LDH - BACSU - GREMLIN Contacts

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LDH - L-lactate dehydrogenase

UniProt:	P13714	Sequences: MNKHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVHAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHFAEQKVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	320 (302)
Sequences:	4937 (2829)
Seq/√Len:	162.8

ECOLI - MDH
BACSU - LDH MDH
HALSA - MDH
SULSO - MDH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_A	74_A	4.268	1.00
76_I	244_T	3.004	1.00
216_D	220_N	2.936	1.00
296_K	300_L	2.864	1.00
78_C	244_T	2.662	1.00
99_L	131_A	2.517	1.00
121_A	240_L	2.464	1.00
9_A	71_C	2.423	1.00
83_A	97_K	2.415	1.00
106_V	132_T	2.374	1.00
27_Q	245_K	2.324	1.00
71_C	113_G	2.305	1.00
208_Q	212_D	2.297	1.00
304_G	308_N	2.260	1.00
252_N	279_N	2.237	1.00
108_E	111_A	2.197	1.00
217_D	224_H	2.179	1.00
267_A	299_F	2.154	1.00
252_N	284_A	2.148	1.00
272_I	299_F	2.140	1.00
279_N	284_A	2.103	1.00
140_K	262_D	2.054	1.00
162_Y	210_E	1.989	1.00
213_Q	217_D	1.975	1.00
106_V	136_S	1.970	1.00
110_M	138_L	1.950	1.00
7_K	32_E	1.923	1.00
138_L	142_R	1.910	1.00
133_W	271_Y	1.906	1.00
276_A	283_I	1.886	1.00
104_G	108_E	1.877	1.00
163_F	191_V	1.867	1.00
175_I	185_V	1.842	1.00
272_I	303_A	1.842	1.00
103_K	107_S	1.832	1.00
117_I	247_I	1.818	1.00
172_A	189_A	1.817	1.00
297_E	301_H	1.801	1.00
261_L	274_V	1.795	1.00
7_K	34_V	1.785	1.00
300_L	304_G	1.782	1.00
277_V	285_G	1.778	1.00
95_V	309_I	1.763	1.00
267_A	300_L	1.744	1.00
102_F	132_T	1.686	1.00
107_S	111_A	1.682	1.00
259_T	276_A	1.669	1.00
107_S	135_F	1.662	1.00
8_V	30_T	1.656	1.00
260_Y	271_Y	1.626	1.00
293_E	296_K	1.619	1.00
43_A	47_V	1.614	1.00
148_T	273_G	1.612	1.00
183_L	295_E	1.585	1.00
100_K	103_K	1.568	1.00
293_E	297_E	1.558	1.00
89_E	97_K	1.543	1.00
8_V	24_L	1.534	1.00
13_A	35_V	1.528	1.00
10_L	21_A	1.515	1.00
174_I	184_P	1.511	1.00
130_Y	310_L	1.511	1.00
118_F	132_T	1.501	1.00
298_Q	301_H	1.483	1.00
281_G	284_A	1.480	1.00
129_T	271_Y	1.477	1.00
212_D	216_D	1.477	1.00
207_K	210_E	1.471	1.00
68_Y	112_S	1.470	1.00
51_N	161_E	1.456	1.00
160_S	170_V	1.452	1.00
130_Y	134_K	1.445	1.00
149_T	239_S	1.439	1.00
245_K	249_H	1.433	1.00
103_K	135_F	1.432	1.00
85_Q	222_A	1.431	1.00
20_Y	240_L	1.431	1.00
68_Y	111_A	1.409	1.00
