TRPA - HALSA - GREMLIN Contacts

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TRPA - Tryptophan synthase alpha chain

UniProt:	Q9HSB9	Sequences: MTRSDLAAAFDDGPALVSYVVAGDPTPAATAEYIDALVDGGTDVIELGLPFSEPVAEGTTIQNAIKRALDAGMTPDAYLDLVARIDADVPVVCMTYYNLLFQYGDRAGPAAFVSAAAEAGVSGFVVPDLPVDESGPLREACRAHGLDLVFVVAPTTTADRRERMLDLTTGFVYVQGRVGTTGAREEVSAATPDALAALQHTDIPKAVGFGVSSGEQAREITASGADGVIVGSAYVDTVADGVADDDPPSVVADRLRDLAAELKAGAARGVPEPEHK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	276 (248)
Sequences:	3769 (2451)
Seq/√Len:	155.7

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
26_T	29_A	3.735	1.00
24_D	67_R	3.242	1.00
158_A	197_A	3.058	1.00
103_Y	115_A	3.050	1.00
63_N	239_A	2.869	1.00
142_R	169_T	2.825	1.00
31_A	84_R	2.593	1.00
206_A	227_G	2.428	1.00
21_V	65_I	2.392	1.00
35_D	86_D	2.283	1.00
18_S	42_T	2.204	1.00
113_V	141_C	2.189	1.00
115_A	118_E	2.174	1.00
152_V	161_R	2.163	1.00
36_A	40_G	2.155	1.00
147_D	169_T	2.076	1.00
74_T	77_A	2.035	1.00
4_S	7_A	2.014	1.00
110_A	140_A	1.968	1.00
68_A	73_M	1.946	1.00
114_S	144_H	1.926	1.00
256_R	260_A	1.922	1.00
34_I	45_I	1.918	1.00
34_I	85_I	1.911	1.00
39_D	256_R	1.883	1.00
77_A	80_D	1.873	1.00
83_A	118_E	1.848	1.00
38_V	89_V	1.845	1.00
17_V	206_A	1.840	1.00
7_A	11_D	1.833	1.00
40_G	256_R	1.822	1.00
214_G	218_R	1.822	1.00
76_D	115_A	1.801	1.00
100_L	126_V	1.778	1.00
49_L	75_P	1.761	1.00
4_S	8_A	1.746	1.00
15_A	227_G	1.708	1.00
213_S	216_Q	1.695	1.00
114_S	118_E	1.690	1.00
38_V	88_D	1.674	1.00
80_D	83_A	1.646	1.00
95_T	100_L	1.644	1.00
117_A	144_H	1.636	1.00
176_G	207_V	1.628	1.00
199_Q	226_D	1.614	1.00
95_T	99_L	1.605	1.00
196_A	200_H	1.596	1.00
199_Q	205_K	1.592	1.00
126_V	137_L	1.592	1.00
162_E	166_D	1.591	1.00
83_A	115_A	1.582	1.00
174_V	205_K	1.580	1.00
73_M	77_A	1.573	1.00
19_Y	65_I	1.557	1.00
34_I	91_V	1.553	1.00
36_A	39_D	1.516	1.00
33_Y	238_V	1.514	1.00
207_V	220_I	1.504	1.00
236_D	240_D	1.502	1.00
111_A	114_S	1.485	1.00
110_A	143_A	1.475	1.00
115_A	119_A	1.470	1.00
141_C	148_L	1.424	1.00
111_A	115_A	1.418	1.00
116_A	146_L	1.412	1.00
44_V	92_V	1.392	1.00
31_A	35_D	1.385	1.00
156_T	161_R	1.370	1.00
66_K	70_D	1.368	1.00
73_M	78_Y	1.359	1.00
97_Y	129_L	1.348	1.00
206_A	229_I	1.336	1.00
207_V	225_A	1.324	1.00
138_R	142_R	1.319	1.00
24_D	239_A	1.305	1.00
242_V	245_D	1.300	1.00
76_D	103_Y	1.297	1.00
161_R	198_L	1.292	1.00
32_E	35_D	1.283	1.00
