YBIS - ECOLI - GREMLIN Contacts

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YBIS - Probable L,D-transpeptidase YbiS

UniProt:	P0AAX8	Sequences: MNMKLKTLFAAAFAVVGFCSTASAVTYPLPTDGSRLVGQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQLILPDTVHEGIVINSAEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRVQFIDEPVKATTEPDGSRYIEVHNPLSTTEAQFEGQEIVPITLTKSVQTVTGQPDVDQVVLDEAIKNRSGMPVRLN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13324
Length:	306 (289)
Sequences:	557 (347)
Seq/√Len:	20.4

ECOLI - YBIS YCFS ERFK YNHG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_T	234_I	5.088	1.00
140_T	188_G	4.823	1.00
144_R	186_Y	4.530	1.00
131_G	207_S	4.426	1.00
107_E	239_K	4.290	1.00
160_E	208_H	3.890	1.00
155_A	159_A	3.765	1.00
111_Y	239_K	3.427	1.00
250_I	291_L	3.420	1.00
180_M	192_A	3.385	1.00
107_E	111_Y	3.005	0.99
123_L	220_F	2.490	0.97
91_L	122_V	2.490	0.97
132_K	208_H	2.466	0.97
158_H	170_A	2.339	0.96
126_G	207_S	2.333	0.96
152_T	174_A	2.326	0.96
105_S	187_I	2.256	0.95
242_T	248_R	2.249	0.95
186_Y	192_A	2.232	0.95
92_I	241_T	2.215	0.95
201_G	206_V	2.150	0.94
48_G	80_K	2.134	0.94
96_T	113_Y	2.125	0.94
58_A	67_M	2.108	0.93
142_V	185_L	2.104	0.93
215_N	219_K	2.090	0.93
202_I	206_V	2.077	0.93
157_M	208_H	2.014	0.92
36_L	92_I	1.991	0.91
212_R	239_K	1.965	0.91
184_A	218_I	1.942	0.90
152_T	171_V	1.923	0.90
67_M	85_L	1.913	0.89
58_A	216_E	1.909	0.89
148_G	182_L	1.872	0.88
150_T	174_A	1.871	0.88
103_I	211_V	1.849	0.88
161_Y	166_E	1.838	0.87
251_E	302_P	1.827	0.87
154_T	157_M	1.821	0.87
35_R	241_T	1.736	0.84
75_D	78_L	1.722	0.83
250_I	294_A	1.720	0.83
130_L	207_S	1.707	0.83
125_I	211_V	1.701	0.83
58_A	199_N	1.685	0.82
291_L	305_L	1.677	0.82
111_Y	234_I	1.677	0.82
129_Q	160_E	1.676	0.82
63_G	201_G	1.636	0.80
43_I	60_Y	1.595	0.78
184_A	192_A	1.583	0.78
288_Q	291_L	1.577	0.78
156_K	208_H	1.575	0.77
22_A	37_V	1.549	0.76
132_K	137_N	1.507	0.74
159_A	163_A	1.503	0.74
57_A	67_M	1.478	0.73
154_T	190_L	1.475	0.73
49_N	180_M	1.469	0.72
139_T	230_R	1.453	0.71
75_D	200_F	1.447	0.71
54_E	214_R	1.438	0.71
45_I	48_G	1.409	0.69
153_P	158_H	1.407	0.69
139_T	232_Q	1.403	0.69
286_V	291_L	1.390	0.68
162_R	167_P	1.389	0.68
156_K	190_L	1.352	0.66
63_G	75_D	1.345	0.65
250_I	305_L	1.342	0.65
199_N	202_I	1.339	0.65
126_G	131_G	1.336	0.65
37_V	91_L	1.329	0.64
37_V	60_Y	1.324	0.64
48_G	81_G	1.307	0.63
87_I	222_F	1.285	0.62
123_L	192_A	1.264	0.60
84_V	113_Y	1.258	0.60
162_R	303_V	1.249	0.59
78_L	200_F	1.249	0.59
17_G	21_T	1.237	0.59
183_Y	223_E	1.225	0.58
235_D	256_L	1.222	0.58
105_S	233_F	1.216	0.57
219_K	223_E	1.212	0.57
132_K	160_E	1.210	0.57
96_T	236_E	1.200	0.56
65_S	76_T	1.198	0.56
58_A	214_R	1.195	0.56
36_L	249_Y	1.193	0.56
30_P	114_P	1.187	0.55
101_I	142_V	1.186	0.55
227_V	287_D	1.176	0.55