41_E	44_M	1.406	1.00
51_N	157_F	1.385	1.00
159_L	170_V	1.363	1.00
149_T	255_L	1.352	1.00
69_E	72_K	1.348	1.00
301_H	304_G	1.333	1.00
294_K	298_Q	1.331	1.00
79_I	120_V	1.322	1.00
250_N	280_R	1.311	1.00
184_P	215_V	1.311	1.00
71_C	74_A	1.297	1.00
307_K	311_K	1.295	1.00
90_T	93_E	1.294	1.00
220_N	223_Y	1.290	1.00
171_H	190_N	1.283	1.00
120_V	132_T	1.278	1.00
53_G	238_M	1.274	1.00
41_E	227_E	1.274	1.00
146_S	240_L	1.272	1.00
22_F	237_A	1.271	1.00
166_A	169_N	1.271	1.00
64_S	70_D	1.266	1.00
181_T	305_V	1.263	1.00
109_V	118_F	1.261	1.00
162_Y	213_Q	1.253	1.00
297_E	300_L	1.249	1.00
224_H	227_E	1.236	1.00
169_N	192_G	1.233	1.00
308_N	312_P	1.228	1.00
267_A	303_A	1.227	1.00
83_A	86_K	1.226	1.00
102_F	106_V	1.215	1.00
7_K	73_D	1.209	1.00
110_M	137_G	1.201	1.00
259_T	283_I	1.196	1.00
187_S	295_E	1.195	1.00
76_I	119_L	1.189	1.00
262_D	268_D	1.189	1.00
75_D	114_F	1.184	1.00
138_L	143_V	1.177	1.00
20_Y	244_T	1.167	1.00
133_W	260_Y	1.165	1.00
24_L	33_L	1.164	1.00
40_K	67_T	1.160	1.00
77_V	109_V	1.155	1.00
125_V	145_G	1.150	1.00
41_E	228_K	1.149	1.00
254_I	277_V	1.143	1.00
216_D	219_K	1.142	1.00
20_Y	78_C	1.137	1.00
277_V	284_A	1.132	1.00
131_A	135_F	1.126	1.00
261_L	264_Q	1.126	1.00
187_S	292_N	1.121	1.00
52_H	221_A	1.117	1.00
109_V	138_L	1.117	1.00
113_G	116_G	1.117	1.00
22_F	26_N	1.116	1.00
91_R	123_N	1.112	1.00
300_L	303_A	1.109	1.00
123_N	178_H	1.105	1.00
94_L	98_N	1.105	1.00
24_L	29_I	1.104	1.00
242_R	253_S	1.102	1.00
144_I	247_I	1.087	1.00
97_K	100_K	1.084	1.00
224_H	228_K	1.083	1.00
34_V	70_D	1.079	0.99
91_R	178_H	1.078	0.99
257_V	276_A	1.077	0.99
104_G	107_S	1.076	0.99
79_I	132_T	1.076	0.99
20_Y	237_A	1.064	0.99
115_D	139_P	1.054	0.99
301_H	305_V	1.048	0.99
39_N	42_K	1.044	0.99
125_V	129_T	1.043	0.99
77_V	116_G	1.041	0.99
198_E	290_N	1.034	0.99
141_E	281_G	1.024	0.99
96_E	100_K	1.022	0.99
45_G	228_K	1.022	0.99
139_P	142_R	1.021	0.99
210_E	213_Q	1.020	0.99
32_E	62_K	1.019	0.99
117_I	142_R	1.018	0.99
194_V	198_E	1.014	0.99
65_Y	70_D	1.014	0.99
67_T	70_D	1.012	0.99
85_Q	226_I	1.007	0.99
93_E	96_E	1.002	0.99
277_V	287_T	1.000	0.99
190_N	193_G	0.999	0.99
119_L	243_I	0.993	0.99
15_F	233_Y	0.993	0.99
156_R	171_H	0.988	0.99
181_T	302_S	0.987	0.99
145_G	258_S	0.984	0.99
294_K	297_E	0.975	0.99
102_F	128_L	0.974	0.99
