PDXS - SULSO - GREMLIN Contacts

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PDXS - Pyridoxal biosynthesis lyase PdxS

UniProt:	Q9UWX3	Sequences: MRLYELSFAQIEDFFYKLAEVKDIIKDHGLLEFLPEFKKLDSTVHTGTTRVKHAFPIFQKGGVVMDITNVQQAQIAEEAGAVAVMVLDKLPYDVRKSGGVARMADPKIIEEVMSSITIPVMAKVRIGHYYEAKLLEALGVDMIDESEVLTPADEEHHINKWEFSVPFVNGARNLGEALRRTSEGASMIRTKGEAGTGNVSEAVKHMKIINSEIRSLISMSEEDRVKKAREYQVPYQIVELTAKIKRLPIVNFAAGGIATPADAALMMWLGADGLFVGSGIFKSQDPDERAKAVVLAAACWEYPEIVLEAQKMISEQKSMMGIDIKSLKPEELLQVRGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	338 (291)
Sequences:	889 (231)
Seq/√Len:	13.5

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
134_L	306_V	5.867	1.00
171_A	209_I	4.663	1.00
133_K	268_W	4.140	1.00
110_E	311_K	3.999	1.00
182_S	225_V	3.825	0.99
104_A	108_I	3.765	0.99
194_A	333_L	3.486	0.99
206_M	271_A	3.303	0.98
198_N	324_I	3.161	0.98
173_N	212_E	3.097	0.98
250_V	273_G	3.086	0.97
284_Q	320_M	3.038	0.97
159_N	162_E	2.922	0.96
240_L	244_I	2.889	0.96
70_V	111_E	2.857	0.96
216_L	238_V	2.834	0.96
190_T	251_N	2.801	0.95
48_T	52_K	2.667	0.94
78_E	287_D	2.590	0.93
104_A	334_Q	2.588	0.93
332_L	335_V	2.568	0.93
216_L	242_A	2.532	0.92
198_N	323_D	2.385	0.90
49_T	53_H	2.329	0.88
306_V	309_A	2.308	0.88
107_K	312_M	2.306	0.88
69_N	111_E	2.299	0.88
113_M	139_G	2.159	0.84
227_K	231_Y	2.159	0.84
55_F	59_Q	2.117	0.83
225_V	235_Y	2.097	0.82
130_Y	264_A	2.058	0.81
107_K	311_K	1.964	0.78
206_M	266_M	1.941	0.77
305_I	309_A	1.937	0.77
284_Q	315_E	1.911	0.76
136_E	164_S	1.894	0.75
246_R	272_D	1.869	0.74
198_N	201_E	1.854	0.74
257_I	297_A	1.842	0.73
219_M	227_K	1.778	0.70
329_P	335_V	1.771	0.70
199_V	257_I	1.771	0.70
295_L	308_E	1.754	0.69
198_N	204_K	1.752	0.69
55_F	142_M	1.745	0.69
129_Y	268_W	1.732	0.68
201_E	204_K	1.730	0.68
178_L	237_I	1.688	0.66
250_V	271_A	1.685	0.66
182_S	235_Y	1.680	0.66
154_E	200_S	1.654	0.65
47_G	51_V	1.650	0.64
113_M	140_V	1.632	0.63
320_M	323_D	1.631	0.63
304_E	308_E	1.624	0.63
274_L	297_A	1.620	0.63
93_D	282_K	1.614	0.63
107_K	111_E	1.545	0.59
295_L	299_C	1.530	0.58
129_Y	133_K	1.516	0.58
173_N	208_I	1.502	0.57
105_D	313_I	1.480	0.56
54_A	58_F	1.464	0.55
250_V	272_D	1.425	0.53
59_Q	142_M	1.413	0.52
221_E	239_E	1.405	0.52
154_E	204_K	1.403	0.52
