TRPA - SULSO - GREMLIN Contacts

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TRPA - Tryptophan synthase alpha chain

UniProt:	P50382	Sequences: MEMGKMLVVYMTLGYPNVQSFKDFIIGAVENGADILELGIPPKYAKYDGPVIRKSYDKVKGLDIWPLIEDIRKDVGVPIIALTYLEDWVDQLENFLNMIKDVKLDGILFPDLLIDYIDDLDKIDGIIKNKGLKNVIFTSPSVPDLLIHKVSKISDLFLYYGVRPTTGVPIPVSVKQLINRVRNLVENKLIVGFGLSSESDLRDALSAGADGIAIGTVFIEEIERNGVKSAINLVKKFRAILDEYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	245 (232)
Sequences:	3716 (2388)
Seq/√Len:	156.8

ECOLI - TRPA
BACSU - TRPA
HALSA - TRPA
SULSO - TRPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_N	20_S	3.814	1.00
26_I	74_D	3.617	1.00
15_Y	58_K	3.360	1.00
144_D	180_R	3.148	1.00
91_Q	98_M	3.073	1.00
54_K	223_E	2.911	1.00
128_K	155_D	2.843	1.00
72_R	105_D	2.793	1.00
22_K	70_D	2.614	1.00
190_I	211_G	2.445	1.00
12_T	56_Y	2.386	1.00
98_M	101_D	2.276	1.00
9_V	33_A	2.266	1.00
138_T	147_I	2.215	1.00
96_L	127_I	2.178	1.00
27_G	31_N	2.176	1.00
70_D	73_K	2.156	1.00
133_K	155_D	2.103	1.00
97_N	130_K	2.004	1.00
25_I	36_L	1.964	1.00
93_E	126_I	1.951	1.00
29_V	77_V	1.906	1.00
59_V	62_L	1.899	1.00
8_V	190_I	1.848	1.00
25_I	71_I	1.839	1.00
198_E	202_R	1.835	1.00
88_W	109_F	1.798	1.00
63_D	66_P	1.793	1.00
69_E	101_D	1.781	1.00
6_M	211_G	1.764	1.00
197_S	200_D	1.744	1.00
97_N	101_D	1.721	1.00
29_V	76_G	1.695	1.00
83_T	87_D	1.683	1.00
179_N	183_N	1.661	1.00
100_K	130_K	1.656	1.00
83_T	88_W	1.647	1.00
182_R	189_L	1.635	1.00
10_Y	56_Y	1.630	1.00
161_G	191_V	1.601	1.00
148_H	152_K	1.593	1.00
182_R	210_D	1.582	1.00
66_P	69_E	1.572	1.00
220_E	224_R	1.563	1.00
109_F	123_I	1.538	1.00
160_Y	189_L	1.534	1.00
31_N	235_K	1.523	1.00
69_E	98_M	1.521	1.00
93_E	129_N	1.521	1.00
191_V	204_A	1.508	1.00
94_N	97_N	1.489	1.00
24_F	222_I	1.484	1.00
27_G	30_E	1.478	1.00
25_I	79_I	1.472	1.00
127_I	134_N	1.466	1.00
98_M	102_V	1.449	1.00
85_L	112_L	1.427	1.00
148_H	184_L	1.413	1.00
35_I	80_I	1.409	1.00
124_D	128_K	1.402	1.00
22_K	26_I	1.397	1.00
232_N	236_K	1.393	1.00
99_I	132_L	1.391	1.00
94_N	98_M	1.381	1.00
142_V	147_I	1.371	1.00
233_L	236_K	1.356	1.00
233_L	238_R	1.352	1.00
23_D	26_I	1.350	1.00
233_L	237_F	1.348	1.00
147_I	181_V	1.346	1.00
190_I	213_A	1.343	1.00
191_V	209_A	1.340	1.00
15_Y	223_E	1.325	1.00
