MDH - SULSO - GREMLIN Contacts

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MDH - Probable malate dehydrogenase

UniProt:	Q97VN4	Sequences: MVKIAFIGVGKIGQTIAYSVIFDGLASEAILYDIVPELPEKFEHELRHAIATRGLSTEVIGTNSLDDVTNADIILIMAGKPRKPGMSRRDLFIDNAKIQIDLAKQLPPKNPGALYIMVANPVDMMASVFMRFSKQFTISTGDAVETMRLRSYIAKKLKVPANKVTGYVAGEHGEDAVVLWSTVKVNGKPFEEVAKGLTKEEVENYVKSIPGEIIRVMGGTTWGPATIIKDIVRSVVFNEGRVMSIATPRTYQGEIIHISVPIVVGAEIGPSLEGVLPESDRQRLNKSVEDFYRVYKENLDHLLQTVKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (293)
Sequences:	4907 (2855)
Seq/√Len:	166.8

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
5_A	71_A	4.270	1.00
73_I	232_V	3.037	1.00
281_R	285_N	2.955	1.00
204_N	208_S	2.910	1.00
96_A	128_V	2.651	1.00
75_L	232_V	2.648	1.00
80_K	94_D	2.494	1.00
118_V	228_I	2.491	1.00
5_A	68_V	2.467	1.00
103_A	129_F	2.389	1.00
68_V	110_N	2.359	1.00
205_Y	212_E	2.315	1.00
23_D	233_R	2.312	1.00
196_G	200_E	2.284	1.00
289_E	293_R	2.236	1.00
240_G	265_G	2.234	1.00
105_Q	108_P	2.182	1.00
258_I	284_L	2.162	1.00
265_G	269_G	2.092	1.00
253_G	284_L	2.068	1.00
240_G	269_G	2.068	1.00
134_K	248_P	2.000	1.00
201_E	205_Y	1.974	1.00
156_K	198_T	1.972	1.00
130_M	257_H	1.968	1.00
107_P	132_F	1.968	1.00
169_A	179_L	1.953	1.00
101_D	105_Q	1.948	1.00
262_I	268_I	1.933	1.00
157_L	185_V	1.928	1.00
258_I	288_V	1.882	1.00
166_G	183_V	1.853	1.00
253_G	285_N	1.851	1.00
100_I	104_K	1.844	1.00
285_N	289_E	1.819	1.00
114_L	235_V	1.818	1.00
263_V	270_P	1.816	1.00
92_F	294_V	1.792	1.00
142_D	259_S	1.785	1.00
282_Q	286_K	1.777	1.00
132_F	136_F	1.745	1.00
99_Q	129_F	1.714	1.00
4_I	26_A	1.712	1.00
3_K	28_E	1.669	1.00
3_K	30_I	1.664	1.00
104_K	108_P	1.664	1.00
140_T	228_I	1.649	1.00
39_P	43_E	1.644	1.00
177_V	280_D	1.599	1.00
278_E	281_R	1.578	1.00
4_I	20_V	1.548	1.00
97_K	100_I	1.547	1.00
168_V	178_V	1.544	1.00
127_S	295_Y	1.531	1.00
86_M	94_D	1.531	1.00
9_V	31_L	1.531	1.00
126_A	257_H	1.524	1.00
65_L	109_K	1.515	1.00
82_R	210_P	1.505	1.00
6_F	17_A	1.503	1.00
278_E	282_Q	1.502	1.00
283_R	286_K	1.493	1.00
233_R	237_F	1.487	1.00
16_I	228_I	1.482	1.00
247_T	262_I	1.477	1.00
127_S	131_R	1.477	1.00
47_R	155_K	1.474	1.00
115_Y	129_F	1.469	1.00
37_E	40_E	1.444	1.00
143_A	227_I	1.439	1.00
66_D	69_T	1.422	1.00
65_L	108_P	1.415	1.00
