PKSI - BACSU - GREMLIN Contacts

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PKSI - Putative polyketide biosynthesis enoyl-CoA isomerase PksI

UniProt:	P40802	Sequences: MTHSVVELIEIESAIIQVKMQDRTHKNAFSQELTDDLIQAFEYIRQNPKYKAVILTGYDNYFASGGTQEGLLRIQQGLTKFTDDNLYSLALDCEIPVIAAMQGHGIGGGFVMGLFADIVILSRESVYTANFMKYGFTPGMGATFIVPKKLGFSLAQEILLNAGSYRGADLEKRGVPFKVLPRAEVLDYAVELAQELAEKPRNSLVTLKDHLVAPLRDQLPRVIEQELMMHEKTFHHEEVKSRIKGLYGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	249 (238)
Sequences:	30241 (19880)
Seq/√Len:	1288.6

ECOLI - PAAG MENB PAAF SCPB CAID FADB FADJ
BACSU - PKSI MENB FADB YNGF YHAR PKSH FADN
HALSA - Q9HS32 Q9HQN4 Q9HQ61 Q9HNM6
SULSO - Q7LXQ1 Q97VK0 Q97WU7 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
126_V	164_S	3.288	1.00
123_R	181_P	3.122	1.00
178_K	188_Y	3.089	1.00
121_L	176_P	2.964	1.00
188_Y	191_E	2.875	1.00
99_A	116_A	2.847	1.00
17_Q	190_V	2.656	1.00
45_R	94_E	2.542	1.00
42_E	89_L	2.463	1.00
163_G	195_E	2.332	1.00
124_E	182_R	2.305	1.00
218_Q	221_R	2.253	1.00
169_D	172_K	2.209	1.00
157_E	163_G	2.189	1.00
166_R	169_D	2.183	1.00
133_K	199_K	2.077	1.00
154_L	173_R	2.076	1.00
26_K	61_Y	2.070	1.00
159_L	207_L	2.062	1.00
17_Q	56_T	2.061	1.00
38_I	89_L	1.945	1.00
32_E	36_D	1.919	1.00
14_A	51_K	1.907	1.00
100_A	189_A	1.907	1.00
106_I	128_T	1.875	1.00
123_R	168_A	1.872	1.00
21_Q	58_Y	1.863	1.00
19_K	58_Y	1.848	1.00
26_K	60_N	1.828	1.00
11_I	16_I	1.799	1.00
100_A	186_L	1.799	1.00
156_Q	212_V	1.793	1.00
120_I	180_L	1.791	1.00
157_E	177_F	1.779	1.00
19_K	56_T	1.777	1.00
117_D	208_K	1.758	1.00
9_I	16_I	1.750	1.00
16_I	44_I	1.735	1.00
43_Y	47_N	1.733	1.00
184_E	187_D	1.733	1.00
190_V	194_Q	1.728	1.00
11_I	47_N	1.723	1.00
53_V	93_C	1.685	1.00
123_R	182_R	1.658	1.00
169_D	173_R	1.650	1.00
152_F	156_Q	1.594	1.00
16_I	50_Y	1.593	1.00
168_A	172_K	1.576	1.00
120_I	192_L	1.550	1.00
119_V	149_K	1.519	1.00
184_E	188_Y	1.513	1.00
157_E	178_K	1.507	1.00
121_L	127_Y	1.506	1.00
44_I	53_V	1.495	1.00
113_G	119_V	1.479	1.00
119_V	153_S	1.478	1.00
122_S	182_R	1.474	1.00
180_L	188_Y	1.460	1.00
52_A	193_A	1.443	1.00
45_R	89_L	1.439	1.00
12_E	190_V	1.435	1.00
18_V	40_A	1.434	1.00
156_Q	211_L	1.434	1.00
60_N	102_Q	1.428	1.00
88_S	92_D	1.418	1.00
101_M	113_G	1.410	1.00
13_S	194_Q	1.409	1.00
88_S	220_P	1.396	1.00
91_L	145_I	1.388	1.00
156_Q	160_L	1.383	1.00
