LYTE - BACSU - GREMLIN Contacts

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LYTE - Probable peptidoglycan endopeptidase LytE

UniProt:	P54421	Sequences: MKKQIITATTAVVLGSTLFAGAASAQSIKVKKGDTLWDLSRKYDTTISKIKSENHLRSDIIYVGQTLSINGKSTSSKSSSSSSSSSTYKVKSGDSLWKISKKYGMTINELKKLNGLKSDLLRVGQVLKLKGSTSSSSSSSSKVSSSSTSTYKVKSGDSLSKIASKYGTTVSKLKSLNGLKSDVIYVNQVLKVKGTSTSSSKPASSSSSSSSKTSSTSLNVSKLVSDAKALVGTPYKWGGTTTSGFDCSGFIWYVLNKQTSVGRTSTAGYWSSMKSIASPSVGDFVFFTTYKSGPSHMGIYIGNNSFIHAGSDGVQISSLNNSYWKPRYLGAKRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	334 (292)
Sequences:	1927 (1798)
Seq/√Len:	105.2

ECOLI - MEPH YAFL MEPS NLPC
BACSU - LYTE LYTF CWLS YDDH CWLO YKFC PGDS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
230_L	233_T	4.072	1.00
301_I	316_I	3.998	1.00
231_V	307_I	3.732	1.00
228_K	307_I	3.201	1.00
239_G	244_G	3.182	1.00
251_I	299_I	2.815	1.00
228_K	316_I	2.775	1.00
240_T	263_R	2.763	1.00
224_V	301_I	2.745	1.00
275_S	278_S	2.646	1.00
252_W	263_R	2.501	1.00
241_T	244_G	2.492	1.00
233_T	241_T	2.474	1.00
226_D	253_Y	2.472	1.00
251_I	268_G	2.466	1.00
251_I	284_F	2.395	1.00
262_G	271_S	2.388	1.00
245_F	253_Y	2.275	1.00
287_F	306_F	2.269	1.00
233_T	245_F	2.160	1.00
253_Y	257_K	2.142	1.00
233_T	244_G	2.081	1.00
276_I	279_P	2.052	1.00
234_P	244_G	2.051	1.00
287_F	298_G	2.045	1.00
226_D	257_K	2.033	1.00
172_K	175_S	2.031	1.00
288_T	295_S	2.020	1.00
100_S	103_Y	2.002	1.00
172_K	176_L	1.995	1.00
251_I	261_V	1.893	1.00
265_S	269_Y	1.833	1.00
175_S	179_L	1.807	1.00
100_S	104_G	1.791	1.00
141_S	145_S	1.769	1.00
310_G	315_Q	1.749	1.00
264_T	267_A	1.748	1.00
185_Y	189_V	1.730	1.00
287_F	328_Y	1.730	1.00
250_F	254_V	1.721	1.00
286_F	297_M	1.707	1.00
221_S	225_S	1.695	1.00
184_I	188_Q	1.683	1.00
186_V	190_L	1.666	1.00
162_I	166_Y	1.603	1.00
177_N	181_S	1.593	1.00
233_T	239_G	1.585	1.00
173_L	177_N	1.583	1.00
46_T	50_I	1.579	1.00
184_I	187_N	1.571	1.00
269_Y	294_P	1.564	1.00
189_V	193_K	1.563	1.00
226_D	245_F	1.556	1.00
226_D	230_L	1.531	1.00
276_I	328_Y	1.523	1.00
288_T	327_R	1.523	1.00
97_W	104_G	1.497	1.00
158_S	161_K	1.487	1.00
179_L	183_V	1.469	1.00
165_K	169_T	1.464	1.00
298_G	306_F	1.457	1.00
186_V	189_V	1.454	1.00
166_Y	170_V	1.444	1.00
158_S	162_I	1.439	1.00
276_I	320_N	1.436	1.00
231_V	316_I	1.434	1.00
227_A	307_I	1.425	1.00
