TRPA - ECOLI - GREMLIN Contacts

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TRPA - Tryptophan synthase alpha chain

UniProt:	P0A877	Sequences: MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSDPLADGPTIQNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11024
Length:	268 (256)
Sequences:	3775 (2487)
Seq/√Len:	155.4

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
29_G	32_Q	3.619	1.00
38_D	91_K	3.501	1.00
27_D	70_R	3.142	1.00
109_K	117_Q	2.910	1.00
66_N	242_E	2.775	1.00
144_L	171_R	2.634	1.00
160_D	199_K	2.539	1.00
34_L	87_L	2.493	1.00
209_L	230_G	2.354	1.00
42_E	256_K	2.330	1.00
89_R	124_D	2.303	1.00
24_T	68_T	2.297	1.00
43_A	256_K	2.212	1.00
21_P	45_A	2.142	1.00
115_Y	143_A	2.132	1.00
117_Q	120_K	2.123	1.00
154_C	163_L	2.092	1.00
87_L	90_Q	2.076	1.00
5_E	149_A	1.986	1.00
149_A	171_R	1.978	1.00
77_T	80_Q	1.975	1.00
3_R	124_D	1.965	1.00
39_T	43_A	1.935	1.00
233_S	262_M	1.930	1.00
7_L	10_Q	1.920	1.00
112_D	142_A	1.912	1.00
71_A	76_V	1.901	1.00
7_L	11_L	1.901	1.00
116_A	146_H	1.865	1.00
37_I	88_I	1.859	1.00
256_K	260_Q	1.843	1.00
37_I	48_L	1.822	1.00
80_Q	83_E	1.808	1.00
41_I	95_I	1.804	1.00
86_A	120_K	1.799	1.00
217_P	221_K	1.732	1.00
10_Q	14_R	1.730	1.00
79_A	117_Q	1.721	1.00
52_I	78_P	1.713	1.00
106_V	128_V	1.709	1.00
20_V	209_L	1.707	1.00
18_A	230_G	1.704	1.00
216_A	219_Q	1.636	1.00
116_A	120_K	1.632	1.00
4_Y	47_A	1.624	1.00
83_E	86_A	1.611	1.00
119_E	146_H	1.606	1.00
201_K	208_P	1.596	1.00
101_M	106_V	1.594	1.00
22_F	68_T	1.568	1.00
178_S	210_Q	1.565	1.00
41_I	94_T	1.549	1.00
101_M	105_L	1.548	1.00
128_V	139_F	1.542	1.00
164_R	168_S	1.541	1.00
86_A	117_Q	1.520	1.00
201_K	229_A	1.510	1.00
198_A	202_E	1.499	1.00
176_L	208_P	1.485	1.00
76_V	80_Q	1.475	1.00
113_E	116_A	1.452	1.00
239_K	243_Q	1.451	1.00
36_I	241_I	1.426	1.00
37_I	97_I	1.425	1.00
112_D	145_R	1.418	1.00
158_A	163_L	1.416	1.00
117_Q	121_V	1.395	1.00
143_A	150_P	1.391	1.00
39_T	256_K	1.389	1.00
118_C	148_V	1.389	1.00
113_E	117_Q	1.388	1.00
39_T	42_E	1.375	1.00
69_L	73_A	1.356	1.00
76_V	81_C	1.355	1.00
47_A	98_G	1.354	1.00
164_R	203_Y	1.351	1.00
34_L	38_D	1.327	1.00
79_A	109_K	1.326	1.00
103_A	131_V	1.324	1.00
140_R	144_L	1.319	1.00
35_K	38_D	1.274	1.00
210_Q	228_A	1.268	1.00
27_D	242_E	1.257	1.00
6_S	9_A	1.257	1.00
214_I	231_A	1.256	1.00
209_L	232_I	1.252	1.00
36_I	255_L	1.248	1.00
257_V	261_P	1.247	1.00
9_A	13_E	1.242	1.00
