TDH - BACSU - GREMLIN Contacts

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TDH - L-threonine 3-dehydrogenase

UniProt:	O31776	Sequences: MQSGKMKALMKKDGAFGAVLTEVPIPEIDKHEVLIKVKAASICGTDVHIYNWDQWARQRIKTPYVFGHEFSGIVEGVGENVSSVKVGEYVSAETHIVCGECVPCLTGKSHVCTNTAIIGVDTAGCFAEYVKVPADNIWRNPADMDPSIASIQEPLGNAVHTVLESQPAGGTTAVIGCGPIGLMAVAVAKAAGASQVIAIDKNEYRLRLAKQMGATCTVSIEKEDPLKIVSALTSGEGADLVCEMSGHPSAIAQGLAMAANGGRFHILSLPEHPVTIDLTNKVVFKGLTIQGITGRKMFSTWRQVSQLISSNMIDLAPVITHQFPLEEFEKGFELMRSGQCGKVILIP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	347 (304)
Sequences:	52764 (36364)
Seq/√Len:	2085.6

ECOLI - YBDR GATD YDJL TDH RSPB YDJJ YGGP YPHC FRMA AHR YJJN YAHK ADHP IDND QOR1 YCJQ ACUI CURA
BACSU - TDH ADHB YJMD DHSO YYCR BDHA ADHA YOGA YHFP YFMJ
HALSA - Q9HMB6 Q9HP38 GLCDH Q9HR85 Q9HQS8
SULSO - ADH Q7LXK1 Q97ZV3 Q97YT7 Q97XR4 Q97VV5 Q97YM2 Q97TZ4 Q97V32 Q97WA1 Q97VW0 GLCD2 GLCD1 Q97W06 GLCD3 Q97VB8 Q97UW5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
327_E	330_K	2.988	1.00
38_K	146_P	2.910	1.00
36_K	75_E	2.811	1.00
38_K	73_I	2.746	1.00
34_L	75_E	2.656	1.00
33_V	137_I	2.640	1.00
189_K	215_T	2.555	1.00
145_D	148_I	2.525	1.00
171_T	195_Q	2.503	1.00
89_Y	140_N	2.416	1.00
88_E	139_R	2.395	1.00
85_K	88_E	2.363	1.00
228_I	231_A	2.324	1.00
70_F	125_C	2.319	1.00
207_R	211_Q	2.277	1.00
323_F	334_L	2.266	1.00
167_P	170_G	2.265	1.00
36_K	73_I	2.257	1.00
25_I	129_Y	2.201	1.00
195_Q	216_C	2.185	1.00
36_K	129_Y	2.180	1.00
147_S	322_Q	2.130	1.00
206_L	210_K	2.094	1.00
172_T	188_A	2.079	1.00
10_M	21_T	2.069	1.00
306_Q	310_S	2.069	1.00
83_S	134_A	2.048	1.00
321_H	334_L	2.005	1.00
31_H	80_N	2.001	1.00
30_K	79_E	1.998	1.00
163_L	191_A	1.984	1.00
185_V	214_A	1.977	1.00
29_D	32_E	1.959	1.00
324_P	327_E	1.948	1.00
89_Y	146_P	1.945	1.00
143_D	309_S	1.931	1.00
70_F	92_A	1.927	1.00
30_K	80_N	1.914	1.00
71_S	146_P	1.899	1.00
333_E	337_S	1.857	1.00
170_G	263_R	1.838	1.00
27_E	76_G	1.833	1.00
207_R	210_K	1.772	1.00
75_E	129_Y	1.768	1.00
34_L	131_K	1.767	1.00
173_A	238_A	1.756	1.00
163_L	303_Q	1.753	1.00
51_N	336_R	1.746	1.00
173_A	199_I	1.743	1.00
330_K	333_E	1.740	1.00
203_E	207_R	1.732	1.00
206_L	217_T	1.719	1.00
323_F	331_G	1.685	1.00
239_D	259_A	1.685	1.00
190_A	312_M	1.666	1.00
140_N	146_P	1.653	1.00
334_L	339_Q	1.652	1.00
197_I	238_A	1.651	1.00
263_R	288_T	1.646	1.00
200_D	206_L	1.639	1.00
330_K	334_L	1.623	1.00
