YXJB - BACSU - GREMLIN Contacts

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YXJB - Putative 23S rRNA (guanine-N(1)-)-methyltransferase YxjB

UniProt:	P42313	Sequences: MKRTVDFSMFRCPLCDSSMDAASGKSLICTERGHTFDLSRHGYVNFLTKPVKTSYGAELFEARSRLIGECGFFDPLHDAIAELISHPKSGHEAFTILDSGCGEGSHLNALCGFDYAGKAAIGTGIDLSKDGILKASKAFKDLMWAVADVARAPFHDRQFDVVLSIFSPSNYAEFHRLLKNDGMLIKVVPRSDYLIELRQFLYTDSPRRTYSNTAAVERFTANAAHSRPVRLRYVKTLDQQAIHWLLKMTPLAWSAPKDRVSLLKEMKSADITVDVDILIGMK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	282 (261)
Sequences:	1537 (1191)
Seq/√Len:	73.7

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
65_R	244_W	6.269	1.00
160_D	179_K	4.529	1.00
196_E	272_T	4.445	1.00
97_L	159_F	4.150	1.00
173_E	176_R	4.045	1.00
101_C	124_G	3.630	1.00
152_A	177_L	3.575	1.00
99_S	174_F	3.037	1.00
238_D	241_A	2.921	1.00
185_I	277_I	2.848	1.00
76_L	275_V	2.824	1.00
185_I	279_I	2.800	1.00
27_L	44_V	2.786	1.00
26_S	35_T	2.764	1.00
79_A	229_V	2.684	1.00
234_V	270_D	2.572	1.00
154_F	159_F	2.407	1.00
236_T	270_D	2.360	1.00
99_S	149_V	2.352	1.00
192_D	232_R	2.287	1.00
72_F	241_A	2.248	1.00
230_R	274_D	2.219	1.00
75_P	233_Y	2.153	1.00
178_L	182_G	2.127	1.00
233_Y	273_V	2.071	1.00
79_A	83_L	2.066	1.00
41_H	133_L	2.045	1.00
70_C	241_A	2.006	1.00
110_L	163_L	1.983	1.00
74_D	78_D	1.981	1.00
162_V	174_F	1.917	1.00
10_F	145_A	1.916	1.00
192_D	272_T	1.889	1.00
156_D	173_E	1.855	1.00
84_I	161_V	1.822	1.00
14_L	48_T	1.812	1.00
97_L	177_L	1.771	1.00
77_H	109_A	1.768	1.00
159_F	177_L	1.749	1.00
97_L	154_F	1.725	1.00
60_F	131_G	1.724	1.00
174_F	178_L	1.710	1.00
135_A	144_W	1.696	1.00
235_K	273_V	1.662	1.00
174_F	184_L	1.641	1.00
39_S	43_Y	1.560	0.99
34_H	37_D	1.544	0.99
101_C	135_A	1.543	0.99
17_S	32_R	1.539	0.99
152_A	173_E	1.533	0.99
159_F	162_V	1.518	0.99
261_S	265_E	1.514	0.99
175_H	223_A	1.498	0.99
86_H	227_R	1.488	0.99
232_R	274_D	1.486	0.99
28_I	35_T	1.477	0.99
72_F	237_L	1.475	0.99
156_D	176_R	1.475	0.99
190_R	276_D	1.458	0.99
107_L	122_G	1.448	0.99
183_M	279_I	1.448	0.99
198_R	205_S	1.447	0.99
241_A	244_W	1.428	0.99
239_Q	242_I	1.426	0.99
69_E	138_A	1.388	0.98
11_R	155_H	1.372	0.98
79_A	82_E	1.370	0.98
256_P	260_V	1.368	0.98
166_F	193_Y	1.361	0.98
66_L	72_F	1.356	0.98
21_A	38_L	1.350	0.98
262_L	266_M	1.349	0.98
80_I	185_I	1.347	0.98
153_P	173_E	1.346	0.98
145_A	154_F	1.338	0.98
150_A	170_N	1.335	0.98
108_N	139_F	1.333	0.98
87_P	183_M	1.333	0.98
67_I	71_G	1.325	0.98
12_C	15_C	1.322	0.98
164_S	174_F	1.306	0.98
225_H	278_L	1.303	0.98
196_E	271_I	1.292	0.97
