SYGA - BACSU - GREMLIN Contacts

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SYGA - Glycine--tRNA ligase alpha subunit

UniProt:	P54380	Sequences: MNIQDMILTLQKHWSSQGCVLMQAYDVEKGAGTMSPYTFLRSIGPEPWKVAYVEPSRRPADGRYGENPNRLYQHHQFQVIIKPSPDNIQELYLDSLRALGIDPLEHDIRFVEDNWENPSLGCAGLGWEVWLDGMEITQFTYFQQVGGLECKPVSVEITYGIERLASYIQDKENVFDLEWTSGFTVKDLFMMAEYEHSVYTFETSDVDMLFQLFSTYEKEAIKQMDNGLVHPAYDYVLKCSHTFNLLDAKGAISVTERTGYIARVRNLARKVAKTYYEEREKLGFPMLKGEGSSHE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	295 (281)
Sequences:	1020 (300)
Seq/√Len:	17.9

ECOLI - SYGA
BACSU - SYGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_Q	77_F	5.035	1.00
13_H	94_D	4.652	1.00
35_S	54_E	4.582	1.00
190_M	194_Y	4.250	1.00
49_K	81_I	3.883	1.00
88_I	155_V	3.587	1.00
34_M	117_N	3.419	1.00
46_E	279_R	3.380	1.00
102_D	105_E	3.098	0.99
72_Y	200_T	3.069	0.99
211_Q	215_T	3.037	0.99
94_D	97_R	2.946	0.99
117_N	120_L	2.928	0.99
191_M	195_E	2.851	0.98
189_F	192_A	2.783	0.98
71_L	174_V	2.579	0.97
87_N	91_L	2.476	0.96
29_K	54_E	2.454	0.96
203_T	226_N	2.453	0.96
6_M	165_A	2.448	0.96
39_F	272_A	2.432	0.96
80_I	154_S	2.424	0.95
42_S	150_C	2.323	0.94
212_L	215_T	2.289	0.94
217_E	263_R	2.273	0.94
2_N	5_D	2.254	0.93
75_H	189_F	2.252	0.93
28_E	238_K	2.229	0.93
203_T	223_Q	2.206	0.92
12_K	16_S	2.109	0.91
106_H	132_D	2.109	0.91
72_Y	75_H	2.100	0.90
74_H	200_T	2.083	0.90
34_M	240_S	2.070	0.90
9_T	98_A	2.058	0.89
192_A	196_H	2.035	0.89
279_R	282_L	1.997	0.88
136_I	164_L	1.997	0.88
196_H	234_D	1.989	0.88
97_R	103_P	1.976	0.87
20_V	183_F	1.960	0.87
150_C	153_V	1.938	0.86
81_I	88_I	1.907	0.85
178_E	182_G	1.885	0.85
205_D	222_K	1.878	0.85
6_M	99_L	1.875	0.84
175_F	186_K	1.847	0.84
2_N	181_S	1.829	0.83
50_V	154_S	1.820	0.83
53_V	56_S	1.813	0.82
164_L	168_I	1.790	0.82
137_T	157_I	1.787	0.81
119_S	261_I	1.747	0.80
43_I	276_Y	1.739	0.80
75_H	200_T	1.731	0.79
206_V	251_A	1.712	0.78
198_V	203_T	1.690	0.78
9_T	12_K	1.687	0.77
62_G	201_F	1.658	0.76
148_L	276_Y	1.626	0.75
87_N	157_I	1.624	0.75
97_R	104_L	1.604	0.74
73_Q	200_T	1.590	0.73
258_T	262_A	1.588	0.73
103_P	108_I	1.584	0.73
198_V	202_E	1.577	0.72
45_P	279_R	1.545	0.71
220_A	236_V	1.523	0.70
178_E	181_S	1.512	0.69
11_Q	23_Q	1.502	0.69
89_Q	110_F	1.492	0.68
216_Y	235_Y	1.490	0.68
34_M	237_L	1.482	0.67
194_Y	198_V	1.450	0.66
191_M	194_Y	1.424	0.64
178_E	184_T	1.421	0.64
212_L	216_Y	1.411	0.64
216_Y	242_T	1.404	0.63
36_P	234_D	1.399	0.63
26_D	57_R	1.393	0.62
269_R	273_K	1.383	0.62
87_N	90_E	1.381	0.62
5_D	9_T	1.362	0.61
2_N	180_T	1.358	0.60
3_I	161_I	1.345	0.60
208_M	215_T	1.326	0.59
50_V	80_I	1.319	0.58
25_Y	234_D	1.315	0.58
117_N	240_S	1.309	0.58
46_E	282_L	1.286	0.56
92_Y	96_L	1.273	0.55
