PABC - ECOLI - GREMLIN Contacts

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PABC - Aminodeoxychorismate lyase

UniProt:	P28305	Sequences: MFLINGHKQESLAVSDRATQFGDGCFTTARVIDGKVSLLSAHIQRLQDACQRLMISCDFWPQLEQEMKTLAAEQQNGVLKVVISRGSGGRGYSTLNSGPATRILSVTAYPAHYDRLRNEGITLALSPVRLGRNPHLAGIKHLNRLEQVLIRSHLEQTNADEALVLDSEGWVTECCAANLFWRKGNVVYTPRLDQAGVNGIMRQFCIRLLAQSSYQLVEVQASLEESLQADEMVICNALMPVMPVCACGDVSFSSATLYEYLAPLCERPN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11493
Length:	269 (255)
Sequences:	9067 (6033)
Seq/√Len:	377.8

ECOLI - PABC ILVE
BACSU - ILVE1 PABC ILVE2 DAAA
HALSA - Q9HS64 Q9HNF8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
186_V	217_V	4.406	1.00
122_T	246_A	4.229	1.00
186_V	215_Q	3.048	1.00
219_V	225_E	2.999	1.00
187_V	209_L	2.997	1.00
24_G	142_L	2.986	1.00
198_N	203_Q	2.579	1.00
170_W	220_Q	2.421	1.00
41_A	203_Q	2.359	1.00
188_Y	219_V	2.358	1.00
174_C	177_A	2.177	1.00
54_M	156_Q	2.140	1.00
124_A	159_A	2.121	1.00
183_K	230_D	2.075	1.00
125_L	248_G	2.049	1.00
124_A	157_T	2.020	1.00
65_Q	69_T	1.975	1.00
232_M	244_V	1.973	1.00
178_N	199_G	1.971	1.00
206_I	216_L	1.957	1.00
25_C	49_A	1.940	1.00
212_S	264_L	1.932	1.00
38_L	204_F	1.886	1.00
69_T	72_A	1.838	1.00
74_Q	77_G	1.759	1.00
259_E	263_P	1.758	1.00
125_L	223_L	1.749	1.00
203_Q	207_R	1.739	1.00
40_S	64_E	1.738	1.00
46_L	83_I	1.734	1.00
23_D	85_R	1.729	1.00
123_L	244_V	1.685	1.00
181_W	221_A	1.682	1.00
50_C	83_I	1.675	1.00
51_Q	57_C	1.668	1.00
32_I	240_P	1.667	1.00
153_H	157_T	1.651	1.00
123_L	174_C	1.647	1.00
180_F	235_C	1.624	1.00
212_S	260_Y	1.618	1.00
260_Y	264_L	1.560	1.00
166_D	170_W	1.551	1.00
25_C	50_C	1.531	1.00
69_T	73_E	1.517	1.00
246_A	249_D	1.515	1.00
29_A	36_V	1.511	1.00
179_L	232_M	1.499	1.00
44_Q	48_D	1.498	1.00
232_M	247_C	1.493	1.00
41_A	207_R	1.489	1.00
205_C	235_C	1.486	1.00
191_R	220_Q	1.485	1.00
47_Q	57_C	1.481	1.00
39_L	43_I	1.477	1.00
181_W	229_A	1.467	1.00
64_E	68_K	1.461	1.00
122_T	245_C	1.455	1.00
66_E	102_R	1.454	1.00
121_I	160_D	1.454	1.00
55_I	83_I	1.451	1.00
182_R	257_L	1.443	1.00
55_I	100_A	1.443	1.00
170_W	222_S	1.442	1.00
31_V	71_A	1.432	1.00
174_C	234_I	1.430	1.00
123_L	163_L	1.422	1.00
122_T	160_D	1.398	1.00
181_W	188_Y	1.392	1.00
73_E	77_G	1.390	1.00
48_D	51_Q	1.388	1.00
194_Q	220_Q	1.379	1.00
40_S	44_Q	1.378	1.00
39_L	64_E	1.375	1.00
187_V	214_Y	1.366	1.00
182_R	187_V	1.352	1.00
65_Q	68_K	1.332	1.00
180_F	233_V	1.318	1.00
207_R	211_Q	1.317	1.00
49_A	139_I	1.313	1.00