32_Q	35_K	1.230	1.00
23_V	36_I	1.229	1.00
176_L	196_L	1.217	1.00
118_C	123_V	1.212	1.00
160_D	202_E	1.203	1.00
83_E	87_L	1.200	1.00
163_L	200_L	1.192	1.00
217_P	261_P	1.190	1.00
82_F	118_C	1.183	1.00
30_I	34_L	1.178	1.00
136_S	152_F	1.176	1.00
5_E	9_A	1.176	1.00
103_A	111_I	1.168	1.00
25_L	50_L	1.162	1.00
106_V	114_F	1.160	1.00
39_T	252_L	1.149	1.00
253_A	257_V	1.139	1.00
6_S	10_Q	1.138	1.00
98_G	151_I	1.138	1.00
141_Q	145_R	1.136	1.00
52_I	99_L	1.134	1.00
215_S	239_K	1.119	1.00
48_L	95_I	1.115	1.00
115_Y	142_A	1.113	1.00
179_R	186_E	1.113	1.00
170_G	206_A	1.109	1.00
30_I	80_Q	1.099	0.99
165_Q	168_S	1.098	0.99
250_K	254_A	1.093	0.99
239_K	242_E	1.084	0.99
66_N	69_L	1.080	0.99
103_A	139_F	1.077	0.99
100_L	127_L	1.075	0.99
195_H	198_A	1.069	0.99
17_G	225_D	1.068	0.99
27_D	238_V	1.067	0.99
174_T	204_N	1.056	0.99
192_P	195_H	1.055	0.99
194_N	198_A	1.054	0.99
7_L	47_A	1.032	0.99
79_A	113_E	1.023	0.99
3_R	89_R	1.023	0.99
119_E	147_N	1.019	0.99
137_A	141_Q	1.019	0.99
109_K	113_E	1.007	0.99
24_T	67_A	1.006	0.99
160_D	203_Y	1.006	0.99
79_A	83_E	1.003	0.99
42_E	91_K	1.000	0.99
114_F	126_V	0.991	0.99
38_D	42_E	0.989	0.99
34_L	91_K	0.989	0.99
115_Y	126_V	0.989	0.99
11_L	18_A	0.988	0.99
236_A	240_I	0.975	0.99
21_P	237_I	0.971	0.99
218_D	222_A	0.968	0.99
41_I	93_P	0.968	0.99
240_I	244_H	0.965	0.99
160_D	164_R	0.954	0.98
150_P	171_R	0.948	0.98
254_A	257_V	0.942	0.98
30_I	76_V	0.938	0.98
34_L	84_M	0.937	0.98
240_I	254_A	0.936	0.98
63_T	239_K	0.933	0.98
186_E	219_Q	0.933	0.98
244_H	254_A	0.931	0.98
258_F	261_P	0.931	0.98
86_A	121_V	0.928	0.98
185_A	239_K	0.926	0.98
258_F	262_M	0.921	0.98
157_N	180_A	0.919	0.98
133_V	169_Y	0.908	0.98
63_T	185_A	0.904	0.98
82_F	117_Q	0.904	0.98
20_V	47_A	0.903	0.98
70_R	242_E	0.902	0.98
112_D	116_A	0.895	0.98
10_Q	13_E	0.894	0.98
255_L	258_F	0.891	0.98
196_L	199_K	0.887	0.98
19_F	237_I	0.887	0.98
38_D	41_I	0.884	0.98
225_D	231_A	0.877	0.97
21_P	40_L	0.874	0.97
176_L	200_L	0.868	0.97
244_H	251_M	0.863	0.97
29_G	74_A	0.860	0.97
220_V	231_A	0.860	0.97
252_L	256_K	0.857	0.97
85_L	97_I	0.851	0.97
115_Y	148_V	0.850	0.97
25_L	81_C	0.850	0.97
50_L	85_L	0.849	0.97
70_R	73_A	0.846	0.97
154_C	170_G	0.843	0.97
251_M	254_A	0.838	0.97
30_I	33_S	0.833	0.96
22_F	51_G	0.830	0.96
98_G	125_S	0.829	0.96
116_A	119_E	0.828	0.96
240_I	243_Q	0.826	0.96
194_N	222_A	0.824	0.96
245_I	248_P	0.822	0.96
25_L	84_M	0.822	0.96
