YGBM - ECOLI - GREMLIN Contacts

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YGBM - Putative hydroxypyruvate isomerase YgbM

UniProt:	Q46891	Sequences: MPRFAANLSMMFTEVPFIERFAAARKAGFDAVEFLFPYNYSTLQIQKQLEQNHLTLALFNTAPGDINAGEWGLSALPGREHEAHADIDLALEYALALNCEQVHVMAGVVPAGEDAERYRAVFIDNIRYAADRFAPHGKRILVEALSPGVKPHYLFSSQYQALAIVEEVARDNVFIQLDTFHAQKVDGNLTHLIRDYAGKYAHVQIAGLPDRHEPDDGEINYPWLFRLFDEVGYQGWIGCEYKPRGLTEEGLGWFDAWR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13107
Length:	258 (219)
Sequences:	14794 (10618)
Seq/√Len:	717.5

ECOLI - YGBM HYI FRLC YCJR ULAE SGBU YIHM END4
BACSU - IOLI IOLH YFIH IOLE END4
SULSO - Q97UI8 Q97UG9 Q97UI3 Q7LX49

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
174_F	201_A	3.129	1.00
88_D	132_R	3.122	1.00
22_A	52_N	2.971	1.00
46_Q	50_E	2.828	1.00
220_N	223_W	2.710	1.00
92_E	136_H	2.588	1.00
31_A	236_W	2.551	1.00
194_R	227_L	2.505	1.00
123_I	167_E	2.467	1.00
207_G	215_D	2.424	1.00
47_K	51_Q	2.389	1.00
92_E	132_R	2.326	1.00
139_R	174_F	2.212	1.00
139_R	201_A	2.195	1.00
16_P	19_E	2.153	1.00
141_L	201_A	2.151	1.00
18_I	48_Q	2.143	1.00
162_L	195_D	2.135	1.00
95_L	136_H	2.104	1.00
131_D	170_R	2.097	1.00
119_R	163_A	1.949	1.00
163_A	167_E	1.927	1.00
22_A	26_K	1.924	1.00
194_R	230_E	1.842	1.00
101_Q	141_L	1.794	1.00
227_L	230_E	1.782	1.00
84_H	128_Y	1.776	1.00
49_L	56_L	1.752	1.00
48_Q	51_Q	1.751	1.00
48_Q	52_N	1.742	1.00
43_L	96_A	1.712	1.00
91_L	136_H	1.711	1.00
132_R	135_P	1.703	1.00
81_H	85_A	1.703	1.00
119_R	167_E	1.680	1.00
188_N	191_H	1.658	1.00
130_A	173_V	1.640	1.00
162_L	166_E	1.598	1.00
134_A	172_N	1.569	1.00
79_R	82_E	1.566	1.00
141_L	176_Q	1.553	1.00
203_V	228_F	1.553	1.00
120_A	167_E	1.530	1.00
85_A	89_L	1.528	1.00
132_R	136_H	1.521	1.00
226_R	230_E	1.521	1.00
25_R	52_N	1.521	1.00
191_H	195_D	1.503	1.00
123_I	127_R	1.500	1.00
222_P	226_R	1.470	1.00
117_R	120_A	1.465	1.00
18_I	51_Q	1.464	1.00
120_A	124_D	1.464	1.00
94_A	99_C	1.461	1.00
44_Q	47_K	1.454	1.00
89_L	92_E	1.437	1.00
207_G	217_G	1.429	1.00
21_F	52_N	1.422	1.00
190_T	223_W	1.418	1.00
131_D	135_P	1.409	1.00
91_L	133_F	1.398	1.00
124_D	127_R	1.392	1.00
179_T	224_L	1.380	1.00
88_D	128_Y	1.369	1.00
227_L	231_V	1.363	1.00
80_E	125_N	1.351	1.00
210_D	213_E	1.343	1.00
23_A	26_K	1.316	1.00
41_S	44_Q	1.316	1.00
130_A	168_V	1.309	1.00
85_A	88_D	1.286	1.00
134_A	170_R	1.277	1.00
174_F	199_K	1.277	1.00
19_E	22_A	1.275	1.00
157_S	160_Q	1.258	1.00
101_Q	139_R	1.254	1.00
44_Q	48_Q	1.253	1.00
47_K	50_E	1.248	1.00
123_I	168_V	1.241	1.00
197_A	231_V	1.240	1.00
84_H	88_D	1.230	1.00
22_A	48_Q	1.227	1.00
166_E	199_K	1.225	1.00
137_G	172_N	1.213	1.00
25_R	53_H	1.199	1.00
121_V	124_D	1.196	1.00
162_L	196_Y	1.193	1.00
43_L	47_K	1.190	1.00
161_A	175_I	1.188	1.00
159_Y	195_D	1.178	1.00
190_T	194_R	1.174	1.00
128_Y	131_D	1.166	1.00
91_L	132_R	1.154	1.00
88_D	92_E	1.147	1.00
91_L	138_K	1.142	1.00
88_D	135_P	1.127	1.00
