DMLA - ECOLI - GREMLIN Contacts

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DMLA - D-malate dehydrogenase [decarboxylating]

UniProt:	P76251	Sequences: MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKIILR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13507
Length:	361 (336)
Sequences:	6915 (3061)
Seq/√Len:	167.0

ECOLI - DMLA LEU3 IDH
BACSU - TTUC LEU3 IDH
HALSA - Q9HNZ7
SULSO - Q97WN0 LEU3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
179_Q	215_E	4.231	1.00
172_R	212_N	3.929	1.00
171_L	206_V	3.128	1.00
22_E	352_A	3.084	1.00
172_R	176_E	2.906	1.00
25_R	353_D	2.797	1.00
6_R	39_S	2.791	1.00
309_D	326_L	2.692	1.00
225_I	229_R	2.687	1.00
335_H	358_I	2.672	1.00
60_D	64_E	2.424	1.00
331_E	358_I	2.418	1.00
354_A	357_K	2.371	1.00
164_R	168_D	2.366	1.00
20_L	300_T	2.318	1.00
28_Q	40_F	2.317	1.00
9_A	24_I	2.281	1.00
22_E	25_R	2.277	1.00
187_T	219_D	2.138	1.00
309_D	323_N	2.118	1.00
206_V	218_W	2.099	1.00
185_T	219_D	2.081	1.00
24_I	42_Q	2.063	1.00
56_K	60_D	2.055	1.00
43_M	65_Q	2.055	1.00
8_A	65_Q	2.017	1.00
332_V	358_I	1.998	1.00
130_Y	177_L	1.982	1.00
302_W	329_I	1.980	1.00
298_I	355_I	1.968	1.00
67_S	100_F	1.959	1.00
171_L	241_V	1.949	1.00
168_D	205_R	1.949	1.00
301_I	355_I	1.942	1.00
168_D	208_A	1.938	1.00
293_N	347_T	1.902	1.00
185_T	217_R	1.889	1.00
176_E	213_Y	1.880	1.00
293_N	349_P	1.876	1.00
44_E	53_H	1.868	1.00
233_Q	236_R	1.840	1.00
15_I	295_A	1.832	1.00
164_R	208_A	1.815	1.00
17_K	21_P	1.807	1.00
323_N	327_A	1.800	1.00
50_Y	59_P	1.797	1.00
64_E	68_R	1.789	1.00
207_E	220_K	1.762	1.00
305_A	326_L	1.756	1.00
352_A	356_C	1.736	1.00
189_A	226_L	1.708	1.00
172_R	213_Y	1.708	1.00
110_R	330_E	1.700	1.00
168_D	172_R	1.687	1.00
153_H	165_R	1.668	1.00
337_P	354_A	1.667	1.00
205_R	208_A	1.650	1.00
67_S	99_E	1.637	1.00
353_D	357_K	1.612	1.00
8_A	69_F	1.594	1.00
160_S	243_S	1.580	1.00
279_F	311_L	1.571	1.00
113_P	334_A	1.566	1.00
30_A	325_I	1.559	1.00
106_L	130_Y	1.528	1.00
49_E	53_H	1.522	1.00
146_R	204_E	1.521	1.00
337_P	346_A	1.515	1.00
64_E	67_S	1.514	1.00
23_G	304_G	1.498	1.00
347_T	350_Q	1.498	1.00
63_H	99_E	1.497	1.00
103_Y	271_P	1.496	1.00
95_K	99_E	1.490	1.00
175_F	210_A	1.489	1.00
25_R	356_C	1.481	1.00
4_T	39_S	1.478	1.00
309_D	322_H	1.462	1.00
209_M	212_N	1.459	1.00
172_R	209_M	1.457	1.00
132_V	173_Y	1.451	1.00
231_V	253_L	1.451	1.00
36_F	321_A	1.441	1.00
176_E	180_S	1.435	1.00
188_S	206_V	1.432	1.00
29_A	356_C	1.408	1.00
40_F	304_G	1.407	1.00
41_E	68_R	1.397	1.00
4_T	37_A	1.396	1.00