100_L	112_F	1.283	1.00
6_L	10_F	1.277	1.00
80_D	84_R	1.276	1.00
36_A	256_R	1.271	1.00
29_A	32_E	1.269	1.00
97_Y	105_D	1.264	1.00
211_V	228_V	1.248	1.00
22_A	47_L	1.241	1.00
20_V	33_Y	1.233	1.00
116_A	121_V	1.225	1.00
174_V	194_A	1.224	1.00
27_P	31_A	1.222	1.00
134_S	150_F	1.221	1.00
79_L	116_A	1.208	1.00
253_D	257_D	1.202	1.00
33_Y	255_L	1.188	1.00
211_V	220_I	1.186	1.00
92_V	149_V	1.184	1.00
113_V	140_A	1.176	1.00
250_V	254_R	1.168	1.00
139_E	143_A	1.166	1.00
163_R	166_D	1.155	1.00
212_S	236_D	1.154	1.00
14_P	222_A	1.130	1.00
168_T	203_I	1.127	1.00
49_L	93_C	1.125	1.00
236_D	239_A	1.122	1.00
27_P	77_A	1.122	1.00
255_L	258_L	1.121	1.00
158_A	200_H	1.114	1.00
45_I	89_V	1.114	1.00
190_A	193_D	1.100	0.99
94_M	125_V	1.095	0.99
24_D	235_V	1.093	0.99
172_V	201_T	1.093	0.99
177_R	184_R	1.091	0.99
192_P	196_A	1.086	0.99
76_D	111_A	1.085	0.99
36_A	252_A	1.082	0.99
148_L	169_T	1.079	0.99
63_N	66_K	1.078	0.99
103_Y	111_A	1.075	0.99
193_D	196_A	1.075	0.99
97_Y	137_L	1.059	0.99
38_V	87_A	1.047	0.99
5_D	9_A	1.047	0.99
135_G	139_E	1.042	0.99
117_A	145_G	1.037	0.99
21_V	64_A	1.032	0.99
113_V	124_F	1.006	0.99
76_D	80_D	1.005	0.99
112_F	124_F	1.003	0.99
237_T	254_R	0.996	0.99
31_A	81_L	0.994	0.99
244_D	250_V	0.987	0.99
35_D	39_D	0.986	0.99
4_S	44_V	0.982	0.99
215_E	219_E	0.977	0.99
27_P	73_M	0.977	0.99
241_G	251_V	0.971	0.99
60_T	183_A	0.961	0.99
18_S	234_Y	0.959	0.99
184_R	216_Q	0.958	0.99
60_T	236_D	0.956	0.99
47_L	82_V	0.947	0.98
217_A	228_V	0.945	0.98
183_A	236_D	0.945	0.98
131_V	167_L	0.943	0.98
110_A	114_S	0.941	0.98
233_A	237_T	0.941	0.98
155_T	178_V	0.938	0.98
5_D	8_A	0.937	0.98
83_A	119_A	0.934	0.98
7_A	10_F	0.933	0.98
113_V	137_L	0.931	0.98
8_A	15_A	0.929	0.98
241_G	244_D	0.927	0.98
79_L	115_A	0.925	0.98
237_T	241_G	0.925	0.98
82_V	91_V	0.912	0.98
194_A	197_A	0.910	0.98
17_V	44_V	0.905	0.98
67_R	239_A	0.905	0.98
222_A	228_V	0.900	0.98
240_D	254_R	0.897	0.98
67_R	70_D	0.894	0.98
35_D	38_V	0.892	0.98
113_V	146_L	0.890	0.98
26_T	71_A	0.888	0.98
158_A	162_E	0.886	0.98
16_L	234_Y	0.886	0.98
87_A	91_V	0.884	0.98
22_A	81_L	0.870	0.97
31_A	34_I	0.865	0.97
18_S	37_L	0.863	0.97
151_V	175_Q	0.862	0.97
251_V	254_R	0.861	0.97
19_Y	48_G	0.860	0.97
22_A	78_Y	0.858	0.97
241_G	254_R	0.858	0.97
110_A	144_H	0.856	0.97
237_T	240_D	0.856	0.97
172_V	198_L	0.855	0.97
152_V	168_T	0.854	0.97
163_R	167_L	0.851	0.97