258_A	264_F	1.617	1.00
78_G	81_V	1.611	1.00
175_I	254_G	1.577	1.00
216_C	232_L	1.553	1.00
203_E	219_S	1.552	1.00
84_V	139_R	1.550	1.00
223_E	228_I	1.535	1.00
148_I	316_A	1.534	1.00
140_N	149_A	1.533	1.00
219_S	222_K	1.523	1.00
224_D	227_K	1.515	1.00
77_V	86_V	1.510	1.00
195_Q	215_T	1.508	1.00
9_L	328_F	1.508	1.00
208_L	211_Q	1.505	1.00
7_K	22_E	1.500	1.00
32_E	133_P	1.500	1.00
203_E	222_K	1.485	1.00
263_R	290_Q	1.483	1.00
258_A	287_L	1.477	1.00
126_F	332_F	1.466	1.00
34_L	129_Y	1.465	1.00
76_G	86_V	1.463	1.00
28_I	131_K	1.456	1.00
37_V	70_F	1.452	1.00
84_V	88_E	1.452	1.00
89_Y	142_A	1.445	1.00
258_A	262_G	1.431	1.00
73_I	89_Y	1.414	1.00
185_V	198_A	1.409	1.00
7_K	128_E	1.389	1.00
28_I	34_L	1.388	1.00
31_H	133_P	1.386	1.00
32_E	131_K	1.376	1.00
241_V	254_G	1.358	1.00
39_A	147_S	1.356	1.00
241_V	258_A	1.342	1.00
329_E	333_E	1.338	1.00
50_Y	332_F	1.337	1.00
74_V	84_V	1.333	1.00
13_D	19_V	1.331	1.00
177_C	198_A	1.319	1.00
33_V	84_V	1.306	1.00
34_L	76_G	1.288	1.00
7_K	326_E	1.285	1.00
320_T	334_L	1.284	1.00
227_K	231_A	1.273	1.00
171_T	197_I	1.272	1.00
73_I	146_P	1.261	1.00
184_A	242_C	1.247	1.00
201_K	206_L	1.243	1.00
201_K	220_I	1.242	1.00
306_Q	309_S	1.241	1.00
9_L	20_L	1.228	1.00
152_Q	308_I	1.224	1.00
175_I	199_I	1.222	1.00
8_A	23_V	1.204	1.00
190_A	307_L	1.204	1.00
13_D	17_G	1.204	1.00
165_S	240_L	1.200	1.00
159_V	163_L	1.184	1.00
38_K	89_Y	1.167	1.00
84_V	137_I	1.164	1.00
210_K	217_T	1.148	1.00
14_G	17_G	1.139	1.00
206_L	219_S	1.137	1.00
228_I	232_L	1.133	1.00
28_I	32_E	1.131	1.00
25_I	34_L	1.128	1.00
171_T	239_D	1.123	1.00
31_H	134_A	1.103	1.00
35_I	72_G	1.102	1.00
203_E	206_L	1.098	1.00
75_E	86_V	1.097	1.00
303_Q	306_Q	1.097	1.00
37_V	130_V	1.097	1.00
198_A	214_A	1.082	1.00
132_V	137_I	1.073	1.00
170_G	239_D	1.063	1.00
42_I	331_G	1.047	1.00
9_L	325_L	1.042	1.00
163_L	300_T	1.042	1.00
39_A	146_P	1.041	1.00
208_L	340_C	1.036	1.00
50_Y	336_R	1.034	1.00
328_F	345_L	1.028	1.00
224_D	228_I	1.017	1.00
156_G	183_M	1.014	1.00
158_A	187_V	1.010	1.00
256_A	281_K	1.008	1.00
160_H	300_T	1.007	1.00
302_R	306_Q	1.007	1.00
245_S	250_A	1.007	1.00
307_L	312_M	1.005	1.00
210_K	216_C	1.002	1.00
35_I	90_V	0.998	1.00
20_L	326_E	0.991	1.00
38_K	71_S	0.990	1.00
43_C	69_E	0.988	1.00
211_Q	317_P	0.987	1.00
43_C	68_H	0.984	1.00
40_A	126_F	0.977	1.00
233_T	237_G	0.969	1.00
222_K	228_I	0.967	1.00
188_A	193_A	0.964	1.00