155_H	158_Q	1.289	0.97
94_F	160_D	1.252	0.97
76_L	187_V	1.246	0.97
190_R	274_D	1.242	0.97
132_I	135_A	1.201	0.96
38_L	44_V	1.199	0.96
132_I	146_V	1.194	0.96
17_S	30_T	1.192	0.96
59_L	128_S	1.183	0.96
59_L	166_F	1.178	0.96
246_L	260_V	1.147	0.95
188_V	278_L	1.129	0.94
246_L	255_A	1.117	0.94
95_T	159_F	1.115	0.94
184_L	219_F	1.113	0.94
77_H	105_S	1.096	0.94
125_I	147_A	1.091	0.93
9_M	95_T	1.091	0.93
27_L	38_L	1.084	0.93
168_P	189_P	1.070	0.93
78_D	82_E	1.064	0.93
106_H	193_Y	1.058	0.92
73_F	98_D	1.042	0.92
123_T	154_F	1.036	0.91
66_L	73_F	1.032	0.91
153_P	176_R	1.021	0.91
123_T	145_A	1.018	0.91
15_C	29_C	1.016	0.91
111_C	122_G	1.005	0.90
228_P	278_L	1.002	0.90
101_C	144_W	1.001	0.90
173_E	177_L	0.982	0.89
20_D	24_G	0.970	0.89
28_I	33_G	0.959	0.88
73_F	106_H	0.959	0.88
79_A	231_L	0.959	0.88
20_D	30_T	0.951	0.88
98_D	101_C	0.948	0.87
232_R	273_V	0.947	0.87
123_T	159_F	0.938	0.87
59_L	193_Y	0.937	0.87
79_A	277_I	0.936	0.87
183_M	226_S	0.936	0.87
95_T	160_D	0.931	0.86
12_C	29_C	0.919	0.86
67_I	105_S	0.916	0.86
10_F	143_M	0.915	0.85
190_R	232_R	0.912	0.85
67_I	106_H	0.911	0.85
77_H	110_L	0.909	0.85
213_T	217_E	0.905	0.85
162_V	178_L	0.904	0.85
45_N	146_V	0.903	0.85
36_F	39_S	0.903	0.85
237_L	241_A	0.902	0.85
152_A	176_R	0.896	0.84
84_I	185_I	0.891	0.84
212_N	215_A	0.890	0.84
18_S	155_H	0.887	0.84
93_A	160_D	0.886	0.84
165_I	189_P	0.885	0.84
106_H	166_F	0.882	0.83
10_F	154_F	0.876	0.83
153_P	177_L	0.876	0.83
95_T	179_K	0.871	0.83
138_A	142_L	0.871	0.83
271_I	274_D	0.868	0.82
23_S	82_E	0.867	0.82
83_L	227_R	0.864	0.82
187_V	277_I	0.860	0.82
80_I	165_I	0.860	0.82
67_I	166_F	0.860	0.82
258_D	261_S	0.859	0.82
169_S	186_K	0.859	0.82
82_E	86_H	0.858	0.82
91_H	94_F	0.855	0.81
257_K	261_S	0.854	0.81
20_D	23_S	0.848	0.81
194_L	245_L	0.847	0.81
259_R	262_L	0.846	0.81
257_K	260_V	0.845	0.81
26_S	44_V	0.842	0.80
49_K	54_S	0.839	0.80
11_R	18_S	0.839	0.80
67_I	193_Y	0.839	0.80
247_K	260_V	0.834	0.80
17_S	23_S	0.830	0.79
245_L	249_T	0.830	0.79
74_D	105_S	0.829	0.79
231_L	277_I	0.827	0.79
168_P	248_M	0.826	0.79
198_R	201_L	0.819	0.78
131_G	237_L	0.819	0.78
240_Q	243_H	0.817	0.78
26_S	238_D	0.817	0.78
107_L	142_L	0.814	0.78
41_H	137_K	0.809	0.78
147_A	152_A	0.808	0.78
228_P	276_D	0.806	0.77
266_M	269_A	0.801	0.77
14_L	49_K	0.798	0.77
100_G	167_S	0.798	0.77
80_I	187_V	0.796	0.77
63_R	166_F	0.787	0.76
47_L	127_L	0.785	0.76
242_I	268_S	0.783	0.75
166_F	248_M	0.780	0.75
37_D	43_Y	0.777	0.75
23_S	28_I	0.776	0.75
167_S	188_V	0.773	0.74
107_L	163_L	0.765	0.74