54_N	58_S	1.421	1.00
226_D	229_A	1.416	1.00
292_S	295_S	1.416	1.00
310_G	313_G	1.414	1.00
190_L	194_G	1.406	1.00
83_S	86_S	1.401	1.00
152_K	156_G	1.400	1.00
173_L	183_V	1.398	1.00
262_G	265_S	1.390	1.00
176_L	179_L	1.383	1.00
240_T	252_W	1.370	1.00
263_R	266_T	1.354	1.00
306_F	319_L	1.343	0.99
230_L	241_T	1.323	0.99
252_W	256_N	1.315	0.99
220_V	224_V	1.308	0.99
269_Y	286_F	1.305	0.99
148_T	152_K	1.295	0.99
155_S	159_L	1.285	0.99
166_Y	169_T	1.285	0.99
86_S	89_K	1.281	0.99
279_P	285_V	1.278	0.99
159_L	162_I	1.278	0.99
284_F	297_M	1.277	0.99
180_K	183_V	1.270	0.99
162_I	165_K	1.267	0.99
269_Y	330_G	1.261	0.99
170_V	174_K	1.260	0.99
53_E	57_R	1.245	0.99
242_T	245_F	1.243	0.99
55_H	58_S	1.242	0.99
156_G	160_S	1.238	0.99
199_S	202_P	1.229	0.99
262_G	267_A	1.226	0.99
90_V	93_G	1.226	0.99
188_Q	191_K	1.225	0.99
252_W	264_T	1.217	0.99
82_S	89_K	1.210	0.99
187_N	190_L	1.208	0.99
170_V	173_L	1.205	0.99
308_H	317_S	1.203	0.99
266_T	269_Y	1.201	0.99
180_K	184_I	1.200	0.99
174_K	178_G	1.197	0.99
173_L	176_L	1.192	0.99
182_D	186_V	1.182	0.99
226_D	258_Q	1.181	0.99
228_K	301_I	1.176	0.99
263_R	267_A	1.173	0.99
79_S	86_S	1.158	0.98
176_L	180_K	1.154	0.98
64_G	68_S	1.152	0.98
93_G	104_G	1.149	0.98
226_D	254_V	1.135	0.98
221_S	281_V	1.133	0.98
267_A	270_W	1.117	0.98
107_I	110_L	1.115	0.98
254_V	258_Q	1.107	0.98
111_K	114_N	1.106	0.98
308_H	320_N	1.091	0.98
163_A	166_Y	1.084	0.98
200_S	203_A	1.082	0.98
65_Q	69_I	1.080	0.98
225_S	228_K	1.071	0.97
198_S	201_K	1.070	0.97
93_G	103_Y	1.053	0.97
89_K	93_G	1.051	0.97
166_Y	176_L	1.051	0.97
35_T	38_D	1.047	0.97
185_Y	188_Q	1.044	0.97
266_T	294_P	1.043	0.97
288_T	293_G	1.039	0.97
307_I	316_I	1.038	0.97
179_L	182_D	1.035	0.97
157_D	161_K	1.034	0.97
187_N	191_K	1.031	0.97
287_F	295_S	1.030	0.97
167_G	171_S	1.029	0.97
236_K	239_G	1.024	0.97
100_S	105_M	1.023	0.97
174_K	177_N	1.021	0.97
120_L	123_V	1.015	0.96
169_T	172_K	1.015	0.96
286_F	294_P	1.013	0.96
308_H	315_Q	1.006	0.96
83_S	90_V	1.004	0.96
298_G	308_H	1.000	0.96
224_V	307_I	0.998	0.96
168_T	172_K	0.988	0.96
222_K	258_Q	0.987	0.96
236_K	312_D	0.975	0.95
281_V	301_I	0.973	0.95
88_Y	93_G	0.969	0.95
191_K	194_G	0.966	0.95
230_L	245_F	0.965	0.95
229_A	233_T	0.962	0.95
78_S	85_S	0.961	0.95
97_W	101_K	0.961	0.95
269_Y	272_S	0.960	0.95
