LDCA - ECOLI - GREMLIN Contacts

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LDCA - Murein tetrapeptide carboxypeptidase

UniProt:	P76008	Sequences: MSLFHLIAPSGYCIKQHAALRGIQRLTDAGHQVNNVEVIARRCERFAGTETERLEDLNSLARLTTPNTIVLAVRGGYGASRLLADIDWQALVARQQHDPLLICGHSDFTAIQCGLLAHGNVITFSGPMLVANFGADELNAFTEHHFWLALRNETFTIEWQGEGPTCRAEGTLWGGNLAMLISLIGTPWMPKIENGILVLEDINEHPFRVERMLLQLYHAGILPRQKAIILGSFSGSTPNDYDAGYNLESVYAFLRSRLSIPLITGLDFGHEQRTVTLPLGAHAILNNTREGTQLTISGHPVLKM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13898
Length:	304 (282)
Sequences:	2952 (2256)
Seq/√Len:	134.4

ECOLI - LDCA
BACSU - LDC YOCD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
169_E	284_I	4.745	1.00
2_S	68_T	3.915	1.00
5_H	60_L	3.800	1.00
10_S	79_A	3.514	1.00
3_L	32_Q	3.468	1.00
49_T	52_E	3.066	1.00
41_R	52_E	2.986	1.00
193_E	224_R	2.917	1.00
50_E	81_R	2.854	1.00
169_E	282_H	2.795	1.00
34_N	63_L	2.787	1.00
3_L	34_N	2.766	1.00
31_H	151_R	2.713	1.00
8_A	73_V	2.697	1.00
4_F	31_H	2.520	1.00
6_L	73_V	2.302	1.00
23_I	27_T	2.233	1.00
58_N	90_A	2.213	1.00
167_R	286_N	2.208	1.00
217_Y	257_R	2.177	1.00
54_L	85_D	2.172	1.00
196_I	283_A	2.154	1.00
167_R	284_I	2.149	1.00
194_N	226_K	2.147	1.00
172_L	277_L	2.134	1.00
69_I	101_L	2.093	1.00
227_A	285_L	2.059	1.00
55_E	59_S	2.010	1.00
171_T	195_G	2.000	1.00
38_V	56_D	1.999	1.00
34_N	66_P	1.997	1.00
189_M	221_I	1.973	1.00
38_V	41_R	1.926	1.00
225_Q	228_I	1.883	1.00
165_T	288_T	1.878	1.00
199_L	230_L	1.832	1.00
228_I	260_I	1.806	1.00
197_L	225_Q	1.805	1.00
54_L	58_N	1.796	1.00
27_T	32_Q	1.771	1.00
64_T	98_D	1.749	1.00
139_N	273_R	1.745	1.00
5_H	66_P	1.708	1.00
35_N	39_I	1.688	1.00
147_W	151_R	1.661	1.00
22_G	129_L	1.637	1.00
7_I	60_L	1.635	1.00
229_I	266_L	1.633	1.00
29_A	147_W	1.617	1.00
23_I	35_N	1.587	1.00
58_N	62_R	1.569	1.00
24_Q	27_T	1.560	1.00
3_L	65_T	1.560	1.00
198_V	279_L	1.551	1.00
57_L	61_A	1.551	1.00
37_E	59_S	1.531	1.00
23_I	33_V	1.529	1.00
229_I	285_L	1.526	1.00
3_L	66_P	1.522	1.00
51_T	85_D	1.515	1.00
122_I	281_A	1.508	1.00
172_L	283_A	1.504	1.00
24_Q	28_D	1.490	1.00
62_R	90_A	1.436	1.00
144_H	148_L	1.418	1.00
141_F	275_V	1.416	1.00
197_L	222_L	1.411	1.00
228_I	255_R	1.381	1.00
31_H	147_W	1.379	1.00
68_T	98_D	1.362	1.00
222_L	260_I	1.362	1.00
171_T	282_H	1.348	1.00
51_T	55_E	1.340	1.00
8_A	39_I	1.339	1.00
192_I	221_I	1.338	1.00
184_I	219_A	1.331	1.00
198_V	277_L	1.322	1.00
5_H	34_N	1.304	1.00
112_Q	123_T	1.281	1.00
214_L	254_L	1.275	1.00
124_F	276_T	1.263	1.00
116_L	279_L	1.263	1.00
125_S	176_N	1.254	1.00
61_A	121_V	1.253	1.00
225_Q	260_I	1.251	1.00
20_L	23_I	1.247	1.00
88_W	114_G	1.242	1.00
61_A	91_L	1.231	1.00
38_V	52_E	1.227	1.00
168_A	227_A	1.219	1.00
