YFIF - ECOLI - GREMLIN Contacts

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YFIF - Uncharacterized tRNA/rRNA methyltransferase YfiF

UniProt:	P0AGJ5	Sequences: MNDEMKGKSGKVKVMYVRSDDDSDKRTHNPRTGKGGGRPGKSRADGGRRPARDDKQSQPRDRKWEDSPWRTVSRAPGDETPEKADHGGISGKSFIDPEVLRRQRAEETRVYGENACQALFQSRPEAIVRAWFIQSVTPRFKEALRWMAANRKAYHVVDEAELTKASGTEHHGGVCFLIKKRNGTTVQQWVSQAGAQDCVLALENESNPHNLGGMMRSCAHFGVKGVVVQDAALLESGAAIRTAEGGAEHVQPITGDNIVNVLDDFRQAGYTVVTTSSEQGKPLFKTSLPAKMVLVLGQEYEGLPDAARDPNDLRVKIDGTGNVAGLNISVATGVLLGEWWRQNKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11786
Length:	345 (283)
Sequences:	1534 (1079)
Seq/√Len:	64.2

ECOLI - YFIF RLMB TRML
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
338_E	341_R	4.937	1.00
218_C	223_V	4.879	1.00
201_A	293_V	3.858	1.00
296_L	328_I	3.705	1.00
330_V	333_G	3.429	1.00
215_M	226_V	3.369	1.00
274_T	311_N	3.351	1.00
214_M	332_T	3.097	1.00
305_D	309_D	2.930	1.00
274_T	303_L	2.566	1.00
266_R	312_D	2.564	1.00
200_L	223_V	2.451	1.00
130_A	176_F	2.445	1.00
275_T	335_L	2.438	1.00
63_K	66_D	2.425	1.00
296_L	332_T	2.290	1.00
273_V	292_M	2.222	1.00
172_G	207_N	2.214	1.00
143_A	174_V	2.205	1.00
110_V	119_L	2.201	1.00
338_E	342_Q	2.196	1.00
61_D	64_W	2.078	1.00
200_L	218_C	2.036	1.00
259_V	310_P	1.991	1.00
201_A	262_L	1.971	1.00
274_T	314_R	1.953	1.00
199_V	265_F	1.911	1.00
68_P	73_S	1.877	1.00
73_S	77_G	1.864	1.00
263_D	310_P	1.850	1.00
186_V	265_F	1.825	1.00
66_D	69_W	1.815	1.00
219_A	250_V	1.808	1.00
69_W	73_S	1.789	1.00
60_R	63_K	1.752	1.00
276_S	314_R	1.749	1.00
295_V	311_N	1.723	0.99
68_P	71_T	1.711	0.99
200_L	214_M	1.709	0.99
270_Y	293_V	1.707	0.99
63_K	70_R	1.695	0.99
225_G	253_I	1.691	0.99
185_T	188_Q	1.688	0.99
127_I	176_F	1.676	0.99
62_R	70_R	1.670	0.99
62_R	66_D	1.652	0.99
201_A	258_I	1.625	0.99
213_G	329_S	1.612	0.99
166_S	175_C	1.602	0.99
221_F	334_V	1.601	0.99
219_A	321_G	1.581	0.99
262_L	293_V	1.579	0.99
65_E	68_P	1.555	0.99
259_V	307_A	1.550	0.99
294_L	339_W	1.540	0.99
116_C	176_F	1.536	0.99
186_V	255_G	1.536	0.99
65_E	71_T	1.522	0.99
129_R	155_H	1.521	0.99
69_W	74_R	1.520	0.99
65_E	69_W	1.493	0.98
215_M	239_A	1.493	0.98
71_T	75_A	1.471	0.98
281_K	313_L	1.458	0.98
61_D	66_D	1.457	0.98
170_H	241_R	1.450	0.98
61_D	70_R	1.447	0.98
276_S	308_R	1.423	0.98
70_R	73_S	1.418	0.98
256_D	260_N	1.392	0.98
71_T	76_P	1.390	0.97
200_L	336_L	1.390	0.97
282_P	285_K	1.383	0.97
203_E	304_P	1.383	0.97
265_F	293_V	1.378	0.97
68_P	72_V	1.377	0.97
63_K	68_P	1.375	0.97
60_R	66_D	1.375	0.97
199_V	227_V	1.371	0.97
197_D	291_K	1.369	0.97
71_T	77_G	1.363	0.97
61_D	67_S	1.341	0.97
66_D	70_R	1.324	0.97
215_M	250_V	1.321	0.97
62_R	65_E	1.312	0.96
60_R	65_E	1.303	0.96
69_W	72_V	1.299	0.96