252_W	268_G	0.953	0.95
224_V	228_K	0.950	0.95
279_P	319_L	0.949	0.95
310_G	314_V	0.946	0.95
230_L	250_F	0.946	0.95
50_I	54_N	0.944	0.95
279_P	328_Y	0.942	0.95
102_K	105_M	0.940	0.94
134_S	138_S	0.939	0.94
230_L	254_V	0.935	0.94
305_S	316_I	0.933	0.94
54_N	57_R	0.928	0.94
228_K	231_V	0.927	0.94
107_I	111_K	0.925	0.94
153_V	157_D	0.922	0.94
169_T	173_L	0.918	0.94
110_L	113_L	0.916	0.94
51_K	55_H	0.915	0.94
149_S	153_V	0.915	0.94
233_T	314_V	0.914	0.94
82_S	86_S	0.912	0.94
234_P	237_W	0.907	0.93
237_W	244_G	0.902	0.93
241_T	245_F	0.900	0.93
269_Y	329_L	0.899	0.93
124_G	128_K	0.898	0.93
82_S	85_S	0.895	0.93
152_K	155_S	0.894	0.93
90_V	94_D	0.894	0.93
191_K	195_T	0.894	0.93
187_N	195_T	0.889	0.93
50_I	58_S	0.889	0.93
166_Y	172_K	0.889	0.93
45_T	49_K	0.887	0.93
120_L	124_G	0.887	0.93
85_S	100_S	0.885	0.92
220_V	281_V	0.879	0.92
164_S	168_T	0.878	0.92
285_V	298_G	0.877	0.92
109_E	113_L	0.876	0.92
304_N	319_L	0.874	0.92
301_I	307_I	0.869	0.92
80_S	84_S	0.868	0.92
265_S	294_P	0.867	0.92
220_V	309_A	0.865	0.92
252_W	261_V	0.858	0.91
233_T	253_Y	0.853	0.91
281_V	300_Y	0.853	0.91
159_L	169_T	0.852	0.91
148_T	151_Y	0.849	0.91
160_S	163_A	0.847	0.91
59_D	62_Y	0.844	0.91
219_N	222_K	0.836	0.90
86_S	90_V	0.835	0.90
230_L	244_G	0.834	0.90
96_L	100_S	0.827	0.90
85_S	89_K	0.827	0.90
39_L	42_K	0.825	0.90
240_T	264_T	0.822	0.89
168_T	171_S	0.822	0.89
287_F	319_L	0.821	0.89
206_S	209_S	0.817	0.89
51_K	54_N	0.817	0.89
127_L	130_K	0.816	0.89
250_F	258_Q	0.809	0.89
268_G	284_F	0.809	0.89
97_W	100_S	0.801	0.88
261_V	268_G	0.797	0.88
171_S	175_S	0.797	0.88
148_T	183_V	0.796	0.88
295_S	312_D	0.794	0.88
98_K	102_K	0.793	0.88
252_W	265_S	0.792	0.88
47_I	51_K	0.782	0.87
65_Q	68_S	0.782	0.87
240_T	249_G	0.779	0.87
201_K	204_S	0.773	0.86
154_K	158_S	0.769	0.86
145_S	149_S	0.767	0.86
115_G	118_S	0.766	0.86
275_S	279_P	0.759	0.85
185_Y	192_V	0.759	0.85
223_L	258_Q	0.757	0.85
86_S	92_S	0.756	0.85
97_W	103_Y	0.754	0.85
230_L	258_Q	0.753	0.85
295_S	327_R	0.752	0.85
188_Q	192_V	0.750	0.85
66_T	70_N	0.748	0.84
147_S	151_Y	0.746	0.84
47_I	54_N	0.746	0.84
266_T	286_F	0.744	0.84
135_S	139_S	0.739	0.84
124_G	130_K	0.736	0.84
144_S	148_T	0.734	0.83
109_E	114_N	0.733	0.83
189_V	192_V	0.732	0.83
233_T	243_S	0.732	0.83
203_A	209_S	0.730	0.83
256_N	260_S	0.724	0.83