99_I	104_L	1.306	1.00
85_L	92_L	1.304	1.00
20_S	23_D	1.294	1.00
195_L	212_I	1.280	1.00
13_L	38_L	1.273	1.00
11_M	24_F	1.270	1.00
88_W	95_F	1.270	1.00
230_A	233_L	1.264	1.00
160_Y	177_L	1.262	1.00
65_W	99_I	1.256	1.00
40_I	81_A	1.246	1.00
225_N	233_L	1.245	1.00
118_D	125_G	1.237	1.00
117_I	136_I	1.231	1.00
66_P	70_D	1.220	1.00
229_S	233_L	1.217	1.00
18_V	22_K	1.211	1.00
196_S	220_E	1.207	1.00
80_I	135_V	1.188	1.00
149_K	152_K	1.185	1.00
195_L	204_A	1.185	1.00
125_G	129_N	1.153	1.00
154_S	187_N	1.152	1.00
30_E	235_K	1.141	1.00
96_L	126_I	1.140	1.00
18_V	63_D	1.140	1.00
82_L	108_L	1.128	1.00
15_Y	219_I	1.127	1.00
54_K	57_D	1.126	1.00
5_K	206_S	1.117	1.00
162_V	169_P	1.108	1.00
36_L	77_V	1.108	1.00
144_D	183_N	1.106	1.00
158_L	185_V	1.097	0.99
176_Q	179_N	1.096	0.99
175_K	179_N	1.096	0.99
85_L	123_I	1.085	0.99
220_E	223_E	1.084	0.99
100_K	131_G	1.078	0.99
144_D	184_L	1.072	0.99
91_Q	94_N	1.058	0.99
12_T	55_S	1.054	0.99
232_N	235_K	1.052	0.99
199_S	203_D	1.049	0.99
221_E	225_N	1.048	0.99
134_N	155_D	1.045	0.99
69_E	102_V	1.038	0.99
217_V	221_E	1.037	0.99
95_F	107_I	1.012	0.99
168_V	220_E	1.012	0.99
22_K	74_D	1.006	0.99
29_V	75_V	0.999	0.99
96_L	107_I	0.995	0.99
30_E	74_D	0.992	0.99
144_D	148_H	0.991	0.99
26_I	75_V	0.991	0.99
9_V	218_F	0.983	0.99
169_P	200_D	0.981	0.99
18_V	62_L	0.978	0.99
26_I	30_E	0.966	0.99
51_V	220_E	0.962	0.99
177_L	180_R	0.962	0.99
22_K	67_L	0.957	0.99
51_V	168_V	0.951	0.99
201_L	212_I	0.949	0.98
231_I	235_K	0.945	0.98
141_S	163_R	0.944	0.98
149_K	153_I	0.944	0.98
114_I	153_I	0.942	0.98
225_N	230_A	0.938	0.98
17_N	60_K	0.937	0.98
58_K	223_E	0.922	0.98
96_L	123_I	0.920	0.98
80_I	106_G	0.915	0.98
26_I	29_V	0.914	0.98
8_V	35_I	0.910	0.98
226_G	229_S	0.895	0.98
206_S	212_I	0.884	0.98
38_L	68_I	0.883	0.98
126_I	130_K	0.880	0.98
93_E	97_N	0.878	0.97
9_V	28_A	0.876	0.97
65_W	98_M	0.875	0.97
96_L	132_L	0.870	0.97
68_I	79_I	0.866	0.97
22_K	25_I	0.865	0.97
138_T	142_V	0.857	0.97
13_L	67_L	0.854	0.97
221_E	224_R	0.847	0.97
97_N	100_K	0.845	0.97
75_V	79_I	0.844	0.97
13_L	64_I	0.843	0.97
10_Y	39_G	0.841	0.97
18_V	21_F	0.837	0.97
231_I	238_R	0.827	0.96
196_S	200_D	0.825	0.96
118_D	153_I	0.823	0.96
151_S	184_L	0.822	0.96
20_S	24_F	0.821	0.96
138_T	154_S	0.812	0.96