165_Q	169_Y	0.819	0.96
210_Q	224_I	0.818	0.96
115_Y	139_F	0.814	0.96
174_T	200_L	0.810	0.96
153_I	177_L	0.808	0.96
237_I	259_V	0.807	0.96
9_A	12_K	0.806	0.96
138_P	142_A	0.804	0.96
41_I	48_L	0.803	0.96
136_S	140_R	0.800	0.96
152_F	170_G	0.790	0.95
33_S	84_M	0.790	0.95
215_S	219_Q	0.789	0.95
97_I	123_V	0.788	0.95
37_I	50_L	0.783	0.95
34_L	37_I	0.781	0.95
4_Y	125_S	0.779	0.95
86_A	90_Q	0.770	0.95
37_I	95_I	0.769	0.94
88_I	97_I	0.768	0.94
155_P	158_A	0.766	0.94
30_I	83_E	0.766	0.94
32_Q	36_I	0.761	0.94
111_I	142_A	0.760	0.94
64_I	238_V	0.758	0.94
38_D	93_P	0.757	0.94
154_C	200_L	0.756	0.94
11_L	16_E	0.755	0.94
194_N	226_A	0.753	0.94
152_F	169_Y	0.750	0.94
233_S	258_F	0.748	0.94
111_I	138_P	0.747	0.94
19_F	259_V	0.746	0.94
36_I	252_L	0.743	0.93
257_V	260_Q	0.743	0.93
126_V	150_P	0.740	0.93
142_A	146_H	0.738	0.93
152_F	166_I	0.734	0.93
85_L	123_V	0.732	0.93
129_A	232_I	0.732	0.93
30_I	84_M	0.732	0.93
221_K	226_A	0.731	0.93
112_D	146_H	0.731	0.93
111_I	139_F	0.730	0.93
218_D	221_K	0.728	0.93
237_I	255_L	0.723	0.92
243_Q	254_A	0.720	0.92
88_I	93_P	0.719	0.92
154_C	158_A	0.718	0.92
185_A	189_A	0.718	0.92
185_A	215_S	0.713	0.92
137_A	169_Y	0.712	0.92
33_S	50_L	0.711	0.92
176_L	227_G	0.710	0.92
79_A	82_F	0.709	0.92
54_F	58_L	0.704	0.91
138_P	141_Q	0.703	0.91
59_A	212_F	0.701	0.91
167_A	206_A	0.700	0.91
167_A	204_N	0.699	0.91
167_A	174_T	0.698	0.91
250_K	253_A	0.696	0.91
244_H	250_K	0.695	0.91
30_I	74_A	0.694	0.91
200_L	204_N	0.694	0.91
133_V	165_Q	0.694	0.91
252_L	255_L	0.693	0.91
253_A	256_K	0.692	0.91
133_V	152_F	0.692	0.91
167_A	203_Y	0.691	0.91
62_P	66_N	0.690	0.91
93_P	97_I	0.688	0.90
17_G	231_A	0.686	0.90
211_G	234_G	0.685	0.90
214_I	220_V	0.681	0.90
220_V	225_D	0.679	0.90
236_A	239_K	0.673	0.90
171_R	206_A	0.671	0.89
40_L	259_V	0.671	0.89
237_I	258_F	0.669	0.89
197_V	208_P	0.668	0.89
21_P	47_A	0.667	0.89
134_E	162_L	0.661	0.89
32_Q	252_L	0.660	0.89
115_Y	146_H	0.658	0.88
52_I	81_C	0.658	0.88
26_G	76_V	0.654	0.88
186_E	189_A	0.650	0.88
224_I	227_G	0.643	0.87
65_Q	96_P	0.643	0.87
240_I	258_F	0.642	0.87
186_E	215_S	0.638	0.87
163_L	167_A	0.637	0.87
160_D	163_L	0.636	0.87
119_E	148_V	0.635	0.87
142_A	145_R	0.629	0.86
159_D	199_K	0.628	0.86
234_G	238_V	0.628	0.86
126_V	143_A	0.626	0.86
99_L	123_V	0.623	0.86
40_L	45_A	0.622	0.86
152_F	174_T	0.618	0.85
248_P	252_L	0.616	0.85
33_S	41_I	0.615	0.85
54_F	103_A	0.614	0.85
