SERA - ECOLI - GREMLIN Contacts

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SERA - D-3-phosphoglycerate dehydrogenase

UniProt:	P0A9T0	Sequences: MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10944
Length:	410 (312)
Sequences:	7710 (4970)
Seq/√Len:	281.3

ECOLI - SERA PDXB GHRB LDHD GHRA
BACSU - SERA YOAD TKRA
HALSA - Q9HMR0 Q9HSS1 Q9HPW9
SULSO - Q97ZK1 Q97U35

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
222_G	225_E	4.450	1.00
245_D	248_A	3.737	1.00
223_A	251_D	3.432	1.00
231_P	257_H	2.770	1.00
198_S	228_L	2.713	1.00
154_L	170_A	2.653	1.00
196_H	199_D	2.595	1.00
153_K	176_Y	2.574	1.00
67_E	96_K	2.495	1.00
219_N	267_P	2.347	1.00
67_E	71_N	2.253	1.00
117_I	170_A	2.249	1.00
254_A	284_F	2.223	1.00
124_L	206_V	2.201	1.00
202_N	228_L	2.172	1.00
201_L	225_E	2.153	1.00
126_G	129_E	2.119	1.00
153_K	178_Y	2.110	1.00
221_M	226_I	2.099	1.00
227_S	257_H	2.031	1.00
155_G	200_L	2.026	1.00
233_S	258_L	2.024	1.00
152_K	299_E	2.005	1.00
314_K	319_G	1.998	1.00
117_I	173_L	1.936	1.00
213_E	242_T	1.926	1.00
55_H	77_V	1.914	1.00
155_G	204_S	1.897	1.00
44_D	68_D	1.895	1.00
235_L	244_V	1.862	1.00
178_Y	203_M	1.854	1.00
251_D	255_S	1.842	1.00
118_G	127_V	1.832	1.00
53_D	75_K	1.805	1.00
14_L	54_A	1.799	1.00
250_C	284_F	1.795	1.00
154_L	175_M	1.794	1.00
123_L	260_G	1.761	1.00
201_L	221_M	1.757	1.00
94_A	101_V	1.743	1.00
254_A	280_P	1.742	1.00
21_Q	25_E	1.737	1.00
93_A	96_K	1.732	1.00
234_L	260_G	1.725	1.00
234_L	259_A	1.724	1.00
199_D	203_M	1.719	1.00
131_N	135_H	1.692	1.00
44_D	66_T	1.679	1.00
43_D	46_Q	1.667	1.00
115_L	294_G	1.652	1.00
116_V	166_L	1.649	1.00
71_N	97_R	1.646	1.00
219_N	245_D	1.643	1.00
223_A	227_S	1.624	1.00
209_L	243_V	1.611	1.00
215_P	218_K	1.586	1.00
224_K	228_L	1.577	1.00
226_I	235_L	1.576	1.00
25_E	29_A	1.566	1.00
70_I	97_R	1.558	1.00
156_I	163_G	1.544	1.00
213_E	218_K	1.521	1.00
170_A	175_M	1.517	1.00
100_P	324_A	1.515	1.00
229_M	233_S	1.515	1.00
55_H	75_K	1.502	1.00
44_D	48_K	1.499	1.00
70_I	79_I	1.494	1.00
205_D	230_K	1.472	1.00
226_I	252_A	1.459	1.00
25_E	28_R	1.459	1.00
56_F	78_A	1.457	1.00
200_L	204_S	1.451	1.00
250_C	254_A	1.442	1.00
195_Q	199_D	1.431	1.00
166_L	208_S	1.430	1.00
211_V	243_V	1.428	1.00
198_S	225_E	1.426	1.00
314_K	322_L	1.420	1.00
78_A	102_F	1.420	1.00
95_A	326_N	1.414	1.00
166_L	210_H	1.389	1.00
284_F	287_V	1.387	1.00