11_P	42_Q	1.396	1.00
183_R	238_D	1.394	1.00
24_I	28_Q	1.381	1.00
293_N	348_T	1.374	1.00
114_G	334_A	1.369	1.00
294_I	340_P	1.344	1.00
131_V	251_S	1.339	1.00
10_I	45_W	1.328	1.00
23_G	73_Y	1.304	1.00
298_I	351_V	1.293	1.00
8_A	43_M	1.288	1.00
41_E	69_F	1.283	1.00
346_A	354_A	1.269	1.00
227_C	250_L	1.269	1.00
132_V	177_L	1.258	1.00
332_V	354_A	1.257	1.00
79_W	82_T	1.256	1.00
6_R	41_E	1.255	1.00
58_M	63_H	1.249	1.00
201_Y	205_R	1.247	1.00
221_Q	229_R	1.245	1.00
23_G	300_T	1.228	1.00
184_K	238_D	1.223	1.00
158_Q	197_I	1.220	1.00
188_S	220_K	1.217	1.00
154_E	164_R	1.214	1.00
41_E	65_Q	1.205	1.00
327_A	331_E	1.201	1.00
351_V	355_I	1.197	1.00
346_A	350_Q	1.197	1.00
176_E	179_Q	1.195	1.00
308_L	321_A	1.195	1.00
171_L	209_M	1.190	1.00
24_I	40_F	1.184	1.00
160_S	197_I	1.180	1.00
27_L	38_L	1.180	1.00
221_Q	225_I	1.179	1.00
207_E	211_E	1.179	1.00
26_V	325_I	1.161	1.00
50_Y	54_H	1.159	1.00
204_E	208_A	1.158	1.00
230_F	240_V	1.157	1.00
356_C	359_I	1.157	1.00
131_V	254_G	1.155	1.00
221_Q	226_L	1.152	1.00
221_Q	237_F	1.152	1.00
9_A	42_Q	1.151	1.00
168_D	209_M	1.146	1.00
66_L	72_I	1.143	1.00
129_F	230_F	1.138	1.00
164_R	205_R	1.123	1.00
350_Q	353_D	1.123	1.00
175_F	213_Y	1.110	1.00
44_E	49_E	1.106	1.00
101_D	169_R	1.104	1.00
44_E	50_Y	1.104	1.00
8_A	66_L	1.104	1.00
27_L	304_G	1.098	1.00
208_A	211_E	1.098	1.00
167_V	171_L	1.096	1.00
227_C	253_L	1.095	1.00
73_Y	304_G	1.085	1.00
110_R	128_D	1.084	1.00
30_A	321_A	1.084	1.00
293_N	350_Q	1.076	1.00
324_G	359_I	1.072	1.00
106_L	132_V	1.069	1.00
175_F	216_I	1.068	0.99
25_R	349_P	1.066	0.99
289_I	295_A	1.061	0.99
186_L	218_W	1.061	0.99
192_S	203_D	1.056	0.99
181_R	238_D	1.055	0.99
223_I	249_I	1.055	0.99
54_H	61_D	1.053	0.99
331_E	335_H	1.051	0.99
179_Q	184_K	1.051	0.99
177_L	181_R	1.044	0.99
74_F	93_L	1.039	0.99
21_P	25_R	1.030	0.99
314_G	321_A	1.026	0.99
162_F	243_S	1.024	0.99
354_A	358_I	1.023	0.99
126_D	235_E	1.021	0.99
139_E	160_S	1.020	0.99
43_M	69_F	1.013	0.99
189_A	223_I	1.013	0.99
44_E	54_H	1.012	0.99
314_G	320_Q	1.005	0.99
25_R	352_A	1.003	0.99
144_G	159_E	1.000	0.99
139_E	243_S	0.998	0.99
59_P	62_W	0.993	0.99
229_R	236_R	0.992	0.99
179_Q	216_I	0.990	0.99
135_N	268_N	0.989	0.99
298_I	333_I	0.988	0.99
22_E	349_P	0.988	0.99
110_R	326_L	0.985	0.99
61_D	64_E	0.975	0.99
23_G	301_I	0.973	0.99
219_D	236_R	0.969	0.99
294_I	345_N	0.968	0.99
302_W	326_L	0.967	0.99
26_V	356_C	0.965	0.99
174_A	186_L	0.963	0.99
323_N	326_L	0.956	0.99
162_F	167_V	0.955	0.99
206_V	241_V	0.952	0.99
340_P	345_N	0.952	0.99