164_R	202_E	0.613	0.85
88_I	95_I	0.609	0.84
66_N	70_R	0.608	0.84
111_I	115_Y	0.607	0.84
126_V	148_V	0.607	0.84
22_F	67_A	0.607	0.84
31_E	87_L	0.607	0.84
98_G	153_I	0.606	0.84
85_L	99_L	0.602	0.84
127_L	173_Y	0.601	0.84
233_S	236_A	0.600	0.83
199_K	202_E	0.599	0.83
103_A	107_F	0.599	0.83
217_P	220_V	0.598	0.83
197_V	227_G	0.596	0.83
86_A	168_S	0.594	0.83
195_H	199_K	0.593	0.83
214_I	224_I	0.592	0.83
129_A	176_L	0.590	0.82
100_L	232_I	0.590	0.82
51_G	230_G	0.585	0.82
61_G	212_F	0.583	0.82
194_N	227_G	0.583	0.82
81_C	85_L	0.580	0.81
237_I	240_I	0.575	0.81
97_I	124_D	0.575	0.81
25_L	85_L	0.575	0.81
4_Y	8_F	0.574	0.81
84_M	87_L	0.570	0.80
164_R	167_A	0.570	0.80
50_L	97_I	0.564	0.80
251_M	255_L	0.562	0.79
139_F	150_P	0.562	0.79
52_I	101_M	0.561	0.79
18_A	46_D	0.558	0.79
54_F	179_R	0.557	0.79
60_D	127_L	0.556	0.79
37_I	41_I	0.555	0.78
241_I	251_M	0.554	0.78
4_Y	98_G	0.553	0.78
204_N	208_P	0.553	0.78
222_A	226_A	0.551	0.78
149_A	172_G	0.548	0.78
236_A	258_F	0.548	0.78
47_A	209_L	0.546	0.77
35_K	91_K	0.542	0.77
41_I	88_I	0.542	0.77
238_V	242_E	0.540	0.77
158_A	162_L	0.539	0.76
195_H	202_E	0.539	0.76
126_V	139_F	0.538	0.76
8_F	11_L	0.536	0.76
54_F	104_N	0.535	0.76
31_E	34_L	0.535	0.76
161_D	165_Q	0.530	0.75
35_K	248_P	0.530	0.75
154_C	193_L	0.529	0.75
155_P	177_L	0.526	0.75
132_P	135_E	0.526	0.75
63_T	235_S	0.526	0.75
94_T	253_A	0.525	0.75
58_L	103_A	0.524	0.74
52_I	114_F	0.522	0.74
60_D	152_F	0.522	0.74
139_F	143_A	0.520	0.74
183_T	212_F	0.520	0.74
221_K	225_D	0.520	0.74
72_F	105_L	0.519	0.74
23_V	37_I	0.519	0.74
184_G	212_F	0.519	0.74
59_A	177_L	0.518	0.74
12_K	15_K	0.517	0.73
54_F	151_I	0.516	0.73
3_R	94_T	0.514	0.73
163_L	199_K	0.514	0.73
8_F	18_A	0.513	0.73
28_P	36_I	0.512	0.73
191_L	195_H	0.511	0.73
61_G	183_T	0.510	0.72
134_E	165_Q	0.505	0.72
252_L	259_V	0.502	0.71
216_A	258_F	0.501	0.71
228_A	231_A	0.500	0.71
56_D	178_S	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	0.8918	100	0.398	Contact Map
3thaA	2	0.9254	100	0.43	Contact Map
4ht3A	1	1	100	0.451	Contact Map
2ekcA	1	0.9664	100	0.451	Contact Map
3vndA	3	0.9627	100	0.455	Contact Map
3navA	2	0.9701	100	0.462	Contact Map
1rd5A	6	0.9739	100	0.49	Contact Map
1geqA	1	0.9142	100	0.521	Contact Map
3cu2A	2	0.806	100	0.597	Contact Map
2f6uA	2	0.7164	100	0.639	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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