HMGCL - BACSU - GREMLIN Contacts

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HMGCL - Hydroxymethylglutaryl-CoA lyase YngG

UniProt:	O34873	Sequences: MPYPKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAIDVAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHILKQVNNDAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTIGAANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLGGCPYAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLSAAKWIEEKMGKPLPSRNLQVFKSS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	299 (275)
Sequences:	10426 (5403)
Seq/√Len:	325.8

ECOLI - LEU1 HOA
BACSU - HMGCL LEU1
SULSO - HOSA Q980Z1 LEU1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
189_E	225_M	3.230	1.00
132_Q	172_S	3.155	1.00
88_E	130_D	2.863	1.00
107_T	151_E	2.850	1.00
206_L	222_A	2.776	1.00
39_R	272_K	2.741	1.00
189_E	224_Q	2.569	1.00
164_E	198_R	2.549	1.00
116_S	119_E	2.468	1.00
125_K	129_N	2.304	1.00
193_E	225_M	2.282	1.00
221_T	224_Q	2.267	1.00
106_E	117_T	2.198	1.00
36_Q	279_W	2.181	1.00
115_K	123_I	2.152	1.00
156_I	194_A	2.098	1.00
26_A	29_D	2.060	1.00
48_T	62_A	2.056	1.00
272_K	275_S	1.968	1.00
269_K	272_K	1.952	1.00
196_L	228_T	1.941	1.00
163_S	174_L	1.937	1.00
219_M	255_I	1.904	1.00
158_Q	161_R	1.903	1.00
193_E	197_A	1.887	1.00
186_A	224_Q	1.875	1.00
125_K	169_F	1.867	1.00
31_I	68_G	1.861	1.00
165_A	168_E	1.849	1.00
196_L	204_I	1.839	1.00
164_E	168_E	1.835	1.00
223_L	230_F	1.821	1.00
125_K	165_A	1.805	1.00
194_A	198_R	1.804	1.00
36_Q	276_A	1.789	1.00
160_I	194_A	1.728	1.00
84_Q	126_Q	1.726	1.00
122_H	126_Q	1.715	1.00
6_K	265_K	1.688	1.00
220_V	258_M	1.687	1.00
188_V	208_F	1.677	1.00
137_T	172_S	1.659	1.00
122_H	125_K	1.658	1.00
189_E	193_E	1.653	1.00
129_N	133_K	1.653	1.00
221_T	225_M	1.649	1.00
50_F	78_A	1.643	1.00
118_S	161_R	1.641	1.00
161_R	165_A	1.625	1.00
64_D	68_G	1.618	1.00
219_M	230_F	1.602	1.00
91_L	134_A	1.572	1.00
27_T	61_D	1.568	1.00
131_A	138_T	1.563	1.00
186_A	190_T	1.552	1.00
208_F	219_M	1.539	1.00
36_Q	275_S	1.533	1.00
260_E	265_K	1.510	1.00
256_V	268_V	1.497	1.00
124_L	162_L	1.497	1.00
192_L	206_L	1.493	1.00
130_D	133_K	1.488	1.00
85_R	88_E	1.486	1.00
189_E	221_T	1.470	1.00
36_Q	39_R	1.454	1.00
188_V	206_L	1.453	1.00
213_G	254_D	1.452	1.00
164_E	199_F	1.450	1.00
232_G	252_T	1.446	1.00
223_L	259_L	1.444	1.00
88_E	92_E	1.428	1.00
167_F	200_P	1.424	1.00
160_I	198_R	1.412	1.00
128_N	138_T	1.394	1.00
118_S	122_H	1.392	1.00
157_E	161_R	1.385	1.00
279_W	283_K	1.384	1.00
277_A	288_L	1.383	1.00
29_D	283_K	1.382	1.00
104_A	154_V	1.369	1.00
219_M	250_A	1.361	1.00
206_L	230_F	1.353	1.00
115_K	119_E	1.352	1.00
130_D	134_A	1.351	1.00
