YNHG - ECOLI - GREMLIN Contacts

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YNHG - Probable L,D-transpeptidase YnhG

UniProt:	P76193	Sequences: MKRASLLTLTLIGAFSAIQAAWAVDYPLPPTGSRLVGQNQTYTVQEGDKNLQAIARRFDTAAMLILEANNTIAPVPKPGTTITIPSQLLLPDAPRQGIIVNLAELRLYYYPPGENIVQVYPIGIGLQGLETPVMETRVGQKIPNPTWTPTAGIRQRSLERGIKLPPVVPAGPNNPLGRYALRLAHGNGEYLIHGTSAPDSVGLRVSSGCIRMNAPDIKALFSSVRTGTPVKVINEPVKYSVEPNGMRYVEVHRPLSAEEQQNVQTMPYTLPAGFTQFKDNKAVDQKLVDKALYRRAGYPVSVSSGATPAASNAPSVESAQNGEPEQGNMLRVTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14015
Length:	334 (292)
Sequences:	562 (344)
Seq/√Len:	20.1

ECOLI - YNHG YCFS YBIS ERFK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
93_A	233_I	5.324	1.00
136_T	184_A	5.043	1.00
140_Q	182_R	4.602	1.00
104_E	238_K	4.172	1.00
151_A	155_Q	3.844	1.00
156_R	207_S	3.766	1.00
128_G	206_S	3.737	1.00
108_Y	238_K	3.273	1.00
249_V	288_V	3.051	0.99
148_T	170_A	2.945	0.99
104_E	108_Y	2.901	0.99
176_L	191_L	2.864	0.99
123_G	206_S	2.786	0.99
129_L	207_S	2.705	0.98
120_Y	219_A	2.492	0.97
56_R	65_I	2.429	0.97
214_A	218_K	2.426	0.97
88_L	119_V	2.388	0.96
154_R	166_P	2.357	0.96
146_T	170_A	2.281	0.95
89_L	240_S	2.212	0.95
157_S	162_I	2.154	0.94
93_A	110_Y	2.080	0.93
180_A	217_I	2.060	0.92
150_T	189_E	2.033	0.92
153_I	207_S	2.013	0.91
15_F	22_W	1.978	0.90
155_Q	159_E	1.970	0.90
21_A	36_V	1.914	0.89
138_V	181_L	1.911	0.89
148_T	167_V	1.911	0.89
56_R	215_P	1.904	0.89
47_G	77_K	1.900	0.89
241_V	247_R	1.894	0.88
61_A	200_S	1.865	0.88
182_R	191_L	1.863	0.88
56_R	198_P	1.834	0.87
65_I	82_I	1.832	0.87
200_S	205_V	1.806	0.86
152_G	189_E	1.795	0.85
55_A	65_I	1.790	0.85
122_I	210_I	1.781	0.85
211_R	238_K	1.780	0.85
249_V	302_V	1.734	0.83
108_Y	233_I	1.726	0.83
100_V	210_I	1.677	0.81
250_E	299_P	1.666	0.81
102_L	183_L	1.654	0.80
144_N	178_R	1.645	0.80
158_L	163_K	1.629	0.79
35_L	89_L	1.546	0.76
61_A	73_A	1.543	0.75
52_Q	213_N	1.542	0.75
25_D	42_Y	1.539	0.75
150_T	153_I	1.514	0.74
34_R	240_S	1.507	0.74
180_A	191_L	1.479	0.72
127_Q	206_S	1.476	0.72
152_G	207_S	1.473	0.72
123_G	128_G	1.459	0.71
73_A	199_D	1.437	0.70
126_L	156_R	1.437	0.70
76_P	79_G	1.426	0.69
48_D	176_L	1.426	0.69
44_V	78_P	1.415	0.69
192_I	212_M	1.411	0.68
149_P	154_R	1.407	0.68
