YOAD - BACSU - GREMLIN Contacts

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YOAD - Putative 2-hydroxyacid dehydrogenase YoaD

UniProt:	O34815	Sequences: MKNTMKRMFCSMTVLVTAPYNEEGRKELENLFGSVAYQSWKEQGRAYREDELIQLLKATNATGLITELDQVTDSVFASVPELSFVGVCRGMPSNVDVAAASKRGIPVFYTPGRNAQAVAEMFIGNVISFLRHTSASNQWLKDGEWDSDYLQAYVKFKGNELTGKTVGMIGFGAVGQRIAKLLTAFDCKIKYYDPYIQDDHPLYEKASLKTVFSDSDIVSVHLPRTEETLGLIDRQYFDLMKESAIFVNTSRAVVVNREDLLFVLKEHKISGAILDVFYHEPPEESDYELISLPNVLATPHLAGATFEVEDHHVTILNKALKKWKGEKTLNIQTMYNKDALKTGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	344 (287)
Sequences:	18236 (12633)
Seq/√Len:	745.7

ECOLI - SERA GHRB LDHD GHRA PDXB
BACSU - YOAD SERA TKRA
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
233_D	236_Y	4.413	1.00
234_R	262_F	3.215	1.00
256_N	259_D	3.173	1.00
166_V	182_L	2.708	1.00
265_K	292_L	2.494	1.00
165_T	188_K	2.480	1.00
224_R	253_V	2.436	1.00
209_K	239_L	2.312	1.00
242_E	268_K	2.303	1.00
165_T	190_K	2.279	1.00
167_G	211_V	2.202	1.00
212_F	236_Y	2.162	1.00
60_N	83_S	2.131	1.00
207_S	210_T	2.112	1.00
213_S	239_L	2.072	1.00
123_I	182_L	2.055	1.00
230_G	278_Y	2.048	1.00
190_K	214_D	2.038	1.00
73_D	102_K	2.018	1.00
137_N	141_K	2.005	1.00
171_F	191_Y	2.004	1.00
322_K	327_K	1.955	1.00
167_G	215_S	1.918	1.00
130_L	217_I	1.898	1.00
262_F	266_E	1.887	1.00
132_H	135_A	1.885	1.00
238_D	268_K	1.873	1.00
177_R	180_K	1.829	1.00
244_A	269_I	1.829	1.00
124_G	133_T	1.826	1.00
232_I	237_F	1.812	1.00
246_F	255_V	1.807	1.00
73_D	77_A	1.795	1.00
245_I	271_G	1.792	1.00
123_I	185_F	1.761	1.00
84_F	108_F	1.752	1.00
261_L	292_L	1.747	1.00
265_K	288_E	1.741	1.00
230_G	256_N	1.723	1.00
292_L	295_V	1.698	1.00
126_V	217_I	1.697	1.00
168_M	175_G	1.668	1.00
166_V	187_C	1.660	1.00
58_A	81_E	1.643	1.00
209_K	236_Y	1.643	1.00
49_E	74_S	1.619	1.00
216_D	241_K	1.607	1.00
99_A	102_K	1.601	1.00
77_A	103_R	1.600	1.00
121_M	302_A	1.595	1.00
234_R	238_D	1.591	1.00
260_L	272_A	1.591	1.00
210_T	214_D	1.577	1.00
128_S	134_S	1.570	1.00
212_F	232_I	1.564	1.00
164_K	307_E	1.551	1.00
106_P	332_Q	1.546	1.00
129_F	271_G	1.545	1.00
237_F	263_V	1.539	1.00
125_N	273_I	1.529	1.00
226_E	229_L	1.520	1.00
257_R	278_Y	1.500	1.00
182_L	187_C	1.496	1.00
160_E	311_H	1.496	1.00
235_Q	239_L	1.486	1.00
159_N	164_K	1.469	1.00
122_F	178_I	1.441	1.00
168_M	219_S	1.440	1.00
49_E	72_T	1.438	1.00
76_F	103_R	1.438	1.00
245_I	270_S	1.436	1.00
48_R	51_E	1.430	1.00
224_R	229_L	1.425	1.00
232_I	236_Y	1.424	1.00
178_I	221_H	1.421	1.00
220_V	254_V	1.401	1.00
100_A	107_V	1.400	1.00
321_K	325_G	1.400	1.00
240_M	244_A	1.397	1.00
234_R	259_D	1.392	1.00
221_H	249_T	1.388	1.00
177_R	181_L	1.382	1.00
222_L	254_V	1.379	1.00
120_E	181_L	1.370	1.00
116_Q	162_T	1.366	1.00
188_K	214_D	1.345	1.00
261_L	265_K	1.344	1.00
322_K	330_N	1.335	1.00
236_Y	239_L	1.331	1.00