264_Q	287_T	0.972	0.99
133_W	143_V	0.971	0.99
106_V	118_F	0.967	0.99
34_V	74_A	0.962	0.99
308_N	311_K	0.961	0.99
299_F	303_A	0.960	0.99
18_S	46_D	0.960	0.99
29_I	249_H	0.945	0.99
36_I	68_Y	0.944	0.99
89_E	93_E	0.938	0.99
160_S	167_P	0.934	0.99
42_K	46_D	0.934	0.99
18_S	237_A	0.931	0.98
83_A	101_I	0.930	0.98
168_Q	251_E	0.929	0.98
21_A	35_V	0.928	0.98
75_D	115_D	0.924	0.98
185_V	291_L	0.924	0.98
77_V	113_G	0.922	0.98
78_C	119_L	0.921	0.98
157_F	161_E	0.913	0.98
43_A	66_G	0.910	0.98
181_T	301_H	0.906	0.98
220_N	227_E	0.902	0.98
74_A	77_V	0.902	0.98
27_Q	241_A	0.900	0.98
66_G	70_D	0.899	0.98
263_G	266_G	0.892	0.98
237_A	241_A	0.891	0.98
127_I	309_I	0.889	0.98
73_D	114_F	0.888	0.98
72_K	112_S	0.887	0.98
129_T	145_G	0.886	0.98
304_G	311_K	0.883	0.98
291_L	299_F	0.881	0.98
76_I	248_L	0.881	0.98
106_V	135_F	0.879	0.98
155_F	172_A	0.878	0.98
222_A	226_I	0.877	0.98
158_M	217_D	0.875	0.98
79_I	102_F	0.871	0.98
29_I	241_A	0.871	0.98
194_V	199_L	0.871	0.98
140_K	260_Y	0.866	0.98
85_Q	223_Y	0.854	0.97
240_L	244_T	0.852	0.97
245_K	251_E	0.851	0.97
279_N	282_G	0.842	0.97
6_N	248_L	0.836	0.97
102_F	120_V	0.827	0.97
152_S	156_R	0.826	0.97
13_A	46_D	0.825	0.97
175_I	183_L	0.824	0.97
256_T	273_G	0.824	0.97
155_F	184_P	0.823	0.97
69_E	112_S	0.821	0.97
158_M	161_E	0.818	0.97
15_F	18_S	0.815	0.96
243_I	257_V	0.809	0.96
40_K	44_M	0.809	0.96
119_L	244_T	0.805	0.96
60_P	166_A	0.804	0.96
44_M	228_K	0.801	0.96
87_P	227_E	0.799	0.96
274_V	286_I	0.796	0.96
265_Y	269_D	0.795	0.96
209_E	213_Q	0.793	0.96
23_A	237_A	0.790	0.96
119_L	247_I	0.789	0.96
195_P	198_E	0.788	0.96
309_I	312_P	0.785	0.96
20_Y	24_L	0.783	0.96
149_T	243_I	0.783	0.96
304_G	307_K	0.782	0.96
101_I	122_T	0.782	0.96
68_Y	105_I	0.781	0.96
252_N	277_V	0.778	0.95
130_Y	133_W	0.776	0.95
85_Q	94_L	0.770	0.95
165_A	170_V	0.770	0.95
106_V	110_M	0.765	0.95
85_Q	89_E	0.765	0.95
11_I	105_I	0.764	0.95
215_V	219_K	0.763	0.95
159_L	163_F	0.761	0.95
125_V	147_G	0.760	0.95
34_V	66_G	0.758	0.95
20_Y	80_C	0.755	0.95
73_D	115_D	0.754	0.95
262_D	287_T	0.753	0.95
305_V	309_I	0.752	0.95
40_K	66_G	0.751	0.94
186_W	218_V	0.750	0.94
165_A	191_V	0.748	0.94
10_L	20_Y	0.745	0.94
180_D	223_Y	0.745	0.94
139_P	143_V	0.745	0.94
90_T	180_D	0.744	0.94
163_F	170_V	0.743	0.94