223_A	248_A	1.383	1.00
306_L	310_G	1.377	1.00
114_E	169_L	1.375	1.00
120_L	206_V	1.368	1.00
307_E	323_S	1.361	1.00
221_M	225_E	1.354	1.00
123_L	234_L	1.330	1.00
48_K	72_A	1.329	1.00
159_Y	179_F	1.322	1.00
176_Y	193_Q	1.319	1.00
165_Q	168_I	1.316	1.00
93_A	97_R	1.308	1.00
36_E	54_A	1.300	1.00
208_S	238_A	1.296	1.00
89_V	94_A	1.291	1.00
67_E	93_A	1.281	1.00
247_P	280_P	1.280	1.00
315_Y	321_T	1.279	1.00
210_H	238_A	1.276	1.00
253_L	287_V	1.267	1.00
157_I	207_V	1.259	1.00
30_A	313_I	1.251	1.00
66_T	69_V	1.245	1.00
192_T	195_Q	1.245	1.00
132_A	136_R	1.244	1.00
226_I	229_M	1.242	1.00
156_I	208_S	1.241	1.00
78_A	312_L	1.236	1.00
78_A	315_Y	1.231	1.00
108_N	295_G	1.229	1.00
122_L	128_P	1.226	1.00
168_I	174_G	1.214	1.00
157_I	220_M	1.211	1.00
232_G	257_H	1.208	1.00
70_I	94_A	1.207	1.00
198_S	224_K	1.205	1.00
92_D	96_K	1.205	1.00
178_Y	195_Q	1.204	1.00
201_L	207_V	1.192	1.00
195_Q	200_L	1.186	1.00
147_F	152_K	1.184	1.00
24_L	28_R	1.180	1.00
71_N	93_A	1.180	1.00
123_L	288_L	1.173	1.00
157_I	221_M	1.171	1.00
313_I	317_D	1.169	1.00
176_Y	203_M	1.168	1.00
148_E	303_N	1.164	1.00
22_K	302_E	1.159	1.00
118_G	121_L	1.152	1.00
157_I	211_V	1.148	1.00
123_L	262_A	1.135	1.00
207_V	233_S	1.131	1.00
209_L	235_L	1.125	1.00
249_L	261_A	1.125	1.00
100_P	321_T	1.122	1.00
220_M	243_V	1.120	1.00
51_I	73_A	1.120	1.00
239_S	243_V	1.120	1.00
226_I	257_H	1.115	1.00
225_E	228_L	1.114	1.00
26_S	313_I	1.107	1.00
246_I	267_P	1.091	1.00
56_F	312_L	1.088	1.00
80_G	308_V	1.084	1.00
159_Y	164_T	1.077	1.00
254_A	283_E	1.075	1.00
165_Q	169_L	1.074	1.00
12_K	53_D	1.072	1.00
91_L	95_A	1.067	1.00
30_A	317_D	1.066	1.00
83_C	88_Q	1.063	1.00
132_A	135_H	1.061	1.00
81_C	89_V	1.058	1.00
116_V	238_A	1.058	1.00
221_M	235_L	1.056	1.00
132_A	285_D	1.051	1.00
222_G	248_A	1.051	1.00
115_L	290_T	1.051	1.00
157_I	209_L	1.049	1.00
110_R	150_R	1.046	1.00
222_G	245_D	1.045	1.00
271_A	279_S	1.043	1.00
128_P	131_N	1.040	1.00
193_Q	203_M	1.040	1.00
224_K	227_S	1.033	1.00
121_L	173_L	1.031	1.00
207_V	229_M	1.031	1.00
175_M	206_V	1.028	1.00
31_G	313_I	1.028	1.00
230_K	233_S	1.026	1.00
46_Q	49_E	1.023	1.00
232_G	258_L	1.021	1.00
310_G	314_K	1.020	1.00
253_L	286_N	1.017	1.00
266_F	289_L	1.015	1.00
150_R	174_G	1.012	1.00
48_K	68_D	1.010	1.00
218_K	242_T	1.008	1.00
212_P	217_T	1.007	1.00
247_P	267_P	1.002	1.00
109_T	165_Q	0.998	1.00