71_L	103_C	1.218	1.00
112_Q	125_S	1.211	1.00
101_L	124_F	1.209	1.00
7_I	86_I	1.208	1.00
232_S	267_D	1.208	1.00
112_Q	279_L	1.207	1.00
125_S	274_T	1.201	1.00
246_N	249_S	1.199	1.00
84_A	218_H	1.190	0.99
248_E	264_T	1.185	0.99
79_A	111_I	1.178	0.99
25_R	29_A	1.178	0.99
115_L	119_G	1.166	0.99
9_P	108_F	1.161	0.99
36_V	56_D	1.158	0.99
230_L	233_F	1.148	0.99
206_P	250_V	1.129	0.99
184_I	189_M	1.123	0.99
174_G	198_V	1.112	0.99
144_H	147_W	1.110	0.99
103_C	126_G	1.106	0.99
181_I	184_I	1.104	0.99
81_R	210_E	1.102	0.99
112_Q	116_L	1.097	0.99
6_L	129_L	1.094	0.99
286_N	292_T	1.089	0.99
286_N	289_R	1.085	0.99
188_W	218_H	1.073	0.99
159_W	162_E	1.072	0.99
5_H	36_V	1.070	0.99
86_I	91_L	1.060	0.99
16_Q	20_L	1.058	0.99
83_L	110_A	1.057	0.99
103_C	276_T	1.055	0.99
102_I	115_L	1.042	0.99
204_E	208_R	1.041	0.99
72_A	108_F	1.030	0.99
180_L	199_L	1.028	0.98
35_N	40_A	1.028	0.98
232_S	271_E	1.027	0.98
87_D	91_L	1.020	0.98
52_E	55_E	1.020	0.98
27_T	33_V	1.013	0.98
228_I	262_L	1.013	0.98
148_L	152_N	1.012	0.98
204_E	211_R	1.008	0.98
20_L	24_Q	1.001	0.98
91_L	119_G	1.001	0.98
284_I	293_Q	1.001	0.98
219_A	222_L	0.995	0.98
61_A	98_D	0.993	0.98
4_F	33_V	0.987	0.98
115_L	123_T	0.986	0.98
34_N	65_T	0.986	0.98
54_L	86_I	0.981	0.98
201_D	233_F	0.980	0.98
189_M	192_I	0.973	0.98
184_I	215_Q	0.973	0.98
146_F	150_L	0.973	0.98
118_H	187_P	0.973	0.98
110_A	179_M	0.966	0.98
198_V	268_F	0.957	0.98
196_I	227_A	0.956	0.98
263_I	287_N	0.949	0.97
113_C	180_L	0.946	0.97
102_I	108_F	0.938	0.97
36_V	60_L	0.934	0.97
268_F	277_L	0.932	0.97
283_A	294_L	0.928	0.97
122_I	278_P	0.915	0.97
63_L	100_L	0.909	0.97
54_L	82_L	0.908	0.97
192_I	224_R	0.908	0.97
74_R	78_G	0.904	0.97
3_L	33_V	0.904	0.97
184_I	216_L	0.901	0.97
32_Q	65_T	0.898	0.96
78_G	210_E	0.895	0.96
128_M	131_A	0.894	0.96
178_A	201_D	0.890	0.96
42_R	48_G	0.890	0.96
176_N	233_F	0.884	0.96
263_I	285_L	0.884	0.96
3_L	68_T	0.883	0.96
80_S	179_M	0.880	0.96
204_E	212_M	0.880	0.96
58_N	86_I	0.879	0.96
221_I	224_R	0.879	0.96
90_A	98_D	0.876	0.96
2_S	69_I	0.862	0.96
13_C	73_V	0.861	0.95
209_V	247_L	0.859	0.95
182_S	215_Q	0.857	0.95
80_S	218_H	0.856	0.95
4_F	151_R	0.855	0.95
167_R	288_T	0.851	0.95
255_R	258_L	0.851	0.95
255_R	262_L	0.851	0.95
57_L	86_I	0.849	0.95
61_A	102_I	0.847	0.95
29_A	143_E	0.840	0.95
186_T	215_Q	0.837	0.95
227_A	287_N	0.837	0.95
21_R	24_Q	0.837	0.95
26_L	71_L	0.837	0.95
181_I	212_M	0.836	0.95
205_H	208_R	0.834	0.95
74_R	128_M	0.833	0.95
148_L	154_T	0.832	0.95
173_W	195_G	0.830	0.95
22_G	26_L	0.829	0.94
43_C	49_T	0.827	0.94
214_L	253_F	0.827	0.94
145_H	276_T	0.824	0.94
149_A	276_T	0.823	0.94
168_A	285_L	0.822	0.94
6_L	23_I	0.821	0.94
50_E	210_E	0.821	0.94
77_Y	207_F	0.819	0.94
