PDXS - HALSA - GREMLIN Contacts

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PDXS - Pyridoxal biosynthesis lyase PdxS

UniProt:	Q9HP57	Sequences: MATETDLEELRRGSELVKRGFAKMQKGGVIMDVVNREQARIAEDVGAVAVMNLEAVPADIRKRGGVARMADPASLTGIIEEVSIPVMGKSRIGHRKEAEILQAVGADMIDESEVLTPADDEYHIDKREFTAPFVCGARNLGEALRRIDEGAAMIRTKGEAGTGDVNQAVHHQRNIKSAIRKLEGMDYEERDMWARDHEAPRELVHETAEMGRLPVVNFAAGGIATPADAALMMHHGCDGIFVGSGIFGAENPEAMGRAVVDAVNNHDDPERLAEIASNIGEGMQGDPNADLPEDERMQDRGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	302 (290)
Sequences:	894 (253)
Seq/√Len:	14.9

BACSU - PDXS
HALSA - PDXS
SULSO - PDXS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
100_I	272_L	5.809	1.00
137_A	175_I	4.604	1.00
99_E	234_H	4.100	1.00
76_T	277_S	3.997	1.00
148_D	191_D	3.848	1.00
70_A	74_S	3.831	1.00
160_A	297_M	3.540	0.99
164_D	288_N	3.290	0.99
172_Q	237_C	3.176	0.99
216_V	239_G	3.170	0.98
125_D	128_E	3.123	0.98
250_E	284_Q	3.063	0.98
206_E	210_M	2.927	0.97
182_L	204_V	2.841	0.97
139_N	178_A	2.828	0.97
36_R	77_G	2.825	0.97
156_T	217_N	2.825	0.97
14_S	18_K	2.728	0.96
296_R	299_D	2.676	0.96
182_L	208_A	2.595	0.95
73_A	278_N	2.464	0.93
70_A	298_Q	2.443	0.93
44_D	253_E	2.441	0.93
15_E	19_R	2.390	0.92
272_L	275_I	2.343	0.91
164_D	287_P	2.280	0.90
35_N	77_G	2.231	0.89
191_D	201_R	2.151	0.87
73_A	277_S	2.144	0.87
193_W	197_H	2.138	0.87
21_F	25_Q	2.108	0.86
120_D	166_N	2.077	0.85
79_I	105_G	2.060	0.84
167_Q	170_H	1.939	0.80
271_R	275_I	1.937	0.80
172_Q	232_M	1.922	0.80
165_V	223_I	1.892	0.79
293_E	299_D	1.850	0.77
96_K	230_A	1.847	0.77
185_M	193_W	1.841	0.77
102_Q	130_T	1.838	0.77
250_E	281_E	1.837	0.77
240_I	263_V	1.832	0.76
164_D	167_Q	1.816	0.76
261_D	274_E	1.795	0.75
212_R	238_D	1.794	0.75
21_F	108_M	1.793	0.75
164_D	170_H	1.738	0.72
144_L	203_L	1.716	0.71
284_Q	287_P	1.709	0.71
270_E	274_E	1.693	0.70
223_I	263_V	1.682	0.70
13_G	17_V	1.663	0.69
148_D	201_R	1.646	0.68
79_I	106_A	1.640	0.68
216_V	237_C	1.627	0.67
95_R	234_H	1.624	0.67
59_D	248_G	1.541	0.63
73_A	77_G	1.536	0.63
120_D	164_D	1.532	0.62
182_L	193_W	1.524	0.62
95_R	99_E	1.520	0.62
261_D	265_N	1.512	0.61
20_G	24_M	1.499	0.61
71_D	279_I	1.497	0.61
207_T	210_M	1.474	0.59
25_Q	108_M	1.463	0.59
139_N	174_N	1.439	0.57
14_S	20_G	1.414	0.56
60_I	65_G	1.405	0.56
156_T	219_A	1.379	0.54
18_K	152_A	1.376	0.54
23_K	108_M	1.366	0.53
148_D	199_A	1.338	0.52
120_D	170_H	1.329	0.51
216_V	238_D	1.326	0.51
250_E	287_P	1.312	0.50
180_R	189_E	1.305	0.50
138_R	217_N	1.304	0.50
23_K	239_G	1.297	0.50
96_K	99_E	1.292	0.49
147_I	154_I	1.290	0.49
144_L	207_T	1.281	0.49
206_E	209_E	1.273	0.48
167_Q	288_N	1.267	0.48
121_E	177_S	1.257	0.47
139_N	198_E	1.243	0.47
174_N	178_A	1.229	0.46
273_A	277_S	1.225	0.46
255_M	281_E	1.224	0.45
15_E	152_A	1.224	0.45
254_A	278_N	1.223	0.45