8_T	44_Y	1.326	1.00
109_N	120_S	1.315	1.00
63_I	67_K	1.290	1.00
104_A	142_L	1.286	1.00
40_T	276_A	1.282	1.00
106_E	155_P	1.282	1.00
84_Q	130_D	1.281	1.00
183_A	188_V	1.267	1.00
31_I	65_V	1.266	1.00
235_G	277_A	1.257	1.00
87_L	134_A	1.256	1.00
157_E	194_A	1.234	1.00
35_N	70_D	1.225	1.00
33_W	280_I	1.223	1.00
16_D	249_N	1.208	1.00
119_E	122_H	1.203	1.00
208_F	222_A	1.200	1.00
81_V	86_G	1.197	1.00
112_N	149_P	1.193	1.00
190_T	194_A	1.190	1.00
164_E	167_F	1.184	1.00
84_Q	88_E	1.184	1.00
107_T	111_K	1.184	1.00
276_A	279_W	1.183	1.00
194_A	197_A	1.180	1.00
206_L	227_I	1.179	1.00
256_V	273_L	1.176	1.00
32_T	36_Q	1.173	1.00
274_L	278_K	1.171	1.00
156_I	190_T	1.171	1.00
257_Y	270_L	1.170	1.00
192_L	204_I	1.167	1.00
91_L	136_L	1.148	1.00
228_T	264_I	1.147	1.00
87_L	127_V	1.142	1.00
25_I	284_M	1.133	1.00
64_D	67_K	1.130	1.00
109_N	117_T	1.119	1.00
153_D	187_Q	1.115	1.00
14_P	34_I	1.115	1.00
35_N	68_G	1.114	1.00
163_S	199_F	1.109	1.00
188_V	222_A	1.105	1.00
140_A	166_L	1.100	1.00
176_L	195_L	1.098	1.00
42_L	268_V	1.095	1.00
155_P	158_Q	1.089	1.00
7_V	264_I	1.086	1.00
38_S	72_E	1.085	1.00
167_F	202_N	1.083	1.00
260_E	266_T	1.079	1.00
163_S	195_L	1.048	1.00
250_A	255_I	1.044	1.00
125_K	168_E	1.042	1.00
35_N	72_E	1.042	1.00
32_T	282_E	1.041	1.00
103_S	108_H	1.040	1.00
117_T	158_Q	1.038	1.00
38_S	71_R	1.037	1.00
232_G	255_I	1.036	1.00
161_R	164_E	1.033	1.00
54_K	60_R	1.028	1.00
7_V	223_L	1.027	1.00
104_A	162_L	1.022	1.00
165_A	169_F	1.021	1.00
102_M	109_N	1.019	1.00
37_L	45_I	1.018	1.00
36_Q	272_K	1.016	1.00
126_Q	129_N	1.013	1.00
103_S	106_E	1.010	1.00
121_L	162_L	1.009	1.00
124_L	166_L	0.999	1.00
68_G	71_R	0.996	1.00
176_L	191_V	0.994	1.00
184_N	187_Q	0.990	1.00
60_R	63_I	0.989	1.00
192_L	227_I	0.961	1.00
12_V	249_N	0.959	1.00
18_L	25_I	0.958	1.00
44_Y	137_T	0.951	1.00
27_T	31_I	0.945	1.00
223_L	264_I	0.945	1.00
76_T	79_A	0.944	1.00
216_L	255_I	0.940	1.00
115_K	120_S	0.938	1.00
140_A	171_I	0.937	1.00
9_I	256_V	0.936	1.00
60_R	64_D	0.934	1.00
32_T	279_W	0.934	1.00
6_K	267_N	0.933	1.00
35_N	38_S	0.931	1.00
110_R	114_N	0.930	1.00
89_N	92_E	0.928	1.00
14_P	45_I	0.926	1.00
110_R	116_S	0.926	1.00
8_T	229_V	0.921	1.00
61_D	64_D	0.916	1.00
216_L	258_M	0.916	1.00
147_G	182_A	0.915	1.00
255_I	259_L	0.907	1.00
215_A	250_A	0.907	1.00
128_N	169_F	0.898	1.00
148_C	151_E	0.894	1.00
192_L	225_M	0.891	1.00
12_V	46_E	0.890	1.00
220_V	262_M	0.888	1.00
278_K	282_E	0.888	1.00
160_I	164_E	0.888	1.00
199_F	202_N	0.886	1.00
29_D	32_T	0.884	1.00
251_A	254_D	0.883	1.00
121_L	165_A	0.879	1.00
160_I	195_L	0.878	1.00
87_L	91_L	0.877	1.00
140_A	162_L	0.867	1.00
196_L	201_A	0.867	1.00