120_Y	191_L	1.406	0.68
129_L	156_R	1.380	0.67
183_L	190_Y	1.364	0.66
201_V	205_V	1.363	0.66
249_V	291_A	1.362	0.66
129_L	134_M	1.352	0.65
283_V	288_V	1.346	0.65
285_Q	288_V	1.340	0.64
93_A	235_E	1.332	0.64
75_V	199_D	1.330	0.64
102_L	232_V	1.326	0.64
30_P	95_R	1.313	0.63
81_T	110_Y	1.310	0.63
36_V	103_A	1.303	0.62
135_E	231_K	1.296	0.62
234_N	255_L	1.272	0.60
135_E	229_P	1.268	0.60
181_L	218_K	1.266	0.60
202_G	230_V	1.263	0.60
154_R	164_L	1.259	0.59
56_R	213_N	1.257	0.59
105_L	206_S	1.256	0.59
237_V	285_Q	1.247	0.59
144_N	227_G	1.243	0.58
55_A	213_N	1.233	0.58
72_I	80_T	1.232	0.58
181_L	248_Y	1.228	0.57
142_I	226_T	1.227	0.57
35_L	248_Y	1.227	0.57
36_V	88_L	1.220	0.57
134_M	185_H	1.219	0.57
141_K	184_A	1.209	0.56
198_P	201_V	1.209	0.56
95_R	191_L	1.199	0.56
52_Q	56_R	1.196	0.55
42_Y	58_F	1.191	0.55
289_D	292_L	1.189	0.55
74_P	128_G	1.188	0.55
44_V	47_G	1.183	0.55
11_L	16_S	1.173	0.54
149_P	238_K	1.168	0.54
157_S	199_D	1.167	0.54
90_L	201_V	1.165	0.53
41_T	81_T	1.150	0.52
104_E	211_R	1.145	0.52
178_R	214_A	1.137	0.52
97_G	117_V	1.133	0.51
107_L	245_G	1.127	0.51
64_L	203_L	1.114	0.50
24_V	59_D	1.112	0.50
68_A	85_P	1.103	0.49
125_G	211_R	1.096	0.49
218_K	222_S	1.093	0.49
241_V	245_G	1.088	0.48
131_T	210_I	1.087	0.48
44_V	77_K	1.086	0.48
167_V	170_A	1.081	0.48
107_L	196_S	1.079	0.48
139_G	184_A	1.069	0.47
47_G	78_P	1.058	0.46
200_S	203_L	1.056	0.46
124_I	128_G	1.047	0.46
179_Y	222_S	1.046	0.46
251_V	291_A	1.046	0.46
183_L	214_A	1.041	0.45
85_P	106_R	1.040	0.45
9_L	16_S	1.040	0.45
98_I	224_V	1.039	0.45
40_Q	86_S	1.032	0.45
158_L	300_V	1.022	0.44
288_V	302_V	1.022	0.44
17_A	20_A	1.020	0.44
92_D	235_E	1.017	0.44
99_I	169_P	1.011	0.43
35_L	87_Q	1.004	0.43
164_L	299_P	0.997	0.43
67_E	253_R	0.996	0.42
51_L	65_I	0.994	0.42
291_A	300_V	0.987	0.42
284_D	290_K	0.985	0.42
61_A	70_N	0.978	0.41
14_A	18_I	0.972	0.41
72_I	103_A	0.967	0.41
77_K	80_T	0.966	0.41
71_T	300_V	0.961	0.40
84_I	221_F	0.961	0.40
16_S	20_A	0.960	0.40
164_L	205_V	0.957	0.40
26_Y	36_V	0.957	0.40
125_G	190_Y	0.950	0.40
137_R	227_G	0.950	0.40
157_S	163_K	0.949	0.39
54_I	153_I	0.946	0.39
252_H	299_P	0.945	0.39
98_I	138_V	0.943	0.39
183_L	191_L	0.941	0.39
26_Y	29_P	0.940	0.39
131_T	218_K	0.934	0.39
159_E	167_V	0.931	0.38