36_I	71_C	0.742	0.94
68_Y	72_K	0.742	0.94
79_I	105_I	0.737	0.94
110_M	136_S	0.737	0.94
78_C	240_L	0.734	0.94
94_L	226_I	0.731	0.94
15_F	231_A	0.731	0.94
225_I	235_G	0.729	0.94
274_V	285_G	0.727	0.93
92_L	127_I	0.726	0.93
116_G	138_L	0.725	0.93
143_V	271_Y	0.719	0.93
24_L	241_A	0.717	0.93
102_F	135_F	0.717	0.93
223_Y	227_E	0.716	0.93
21_A	50_L	0.716	0.93
117_I	144_I	0.711	0.93
213_Q	216_D	0.710	0.93
133_W	136_S	0.709	0.93
81_A	101_I	0.709	0.93
212_D	294_K	0.707	0.93
132_T	136_S	0.706	0.92
197_S	211_L	0.705	0.92
23_A	26_N	0.703	0.92
44_M	66_G	0.703	0.92
155_F	189_A	0.703	0.92
134_K	137_G	0.703	0.92
263_G	288_E	0.700	0.92
19_S	234_Y	0.698	0.92
91_R	94_L	0.697	0.92
6_N	31_D	0.695	0.92
110_M	116_G	0.694	0.92
46_D	237_A	0.693	0.92
250_N	279_N	0.690	0.92
133_W	140_K	0.687	0.91
74_A	113_G	0.684	0.91
243_I	255_L	0.683	0.91
19_S	233_Y	0.680	0.91
206_Y	210_E	0.678	0.91
24_L	244_T	0.675	0.91
270_V	307_K	0.674	0.91
257_V	278_V	0.674	0.91
130_Y	269_D	0.672	0.91
96_E	312_P	0.670	0.90
174_I	215_V	0.667	0.90
134_K	260_Y	0.665	0.90
6_N	75_D	0.664	0.90
267_A	296_K	0.664	0.90
19_S	23_A	0.661	0.90
156_R	242_R	0.660	0.90
100_K	104_G	0.659	0.90
148_T	181_T	0.659	0.90
235_G	238_M	0.659	0.90
136_S	143_V	0.659	0.90
110_M	118_F	0.658	0.90
9_A	34_V	0.657	0.90
270_V	303_A	0.656	0.89
188_H	289_L	0.654	0.89
206_Y	209_E	0.653	0.89
24_L	30_T	0.648	0.89
141_E	284_A	0.647	0.89
91_R	151_D	0.645	0.89
92_L	309_I	0.645	0.89
222_A	231_A	0.643	0.88
175_I	289_L	0.641	0.88
9_A	113_G	0.641	0.88
246_A	255_L	0.641	0.88
222_A	232_T	0.639	0.88
68_Y	108_E	0.634	0.88
183_L	302_S	0.632	0.88
303_A	307_K	0.632	0.88
291_L	300_L	0.632	0.88
140_K	271_Y	0.629	0.87
163_F	206_Y	0.626	0.87
52_H	157_F	0.625	0.87
47_V	51_N	0.624	0.87
39_N	43_A	0.623	0.87
226_I	231_A	0.622	0.87
99_L	135_F	0.621	0.87
25_I	33_L	0.620	0.87
108_E	112_S	0.619	0.87
220_N	224_H	0.618	0.86
267_A	307_K	0.617	0.86
146_S	258_S	0.616	0.86
109_V	112_S	0.616	0.86
92_L	305_V	0.615	0.86
30_T	33_L	0.614	0.86
143_V	146_S	0.613	0.86
178_H	222_A	0.612	0.86
121_A	146_S	0.609	0.86
80_C	121_A	0.608	0.86
215_V	298_Q	0.605	0.85
86_K	97_K	0.605	0.85
160_S	165_A	0.603	0.85
82_G	122_T	0.602	0.85
253_S	277_V	0.602	0.85
151_D	154_R	0.600	0.85
18_S	234_Y	0.597	0.85
185_V	188_H	0.593	0.84
267_A	272_I	0.589	0.84
