PAAF - ECOLI - GREMLIN Contacts

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PAAF - 2,3-dehydroadipyl-CoA hydratase

UniProt:	P76082	Sequences: MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRTPDFKGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13740
Length:	255 (244)
Sequences:	30188 (19768)
Seq/√Len:	1265.5

ECOLI - PAAF PAAG MENB CAID SCPB FADB FADJ
BACSU - FADB MENB YNGF YHAR PKSH PKSI FADN
HALSA - Q9HS32 Q9HQN4 Q9HQ61
SULSO - Q97WU7 Q7LXQ1 Q97VK0 Q97YL2 Q97VK1 Q97VS6 Q97VU5 Q980Z9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_R	162_S	3.179	1.00
121_E	179_P	3.038	1.00
176_D	186_Y	3.022	1.00
119_A	174_V	2.909	1.00
97_A	114_C	2.795	1.00
186_Y	189_Q	2.779	1.00
14_L	188_L	2.644	1.00
42_A	92_N	2.483	1.00
39_E	87_R	2.466	1.00
23_R	57_R	2.283	1.00
161_E	193_K	2.277	1.00
122_N	180_S	2.276	1.00
5_I	18_N	2.222	1.00
167_Q	170_Q	2.186	1.00
216_A	219_A	2.171	1.00
164_T	167_Q	2.146	1.00
8_R	13_L	2.101	1.00
155_K	161_E	2.085	1.00
152_L	171_A	2.033	1.00
157_V	205_A	2.016	1.00
14_L	53_T	2.005	1.00
131_T	197_H	2.001	1.00
8_R	44_D	1.951	1.00
11_R	48_S	1.908	1.00
6_V	13_L	1.887	1.00
35_V	87_R	1.875	1.00
98_A	187_A	1.868	1.00
121_E	166_Q	1.851	1.00
29_A	33_Q	1.845	1.00
18_N	55_N	1.842	1.00
239_E	248_R	1.832	1.00
104_L	126_G	1.828	1.00
242_S	246_Q	1.817	1.00
16_T	55_N	1.809	1.00
98_A	184_L	1.797	1.00
23_R	58_F	1.795	1.00
118_V	178_F	1.774	1.00
13_L	41_A	1.731	1.00
182_L	185_E	1.730	1.00
154_S	210_R	1.726	1.00
16_T	53_T	1.713	1.00
155_K	175_S	1.708	1.00
188_L	192_S	1.705	1.00
40_A	44_D	1.688	1.00
50_C	91_F	1.663	1.00
121_E	180_S	1.658	1.00
115_D	206_K	1.646	1.00
167_Q	171_A	1.628	1.00
150_K	154_S	1.620	1.00
13_L	47_I	1.590	1.00
182_L	186_Y	1.566	1.00
32_M	80_T	1.565	1.00
166_Q	170_Q	1.556	1.00
118_V	190_L	1.548	1.00
119_A	125_F	1.489	1.00
155_K	176_D	1.486	1.00
178_F	186_Y	1.475	1.00
120_G	180_S	1.464	1.00
41_A	50_C	1.453	1.00
117_V	147_S	1.445	1.00
117_V	151_S	1.445	1.00
9_Q	188_L	1.436	1.00
42_A	87_R	1.434	1.00
111_A	117_V	1.429	1.00
15_L	37_E	1.425	1.00
10_Q	192_S	1.419	1.00
49_V	191_A	1.413	1.00
154_S	209_L	1.405	1.00
86_A	218_Q	1.397	1.00
99_V	111_A	1.393	1.00
86_A	90_A	1.385	1.00
6_V	41_A	1.375	1.00
169_Q	177_V	1.375	1.00
154_S	158_L	1.373	1.00
100_N	120_G	1.345	1.00
5_I	55_N	1.339	1.00
204_A	230_L	1.332	1.00
9_Q	192_S	1.328	1.00