105_L	142_I	0.931	0.38
96_Q	113_G	0.927	0.38
205_V	299_P	0.926	0.38
149_P	211_R	0.925	0.38
39_N	122_I	0.923	0.38
29_P	32_G	0.917	0.38
44_V	79_G	0.911	0.37
20_A	276_Q	0.911	0.37
125_G	297_G	0.907	0.37
25_D	283_V	0.907	0.37
290_K	294_R	0.906	0.37
108_Y	212_M	0.900	0.36
136_T	255_L	0.896	0.36
250_E	295_R	0.893	0.36
155_Q	291_A	0.892	0.36
54_I	201_V	0.891	0.36
139_G	182_R	0.890	0.36
157_S	197_A	0.890	0.36
276_Q	302_V	0.883	0.35
47_G	176_L	0.881	0.35
137_R	226_T	0.881	0.35
238_K	250_E	0.877	0.35
134_M	198_P	0.871	0.35
10_T	14_A	0.865	0.34
246_M	301_S	0.864	0.34
63_M	74_P	0.863	0.34
129_L	189_E	0.862	0.34
44_V	245_G	0.858	0.34
151_A	166_P	0.852	0.34
74_P	123_G	0.852	0.34
261_Q	266_M	0.850	0.34
72_I	76_P	0.843	0.33
19_Q	201_V	0.843	0.33
201_V	251_V	0.840	0.33
26_Y	117_V	0.832	0.33
48_D	54_I	0.832	0.33
28_L	111_P	0.828	0.32
173_N	218_K	0.824	0.32
113_G	221_F	0.824	0.32
130_E	196_S	0.818	0.32
94_P	111_P	0.811	0.31
118_Q	219_A	0.811	0.31
100_V	232_V	0.809	0.31
134_M	184_A	0.808	0.31
251_V	292_L	0.805	0.31
252_H	295_R	0.799	0.31
287_L	291_A	0.798	0.31
149_P	190_Y	0.795	0.30
131_T	195_T	0.795	0.30
135_E	227_G	0.788	0.30
86_S	155_Q	0.781	0.30
64_L	240_S	0.781	0.30
27_P	30_P	0.780	0.30
225_R	228_T	0.780	0.30
103_A	123_G	0.779	0.30
234_N	254_P	0.778	0.30
30_P	143_P	0.775	0.29
100_V	274_F	0.773	0.29
245_G	256_S	0.771	0.29
179_Y	218_K	0.770	0.29
240_S	257_A	0.760	0.29
94_P	155_Q	0.755	0.28
61_A	106_R	0.755	0.28
143_P	179_Y	0.752	0.28
84_I	219_A	0.751	0.28
218_K	255_L	0.751	0.28
183_L	210_I	0.751	0.28
61_A	85_P	0.747	0.28
54_I	223_S	0.745	0.28
166_P	284_D	0.742	0.28
201_V	206_S	0.740	0.27
106_R	202_G	0.738	0.27
50_N	78_P	0.737	0.27
110_Y	233_I	0.736	0.27
62_A	139_G	0.734	0.27
160_R	173_N	0.734	0.27
70_N	200_S	0.732	0.27
273_G	277_F	0.729	0.27
204_R	234_N	0.729	0.27
142_I	182_R	0.726	0.27
102_L	144_N	0.726	0.27
120_Y	262_N	0.724	0.27
191_L	203_L	0.722	0.27
181_L	221_F	0.722	0.27
155_Q	283_V	0.721	0.27
32_G	36_V	0.719	0.26
91_P	174_N	0.713	0.26
204_R	245_G	0.707	0.26
226_T	284_D	0.706	0.26
72_I	270_L	0.705	0.26
125_G	217_I	0.703	0.26
250_E	297_G	0.701	0.26
31_T	110_Y	0.701	0.26
107_L	204_R	0.700	0.25
45_Q	48_D	0.698	0.25
28_L	94_P	0.698	0.25
105_L	182_R	0.697	0.25
62_A	200_S	0.696	0.25
