TYRA - BACSU - GREMLIN Contacts

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TYRA - Prephenate dehydrogenase

UniProt:	P20692	Sequences: MNQMKDTILLAGLGLIGGSIALAIKKNHPGKRIIGIDISDEQAVAALKLGVIDDRADSFISGVKEAATVIIATPVEQTLVMLEELAHSGIEHELLITDVGSTKQKVVDYADQVLPSRYQFVGGHPMAGSHKSGVAAAKEFLFENAFYILTPGQKTDKQAVEQLKNLLKGTNAHFVEMSPEEHDGVTSVISHFPHIVAASLVHQTHHSENLYPLVKRFAAGGFRDITRIASSSPAMWRDILLHNKDKILDRFDEWIREIDKIRTYVEQEDAENLFRYFKTAKDYRDGLPLRQKGAIPAFYDLYVDVPDHPGVISEITAILAAERISITNIRIIETREDINGILRISFQSDDDRKRAEQCIEARAEYETFYAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	371 (287)
Sequences:	2112 (1487)
Seq/√Len:	87.8

BACSU - TYRA
HALSA - Q9HQB8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
252_D	262_R	4.339	1.00
32_R	54_D	4.112	1.00
45_A	135_A	3.746	1.00
255_I	259_D	3.445	1.00
281_K	285_D	3.369	1.00
97_T	123_G	3.167	1.00
22_L	137_A	2.981	1.00
7_T	32_R	2.967	1.00
255_I	262_R	2.826	1.00
252_D	266_E	2.627	1.00
164_K	176_E	2.607	1.00
20_I	170_T	2.490	1.00
23_A	170_T	2.373	1.00
164_K	168_K	2.350	1.00
244_K	268_E	2.313	1.00
121_V	163_L	2.308	1.00
264_Y	272_N	2.275	1.00
269_D	272_N	2.271	1.00
25_K	53_D	2.262	1.00
230_S	285_D	2.224	1.00
192_F	247_I	2.199	1.00
155_T	160_V	2.144	1.00
248_L	266_E	1.960	1.00
7_T	34_I	1.958	1.00
126_M	186_T	1.954	1.00
40_D	44_V	1.951	1.00
110_A	120_F	1.936	1.00
129_S	138_K	1.934	1.00
8_I	24_I	1.923	1.00
51_V	134_V	1.916	1.00
35_G	52_I	1.910	1.00
148_I	177_M	1.896	1.00
197_A	229_A	1.885	1.00
52_I	55_R	1.882	1.00
82_L	110_A	1.855	1.00
240_L	247_I	1.847	1.00
73_T	81_M	1.833	1.00
75_V	102_T	1.826	1.00
123_G	149_L	1.816	1.00
37_D	42_Q	1.802	1.00
178_S	181_E	1.799	1.00
71_I	82_L	1.782	1.00
9_L	66_A	1.779	1.00
13_L	35_G	1.763	1.00
58_S	61_S	1.751	1.00
43_A	55_R	1.749	1.00
7_T	65_E	1.747	1.00
49_L	134_V	1.733	1.00
26_K	139_E	1.721	1.00
44_V	48_K	1.699	1.00
71_I	81_M	1.692	1.00
45_A	48_K	1.686	1.00
91_E	94_L	1.683	1.00
195_I	261_I	1.658	1.00
21_A	51_V	1.642	1.00
70_I	97_T	1.627	1.00
104_Q	108_D	1.623	1.00
251_F	258_I	1.619	1.00
24_I	166_L	1.549	1.00
184_G	249_D	1.539	1.00
78_T	100_G	1.537	1.00
275_R	279_T	1.512	1.00
43_A	52_I	1.509	1.00
104_Q	180_E	1.496	1.00
80_V	84_E	1.459	0.99
18_G	137_A	1.448	0.99
200_L	225_I	1.446	0.99
262_R	266_E	1.441	0.99
107_V	179_P	1.431	0.99
20_I	70_I	1.421	0.99
79_L	112_Q	1.420	0.99
240_L	277_F	1.415	0.99
237_R	270_A	1.398	0.99
165_N	168_K	1.389	0.99
71_I	78_T	1.380	0.99
230_S	281_K	1.370	0.99
20_I	166_L	1.350	0.99
195_I	240_L	1.338	0.99
79_L	109_Y	1.335	0.99
97_T	163_L	1.316	0.99
196_V	254_W	1.297	0.99
43_A	57_D	1.281	0.99
234_A	274_F	1.275	0.98
274_F	278_K	1.275	0.98
189_I	220_G	1.268	0.98
161_E	164_K	1.265	0.98
248_L	262_R	1.264	0.98
34_I	65_E	1.257	0.98
181_E	213_L	1.252	0.98
105_K	242_H	1.236	0.98
