LDHD - ECOLI - GREMLIN Contacts

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LDHD - D-lactate dehydrogenase

UniProt:	P52643	Sequences: MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPVLEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRIHRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSAAALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVNTSRGALIDSQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLTAEALTSISQTTLQNLSNLEKGETCPNELV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13186
Length:	329 (287)
Sequences:	18894 (13087)
Seq/√Len:	772.5

ECOLI - LDHD SERA GHRB GHRA PDXB
BACSU - SERA TKRA YOAD
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
216_N	219_A	4.445	1.00
217_E	245_E	3.239	1.00
239_D	242_A	3.108	1.00
147_A	163_L	2.737	1.00
248_K	287_C	2.527	1.00
146_T	169_R	2.522	1.00
207_L	236_A	2.465	1.00
46_E	70_K	2.421	1.00
192_P	222_Q	2.343	1.00
146_T	171_L	2.279	1.00
225_N	251_K	2.262	1.00
148_G	194_L	2.202	1.00
195_F	219_A	2.182	1.00
171_L	197_E	2.098	1.00
152_T	172_A	2.066	1.00
196_S	222_Q	2.065	1.00
213_H	261_E	2.049	1.00
110_I	163_L	2.038	1.00
190_D	193_T	2.034	1.00
124_Y	128_R	2.029	1.00
58_R	89_E	1.992	1.00
317_N	322_E	1.949	1.00
119_R	122_R	1.919	1.00
148_G	198_S	1.913	1.00
221_E	251_K	1.902	1.00
158_A	161_R	1.897	1.00
117_N	200_V	1.894	1.00
245_E	249_N	1.890	1.00
71_Y	95_V	1.852	1.00
111_G	120_I	1.831	1.00
215_L	220_F	1.822	1.00
169_R	187_E	1.811	1.00
44_G	68_G	1.807	1.00
58_R	62_E	1.800	1.00
227_V	252_I	1.790	1.00
248_K	283_R	1.789	1.00
229_I	238_I	1.777	1.00
113_M	200_V	1.748	1.00
228_M	254_S	1.745	1.00
213_H	239_D	1.736	1.00
110_I	166_F	1.728	1.00
244_I	287_C	1.712	1.00
192_P	219_A	1.694	1.00
86_A	89_E	1.643	1.00
287_C	290_V	1.633	1.00
217_E	221_E	1.629	1.00
149_V	156_G	1.622	1.00
220_F	246_A	1.616	1.00
147_A	168_M	1.609	1.00
115_T	121_H	1.605	1.00
112_M	256_G	1.605	1.00
193_T	197_E	1.599	1.00
35_T	59_P	1.594	1.00
199_D	224_K	1.581	1.00
108_H	297_A	1.565	1.00
209_P	212_Y	1.556	1.00
145_K	302_E	1.551	1.00
62_E	90_L	1.544	1.00
34_L	37_K	1.514	1.00
243_A	255_L	1.513	1.00
116_L	254_S	1.511	1.00
240_S	261_E	1.505	1.00
218_A	222_Q	1.504	1.00
140_F	145_K	1.504	1.00
35_T	57_S	1.485	1.00
171_L	189_V	1.485	1.00
28_E	45_C	1.475	1.00
215_L	219_A	1.474	1.00
195_F	215_L	1.470	1.00
207_L	212_Y	1.470	1.00
103_E	143_Y	1.460	1.00
163_L	168_M	1.454	1.00
316_S	320_K	1.452	1.00
141_T	306_S	1.440	1.00
223_M	227_V	1.434	1.00
159_M	204_H	1.429	1.00
107_E	162_I	1.428	1.00
203_L	237_L	1.417	1.00
244_I	248_K	1.413	1.00
109_A	159_M	1.412	1.00
228_M	253_G	1.407	1.00
169_R	197_E	1.403	1.00
217_E	242_A	1.398	1.00
158_A	162_I	1.382	1.00
204_H	232_T	1.381	1.00
46_E	68_G	1.369	1.00
219_A	222_Q	1.369	1.00
87_A	94_V	1.367	1.00
61_L	90_L	1.357	1.00
125_Q	128_R	1.346	1.00