124_L	234_L	0.998	1.00
157_I	197_L	0.992	1.00
254_A	286_N	0.983	1.00
206_V	234_L	0.980	1.00
302_E	306_L	0.979	1.00
52_R	72_A	0.976	1.00
211_V	220_M	0.962	1.00
90_D	93_A	0.959	1.00
122_L	288_L	0.957	1.00
12_K	32_Y	0.956	1.00
119_E	262_A	0.948	1.00
89_V	101_V	0.946	1.00
26_S	309_A	0.944	1.00
153_K	204_S	0.937	1.00
133_K	138_V	0.934	1.00
181_D	185_K	0.930	1.00
249_L	258_L	0.926	1.00
197_L	201_L	0.926	1.00
26_S	306_L	0.925	1.00
164_T	185_K	0.918	1.00
250_C	280_P	0.918	1.00
79_I	94_A	0.918	1.00
57_I	65_L	0.911	1.00
81_C	88_Q	0.910	1.00
26_S	310_G	0.910	1.00
178_Y	204_S	0.904	1.00
110_R	165_Q	0.902	1.00
134_A	282_C	0.901	1.00
156_I	167_G	0.898	1.00
56_F	316_S	0.894	1.00
164_T	188_L	0.889	1.00
111_S	148_E	0.889	1.00
49_E	52_R	0.887	1.00
233_S	257_H	0.886	1.00
22_K	25_E	0.882	1.00
195_Q	203_M	0.879	1.00
140_N	143_A	0.879	1.00
268_T	271_A	0.877	1.00
23_A	305_G	0.873	1.00
153_K	203_M	0.867	1.00
48_K	69_V	0.865	1.00
268_T	272_T	0.863	1.00
191_A	195_Q	0.860	1.00
68_D	71_N	0.859	1.00
227_S	255_S	0.857	1.00
186_L	189_G	0.854	1.00
156_I	166_L	0.851	1.00
310_G	322_L	0.848	1.00
219_N	222_G	0.848	1.00
246_I	268_T	0.844	1.00
251_D	254_A	0.843	1.00
128_P	132_A	0.838	1.00
252_A	258_L	0.838	1.00
198_S	202_N	0.837	1.00
197_L	220_M	0.837	1.00
92_D	95_A	0.835	1.00
26_S	29_A	0.828	1.00
58_G	308_V	0.823	1.00
74_E	97_R	0.818	0.99
197_L	225_E	0.810	0.99
67_E	90_D	0.810	0.99
46_Q	50_S	0.808	0.99
106_F	161_H	0.807	0.99
65_L	69_V	0.806	0.99
45_E	49_E	0.800	0.99
180_Y	197_L	0.793	0.99
117_I	166_L	0.784	0.99
120_L	236_I	0.784	0.99
201_L	229_M	0.778	0.99
51_I	57_I	0.778	0.99
12_K	34_N	0.775	0.99
119_E	288_L	0.775	0.99
12_K	36_E	0.770	0.99
232_G	255_S	0.768	0.99
209_L	221_M	0.767	0.99
117_I	154_L	0.764	0.99
262_A	288_L	0.761	0.99
110_R	114_E	0.759	0.99
184_N	189_G	0.758	0.99
201_L	228_L	0.756	0.99
70_I	99_I	0.756	0.99
106_F	109_T	0.755	0.99
78_A	316_S	0.751	0.99
103_N	325_V	0.751	0.99
199_D	202_N	0.750	0.99
111_S	297_T	0.749	0.99
130_A	293_I	0.743	0.99
147_F	232_G	0.740	0.99
146_S	297_T	0.740	0.99
207_V	235_L	0.740	0.99
211_V	239_S	0.738	0.99
65_L	70_I	0.737	0.99
178_Y	200_L	0.737	0.99
184_N	194_V	0.737	0.99
213_E	217_T	0.736	0.99
166_L	170_A	0.736	0.99
246_I	279_S	0.733	0.99
235_L	258_L	0.731	0.99
185_K	188_L	0.730	0.99
36_E	50_S	0.730	0.99
115_L	119_E	0.728	0.99
128_P	288_L	0.724	0.99