253_G	288_V	1.413	1.00
200_E	204_N	1.412	1.00
47_R	151_S	1.404	1.00
154_A	164_V	1.392	1.00
153_I	164_V	1.389	1.00
76_I	117_M	1.368	1.00
68_V	71_A	1.343	1.00
41_K	216_V	1.332	1.00
178_V	203_E	1.331	1.00
279_S	283_R	1.320	1.00
117_M	129_F	1.319	1.00
286_K	289_E	1.312	1.00
292_Y	296_K	1.284	1.00
72_D	111_P	1.281	1.00
175_D	290_D	1.272	1.00
49_A	226_T	1.271	1.00
106_L	115_Y	1.264	1.00
18_Y	225_A	1.260	1.00
160_P	163_K	1.260	1.00
73_I	116_I	1.256	1.00
99_Q	103_A	1.255	1.00
181_S	280_D	1.242	1.00
293_R	297_E	1.235	1.00
156_K	201_E	1.229	1.00
74_I	106_L	1.226	1.00
37_E	215_R	1.216	1.00
208_S	211_G	1.216	1.00
238_N	266_A	1.212	1.00
248_P	254_E	1.208	1.00
212_E	216_V	1.207	1.00
87_S	90_D	1.204	1.00
106_L	132_F	1.201	1.00
36_P	64_S	1.191	1.00
163_K	186_N	1.189	1.00
3_K	70_N	1.189	1.00
122_V	139_S	1.188	1.00
263_V	269_G	1.187	1.00
212_E	215_R	1.182	1.00
16_I	232_V	1.181	1.00
16_I	75_L	1.180	1.00
61_G	67_D	1.180	1.00
138_I	235_V	1.177	1.00
20_V	29_A	1.168	1.00
282_Q	285_N	1.167	1.00
230_D	241_R	1.163	1.00
37_E	216_V	1.163	1.00
181_S	277_P	1.163	1.00
114_L	136_F	1.156	1.00
285_N	288_V	1.153	1.00
204_N	207_K	1.153	1.00
20_V	25_L	1.152	1.00
242_V	246_A	1.150	1.00
143_A	243_M	1.148	1.00
18_Y	22_F	1.143	1.00
110_N	113_A	1.140	1.00
80_K	83_K	1.135	1.00
195_K	198_T	1.120	1.00
94_D	97_K	1.119	1.00
250_T	272_L	1.119	1.00
165_T	184_K	1.113	1.00
130_M	137_T	1.111	1.00
135_Q	267_E	1.110	1.00
188_K	192_E	1.108	1.00
120_N	172_H	1.104	1.00
48_H	209_I	1.103	1.00
88_R	120_N	1.099	1.00
74_I	113_A	1.096	1.00
192_E	275_V	1.087	1.00
101_D	104_K	1.087	1.00
112_G	133_S	1.084	1.00
198_T	201_E	1.083	1.00
82_R	214_I	1.081	1.00
242_V	263_V	1.081	1.00
35_V	38_L	1.077	1.00
16_I	225_A	1.075	1.00
88_R	172_H	1.074	1.00
93_I	97_K	1.073	1.00
30_I	67_D	1.067	0.99
91_L	95_N	1.057	0.99
103_A	115_Y	1.055	0.99
76_I	129_F	1.048	0.99
286_K	290_D	1.048	0.99
99_Q	125_M	1.047	0.99
122_V	126_A	1.041	0.99
263_V	272_L	1.021	0.99
72_D	112_G	1.017	0.99
25_L	237_F	1.015	0.99
293_R	296_K	1.012	0.99
11_K	221_T	1.011	0.99
116_I	231_I	1.011	0.99
62_T	67_D	1.011	0.99
175_D	287_S	1.008	0.99
14_Q	42_F	1.001	0.99
162_N	239_E	0.995	0.99
284_L	288_V	0.993	0.99
154_A	161_A	0.992	0.99
64_S	67_D	0.991	0.99
247_T	268_I	0.963	0.99