181_I	215_Q	0.819	0.94
156_T	291_G	0.818	0.94
192_I	195_G	0.816	0.94
186_T	189_M	0.816	0.94
10_S	108_F	0.813	0.94
158_E	161_G	0.813	0.94
37_E	55_E	0.808	0.94
78_G	81_R	0.808	0.94
177_L	216_L	0.808	0.94
278_P	281_A	0.802	0.93
19_A	23_I	0.799	0.93
156_T	293_Q	0.798	0.93
116_L	173_W	0.796	0.93
105_H	274_T	0.795	0.93
166_C	287_N	0.794	0.93
84_A	188_W	0.792	0.93
50_E	54_L	0.792	0.93
230_L	264_T	0.790	0.93
177_L	212_M	0.790	0.93
99_P	121_V	0.790	0.93
7_I	70_V	0.789	0.93
4_F	71_L	0.788	0.93
148_L	153_E	0.784	0.93
7_I	56_D	0.775	0.92
20_L	27_T	0.773	0.92
4_F	69_I	0.771	0.92
179_M	182_S	0.768	0.92
114_G	188_W	0.767	0.92
80_S	182_S	0.766	0.92
58_N	88_W	0.765	0.92
35_N	38_V	0.764	0.92
217_Y	254_L	0.763	0.92
201_D	204_E	0.760	0.91
173_W	190_P	0.756	0.91
140_A	144_H	0.753	0.91
178_A	182_S	0.753	0.91
110_A	183_L	0.751	0.91
57_L	82_L	0.747	0.91
116_L	123_T	0.742	0.91
9_P	111_I	0.740	0.90
287_N	292_T	0.740	0.90
46_F	50_E	0.737	0.90
88_W	119_G	0.736	0.90
232_S	265_G	0.734	0.90
72_A	102_I	0.734	0.90
147_W	150_L	0.734	0.90
143_E	147_W	0.732	0.90
145_H	149_A	0.730	0.90
101_L	150_L	0.730	0.90
217_Y	253_F	0.727	0.90
177_L	204_E	0.727	0.90
146_F	149_A	0.725	0.89
50_E	78_G	0.725	0.89
20_L	40_A	0.723	0.89
160_Q	163_G	0.721	0.89
217_Y	258_L	0.720	0.89
83_L	188_W	0.713	0.89
199_L	213_L	0.713	0.89
23_I	129_L	0.712	0.89
101_L	122_I	0.710	0.88
57_L	102_I	0.707	0.88
46_F	78_G	0.705	0.88
80_S	214_L	0.704	0.88
88_W	91_L	0.703	0.88
204_E	207_F	0.698	0.88
108_F	111_I	0.697	0.88
178_A	212_M	0.697	0.88
215_Q	219_A	0.695	0.87
286_N	293_Q	0.691	0.87
217_Y	223_P	0.691	0.87
9_P	57_L	0.690	0.87
203_N	235_G	0.688	0.87
285_L	294_L	0.682	0.86
6_L	35_N	0.679	0.86
199_L	228_I	0.678	0.86
286_N	290_E	0.676	0.86
26_L	33_V	0.675	0.86
11_G	74_R	0.673	0.86
44_E	48_G	0.672	0.86
248_E	252_A	0.671	0.86
142_T	273_R	0.671	0.86
105_H	125_S	0.670	0.85
177_L	209_V	0.669	0.85
190_P	221_I	0.667	0.85
91_L	115_L	0.666	0.85
19_A	35_N	0.664	0.85
59_S	63_L	0.662	0.85
165_T	287_N	0.660	0.85
207_F	210_E	0.654	0.84
89_Q	96_Q	0.654	0.84
145_H	148_L	0.654	0.84
157_I	275_V	0.654	0.84
209_V	236_S	0.652	0.84
178_A	208_R	0.651	0.84
17_H	21_R	0.650	0.84
5_H	63_L	0.649	0.84
206_P	236_S	0.649	0.84
63_L	66_P	0.647	0.83
39_I	73_V	0.646	0.83
83_L	114_G	0.646	0.83
183_L	190_P	0.640	0.83
79_A	110_A	0.637	0.82
78_G	202_I	0.636	0.82
254_L	257_R	0.636	0.82
8_A	232_S	0.632	0.82
214_L	218_H	0.630	0.82
197_L	221_I	0.630	0.82
216_L	221_I	0.625	0.81
77_Y	204_E	0.624	0.81
84_A	217_Y	0.623	0.81
124_F	278_P	0.623	0.81
114_G	119_G	0.622	0.81
208_R	212_M	0.620	0.81
60_L	66_P	0.620	0.81
233_F	247_L	0.616	0.80
101_L	276_T	0.616	0.80
74_R	202_I	0.613	0.80
171_T	194_N	0.613	0.80
6_L	22_G	0.612	0.80