154_E	198_N	1.402	0.52
216_L	227_K	1.378	0.50
214_R	223_D	1.365	0.50
58_F	298_A	1.364	0.50
190_T	253_A	1.356	0.49
48_T	54_A	1.349	0.49
155_E	211_S	1.331	0.48
57_I	273_G	1.321	0.47
49_T	186_S	1.317	0.47
241_T	244_I	1.315	0.47
233_V	238_V	1.314	0.47
130_Y	133_K	1.310	0.47
240_L	243_K	1.308	0.47
94_V	99_G	1.306	0.46
181_T	188_I	1.291	0.46
172_R	251_N	1.281	0.45
284_Q	323_D	1.280	0.45
92_Y	320_M	1.278	0.45
52_K	186_S	1.276	0.45
53_H	186_S	1.265	0.44
57_I	142_M	1.265	0.44
208_I	212_E	1.249	0.43
201_E	324_I	1.237	0.43
288_E	312_M	1.224	0.42
307_L	311_K	1.219	0.42
235_Y	239_E	1.210	0.41
159_N	171_A	1.206	0.41
210_N	214_R	1.200	0.41
253_A	271_A	1.178	0.40
129_Y	158_I	1.167	0.39
182_S	233_V	1.167	0.39
173_N	232_Q	1.135	0.38
182_S	234_P	1.133	0.37
92_Y	96_K	1.133	0.37
101_A	201_E	1.122	0.37
172_R	190_T	1.121	0.37
250_V	253_A	1.121	0.37
178_L	241_T	1.121	0.37
241_T	246_R	1.119	0.37
323_D	326_S	1.118	0.37
208_I	334_Q	1.113	0.36
328_K	331_E	1.108	0.36
228_A	237_I	1.091	0.35
51_V	54_A	1.090	0.35
47_G	52_K	1.083	0.35
78_E	117_T	1.083	0.35
284_Q	322_I	1.082	0.35
227_K	242_A	1.076	0.35
172_R	265_L	1.070	0.34
244_I	272_D	1.070	0.34
74_Q	77_E	1.066	0.34
107_K	110_E	1.050	0.33
188_I	199_V	1.047	0.33
200_S	207_K	1.044	0.33
138_L	307_L	1.039	0.33
225_V	229_R	1.038	0.33
289_R	315_E	1.035	0.33
92_Y	284_Q	1.027	0.32
89_K	104_A	1.014	0.32
74_Q	78_E	1.004	0.31
57_I	250_V	1.002	0.31
171_A	188_I	0.999	0.31
330_E	335_V	0.996	0.31
217_I	245_K	0.989	0.31
211_S	238_V	0.988	0.31
211_S	219_M	0.985	0.30
68_T	72_Q	0.983	0.30
299_C	302_Y	0.983	0.30
105_D	314_S	0.979	0.30
129_Y	289_R	0.970	0.30
223_D	229_R	0.969	0.30
124_V	158_I	0.969	0.30
134_L	261_A	0.968	0.30
109_I	194_A	0.967	0.30
206_M	210_N	0.965	0.30
97_S	104_A	0.964	0.29
223_D	233_V	0.963	0.29
283_S	286_P	0.960	0.29
162_E	221_E	0.958	0.29
54_A	72_Q	0.946	0.29
90_L	94_V	0.940	0.28
54_A	140_V	0.939	0.28
108_I	111_E	0.937	0.28
52_K	140_V	0.926	0.28
53_H	59_Q	0.924	0.28
240_L	246_R	0.921	0.28
112_V	186_S	0.917	0.27
47_G	53_H	0.916	0.27
94_V	101_A	0.915	0.27
158_I	163_F	0.912	0.27
219_M	229_R	0.903	0.27
219_M	231_Y	0.901	0.27
272_D	327_L	0.897	0.27
198_N	322_I	0.896	0.27
142_M	250_V	0.895	0.27
266_M	307_L	0.894	0.26
214_R	233_V	0.892	0.26
134_L	309_A	0.885	0.26