149_V	202_S	1.343	1.00
317_N	325_P	1.330	1.00
212_Y	236_A	1.325	1.00
47_A	71_Y	1.307	1.00
103_E	158_A	1.298	1.00
205_C	237_L	1.292	1.00
42_A	64_L	1.289	1.00
233_S	237_L	1.285	1.00
313_Q	317_N	1.284	1.00
39_A	63_E	1.269	1.00
203_L	229_I	1.257	1.00
187_E	197_E	1.241	1.00
194_L	198_S	1.240	1.00
57_S	60_V	1.239	1.00
309_Q	313_Q	1.238	1.00
126_R	131_N	1.230	1.00
58_R	86_A	1.219	1.00
108_H	112_M	1.217	1.00
125_Q	129_D	1.209	1.00
260_Y	292_F	1.204	1.00
149_V	160_L	1.203	1.00
109_A	232_T	1.193	1.00
150_I	205_C	1.191	1.00
114_M	166_F	1.183	1.00
85_D	89_E	1.180	1.00
192_P	218_A	1.177	1.00
116_L	228_M	1.177	1.00
159_M	202_S	1.172	1.00
150_I	215_L	1.171	1.00
161_R	167_G	1.161	1.00
101_D	298_F	1.160	1.00
318_L	324_C	1.147	1.00
61_L	87_A	1.147	1.00
150_I	214_L	1.143	1.00
116_L	256_G	1.142	1.00
152_T	157_V	1.141	1.00
224_K	227_V	1.137	1.00
74_L	82_V	1.134	1.00
218_A	221_E	1.134	1.00
202_S	232_T	1.130	1.00
111_G	114_M	1.127	1.00
71_Y	318_L	1.126	1.00
121_H	124_Y	1.122	1.00
106_A	162_I	1.117	1.00
86_A	90_L	1.116	1.00
130_A	286_A	1.111	1.00
116_L	291_L	1.104	1.00
200_V	228_M	1.104	1.00
214_L	237_L	1.100	1.00
82_V	87_A	1.100	1.00
171_L	198_S	1.097	1.00
265_D	282_R	1.096	1.00
220_F	229_I	1.088	1.00
201_I	223_M	1.087	1.00
62_E	86_A	1.081	1.00
146_T	197_E	1.071	1.00
191_L	219_A	1.070	1.00
226_G	251_K	1.061	1.00
241_Q	283_R	1.057	1.00
37_K	40_K	1.052	1.00
248_K	286_A	1.051	1.00
150_I	201_I	1.043	1.00
73_A	314_N	1.041	1.00
240_S	262_N	1.038	1.00
103_E	162_I	1.036	1.00
108_H	293_T	1.035	1.00
247_L	290_V	1.033	1.00
313_Q	325_P	1.030	1.00
35_T	39_A	1.020	1.00
216_N	242_A	1.019	1.00
113_M	147_A	1.015	1.00
174_D	178_S	1.013	1.00
85_D	88_K	1.010	1.00
177_P	188_Y	1.004	1.00
164_K	185_G	1.002	1.00
175_P	210_E	0.998	1.00
113_M	163_L	0.996	1.00
93_K	324_C	0.985	1.00
191_L	195_F	0.981	1.00
189_V	194_L	0.970	1.00
189_V	193_T	0.966	1.00
150_I	191_L	0.965	1.00
112_M	291_L	0.962	1.00
244_I	283_R	0.960	1.00
108_H	256_G	0.960	1.00
161_R	164_K	0.959	1.00
246_A	251_K	0.952	1.00
240_S	282_R	0.950	1.00
28_E	41_T	0.945	1.00
305_T	309_Q	0.945	1.00
47_A	315_L	0.945	1.00
73_A	311_T	0.944	1.00
206_P	211_N	0.943	1.00
84_L	88_K	0.940	1.00
73_A	95_V	0.937	1.00
74_L	81_N	0.924	1.00
157_V	178_S	0.922	1.00
110_I	162_I	0.921	1.00
189_V	197_E	0.917	1.00
61_L	72_I	0.912	1.00
172_A	186_V	0.910	1.00
215_L	229_I	0.905	1.00
104_A	141_T	0.904	1.00
216_N	239_D	0.903	1.00
83_D	86_A	0.902	1.00
198_S	201_I	0.899	1.00
205_C	214_L	0.894	1.00
117_N	140_F	0.893	1.00
220_F	251_K	0.892	1.00
82_V	94_V	0.891	1.00
240_S	284_L	0.888	1.00
246_A	252_I	0.887	1.00
40_K	43_N	0.877	1.00
159_M	163_L	0.873	1.00
150_I	203_L	0.873	1.00
125_Q	288_H	0.868	1.00
115_T	120_I	0.863	1.00
117_N	145_K	0.860	1.00
147_A	202_S	0.856	1.00
115_T	291_L	0.854	1.00