35_V	39_E	1.316	1.00
99_V	103_A	1.314	1.00
38_L	91_F	1.312	1.00
100_N	122_N	1.309	1.00
108_C	127_L	1.307	1.00
152_L	155_K	1.302	1.00
89_Q	143_R	1.297	1.00
53_T	100_N	1.290	1.00
156_M	163_I	1.287	1.00
57_R	100_N	1.286	1.00
88_L	95_L	1.282	1.00
28_N	67_E	1.272	1.00
183_T	187_A	1.266	1.00
9_Q	14_L	1.264	1.00
161_E	167_Q	1.261	1.00
126_G	162_S	1.230	1.00
184_L	188_L	1.214	1.00
42_A	91_F	1.197	1.00
27_N	30_L	1.195	1.00
207_Q	211_Q	1.195	1.00
14_L	184_L	1.194	1.00
102_Y	124_R	1.192	1.00
35_V	83_Q	1.188	1.00
58_F	102_Y	1.186	1.00
130_I	160_G	1.185	1.00
151_S	175_S	1.184	1.00
53_T	184_L	1.177	1.00
197_H	202_L	1.174	1.00
152_L	167_Q	1.169	1.00
237_R	241_I	1.168	1.00
184_L	187_A	1.167	1.00
33_Q	37_E	1.155	1.00
215_V	219_A	1.141	1.00
17_L	30_L	1.135	1.00
19_R	22_A	1.129	1.00
120_G	183_T	1.112	1.00
7_S	16_T	1.095	1.00
8_R	46_S	1.091	1.00
215_V	223_Q	1.086	1.00
163_I	171_A	1.082	1.00
149_G	152_L	1.077	1.00
165_A	177_V	1.072	1.00
22_A	66_N	1.069	1.00
200_L	236_D	1.061	1.00
8_R	40_A	1.055	1.00
17_L	60_A	1.045	1.00
185_E	189_Q	1.043	1.00
33_Q	36_N	1.042	1.00
60_A	107_G	1.041	1.00
211_Q	223_Q	1.041	1.00
90_A	218_Q	1.039	1.00
28_N	32_M	1.034	1.00
36_N	40_A	1.005	1.00
7_S	14_L	0.997	1.00
19_R	64_D	0.994	1.00
95_L	114_C	0.990	1.00
116_V	190_L	0.990	1.00
50_C	93_K	0.985	1.00
5_I	16_T	0.985	1.00
81_R	138_A	0.968	1.00
37_E	40_A	0.959	1.00
109_E	140_G	0.957	1.00
148_V	152_L	0.956	1.00
199_P	203_Q	0.954	1.00
147_S	151_S	0.944	1.00
92_N	203_Q	0.943	1.00
51_V	187_A	0.935	1.00
191_A	195_A	0.928	1.00
166_Q	169_Q	0.923	1.00
53_T	98_A	0.922	1.00
108_C	125_F	0.920	1.00
169_Q	174_V	0.916	1.00
50_C	95_L	0.909	1.00
124_R	164_T	0.907	1.00
238_H	242_S	0.903	1.00
179_P	182_L	0.896	1.00
98_A	183_T	0.893	1.00
219_A	222_A	0.892	1.00
207_Q	227_L	0.887	1.00
12_V	49_V	0.887	1.00
130_I	205_A	0.880	1.00
204_A	207_Q	0.877	1.00
75_A	79_D	0.876	1.00
141_T	224_E	0.874	1.00
14_L	51_V	0.873	1.00
47_I	93_K	0.871	1.00
223_Q	226_Q	0.866	1.00
204_A	227_L	0.857	1.00
189_Q	193_K	0.853	1.00
31_L	84_L	0.848	1.00
142_Q	220_G	0.847	1.00
150_K	213_Q	0.846	1.00
56_A	100_N	0.839	1.00
135_M	231_L	0.836	1.00
8_R	47_I	0.829	1.00
99_V	125_F	0.829	1.00
100_N	183_T	0.828	1.00
121_E	177_V	0.827	1.00
35_V	80_T	0.826	1.00
185_E	188_L	0.825	1.00
120_G	181_D	0.819	1.00
45_T	93_K	0.816	1.00
186_Y	190_L	0.815	1.00
188_L	191_A	0.815	1.00