128_V	179_K	1.299	0.96
270_Y	291_K	1.293	0.96
64_W	72_V	1.293	0.96
262_L	310_P	1.287	0.96
294_L	335_L	1.286	0.96
223_V	250_V	1.281	0.96
190_V	270_Y	1.278	0.96
246_G	323_V	1.278	0.96
199_V	268_A	1.270	0.96
62_R	69_W	1.266	0.96
273_V	315_V	1.248	0.95
70_R	74_R	1.243	0.95
202_L	211_L	1.243	0.95
195_A	224_K	1.243	0.95
62_R	68_P	1.240	0.95
238_A	329_S	1.240	0.95
67_S	70_R	1.238	0.95
257_N	260_N	1.235	0.95
127_I	130_A	1.234	0.95
72_V	75_A	1.216	0.95
205_E	342_Q	1.211	0.94
219_A	323_V	1.207	0.94
60_R	64_W	1.201	0.94
136_V	204_N	1.158	0.93
62_R	71_T	1.153	0.93
76_P	80_T	1.145	0.93
64_W	70_R	1.139	0.92
67_S	73_S	1.131	0.92
84_A	87_G	1.128	0.92
62_R	67_S	1.120	0.92
66_D	72_V	1.118	0.92
91_G	100_L	1.114	0.92
217_S	221_F	1.111	0.91
286_T	315_V	1.107	0.91
117_Q	142_E	1.105	0.91
263_D	267_Q	1.091	0.91
273_V	313_L	1.087	0.91
260_N	306_A	1.086	0.90
91_G	99_V	1.082	0.90
75_A	78_D	1.081	0.90
159_E	163_T	1.068	0.90
196_Q	290_A	1.065	0.90
76_P	79_E	1.062	0.89
187_Q	264_D	1.060	0.89
73_S	76_P	1.057	0.89
62_R	72_V	1.050	0.89
123_R	150_N	1.046	0.89
221_F	283_L	1.041	0.89
284_F	341_R	1.038	0.88
124_P	248_E	1.037	0.88
61_D	65_E	1.029	0.88
88_G	94_F	1.020	0.87
308_R	314_R	1.009	0.87
161_E	164_K	1.007	0.87
66_D	73_S	1.007	0.87
66_D	76_P	1.007	0.87
118_A	249_H	1.002	0.87
311_N	314_R	1.002	0.87
103_Q	107_E	1.000	0.86
266_R	272_V	1.000	0.86
111_Y	118_A	0.994	0.86
78_D	83_K	0.993	0.86
61_D	68_P	0.990	0.86
236_S	248_E	0.989	0.86
162_L	175_C	0.979	0.85
88_G	91_G	0.976	0.85
264_D	267_Q	0.974	0.85
227_V	255_G	0.971	0.85
87_G	90_S	0.960	0.84
63_K	76_P	0.959	0.84
207_N	300_Y	0.953	0.84
65_E	77_G	0.951	0.84
80_T	87_G	0.947	0.83
69_W	76_P	0.942	0.83
190_V	268_A	0.939	0.83
274_T	295_V	0.934	0.82
88_G	92_K	0.933	0.82
240_I	247_A	0.930	0.82
204_N	298_Q	0.925	0.82
287_S	290_A	0.925	0.82
280_G	316_K	0.921	0.82
65_E	70_R	0.913	0.81
109_R	175_C	0.905	0.80
67_S	71_T	0.899	0.80
63_K	75_A	0.898	0.80
87_G	91_G	0.898	0.80
62_R	75_A	0.895	0.80
209_H	242_T	0.891	0.79
283_L	335_L	0.890	0.79
67_S	74_R	0.882	0.79
203_E	303_L	0.878	0.78
64_W	71_T	0.877	0.78
87_G	96_D	0.873	0.78
241_R	337_G	0.870	0.78
77_G	83_K	0.860	0.77
153_A	227_V	0.858	0.77
64_W	68_P	0.853	0.76
71_T	78_D	0.851	0.76
79_E	83_K	0.850	0.76
242_T	329_S	0.848	0.76
63_K	69_W	0.847	0.76
72_V	78_D	0.846	0.76
136_V	140_F	0.842	0.75
189_W	253_I	0.837	0.75
339_W	342_Q	0.833	0.75
203_E	295_V	0.831	0.74
68_P	75_A	0.828	0.74
186_V	227_V	0.827	0.74
72_V	76_P	0.825	0.74
83_K	90_S	0.824	0.74
73_S	78_D	0.823	0.74
287_S	342_Q	0.814	0.73
162_L	171_H	0.812	0.73
70_R	75_A	0.811	0.73
78_D	82_E	0.810	0.72
85_D	90_S	0.806	0.72
228_V	234_L	0.805	0.72
64_W	67_S	0.805	0.72
68_P	77_G	0.802	0.72
295_V	307_A	0.799	0.71
63_K	71_T	0.798	0.71