171_E	179_V	1.381	1.00
101_M	105_G	1.371	1.00
102_Q	122_S	1.356	1.00
110_F	129_A	1.344	1.00
102_Q	124_E	1.342	1.00
12_E	194_Q	1.338	1.00
41_F	93_C	1.337	1.00
206_T	232_K	1.334	1.00
56_T	102_Q	1.316	1.00
90_A	97_V	1.315	1.00
38_I	42_E	1.314	1.00
158_I	165_Y	1.313	1.00
12_E	17_Q	1.307	1.00
154_L	157_E	1.306	1.00
185_V	189_A	1.294	1.00
163_G	169_D	1.284	1.00
31_Q	70_G	1.283	1.00
9_I	44_I	1.250	1.00
128_T	164_S	1.243	1.00
30_S	33_L	1.234	1.00
22_D	25_H	1.228	1.00
209_D	213_A	1.222	1.00
132_M	162_A	1.215	1.00
38_I	85_N	1.213	1.00
153_S	177_F	1.201	1.00
104_H	126_V	1.192	1.00
186_L	190_V	1.190	1.00
154_L	169_D	1.190	1.00
36_D	40_A	1.189	1.00
45_R	93_C	1.188	1.00
239_V	243_I	1.183	1.00
61_Y	104_H	1.173	1.00
217_D	221_R	1.171	1.00
186_L	189_A	1.169	1.00
199_K	204_L	1.161	1.00
20_M	33_L	1.154	1.00
17_Q	186_L	1.152	1.00
56_T	186_L	1.129	1.00
25_H	69_E	1.124	1.00
165_Y	173_R	1.123	1.00
20_M	63_A	1.115	1.00
217_D	225_Q	1.106	1.00
63_A	109_G	1.096	1.00
122_S	185_V	1.090	1.00
213_A	225_Q	1.077	1.00
167_G	179_V	1.076	1.00
151_G	154_L	1.072	1.00
36_D	39_Q	1.058	1.00
39_Q	43_Y	1.046	1.00
202_N	238_E	1.046	1.00
31_Q	35_D	1.040	1.00
187_D	191_E	1.033	1.00
53_V	95_I	1.030	1.00
92_D	220_P	1.030	1.00
111_V	142_A	1.017	1.00
118_I	192_L	1.002	1.00
193_A	197_A	0.997	1.00
150_L	154_L	0.993	1.00
97_V	116_A	0.989	1.00
22_D	67_T	0.988	1.00
221_R	224_E	0.956	1.00
40_A	43_Y	0.950	1.00
149_K	153_S	0.949	1.00
143_T	226_E	0.944	1.00
94_E	205_V	0.943	1.00
171_E	176_P	0.943	1.00
59_D	102_Q	0.942	1.00
17_Q	54_I	0.933	1.00
56_T	100_A	0.927	1.00
54_I	189_A	0.925	1.00
201_R	205_V	0.925	1.00
168_A	171_E	0.923	1.00
11_I	43_Y	0.916	1.00
240_K	244_K	0.915	1.00
126_V	166_R	0.915	1.00
181_P	184_E	0.910	1.00
100_A	185_V	0.908	1.00
110_F	127_Y	0.907	1.00
209_D	229_M	0.907	1.00
53_V	97_V	0.906	1.00
11_I	49_K	0.897	1.00
50_Y	95_I	0.892	1.00
190_V	193_A	0.888	1.00
34_T	86_L	0.887	1.00
132_M	207_L	0.881	1.00
48_P	95_I	0.879	1.00
15_I	52_A	0.869	1.00
26_K	64_S	0.867	1.00
206_T	209_D	0.862	1.00
137_T	233_T	0.851	1.00
241_S	245_G	0.850	1.00
102_Q	185_V	0.849	1.00
206_T	229_M	0.846	1.00
10_E	19_K	0.845	1.00
225_Q	228_M	0.840	1.00
191_E	195_E	0.836	1.00
144_F	222_V	0.835	1.00
101_M	127_Y	0.829	1.00
206_T	233_T	0.829	1.00
111_V	131_F	0.829	1.00
152_F	215_L	0.826	1.00
118_I	177_F	0.816	1.00
122_S	183_A	0.811	1.00