188_K	204_E	1.322	1.00
318_K	322_K	1.274	1.00
211_V	215_S	1.271	1.00
314_T	318_K	1.264	1.00
116_Q	177_R	1.260	1.00
138_Q	141_K	1.256	1.00
229_L	253_V	1.236	1.00
53_I	78_S	1.235	1.00
60_N	81_E	1.234	1.00
203_Y	206_A	1.225	1.00
73_D	99_A	1.218	1.00
220_V	246_F	1.212	1.00
190_K	206_A	1.212	1.00
114_N	303_G	1.208	1.00
61_A	84_F	1.203	1.00
76_F	100_A	1.202	1.00
138_Q	142_D	1.200	1.00
209_K	235_Q	1.198	1.00
250_S	254_V	1.197	1.00
180_K	186_D	1.196	1.00
127_I	185_F	1.194	1.00
168_M	179_A	1.192	1.00
178_I	219_S	1.184	1.00
129_F	245_I	1.182	1.00
169_I	232_I	1.181	1.00
121_M	125_N	1.180	1.00
169_I	222_L	1.167	1.00
277_F	297_A	1.158	1.00
122_F	249_T	1.156	1.00
282_P	287_Y	1.154	1.00
84_F	323_W	1.152	1.00
219_S	249_T	1.152	1.00
129_F	296_L	1.150	1.00
72_T	75_V	1.145	1.00
231_L	254_V	1.145	1.00
323_W	329_L	1.140	1.00
56_L	79_V	1.139	1.00
237_F	246_F	1.134	1.00
241_K	244_A	1.131	1.00
243_S	268_K	1.130	1.00
98_A	102_K	1.129	1.00
171_F	176_Q	1.128	1.00
119_A	181_L	1.122	1.00
169_I	231_L	1.121	1.00
95_V	100_A	1.119	1.00
99_A	103_R	1.118	1.00
217_I	245_I	1.112	1.00
124_G	127_I	1.108	1.00
87_V	95_V	1.107	1.00
139_W	144_E	1.103	1.00
235_Q	238_D	1.092	1.00
129_F	273_I	1.091	1.00
49_E	53_I	1.090	1.00
283_E	286_D	1.085	1.00
134_S	137_N	1.077	1.00
218_V	240_M	1.068	1.00
169_I	218_V	1.066	1.00
190_K	215_S	1.058	1.00
165_T	214_D	1.055	1.00
258_E	288_E	1.053	1.00
121_M	298_T	1.051	1.00
265_K	291_S	1.047	1.00
143_G	291_S	1.047	1.00
315_I	331_I	1.046	1.00
264_L	295_V	1.044	1.00
233_D	259_D	1.042	1.00
77_A	99_A	1.040	1.00
86_G	319_A	1.034	1.00
51_E	54_Q	1.034	1.00
257_R	279_H	1.032	1.00
126_V	166_V	1.028	1.00
206_A	210_T	1.020	1.00
116_Q	181_L	1.015	1.00
98_A	101_S	1.015	1.00
318_K	330_N	1.009	1.00
193_D	197_Q	1.001	1.00
194_P	227_E	0.999	1.00
208_L	236_Y	0.990	1.00
204_E	214_D	0.988	1.00
169_I	208_L	0.986	1.00
208_L	212_F	0.985	1.00
76_F	85_V	0.979	1.00
106_P	329_L	0.977	1.00
125_N	296_L	0.970	1.00
31_L	321_K	0.964	1.00
126_V	182_L	0.964	1.00
257_R	287_Y	0.956	1.00
279_H	283_E	0.954	1.00
97_V	101_S	0.949	1.00
121_M	273_I	0.947	1.00
206_A	211_V	0.946	1.00
310_D	314_T	0.943	1.00
223_P	228_T	0.939	1.00
263_V	268_K	0.938	1.00
87_V	94_N	0.929	1.00
237_F	268_K	0.927	1.00
233_D	256_N	0.926	1.00
180_K	183_T	0.920	1.00
261_L	288_E	0.919	1.00
86_G	108_F	0.918	1.00
123_I	181_L	0.918	1.00
222_L	231_L	0.912	1.00
176_Q	197_Q	0.910	1.00
54_Q	57_K	0.908	1.00
96_D	99_A	0.906	1.00
199_D	202_L	0.893	1.00
169_I	220_V	0.890	1.00
117_A	160_E	0.887	1.00
215_S	218_V	0.887	1.00
138_Q	293_P	0.885	1.00
232_I	246_F	0.883	1.00
130_L	159_N	0.883	1.00
86_G	316_L	0.882	1.00
237_F	240_M	0.875	1.00
263_V	269_I	0.872	1.00
128_S	133_T	0.859	1.00
168_M	178_I	0.856	1.00
128_S	296_L	0.852	1.00
160_E	305_T	0.851	1.00
178_I	182_L	0.850	1.00
166_V	219_S	0.849	1.00