9_A	20_L	0.949	0.99
50_Y	62_W	0.949	0.99
6_R	68_R	0.947	0.99
321_A	324_G	0.946	0.99
56_K	95_K	0.944	0.99
313_N	321_A	0.943	0.99
298_I	329_I	0.942	0.99
138_G	160_S	0.942	0.99
19_V	300_T	0.942	0.99
118_P	123_Q	0.936	0.99
18_E	291_G	0.935	0.99
186_L	239_V	0.933	0.99
232_M	256_A	0.932	0.99
104_V	170_I	0.932	0.99
113_P	125_G	0.930	0.99
179_Q	213_Y	0.929	0.99
186_L	209_M	0.929	0.99
190_T	203_D	0.925	0.99
129_F	254_G	0.923	0.99
22_E	293_N	0.923	0.99
45_W	92_S	0.918	0.98
114_G	330_E	0.914	0.98
165_R	168_D	0.911	0.98
30_A	304_G	0.910	0.98
11_P	21_P	0.910	0.98
175_F	186_L	0.907	0.98
289_I	294_I	0.903	0.98
26_V	359_I	0.899	0.98
186_L	241_V	0.894	0.98
210_A	218_W	0.894	0.98
281_P	300_T	0.892	0.98
333_I	338_K	0.891	0.98
155_V	161_V	0.883	0.98
229_R	233_Q	0.883	0.98
138_G	243_S	0.876	0.98
52_S	81_D	0.876	0.98
289_I	340_P	0.874	0.98
26_V	301_I	0.873	0.98
307_M	312_G	0.872	0.98
19_V	75_G	0.871	0.98
9_A	40_F	0.869	0.98
106_L	173_Y	0.867	0.98
331_E	334_A	0.863	0.98
343_K	346_A	0.857	0.98
112_F	330_E	0.853	0.98
61_D	65_Q	0.851	0.97
5_M	313_N	0.848	0.97
22_E	353_D	0.847	0.97
305_A	309_D	0.846	0.97
270_N	273_R	0.846	0.97
186_L	216_I	0.840	0.97
186_L	210_A	0.839	0.97
65_Q	69_F	0.837	0.97
155_V	163_T	0.835	0.97
288_D	340_P	0.835	0.97
188_S	218_W	0.834	0.97
145_G	157_I	0.832	0.97
332_V	355_I	0.829	0.97
304_G	307_M	0.829	0.97
52_S	79_W	0.827	0.97
267_A	279_F	0.823	0.97
109_V	254_G	0.822	0.97
36_F	314_G	0.821	0.97
301_I	329_I	0.821	0.97
223_I	227_C	0.820	0.97
328_A	332_V	0.813	0.97
20_L	75_G	0.811	0.97
332_V	337_P	0.810	0.97
113_P	330_E	0.808	0.97
71_A	311_L	0.808	0.97
192_S	222_H	0.805	0.97
101_D	136_T	0.795	0.96
5_M	36_F	0.795	0.96
190_T	220_K	0.795	0.96
51_Y	57_M	0.794	0.96
156_V	201_Y	0.791	0.96
189_A	240_V	0.791	0.96
23_G	27_L	0.791	0.96
210_A	214_P	0.791	0.96
205_R	209_M	0.789	0.96
146_R	156_V	0.788	0.96
104_V	173_Y	0.785	0.96
187_T	221_Q	0.785	0.96
292_K	340_P	0.784	0.96
30_A	36_F	0.781	0.96
148_N	155_V	0.776	0.96
346_A	351_V	0.773	0.96
10_I	66_L	0.772	0.96
43_M	62_W	0.770	0.95
304_G	308_L	0.766	0.95
339_T	351_V	0.764	0.95
226_L	240_V	0.760	0.95
139_E	245_L	0.760	0.95
174_A	241_V	0.758	0.95
131_V	250_L	0.758	0.95
22_E	356_C	0.757	0.95
76_A	283_H	0.756	0.95
171_L	218_W	0.756	0.95
230_F	254_G	0.756	0.95
63_H	67_S	0.752	0.95
160_S	245_L	0.752	0.95
43_M	61_D	0.749	0.95
109_V	258_T	0.749	0.95
327_A	330_E	0.749	0.95
223_I	243_S	0.745	0.95
209_M	213_Y	0.745	0.95
45_W	96_F	0.743	0.95
189_A	250_L	0.741	0.94
48_C	52_S	0.741	0.94