158_A	184_A	0.956	1.00
40_A	125_C	0.950	1.00
144_M	149_A	0.949	1.00
161_T	267_L	0.948	1.00
126_F	328_F	0.948	1.00
10_M	65_V	0.944	1.00
77_V	81_V	0.942	1.00
226_L	256_A	0.941	1.00
174_V	184_A	0.940	1.00
334_L	343_V	0.932	1.00
10_M	23_V	0.930	1.00
282_V	289_I	0.930	1.00
185_V	196_V	0.925	1.00
47_V	335_M	0.917	1.00
25_I	76_G	0.913	1.00
243_E	246_G	0.912	1.00
174_V	188_A	0.909	1.00
333_E	336_R	0.909	1.00
177_C	200_D	0.906	1.00
176_G	198_A	0.901	1.00
252_A	256_A	0.898	1.00
85_K	139_R	0.892	1.00
197_I	216_C	0.891	1.00
159_V	303_Q	0.891	1.00
81_V	134_A	0.891	1.00
229_V	238_A	0.890	1.00
187_V	304_V	0.888	1.00
64_Y	123_A	0.884	1.00
27_E	34_L	0.884	1.00
36_K	128_E	0.882	1.00
199_I	220_I	0.882	1.00
23_V	123_A	0.879	1.00
253_Q	256_A	0.877	1.00
202_N	205_R	0.875	1.00
31_H	78_G	0.873	1.00
201_K	221_E	0.872	1.00
335_M	343_V	0.872	1.00
226_L	253_Q	0.871	1.00
82_S	134_A	0.867	1.00
155_L	183_M	0.866	1.00
41_S	69_E	0.864	1.00
170_G	240_L	0.862	1.00
197_I	218_V	0.860	1.00
173_A	257_M	0.859	1.00
126_F	345_L	0.859	1.00
202_N	219_S	0.856	1.00
200_D	217_T	0.854	1.00
13_D	16_F	0.853	1.00
175_I	241_V	0.850	1.00
198_A	209_A	0.850	1.00
171_T	238_A	0.847	1.00
70_F	130_V	0.845	1.00
25_I	75_E	0.844	1.00
182_L	208_L	0.844	1.00
39_A	344_I	0.843	1.00
204_Y	207_R	0.843	1.00
281_K	285_K	0.842	1.00
323_F	327_E	0.837	1.00
205_R	340_C	0.828	1.00
303_Q	307_L	0.826	1.00
8_A	65_V	0.826	1.00
226_L	230_S	0.821	1.00
161_T	242_C	0.821	1.00
142_A	309_S	0.816	1.00
299_S	303_Q	0.815	1.00
91_S	305_S	0.801	1.00
187_V	307_L	0.800	1.00
31_H	79_E	0.799	1.00
162_V	188_A	0.797	1.00
261_G	286_G	0.796	1.00
43_C	46_D	0.796	1.00
227_K	230_S	0.793	1.00
42_I	335_M	0.789	1.00
9_L	329_E	0.786	1.00
161_T	184_A	0.781	1.00
172_T	193_A	0.776	1.00
158_A	183_M	0.773	1.00
90_V	137_I	0.772	1.00
158_A	180_I	0.769	1.00
7_K	20_L	0.769	1.00
209_A	214_A	0.766	1.00
323_F	345_L	0.763	1.00
234_S	237_G	0.761	1.00
9_L	18_A	0.758	1.00
29_D	131_K	0.756	1.00
197_I	232_L	0.756	1.00
254_G	264_F	0.756	1.00
224_D	253_Q	0.756	1.00
42_I	126_F	0.752	1.00
226_L	257_M	0.751	1.00
177_C	209_A	0.749	1.00
92_A	132_V	0.746	1.00
201_K	209_A	0.745	1.00
191_A	303_Q	0.745	1.00
241_V	264_F	0.744	1.00
20_L	325_L	0.744	1.00
144_M	308_I	0.740	1.00
196_V	215_T	0.738	1.00
225_P	253_Q	0.738	1.00
163_L	187_V	0.738	1.00
282_V	291_G	0.737	1.00
45_T	68_H	0.734	1.00
316_A	319_I	0.733	1.00
23_V	65_V	0.733	1.00
299_S	302_R	0.733	1.00