286_N	291_G	0.610	0.80
16_Q	40_A	0.610	0.80
213_L	254_L	0.607	0.79
178_A	202_I	0.604	0.79
248_E	265_G	0.603	0.79
79_A	102_I	0.603	0.79
78_G	201_D	0.601	0.79
252_A	256_S	0.599	0.78
186_T	218_H	0.596	0.78
3_L	63_L	0.595	0.78
96_Q	119_G	0.589	0.77
58_N	87_D	0.588	0.77
217_Y	222_L	0.586	0.77
77_Y	210_E	0.585	0.77
50_E	82_L	0.585	0.77
123_T	279_L	0.578	0.76
281_A	294_L	0.578	0.76
2_S	99_P	0.577	0.76
79_A	108_F	0.577	0.76
87_D	99_P	0.577	0.76
72_A	79_A	0.575	0.76
46_F	81_R	0.575	0.76
227_A	263_I	0.572	0.75
289_R	293_Q	0.572	0.75
209_V	212_M	0.565	0.74
36_V	39_I	0.565	0.74
191_K	195_G	0.564	0.74
223_P	258_L	0.563	0.74
200_E	231_G	0.562	0.74
252_A	262_L	0.561	0.74
78_G	207_F	0.558	0.73
11_G	203_N	0.558	0.73
8_A	47_A	0.558	0.73
177_L	210_E	0.554	0.73
210_E	254_L	0.552	0.73
29_A	151_R	0.550	0.72
29_A	218_H	0.550	0.72
221_I	225_Q	0.550	0.72
116_L	280_G	0.549	0.72
7_I	36_V	0.548	0.72
168_A	287_N	0.548	0.72
58_N	122_I	0.548	0.72
160_Q	164_P	0.548	0.72
58_N	82_L	0.547	0.72
148_L	155_F	0.547	0.72
285_L	288_T	0.547	0.72
69_I	99_P	0.546	0.72
13_C	19_A	0.546	0.72
180_L	216_L	0.545	0.72
58_N	85_D	0.544	0.72
157_I	160_Q	0.542	0.71
182_S	211_R	0.540	0.71
2_S	31_H	0.537	0.71
18_A	135_A	0.529	0.69
117_A	189_M	0.529	0.69
82_L	86_I	0.528	0.69
251_Y	264_T	0.528	0.69
101_L	278_P	0.528	0.69
89_Q	193_E	0.528	0.69
103_C	124_F	0.527	0.69
251_Y	255_R	0.526	0.69
59_S	62_R	0.523	0.69
81_R	207_F	0.522	0.68
109_T	216_L	0.522	0.68
127_P	276_T	0.522	0.68
191_K	224_R	0.522	0.68
22_G	134_G	0.522	0.68
196_I	285_L	0.521	0.68
109_T	175_G	0.520	0.68
199_L	218_H	0.519	0.68
44_E	244_G	0.519	0.68
58_N	123_T	0.519	0.68
21_R	25_R	0.518	0.68
210_E	253_F	0.517	0.68
113_C	190_P	0.516	0.68
149_A	152_N	0.516	0.68
26_L	224_R	0.514	0.67
198_V	253_F	0.514	0.67
81_R	204_E	0.513	0.67
230_L	255_R	0.513	0.67
230_L	251_Y	0.512	0.67
44_E	245_Y	0.511	0.67
22_G	73_V	0.510	0.67
284_I	291_G	0.509	0.67
9_P	126_G	0.508	0.66
201_D	209_V	0.508	0.66
74_R	204_E	0.506	0.66
7_I	38_V	0.506	0.66
283_A	292_T	0.505	0.66
74_R	207_F	0.504	0.66
177_L	237_T	0.504	0.66
137_E	140_A	0.503	0.66
68_T	101_L	0.503	0.66
113_C	173_W	0.501	0.65
58_N	61_A	0.500	0.65

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
3tlaA	2	0.9638	100	0.084	Contact Map
4e5sA	2	0.9539	100	0.095	Contact Map
4jvoA	2	0.9539	100	0.1	Contact Map
4injA	2	0.9507	100	0.107	Contact Map
1zl0A	1	0.9342	100	0.116	Contact Map
4eysA	3	0.9375	100	0.139	Contact Map
3g23A	2	0.8717	100	0.16	Contact Map
4z0nA	1	0.5329	79.9	0.95	Contact Map
4yleA	1	0.477	77.6	0.952	Contact Map
4jenA	2	0.3783	76.7	0.952	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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