153_P	212_R	1.172	0.54
203_G	231_V	1.172	0.54
193_I	213_L	1.170	0.54
187_I	192_A	1.168	0.54
16_V	23_S	1.163	0.54
116_G	142_V	1.155	0.53
63_G	72_P	1.152	0.53
107_E	212_R	1.145	0.53
12_A	17_G	1.143	0.53
88_P	109_R	1.142	0.52
185_L	249_Y	1.140	0.52
27_Y	37_V	1.138	0.52
146_K	227_V	1.137	0.52
187_I	191_Y	1.137	0.52
50_T	81_G	1.133	0.52
74_V	83_T	1.105	0.50
93_L	100_G	1.104	0.50
92_I	263_F	1.103	0.50
134_T	211_V	1.089	0.49
252_V	294_A	1.089	0.49
11_A	14_A	1.088	0.49
201_G	204_L	1.083	0.49
148_G	228_G	1.080	0.48
40_N	125_I	1.077	0.48
158_H	168_L	1.064	0.47
251_E	298_R	1.057	0.47
292_D	295_I	1.054	0.47
226_P	229_T	1.052	0.47
238_V	288_Q	1.051	0.47
45_I	82_G	1.045	0.46
29_L	114_P	1.041	0.46
30_P	188_G	1.040	0.46
108_M	207_S	1.032	0.45
73_G	303_V	1.026	0.45
26_T	43_I	1.024	0.45
31_T	98_H	1.023	0.45
49_N	56_F	1.017	0.44
53_L	67_M	1.016	0.44
37_V	266_Q	1.014	0.44
187_I	215_N	1.013	0.44
102_V	173_P	1.012	0.44
242_T	246_G	1.012	0.44
76_T	131_G	1.010	0.44
110_L	197_N	1.009	0.44
69_E	254_N	1.009	0.44
110_L	246_G	1.009	0.44
141_K	227_V	1.006	0.44
182_L	215_N	1.004	0.43
45_I	80_K	1.003	0.43
55_Y	77_F	1.002	0.43
161_Y	200_F	0.999	0.43
66_N	241_T	0.994	0.43
287_D	293_E	0.992	0.43
187_I	211_V	0.984	0.42
15_V	19_C	0.984	0.42
253_H	302_P	0.983	0.42
153_P	191_Y	0.982	0.42
95_D	236_E	0.979	0.42
185_L	219_K	0.978	0.42
108_M	146_K	0.969	0.41
64_L	143_E	0.967	0.41
153_P	239_K	0.966	0.41
294_A	303_V	0.963	0.41
25_V	61_Q	0.963	0.41
74_V	106_A	0.959	0.41
56_F	224_K	0.959	0.41
57_A	214_R	0.957	0.40
64_L	76_T	0.957	0.40
74_V	79_P	0.956	0.40
54_E	58_A	0.947	0.40
66_N	204_L	0.946	0.40
36_L	90_Q	0.945	0.40
66_N	305_L	0.938	0.39
36_L	241_T	0.931	0.39
42_V	84_V	0.923	0.38
37_V	106_A	0.915	0.38
155_A	170_A	0.912	0.38
45_I	81_G	0.912	0.38
148_G	183_Y	0.912	0.38
135_P	165_G	0.910	0.38
128_G	212_R	0.905	0.37
127_I	131_G	0.905	0.37
247_S	304_R	0.904	0.37
20_S	44_T	0.902	0.37
87_I	220_F	0.900	0.37
48_G	180_M	0.899	0.37
141_K	228_G	0.897	0.37
205_R	235_D	0.881	0.36
146_K	186_Y	0.874	0.35
30_P	140_T	0.872	0.35
80_K	83_T	0.871	0.35
13_F	19_C	0.871	0.35
101_I	225_V	0.870	0.35
170_A	287_D	0.864	0.35
79_P	88_P	0.864	0.35
111_Y	213_L	0.863	0.35
112_Y	229_T	0.859	0.34
87_I	233_F	0.855	0.34
70_A	88_P	0.854	0.34
139_T	228_G	0.839	0.33
63_G	109_R	0.838	0.33
87_I	183_Y	0.830	0.33
12_A	18_F	0.827	0.33
213_L	218_I	0.825	0.32
206_V	302_P	0.824	0.32
140_T	256_L	0.817	0.32
113_Y	234_I	0.814	0.32
93_L	202_I	0.814	0.32
158_H	212_R	0.812	0.32
293_E	297_N	0.802	0.31
163_A	285_D	0.800	0.31
76_T	126_G	0.798	0.31
38_G	88_P	0.795	0.31
143_E	186_Y	0.792	0.31
98_H	153_P	0.789	0.30
41_Q	89_Q	0.786	0.30
132_K	190_L	0.784	0.30
109_R	203_G	0.783	0.30
20_S	23_S	0.782	0.30
239_K	251_E	0.780	0.30
34_S	202_I	0.778	0.30
160_E	206_V	0.775	0.30