14_A	17_A	0.694	0.25
12_I	16_S	0.694	0.25
24_V	283_V	0.691	0.25
251_V	301_S	0.688	0.25
164_L	250_E	0.688	0.25
31_T	58_F	0.687	0.25
64_L	302_V	0.685	0.25
76_P	203_L	0.685	0.25
116_I	226_T	0.683	0.25
152_G	156_R	0.675	0.24
149_P	212_M	0.674	0.24
29_P	111_P	0.674	0.24
60_T	159_E	0.673	0.24
105_L	191_L	0.672	0.24
156_R	205_V	0.669	0.24
126_L	129_L	0.668	0.24
113_G	138_V	0.666	0.24
95_R	149_P	0.666	0.24
168_V	232_V	0.664	0.24
68_A	83_T	0.660	0.24
50_N	126_L	0.658	0.23
241_V	281_K	0.656	0.23
84_I	179_Y	0.655	0.23
37_G	85_P	0.654	0.23
105_L	207_S	0.653	0.23
134_M	191_L	0.651	0.23
104_E	149_P	0.648	0.23
42_Y	89_L	0.647	0.23
94_P	302_V	0.647	0.23
157_S	203_L	0.645	0.23
63_M	102_L	0.644	0.23
237_V	251_V	0.644	0.23
181_L	217_I	0.640	0.23
268_Y	271_P	0.637	0.22
64_L	140_Q	0.635	0.22
16_S	179_Y	0.635	0.22
11_L	17_A	0.635	0.22
123_G	194_G	0.635	0.22
43_T	287_L	0.632	0.22
9_L	276_Q	0.631	0.22
138_V	144_N	0.631	0.22
72_I	75_V	0.631	0.22
17_A	21_A	0.628	0.22
16_S	302_V	0.626	0.22
35_L	80_T	0.626	0.22
183_L	217_I	0.625	0.22
289_D	293_Y	0.625	0.22
59_D	283_V	0.623	0.22
60_T	66_L	0.621	0.22
43_T	144_N	0.621	0.22
25_D	114_E	0.620	0.22
10_T	18_I	0.620	0.22
56_R	199_D	0.616	0.22
33_S	103_A	0.615	0.22
166_P	225_R	0.615	0.22
131_T	198_P	0.607	0.21
31_T	95_R	0.606	0.21
20_A	57_R	0.605	0.21
206_S	233_I	0.604	0.21
74_P	84_I	0.604	0.21
29_P	255_L	0.603	0.21
159_E	188_G	0.603	0.21
121_P	216_D	0.603	0.21
104_E	200_S	0.601	0.21
154_R	211_R	0.600	0.21
51_L	122_I	0.599	0.21
27_P	31_T	0.598	0.21
23_A	29_P	0.598	0.21
115_N	251_V	0.597	0.21
12_I	20_A	0.597	0.21
104_E	217_I	0.596	0.21
114_E	249_V	0.595	0.21
134_M	214_A	0.594	0.21
58_F	302_V	0.593	0.21
167_V	248_Y	0.593	0.21
41_T	163_K	0.591	0.20
123_G	127_Q	0.589	0.20
35_L	44_V	0.588	0.20
52_Q	199_D	0.588	0.20
141_K	228_T	0.587	0.20
197_A	205_V	0.586	0.20
172_P	227_G	0.585	0.20
97_G	190_Y	0.585	0.20
34_R	95_R	0.585	0.20
62_A	194_G	0.584	0.20
204_R	255_L	0.584	0.20
152_G	197_A	0.583	0.20
262_N	265_T	0.583	0.20
62_A	119_V	0.581	0.20
142_I	184_A	0.580	0.20
137_R	296_A	0.576	0.20
197_A	295_R	0.575	0.20
70_N	212_M	0.574	0.20
110_Y	118_Q	0.569	0.20
158_L	168_V	0.568	0.20
183_L	194_G	0.564	0.19
12_I	158_L	0.562	0.19
34_R	66_L	0.562	0.19
33_S	108_Y	0.562	0.19