100_G	131_G	0.765	0.74
67_I	128_S	0.764	0.74
39_S	133_L	0.764	0.74
192_D	196_E	0.762	0.73
192_D	195_I	0.761	0.73
149_V	164_S	0.759	0.73
210_Y	213_T	0.756	0.73
83_L	229_V	0.755	0.73
273_V	278_L	0.754	0.73
21_A	25_K	0.754	0.73
63_R	250_P	0.749	0.72
17_S	82_E	0.747	0.72
35_T	38_L	0.746	0.72
80_I	162_V	0.739	0.71
256_P	259_R	0.738	0.71
49_K	148_D	0.736	0.71
208_R	214_A	0.734	0.71
29_C	34_H	0.731	0.70
246_L	252_A	0.728	0.70
26_S	38_L	0.727	0.70
192_D	274_D	0.724	0.69
11_R	16_D	0.723	0.69
108_N	138_A	0.721	0.69
98_D	127_L	0.718	0.69
212_N	219_F	0.718	0.69
189_P	248_M	0.718	0.69
251_L	275_V	0.713	0.68
235_K	271_I	0.713	0.68
21_A	44_V	0.708	0.68
15_C	167_S	0.706	0.68
247_K	252_A	0.706	0.68
124_G	144_W	0.705	0.67
125_I	145_A	0.705	0.67
47_L	98_D	0.705	0.67
243_H	264_K	0.703	0.67
258_D	262_L	0.701	0.67
66_L	167_S	0.700	0.67
15_C	168_P	0.691	0.66
163_L	187_V	0.688	0.66
260_V	263_L	0.687	0.65
87_P	227_R	0.686	0.65
14_L	36_F	0.685	0.65
95_T	121_I	0.685	0.65
76_L	277_I	0.684	0.65
84_I	132_I	0.683	0.65
149_V	167_S	0.679	0.65
54_S	59_L	0.678	0.64
100_G	127_L	0.676	0.64
51_V	151_R	0.670	0.63
82_E	85_S	0.670	0.63
50_P	55_Y	0.669	0.63
178_L	184_L	0.666	0.63
94_F	120_A	0.665	0.63
49_K	55_Y	0.665	0.63
77_H	81_A	0.660	0.62
98_D	104_G	0.659	0.62
108_N	112_G	0.658	0.62
84_I	242_I	0.657	0.62
36_F	136_S	0.655	0.62
25_K	40_R	0.655	0.62
48_T	52_K	0.655	0.62
109_A	112_G	0.653	0.61
175_H	181_D	0.651	0.61
195_I	272_T	0.651	0.61
193_Y	250_P	0.650	0.61
63_R	193_Y	0.647	0.61
164_S	169_S	0.646	0.61
198_R	202_Y	0.643	0.60
164_S	170_N	0.641	0.60
75_P	231_L	0.640	0.60
136_S	139_F	0.640	0.60
144_W	251_L	0.639	0.60
164_S	188_V	0.638	0.60
144_W	150_A	0.638	0.60
151_R	156_D	0.638	0.60
20_D	82_E	0.637	0.60
273_V	276_D	0.636	0.59
127_L	146_V	0.636	0.59
66_L	131_G	0.636	0.59
122_G	139_F	0.632	0.59
98_D	125_I	0.632	0.59
33_G	37_D	0.631	0.59
43_Y	46_F	0.630	0.59
82_E	270_D	0.630	0.59
59_L	148_D	0.629	0.59
242_I	269_A	0.627	0.58
211_S	214_A	0.627	0.58
76_L	80_I	0.625	0.58
216_V	219_F	0.623	0.58
63_R	67_I	0.620	0.58
139_F	144_W	0.620	0.58
46_F	54_S	0.618	0.57
129_K	146_V	0.617	0.57
246_L	251_L	0.616	0.57
117_G	120_A	0.616	0.57
157_R	179_K	0.616	0.57
39_S	66_L	0.612	0.57
213_T	220_T	0.612	0.57
84_I	110_L	0.609	0.56
262_L	265_E	0.608	0.56
234_V	262_L	0.607	0.56
235_K	269_A	0.607	0.56
50_P	127_L	0.606	0.56
150_A	169_S	0.606	0.56
96_I	161_V	0.604	0.56
18_S	93_A	0.603	0.55
23_S	120_A	0.603	0.55
77_H	106_H	0.602	0.55
60_F	130_D	0.601	0.55
150_A	249_T	0.600	0.55
101_C	202_Y	0.597	0.55