104_L	162_S	0.812	1.00
99_V	117_V	0.808	1.00
169_Q	176_D	0.796	1.00
38_L	88_L	0.796	1.00
39_E	43_T	0.791	1.00
148_V	156_M	0.787	1.00
156_M	171_A	0.787	1.00
204_A	231_L	0.786	1.00
116_V	175_S	0.786	1.00
157_V	209_L	0.777	1.00
23_R	61_A	0.776	1.00
144_L	148_V	0.775	1.00
109_E	129_E	0.769	1.00
66_N	245_L	0.764	1.00
28_N	80_T	0.764	1.00
15_L	50_C	0.763	1.00
208_A	227_L	0.761	1.00
39_E	83_Q	0.759	1.00
42_A	93_K	0.758	1.00
35_V	84_L	0.758	1.00
32_M	36_N	0.758	1.00
176_D	190_L	0.752	1.00
26_L	30_L	0.750	1.00
187_A	191_A	0.748	1.00
52_I	114_C	0.745	1.00
142_Q	145_I	0.744	1.00
41_A	47_I	0.743	1.00
131_T	162_S	0.742	1.00
223_Q	227_L	0.736	1.00
92_N	207_Q	0.733	1.00
91_F	95_L	0.727	1.00
155_K	159_S	0.727	1.00
227_L	230_L	0.726	1.00
235_E	238_H	0.726	1.00
149_G	153_A	0.723	1.00
19_R	27_N	0.722	1.00
58_F	100_N	0.722	1.00
189_Q	192_S	0.719	1.00
27_N	67_E	0.717	1.00
165_A	174_V	0.715	1.00
112_L	173_L	0.712	1.00
217_L	221_L	0.708	1.00
85_W	113_L	0.706	1.00
198_S	236_D	0.705	1.00
168_A	173_L	0.702	1.00
211_Q	215_V	0.702	1.00
79_D	225_R	0.700	1.00
241_I	245_L	0.698	1.00
194_M	202_L	0.695	1.00
105_G	128_P	0.692	1.00
193_K	197_H	0.691	1.00
100_N	180_S	0.690	1.00
72_D	76_T	0.689	1.00
118_V	176_D	0.683	1.00
23_R	102_Y	0.681	1.00
79_D	83_Q	0.680	1.00
129_E	137_G	0.676	1.00
48_S	199_P	0.676	1.00
222_A	226_Q	0.676	1.00
6_V	37_E	0.673	1.00
99_V	123_A	0.671	1.00
192_S	196_R	0.666	1.00
178_F	183_T	0.666	1.00
30_L	33_Q	0.665	1.00
159_S	190_L	0.664	1.00
29_A	32_M	0.663	1.00
6_V	40_A	0.659	1.00
200_L	234_T	0.655	1.00
11_R	46_S	0.653	1.00
150_K	210_R	0.650	1.00
51_V	98_A	0.648	1.00
225_R	229_T	0.648	1.00
44_D	47_I	0.647	1.00
96_I	191_A	0.644	1.00
12_V	51_V	0.643	1.00
125_F	174_V	0.643	1.00
119_A	123_A	0.642	1.00
129_E	136_P	0.640	1.00
208_A	223_Q	0.639	1.00
118_V	187_A	0.639	1.00
22_A	25_A	0.637	1.00
69_A	242_S	0.635	1.00
41_A	93_K	0.633	1.00
190_L	193_K	0.630	1.00
152_L	169_Q	0.629	1.00
226_Q	230_L	0.628	1.00
19_R	25_A	0.628	1.00
91_F	94_P	0.627	1.00
104_L	128_P	0.627	1.00
39_E	42_A	0.624	1.00
174_V	177_V	0.621	1.00
52_I	95_L	0.621	1.00
218_Q	222_A	0.620	1.00
135_M	208_A	0.616	1.00
97_A	117_V	0.614	1.00
51_V	188_L	0.613	1.00
37_E	41_A	0.613	1.00
126_G	160_G	0.610	1.00
136_P	205_A	0.606	1.00
8_R	11_R	0.606	1.00
63_A	68_M	0.604	1.00
75_A	229_T	0.603	1.00
150_K	209_L	0.599	1.00
36_N	39_E	0.598	1.00