246_A	251_S	1.312	1.00
181_W	232_M	1.306	1.00
183_K	228_Q	1.306	1.00
38_L	41_A	1.303	1.00
202_R	218_E	1.297	1.00
260_Y	263_P	1.296	1.00
209_L	214_Y	1.273	1.00
48_D	198_N	1.266	1.00
132_R	167_S	1.261	1.00
36_V	39_L	1.249	1.00
222_S	225_E	1.243	1.00
70_L	104_L	1.238	1.00
163_L	179_L	1.230	1.00
152_S	156_Q	1.227	1.00
236_N	239_M	1.225	1.00
41_A	44_Q	1.223	1.00
36_V	67_M	1.221	1.00
20_Q	80_K	1.191	1.00
44_Q	60_W	1.186	1.00
189_T	202_R	1.185	1.00
68_K	72_A	1.181	1.00
33_D	75_Q	1.174	1.00
188_Y	217_V	1.169	1.00
18_A	84_S	1.162	1.00
231_E	258_Y	1.161	1.00
47_Q	60_W	1.143	1.00
251_S	254_S	1.137	1.00
16_D	84_S	1.131	1.00
67_M	79_L	1.130	1.00
52_R	139_I	1.128	1.00
150_I	164_V	1.123	1.00
221_A	225_E	1.119	1.00
227_L	250_V	1.117	1.00
62_Q	65_Q	1.115	1.00
18_A	24_G	1.108	1.00
224_E	228_Q	1.107	1.00
151_R	155_E	1.106	1.00
61_P	65_Q	1.091	1.00
25_C	46_L	1.078	1.00
66_E	104_L	1.078	1.00
191_R	219_V	1.073	1.00
126_S	162_A	1.072	1.00
182_R	231_E	1.070	1.00
202_R	206_I	1.068	1.00
183_K	225_E	1.067	1.00
183_K	188_Y	1.059	1.00
31_V	77_G	1.054	1.00
180_F	202_R	1.052	1.00
234_I	244_V	1.052	1.00
123_L	234_I	1.050	1.00
67_M	104_L	1.042	1.00
127_P	153_H	1.028	1.00
188_Y	221_A	1.026	1.00
191_R	218_E	1.025	1.00
153_H	156_Q	1.023	1.00
41_A	204_F	1.020	1.00
43_I	64_E	1.018	1.00
192_L	202_R	1.010	1.00
82_V	103_I	1.000	1.00
214_Y	257_L	0.994	1.00
70_L	106_V	0.993	1.00
47_Q	51_Q	0.988	1.00
169_G	224_E	0.982	1.00
44_Q	47_Q	0.981	1.00
192_L	198_N	0.978	1.00
52_R	138_G	0.974	1.00
245_C	255_A	0.973	1.00
180_F	206_I	0.972	1.00
161_E	175_C	0.960	1.00
26_F	144_R	0.958	1.00
256_T	259_E	0.956	1.00
163_L	226_S	0.952	1.00
171_V	179_L	0.951	1.00
93_S	96_N	0.950	1.00
86_G	101_T	0.944	1.00
9_Q	13_A	0.938	1.00
165_L	223_L	0.938	1.00
190_P	221_A	0.935	1.00
166_D	195_A	0.934	1.00
178_N	235_C	0.931	1.00
48_D	138_G	0.928	1.00
7_H	11_S	0.927	1.00
83_I	102_R	0.922	1.00
19_T	84_S	0.922	1.00
120_G	245_C	0.921	1.00
25_C	83_I	0.920	1.00
171_V	181_W	0.917	1.00
82_V	142_L	0.911	1.00
73_E	76_N	0.911	1.00
209_L	261_L	0.907	1.00
259_E	262_A	0.907	1.00
43_I	47_Q	0.901	1.00
16_D	86_G	0.899	1.00
209_L	216_L	0.895	1.00
57_C	83_I	0.892	1.00
48_D	52_R	0.887	1.00
199_G	235_C	0.885	1.00
121_I	242_M	0.879	1.00
209_L	212_S	0.878	1.00
210_A	218_E	0.877	1.00
157_T	248_G	0.874	1.00
59_F	62_Q	0.862	1.00
66_E	69_T	0.856	1.00
54_M	152_S	0.855	1.00
161_E	177_A	0.853	1.00
187_V	233_V	0.851	1.00
150_I	162_A	0.851	1.00
14_V	103_I	0.847	1.00
161_E	174_C	0.847	1.00