63_V	85_L	1.235	0.98
95_L	159_A	1.231	0.98
252_D	255_I	1.230	0.98
111_D	154_K	1.227	0.98
67_A	91_E	1.217	0.98
107_V	122_G	1.216	0.98
203_Q	257_E	1.215	0.98
237_R	274_F	1.203	0.98
73_T	77_Q	1.200	0.98
16_I	99_V	1.187	0.98
123_G	147_Y	1.185	0.98
132_S	277_F	1.183	0.97
107_V	152_G	1.182	0.97
79_L	83_E	1.181	0.97
175_V	217_F	1.178	0.97
70_I	99_V	1.177	0.97
83_E	109_Y	1.172	0.97
65_E	91_E	1.170	0.97
26_K	143_E	1.162	0.97
45_A	49_L	1.137	0.97
186_T	189_I	1.134	0.97
140_F	143_E	1.133	0.97
109_Y	112_Q	1.125	0.97
147_Y	167_L	1.125	0.97
34_I	54_D	1.114	0.96
68_T	166_L	1.113	0.96
177_M	213_L	1.112	0.96
231_S	277_F	1.111	0.96
9_L	36_I	1.109	0.96
101_S	239_I	1.103	0.96
93_E	118_Y	1.103	0.96
11_A	85_L	1.103	0.96
8_I	68_T	1.100	0.96
157_K	161_E	1.099	0.96
221_G	228_I	1.091	0.96
11_A	81_M	1.087	0.96
95_L	162_Q	1.086	0.96
16_I	142_F	1.085	0.96
263_T	267_Q	1.076	0.96
167_L	174_F	1.070	0.95
63_V	69_V	1.066	0.95
107_V	120_F	1.065	0.95
42_Q	134_V	1.065	0.95
39_S	42_Q	1.064	0.95
63_V	66_A	1.062	0.95
25_K	33_I	1.058	0.95
6_D	31_K	1.048	0.95
47_L	55_R	1.044	0.95
77_Q	80_V	1.044	0.95
11_A	36_I	1.039	0.95
22_L	49_L	1.039	0.95
126_M	167_L	1.026	0.94
24_I	29_P	1.025	0.94
147_Y	172_A	1.023	0.94
221_G	225_I	1.022	0.94
23_A	139_E	1.021	0.94
241_L	270_A	1.019	0.94
102_T	105_K	1.015	0.94
18_G	22_L	1.015	0.94
194_H	228_I	1.012	0.94
231_S	236_W	1.012	0.94
99_V	142_F	1.011	0.94
93_E	119_Q	1.006	0.94
44_V	47_L	1.002	0.94
75_V	100_G	1.000	0.93
38_I	73_T	0.999	0.93
108_D	112_Q	0.998	0.93
194_H	236_W	0.997	0.93
121_V	155_T	0.992	0.93
156_D	159_A	0.990	0.93
87_H	90_I	0.987	0.93
272_N	275_R	0.985	0.93
152_G	155_T	0.984	0.93
82_L	86_A	0.984	0.93
236_W	239_I	0.983	0.93
119_Q	156_D	0.974	0.93
202_H	279_T	0.971	0.92
278_K	282_D	0.963	0.92
56_A	62_G	0.962	0.92
13_L	37_D	0.953	0.92
10_L	21_A	0.953	0.92
52_I	56_A	0.949	0.92
161_E	168_K	0.945	0.91
13_L	42_Q	0.945	0.91
90_I	96_I	0.940	0.91
115_P	118_Y	0.935	0.91
206_H	257_E	0.914	0.90
126_M	220_G	0.909	0.90
187_S	246_K	0.907	0.90
59_F	85_L	0.905	0.90
228_I	236_W	0.905	0.90
10_L	17_G	0.903	0.89
46_A	52_I	0.903	0.89
198_A	261_I	0.890	0.89
101_S	191_H	0.888	0.89
195_I	251_F	0.887	0.89
34_I	56_A	0.881	0.88
275_R	278_K	0.865	0.87
83_E	87_H	0.861	0.87
47_L	54_D	0.859	0.87
244_K	248_L	0.858	0.87
106_V	120_F	0.856	0.87
111_D	117_R	0.855	0.87
261_I	276_Y	0.854	0.87
221_G	231_S	0.853	0.87
225_I	230_S	0.851	0.86
76_E	238_D	0.850	0.86
166_L	170_T	0.850	0.86
263_T	266_E	0.848	0.86
202_H	276_Y	0.841	0.86
21_A	35_G	0.839	0.86
157_K	176_E	0.838	0.86
163_L	167_L	0.838	0.86
11_A	59_F	0.832	0.85
69_V	94_L	0.829	0.85
96_I	114_L	0.828	0.85
150_T	179_P	0.827	0.85
41_E	44_V	0.825	0.85
6_D	162_Q	0.820	0.84
23_A	140_F	0.818	0.84
60_I	84_E	0.816	0.84
111_D	152_G	0.814	0.84