143_Y	167_G	0.849	1.00
39_A	60_V	0.848	1.00
203_L	215_L	0.842	1.00
141_T	300_T	0.842	1.00
262_N	279_D	0.842	1.00
110_I	159_M	0.841	1.00
76_C	81_N	0.839	1.00
314_N	317_N	0.838	1.00
149_V	159_M	0.838	1.00
102_P	158_A	0.829	1.00
220_F	223_M	0.823	1.00
117_N	228_M	0.821	1.00
105_V	297_A	0.816	1.00
59_P	62_E	0.816	1.00
179_A	182_L	0.816	1.00
254_S	291_L	0.815	1.00
43_N	63_E	0.808	1.00
172_A	188_Y	0.807	1.00
47_A	319_E	0.806	1.00
243_A	252_I	0.805	1.00
238_I	243_A	0.805	1.00
121_H	125_Q	0.805	1.00
142_M	168_M	0.804	1.00
226_G	253_G	0.804	1.00
241_Q	245_E	0.802	1.00
245_E	248_K	0.802	1.00
140_F	302_E	0.797	1.00
195_F	201_I	0.792	1.00
49_C	311_T	0.788	1.00
71_Y	315_L	0.788	1.00
201_I	227_V	0.781	1.00
152_T	160_L	0.774	1.00
37_K	41_T	0.773	1.00
103_E	107_E	0.764	1.00
48_V	56_G	0.764	1.00
241_Q	261_E	0.759	1.00
111_G	115_T	0.757	1.00
168_M	200_V	0.755	1.00
207_L	211_N	0.752	1.00
192_P	196_S	0.749	1.00
255_L	290_V	0.746	1.00
102_P	154_K	0.745	1.00
262_N	265_D	0.743	1.00
160_L	170_L	0.742	1.00
110_I	113_M	0.742	1.00
109_A	204_H	0.742	1.00
103_E	141_T	0.741	1.00
140_F	301_A	0.738	1.00
72_I	87_A	0.736	1.00
107_E	118_R	0.733	1.00
257_M	290_V	0.733	1.00
247_L	289_N	0.733	1.00
221_E	249_N	0.724	1.00
109_A	202_S	0.722	1.00
195_F	222_Q	0.721	1.00
42_A	48_V	0.721	1.00
226_G	252_I	0.716	1.00
123_A	296_Q	0.713	1.00
260_Y	265_D	0.713	1.00
25_F	316_S	0.711	1.00
146_T	198_S	0.711	1.00
117_N	121_H	0.708	1.00
173_F	191_L	0.708	1.00
44_G	65_K	0.708	1.00
99_A	154_K	0.705	1.00
306_S	309_Q	0.703	1.00
181_A	188_Y	0.701	1.00
238_I	255_L	0.700	1.00
104_A	303_A	0.699	1.00
191_L	214_L	0.699	1.00
58_R	83_D	0.698	1.00
193_T	196_S	0.696	1.00
127_T	285_S	0.696	1.00
162_I	166_F	0.694	1.00
143_Y	306_S	0.690	1.00
217_E	251_K	0.689	1.00
79_F	84_L	0.688	1.00
113_M	159_M	0.688	1.00
97_V	310_T	0.687	1.00
140_F	226_G	0.687	1.00
174_D	177_P	0.686	1.00
182_L	185_G	0.680	1.00
113_M	142_M	0.678	1.00
228_M	256_G	0.678	1.00
109_A	112_M	0.677	1.00
97_V	307_I	0.674	1.00
58_R	90_L	0.674	1.00
39_A	59_P	0.672	1.00
203_L	233_S	0.667	1.00
243_A	257_M	0.667	1.00
265_D	285_S	0.666	1.00
146_T	224_K	0.664	1.00
313_Q	316_S	0.664	1.00
36_E	40_K	0.658	1.00
148_G	173_F	0.657	1.00
181_A	185_G	0.657	1.00
74_L	79_F	0.656	1.00
30_F	33_L	0.652	1.00
265_D	279_D	0.650	1.00
301_A	305_T	0.648	1.00
73_A	315_L	0.647	1.00
201_I	224_K	0.646	1.00
145_K	200_V	0.644	1.00
104_A	107_E	0.640	1.00
212_Y	261_E	0.639	1.00
312_L	316_S	0.634	1.00
124_Y	127_T	0.633	1.00
282_R	286_A	0.632	1.00
245_E	251_K	0.630	1.00
113_M	230_V	0.629	1.00
106_A	158_A	0.625	1.00
195_F	223_M	0.623	1.00
104_A	300_T	0.620	1.00
205_C	233_S	0.618	1.00
80_N	207_L	0.617	1.00
181_A	186_V	0.617	1.00
59_P	63_E	0.616	1.00
256_G	291_L	0.615	1.00
108_H	111_G	0.615	1.00
99_A	310_T	0.615	1.00
248_K	288_H	0.612	1.00