160_Y	181_V	0.811	0.96
29_V	36_L	0.803	0.96
7_L	218_F	0.802	0.96
229_S	232_N	0.799	0.96
158_L	181_V	0.797	0.96
160_Y	208_G	0.797	0.96
71_I	79_I	0.795	0.95
93_E	130_K	0.793	0.95
136_I	154_S	0.792	0.95
107_I	134_N	0.789	0.95
25_I	77_V	0.784	0.95
92_L	126_I	0.783	0.95
92_L	123_I	0.780	0.95
138_T	181_V	0.776	0.95
136_I	153_I	0.771	0.95
202_R	207_A	0.767	0.95
52_I	219_I	0.766	0.94
175_K	203_D	0.765	0.94
69_E	73_K	0.762	0.94
110_P	213_A	0.759	0.94
18_V	66_P	0.757	0.94
18_V	60_K	0.749	0.94
230_A	237_F	0.749	0.94
221_E	233_L	0.747	0.94
79_I	104_L	0.745	0.94
96_L	130_K	0.735	0.93
71_I	75_V	0.733	0.93
21_F	38_L	0.726	0.93
192_G	215_G	0.726	0.93
178_I	189_L	0.725	0.93
136_I	150_V	0.721	0.93
139_S	142_V	0.717	0.92
234_V	237_F	0.717	0.92
195_L	201_L	0.716	0.92
18_V	67_L	0.712	0.92
25_I	38_L	0.710	0.92
50_P	54_K	0.709	0.92
151_S	187_N	0.706	0.92
168_V	196_S	0.704	0.92
21_F	67_L	0.702	0.92
40_I	64_I	0.699	0.91
230_A	238_R	0.698	0.91
19_Q	70_D	0.698	0.91
175_K	207_A	0.698	0.91
42_P	46_K	0.698	0.91
204_A	212_I	0.698	0.91
47_Y	193_F	0.696	0.91
198_E	201_L	0.692	0.91
9_V	35_I	0.692	0.91
169_P	172_V	0.691	0.91
68_I	104_L	0.691	0.91
53_R	78_P	0.690	0.91
114_I	149_K	0.689	0.91
155_D	187_N	0.688	0.91
117_I	124_D	0.687	0.91
92_L	96_L	0.680	0.90
180_R	183_N	0.677	0.90
217_V	220_E	0.677	0.90
151_S	158_L	0.673	0.90
107_I	127_I	0.673	0.90
80_I	137_F	0.673	0.90
199_S	202_R	0.671	0.90
92_L	119_D	0.669	0.89
201_L	206_S	0.666	0.89
170_I	173_S	0.663	0.89
169_P	196_S	0.662	0.89
10_Y	55_S	0.656	0.89
81_A	104_L	0.654	0.88
114_I	136_I	0.653	0.88
214_I	217_V	0.645	0.88
69_E	152_K	0.645	0.88
147_I	151_S	0.643	0.88
215_G	219_I	0.642	0.87
68_I	81_A	0.639	0.87
42_P	85_L	0.637	0.87
5_K	212_I	0.630	0.86
225_N	229_S	0.630	0.86
115_D	146_L	0.629	0.86
100_K	132_L	0.628	0.86
119_D	126_I	0.628	0.86
136_I	158_L	0.617	0.85
85_L	89_V	0.616	0.85
144_D	147_I	0.614	0.85
71_I	77_V	0.612	0.85
115_D	149_K	0.611	0.85
35_I	190_I	0.609	0.85
79_I	105_D	0.608	0.84
218_F	234_V	0.608	0.84
181_V	185_V	0.605	0.84
108_L	157_F	0.604	0.84
202_R	206_S	0.603	0.84
30_E	231_I	0.602	0.84
49_G	193_F	0.596	0.83
175_K	208_G	0.595	0.83
218_F	221_E	0.595	0.83
82_L	213_A	0.594	0.83
178_I	208_G	0.591	0.83
185_V	188_K	0.590	0.83
6_M	34_D	0.588	0.82