263_A	293_V	0.879	0.26
90_L	138_L	0.877	0.26
187_M	250_V	0.874	0.26
245_K	302_Y	0.874	0.26
198_N	326_S	0.859	0.25
49_T	59_Q	0.858	0.25
216_L	241_T	0.857	0.25
132_A	158_I	0.852	0.25
212_E	215_S	0.851	0.25
305_I	308_E	0.851	0.25
211_S	220_S	0.847	0.25
150_T	331_E	0.843	0.24
68_T	172_R	0.839	0.24
48_T	51_V	0.839	0.24
56_P	60_K	0.832	0.24
210_N	218_S	0.830	0.24
215_S	218_S	0.827	0.24
196_T	199_V	0.823	0.24
156_H	232_Q	0.822	0.24
57_I	110_E	0.819	0.23
82_V	298_A	0.814	0.23
253_A	272_D	0.812	0.23
130_Y	306_V	0.809	0.23
101_A	150_T	0.807	0.23
289_R	320_M	0.803	0.23
268_W	300_W	0.802	0.23
110_E	114_S	0.799	0.23
97_S	194_A	0.796	0.23
70_V	138_L	0.791	0.22
322_I	328_K	0.789	0.22
50_R	53_H	0.789	0.22
331_E	335_V	0.787	0.22
209_I	253_A	0.786	0.22
97_S	334_Q	0.785	0.22
70_V	108_I	0.783	0.22
212_E	219_M	0.780	0.22
227_K	271_A	0.774	0.22
130_Y	268_W	0.774	0.22
315_E	320_M	0.773	0.22
47_G	54_A	0.772	0.22
324_I	333_L	0.772	0.22
221_E	242_A	0.771	0.22
88_D	94_V	0.767	0.22
68_T	190_T	0.767	0.22
108_I	334_Q	0.764	0.21
124_V	172_R	0.763	0.21
201_E	325_K	0.762	0.21
326_S	332_L	0.760	0.21
242_A	246_R	0.757	0.21
53_H	250_V	0.756	0.21
72_Q	96_K	0.752	0.21
297_A	309_A	0.748	0.21
117_T	324_I	0.748	0.21
133_K	303_P	0.748	0.21
68_T	104_A	0.747	0.21
97_S	333_L	0.743	0.21
109_I	334_Q	0.740	0.21
187_M	273_G	0.740	0.21
100_V	196_T	0.740	0.21
130_Y	289_R	0.739	0.21
101_A	198_N	0.739	0.21
104_A	109_I	0.738	0.21
199_V	289_R	0.738	0.21
92_Y	268_W	0.736	0.20
225_V	233_V	0.735	0.20
226_K	232_Q	0.733	0.20
214_R	245_K	0.729	0.20
234_P	237_I	0.728	0.20
217_I	242_A	0.727	0.20
227_K	238_V	0.724	0.20
203_V	265_L	0.719	0.20
285_D	331_E	0.717	0.20
232_Q	299_C	0.716	0.20
274_L	287_D	0.713	0.20
169_N	310_Q	0.712	0.20
284_Q	312_M	0.712	0.20
94_V	318_S	0.712	0.20
49_T	54_A	0.711	0.20
199_V	266_M	0.710	0.20
229_R	232_Q	0.709	0.20
53_H	161_W	0.708	0.19
218_S	222_E	0.707	0.19
133_K	300_W	0.705	0.19
52_K	58_F	0.704	0.19
113_M	138_L	0.703	0.19
59_Q	272_D	0.700	0.19
206_M	209_I	0.699	0.19
194_A	209_I	0.696	0.19
257_I	263_A	0.695	0.19
52_K	56_P	0.695	0.19
203_V	253_A	0.695	0.19
154_E	172_R	0.694	0.19
78_E	299_C	0.691	0.19
133_K	158_I	0.690	0.19
172_R	253_A	0.685	0.19
110_E	199_V	0.683	0.19
216_L	224_R	0.681	0.19
324_I	327_L	0.681	0.19