228_F	231_V	1.107	1.00
156_S	160_Q	1.105	1.00
81_H	128_Y	1.104	1.00
46_Q	96_A	1.093	1.00
133_F	140_I	1.092	1.00
223_W	227_L	1.090	1.00
18_I	44_Q	1.085	1.00
31_A	57_A	1.080	1.00
192_L	196_Y	1.077	1.00
162_L	199_K	1.069	1.00
177_L	182_A	1.065	1.00
134_A	171_D	1.056	1.00
163_A	166_E	1.043	1.00
29_F	239_C	1.042	1.00
119_R	123_I	1.037	1.00
194_R	231_V	1.030	1.00
23_A	27_A	1.028	1.00
21_F	49_L	1.026	1.00
127_R	168_V	1.020	1.00
87_I	129_A	1.010	1.00
191_H	194_R	1.005	1.00
39_N	96_A	1.004	1.00
193_I	231_V	1.002	1.00
130_A	170_R	1.002	1.00
49_L	54_L	0.998	1.00
33_E	58_L	0.996	1.00
21_F	48_Q	0.989	1.00
100_E	139_R	0.981	1.00
76_L	79_R	0.977	1.00
31_A	55_T	0.971	1.00
180_F	206_A	0.970	1.00
127_R	131_D	0.969	1.00
144_A	182_A	0.967	1.00
33_E	202_H	0.958	1.00
101_Q	201_A	0.954	1.00
34_F	56_L	0.952	1.00
178_D	240_E	0.947	1.00
24_A	32_V	0.947	1.00
82_E	85_A	0.947	1.00
219_I	224_L	0.945	1.00
131_D	134_A	0.939	1.00
206_A	242_K	0.930	1.00
205_I	221_Y	0.925	1.00
181_H	206_A	0.922	1.00
190_T	227_L	0.921	1.00
92_E	96_A	0.919	1.00
59_F	94_A	0.913	1.00
25_R	30_D	0.910	1.00
92_E	95_L	0.906	1.00
15_V	23_A	0.897	1.00
127_R	169_A	0.897	1.00
88_D	136_H	0.896	1.00
175_I	196_Y	0.893	1.00
116_E	120_A	0.875	1.00
115_A	160_Q	0.873	1.00
18_I	22_A	0.871	1.00
221_Y	225_F	0.868	1.00
130_A	172_N	0.868	1.00
124_D	128_Y	0.866	1.00
77_P	81_H	0.861	1.00
94_A	102_V	0.858	1.00
84_H	125_N	0.857	1.00
119_R	160_Q	0.857	1.00
158_Q	195_D	0.855	1.00
114_D	117_R	0.837	1.00
209_P	218_E	0.831	1.00
22_A	51_Q	0.831	1.00
57_A	236_W	0.831	1.00
86_D	89_L	0.830	1.00
159_Y	163_A	0.830	1.00
115_A	118_Y	0.828	1.00
49_L	52_N	0.824	1.00
43_L	46_Q	0.818	1.00
139_R	172_N	0.811	1.00
225_F	229_D	0.803	1.00
126_I	173_V	0.798	1.00
223_W	226_R	0.797	1.00
30_D	55_T	0.797	1.00
103_H	176_Q	0.793	1.00
193_I	227_L	0.792	1.00
168_V	173_V	0.792	1.00
116_E	163_A	0.792	1.00
55_T	100_E	0.788	1.00
165_V	175_I	0.786	1.00
180_F	208_L	0.786	1.00
165_V	199_K	0.784	1.00
122_F	164_I	0.770	1.00
158_Q	187_G	0.770	1.00
183_Q	218_E	0.768	1.00
56_L	99_C	0.767	1.00
42_T	96_A	0.766	1.00
95_L	138_K	0.761	1.00
93_Y	97_L	0.757	1.00
160_Q	163_A	0.757	1.00
24_A	29_F	0.751	1.00
129_A	140_I	0.746	1.00
127_R	170_R	0.745	1.00
155_F	161_A	0.745	1.00
179_T	221_Y	0.735	1.00
169_A	172_N	0.733	1.00
42_T	93_Y	0.733	1.00
128_Y	132_R	0.723	1.00
155_F	164_I	0.720	1.00
55_T	236_W	0.720	1.00
205_I	237_I	0.719	1.00
193_I	200_Y	0.718	1.00
143_E	240_E	0.711	1.00
121_V	125_N	0.708	1.00
80_E	124_D	0.706	1.00
150_K	153_Y	0.699	1.00
176_Q	202_H	0.698	1.00
78_G	82_E	0.697	1.00
15_V	19_E	0.696	1.00
62_A	90_A	0.692	1.00
74_S	79_R	0.691	1.00
117_R	121_V	0.690	1.00
202_H	238_G	0.690	1.00
84_H	129_A	0.689	1.00
95_L	137_G	0.686	1.00
225_F	237_I	0.684	1.00
125_N	128_Y	0.681	1.00
89_L	93_Y	0.680	1.00
22_A	25_R	0.677	1.00
18_I	52_N	0.675	1.00
33_E	238_G	0.674	1.00
76_L	80_E	0.669	1.00
183_Q	219_I	0.669	1.00
177_L	193_I	0.666	1.00