43_I	67_M	0.838	1.00
124_A	248_G	0.829	1.00
184_G	230_D	0.829	1.00
123_L	161_E	0.827	1.00
185_N	215_Q	0.827	1.00
16_D	88_G	0.821	1.00
20_Q	82_V	0.820	1.00
12_L	19_T	0.814	1.00
229_A	232_M	0.813	1.00
50_C	57_C	0.812	1.00
210_A	215_Q	0.812	1.00
47_Q	63_L	0.809	1.00
126_S	153_H	0.807	1.00
117_R	262_A	0.807	1.00
168_E	220_Q	0.807	1.00
39_L	67_M	0.805	1.00
31_V	36_V	0.804	1.00
32_I	37_S	0.803	1.00
207_R	210_A	0.802	1.00
193_D	220_Q	0.796	1.00
231_E	255_A	0.794	1.00
116_L	160_D	0.787	1.00
188_Y	225_E	0.784	1.00
41_A	200_I	0.783	1.00
20_Q	105_S	0.782	1.00
37_S	204_F	0.781	1.00
94_T	152_S	0.777	1.00
173_E	197_V	0.776	1.00
150_I	175_C	0.773	1.00
10_E	14_V	0.768	1.00
43_I	63_L	0.767	1.00
117_R	120_G	0.766	1.00
172_T	196_G	0.766	1.00
165_L	171_V	0.760	1.00
257_L	260_Y	0.758	1.00
50_C	55_I	0.754	1.00
62_Q	66_E	0.753	1.00
31_V	79_L	0.753	1.00
151_R	176_A	0.752	1.00
206_I	218_E	0.752	1.00
151_R	161_E	0.751	1.00
71_A	77_G	0.750	1.00
11_S	14_V	0.745	1.00
180_F	189_T	0.744	1.00
211_Q	264_L	0.744	1.00
29_A	67_M	0.744	1.00
204_F	207_R	0.740	1.00
182_R	233_V	0.738	1.00
30_R	76_N	0.734	1.00
17_R	23_D	0.734	1.00
29_A	81_V	0.728	1.00
252_F	255_A	0.724	1.00
87_S	101_T	0.724	1.00
93_S	155_E	0.722	1.00
30_R	237_A	0.721	1.00
18_A	142_L	0.718	1.00
53_L	141_H	0.717	1.00
129_R	134_P	0.717	1.00
152_S	155_E	0.717	1.00
22_G	143_N	0.717	1.00
28_T	78_V	0.716	1.00
206_I	210_A	0.715	1.00
154_L	158_N	0.709	1.00
225_E	228_Q	0.709	1.00
53_L	145_L	0.707	1.00
28_T	238_L	0.705	1.00
10_E	103_I	0.704	0.99
185_N	230_D	0.703	0.99
119_E	160_D	0.703	0.99
27_T	49_A	0.702	0.99
224_E	227_L	0.701	0.99
61_P	64_E	0.700	0.99
179_L	190_P	0.700	0.99
159_A	248_G	0.694	0.99
118_N	259_E	0.694	0.99
33_D	76_N	0.692	0.99
169_G	223_L	0.689	0.99
122_T	159_A	0.689	0.99
58_D	62_Q	0.686	0.99
126_S	150_I	0.682	0.99
90_R	93_S	0.679	0.99
84_S	103_I	0.676	0.99
30_R	240_P	0.675	0.99
78_V	107_T	0.674	0.99
177_A	234_I	0.673	0.99
63_L	102_R	0.672	0.99
36_V	79_L	0.671	0.99
226_S	232_M	0.670	0.99
19_T	103_I	0.661	0.99
239_M	242_M	0.660	0.99
84_S	101_T	0.658	0.99
204_F	208_L	0.658	0.99
23_D	148_V	0.656	0.99
191_R	194_Q	0.652	0.99
208_L	212_S	0.651	0.99
256_T	260_Y	0.651	0.99
201_M	265_C	0.649	0.99
189_T	218_E	0.649	0.99
150_I	153_H	0.643	0.99
223_L	227_L	0.643	0.99
78_V	238_L	0.641	0.99
241_V	261_L	0.640	0.99
38_L	200_I	0.637	0.99
141_H	145_L	0.632	0.99
125_L	165_L	0.629	0.99
232_M	252_F	0.626	0.99
77_G	106_V	0.625	0.99
92_Y	147_Q	0.624	0.99