42_S	80_I	1.264	0.55
34_M	120_L	1.247	0.54
13_H	102_D	1.237	0.53
112_E	144_Q	1.235	0.53
8_L	11_Q	1.219	0.52
2_N	178_E	1.204	0.51
227_G	277_E	1.199	0.51
192_A	230_H	1.197	0.51
4_Q	28_E	1.183	0.50
123_A	149_E	1.160	0.48
208_M	212_L	1.148	0.48
274_T	277_E	1.143	0.47
74_H	189_F	1.141	0.47
114_N	272_A	1.134	0.47
29_K	237_L	1.132	0.47
102_D	157_I	1.126	0.46
114_N	262_A	1.111	0.45
7_I	161_I	1.108	0.45
174_V	202_E	1.078	0.43
54_E	234_D	1.077	0.43
236_V	271_V	1.061	0.42
123_A	144_Q	1.056	0.42
209_L	245_L	1.051	0.42
35_S	234_D	1.048	0.42
17_Q	87_N	1.037	0.41
43_I	224_M	1.036	0.41
206_V	210_F	1.009	0.39
111_V	130_W	1.003	0.39
145_V	164_L	1.002	0.39
273_K	277_E	0.994	0.39
49_K	87_N	0.988	0.38
147_G	269_R	0.988	0.38
22_M	150_C	0.985	0.38
220_A	267_L	0.977	0.38
204_S	245_L	0.976	0.37
3_I	6_M	0.969	0.37
210_F	214_S	0.964	0.37
177_L	190_M	0.953	0.36
22_M	35_S	0.953	0.36
196_H	230_H	0.951	0.36
235_Y	239_C	0.949	0.36
224_M	270_K	0.943	0.36
204_S	251_A	0.942	0.36
239_C	258_T	0.942	0.36
114_N	263_R	0.938	0.35
25_Y	132_D	0.937	0.35
21_L	51_A	0.936	0.35
29_K	35_S	0.936	0.35
132_D	219_E	0.927	0.35
22_M	164_L	0.920	0.34
277_E	280_E	0.916	0.34
278_E	282_L	0.907	0.34
4_Q	238_K	0.889	0.33
114_N	177_L	0.888	0.33
60_A	117_N	0.885	0.32
5_D	101_I	0.884	0.32
51_A	77_F	0.882	0.32
117_N	139_F	0.881	0.32
214_S	264_V	0.872	0.32
228_L	231_P	0.871	0.32
109_R	130_W	0.869	0.32
191_M	282_L	0.868	0.32
111_V	128_E	0.866	0.31
146_G	272_A	0.862	0.31
114_N	150_C	0.861	0.31
134_M	167_Y	0.856	0.31
187_D	274_T	0.854	0.31
242_T	245_L	0.846	0.30
56_S	74_H	0.842	0.30
117_N	264_V	0.842	0.30
194_Y	200_T	0.841	0.30
29_K	72_Y	0.838	0.30
12_K	101_I	0.831	0.30
56_S	71_L	0.829	0.29
211_Q	214_S	0.828	0.29
97_R	102_D	0.825	0.29
84_S	151_K	0.822	0.29
227_G	274_T	0.818	0.29
222_K	226_N	0.817	0.29
81_I	155_V	0.817	0.29
5_D	8_L	0.815	0.29
75_H	192_A	0.811	0.29
2_N	168_I	0.808	0.28
202_E	230_H	0.804	0.28
197_S	233_Y	0.803	0.28
149_E	262_A	0.797	0.28
13_H	191_M	0.794	0.28
43_I	148_L	0.787	0.27
39_F	131_L	0.786	0.27
114_N	196_H	0.786	0.27
57_R	119_S	0.773	0.27
132_D	255_T	0.770	0.27
24_A	112_E	0.762	0.26
39_F	268_A	0.762	0.26
266_N	269_R	0.758	0.26
256_E	263_R	0.757	0.26
123_A	258_T	0.756	0.26
129_V	146_G	0.756	0.26
137_T	169_Q	0.747	0.25
9_T	207_D	0.746	0.25
114_N	258_T	0.746	0.25
94_D	98_A	0.742	0.25
148_L	236_V	0.733	0.25
168_I	206_V	0.732	0.25
254_V	269_R	0.731	0.25
190_M	224_M	0.727	0.25
101_I	108_I	0.726	0.25
123_A	147_G	0.726	0.25
60_A	99_L	0.725	0.24
72_Y	194_Y	0.725	0.24
60_A	74_H	0.722	0.24
173_N	271_V	0.720	0.24
60_A	200_T	0.718	0.24
175_F	201_F	0.718	0.24
111_V	134_M	0.717	0.24
29_K	56_S	0.717	0.24
216_Y	239_C	0.717	0.24
42_S	145_V	0.716	0.24