127_R	167_E	0.665	1.00
203_V	237_I	0.664	1.00
60_N	105_M	0.662	1.00
39_N	43_L	0.657	1.00
19_E	23_A	0.655	1.00
183_Q	189_L	0.652	1.00
21_F	32_V	0.652	1.00
40_Y	44_Q	0.651	1.00
144_A	161_A	0.645	1.00
78_G	81_H	0.644	1.00
102_V	133_F	0.643	1.00
90_A	102_V	0.641	1.00
46_Q	98_N	0.635	1.00
21_F	25_R	0.632	1.00
126_I	164_I	0.630	1.00
45_I	48_Q	0.629	1.00
42_T	97_L	0.627	1.00
193_I	196_Y	0.626	1.00
133_F	138_K	0.624	1.00
130_A	140_I	0.624	1.00
232_G	235_G	0.624	1.00
80_E	121_V	0.622	1.00
39_N	42_T	0.621	1.00
143_E	204_Q	0.619	1.00
182_A	192_L	0.619	1.00
21_F	54_L	0.619	1.00
198_G	231_V	0.619	1.00
84_H	87_I	0.617	1.00
197_A	200_Y	0.616	1.00
193_I	197_A	0.614	1.00
20_R	24_A	0.613	1.00
203_V	233_Y	0.612	1.00
130_A	134_A	0.599	1.00
177_L	192_L	0.598	1.00
21_F	45_I	0.595	1.00
101_Q	202_H	0.592	1.00
104_V	140_I	0.589	1.00
165_V	169_A	0.587	1.00
197_A	227_L	0.584	1.00
123_I	164_I	0.584	1.00
131_D	172_N	0.578	1.00
193_I	224_L	0.576	1.00
144_A	155_F	0.576	1.00
202_H	233_Y	0.576	1.00
228_F	233_Y	0.576	1.00
162_L	165_V	0.575	1.00
206_A	241_Y	0.572	1.00
59_F	99_C	0.569	1.00
77_P	121_V	0.567	1.00
77_P	80_E	0.562	1.00
158_Q	191_H	0.561	1.00
164_I	168_V	0.560	1.00
205_I	225_F	0.559	1.00
94_A	138_K	0.558	1.00
80_E	84_H	0.554	1.00
25_R	54_L	0.554	1.00
193_I	228_F	0.553	1.00
74_S	83_A	0.551	1.00
169_A	199_K	0.550	1.00
57_A	238_G	0.549	1.00
39_N	97_L	0.548	1.00
49_L	53_H	0.547	1.00
177_L	200_Y	0.546	1.00
158_Q	196_Y	0.545	1.00
100_E	137_G	0.544	1.00
178_D	206_A	0.543	1.00
119_R	164_I	0.542	1.00
161_A	165_V	0.542	1.00
175_I	200_Y	0.538	1.00
229_D	232_G	0.538	1.00
72_G	125_N	0.538	1.00
72_G	75_A	0.538	1.00
82_E	86_D	0.537	1.00
158_Q	162_L	0.537	1.00
143_E	181_H	0.535	1.00
202_H	236_W	0.532	1.00
122_F	126_I	0.532	1.00
84_H	132_R	0.530	1.00
58_L	103_H	0.529	1.00
42_T	46_Q	0.528	1.00
179_T	205_I	0.528	1.00
214_P	217_G	0.526	1.00
120_A	123_I	0.525	1.00
204_Q	238_G	0.524	1.00
107_G	110_P	0.522	1.00
196_Y	200_Y	0.520	1.00
60_N	103_H	0.519	1.00
203_V	224_L	0.518	1.00
95_L	100_E	0.517	1.00
17_F	45_I	0.516	1.00
105_M	181_H	0.514	1.00
133_F	136_H	0.513	1.00
50_E	96_A	0.513	1.00
165_V	173_V	0.513	1.00
130_A	133_F	0.511	1.00
184_K	208_L	0.510	1.00
229_D	237_I	0.509	1.00
183_Q	208_L	0.508	0.99
168_V	171_D	0.508	0.99
92_E	135_P	0.507	0.99
61_T	90_A	0.503	0.99
180_F	242_K	0.503	0.99
141_L	174_F	0.500	0.99
33_E	204_Q	0.500	0.99

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
1k77A	1	1	100	0.16	Contact Map
3ngfA	1	0.9961	100	0.196	Contact Map
3kwsA	2	0.969	100	0.238	Contact Map
1i60A	1	0.9574	100	0.238	Contact Map
2qulA	2	0.9651	100	0.243	Contact Map
2hk0A	3	0.9612	100	0.245	Contact Map
3qc0A	2	0.9612	100	0.245	Contact Map
2zvrA	2	0.9729	100	0.246	Contact Map
3wqoA	2	0.9651	100	0.249	Contact Map
3vylA	4	0.9651	100	0.253	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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