48_G	172_V	0.773	0.30
269_V	272_T	0.772	0.30
161_Y	201_G	0.772	0.30
235_D	255_P	0.771	0.29
137_N	199_N	0.767	0.29
99_E	116_G	0.766	0.29
12_A	20_S	0.766	0.29
21_T	59_E	0.766	0.29
55_Y	166_E	0.762	0.29
97_V	114_P	0.762	0.29
191_Y	300_G	0.759	0.29
248_R	290_V	0.758	0.29
198_A	298_R	0.757	0.29
128_G	300_G	0.754	0.29
18_F	21_T	0.753	0.29
241_T	258_T	0.751	0.28
202_I	207_S	0.748	0.28
133_D	197_N	0.746	0.28
163_A	171_V	0.745	0.28
26_T	286_V	0.743	0.28
98_H	192_A	0.740	0.28
121_I	220_F	0.733	0.27
137_N	215_N	0.731	0.27
128_G	187_I	0.731	0.27
142_V	261_A	0.730	0.27
168_L	187_I	0.729	0.27
129_Q	132_K	0.727	0.27
173_P	212_R	0.726	0.27
172_V	233_F	0.725	0.27
66_N	161_Y	0.724	0.27
36_L	83_T	0.722	0.27
70_A	186_Y	0.719	0.27
183_Y	219_K	0.719	0.27
153_P	200_F	0.718	0.27
147_A	183_Y	0.717	0.27
34_S	244_P	0.717	0.27
89_Q	159_A	0.716	0.27
85_L	154_T	0.715	0.27
35_R	125_I	0.715	0.27
63_G	88_P	0.708	0.26
35_R	98_H	0.707	0.26
213_L	291_L	0.706	0.26
205_R	246_G	0.702	0.26
65_S	105_S	0.701	0.26
36_L	277_V	0.700	0.26
37_V	183_Y	0.698	0.26
108_M	208_H	0.695	0.26
45_I	246_G	0.694	0.25
161_Y	198_A	0.694	0.25
31_T	147_A	0.692	0.25
26_T	117_T	0.691	0.25
158_H	239_K	0.691	0.25
88_P	203_G	0.687	0.25
22_A	31_T	0.685	0.25
156_K	160_E	0.683	0.25
154_T	189_R	0.682	0.25
164_A	177_D	0.681	0.25
180_M	202_I	0.673	0.24
134_T	199_N	0.671	0.24
62_M	267_E	0.670	0.24
128_G	191_Y	0.670	0.24
128_G	218_I	0.669	0.24
141_K	230_R	0.668	0.24
44_T	148_G	0.667	0.24
126_G	195_G	0.666	0.24
183_Y	218_I	0.665	0.24
105_S	197_N	0.665	0.24
13_F	21_T	0.665	0.24
18_F	22_A	0.664	0.24
107_E	153_P	0.662	0.24
92_I	119_T	0.661	0.24
72_P	213_L	0.658	0.24
77_F	214_R	0.657	0.24
100_G	120_V	0.657	0.24
25_V	286_V	0.654	0.24
253_H	298_R	0.650	0.23
170_A	226_P	0.643	0.23
70_A	229_T	0.641	0.23
61_Q	233_F	0.640	0.23
56_F	157_M	0.637	0.23
134_T	219_K	0.635	0.23
202_I	216_E	0.634	0.23
37_V	122_V	0.634	0.23
195_G	221_L	0.633	0.23
185_L	278_Q	0.633	0.23
161_Y	168_L	0.631	0.22
87_I	253_H	0.626	0.22
202_I	252_V	0.625	0.22
141_K	299_S	0.625	0.22
106_A	269_V	0.618	0.22
198_A	206_V	0.617	0.22
189_R	233_F	0.616	0.22
74_V	78_L	0.615	0.22
171_V	174_A	0.610	0.22
238_V	252_V	0.607	0.21
116_G	139_T	0.607	0.21
93_L	120_V	0.607	0.21
77_F	132_K	0.603	0.21
199_N	215_N	0.603	0.21
44_T	290_V	0.600	0.21
153_P	213_L	0.600	0.21
63_G	77_F	0.599	0.21
219_K	256_L	0.599	0.21
64_L	195_G	0.595	0.21
107_E	218_I	0.594	0.21
13_F	250_I	0.594	0.21
63_G	79_P	0.592	0.21
64_L	68_M	0.591	0.21
65_S	108_M	0.590	0.21
104_N	107_E	0.590	0.21
46_P	113_Y	0.589	0.21
238_V	250_I	0.588	0.21
251_E	300_G	0.587	0.21
287_D	290_V	0.586	0.20
26_T	121_I	0.584	0.20
76_T	207_S	0.584	0.20
65_S	199_N	0.584	0.20
14_A	19_C	0.583	0.20
97_V	305_L	0.583	0.20
168_L	251_E	0.583	0.20
241_T	244_P	0.582	0.20