197_T	201_K	0.717	0.82
142_K	145_S	0.715	0.82
263_R	271_S	0.715	0.82
163_A	167_G	0.715	0.82
79_S	82_S	0.714	0.82
207_S	210_S	0.714	0.82
242_T	253_Y	0.713	0.82
250_F	310_G	0.713	0.82
78_S	92_S	0.711	0.81
196_S	200_S	0.710	0.81
93_G	97_W	0.709	0.81
287_F	320_N	0.708	0.81
199_S	205_S	0.708	0.81
53_E	56_L	0.703	0.81
166_Y	179_L	0.701	0.80
213_T	216_T	0.700	0.80
245_F	255_L	0.697	0.80
159_L	163_A	0.694	0.80
205_S	209_S	0.693	0.80
265_S	286_F	0.692	0.80
167_G	170_V	0.689	0.79
82_S	90_V	0.686	0.79
204_S	208_S	0.685	0.79
242_T	308_H	0.684	0.79
87_T	91_K	0.681	0.79
223_L	261_V	0.681	0.79
111_K	118_S	0.681	0.79
255_L	259_T	0.679	0.78
255_L	261_V	0.676	0.78
32_K	35_T	0.676	0.78
166_Y	174_K	0.669	0.77
299_I	307_I	0.669	0.77
261_V	272_S	0.669	0.77
51_K	58_S	0.668	0.77
255_L	258_Q	0.666	0.77
89_K	104_G	0.666	0.77
218_L	221_S	0.658	0.76
139_S	143_V	0.654	0.76
259_T	272_S	0.653	0.76
69_I	76_S	0.651	0.75
161_K	164_S	0.647	0.75
99_I	104_G	0.647	0.75
96_L	99_I	0.646	0.75
206_S	210_S	0.645	0.75
200_S	205_S	0.644	0.75
173_L	179_L	0.644	0.75
177_N	180_K	0.643	0.74
114_N	118_S	0.641	0.74
131_G	135_S	0.640	0.74
169_T	183_V	0.636	0.74
269_Y	274_K	0.635	0.74
97_W	105_M	0.634	0.73
202_P	207_S	0.629	0.73
121_L	124_G	0.627	0.73
171_S	174_K	0.626	0.73
202_P	205_S	0.625	0.72
120_L	128_K	0.624	0.72
276_I	285_V	0.624	0.72
106_T	110_L	0.623	0.72
200_S	204_S	0.622	0.72
160_S	164_S	0.621	0.72
194_G	197_T	0.621	0.72
169_T	180_K	0.618	0.72
50_I	53_E	0.618	0.72
47_I	53_E	0.617	0.71
36_L	39_L	0.617	0.71
254_V	257_K	0.616	0.71
223_L	255_L	0.615	0.71
202_P	208_S	0.613	0.71
268_G	297_M	0.612	0.71
145_S	155_S	0.612	0.71
175_S	183_V	0.611	0.71
96_L	101_K	0.609	0.70
107_I	116_L	0.609	0.70
165_K	168_T	0.608	0.70
59_D	63_V	0.607	0.70
211_S	215_S	0.604	0.70
161_K	165_K	0.603	0.70
140_S	144_S	0.600	0.69
90_V	96_L	0.599	0.69
148_T	159_L	0.599	0.69
48_S	51_K	0.598	0.69
146_S	150_T	0.597	0.69
300_Y	304_N	0.595	0.69
311_S	314_V	0.594	0.69
149_S	152_K	0.594	0.69
151_Y	154_K	0.594	0.69
255_L	272_S	0.592	0.68
39_L	43_Y	0.592	0.68
81_S	85_S	0.592	0.68
34_D	38_D	0.591	0.68
90_V	97_W	0.590	0.68
229_A	250_F	0.590	0.68
143_V	147_S	0.589	0.68
66_T	69_I	0.588	0.68
108_N	112_K	0.587	0.68
181_S	185_Y	0.587	0.68
162_I	169_T	0.585	0.67
187_N	194_G	0.584	0.67
223_L	254_V	0.584	0.67