198_D	202_L	0.848	1.00
118_V	302_A	0.846	1.00
161_L	187_C	0.843	1.00
196_I	201_P	0.841	1.00
27_E	314_T	0.840	1.00
162_T	186_D	0.840	1.00
220_V	232_I	0.834	1.00
53_I	75_V	0.833	1.00
176_Q	200_H	0.832	1.00
130_L	245_I	0.832	1.00
123_I	178_I	0.829	1.00
57_K	78_S	0.828	1.00
61_A	320_L	0.827	1.00
243_S	270_S	0.825	1.00
218_V	244_A	0.823	1.00
187_C	217_I	0.819	1.00
212_F	218_V	0.819	1.00
89_R	94_N	0.818	1.00
84_F	320_L	0.818	1.00
130_L	164_K	0.818	1.00
198_D	201_P	0.816	1.00
95_V	107_V	0.814	1.00
260_L	269_I	0.811	1.00
319_A	322_K	0.807	1.00
116_Q	160_E	0.805	1.00
115_A	177_R	0.805	1.00
264_L	294_N	0.802	1.00
258_E	262_F	0.798	1.00
262_F	265_K	0.798	1.00
257_R	289_L	0.792	1.00
255_V	260_L	0.792	1.00
123_I	126_V	0.790	1.00
51_E	55_L	0.786	1.00
171_F	179_A	0.785	1.00
134_S	138_Q	0.784	1.00
74_S	77_A	0.782	1.00
85_V	100_A	0.778	1.00
27_E	321_K	0.777	1.00
224_R	228_T	0.771	1.00
238_D	266_E	0.761	1.00
122_F	221_H	0.759	1.00
271_G	296_L	0.756	1.00
179_A	189_I	0.755	1.00
61_A	324_K	0.754	1.00
272_A	295_V	0.753	1.00
258_E	278_Y	0.750	1.00
165_T	215_S	0.748	1.00
27_E	31_L	0.743	1.00
62_T	71_V	0.743	1.00
116_Q	120_E	0.742	1.00
181_L	185_F	0.738	1.00
159_N	307_E	0.734	1.00
192_Y	208_L	0.733	1.00
279_H	282_P	0.733	1.00
191_Y	205_K	0.731	1.00
136_S	301_L	0.731	1.00
124_G	128_S	0.730	1.00
73_D	103_R	0.729	1.00
282_P	290_I	0.729	1.00
122_F	219_S	0.722	1.00
120_E	131_R	0.721	1.00
73_D	96_D	0.720	1.00
28_L	32_F	0.720	1.00
274_L	295_V	0.719	1.00
260_L	274_L	0.719	1.00
115_A	173_A	0.718	1.00
140_L	290_I	0.718	1.00
197_Q	200_H	0.717	1.00
130_L	134_S	0.717	1.00
159_N	243_S	0.716	1.00
50_D	54_Q	0.713	1.00
243_S	269_I	0.712	1.00
112_G	173_A	0.711	1.00
159_N	306_F	0.707	1.00
212_F	239_L	0.701	1.00
277_F	282_P	0.697	1.00
234_R	268_K	0.693	1.00
117_A	308_V	0.692	1.00
126_V	178_I	0.691	1.00
126_V	161_L	0.689	1.00
210_T	213_S	0.689	1.00
209_K	213_S	0.687	1.00
27_E	30_N	0.686	1.00
193_D	196_I	0.682	1.00
48_R	52_L	0.677	1.00
208_L	231_L	0.677	1.00
110_T	315_I	0.674	1.00
229_L	278_Y	0.671	1.00
110_T	312_H	0.670	1.00
126_V	247_V	0.668	1.00
167_G	192_Y	0.668	1.00
311_H	314_T	0.668	1.00
245_I	273_I	0.667	1.00
196_I	205_K	0.666	1.00
165_T	241_K	0.665	1.00
255_V	272_A	0.664	1.00
117_A	305_T	0.661	1.00
197_Q	202_L	0.660	1.00
122_F	125_N	0.660	1.00
27_E	318_K	0.657	1.00
113_R	303_G	0.655	1.00
318_K	321_K	0.654	1.00
112_G	315_I	0.653	1.00
86_G	320_L	0.653	1.00
283_E	287_Y	0.650	1.00
32_F	321_K	0.649	1.00
220_V	250_S	0.648	1.00
306_F	310_D	0.647	1.00
222_L	250_S	0.644	1.00
290_I	297_A	0.642	1.00
164_K	217_I	0.642	1.00
87_V	92_P	0.641	1.00
56_L	62_T	0.641	1.00
53_I	74_S	0.640	1.00
162_T	311_H	0.638	1.00
273_I	296_L	0.636	1.00
230_G	233_D	0.633	1.00
79_V	82_L	0.632	1.00
92_P	97_V	0.632	1.00
117_A	120_E	0.629	1.00
29_E	32_F	0.625	1.00