117_I	120_L	0.723	0.99
303_N	306_L	0.723	0.99
120_L	149_A	0.722	0.99
296_S	301_Q	0.721	0.99
116_V	210_H	0.717	0.99
80_G	102_F	0.713	0.99
113_A	169_L	0.713	0.99
249_L	263_I	0.712	0.99
274_S	280_P	0.710	0.99
120_L	154_L	0.709	0.99
117_I	169_L	0.709	0.99
148_E	297_T	0.708	0.99
11_I	55_H	0.708	0.99
247_P	251_D	0.707	0.99
201_L	233_S	0.693	0.98
167_G	177_V	0.691	0.98
111_S	300_A	0.690	0.98
204_S	207_V	0.690	0.98
171_E	191_A	0.688	0.98
182_I	216_S	0.688	0.98
86_T	91_L	0.687	0.98
110_R	169_L	0.686	0.98
45_E	68_D	0.686	0.98
73_A	76_L	0.685	0.98
234_L	262_A	0.685	0.98
120_L	170_A	0.684	0.98
139_W	142_L	0.684	0.98
26_S	30_A	0.684	0.98
147_F	298_Q	0.684	0.98
110_R	148_E	0.684	0.98
59_L	65_L	0.682	0.98
115_L	118_G	0.682	0.98
115_L	262_A	0.681	0.98
185_K	189_G	0.680	0.98
261_A	287_V	0.676	0.98
131_N	289_L	0.676	0.98
23_A	306_L	0.675	0.98
219_N	242_T	0.674	0.98
178_Y	194_V	0.674	0.98
109_T	161_H	0.671	0.98
21_Q	28_R	0.668	0.98
223_A	257_H	0.657	0.98
112_V	294_G	0.655	0.98
246_I	281_L	0.653	0.98
52_R	74_E	0.650	0.97
102_F	321_T	0.648	0.97
58_G	312_L	0.646	0.97
176_Y	192_T	0.644	0.97
253_L	284_F	0.644	0.97
12_K	54_A	0.643	0.97
53_D	74_E	0.643	0.97
168_I	171_E	0.643	0.97
250_C	281_L	0.642	0.97
147_F	259_A	0.642	0.97
235_L	249_L	0.641	0.97
110_R	174_G	0.641	0.97
122_L	127_V	0.640	0.97
149_A	206_V	0.639	0.97
67_E	97_R	0.639	0.97
115_L	127_V	0.639	0.97
252_A	257_H	0.633	0.97
201_L	220_M	0.633	0.97
12_K	55_H	0.630	0.97
70_I	93_A	0.630	0.97
247_P	279_S	0.629	0.97
282_C	289_L	0.627	0.97
272_T	279_S	0.626	0.97
171_E	190_N	0.626	0.97
273_N	280_P	0.626	0.97
250_C	283_E	0.625	0.97
107_S	295_G	0.620	0.97
50_S	54_A	0.618	0.97
250_C	287_V	0.616	0.97
138_V	142_L	0.615	0.96
80_G	312_L	0.612	0.96
244_V	249_L	0.607	0.96
154_L	208_S	0.607	0.96
123_L	236_I	0.607	0.96
250_C	263_I	0.607	0.96
214_N	217_T	0.605	0.96
244_V	261_A	0.604	0.96
311_K	314_K	0.602	0.96
120_L	234_L	0.600	0.96
119_E	238_A	0.600	0.96
157_I	200_L	0.599	0.96
116_V	208_S	0.599	0.96
44_D	69_V	0.597	0.96
115_L	125_R	0.597	0.96
271_A	274_S	0.597	0.96
147_F	206_V	0.596	0.96
104_A	304_I	0.595	0.96
209_L	239_S	0.593	0.96
104_A	107_S	0.593	0.96
124_L	128_P	0.592	0.96
169_L	173_L	0.590	0.96
271_A	282_C	0.590	0.96
127_V	290_T	0.588	0.95
108_N	300_A	0.588	0.95
218_K	267_P	0.588	0.95
263_I	287_V	0.587	0.95
159_Y	163_G	0.586	0.95
197_L	221_M	0.585	0.95