132_R	168_E	0.624	0.99
226_S	247_C	0.623	0.99
221_A	229_A	0.623	0.99
130_L	144_R	0.620	0.99
44_Q	203_Q	0.619	0.99
140_K	197_V	0.617	0.99
67_M	81_V	0.617	0.99
171_V	221_A	0.615	0.99
144_R	147_Q	0.615	0.99
12_L	16_D	0.614	0.99
59_F	63_L	0.608	0.99
37_S	237_A	0.607	0.99
162_A	175_C	0.603	0.98
125_L	247_C	0.602	0.98
210_A	216_L	0.601	0.98
31_V	106_V	0.600	0.98
163_L	232_M	0.600	0.98
19_T	82_V	0.599	0.98
86_G	99_P	0.598	0.98
113_Y	116_L	0.596	0.98
28_T	236_N	0.596	0.98
60_W	64_E	0.595	0.98
183_K	229_A	0.594	0.98
17_R	85_R	0.592	0.98
128_V	153_H	0.590	0.98
180_F	187_V	0.590	0.98
25_C	53_L	0.590	0.98
51_Q	56_S	0.589	0.98
233_V	241_V	0.588	0.98
185_N	214_Y	0.587	0.98
59_F	102_R	0.586	0.98
132_R	135_H	0.585	0.98
59_F	66_E	0.583	0.98
200_I	203_Q	0.582	0.98
140_K	173_E	0.581	0.98
121_I	234_I	0.580	0.98
123_L	247_C	0.578	0.98
90_R	94_T	0.575	0.98
15_S	20_Q	0.572	0.98
32_I	76_N	0.571	0.98
29_A	39_L	0.568	0.98
200_I	204_F	0.567	0.98
131_G	146_E	0.565	0.98
233_V	258_Y	0.560	0.97
36_V	71_A	0.559	0.97
15_S	87_S	0.556	0.97
170_W	194_Q	0.555	0.97
181_W	226_S	0.554	0.97
39_L	68_K	0.551	0.97
192_L	218_E	0.550	0.97
80_K	142_L	0.549	0.97
30_R	37_S	0.548	0.97
36_V	68_K	0.546	0.97
129_R	167_S	0.542	0.97
180_F	205_C	0.542	0.97
27_T	46_L	0.541	0.97
182_R	185_N	0.541	0.97
120_G	242_M	0.541	0.97
258_Y	262_A	0.538	0.97
46_L	81_V	0.536	0.97
154_L	162_A	0.534	0.97
25_C	141_H	0.533	0.97
116_L	242_M	0.533	0.97
125_L	226_S	0.532	0.97
124_A	153_H	0.527	0.96
25_C	139_I	0.526	0.96
13_A	87_S	0.525	0.96
201_M	237_A	0.523	0.96
151_R	175_C	0.523	0.96
45_R	197_V	0.522	0.96
79_L	106_V	0.520	0.96
189_T	196_G	0.520	0.96
186_V	219_V	0.517	0.96
70_L	74_Q	0.516	0.96
189_T	192_L	0.515	0.96
84_S	142_L	0.512	0.96
55_I	85_R	0.511	0.96
131_G	137_A	0.510	0.96
129_R	132_R	0.508	0.96
235_C	241_V	0.507	0.96
227_L	248_G	0.505	0.95
92_Y	144_R	0.504	0.95
154_L	159_A	0.504	0.95
11_S	15_S	0.503	0.95
240_P	265_C	0.502	0.95
37_S	41_A	0.500	0.95

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
1i2kA	2	1	100	0.08	Contact Map
2y4rA	2	0.9963	100	0.098	Contact Map
1iyeA	5	1	100	0.122	Contact Map
3lulA	2	0.9591	100	0.125	Contact Map
2eiyA	5	0.9963	100	0.126	Contact Map
4tm5A	2	0.9851	100	0.13	Contact Map
3u0gA	5	0.9926	100	0.134	Contact Map
3snoA	2	0.8364	100	0.135	Contact Map
4chiA	2	0.9926	100	0.135	Contact Map
3daaA	2	0.9814	100	0.139	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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