271_A	332_L	0.681	0.19
219_M	242_A	0.680	0.19
178_L	228_A	0.677	0.18
219_M	246_R	0.675	0.18
88_D	169_N	0.673	0.18
63_V	263_A	0.672	0.18
78_E	304_E	0.671	0.18
326_S	330_E	0.670	0.18
220_S	225_V	0.667	0.18
320_M	325_K	0.666	0.18
303_P	311_K	0.662	0.18
53_H	240_L	0.660	0.18
295_L	309_A	0.660	0.18
199_V	324_I	0.659	0.18
208_I	234_P	0.658	0.18
105_D	309_A	0.658	0.18
238_V	242_A	0.652	0.18
110_E	240_L	0.652	0.18
57_I	60_K	0.652	0.18
172_R	194_A	0.652	0.18
257_I	293_V	0.651	0.18
172_R	203_V	0.650	0.18
226_K	233_V	0.649	0.18
86_V	94_V	0.647	0.18
68_T	251_N	0.645	0.17
246_R	295_L	0.643	0.17
213_I	241_T	0.643	0.17
246_R	273_G	0.640	0.17
213_I	244_I	0.638	0.17
129_Y	163_F	0.638	0.17
61_G	64_V	0.637	0.17
285_D	314_S	0.637	0.17
209_I	271_A	0.636	0.17
284_Q	289_R	0.635	0.17
49_T	52_K	0.634	0.17
53_H	273_G	0.632	0.17
107_K	164_S	0.630	0.17
253_A	267_M	0.628	0.17
50_R	54_A	0.627	0.17
89_K	94_V	0.626	0.17
63_V	264_A	0.626	0.17
282_K	315_E	0.625	0.17
142_M	297_A	0.624	0.17
63_V	293_V	0.623	0.17
59_Q	133_K	0.623	0.17
60_K	298_A	0.622	0.17
215_S	227_K	0.620	0.17
224_R	234_P	0.619	0.17
49_T	55_F	0.611	0.16
51_V	58_F	0.611	0.16
113_M	299_C	0.610	0.16
130_Y	312_M	0.609	0.16
92_Y	156_H	0.609	0.16
222_E	300_W	0.602	0.16
257_I	264_A	0.601	0.16
111_E	331_E	0.601	0.16
105_D	285_D	0.598	0.16
216_L	231_Y	0.595	0.16
310_Q	314_S	0.593	0.16
96_K	113_M	0.592	0.16
225_V	232_Q	0.591	0.16
178_L	238_V	0.591	0.16
74_Q	288_E	0.590	0.16
217_I	271_A	0.589	0.16
207_K	223_D	0.588	0.16
97_S	108_I	0.588	0.16
86_V	90_L	0.587	0.16
103_M	265_L	0.587	0.16
82_V	323_D	0.586	0.16
139_G	304_E	0.586	0.16
56_P	298_A	0.585	0.16
156_H	220_S	0.585	0.16
274_L	324_I	0.584	0.16
182_S	220_S	0.583	0.16
263_A	271_A	0.582	0.16
55_F	164_S	0.580	0.16
198_N	209_I	0.578	0.16
48_T	165_V	0.577	0.15
267_M	272_D	0.576	0.15
326_S	335_V	0.576	0.15
201_E	286_P	0.575	0.15
285_D	288_E	0.575	0.15
297_A	306_V	0.574	0.15
46_T	53_H	0.573	0.15
108_I	138_L	0.571	0.15
113_M	198_N	0.570	0.15
113_M	143_I	0.568	0.15
208_I	237_I	0.566	0.15
156_H	200_S	0.562	0.15
227_K	241_T	0.561	0.15
236_Q	326_S	0.560	0.15
65_M	87_L	0.560	0.15
232_Q	238_V	0.559	0.15
113_M	142_M	0.558	0.15
90_L	124_V	0.557	0.15
74_Q	117_T	0.557	0.15
68_T	230_E	0.556	0.15