202_H	280_A	0.811	0.84
256_R	263_T	0.810	0.84
10_L	72_A	0.810	0.84
188_V	250_R	0.809	0.84
9_L	62_G	0.809	0.84
177_M	185_V	0.807	0.83
95_L	163_L	0.804	0.83
126_M	147_Y	0.792	0.82
8_I	30_G	0.790	0.82
248_L	255_I	0.787	0.82
108_D	111_D	0.783	0.82
21_A	33_I	0.779	0.81
171_N	187_S	0.776	0.81
188_V	204_T	0.776	0.81
204_T	232_S	0.773	0.81
145_A	220_G	0.772	0.81
13_L	134_V	0.772	0.81
114_L	117_R	0.771	0.81
29_P	166_L	0.769	0.80
188_V	207_S	0.765	0.80
13_L	46_A	0.764	0.80
185_V	217_F	0.762	0.80
109_Y	113_V	0.759	0.80
271_E	275_R	0.758	0.79
28_H	31_K	0.757	0.79
218_A	287_L	0.757	0.79
192_F	250_R	0.754	0.79
186_T	217_F	0.750	0.79
196_V	200_L	0.748	0.79
257_E	260_K	0.747	0.78
122_G	145_A	0.747	0.78
148_I	217_F	0.744	0.78
220_G	228_I	0.743	0.78
201_V	219_A	0.736	0.77
153_Q	178_S	0.733	0.77
111_D	153_Q	0.733	0.77
126_M	198_A	0.728	0.77
104_Q	179_P	0.725	0.76
126_M	189_I	0.722	0.76
22_L	51_V	0.722	0.76
215_K	283_Y	0.721	0.76
195_I	247_I	0.720	0.76
132_S	136_A	0.719	0.76
217_F	288_P	0.719	0.76
259_D	263_T	0.717	0.76
191_H	239_I	0.717	0.76
223_R	237_R	0.716	0.75
96_I	110_A	0.707	0.75
161_E	165_N	0.705	0.74
36_I	56_A	0.704	0.74
73_T	78_T	0.704	0.74
20_I	24_I	0.701	0.74
9_L	63_V	0.701	0.74
228_I	239_I	0.694	0.73
126_M	225_I	0.690	0.73
68_T	163_L	0.688	0.73
75_V	235_M	0.683	0.72
130_H	171_N	0.683	0.72
102_T	265_V	0.681	0.72
69_V	92_H	0.680	0.72
60_I	64_K	0.680	0.72
21_A	194_H	0.680	0.72
146_F	230_S	0.675	0.71
15_L	191_H	0.674	0.71
249_D	266_E	0.673	0.71
254_W	258_I	0.672	0.71
264_Y	269_D	0.671	0.71
68_T	95_L	0.671	0.71
16_I	123_G	0.671	0.71
156_D	160_V	0.670	0.71
105_K	108_D	0.668	0.70
188_V	197_A	0.668	0.70
132_S	232_S	0.666	0.70
165_N	169_G	0.662	0.70
153_Q	162_Q	0.660	0.69
26_K	165_N	0.659	0.69
198_A	217_F	0.657	0.69
151_P	160_V	0.657	0.69
148_I	174_F	0.656	0.69
12_G	17_G	0.656	0.69
192_F	200_L	0.656	0.69
207_S	253_E	0.654	0.69
203_Q	250_R	0.654	0.69
224_D	229_A	0.651	0.68
100_G	235_M	0.648	0.68
56_A	61_S	0.648	0.68
121_V	160_V	0.647	0.68
48_K	135_A	0.646	0.68
97_T	219_A	0.644	0.67
47_L	52_I	0.643	0.67
203_Q	254_W	0.642	0.67
149_L	167_L	0.639	0.67
218_A	280_A	0.639	0.67
197_A	284_R	0.638	0.67
8_I	31_K	0.634	0.66
131_K	285_D	0.632	0.66
252_D	259_D	0.631	0.66
230_S	288_P	0.629	0.66
13_L	52_I	0.628	0.66
160_V	164_K	0.622	0.65
244_K	266_E	0.622	0.65
251_F	262_R	0.622	0.65
113_V	117_R	0.619	0.64
81_M	85_L	0.618	0.64
190_S	224_D	0.618	0.64
162_Q	165_N	0.616	0.64
75_V	242_H	0.615	0.64
159_A	166_L	0.615	0.64
122_G	186_T	0.612	0.64
70_I	166_L	0.610	0.63
206_H	249_D	0.608	0.63
40_D	57_D	0.607	0.63
110_A	117_R	0.605	0.63
22_L	35_G	0.604	0.63
175_V	213_L	0.603	0.62
22_L	134_V	0.600	0.62
130_H	192_F	0.599	0.62
18_G	21_A	0.599	0.62
148_I	186_T	0.598	0.62
158_Q	282_D	0.598	0.62