260_V	264_K	0.595	0.54
157_R	180_N	0.594	0.54
20_D	270_D	0.592	0.54
261_S	270_D	0.592	0.54
100_G	164_S	0.590	0.54
43_Y	129_K	0.587	0.53
93_A	161_V	0.583	0.53
131_G	167_S	0.581	0.53
63_R	168_P	0.581	0.53
162_V	184_L	0.580	0.53
187_V	193_Y	0.579	0.52
34_H	42_G	0.576	0.52
236_T	268_S	0.575	0.52
55_Y	60_F	0.575	0.52
195_I	205_S	0.575	0.52
251_L	271_I	0.572	0.52
25_K	119_A	0.572	0.52
47_L	202_Y	0.571	0.51
149_V	171_Y	0.571	0.51
16_D	32_R	0.571	0.51
45_N	127_L	0.571	0.51
251_L	255_A	0.571	0.51
236_T	267_K	0.570	0.51
60_F	164_S	0.566	0.51
240_Q	267_K	0.561	0.50
166_F	275_V	0.560	0.50
124_G	139_F	0.558	0.50
25_K	38_L	0.556	0.50
34_H	63_R	0.554	0.49
190_R	230_R	0.553	0.49
272_T	275_V	0.552	0.49
204_D	253_W	0.551	0.49
66_L	107_L	0.550	0.49
66_L	237_L	0.550	0.49
168_P	173_E	0.550	0.49
36_F	43_Y	0.550	0.49
119_A	157_R	0.548	0.49
15_C	189_P	0.546	0.48
148_D	254_S	0.546	0.48
62_A	131_G	0.546	0.48
105_S	193_Y	0.544	0.48
103_E	249_T	0.542	0.48
151_R	162_V	0.540	0.48
226_S	279_I	0.540	0.48
55_Y	148_D	0.539	0.48
217_E	220_T	0.538	0.47
83_L	279_I	0.537	0.47
35_T	44_V	0.537	0.47
198_R	244_W	0.536	0.47
60_F	166_F	0.536	0.47
61_E	134_K	0.535	0.47
99_S	164_S	0.534	0.47
154_F	177_L	0.534	0.47
100_G	189_P	0.534	0.47
50_P	53_T	0.534	0.47
166_F	250_P	0.534	0.47
24_G	181_D	0.532	0.47
189_P	250_P	0.531	0.47
66_L	241_A	0.530	0.46
139_F	142_L	0.530	0.46
34_H	40_R	0.524	0.46
195_I	199_Q	0.522	0.45
78_D	179_K	0.521	0.45
179_K	262_L	0.520	0.45
218_R	221_A	0.518	0.45
160_D	269_A	0.518	0.45
187_V	275_V	0.516	0.45
47_L	146_V	0.516	0.45
188_V	216_V	0.512	0.44
129_K	223_A	0.512	0.44
36_F	231_L	0.512	0.44
132_I	144_W	0.511	0.44
25_K	28_I	0.510	0.44
144_W	168_P	0.510	0.44
164_S	167_S	0.508	0.44
82_E	229_V	0.507	0.44
224_A	267_K	0.507	0.44
111_C	142_L	0.507	0.44
18_S	21_A	0.507	0.44
122_G	142_L	0.507	0.44
171_Y	175_H	0.505	0.43
170_N	186_K	0.505	0.43
73_F	132_I	0.505	0.43
133_L	211_S	0.503	0.43
200_F	259_R	0.501	0.43
37_D	40_R	0.501	0.43
239_Q	267_K	0.500	0.43

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	0.9291	100	0.386	Contact Map
2yqzA	1	0.7624	100	0.577	Contact Map
3ccfA	1	0.7163	100	0.595	Contact Map
4hg2A	1	0.7092	99.9	0.61	Contact Map
2p35A	2	0.7305	99.9	0.613	Contact Map
1xxlA	1	0.7057	99.9	0.616	Contact Map
1vl5A	1	0.7021	99.9	0.62	Contact Map
3ujcA	1	0.8262	99.9	0.621	Contact Map
4pneA	2	0.7943	99.9	0.625	Contact Map
2o57A	2	0.8582	99.9	0.628	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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