17_Q	94_D	0.714	0.24
171_K	178_E	0.711	0.24
229_V	278_E	0.709	0.24
99_L	157_I	0.707	0.24
125_L	264_V	0.706	0.24
11_Q	21_L	0.705	0.24
62_G	175_F	0.703	0.23
208_M	218_K	0.702	0.23
137_T	219_E	0.702	0.23
142_F	201_F	0.701	0.23
17_Q	91_L	0.701	0.23
237_L	242_T	0.701	0.23
91_L	125_L	0.700	0.23
261_I	264_V	0.698	0.23
77_F	168_I	0.697	0.23
114_N	131_L	0.696	0.23
22_M	37_Y	0.692	0.23
12_K	15_S	0.691	0.23
52_Y	237_L	0.691	0.23
131_L	239_C	0.690	0.23
165_A	201_F	0.689	0.23
84_S	236_V	0.680	0.22
154_S	272_A	0.675	0.22
6_M	170_D	0.674	0.22
214_S	260_Y	0.673	0.22
150_C	203_T	0.672	0.22
27_V	35_S	0.670	0.22
195_E	230_H	0.670	0.22
24_A	144_Q	0.669	0.22
210_F	260_Y	0.667	0.22
39_F	168_I	0.666	0.22
131_L	236_V	0.665	0.22
149_E	153_V	0.665	0.22
232_A	271_V	0.665	0.22
153_V	263_R	0.665	0.22
29_K	236_V	0.664	0.22
164_L	170_D	0.661	0.22
191_M	279_R	0.659	0.22
149_E	245_L	0.656	0.21
40_L	48_W	0.654	0.21
95_S	159_Y	0.653	0.21
136_I	206_V	0.652	0.21
37_Y	166_S	0.650	0.21
46_E	280_E	0.649	0.21
173_N	176_D	0.649	0.21
57_R	201_F	0.648	0.21
51_A	99_L	0.647	0.21
12_K	91_L	0.647	0.21
34_M	74_H	0.646	0.21
39_F	179_W	0.643	0.21
203_T	234_D	0.643	0.21
80_I	180_T	0.642	0.21
13_H	91_L	0.642	0.21
101_I	183_F	0.635	0.21
41_R	48_W	0.633	0.21
210_F	252_I	0.633	0.21
184_T	267_L	0.633	0.21
155_V	239_C	0.631	0.20
136_I	179_W	0.631	0.20
90_E	144_Q	0.630	0.20
179_W	275_Y	0.630	0.20
240_S	264_V	0.630	0.20
75_H	171_K	0.629	0.20
60_A	120_L	0.627	0.20
221_I	225_D	0.625	0.20
39_F	223_Q	0.625	0.20
145_V	150_C	0.624	0.20
150_C	155_V	0.623	0.20
154_S	250_G	0.623	0.20
2_N	91_L	0.621	0.20
196_H	229_V	0.620	0.20
240_S	268_A	0.618	0.20
125_L	233_Y	0.617	0.20
17_Q	81_I	0.616	0.20
242_T	269_R	0.615	0.20
56_S	75_H	0.614	0.20
56_S	251_A	0.613	0.20
165_A	177_L	0.611	0.20
91_L	94_D	0.610	0.20
132_D	178_E	0.610	0.20
132_D	179_W	0.607	0.20
27_V	105_E	0.606	0.19
208_M	222_K	0.606	0.19
35_S	209_L	0.604	0.19
22_M	80_I	0.604	0.19
205_D	218_K	0.600	0.19
60_A	258_T	0.599	0.19
117_N	220_A	0.598	0.19
3_I	125_L	0.596	0.19
278_E	281_K	0.595	0.19
220_A	264_V	0.594	0.19
108_I	128_E	0.594	0.19
34_M	60_A	0.590	0.19
131_L	179_W	0.589	0.19
255_T	279_R	0.588	0.19
43_I	191_M	0.588	0.19
211_Q	218_K	0.587	0.19
200_T	261_I	0.587	0.19
108_I	236_V	0.586	0.19
66_E	205_D	0.584	0.19
3_I	177_L	0.584	0.19
27_V	60_A	0.584	0.19
34_M	114_N	0.583	0.19
7_I	23_Q	0.582	0.19
77_F	125_L	0.581	0.19
8_L	21_L	0.581	0.19
74_H	167_Y	0.577	0.18
60_A	72_Y	0.575	0.18
191_M	278_E	0.575	0.18
131_L	272_A	0.574	0.18
41_R	234_D	0.574	0.18
200_T	245_L	0.574	0.18
137_T	155_V	0.572	0.18
34_M	234_D	0.572	0.18
88_I	145_V	0.568	0.18
16_S	98_A	0.568	0.18
155_V	220_A	0.566	0.18
145_V	206_V	0.566	0.18