148_D	200_P	1.219	0.45
13_G	18_K	1.208	0.45
176_K	180_R	1.208	0.45
199_A	204_V	1.189	0.44
187_Y	205_H	1.185	0.43
58_A	284_Q	1.182	0.43
125_D	137_A	1.181	0.43
216_V	219_A	1.181	0.43
201_R	205_H	1.177	0.43
189_E	195_R	1.155	0.42
24_M	264_N	1.154	0.42
189_E	199_A	1.144	0.41
40_R	43_E	1.142	0.41
19_R	152_A	1.140	0.41
219_A	237_C	1.132	0.40
100_I	227_A	1.131	0.40
138_R	156_T	1.127	0.40
174_N	298_Q	1.118	0.40
207_T	212_R	1.083	0.38
191_D	195_R	1.079	0.38
193_W	208_A	1.079	0.38
287_P	290_D	1.078	0.38
154_I	165_V	1.068	0.37
183_E	211_G	1.055	0.36
58_A	250_E	1.046	0.36
90_S	124_I	1.044	0.36
95_R	124_I	1.043	0.36
34_V	38_Q	1.042	0.36
17_V	20_G	1.034	0.35
138_R	231_L	1.008	0.34
249_A	252_P	1.003	0.34
58_A	62_K	1.000	0.34
13_G	19_R	1.000	0.34
67_A	167_Q	0.999	0.34
56_V	60_I	0.999	0.34
55_A	70_A	0.998	0.33
153_M	216_V	0.996	0.33
34_V	138_R	0.994	0.33
75_L	160_A	0.993	0.33
206_E	212_R	0.993	0.33
185_M	195_R	0.992	0.33
210_M	238_D	0.986	0.33
74_S	77_G	0.979	0.33
95_R	255_M	0.975	0.32
187_Y	208_A	0.975	0.32
14_S	17_V	0.975	0.32
178_A	185_M	0.973	0.32
104_V	273_A	0.968	0.32
164_D	286_D	0.967	0.32
60_I	67_A	0.963	0.32
76_T	80_E	0.962	0.32
63_R	70_A	0.961	0.32
40_R	44_D	0.958	0.31
73_A	76_T	0.955	0.31
23_K	216_V	0.952	0.31
44_D	83_S	0.951	0.31
96_K	234_H	0.943	0.31
208_A	212_R	0.935	0.30
211_G	268_D	0.934	0.30
137_A	154_I	0.934	0.30
16_L	19_R	0.931	0.30
20_G	106_A	0.918	0.30
166_N	173_R	0.918	0.30
265_N	268_D	0.913	0.29
250_E	286_D	0.910	0.29
20_G	38_Q	0.909	0.29
177_S	185_M	0.906	0.29
200_P	203_L	0.902	0.29
153_M	239_G	0.898	0.29
229_A	259_V	0.898	0.29
116_T	295_E	0.898	0.29
177_S	204_V	0.897	0.29
96_K	255_M	0.892	0.28
176_K	184_G	0.890	0.28
78_I	152_A	0.887	0.28
108_M	216_V	0.883	0.28
18_K	106_A	0.875	0.28
177_S	186_D	0.866	0.27
281_E	284_Q	0.865	0.27
251_N	295_E	0.864	0.27
192_M	198_E	0.864	0.27
232_M	273_A	0.860	0.27
98_A	124_I	0.860	0.27
96_K	272_L	0.859	0.27
36_R	74_S	0.857	0.27
128_E	187_Y	0.855	0.27
263_V	275_I	0.854	0.27
172_Q	176_K	0.850	0.27
124_I	129_F	0.847	0.26
95_R	129_F	0.846	0.26
182_L	207_T	0.846	0.26
294_D	299_D	0.845	0.26
71_D	275_I	0.843	0.26
54_E	60_I	0.843	0.26
15_E	25_Q	0.839	0.26
292_P	295_E	0.838	0.26
180_R	199_A	0.835	0.26
13_G	20_G	0.835	0.26
175_I	219_A	0.829	0.26
183_E	208_A	0.820	0.25
144_L	204_V	0.818	0.25
290_D	294_D	0.809	0.25
271_R	274_E	0.807	0.25
288_N	291_L	0.802	0.24
19_R	25_Q	0.801	0.24
74_S	298_Q	0.801	0.24
238_D	291_L	0.799	0.24
100_I	275_I	0.799	0.24
18_K	24_M	0.798	0.24
56_V	104_V	0.798	0.24
129_F	133_F	0.795	0.24
255_M	284_Q	0.794	0.24
36_R	104_V	0.791	0.24
204_V	208_A	0.789	0.24
182_L	185_M	0.788	0.24
144_L	199_A	0.786	0.24
295_E	299_D	0.785	0.24
67_A	116_T	0.785	0.24
276_A	279_I	0.784	0.24
96_K	238_D	0.784	0.24
19_R	127_R	0.780	0.24
34_V	156_T	0.770	0.23