164_R	201_Y	0.740	0.94
27_L	308_L	0.739	0.94
5_M	311_L	0.739	0.94
265_P	302_W	0.734	0.94
105_N	282_V	0.733	0.94
207_E	218_W	0.724	0.94
45_W	74_F	0.724	0.94
349_P	353_D	0.722	0.94
160_S	246_F	0.721	0.94
65_Q	68_R	0.721	0.94
211_E	214_P	0.720	0.94
204_E	211_E	0.720	0.94
265_P	306_M	0.719	0.94
288_D	295_A	0.718	0.93
128_D	238_D	0.718	0.93
21_P	349_P	0.716	0.93
102_Q	278_L	0.714	0.93
132_V	170_I	0.713	0.93
340_P	347_T	0.712	0.93
137_E	166_G	0.709	0.93
123_Q	126_D	0.704	0.93
173_Y	177_L	0.703	0.93
175_F	218_W	0.702	0.93
73_Y	300_T	0.700	0.93
173_Y	271_P	0.696	0.92
116_P	338_K	0.693	0.92
129_F	257_C	0.693	0.92
109_V	129_F	0.692	0.92
20_L	23_G	0.686	0.92
353_D	356_C	0.686	0.92
203_D	207_E	0.681	0.92
116_P	342_M	0.681	0.92
22_E	301_I	0.680	0.92
226_L	237_F	0.680	0.92
87_I	91_G	0.679	0.91
332_V	351_V	0.679	0.91
286_A	289_I	0.678	0.91
225_I	261_I	0.677	0.91
21_P	42_Q	0.674	0.91
38_L	304_G	0.674	0.91
49_E	52_S	0.671	0.91
349_P	352_A	0.670	0.91
167_V	205_R	0.667	0.91
307_M	311_L	0.666	0.91
207_E	210_A	0.662	0.90
144_G	157_I	0.657	0.90
344_G	350_Q	0.655	0.90
48_C	79_W	0.654	0.90
176_E	212_N	0.654	0.90
170_I	241_V	0.654	0.90
190_T	222_H	0.651	0.90
27_L	40_F	0.651	0.90
48_C	82_T	0.651	0.90
111_L	127_I	0.651	0.90
72_I	278_L	0.648	0.89
301_I	325_I	0.645	0.89
146_R	149_E	0.645	0.89
56_K	61_D	0.641	0.89
7_I	38_L	0.640	0.89
60_D	95_K	0.640	0.89
130_Y	181_R	0.639	0.89
330_E	334_A	0.638	0.89
260_T	299_A	0.637	0.89
30_A	35_G	0.635	0.89
229_R	232_M	0.633	0.88
309_D	314_G	0.632	0.88
124_P	235_E	0.631	0.88
339_T	342_M	0.630	0.88
267_A	306_M	0.630	0.88
189_A	242_A	0.630	0.88
184_K	215_E	0.626	0.88
112_F	302_W	0.625	0.88
338_K	342_M	0.624	0.88
25_R	28_Q	0.624	0.88
279_F	310_F	0.620	0.87
308_L	325_I	0.619	0.87
20_L	24_I	0.619	0.87
158_Q	200_P	0.619	0.87
322_H	326_L	0.618	0.87
320_Q	323_N	0.618	0.87
27_L	325_I	0.617	0.87
210_A	216_I	0.613	0.87
130_Y	239_V	0.612	0.87
295_A	340_P	0.611	0.87
167_V	243_S	0.611	0.87
269_L	310_F	0.607	0.86
5_M	312_G	0.607	0.86
92_S	95_K	0.607	0.86
50_Y	58_M	0.602	0.86
188_S	202_W	0.601	0.86
128_D	183_R	0.601	0.86
282_V	299_A	0.601	0.86
131_V	240_V	0.600	0.86
263_I	342_M	0.600	0.86
173_Y	176_E	0.598	0.85
76_A	300_T	0.597	0.85
143_L	161_V	0.597	0.85
58_M	96_F	0.595	0.85
118_P	124_P	0.592	0.85
313_N	320_Q	0.591	0.85
337_P	358_I	0.591	0.85
62_W	92_S	0.590	0.85
75_G	300_T	0.587	0.84
191_K	224_D	0.586	0.84
324_G	328_A	0.585	0.84
144_G	147_V	0.584	0.84
101_D	165_R	0.584	0.84
90_W	95_K	0.583	0.84
308_L	322_H	0.581	0.84