151_S	155_K	0.959	0.99
30_I	71_A	0.959	0.99
279_S	282_Q	0.959	0.99
80_K	98_I	0.957	0.99
126_A	139_S	0.953	0.99
73_I	236_V	0.949	0.99
32_Y	65_L	0.949	0.99
38_L	42_F	0.949	0.99
90_D	93_I	0.946	0.99
23_D	229_K	0.944	0.99
14_Q	225_A	0.944	0.99
276_L	284_L	0.940	0.99
208_S	215_R	0.940	0.99
86_M	90_D	0.937	0.99
84_P	215_R	0.935	0.99
244_S	247_T	0.932	0.99
17_A	31_L	0.932	0.99
249_R	252_Q	0.929	0.99
179_L	276_L	0.928	0.99
75_L	116_I	0.925	0.99
70_N	111_P	0.924	0.99
184_K	187_G	0.920	0.98
289_E	296_K	0.919	0.98
192_E	195_K	0.917	0.98
175_D	286_K	0.915	0.98
130_M	134_K	0.908	0.98
69_T	109_K	0.907	0.98
189_P	192_E	0.902	0.98
210_P	214_I	0.899	0.98
150_R	165_T	0.897	0.98
133_S	136_F	0.895	0.98
39_P	63_N	0.888	0.98
103_A	107_P	0.884	0.98
149_L	166_G	0.883	0.98
74_I	110_N	0.882	0.98
233_R	239_E	0.878	0.98
71_A	74_I	0.875	0.98
146_T	150_R	0.875	0.98
76_I	99_Q	0.873	0.98
25_L	229_K	0.873	0.98
253_G	281_R	0.873	0.98
124_M	294_V	0.869	0.98
188_K	193_V	0.865	0.98
127_S	130_M	0.859	0.98
116_I	232_V	0.852	0.98
132_F	137_T	0.848	0.97
248_P	272_L	0.844	0.97
82_R	211_G	0.842	0.97
228_I	232_V	0.841	0.97
113_A	132_F	0.840	0.97
66_D	109_K	0.839	0.97
137_T	257_H	0.839	0.97
225_A	229_K	0.836	0.97
260_V	271_S	0.835	0.97
152_Y	205_Y	0.832	0.97
139_S	246_A	0.827	0.97
63_N	67_D	0.826	0.97
9_V	42_F	0.825	0.97
36_P	40_E	0.818	0.97
250_T	260_V	0.818	0.97
60_I	63_N	0.817	0.97
6_F	16_I	0.817	0.97
169_A	177_V	0.816	0.97
203_E	207_K	0.816	0.97
197_L	201_E	0.814	0.97
11_K	14_Q	0.814	0.97
242_V	247_T	0.812	0.97
152_Y	155_K	0.812	0.97
99_Q	117_M	0.802	0.96
289_E	292_Y	0.801	0.96
231_I	245_I	0.799	0.96
65_L	102_L	0.798	0.96
116_I	235_V	0.797	0.96
98_I	119_A	0.796	0.96
30_I	63_N	0.792	0.96
40_E	216_V	0.790	0.96
294_V	297_E	0.786	0.96
245_I	262_I	0.785	0.96
16_I	20_V	0.785	0.96
213_I	223_G	0.783	0.96
143_A	231_I	0.780	0.96
19_S	225_A	0.779	0.96
180_W	206_V	0.773	0.96
260_V	270_P	0.769	0.95
89_R	124_M	0.769	0.95
290_D	294_V	0.765	0.95
71_A	110_N	0.764	0.95
153_I	157_L	0.762	0.95
250_T	270_P	0.762	0.95
82_R	91_L	0.756	0.95
159_V	164_V	0.755	0.95
7_I	102_L	0.753	0.95
191_E	199_K	0.753	0.95
174_E	211_G	0.748	0.95
87_S	174_E	0.747	0.95
76_I	102_L	0.747	0.95
149_L	178_V	0.747	0.95
70_N	112_G	0.746	0.95
159_V	185_V	0.745	0.95