198_A	231_S	0.597	0.62
87_H	94_L	0.596	0.62
267_Q	270_A	0.595	0.61
20_I	68_T	0.594	0.61
76_E	242_H	0.593	0.61
61_S	64_K	0.592	0.61
84_E	89_G	0.591	0.61
99_V	234_A	0.587	0.60
159_A	162_Q	0.586	0.60
18_G	134_V	0.585	0.60
234_A	237_R	0.585	0.60
97_T	147_Y	0.584	0.60
234_A	265_V	0.579	0.59
228_I	231_S	0.578	0.59
22_L	26_K	0.578	0.59
108_D	180_E	0.578	0.59
121_V	167_L	0.577	0.59
253_E	260_K	0.576	0.59
196_V	199_S	0.573	0.59
221_G	229_A	0.573	0.59
222_F	284_R	0.571	0.58
122_G	147_Y	0.570	0.58
7_T	67_A	0.567	0.58
154_K	160_V	0.565	0.57
18_G	35_G	0.564	0.57
37_D	99_V	0.564	0.57
177_M	197_A	0.564	0.57
57_D	61_S	0.562	0.57
191_H	231_S	0.561	0.57
8_I	70_I	0.560	0.57
146_F	173_H	0.559	0.57
64_K	89_G	0.558	0.57
74_P	191_H	0.558	0.57
265_V	268_E	0.557	0.56
117_R	154_K	0.557	0.56
105_K	109_Y	0.557	0.56
134_V	137_A	0.555	0.56
58_S	84_E	0.555	0.56
231_S	281_K	0.555	0.56
248_L	252_D	0.555	0.56
21_A	49_L	0.555	0.56
20_I	99_V	0.554	0.56
219_A	236_W	0.550	0.55
245_D	266_E	0.547	0.55
231_S	239_I	0.547	0.55
86_A	115_P	0.545	0.55
15_L	190_S	0.544	0.55
19_S	141_L	0.544	0.55
78_T	106_V	0.543	0.55
205_H	279_T	0.543	0.55
82_L	113_V	0.541	0.54
122_G	152_G	0.541	0.54
30_G	33_I	0.541	0.54
85_L	90_I	0.540	0.54
192_F	254_W	0.540	0.54
74_P	239_I	0.539	0.54
167_L	186_T	0.538	0.54
80_V	83_E	0.538	0.54
132_S	235_M	0.538	0.54
191_H	224_D	0.537	0.54
194_H	231_S	0.537	0.54
198_A	276_Y	0.536	0.54
158_Q	249_D	0.535	0.53
129_S	137_A	0.532	0.53
187_S	250_R	0.531	0.53
276_Y	279_T	0.531	0.53
191_H	221_G	0.531	0.53
79_L	113_V	0.529	0.53
37_D	288_P	0.528	0.53
18_G	51_V	0.528	0.53
72_A	242_H	0.527	0.52
194_H	197_A	0.527	0.52
161_E	271_E	0.527	0.52
74_P	172_A	0.525	0.52
121_V	159_A	0.524	0.52
34_I	63_V	0.523	0.52
94_L	149_L	0.521	0.52
9_L	34_I	0.519	0.51
192_F	276_Y	0.517	0.51
251_F	265_V	0.516	0.51
74_P	101_S	0.516	0.51
79_L	105_K	0.514	0.51
37_D	52_I	0.514	0.51
44_V	55_R	0.513	0.50
230_S	240_L	0.511	0.50
244_K	265_V	0.511	0.50
127_A	141_L	0.511	0.50
198_A	265_V	0.511	0.50
146_F	225_I	0.511	0.50
141_L	193_P	0.509	0.50
10_L	73_T	0.506	0.50
82_L	123_G	0.504	0.49
22_L	25_K	0.503	0.49
189_I	204_T	0.502	0.49
189_I	213_L	0.501	0.49
147_Y	198_A	0.501	0.49
190_S	227_R	0.500	0.49
190_S	197_A	0.500	0.49

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
3ktdA	2	0.8383	100	0.487	Contact Map
3b1fA	2	0.7628	100	0.508	Contact Map
3ggoA	2	0.7601	100	0.539	Contact Map
4wjiA	2	0.7871	100	0.546	Contact Map
2g5cA	2	0.7493	100	0.548	Contact Map
2pv7A	2	0.7305	100	0.569	Contact Map
2f1kA	2	0.7466	100	0.574	Contact Map
1ygyA	4	0.9137	100	0.708	Contact Map
2izzA	5	0.7116	100	0.732	Contact Map
2b0jA	2	0.6846	100	0.737	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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