210_D	213_G	0.866	1.00
147_G	154_V	0.864	1.00
63_I	89_N	0.862	1.00
10_K	229_V	0.860	1.00
234_A	280_I	0.858	1.00
105_S	136_L	0.856	1.00
79_A	82_P	0.851	1.00
87_L	130_D	0.849	1.00
234_A	276_A	0.846	1.00
137_T	173_E	0.840	1.00
156_I	191_V	0.840	1.00
27_T	64_D	0.833	1.00
260_E	270_L	0.827	1.00
187_Q	190_T	0.826	1.00
142_L	162_L	0.824	1.00
97_E	137_T	0.823	1.00
186_A	221_T	0.819	1.00
220_V	224_Q	0.818	1.00
57_P	61_D	0.817	1.00
7_V	259_L	0.817	1.00
25_I	283_K	0.813	1.00
39_R	72_E	0.808	1.00
204_I	227_I	0.804	1.00
210_D	215_A	0.796	1.00
88_E	134_A	0.794	1.00
173_E	229_V	0.790	1.00
65_V	68_G	0.789	1.00
126_Q	130_D	0.787	1.00
85_R	89_N	0.786	1.00
48_T	66_A	0.785	1.00
178_D	218_N	0.785	1.00
6_K	43_S	0.785	1.00
148_C	163_S	0.781	1.00
106_E	110_R	0.778	1.00
160_I	199_F	0.777	1.00
230_F	259_L	0.775	1.00
164_E	200_P	0.773	1.00
167_F	174_L	0.770	1.00
184_N	262_M	0.769	1.00
275_S	279_W	0.761	1.00
8_T	43_S	0.757	0.99
31_I	35_N	0.755	0.99
192_L	222_A	0.755	0.99
11_E	252_T	0.752	0.99
43_S	267_N	0.747	0.99
62_A	66_A	0.745	0.99
142_L	163_S	0.743	0.99
156_I	160_I	0.741	0.99
191_V	194_A	0.740	0.99
28_E	32_T	0.739	0.99
129_N	169_F	0.734	0.99
9_I	232_G	0.734	0.99
230_F	255_I	0.734	0.99
139_R	173_E	0.733	0.99
256_V	270_L	0.733	0.99
48_T	59_L	0.728	0.99
196_L	225_M	0.727	0.99
117_T	161_R	0.727	0.99
187_Q	191_V	0.726	0.99
167_F	199_F	0.725	0.99
39_R	275_S	0.725	0.99
186_A	189_E	0.721	0.99
121_L	169_F	0.718	0.99
151_E	154_V	0.716	0.99
123_I	126_Q	0.711	0.99
35_N	39_R	0.709	0.99
8_T	173_E	0.708	0.99
216_L	254_D	0.704	0.99
223_L	255_I	0.703	0.99
145_V	177_G	0.702	0.99
47_I	77_Y	0.701	0.99
152_K	183_A	0.700	0.99
258_M	262_M	0.698	0.99
195_L	199_F	0.697	0.99
205_A	229_V	0.694	0.99
117_T	155_P	0.690	0.99
233_S	248_G	0.689	0.99
190_T	193_E	0.689	0.99
44_Y	78_A	0.688	0.99
99_C	175_S	0.687	0.99
28_E	68_G	0.684	0.99
191_V	195_L	0.683	0.99
237_L	286_K	0.682	0.99
32_T	35_N	0.682	0.99
99_C	102_M	0.681	0.99
192_L	196_L	0.680	0.99
95_I	136_L	0.677	0.99
175_S	205_A	0.676	0.99
10_K	44_Y	0.675	0.99
224_Q	262_M	0.674	0.99
51_V	85_R	0.672	0.99
200_P	203_Q	0.670	0.99
33_W	234_A	0.670	0.99
216_L	219_M	0.667	0.99
121_L	161_R	0.664	0.99
33_W	37_L	0.659	0.99
102_M	124_L	0.658	0.99
9_I	252_T	0.658	0.99
163_S	176_L	0.655	0.99
157_E	198_R	0.654	0.98
71_R	96_N	0.649	0.98
25_I	30_K	0.648	0.98
167_F	203_Q	0.646	0.98
63_I	92_E	0.646	0.98
69_I	72_E	0.643	0.98
91_L	96_N	0.642	0.98
278_K	281_E	0.633	0.98
91_L	135_N	0.633	0.98
105_S	154_V	0.632	0.98
237_L	284_M	0.632	0.98
199_F	204_I	0.631	0.98
183_A	187_Q	0.630	0.98
38_S	70_D	0.629	0.98
213_G	251_A	0.628	0.98
7_V	228_T	0.628	0.98
203_Q	228_T	0.628	0.98
211_T	246_S	0.626	0.98