41_F	90_A	0.810	1.00
106_I	164_S	0.810	1.00
42_E	46_Q	0.809	1.00
10_E	17_Q	0.808	1.00
159_L	211_L	0.806	1.00
101_M	119_V	0.806	1.00
171_E	178_K	0.804	1.00
157_E	161_N	0.799	1.00
150_L	158_I	0.797	1.00
44_I	50_Y	0.794	1.00
242_R	245_G	0.792	1.00
42_E	85_N	0.792	1.00
210_H	229_M	0.789	1.00
158_I	173_R	0.787	1.00
55_L	116_A	0.787	1.00
38_I	86_L	0.784	1.00
107_G	130_N	0.782	1.00
123_R	179_V	0.777	1.00
188_Y	192_L	0.777	1.00
18_V	53_V	0.773	1.00
30_S	70_G	0.773	1.00
187_D	190_V	0.773	1.00
178_K	192_L	0.771	1.00
45_R	95_I	0.768	1.00
69_E	247_Y	0.767	1.00
133_K	164_S	0.766	1.00
61_Y	102_Q	0.766	1.00
35_D	39_Q	0.762	1.00
189_A	193_A	0.755	1.00
75_Q	78_L	0.755	1.00
238_E	242_R	0.754	1.00
146_V	150_L	0.752	1.00
225_Q	229_M	0.749	1.00
29_F	33_L	0.744	1.00
87_Y	115_F	0.741	1.00
51_K	201_R	0.741	1.00
237_E	240_K	0.741	1.00
94_E	209_D	0.738	1.00
131_F	139_G	0.731	1.00
227_L	231_E	0.731	1.00
191_E	194_Q	0.725	1.00
241_S	244_K	0.724	1.00
22_D	30_S	0.724	1.00
26_K	104_H	0.722	1.00
200_P	238_E	0.722	1.00
93_C	97_V	0.713	1.00
11_I	50_Y	0.711	1.00
167_G	176_P	0.708	1.00
195_E	199_K	0.703	1.00
219_L	223_I	0.700	1.00
131_F	230_H	0.700	1.00
151_G	155_A	0.700	1.00
213_A	217_D	0.698	1.00
170_L	175_V	0.695	1.00
131_F	138_P	0.693	1.00
11_I	14_A	0.689	1.00
114_L	175_V	0.689	1.00
229_M	232_K	0.688	1.00
196_L	204_L	0.686	1.00
224_E	228_M	0.686	1.00
102_Q	182_R	0.674	1.00
180_L	185_V	0.670	1.00
55_L	97_V	0.669	1.00
243_I	247_Y	0.668	1.00
161_N	192_L	0.668	1.00
33_L	36_D	0.666	1.00
120_I	178_K	0.663	1.00
44_I	95_I	0.663	1.00
101_M	125_S	0.663	1.00
57_G	60_N	0.661	1.00
194_Q	198_E	0.660	1.00
111_V	139_G	0.660	1.00
93_C	96_P	0.657	1.00
47_N	50_Y	0.656	1.00
128_T	162_A	0.656	1.00
22_D	28_A	0.655	1.00
210_H	225_Q	0.652	1.00
152_F	212_V	0.651	1.00
228_M	232_K	0.650	1.00
127_Y	176_P	0.650	1.00
54_I	100_A	0.650	1.00
176_P	179_V	0.646	1.00
15_I	54_I	0.643	1.00
202_N	236_H	0.642	1.00
144_F	147_P	0.641	1.00
37_L	86_L	0.641	1.00
138_P	207_L	0.637	1.00
32_E	35_D	0.632	1.00
137_T	210_H	0.629	1.00
66_G	71_L	0.629	1.00
192_L	195_E	0.628	1.00
40_A	44_I	0.628	1.00
54_I	190_V	0.627	1.00
106_I	130_N	0.627	1.00
121_L	125_S	0.626	1.00
152_F	211_L	0.623	1.00
120_I	189_A	0.619	1.00
99_A	119_V	0.617	1.00
42_E	45_R	0.610	1.00
14_A	49_K	0.608	1.00
52_A	98_I	0.606	1.00
39_Q	42_E	0.606	1.00
25_H	67_T	0.606	1.00
237_E	241_S	0.604	1.00