229_M	232_G	0.584	0.95
114_E	149_A	0.583	0.95
154_L	166_L	0.581	0.95
106_F	307_E	0.581	0.95
110_R	168_I	0.580	0.95
164_T	168_I	0.580	0.95
17_E	63_T	0.580	0.95
191_A	194_V	0.577	0.95
56_F	80_G	0.576	0.95
107_S	304_I	0.575	0.95
27_L	309_A	0.574	0.95
220_M	225_E	0.574	0.95
78_A	100_P	0.572	0.95
79_I	99_I	0.567	0.94
84_I	161_H	0.566	0.94
233_S	252_A	0.566	0.94
226_I	249_L	0.566	0.94
11_I	316_S	0.565	0.94
159_Y	181_D	0.565	0.94
23_A	309_A	0.565	0.94
130_A	144_A	0.564	0.94
102_F	323_S	0.562	0.94
221_M	229_M	0.562	0.94
34_N	37_F	0.561	0.94
57_I	76_L	0.559	0.94
178_Y	192_T	0.556	0.94
56_F	308_V	0.556	0.94
57_I	79_I	0.556	0.94
134_A	266_F	0.556	0.94
42_L	46_Q	0.555	0.94
16_V	63_T	0.552	0.94
147_F	234_L	0.551	0.94
78_A	321_T	0.550	0.94
170_A	177_V	0.548	0.93
295_G	301_Q	0.547	0.93
236_I	262_A	0.546	0.93
147_F	299_E	0.545	0.93
240_R	292_H	0.544	0.93
253_L	258_L	0.543	0.93
311_K	323_S	0.543	0.93
251_D	257_H	0.542	0.93
211_V	217_T	0.540	0.93
131_N	134_A	0.534	0.93
28_R	32_Y	0.533	0.92
120_L	166_L	0.532	0.92
107_S	300_A	0.531	0.92
86_T	103_N	0.530	0.92
102_F	311_K	0.530	0.92
196_H	202_N	0.528	0.92
250_C	289_L	0.527	0.92
124_L	147_F	0.527	0.92
262_A	290_T	0.527	0.92
314_K	320_S	0.525	0.92
135_H	283_E	0.525	0.92
108_N	111_S	0.525	0.92
179_F	194_V	0.524	0.92
290_T	293_I	0.523	0.92
179_F	185_K	0.522	0.92
321_T	324_A	0.522	0.92
312_L	315_Y	0.522	0.92
114_E	125_R	0.522	0.92
14_L	50_S	0.522	0.92
130_A	133_K	0.520	0.92
100_P	315_Y	0.519	0.91
124_L	175_M	0.519	0.91
11_I	77_V	0.518	0.91
261_A	284_F	0.517	0.91
280_P	284_F	0.517	0.91
298_Q	302_E	0.516	0.91
81_C	103_N	0.515	0.91
50_S	53_D	0.515	0.91
179_F	189_G	0.513	0.91
124_L	149_A	0.513	0.91
119_E	122_L	0.510	0.91
207_V	221_M	0.507	0.91
60_R	83_C	0.503	0.90
183_E	216_S	0.502	0.90
274_S	283_E	0.502	0.90
178_Y	199_D	0.500	0.90

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
1sc6A	4	0.9537	100	0.2	Contact Map
3k5pA	3	0.9732	100	0.202	Contact Map
1ygyA	4	0.961	100	0.309	Contact Map
2g76A	2	0.7317	100	0.383	Contact Map
3ba1A	2	0.7585	100	0.391	Contact Map
4g2nA	3	0.7585	100	0.397	Contact Map
4lswA	2	0.7683	100	0.398	Contact Map
2d0iA	2	0.7902	100	0.399	Contact Map
4xkjA	2	0.7756	100	0.402	Contact Map
2w2kA	2	0.7756	100	0.405	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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