275_T	324_A	0.793	0.71
243_A	307_A	0.792	0.71
117_Q	143_A	0.791	0.71
62_R	77_G	0.783	0.70
92_K	95_I	0.778	0.69
295_V	303_L	0.777	0.69
279_Q	316_K	0.777	0.69
220_H	319_G	0.776	0.69
82_E	86_H	0.775	0.69
69_W	77_G	0.770	0.69
74_R	78_D	0.767	0.68
65_E	72_V	0.767	0.68
146_W	150_N	0.765	0.68
243_A	298_Q	0.765	0.68
119_L	241_R	0.765	0.68
219_A	246_G	0.762	0.68
240_I	248_E	0.762	0.68
166_S	333_G	0.761	0.68
298_Q	301_E	0.759	0.68
74_R	79_E	0.758	0.67
84_A	95_I	0.756	0.67
70_R	77_G	0.753	0.67
280_G	313_L	0.751	0.67
104_R	107_E	0.750	0.67
196_Q	224_K	0.749	0.66
222_G	332_T	0.748	0.66
60_R	67_S	0.748	0.66
259_V	263_D	0.747	0.66
66_D	75_A	0.746	0.66
194_G	270_Y	0.746	0.66
115_A	238_A	0.744	0.66
64_W	73_S	0.743	0.66
66_D	71_T	0.742	0.66
65_E	76_P	0.741	0.66
189_W	225_G	0.740	0.66
299_E	302_G	0.737	0.65
86_H	89_I	0.736	0.65
77_G	80_T	0.731	0.65
262_L	269_G	0.729	0.64
142_E	146_W	0.723	0.64
69_W	75_A	0.720	0.63
62_R	73_S	0.719	0.63
271_T	313_L	0.719	0.63
80_T	83_K	0.718	0.63
63_K	73_S	0.717	0.63
258_I	307_A	0.711	0.62
63_K	72_V	0.710	0.62
121_Q	142_E	0.707	0.62
110_V	169_E	0.707	0.62
262_L	312_D	0.705	0.62
65_E	74_R	0.704	0.62
110_V	178_I	0.701	0.61
91_G	96_D	0.701	0.61
271_T	292_M	0.698	0.61
99_V	105_A	0.697	0.61
202_L	207_N	0.696	0.61
68_P	76_P	0.693	0.60
82_E	91_G	0.693	0.60
60_R	70_R	0.693	0.60
303_L	311_N	0.691	0.60
64_W	78_D	0.691	0.60
276_S	301_E	0.688	0.60
172_G	274_T	0.686	0.60
264_D	268_A	0.685	0.60
62_R	76_P	0.682	0.59
209_H	213_G	0.681	0.59
212_G	245_G	0.678	0.59
201_A	227_V	0.678	0.59
202_L	226_V	0.675	0.58
129_R	177_L	0.673	0.58
181_R	235_E	0.667	0.58
60_R	69_W	0.664	0.57
243_A	247_A	0.662	0.57
219_A	320_T	0.661	0.57
205_E	233_L	0.658	0.57
209_H	248_E	0.658	0.57
277_S	319_G	0.658	0.57
288_L	313_L	0.654	0.56
206_S	300_Y	0.653	0.56
76_P	83_K	0.652	0.56
99_V	103_Q	0.652	0.56
109_R	174_V	0.652	0.56
260_N	263_D	0.650	0.56
266_R	271_T	0.649	0.55
90_S	93_S	0.645	0.55
209_H	238_A	0.645	0.55
131_W	155_H	0.640	0.54
261_V	268_A	0.639	0.54
189_W	197_D	0.637	0.54
202_L	214_M	0.634	0.54
82_E	85_D	0.631	0.53
73_S	79_E	0.630	0.53
60_R	71_T	0.629	0.53
86_H	92_K	0.626	0.53
108_T	177_L	0.626	0.53
71_T	79_E	0.624	0.53
99_V	102_R	0.623	0.52
199_V	225_G	0.623	0.52
119_L	337_G	0.618	0.52
86_H	90_S	0.616	0.52
60_R	75_A	0.614	0.51
67_S	72_V	0.614	0.51
60_R	72_V	0.613	0.51
83_K	86_H	0.613	0.51
108_T	243_A	0.612	0.51
303_L	316_K	0.612	0.51
115_A	244_E	0.612	0.51
302_G	325_G	0.611	0.51
262_L	266_R	0.609	0.51
297_G	302_G	0.608	0.51
204_N	304_P	0.608	0.51
235_E	240_I	0.607	0.51
70_R	78_D	0.607	0.51
105_A	285_K	0.605	0.50
224_K	267_Q	0.603	0.50
75_A	193_A	0.603	0.50
215_M	247_A	0.602	0.50
87_G	92_K	0.602	0.50
83_K	87_G	0.601	0.50
70_R	76_P	0.601	0.50