137_N	297_A	0.624	1.00
262_F	268_K	0.624	1.00
329_L	332_Q	0.624	1.00
161_L	185_F	0.623	1.00
190_K	211_V	0.622	1.00
183_T	189_I	0.620	1.00
218_V	241_K	0.617	1.00
76_F	105_I	0.616	1.00
212_F	240_M	0.615	1.00
176_Q	180_K	0.614	1.00
121_M	124_G	0.612	1.00
322_K	329_L	0.611	1.00
206_A	214_D	0.611	1.00
287_Y	291_S	0.611	1.00
191_Y	203_Y	0.611	1.00
53_I	79_V	0.609	1.00
137_N	140_L	0.608	1.00
130_L	187_C	0.608	1.00
166_V	178_I	0.607	1.00
119_A	177_R	0.605	1.00
322_K	328_T	0.605	1.00
243_S	266_E	0.601	1.00
225_T	228_T	0.596	1.00
93_S	224_R	0.596	1.00
80_P	103_R	0.593	1.00
317_N	321_K	0.592	1.00
121_M	131_R	0.591	1.00
304_A	309_E	0.588	1.00
74_S	78_S	0.588	1.00
83_S	323_W	0.587	1.00
125_N	128_S	0.586	1.00
61_A	86_G	0.585	1.00
265_K	293_P	0.585	1.00
113_R	312_H	0.581	1.00
234_R	266_E	0.581	1.00
136_S	299_P	0.580	1.00
58_A	80_P	0.579	1.00
140_L	277_F	0.578	1.00
92_P	109_Y	0.575	1.00
165_T	216_D	0.573	1.00
139_W	142_D	0.572	1.00
230_G	253_V	0.572	1.00
190_K	205_K	0.572	1.00
181_L	184_A	0.572	1.00
55_L	59_T	0.571	1.00
125_N	129_F	0.570	1.00
57_K	80_P	0.569	1.00
164_K	187_C	0.569	1.00
50_D	74_S	0.568	1.00
218_V	246_F	0.567	1.00
118_V	122_F	0.564	1.00
88_C	312_H	0.561	1.00
328_T	332_Q	0.558	1.00
71_V	76_F	0.558	1.00
253_V	278_Y	0.558	1.00
116_Q	186_D	0.558	1.00
112_G	115_A	0.557	1.00
27_E	317_N	0.553	1.00
86_G	110_T	0.552	1.00
263_V	266_E	0.551	1.00
261_L	295_V	0.550	1.00
184_A	187_C	0.549	1.00
171_F	175_G	0.548	1.00
218_V	232_I	0.548	1.00
197_Q	201_P	0.547	1.00
265_K	294_N	0.547	1.00
134_S	296_L	0.546	1.00
31_L	325_G	0.545	1.00
114_N	117_A	0.543	1.00
28_L	31_L	0.540	1.00
126_V	219_S	0.535	1.00
140_L	297_A	0.533	1.00
258_E	287_Y	0.532	1.00
264_L	292_L	0.532	1.00
234_R	263_V	0.528	1.00
244_A	268_K	0.526	1.00
208_L	232_I	0.526	1.00
279_H	287_Y	0.525	1.00
188_K	203_Y	0.525	1.00
257_R	261_L	0.525	1.00
314_T	317_N	0.524	1.00
180_K	184_A	0.524	1.00
123_I	166_V	0.521	1.00
212_F	231_L	0.521	1.00
194_P	197_Q	0.521	1.00
160_E	307_E	0.518	1.00
171_F	193_D	0.516	1.00
108_F	319_A	0.516	1.00
113_R	315_I	0.512	1.00
222_L	228_T	0.512	1.00
316_L	319_A	0.512	1.00
135_A	139_W	0.509	1.00
251_R	300_H	0.509	1.00
287_Y	290_I	0.508	1.00
141_K	291_S	0.506	1.00
84_F	106_P	0.506	1.00
103_R	106_P	0.500	1.00
169_I	211_V	0.500	1.00
53_I	57_K	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
1sc6A	4	0.907	100	0.236	Contact Map
3k5pA	3	0.9273	100	0.237	Contact Map
3ba1A	2	0.907	100	0.248	Contact Map
2g76A	2	0.8692	100	0.252	Contact Map
4g2nA	3	0.9157	100	0.252	Contact Map
4lswA	2	0.9157	100	0.254	Contact Map
1ygyA	4	0.9273	100	0.254	Contact Map
2d0iA	2	0.939	100	0.257	Contact Map
2w2kA	2	0.936	100	0.262	Contact Map
2gcgA	2	0.9273	100	0.265	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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