.46
105_D	131_Q	0.507	0.46
38_L	192_Y	0.507	0.46
25_H	30_A	0.507	0.46
15_E	72_D	0.507	0.46
18_S	255_D	0.506	0.45
11_P	86_A	0.506	0.45
60_A	118_S	0.506	0.45
94_C	118_S	0.506	0.45
221_R	250_A	0.505	0.45
15_E	147_T	0.505	0.45
77_Q	264_L	0.501	0.45
38_L	45_S	0.500	0.45

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
1p91A	2	0.9963	100	0.326	Contact Map
2yqzA	1	0.7955	99.9	0.608	Contact Map
3ccfA	1	0.7435	99.9	0.618	Contact Map
2p35A	2	0.7695	99.9	0.636	Contact Map
3ujcA	1	0.8439	99.9	0.641	Contact Map
4kriA	1	0.9703	99.9	0.643	Contact Map
4xrpC	1	0.8476	99.9	0.644	Contact Map
4rv9A	1	0.9182	99.9	0.646	Contact Map
4obxA	2	0.6431	99.9	0.647	Contact Map
3mggA	2	0.7546	99.9	0.649	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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