5_M	314_G	0.580	0.84
265_P	299_A	0.576	0.83
195_L	198_S	0.576	0.83
154_E	204_E	0.573	0.83
140_Y	280_E	0.569	0.82
7_I	307_M	0.566	0.82
52_S	82_T	0.566	0.82
36_F	313_N	0.565	0.82
143_L	159_E	0.565	0.82
338_K	346_A	0.564	0.82
7_I	40_F	0.564	0.82
30_A	324_G	0.563	0.82
166_G	169_R	0.562	0.82
146_R	196_A	0.562	0.82
150_G	155_V	0.561	0.82
301_I	352_A	0.561	0.82
231_V	257_C	0.560	0.81
180_S	313_N	0.560	0.81
101_D	270_N	0.560	0.81
17_K	49_E	0.559	0.81
337_P	344_G	0.559	0.81
225_I	236_R	0.558	0.81
158_Q	195_L	0.557	0.81
243_S	246_F	0.556	0.81
66_L	100_F	0.556	0.81
23_G	26_V	0.552	0.81
66_L	69_F	0.552	0.81
58_M	95_K	0.550	0.80
337_P	357_K	0.549	0.80
157_I	161_V	0.548	0.80
50_Y	53_H	0.548	0.80
155_V	164_R	0.548	0.80
101_D	137_E	0.548	0.80
91_G	95_K	0.547	0.80
179_Q	210_A	0.544	0.80
21_P	24_I	0.543	0.79
51_Y	87_I	0.543	0.79
103_Y	170_I	0.541	0.79
171_L	205_R	0.541	0.79
176_E	209_M	0.541	0.79
66_L	96_F	0.540	0.79
20_L	73_Y	0.540	0.79
314_G	323_N	0.539	0.79
320_Q	324_G	0.539	0.79
147_V	204_E	0.534	0.78
27_L	30_A	0.533	0.78
103_Y	173_Y	0.533	0.78
248_D	252_D	0.532	0.78
260_T	263_I	0.532	0.78
47_S	50_Y	0.531	0.78
148_N	153_H	0.531	0.78
58_M	62_W	0.529	0.78
10_I	43_M	0.528	0.78
153_H	163_T	0.528	0.78
127_I	235_E	0.527	0.77
56_K	87_I	0.525	0.77
293_N	353_D	0.523	0.77
333_I	342_M	0.522	0.77
269_L	277_S	0.522	0.77
38_L	321_A	0.520	0.77
226_L	250_L	0.520	0.77
57_M	61_D	0.520	0.77
210_A	213_Y	0.519	0.76
277_S	310_F	0.519	0.76
270_N	277_S	0.518	0.76
74_F	96_F	0.518	0.76
88_S	91_G	0.516	0.76
149_E	154_E	0.515	0.76
145_G	155_V	0.515	0.76
225_I	237_F	0.513	0.76
57_M	89_L	0.512	0.75
132_V	174_A	0.510	0.75
150_G	161_V	0.510	0.75
98_R	142_S	0.509	0.75
137_E	163_T	0.507	0.75
86_H	91_G	0.506	0.75
100_F	278_L	0.505	0.74
248_D	283_H	0.504	0.74
179_Q	214_P	0.504	0.74
337_P	345_N	0.503	0.74
178_A	186_L	0.503	0.74
11_P	17_K	0.503	0.74
328_A	355_I	0.502	0.74
144_G	160_S	0.502	0.74
50_Y	56_K	0.501	0.74
130_Y	183_R	0.500	0.74
132_V	251_S	0.500	0.74

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
3flkA	3	0.9889	100	0.021	Contact Map
2y3zA	2	0.9474	100	0.042	Contact Map
1a05A	2	0.9612	100	0.046	Contact Map
1cnzA	2	0.9723	100	0.046	Contact Map
3u1hA	2	0.9418	100	0.047	Contact Map
3r8wA	2	0.964	100	0.048	Contact Map
2e0cA	2	0.9363	100	0.05	Contact Map
3uduA	3	0.9529	100	0.05	Contact Map
1tyoA	2	0.9557	100	0.052	Contact Map
2iv0A	2	0.9584	100	0.055	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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