234_H	266_H	0.762	0.23
23_K	76_T	0.760	0.23
75_L	298_Q	0.759	0.23
44_D	270_E	0.759	0.23
15_E	20_G	0.756	0.23
19_R	216_V	0.755	0.23
22_A	26_K	0.754	0.23
58_A	234_H	0.754	0.23
167_Q	289_A	0.753	0.23
184_G	188_E	0.751	0.22
162_T	165_V	0.746	0.22
63_R	298_Q	0.739	0.22
237_C	296_R	0.737	0.22
290_D	296_R	0.737	0.22
165_V	255_M	0.735	0.22
185_M	197_H	0.735	0.22
219_A	238_D	0.727	0.22
31_M	53_L	0.727	0.22
284_Q	289_A	0.726	0.21
192_M	199_A	0.726	0.21
31_M	51_M	0.725	0.21
160_A	175_I	0.725	0.21
240_I	253_E	0.722	0.21
193_W	237_C	0.721	0.21
274_E	277_S	0.717	0.21
182_L	190_R	0.710	0.21
66_V	162_T	0.706	0.21
219_A	233_M	0.705	0.21
212_R	261_D	0.703	0.21
261_D	275_I	0.702	0.21
181_K	184_G	0.700	0.21
138_R	219_A	0.699	0.20
79_I	265_N	0.692	0.20
52_N	60_I	0.691	0.20
40_R	83_S	0.690	0.20
181_K	197_H	0.688	0.20
34_V	70_A	0.686	0.20
79_I	104_V	0.684	0.20
34_V	217_N	0.684	0.20
55_A	60_I	0.682	0.20
90_S	273_A	0.681	0.20
180_R	211_G	0.680	0.20
27_G	30_I	0.676	0.20
164_D	290_D	0.675	0.20
44_D	265_N	0.674	0.20
48_V	264_N	0.672	0.20
185_M	212_R	0.670	0.19
185_M	208_A	0.667	0.19
99_E	269_P	0.663	0.19
90_S	138_R	0.662	0.19
15_E	18_K	0.661	0.19
99_E	124_I	0.659	0.19
122_Y	198_E	0.659	0.19
195_R	199_A	0.658	0.19
52_N	56_V	0.657	0.19
63_R	288_N	0.656	0.19
195_R	198_E	0.651	0.19
191_D	199_A	0.650	0.19
223_I	229_A	0.650	0.19
90_S	125_D	0.649	0.19
164_D	175_I	0.648	0.19
18_K	22_A	0.647	0.19
99_E	266_H	0.645	0.19
178_A	181_K	0.642	0.18
40_R	254_A	0.642	0.18
58_A	122_Y	0.641	0.18
14_S	131_A	0.641	0.18
67_A	164_D	0.641	0.18
70_A	75_L	0.638	0.18
29_V	229_A	0.636	0.18
144_L	200_P	0.636	0.18
77_G	295_E	0.634	0.18
182_L	197_H	0.633	0.18
135_C	276_A	0.632	0.18
198_E	265_N	0.632	0.18
250_E	278_N	0.628	0.18
83_S	288_N	0.625	0.18
17_V	24_M	0.625	0.18
233_M	238_D	0.622	0.18
19_R	239_G	0.621	0.18
204_V	211_G	0.620	0.18
223_I	230_A	0.620	0.18
165_V	232_M	0.620	0.18
169_V	231_L	0.619	0.18
66_V	116_T	0.615	0.18
105_G	270_E	0.614	0.18
174_N	200_P	0.614	0.18
193_W	204_V	0.612	0.17
63_R	160_A	0.612	0.17
54_E	135_C	0.610	0.17
60_I	282_G	0.610	0.17
204_V	289_A	0.609	0.17
81_E	90_S	0.608	0.17
76_T	206_E	0.608	0.17
120_D	200_P	0.608	0.17
138_R	160_A	0.607	0.17
191_D	198_E	0.605	0.17
38_Q	62_K	0.603	0.17
223_I	259_V	0.603	0.17
19_R	206_E	0.602	0.17
15_E	21_F	0.601	0.17
253_E	257_R	0.599	0.17
63_R	297_M	0.598	0.17
125_D	175_I	0.597	0.17
32_D	53_L	0.596	0.17
16_L	198_E	0.595	0.17
27_G	36_R	0.594	0.17
58_A	148_D	0.593	0.17
172_Q	175_I	0.592	0.17
277_S	294_D	0.591	0.17
176_K	210_M	0.590	0.17
223_I	289_A	0.587	0.17
297_M	300_R	0.584	0.17
186_D	191_D	0.578	0.16
82_V	118_A	0.577	0.16
288_N	296_R	0.577	0.16
120_D	203_L	0.576	0.16
172_Q	223_I	0.575	0.16
252_P	279_I	0.573	0.16
165_V	193_W	0.572	0.16
16_L	20_G	0.570	0.16
190_R	200_P	0.567	0.16
290_D	299_D	0.565	0.16