38_V	45_I	0.848	0.97
30_T	81_L	0.843	0.97
92_V	123_G	0.842	0.97
6_L	9_A	0.841	0.97
251_V	258_L	0.837	0.97
174_V	198_L	0.832	0.96
27_P	30_T	0.832	0.96
114_S	117_A	0.825	0.96
212_S	216_Q	0.824	0.96
257_D	260_A	0.818	0.96
254_R	257_D	0.812	0.96
134_S	138_R	0.807	0.96
136_P	140_A	0.804	0.96
31_A	86_D	0.804	0.96
34_I	89_V	0.802	0.96
34_I	47_L	0.796	0.95
135_G	167_L	0.796	0.95
252_A	256_R	0.795	0.95
150_F	168_T	0.792	0.95
61_I	235_V	0.785	0.95
192_P	219_E	0.785	0.95
140_A	144_H	0.783	0.95
27_P	80_D	0.779	0.95
174_V	224_G	0.779	0.95
237_T	258_L	0.776	0.95
105_D	140_A	0.769	0.94
152_V	198_L	0.764	0.94
150_F	164_M	0.757	0.94
234_Y	259_A	0.753	0.94
218_R	223_S	0.753	0.94
29_A	33_Y	0.751	0.94
127_P	229_I	0.751	0.94
150_F	167_L	0.750	0.94
82_V	121_V	0.750	0.94
27_P	81_L	0.748	0.94
35_D	87_A	0.747	0.94
39_D	86_D	0.746	0.94
192_P	223_S	0.745	0.94
136_P	139_E	0.740	0.93
165_L	203_I	0.740	0.93
51_F	55_V	0.739	0.93
211_V	217_A	0.738	0.93
27_P	71_A	0.738	0.93
124_F	148_L	0.732	0.93
76_D	79_L	0.732	0.93
62_Q	90_P	0.732	0.93
183_A	187_V	0.731	0.93
91_V	121_V	0.728	0.93
153_A	156_T	0.728	0.93
56_A	209_F	0.724	0.93
131_V	163_R	0.722	0.92
33_Y	252_A	0.721	0.92
16_L	259_A	0.720	0.92
91_V	122_S	0.712	0.92
195_L	205_K	0.704	0.91
152_V	156_T	0.703	0.91
131_V	150_F	0.702	0.91
220_I	228_V	0.696	0.91
215_E	218_R	0.695	0.91
30_T	47_L	0.695	0.91
85_I	91_V	0.694	0.91
113_V	144_H	0.689	0.91
183_A	212_S	0.688	0.91
169_T	203_I	0.687	0.90
18_S	44_V	0.685	0.90
252_A	255_L	0.684	0.90
59_T	63_N	0.683	0.90
165_L	172_V	0.681	0.90
14_P	228_V	0.680	0.90
234_Y	255_L	0.678	0.90
132_D	160_R	0.675	0.90
250_V	253_D	0.674	0.90
161_R	165_L	0.669	0.89
19_Y	64_A	0.668	0.89
150_F	172_V	0.668	0.89
214_G	217_A	0.667	0.89
37_L	255_L	0.666	0.89
184_R	212_S	0.664	0.89
217_A	222_A	0.660	0.89
23_G	73_M	0.659	0.89
49_L	78_Y	0.658	0.88
105_D	136_P	0.657	0.88
47_L	91_V	0.657	0.88
105_D	137_L	0.654	0.88
28_A	84_R	0.651	0.88
92_V	151_V	0.650	0.88
97_Y	101_F	0.647	0.88
51_F	97_Y	0.646	0.88
9_A	12_D	0.642	0.87
140_A	143_A	0.640	0.87
230_V	233_A	0.637	0.87
37_L	259_A	0.635	0.87
117_A	146_L	0.634	0.87
184_R	187_V	0.634	0.87
48_G	227_G	0.633	0.87
233_A	236_D	0.632	0.86
208_G	231_G	0.629	0.86
162_E	200_H	0.629	0.86
83_A	166_D	0.628	0.86
37_L	42_T	0.628	0.86
193_D	200_H	0.627	0.86
93_C	121_V	0.625	0.86
85_I	89_V	0.621	0.85
8_A	13_G	0.620	0.85
63_N	67_R	0.615	0.85