71_C	110_M	0.587	0.84
23_A	241_A	0.586	0.83
22_F	234_Y	0.583	0.83
10_L	33_L	0.583	0.83
79_I	106_V	0.583	0.83
262_D	269_D	0.579	0.83
36_I	105_I	0.576	0.82
307_K	310_L	0.574	0.82
92_L	312_P	0.573	0.82
261_L	266_G	0.573	0.82
25_I	50_L	0.573	0.82
183_L	298_Q	0.573	0.82
183_L	215_V	0.573	0.82
171_H	253_S	0.572	0.82
161_E	217_D	0.572	0.82
183_L	291_L	0.566	0.81
98_N	128_L	0.565	0.81
89_E	94_L	0.565	0.81
16_V	121_A	0.562	0.81
125_V	146_S	0.562	0.81
133_W	138_L	0.561	0.81
290_N	296_K	0.558	0.80
246_A	253_S	0.557	0.80
208_Q	294_K	0.555	0.80
159_L	172_A	0.554	0.80
263_G	268_D	0.554	0.80
162_Y	206_Y	0.549	0.79
8_V	33_L	0.549	0.79
45_G	94_L	0.548	0.79
123_N	232_T	0.548	0.79
54_K	59_Q	0.548	0.79
259_T	262_D	0.547	0.79
156_R	172_A	0.545	0.79
242_R	251_E	0.544	0.79
82_G	85_Q	0.543	0.79
19_S	22_F	0.540	0.78
82_G	88_G	0.538	0.78
264_Q	285_G	0.534	0.77
207_K	211_L	0.534	0.77
105_I	109_V	0.533	0.77
124_P	154_R	0.532	0.77
123_N	154_R	0.531	0.77
246_A	251_E	0.530	0.77
194_V	197_S	0.529	0.77
72_K	111_A	0.529	0.77
155_F	183_L	0.529	0.77
267_A	270_V	0.528	0.77
265_Y	289_L	0.527	0.77
17_G	21_A	0.527	0.77
32_E	60_P	0.526	0.76
142_R	281_G	0.525	0.76
259_T	273_G	0.525	0.76
91_R	222_A	0.523	0.76
253_S	256_T	0.522	0.76
46_D	234_Y	0.521	0.76
279_N	283_I	0.521	0.76
13_A	33_L	0.521	0.76
21_A	33_L	0.520	0.76
103_K	131_A	0.519	0.75
103_K	134_K	0.517	0.75
115_D	142_R	0.516	0.75
29_I	245_K	0.516	0.75
247_I	250_N	0.514	0.75
159_L	189_A	0.512	0.74
173_H	256_T	0.509	0.74
11_I	71_C	0.507	0.74
261_L	267_A	0.504	0.73
48_M	228_K	0.504	0.73
57_A	238_M	0.503	0.73
14_G	151_D	0.502	0.73
175_I	291_L	0.501	0.73
39_N	65_Y	0.501	0.73
292_N	296_K	0.500	0.73
48_M	224_H	0.500	0.73
246_A	256_T	0.500	0.73
20_Y	121_A	0.500	0.73

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
3nepX	4	0.9437	100	0.232	Contact Map
2d4aB	4	0.9531	100	0.232	Contact Map
4plzA	4	0.9406	100	0.241	Contact Map
1a5zA	3	0.975	100	0.241	Contact Map
1lldA	3	0.9719	100	0.243	Contact Map
1guzA	4	0.9437	100	0.245	Contact Map
4cl3A	4	0.9563	100	0.246	Contact Map
2hjrA	4	0.9688	100	0.26	Contact Map
4bgvA	4	0.9688	100	0.261	Contact Map
4rorA	4	0.9812	100	0.261	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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