248_A	251_A	0.565	0.18
2_N	6_M	0.564	0.18
214_S	218_K	0.564	0.18
117_N	214_S	0.564	0.18
54_E	189_F	0.563	0.18
119_S	177_L	0.563	0.18
148_L	153_V	0.562	0.18
157_I	266_N	0.562	0.18
43_I	132_D	0.562	0.18
116_E	234_D	0.561	0.18
270_K	273_K	0.561	0.18
26_D	119_S	0.560	0.18
274_T	278_E	0.560	0.18
53_V	222_K	0.558	0.18
34_M	264_V	0.558	0.18
48_W	112_E	0.558	0.18
71_L	197_S	0.557	0.18
106_H	167_Y	0.555	0.18
32_G	56_S	0.553	0.18
217_E	238_K	0.551	0.17
62_G	176_D	0.550	0.17
153_V	181_S	0.548	0.17
184_T	262_A	0.547	0.17
2_N	239_C	0.545	0.17
8_L	252_I	0.545	0.17
194_Y	281_K	0.544	0.17
154_S	172_E	0.543	0.17
37_Y	117_N	0.543	0.17
45_P	152_P	0.543	0.17
207_D	277_E	0.543	0.17
169_Q	178_E	0.542	0.17
183_F	207_D	0.541	0.17
80_I	164_L	0.540	0.17
73_Q	189_F	0.539	0.17
164_L	196_H	0.538	0.17
84_S	152_P	0.537	0.17
250_G	262_A	0.537	0.17
17_Q	49_K	0.536	0.17
57_R	261_I	0.536	0.17
119_S	122_C	0.535	0.17
34_M	150_C	0.534	0.17
171_K	216_Y	0.533	0.17
136_I	237_L	0.533	0.17
90_E	97_R	0.533	0.17
2_N	164_L	0.532	0.17
154_S	171_K	0.532	0.17
10_L	14_W	0.530	0.17
136_I	207_D	0.528	0.17
216_Y	220_A	0.527	0.17
42_S	276_Y	0.527	0.17
219_E	222_K	0.525	0.17
20_V	54_E	0.524	0.17
72_Y	189_F	0.524	0.17
60_A	119_S	0.522	0.16
9_T	170_D	0.522	0.16
119_S	243_F	0.521	0.16
30_G	33_T	0.521	0.16
81_I	154_S	0.521	0.16
26_D	179_W	0.520	0.16
260_Y	264_V	0.518	0.16
20_V	218_K	0.517	0.16
195_E	279_R	0.517	0.16
69_N	171_K	0.517	0.16
54_E	161_I	0.515	0.16
117_N	204_S	0.515	0.16
197_S	251_A	0.515	0.16
167_Y	174_V	0.514	0.16
123_A	223_Q	0.514	0.16
212_L	239_C	0.514	0.16
13_H	87_N	0.513	0.16
186_K	279_R	0.513	0.16
194_Y	275_Y	0.512	0.16
18_G	36_P	0.512	0.16
128_E	260_Y	0.512	0.16
103_P	222_K	0.511	0.16
183_F	187_D	0.509	0.16
262_A	266_N	0.508	0.16
44_G	81_I	0.508	0.16
137_T	275_Y	0.508	0.16
196_H	271_V	0.507	0.16
141_Y	169_Q	0.506	0.16
49_K	80_I	0.506	0.16
43_I	80_I	0.505	0.16
230_H	271_V	0.505	0.16
227_G	281_K	0.504	0.16
145_V	195_E	0.504	0.16
175_F	197_S	0.504	0.16
15_S	49_K	0.504	0.16
13_H	22_M	0.504	0.16
23_Q	72_Y	0.503	0.16
50_V	102_D	0.503	0.16
104_L	273_K	0.503	0.16
221_I	270_K	0.503	0.16
40_L	146_G	0.500	0.16
221_I	224_M	0.500	0.16

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
1j5wA	2	0.9492	100	0.003	Contact Map
3rf1A	2	0.9492	100	0.016	Contact Map
2zzeA	1	0.9153	100	0.703	Contact Map
2ztgA	1	0.9424	100	0.712	Contact Map
3wqyA	2	0.9288	100	0.795	Contact Map
3hy0A	1	0.8576	96.8	0.956	Contact Map
4cs4A	2	0.6034	96.4	0.959	Contact Map
1yfsA	1	0.8746	96	0.96	Contact Map
3dsqA	2	0.5898	95.9	0.961	Contact Map
3l4gA	2	0.6542	84.7	0.971	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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