118_V	186_Y	0.597	1.00
44_D	93_K	0.596	1.00
34_L	84_L	0.594	1.00
129_E	228_F	0.593	1.00
118_V	183_T	0.593	1.00
158_L	202_L	0.591	1.00
166_Q	177_V	0.590	1.00
122_N	165_A	0.590	1.00
235_E	239_E	0.589	1.00
49_V	195_A	0.589	1.00
12_V	188_L	0.587	1.00
12_V	191_A	0.585	1.00
49_V	96_I	0.585	1.00
6_V	15_L	0.584	1.00
75_A	226_Q	0.584	1.00
109_E	137_G	0.583	1.00
147_S	175_S	0.582	1.00
22_A	64_D	0.581	1.00
148_V	153_A	0.578	1.00
163_I	168_A	0.575	1.00
155_K	167_Q	0.574	1.00
83_Q	86_A	0.573	1.00
240_G	243_A	0.572	1.00
102_Y	162_S	0.569	1.00
134_I	237_R	0.566	1.00
48_S	195_A	0.565	1.00
239_E	242_S	0.564	1.00
205_A	208_A	0.562	1.00
38_L	87_R	0.562	1.00
242_S	245_L	0.560	1.00
239_E	243_A	0.560	1.00
182_L	189_Q	0.558	1.00
236_D	240_G	0.557	1.00
200_L	231_L	0.557	1.00
142_Q	146_R	0.552	1.00
127_L	157_V	0.549	1.00
15_L	38_L	0.549	1.00
141_T	220_G	0.547	1.00
76_T	80_T	0.547	1.00
159_S	194_M	0.547	1.00
83_Q	87_R	0.543	1.00
164_T	170_Q	0.543	1.00
154_S	206_K	0.542	1.00
111_A	114_C	0.541	1.00
161_E	176_D	0.541	1.00
148_V	171_A	0.539	1.00
239_E	246_Q	0.537	1.00
72_D	75_A	0.531	1.00
165_A	169_Q	0.530	1.00
105_G	127_L	0.529	1.00
38_L	95_L	0.527	1.00
108_C	173_L	0.527	1.00
113_L	143_R	0.527	1.00
116_V	194_M	0.526	1.00
127_L	140_G	0.525	1.00
159_S	193_K	0.523	1.00
152_L	170_Q	0.522	1.00
109_E	127_L	0.521	1.00
120_G	123_A	0.520	1.00
29_A	67_E	0.519	1.00
15_L	52_I	0.519	1.00
63_A	106_A	0.517	1.00
69_A	245_L	0.515	1.00
130_I	197_H	0.513	1.00
65_L	132_L	0.512	1.00
109_E	139_G	0.511	1.00
135_M	205_A	0.511	1.00
127_L	144_L	0.510	1.00
31_L	35_V	0.507	1.00
106_A	138_A	0.506	1.00
222_A	225_R	0.506	1.00
26_L	106_A	0.505	1.00
130_I	202_L	0.504	1.00
145_I	212_S	0.503	1.00
16_T	184_L	0.502	1.00
100_N	123_A	0.502	1.00
168_A	174_V	0.501	1.00
73_L	76_T	0.500	1.00
40_A	43_T	0.500	1.00
69_A	241_I	0.500	1.00

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
4lk5A	3	0.9725	100	0.075	Contact Map
3tlfA	5	0.9961	100	0.078	Contact Map
4mi2A	3	0.9961	100	0.079	Contact Map
3kqfA	3	1	100	0.08	Contact Map
3g64A	6	1	100	0.08	Contact Map
2fbmA	3	0.9529	100	0.083	Contact Map
1nzyA	4	1	100	0.083	Contact Map
3sllA	6	0.9843	100	0.085	Contact Map
3qreA	3	0.7686	100	0.085	Contact Map
2pbpA	5	1	100	0.085	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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