100_Y	298_F	0.608	1.00
79_F	96_R	0.607	1.00
147_A	159_M	0.605	1.00
30_F	41_T	0.605	1.00
157_V	161_R	0.605	1.00
65_K	69_V	0.602	1.00
73_A	97_V	0.600	1.00
146_T	199_D	0.597	1.00
285_S	292_F	0.596	1.00
47_A	73_A	0.595	1.00
208_T	211_N	0.593	1.00
317_N	323_T	0.592	1.00
281_F	285_S	0.589	1.00
64_L	69_V	0.588	1.00
217_E	249_N	0.588	1.00
43_N	65_K	0.587	1.00
103_E	167_G	0.585	1.00
213_H	216_N	0.584	1.00
171_L	194_L	0.584	1.00
142_M	166_F	0.582	1.00
99_A	102_P	0.582	1.00
126_R	129_D	0.581	1.00
108_H	118_R	0.580	1.00
217_E	246_A	0.579	1.00
61_L	92_L	0.578	1.00
299_L	304_L	0.578	1.00
65_K	68_G	0.576	1.00
162_I	165_G	0.575	1.00
164_K	170_L	0.574	1.00
36_E	59_P	0.574	1.00
112_M	115_T	0.574	1.00
226_G	249_N	0.573	1.00
124_Y	292_F	0.573	1.00
70_K	318_L	0.570	1.00
213_H	236_A	0.569	1.00
279_D	282_R	0.568	1.00
113_M	202_S	0.565	1.00
123_A	294_G	0.565	1.00
75_R	307_I	0.564	1.00
145_K	168_M	0.562	1.00
201_I	215_L	0.559	1.00
117_N	168_M	0.558	1.00
240_S	244_I	0.558	1.00
236_A	261_E	0.555	1.00
105_V	109_A	0.553	1.00
317_N	324_C	0.551	1.00
283_R	287_C	0.550	1.00
36_E	39_A	0.550	1.00
100_Y	307_I	0.550	1.00
65_K	90_L	0.550	1.00
112_M	116_L	0.550	1.00
127_T	260_Y	0.548	1.00
39_A	64_L	0.545	1.00
152_T	188_Y	0.545	1.00
23_F	316_S	0.543	1.00
177_P	181_A	0.543	1.00
56_G	61_L	0.539	1.00
133_S	136_G	0.538	1.00
248_K	289_N	0.536	1.00
50_I	56_G	0.533	1.00
246_A	249_N	0.532	1.00
115_T	124_Y	0.531	1.00
309_Q	312_L	0.531	1.00
171_L	187_E	0.530	1.00
234_R	295_H	0.529	1.00
100_Y	310_T	0.528	1.00
161_R	165_G	0.528	1.00
121_H	291_L	0.528	1.00
122_R	126_R	0.526	1.00
247_L	255_L	0.524	1.00
128_R	286_A	0.523	1.00
71_Y	93_K	0.522	1.00
24_G	320_K	0.521	1.00
182_L	188_Y	0.520	1.00
123_A	137_L	0.520	1.00
205_C	211_N	0.519	1.00
247_L	287_C	0.518	1.00
127_T	292_F	0.516	1.00
241_Q	282_R	0.515	1.00
141_T	302_E	0.514	1.00
180_A	183_E	0.514	1.00
172_A	181_A	0.511	1.00
24_G	316_S	0.510	1.00
244_I	290_V	0.510	1.00
126_R	137_L	0.509	1.00
195_F	214_L	0.508	1.00
191_L	215_L	0.508	1.00
311_T	314_N	0.507	1.00
152_T	174_D	0.506	1.00
90_L	93_K	0.506	1.00
97_V	100_Y	0.504	1.00
110_I	147_A	0.504	1.00
165_G	168_M	0.504	1.00
175_P	178_S	0.504	1.00
41_T	44_G	0.502	1.00
201_I	219_A	0.501	1.00
183_E	186_V	0.501	1.00
160_L	172_A	0.501	1.00
150_I	194_L	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
4cujA	4	1	100	0.186	Contact Map
3wwzA	4	0.997	100	0.203	Contact Map
1xdwA	1	0.997	100	0.204	Contact Map
1dxyA	5	0.997	100	0.205	Contact Map
3wwyA	4	0.997	100	0.206	Contact Map
1ygyA	4	0.9453	100	0.207	Contact Map
1sc6A	4	0.9088	100	0.208	Contact Map
2g76A	2	0.9149	100	0.213	Contact Map
3k5pA	3	0.9453	100	0.215	Contact Map
2yq5A	4	0.9939	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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