222_G	334_V	0.600	0.50
140_F	289_P	0.598	0.50
72_V	95_I	0.597	0.49
220_H	323_V	0.596	0.49
295_V	304_P	0.595	0.49
61_D	69_W	0.592	0.49
134_Q	141_K	0.592	0.49
64_W	76_P	0.591	0.49
65_E	75_A	0.591	0.49
84_A	93_S	0.591	0.49
74_R	77_G	0.590	0.49
79_E	86_H	0.589	0.49
224_K	270_Y	0.588	0.48
262_L	307_A	0.588	0.48
215_M	219_A	0.587	0.48
187_Q	191_S	0.584	0.48
134_Q	158_D	0.584	0.48
206_S	233_L	0.583	0.48
86_H	94_F	0.581	0.48
272_V	293_V	0.581	0.48
82_E	96_D	0.581	0.48
85_D	88_G	0.581	0.48
306_A	309_D	0.580	0.47
262_L	295_V	0.579	0.47
211_L	239_A	0.579	0.47
68_P	83_K	0.578	0.47
308_R	329_S	0.578	0.47
201_A	265_F	0.578	0.47
117_Q	174_V	0.575	0.47
183_G	231_A	0.575	0.47
287_S	313_L	0.574	0.47
159_E	243_A	0.571	0.46
72_V	85_D	0.569	0.46
170_H	232_A	0.565	0.46
198_C	292_M	0.564	0.46
118_A	276_S	0.562	0.45
78_D	86_H	0.562	0.45
131_W	177_L	0.560	0.45
91_G	94_F	0.557	0.45
75_A	83_K	0.553	0.44
71_T	80_T	0.551	0.44
60_R	68_P	0.551	0.44
67_S	75_A	0.551	0.44
62_R	89_I	0.550	0.44
115_A	242_T	0.549	0.44
63_K	74_R	0.549	0.44
213_G	333_G	0.548	0.44
288_L	292_M	0.548	0.44
299_E	325_G	0.547	0.44
84_A	90_S	0.547	0.44
320_T	323_V	0.547	0.44
72_V	77_G	0.544	0.43
323_V	335_L	0.541	0.43
75_A	89_I	0.540	0.43
208_P	296_L	0.538	0.43
144_L	174_V	0.538	0.43
249_H	321_G	0.532	0.42
179_K	254_T	0.530	0.42
61_D	71_T	0.529	0.42
69_W	78_D	0.529	0.42
68_P	74_R	0.527	0.41
302_G	331_A	0.527	0.41
228_V	231_A	0.527	0.41
90_S	96_D	0.525	0.41
281_K	286_T	0.524	0.41
111_Y	168_T	0.523	0.41
79_E	82_E	0.522	0.41
215_M	235_E	0.522	0.41
96_D	145_R	0.522	0.41
145_R	148_A	0.521	0.41
108_T	241_R	0.520	0.41
160_A	163_T	0.520	0.41
167_G	175_C	0.520	0.41
71_T	74_R	0.519	0.41
207_N	244_E	0.518	0.40
168_T	238_A	0.517	0.40
147_M	152_K	0.516	0.40
111_Y	167_G	0.515	0.40
318_D	338_E	0.513	0.40
68_P	78_D	0.512	0.40
64_W	69_W	0.511	0.40
110_V	165_A	0.510	0.40
77_G	81_P	0.510	0.40
81_P	87_G	0.509	0.39
167_G	296_L	0.507	0.39
96_D	99_V	0.507	0.39
208_P	239_A	0.504	0.39
282_P	342_Q	0.504	0.39
284_F	334_V	0.503	0.39
135_S	140_F	0.503	0.39
202_L	205_E	0.503	0.39
78_D	81_P	0.502	0.39
101_R	267_Q	0.502	0.39
210_N	299_E	0.500	0.38
209_H	239_A	0.500	0.38
334_V	341_R	0.500	0.38

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
1ipaA	1	0.7449	100	0.304	Contact Map
3nk6A	2	0.742	100	0.313	Contact Map
1gz0A	2	0.7188	100	0.313	Contact Map
1x7oA	2	0.7333	100	0.333	Contact Map
2i6dA	2	0.7072	100	0.353	Contact Map
1v2xA	2	0.4899	100	0.506	Contact Map
1zjrA	2	0.487	100	0.507	Contact Map
4kgnA	2	0.4377	100	0.51	Contact Map
2ha8A	2	0.4435	100	0.519	Contact Map
3n4jA	2	0.4348	100	0.521	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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