72_L	244_K	0.601	1.00
143_T	222_V	0.601	1.00
207_L	210_H	0.600	1.00
47_N	95_I	0.598	1.00
98_I	193_A	0.598	1.00
154_L	171_E	0.597	1.00
15_I	190_V	0.595	1.00
120_I	185_V	0.595	1.00
160_L	204_L	0.587	1.00
168_A	179_V	0.584	1.00
129_A	142_A	0.581	1.00
202_N	233_T	0.581	1.00
52_A	197_A	0.574	1.00
120_I	188_Y	0.574	1.00
220_P	224_E	0.574	1.00
157_E	169_D	0.574	1.00
124_E	167_G	0.574	1.00
137_T	207_L	0.573	1.00
136_F	239_V	0.573	1.00
111_V	141_G	0.570	1.00
51_K	197_A	0.563	1.00
184_E	191_E	0.562	1.00
165_Y	170_L	0.561	1.00
150_L	155_A	0.561	1.00
85_N	88_S	0.559	1.00
166_R	172_K	0.556	1.00
239_V	242_R	0.554	1.00
86_L	89_L	0.554	1.00
163_G	178_K	0.552	1.00
9_I	43_Y	0.550	1.00
108_G	140_M	0.550	1.00
132_M	199_K	0.549	1.00
104_H	164_S	0.548	1.00
244_K	247_Y	0.548	1.00
18_V	55_L	0.547	1.00
15_I	193_A	0.546	1.00
154_L	172_K	0.545	1.00
118_I	196_L	0.544	1.00
156_Q	208_K	0.543	1.00
85_N	89_L	0.540	1.00
66_G	108_G	0.539	1.00
41_F	89_L	0.539	1.00
30_S	67_T	0.538	1.00
122_S	125_S	0.537	1.00
34_T	38_I	0.537	1.00
75_Q	79_T	0.536	1.00
113_G	116_A	0.536	1.00
68_Q	71_L	0.535	1.00
149_K	177_F	0.535	1.00
111_V	129_A	0.534	1.00
107_G	129_A	0.534	1.00
129_A	159_L	0.533	1.00
150_L	173_R	0.532	1.00
167_G	171_E	0.529	1.00
139_G	142_A	0.529	1.00
110_F	114_L	0.527	1.00
161_N	196_L	0.526	1.00
129_A	146_V	0.526	1.00
29_F	34_T	0.520	1.00
76_Q	79_T	0.519	1.00
135_G	200_P	0.516	1.00
50_Y	53_V	0.516	1.00
18_V	41_F	0.515	1.00
224_E	227_L	0.514	1.00
111_V	145_I	0.514	1.00
161_N	195_E	0.514	1.00
108_G	111_V	0.513	1.00
29_F	108_G	0.512	1.00
32_E	70_G	0.511	1.00
217_D	222_V	0.511	1.00
105_G	110_F	0.510	1.00
110_F	175_V	0.508	1.00
115_F	145_I	0.508	1.00
41_F	97_V	0.507	1.00
68_Q	134_Y	0.506	1.00
19_K	186_L	0.504	1.00
131_F	141_G	0.502	1.00
138_P	159_L	0.501	1.00
170_L	176_P	0.501	1.00
144_F	148_K	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
4q1kA	3	1	100	0.064	Contact Map
4jfcA	3	0.9839	100	0.088	Contact Map
3laoA	3	0.9157	100	0.088	Contact Map
4lk5A	3	0.9679	100	0.09	Contact Map
4mi2A	3	0.9839	100	0.092	Contact Map
3swxA	3	0.992	100	0.092	Contact Map
4u19A	3	0.996	100	0.092	Contact Map
1nzyA	4	0.992	100	0.093	Contact Map
2pbpA	5	0.988	100	0.093	Contact Map
4og1A	3	0.9518	100	0.094	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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