47_G	250_V	0.556	0.15
210_N	244_I	0.556	0.15
124_V	297_A	0.555	0.15
97_S	324_I	0.551	0.15
188_I	247_L	0.551	0.15
235_Y	238_V	0.548	0.15
154_E	325_K	0.547	0.15
286_P	313_I	0.546	0.15
264_A	293_V	0.545	0.15
100_V	150_T	0.545	0.15
207_K	233_V	0.545	0.15
173_N	233_V	0.544	0.15
92_Y	182_S	0.544	0.15
285_D	306_V	0.544	0.15
66_D	126_I	0.543	0.15
58_F	252_F	0.542	0.15
137_A	329_P	0.540	0.14
333_L	337_G	0.540	0.14
257_I	266_M	0.538	0.14
124_V	307_L	0.537	0.14
51_V	117_T	0.537	0.14
78_E	110_E	0.537	0.14
156_H	229_R	0.536	0.14
87_L	191_K	0.535	0.14
90_L	169_N	0.535	0.14
92_Y	257_I	0.535	0.14
190_T	209_I	0.534	0.14
140_V	165_V	0.531	0.14
124_V	143_I	0.529	0.14
47_G	59_Q	0.528	0.14
97_S	101_A	0.527	0.14
320_M	334_Q	0.527	0.14
325_K	332_L	0.527	0.14
312_M	328_K	0.526	0.14
202_A	279_G	0.524	0.14
155_E	204_K	0.523	0.14
123_K	191_K	0.522	0.14
224_R	242_A	0.522	0.14
209_I	300_W	0.519	0.14
198_N	333_L	0.517	0.14
50_R	232_Q	0.517	0.14
87_L	279_G	0.517	0.14
246_R	274_L	0.517	0.14
101_A	327_L	0.516	0.14
90_L	97_S	0.516	0.14
130_Y	272_D	0.516	0.14
287_D	291_K	0.514	0.14
101_A	204_K	0.513	0.14
65_M	85_M	0.513	0.14
257_I	322_I	0.513	0.14
199_V	227_K	0.512	0.14
201_E	326_S	0.511	0.14
114_S	161_W	0.511	0.14
58_F	299_C	0.511	0.14
200_S	265_L	0.510	0.14
216_L	219_M	0.509	0.14
221_E	243_K	0.509	0.14
178_L	213_I	0.509	0.14
97_S	109_I	0.509	0.14
163_F	167_F	0.509	0.14
217_I	241_T	0.509	0.14
207_K	232_Q	0.508	0.14
85_M	279_G	0.508	0.14
77_E	187_M	0.507	0.14
132_A	286_P	0.507	0.14
65_M	279_G	0.506	0.14
191_K	279_G	0.504	0.14
206_M	257_I	0.504	0.14
246_R	250_V	0.503	0.14
45_H	142_M	0.503	0.14
156_H	226_K	0.502	0.13
59_Q	229_R	0.502	0.13
182_S	232_Q	0.501	0.13
163_F	188_I	0.500	0.13
333_L	336_R	0.500	0.13

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	0.8077	100	0.721	Contact Map
2nv1A	5	0.7663	100	0.784	Contact Map
2zbtA	5	0.8225	100	0.789	Contact Map
3o07A	3	0.7633	100	0.806	Contact Map
4adtA	5	0.8077	100	0.81	Contact Map
4qccA	6	0.6538	99.6	0.906	Contact Map
2htmA	3	0.5799	99.5	0.909	Contact Map
3qjaA	1	0.7278	99.5	0.911	Contact Map
1wv2A	3	0.5503	99.5	0.911	Contact Map
1y0eA	2	0.574	99.4	0.913	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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