98_A	252_P	0.564	0.16
167_Q	290_D	0.564	0.16
156_T	175_I	0.563	0.16
58_A	223_I	0.562	0.16
69_M	231_L	0.562	0.16
29_V	230_A	0.560	0.16
90_S	109_I	0.559	0.16
288_N	297_M	0.559	0.16
96_K	278_N	0.555	0.16
20_G	152_A	0.555	0.16
248_G	281_E	0.554	0.16
169_V	219_A	0.554	0.16
25_Q	99_E	0.554	0.16
181_K	193_W	0.554	0.16
179_I	207_T	0.552	0.16
15_E	108_M	0.552	0.16
249_A	279_I	0.552	0.16
40_R	253_E	0.552	0.16
106_A	131_A	0.550	0.16
289_A	296_R	0.549	0.16
193_W	198_E	0.549	0.16
154_I	213_L	0.549	0.16
120_D	138_R	0.549	0.16
117_P	190_R	0.545	0.15
165_V	288_N	0.545	0.15
121_E	200_P	0.545	0.15
125_D	188_E	0.544	0.15
201_R	204_V	0.543	0.15
138_R	169_V	0.542	0.15
23_K	26_K	0.541	0.15
181_K	185_M	0.539	0.15
90_S	263_V	0.539	0.15
122_Y	188_E	0.537	0.15
175_I	232_M	0.537	0.15
12_R	19_R	0.537	0.15
13_G	216_V	0.536	0.15
174_N	203_L	0.535	0.15
71_D	280_G	0.535	0.15
175_I	237_C	0.533	0.15
29_V	223_I	0.533	0.15
35_N	193_W	0.533	0.15
17_V	37_E	0.532	0.15
79_I	109_I	0.528	0.15
175_I	266_H	0.527	0.15
104_V	137_A	0.527	0.15
173_R	198_E	0.527	0.15
16_L	108_M	0.526	0.15
250_E	253_E	0.526	0.15
173_R	199_A	0.525	0.15
17_V	127_R	0.525	0.15
291_L	299_D	0.524	0.15
63_R	79_I	0.524	0.15
29_V	259_V	0.524	0.15
234_H	269_P	0.523	0.15
69_M	131_A	0.523	0.15
74_S	104_V	0.522	0.15
167_Q	252_P	0.521	0.15
100_I	263_V	0.520	0.15
74_S	177_S	0.520	0.15
157_K	168_A	0.519	0.15
290_D	295_E	0.519	0.15
168_A	245_G	0.519	0.15
32_D	51_M	0.519	0.15
125_D	186_D	0.517	0.15
193_W	207_T	0.517	0.15
195_R	235_H	0.517	0.15
44_D	76_T	0.516	0.15
79_I	297_M	0.516	0.15
223_I	253_E	0.515	0.15
21_F	130_T	0.515	0.15
255_M	286_D	0.515	0.15
275_I	279_I	0.514	0.15
212_R	239_G	0.514	0.15
71_D	254_A	0.514	0.15
183_E	207_T	0.513	0.15
21_F	212_R	0.513	0.15
127_R	176_K	0.513	0.15
71_D	239_G	0.512	0.14
36_R	52_N	0.511	0.14
53_L	157_K	0.511	0.14
58_A	179_I	0.510	0.14
166_N	170_H	0.510	0.14
108_M	254_A	0.510	0.14
249_A	256_G	0.509	0.14
188_E	266_H	0.508	0.14
129_F	255_M	0.507	0.14
40_R	73_A	0.505	0.14
58_A	267_D	0.505	0.14
157_K	245_G	0.504	0.14
116_T	123_H	0.503	0.14
89_K	157_K	0.503	0.14
16_L	21_F	0.503	0.14
278_N	292_P	0.502	0.14
26_K	264_N	0.501	0.14
230_A	259_V	0.501	0.14
36_R	81_E	0.500	0.14
56_V	65_G	0.500	0.14
257_R	261_D	0.500	0.14

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
2yzrA	5	0.904	100	0.697	Contact Map
2nv1A	5	0.8576	100	0.769	Contact Map
2zbtA	5	0.9205	100	0.774	Contact Map
3o07A	3	0.8543	100	0.791	Contact Map
4adtA	5	0.904	100	0.796	Contact Map
4qccA	6	0.7318	99.6	0.898	Contact Map
2htmA	3	0.649	99.5	0.901	Contact Map
3qjaA	1	0.7517	99.5	0.903	Contact Map
1wv2A	3	0.6159	99.5	0.905	Contact Map
1xm3A	4	0.6788	99.5	0.906	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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