93_I	297_E	0.744	0.95
16_I	77_M	0.742	0.94
82_R	86_M	0.742	0.94
75_L	228_I	0.741	0.94
211_G	215_R	0.740	0.94
78_A	98_I	0.740	0.94
91_L	214_I	0.740	0.94
19_S	22_F	0.738	0.94
40_E	63_N	0.736	0.94
240_G	263_V	0.733	0.94
107_P	113_A	0.732	0.94
36_P	63_N	0.729	0.94
157_L	164_V	0.727	0.94
32_Y	68_V	0.726	0.94
129_F	137_T	0.723	0.94
11_K	219_G	0.717	0.93
28_E	56_S	0.717	0.93
15_T	222_W	0.711	0.93
15_T	19_S	0.710	0.93
107_P	115_Y	0.706	0.93
134_K	257_H	0.704	0.93
42_F	225_A	0.700	0.93
17_A	46_L	0.699	0.93
168_V	203_E	0.697	0.92
114_L	138_I	0.697	0.92
217_M	220_T	0.695	0.92
210_P	220_T	0.694	0.92
127_S	255_I	0.692	0.92
182_T	274_G	0.691	0.92
150_R	230_D	0.689	0.92
250_T	273_E	0.689	0.92
118_V	140_T	0.688	0.92
201_E	204_N	0.687	0.92
149_L	183_V	0.687	0.92
15_T	221_T	0.686	0.92
20_V	229_K	0.685	0.92
97_K	101_D	0.682	0.92
88_R	145_E	0.682	0.92
20_V	232_V	0.677	0.91
135_Q	269_G	0.674	0.91
177_V	287_S	0.672	0.91
214_I	219_G	0.670	0.91
223_G	226_T	0.666	0.91
42_F	217_M	0.666	0.91
76_I	103_A	0.664	0.91
35_V	39_P	0.664	0.91
5_A	30_I	0.661	0.90
83_K	94_D	0.658	0.90
153_I	166_G	0.655	0.90
194_A	198_T	0.649	0.90
169_A	274_G	0.647	0.89
89_R	294_V	0.646	0.89
253_G	292_Y	0.646	0.89
276_L	285_N	0.646	0.89
240_G	244_S	0.645	0.89
249_R	273_E	0.643	0.89
20_V	26_A	0.641	0.89
65_L	69_T	0.641	0.89
21_I	46_L	0.641	0.89
200_E	279_S	0.640	0.89
53_R	226_T	0.640	0.89
242_V	245_I	0.638	0.89
77_M	118_V	0.637	0.89
112_G	136_F	0.637	0.89
89_R	290_D	0.633	0.88
43_E	47_R	0.628	0.88
68_V	107_P	0.627	0.88
122_V	140_T	0.626	0.88
238_N	241_R	0.625	0.88
32_Y	102_L	0.624	0.88
19_S	229_K	0.624	0.88
5_A	110_N	0.624	0.88
234_S	239_E	0.622	0.87
106_L	109_K	0.622	0.87
79_G	119_A	0.619	0.87
145_E	148_R	0.616	0.87
256_I	292_Y	0.616	0.87
288_V	292_Y	0.613	0.87
136_F	267_E	0.611	0.87
65_L	105_Q	0.611	0.87
142_D	175_D	0.611	0.87
172_H	210_P	0.609	0.86
234_S	244_S	0.609	0.86
250_T	271_S	0.609	0.86
100_I	128_V	0.606	0.86
210_P	219_G	0.605	0.86
196_G	279_S	0.602	0.86
179_L	182_T	0.601	0.86
26_A	29_A	0.600	0.86
89_R	297_E	0.599	0.85
4_I	29_A	0.597	0.85
28_E	59_V	0.597	0.85
208_S	212_E	0.596	0.85
18_Y	222_W	0.596	0.85
48_H	151_S	0.595	0.85
14_Q	222_W	0.595	0.85
149_L	177_V	0.595	0.85
154_A	159_V	0.595	0.85
265_G	268_I	0.594	0.85