107_I	114_N	0.583	0.67
267_A	284_F	0.581	0.67
98_K	103_Y	0.579	0.67
38_D	41_R	0.579	0.67
176_L	184_I	0.578	0.66
305_S	318_S	0.577	0.66
237_W	249_G	0.575	0.66
198_S	204_S	0.573	0.66
93_G	100_S	0.573	0.66
156_G	166_Y	0.572	0.66
186_V	193_K	0.570	0.65
240_T	245_F	0.568	0.65
85_S	90_V	0.567	0.65
80_S	86_S	0.567	0.65
110_L	114_N	0.564	0.65
172_K	179_L	0.564	0.65
181_S	184_I	0.564	0.65
279_P	287_F	0.560	0.64
264_T	298_G	0.560	0.64
178_G	182_D	0.559	0.64
226_D	255_L	0.558	0.64
130_K	133_T	0.557	0.64
52_S	56_L	0.553	0.63
265_S	268_G	0.553	0.63
121_L	130_K	0.552	0.63
266_T	295_S	0.551	0.63
202_P	206_S	0.550	0.63
78_S	82_S	0.550	0.63
131_G	134_S	0.550	0.63
241_T	253_Y	0.549	0.63
88_Y	103_Y	0.548	0.62
106_T	111_K	0.548	0.62
150_T	154_K	0.547	0.62
131_G	138_S	0.545	0.62
122_R	130_K	0.544	0.62
150_T	153_V	0.542	0.62
285_V	319_L	0.541	0.61
270_W	274_K	0.541	0.61
88_Y	96_L	0.541	0.61
205_S	208_S	0.541	0.61
123_V	126_V	0.540	0.61
112_K	115_G	0.539	0.61
192_V	195_T	0.537	0.61
89_K	96_L	0.535	0.61
245_F	314_V	0.533	0.60
203_A	207_S	0.533	0.60
294_P	329_L	0.532	0.60
197_T	203_A	0.532	0.60
274_K	330_G	0.531	0.60
183_V	186_V	0.528	0.60
212_K	215_S	0.526	0.59
152_K	159_L	0.526	0.59
80_S	90_V	0.525	0.59
153_V	160_S	0.524	0.59
197_T	200_S	0.521	0.59
175_S	178_G	0.520	0.58
94_D	97_W	0.519	0.58
230_L	253_Y	0.516	0.58
287_F	326_P	0.515	0.58
319_L	328_Y	0.514	0.58
119_D	122_R	0.513	0.57
109_E	117_K	0.512	0.57
85_S	92_S	0.510	0.57
198_S	202_P	0.508	0.57
220_V	223_L	0.505	0.56
121_L	131_G	0.505	0.56
85_S	93_G	0.505	0.56
202_P	210_S	0.504	0.56
42_K	46_T	0.502	0.56
37_W	40_S	0.501	0.56
142_K	146_S	0.500	0.55
92_S	100_S	0.500	0.55

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
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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
4q4gX	1	0.3802	100	0.421	Contact Map
4xcmA	2	0.6557	100	0.46	Contact Map
2k1gA	1	0.3563	100	0.524	Contact Map
3npfA	2	0.7575	100	0.542	Contact Map
4hpeA	1	0.7216	100	0.543	Contact Map
3h41A	1	0.8563	100	0.555	Contact Map
4fdyA	1	0.7485	100	0.555	Contact Map
4lj1A	1	0.3383	100	0.558	Contact Map
2hbwA	1	0.5808	100	0.561	Contact Map
3pbiA	1	0.5329	100	0.562	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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