42_L	252_T	0.625	0.98
217_A	221_T	0.625	0.98
281_E	287_P	0.622	0.98
40_T	273_L	0.622	0.98
69_I	73_K	0.621	0.98
101_F	177_G	0.620	0.98
32_T	275_S	0.619	0.98
34_I	58_A	0.616	0.98
71_R	77_Y	0.612	0.98
27_T	30_K	0.612	0.98
20_N	23_V	0.611	0.98
166_L	171_I	0.611	0.98
76_T	81_V	0.609	0.98
195_L	204_I	0.606	0.98
91_L	130_D	0.606	0.98
80_L	90_A	0.605	0.98
58_A	61_D	0.603	0.97
49_S	53_P	0.600	0.97
186_A	262_M	0.599	0.97
109_N	154_V	0.598	0.97
157_E	160_I	0.596	0.97
188_V	218_N	0.596	0.97
9_I	266_T	0.590	0.97
44_Y	97_E	0.590	0.97
82_P	127_V	0.589	0.97
178_D	181_G	0.587	0.97
57_P	60_R	0.585	0.97
20_N	286_K	0.584	0.97
70_D	73_K	0.582	0.97
35_N	71_R	0.581	0.97
113_I	120_S	0.579	0.97
152_K	191_V	0.578	0.97
183_A	191_V	0.572	0.97
81_V	98_A	0.572	0.97
119_E	123_I	0.571	0.96
50_F	62_A	0.570	0.96
59_L	89_N	0.567	0.96
172_S	203_Q	0.566	0.96
216_L	250_A	0.566	0.96
275_S	278_K	0.566	0.96
254_D	257_Y	0.565	0.96
270_L	274_L	0.565	0.96
223_L	228_T	0.563	0.96
145_V	176_L	0.562	0.96
147_G	153_D	0.561	0.96
66_A	69_I	0.559	0.96
77_Y	80_L	0.556	0.96
53_P	57_P	0.555	0.96
34_I	45_I	0.549	0.96
77_Y	81_V	0.548	0.96
17_G	233_S	0.546	0.95
76_T	137_T	0.544	0.95
162_L	165_A	0.544	0.95
34_I	69_I	0.543	0.95
185_P	217_A	0.541	0.95
106_E	109_N	0.538	0.95
38_S	69_I	0.538	0.95
122_H	165_A	0.536	0.95
80_L	86_G	0.534	0.95
87_L	98_A	0.534	0.95
105_S	108_H	0.534	0.95
259_L	266_T	0.533	0.95
58_A	62_A	0.533	0.95
278_K	288_L	0.531	0.95
109_N	115_K	0.531	0.95
59_L	62_A	0.531	0.95
279_W	282_E	0.531	0.95
276_A	280_I	0.529	0.95
211_T	245_G	0.529	0.95
19_Q	245_G	0.528	0.95
125_K	166_L	0.527	0.95
12_V	233_S	0.526	0.95
79_A	95_I	0.525	0.94
280_I	284_M	0.524	0.94
90_A	98_A	0.523	0.94
82_P	86_G	0.519	0.94
80_L	83_N	0.519	0.94
20_N	237_L	0.518	0.94
219_M	249_N	0.518	0.94
260_E	267_N	0.517	0.94
210_D	216_L	0.517	0.94
40_T	272_K	0.517	0.94
12_V	16_D	0.517	0.94
100_V	127_V	0.516	0.94
129_N	132_Q	0.516	0.94
147_G	177_G	0.515	0.94
32_T	283_K	0.514	0.94
252_T	273_L	0.513	0.94
34_I	47_I	0.509	0.94
176_L	192_L	0.508	0.93
10_K	99_C	0.507	0.93
6_K	264_I	0.506	0.93
67_K	107_T	0.504	0.93
54_K	59_L	0.502	0.93
9_I	42_L	0.500	0.93

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
2ftpA	3	1	100	0.083	Contact Map
1ydoA	3	0.9967	100	0.085	Contact Map
2cw6A	5	0.99	100	0.11	Contact Map
1ydnA	1	0.9465	100	0.113	Contact Map
3bleA	2	0.9465	100	0.183	Contact Map
4ov4A	2	0.9465	100	0.185	Contact Map
3rmjA	2	0.9365	100	0.194	Contact Map
2ztjA	2	0.903	100	0.204	Contact Map
3ivsA	2	0.8997	100	0.207	Contact Map
3eegA	2	0.8729	100	0.215	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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