105_Q	109_K	0.594	0.85
167_Y	244_S	0.594	0.85
248_P	252_Q	0.593	0.85
275_V	281_R	0.581	0.84
6_F	29_A	0.579	0.83
177_V	283_R	0.577	0.83
276_L	280_D	0.577	0.83
256_I	288_V	0.577	0.83
251_Y	255_I	0.573	0.83
247_T	257_H	0.571	0.83
121_P	148_R	0.570	0.83
41_K	91_L	0.570	0.83
12_I	118_V	0.570	0.83
203_E	283_R	0.569	0.82
95_N	125_M	0.569	0.82
21_I	29_A	0.568	0.82
155_K	205_Y	0.567	0.82
100_I	131_R	0.566	0.82
231_I	243_M	0.564	0.82
292_Y	295_Y	0.562	0.82
160_P	241_R	0.560	0.81
86_M	91_L	0.560	0.81
88_R	91_L	0.557	0.81
177_V	203_E	0.554	0.81
191_E	195_K	0.554	0.81
197_L	200_E	0.553	0.81
15_T	18_Y	0.553	0.81
260_V	273_E	0.552	0.81
70_N	110_N	0.551	0.80
241_R	244_S	0.551	0.80
243_M	246_A	0.551	0.80
232_V	236_V	0.550	0.80
42_F	222_W	0.547	0.80
96_A	100_I	0.546	0.80
103_A	106_L	0.543	0.79
13_G	17_A	0.543	0.79
239_E	242_V	0.540	0.79
36_P	62_T	0.539	0.79
277_P	281_R	0.537	0.79
102_L	106_L	0.534	0.78
3_K	69_T	0.534	0.78
84_P	218_G	0.533	0.78
234_S	243_M	0.531	0.78
258_I	291_F	0.530	0.78
179_L	277_P	0.530	0.78
140_T	143_A	0.528	0.78
177_V	276_L	0.526	0.77
243_M	247_T	0.526	0.77
143_A	234_S	0.525	0.77
169_A	276_L	0.525	0.77
120_N	220_T	0.524	0.77
57_T	160_P	0.522	0.77
253_G	258_I	0.522	0.77
213_I	217_M	0.522	0.77
60_I	64_S	0.522	0.77
138_I	231_I	0.522	0.77
6_F	20_V	0.522	0.77
152_Y	156_K	0.521	0.77
230_D	239_E	0.517	0.76
79_G	82_R	0.515	0.76
25_L	233_R	0.514	0.76
140_T	259_S	0.511	0.75
150_R	166_G	0.510	0.75
138_I	268_I	0.510	0.75
171_E	220_T	0.509	0.75
104_K	107_P	0.509	0.75
153_I	180_W	0.508	0.75
238_N	265_G	0.505	0.74
79_G	85_G	0.502	0.74
10_G	145_E	0.501	0.74
17_A	29_A	0.500	0.74
9_V	29_A	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
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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	0.9675	100	0.255	Contact Map
2d4aB	4	0.9708	100	0.258	Contact Map
4cl3A	4	0.9708	100	0.262	Contact Map
1guzA	4	0.9643	100	0.267	Contact Map
1a5zA	3	0.974	100	0.27	Contact Map
1lldA	3	0.9708	100	0.271	Contact Map
4plzA	4	0.9448	100	0.272	Contact Map
4bgvA	4	0.9903	100	0.278	Contact Map
2v6bA	4	0.8896	100	0.282	Contact Map
4aj2A	4	0.9708	100	0.284	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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