123_I	127_I	0.587	0.82
107_I	132_L	0.587	0.82
133_K	156_L	0.586	0.82
166_T	193_F	0.585	0.82
126_I	129_N	0.585	0.82
119_D	125_G	0.584	0.82
39_G	211_G	0.583	0.82
18_V	70_D	0.582	0.82
151_S	185_V	0.581	0.82
31_N	231_I	0.578	0.81
228_K	231_I	0.577	0.81
54_K	58_K	0.575	0.81
6_M	190_I	0.572	0.81
148_H	151_S	0.571	0.81
176_Q	180_R	0.571	0.81
118_D	149_K	0.568	0.80
25_I	29_V	0.568	0.80
27_G	231_I	0.567	0.80
42_P	86_E	0.566	0.80
13_L	68_I	0.565	0.80
64_I	68_I	0.565	0.80
24_F	234_V	0.565	0.80
29_V	71_I	0.564	0.80
176_Q	183_N	0.564	0.80
148_H	183_N	0.562	0.80
222_I	225_N	0.561	0.79
204_A	208_G	0.560	0.79
42_P	162_V	0.557	0.79
14_G	62_L	0.556	0.79
167_G	193_F	0.553	0.78
142_V	146_L	0.553	0.78
48_D	108_L	0.553	0.78
28_A	33_A	0.553	0.78
44_Y	161_G	0.552	0.78
40_I	83_T	0.550	0.78
22_K	71_I	0.550	0.78
145_L	149_K	0.549	0.78
224_R	233_L	0.549	0.78
38_L	79_I	0.549	0.78
110_P	160_Y	0.546	0.78
19_Q	22_K	0.546	0.78
51_V	216_T	0.545	0.77
203_D	207_A	0.544	0.77
21_F	29_V	0.544	0.77
55_S	219_I	0.542	0.77
123_I	134_N	0.541	0.77
168_V	172_V	0.538	0.77
228_K	235_K	0.538	0.77
227_V	231_I	0.534	0.76
204_A	207_A	0.529	0.75
67_L	70_D	0.529	0.75
168_V	171_P	0.528	0.75
231_I	237_F	0.527	0.75
3_M	6_M	0.527	0.75
235_K	238_R	0.524	0.75
231_I	234_V	0.524	0.75
63_D	67_L	0.521	0.74
40_I	95_F	0.520	0.74
230_A	234_V	0.519	0.74
11_M	21_F	0.519	0.74
68_I	72_R	0.518	0.74
27_G	235_K	0.518	0.74
23_D	228_K	0.518	0.74
4_G	34_D	0.517	0.74
46_K	85_L	0.517	0.74
178_I	191_V	0.517	0.74
48_D	136_I	0.515	0.73
49_G	166_T	0.514	0.73
145_L	148_H	0.513	0.73
26_I	70_D	0.510	0.73
189_L	210_D	0.506	0.72
49_G	167_G	0.504	0.72
147_I	180_R	0.503	0.72
42_P	47_Y	0.502	0.72
25_I	75_V	0.500	0.71
124_D	134_N	0.500	0.71

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
1ujpA	1	0.902	100	0.432	Contact Map
3thaA	2	0.951	100	0.46	Contact Map
2ekcA	1	0.9673	100	0.484	Contact Map
3vndA	3	0.9469	100	0.504	Contact Map
4ht3A	1	0.9837	100	0.505	Contact Map
3navA	2	0.9551	100	0.518	Contact Map
1geqA	1	0.9633	100	0.519	Contact Map
1rd5A	6	0.9673	100	0.532	Contact Map
3cu2A	2	0.8449	100	0.597	Contact Map
2f6uA	2	0.7837	100	0.619	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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