158_A	161_R	0.615	0.85
195_L	224_G	0.613	0.85
19_Y	258_L	0.613	0.85
234_Y	237_T	0.612	0.85
231_G	235_V	0.612	0.85
30_T	38_V	0.611	0.85
78_Y	82_V	0.608	0.84
197_A	200_H	0.608	0.84
104_G	110_A	0.607	0.84
124_F	141_C	0.605	0.84
125_V	171_F	0.599	0.83
162_E	165_L	0.599	0.83
252_A	259_A	0.598	0.83
124_F	146_L	0.596	0.83
81_L	84_R	0.594	0.83
10_F	13_G	0.593	0.83
201_T	204_P	0.591	0.83
31_A	85_I	0.591	0.83
192_P	224_G	0.591	0.83
58_G	209_F	0.588	0.82
105_D	113_V	0.586	0.82
241_G	245_D	0.586	0.82
82_V	93_C	0.584	0.82
165_L	201_T	0.582	0.82
198_L	201_T	0.581	0.81
189_A	193_D	0.580	0.81
147_D	170_G	0.580	0.81
220_I	224_G	0.578	0.81
94_M	229_I	0.577	0.81
8_A	11_D	0.576	0.81
15_A	43_D	0.576	0.81
153_A	175_Q	0.566	0.80
22_A	82_V	0.556	0.79
49_L	95_T	0.555	0.78
9_A	13_G	0.554	0.78
218_R	222_A	0.551	0.78
57_E	125_V	0.550	0.78
34_I	38_V	0.550	0.78
51_F	177_R	0.549	0.78
34_I	87_A	0.548	0.78
181_T	209_F	0.547	0.77
51_F	98_N	0.545	0.77
193_D	197_A	0.544	0.77
127_P	174_V	0.543	0.77
187_V	191_T	0.534	0.76
93_C	116_A	0.534	0.76
44_V	206_A	0.532	0.76
70_D	200_H	0.531	0.75
38_V	86_D	0.525	0.75
28_A	31_A	0.524	0.74
5_D	15_A	0.524	0.74
131_V	164_M	0.524	0.74
44_V	89_V	0.522	0.74
242_V	251_V	0.522	0.74
156_T	160_R	0.522	0.74
245_D	252_A	0.521	0.74
27_P	84_R	0.519	0.74
130_P	133_E	0.519	0.74
20_V	34_I	0.518	0.74
38_V	85_I	0.518	0.74
220_I	223_S	0.517	0.73
5_D	13_G	0.517	0.73
58_G	181_T	0.516	0.73
132_D	163_R	0.516	0.73
49_L	112_F	0.516	0.73
126_V	141_C	0.516	0.73
230_V	258_L	0.513	0.73
186_E	189_A	0.512	0.73
182_G	209_F	0.511	0.73
4_S	86_D	0.510	0.72
254_R	258_L	0.510	0.72
137_L	148_L	0.509	0.72
152_V	191_T	0.509	0.72
235_V	239_A	0.509	0.72
15_A	206_A	0.509	0.72
53_E	176_G	0.506	0.72
51_F	149_V	0.505	0.72
238_V	241_G	0.503	0.71
25_P	33_Y	0.502	0.71
69_L	99_L	0.501	0.71
41_G	89_V	0.501	0.71
241_G	250_V	0.501	0.71
27_P	68_A	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	0.8514	100	0.434	Contact Map
3thaA	2	0.8949	100	0.463	Contact Map
2ekcA	1	0.913	100	0.496	Contact Map
3vndA	3	0.9094	100	0.497	Contact Map
4ht3A	1	0.9457	100	0.499	Contact Map
3navA	2	0.9167	100	0.506	Contact Map
1rd5A	6	0.9239	100	0.526	Contact Map
1geqA	1	0.8768	100	0.546	Contact Map
3cu2A	2	0.779	100	0.631	Contact Map
2f6uA	2	0.6884	100	0.665	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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