64_L	157_S	0.560	0.19
133_V	235_E	0.559	0.19
62_A	74_P	0.559	0.19
35_L	240_S	0.559	0.19
104_E	250_E	0.559	0.19
228_T	245_G	0.557	0.19
51_L	264_Q	0.557	0.19
176_L	183_L	0.556	0.19
123_G	224_V	0.556	0.19
69_N	165_P	0.556	0.19
16_S	43_T	0.556	0.19
179_Y	217_I	0.555	0.19
61_A	76_P	0.554	0.19
76_P	85_P	0.554	0.19
84_I	232_V	0.553	0.19
141_K	236_P	0.549	0.19
157_S	200_S	0.549	0.19
25_D	32_G	0.548	0.19
169_P	211_R	0.548	0.19
25_D	46_E	0.548	0.19
63_M	105_L	0.546	0.19
270_L	275_T	0.543	0.19
9_L	13_G	0.543	0.19
153_I	253_R	0.542	0.18
16_S	19_Q	0.542	0.18
85_P	202_G	0.540	0.18
36_V	58_F	0.540	0.18
155_Q	222_S	0.540	0.18
122_I	296_A	0.539	0.18
195_T	214_A	0.539	0.18
263_V	266_M	0.538	0.18
138_V	260_Q	0.538	0.18
178_R	225_R	0.537	0.18
60_T	65_I	0.536	0.18
212_M	288_V	0.534	0.18
181_L	220_L	0.533	0.18
125_G	183_L	0.533	0.18
131_T	217_I	0.532	0.18
205_V	251_V	0.531	0.18
36_V	163_K	0.531	0.18
50_N	298_Y	0.530	0.18
13_G	272_A	0.529	0.18
121_P	245_G	0.528	0.18
168_V	211_R	0.527	0.18
264_Q	269_T	0.527	0.18
144_N	179_Y	0.527	0.18
88_L	240_S	0.525	0.18
159_E	275_T	0.524	0.18
14_A	22_W	0.521	0.18
268_Y	273_G	0.520	0.18
54_I	144_N	0.519	0.18
103_A	201_V	0.519	0.18
43_T	270_L	0.517	0.18
74_P	102_L	0.515	0.17
105_L	204_R	0.515	0.17
68_A	182_R	0.515	0.17
176_L	297_G	0.515	0.17
189_E	207_S	0.513	0.17
157_S	164_L	0.511	0.17
194_G	220_L	0.511	0.17
45_Q	75_V	0.511	0.17
206_S	256_S	0.511	0.17
146_T	290_K	0.510	0.17
53_A	162_I	0.508	0.17
140_Q	189_E	0.508	0.17
171_G	175_P	0.507	0.17
191_L	207_S	0.506	0.17
252_H	297_G	0.506	0.17
212_M	217_I	0.504	0.17
11_L	115_N	0.504	0.17
195_T	221_F	0.503	0.17
74_P	206_S	0.501	0.17
138_V	164_L	0.501	0.17
141_K	182_R	0.500	0.17
12_I	19_Q	0.500	0.17

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
4lzhA	1	0.8174	100	0.432	Contact Map
4xvoA	1	0.5898	100	0.671	Contact Map
4jmnA	1	0.5868	100	0.684	Contact Map
4a1kA	2	0.494	100	0.689	Contact Map
4k73A	1	0.5629	100	0.749	Contact Map
3vypA	1	0.6856	100	0.758	Contact Map
1zatA	1	0.6257	100	0.763	Contact Map
4qtfA	2	0.7275	100	0.769	Contact Map
5bmqA	3	0.5569	100	0.775	Contact Map
4lpqA	1	0.5479	100	0.786	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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