128_G	134_T	0.579	0.20
252_V	295_I	0.579	0.20
35_R	68_M	0.578	0.20
42_V	167_P	0.577	0.20
93_L	155_A	0.577	0.20
169_P	192_A	0.577	0.20
57_A	202_I	0.576	0.20
13_F	23_S	0.575	0.20
165_G	204_L	0.575	0.20
48_G	77_F	0.574	0.20
168_L	206_V	0.571	0.20
113_Y	188_G	0.571	0.20
71_N	169_P	0.570	0.20
56_F	202_I	0.569	0.20
54_E	77_F	0.568	0.20
161_Y	167_P	0.568	0.20
135_P	251_E	0.567	0.20
72_P	109_R	0.567	0.20
105_S	148_G	0.566	0.20
58_A	215_N	0.565	0.20
97_V	273_L	0.563	0.20
62_M	68_M	0.563	0.20
28_P	31_T	0.563	0.20
162_R	172_V	0.562	0.19
29_L	98_H	0.561	0.19
136_I	141_K	0.561	0.19
192_A	204_L	0.559	0.19
145_K	237_P	0.559	0.19
16_V	277_V	0.558	0.19
117_T	141_K	0.558	0.19
15_V	23_S	0.557	0.19
15_V	18_F	0.556	0.19
13_F	162_R	0.556	0.19
180_M	300_G	0.555	0.19
29_L	97_V	0.555	0.19
267_E	276_S	0.554	0.19
246_G	257_S	0.553	0.19
69_E	78_L	0.552	0.19
108_M	186_Y	0.551	0.19
150_T	171_V	0.549	0.19
43_I	77_F	0.547	0.19
157_M	254_N	0.545	0.19
144_R	190_L	0.544	0.19
24_A	111_Y	0.542	0.19
166_E	204_L	0.542	0.19
176_P	228_G	0.542	0.19
110_L	193_I	0.541	0.19
251_E	294_A	0.540	0.19
68_M	153_P	0.540	0.19
172_V	212_R	0.540	0.19
136_I	236_E	0.539	0.19
13_F	20_S	0.536	0.18
113_Y	121_I	0.535	0.18
21_T	279_T	0.535	0.18
187_I	195_G	0.533	0.18
212_R	300_G	0.532	0.18
11_A	15_V	0.528	0.18
207_S	257_S	0.528	0.18
205_R	256_L	0.528	0.18
142_V	246_G	0.527	0.18
72_P	77_F	0.527	0.18
53_L	125_I	0.527	0.18
76_T	87_I	0.525	0.18
87_I	200_F	0.525	0.18
225_V	229_T	0.525	0.18
147_A	240_A	0.524	0.18
145_K	227_V	0.523	0.18
176_P	273_L	0.523	0.18
46_P	49_N	0.522	0.18
143_E	156_K	0.521	0.18
296_K	305_L	0.521	0.18
42_V	86_N	0.520	0.18
103_I	221_L	0.520	0.18
146_K	233_F	0.519	0.18
182_L	226_P	0.518	0.18
46_P	78_L	0.516	0.18
122_V	216_E	0.515	0.18
110_L	205_R	0.515	0.18
187_I	218_I	0.514	0.18
43_I	92_I	0.514	0.18
61_Q	286_V	0.510	0.17
19_C	23_S	0.510	0.17
67_M	184_A	0.510	0.17
117_T	275_K	0.509	0.17
292_D	296_K	0.509	0.17
156_K	198_A	0.508	0.17
171_V	249_Y	0.506	0.17
145_K	221_L	0.504	0.17
168_L	183_Y	0.502	0.17
66_N	122_V	0.502	0.17
201_G	219_K	0.502	0.17
126_G	130_L	0.501	0.17
142_V	290_V	0.501	0.17
227_V	296_K	0.501	0.17
41_Q	87_I	0.501	0.17
58_A	137_N	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
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
4lzhA	1	0.8987	100	0.402	Contact Map
4xvoA	1	0.6405	100	0.664	Contact Map
4jmnA	1	0.6405	100	0.666	Contact Map
4a1kA	2	0.5359	100	0.68	Contact Map
4k73A	1	0.6144	100	0.74	Contact Map
3vypA	1	0.7484	100	0.754	Contact Map
1zatA	1	0.6797	100	0.762	Contact Map
4qtfA	2	0.7778	100	0.767	Contact Map
5bmqA	3	0.5784	100	0.773	Contact Map
4xxtA	1	0.6144	100	0.784	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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