197_I	229_V	0.731	1.00
249_S	253_Q	0.730	1.00
77_V	85_K	0.730	1.00
193_A	240_L	0.727	1.00
334_L	337_S	0.725	1.00
91_S	140_N	0.725	1.00
43_C	154_P	0.725	1.00
175_I	250_A	0.724	1.00
307_L	311_N	0.724	1.00
28_I	76_G	0.723	1.00
165_S	265_H	0.722	1.00
28_I	78_G	0.717	1.00
188_A	196_V	0.716	1.00
138_W	302_R	0.716	1.00
282_V	287_L	0.715	1.00
238_A	241_V	0.714	1.00
240_L	265_H	0.714	1.00
244_M	267_L	0.712	1.00
33_V	134_A	0.712	1.00
266_I	289_I	0.711	1.00
71_S	150_S	0.711	1.00
319_I	322_Q	0.710	1.00
160_H	286_G	0.708	1.00
307_L	310_S	0.706	1.00
145_D	149_A	0.703	1.00
193_A	196_V	0.695	1.00
321_H	330_K	0.694	1.00
323_F	343_V	0.693	1.00
89_Y	143_D	0.689	1.00
39_A	322_Q	0.687	1.00
125_C	130_V	0.683	1.00
177_C	185_V	0.682	1.00
158_A	162_V	0.679	1.00
138_W	301_W	0.677	1.00
16_F	333_E	0.675	1.00
174_V	198_A	0.674	1.00
252_A	275_T	0.669	1.00
260_N	285_K	0.668	1.00
11_K	17_G	0.666	1.00
157_N	180_I	0.666	1.00
154_P	179_P	0.664	1.00
305_S	309_S	0.664	1.00
229_V	257_M	0.663	1.00
88_E	142_A	0.659	1.00
141_P	309_S	0.658	1.00
44_G	48_H	0.656	1.00
166_Q	263_R	0.656	1.00
277_D	281_K	0.655	1.00
230_S	233_T	0.651	1.00
71_S	140_N	0.651	1.00
138_W	305_S	0.651	1.00
26_P	131_K	0.647	1.00
159_V	304_V	0.645	1.00
33_V	74_V	0.645	1.00
83_S	139_R	0.644	1.00
321_H	343_V	0.636	1.00
39_A	71_S	0.636	1.00
159_V	307_L	0.635	1.00
31_H	135_D	0.634	1.00
71_S	89_Y	0.632	1.00
251_I	264_F	0.630	1.00
189_K	196_V	0.630	1.00
230_S	237_G	0.629	1.00
35_I	92_A	0.628	1.00
247_H	250_A	0.628	1.00
164_E	288_T	0.627	1.00
332_F	336_R	0.624	1.00
243_E	264_F	0.623	1.00
187_V	191_A	0.622	1.00
83_S	86_V	0.621	1.00
206_L	220_I	0.620	1.00
91_S	153_E	0.620	1.00
153_E	157_N	0.619	1.00
161_T	292_I	0.618	1.00
13_D	21_T	0.616	1.00
208_L	212_M	0.615	1.00
186_A	212_M	0.615	1.00
200_D	220_I	0.615	1.00
199_I	218_V	0.614	1.00
185_V	212_M	0.614	1.00
48_H	53_D	0.613	1.00
240_L	263_R	0.612	1.00
200_D	219_S	0.612	1.00
238_A	257_M	0.611	1.00
241_V	257_M	0.611	1.00
206_L	209_A	0.609	1.00
200_D	209_A	0.609	1.00
93_E	138_W	0.608	1.00
281_K	284_F	0.607	1.00
45_T	49_I	0.605	1.00
28_I	80_N	0.603	1.00
152_Q	304_V	0.603	1.00
26_P	129_Y	0.601	1.00
148_I	152_Q	0.600	1.00
15_A	333_E	0.600	1.00
250_A	254_G	0.594	1.00
184_A	267_L	0.593	1.00
185_V	209_A	0.592	1.00
155_L	304_V	0.592	1.00
172_T	240_L	0.592	1.00
37_V	40_A	0.591	1.00
216_C	228_I	0.587	1.00
92_A	137_I	0.584	1.00
157_N	267_L	0.584	1.00
281_K	287_L	0.582	1.00
44_G	178_G	0.581	1.00
24_P	27_E	0.580	1.00
26_P	34_L	0.580	1.00
159_V	300_T	0.579	1.00
47_V	336_R	0.572	1.00
35_I	137_I	0.572	1.00
45_T	48_H	0.572	1.00
298_F	302_R	0.571	1.00
77_V	88_E	0.570	1.00
252_A	281_K	0.568	1.00
243_E	268_S	0.566	1.00
60_I	64_Y	0.566	1.00
209_A	217_T	0.566	1.00
61_K	64_Y	0.564	1.00
173_A	241_V	0.563	1.00
67_G	126_F	0.562	1.00
225_P	229_V	0.561	1.00
82_S	85_K	0.560	1.00
273_P	277_D	0.559	1.00
265_H	292_I	0.558	1.00
166_Q	288_T	0.558	1.00
25_I	131_K	0.557	1.00
283_V	291_G	0.555	1.00
146_P	149_A	0.548	1.00
164_E	300_T	0.548	1.00
40_A	345_L	0.547	1.00
168_A	192_G	0.546	1.00
162_V	187_V	0.545	1.00
218_V	228_I	0.543	1.00
166_Q	290_Q	0.543	1.00
218_V	223_E	0.542	1.00
197_I	233_T	0.540	1.00
71_S	149_A	0.539	1.00
189_K	214_A	0.539	1.00
84_V	134_A	0.538	1.00
183_M	187_V	0.538	1.00
25_I	28_I	0.536	1.00
321_H	327_E	0.535	1.00
287_L	291_G	0.534	1.00
160_H	164_E	0.534	1.00
168_A	191_A	0.534	1.00
35_I	70_F	0.533	1.00
183_M	186_A	0.533	1.00
200_D	205_R	0.532	1.00
92_A	125_C	0.531	1.00
218_V	232_L	0.531	1.00
37_V	92_A	0.531	1.00
47_V	51_N	0.531	1.00
210_K	214_A	0.529	1.00
145_D	322_Q	0.528	1.00
321_H	340_C	0.527	1.00
153_E	156_G	0.525	1.00
134_A	137_I	0.525	1.00
201_K	219_S	0.523	1.00
171_T	233_T	0.522	1.00
183_M	313_I	0.522	1.00
65_V	124_G	0.520	1.00
151_I	344_I	0.519	1.00
182_L	318_V	0.516	1.00
175_I	225_P	0.514	1.00
20_L	328_F	0.513	1.00
26_P	32_E	0.511	1.00
156_G	304_V	0.510	1.00
278_L	281_K	0.509	1.00
17_G	50_Y	0.509	1.00
292_I	295_R	0.507	1.00
308_I	313_I	0.507	1.00
159_V	191_A	0.506	1.00
140_N	144_M	0.506	1.00
161_T	265_H	0.505	1.00
173_A	229_V	0.505	1.00
237_G	259_A	0.503	1.00
77_V	84_V	0.503	1.00
185_V	189_K	0.502	1.00
43_C	342_K	0.501	1.00
28_I	31_H	0.501	1.00
249_S	252_A	0.501	1.00
169_G	193_A	0.500	1.00
320_T	341_G	0.500	1.00
92_A	130_V	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
2d8aA	3	0.9568	100	0.153	Contact Map
2dq4A	4	0.9798	100	0.162	Contact Map
1vj0A	4	0.9769	100	0.173	Contact Map
1h2bA	4	0.9654	100	0.174	Contact Map
4ej6A	1	0.9683	100	0.175	Contact Map
4ilkA	2	0.9625	100	0.175	Contact Map
3ukoA	4	0.9885	100	0.182	Contact Map
3ip1A	4	0.9741	100	0.188	Contact Map
1cdoA	2	0.9827	100	0.189	Contact Map
4rqtA	2	0.9885	100	0.19	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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