SYFA - BACSU - GREMLIN Contacts

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SYFA - Phenylalanine--tRNA ligase alpha subunit

UniProt:	P17921	Sequences: MEEKLKQLEQEALEQVEAASSLKVVNDIRVQYLGKKGPITEVLRGMGKLSAEERPKMGALANEVRERIANAIADKNEKLEEEEMKQKLAGQTIDVTLPGNPVAVGGRHPLTVVIEEIEDLFIGMGYTVEEGPEVETDYYNFESLNLPKEHPARDMQDSFYITEETLMRTQTSPVQTRTMEKHEGKGPVKIICPGKVYRRDNDDATHSHQFMQIEGLVVDKNISMSDLKGTLELVAKKMFGQDREIRLRPSFFPFTEPSVEVDVTCFKCGGNGCSVCKGTGWIEILGAGMVHPNVLKMAGFDPKEYQGFAFGMGVERIAMLKYGIDDIRHFYTNDVRFISQFKQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	344 (326)
Sequences:	3364 (1727)
Seq/√Len:	95.6

ECOLI - SYFA
BACSU - SYFA
HALSA - SYFA
SULSO - SYFA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
220_K	304_E	6.540	1.00
136_T	139_Y	4.177	1.00
216_L	290_V	3.566	1.00
255_T	258_S	3.540	1.00
293_N	296_K	3.465	1.00
21_S	24_V	3.117	1.00
265_C	276_C	3.015	1.00
259_V	287_A	2.950	1.00
244_E	264_T	2.788	1.00
138_Y	143_S	2.698	1.00
137_D	142_E	2.670	1.00
232_E	245_I	2.645	1.00
75_K	78_K	2.563	1.00
15_Q	31_Q	2.537	1.00
116_E	321_K	2.454	1.00
45_G	48_K	2.404	1.00
117_I	213_I	2.395	1.00
215_G	310_F	2.393	1.00
296_K	302_P	2.371	1.00
126_Y	230_T	2.320	1.00
224_M	259_V	2.301	1.00
231_L	285_L	2.270	1.00
50_S	53_E	2.255	1.00
300_F	305_Y	2.196	1.00
217_V	222_I	2.170	1.00
11_E	15_Q	2.167	1.00
13_L	71_A	2.140	1.00
296_K	303_K	2.133	1.00
284_I	317_I	2.122	1.00
76_N	80_E	2.116	1.00
20_S	24_V	2.098	1.00
82_E	86_Q	2.068	1.00
276_C	280_G	2.045	1.00
139_Y	180_E	2.041	1.00
142_E	148_K	2.027	1.00
11_E	38_P	2.022	1.00
9_E	67_R	1.944	1.00
6_K	10_Q	1.939	1.00
226_D	229_G	1.922	1.00
7_Q	11_E	1.909	1.00
70_N	74_D	1.858	1.00
86_Q	90_G	1.847	1.00
31_Q	38_P	1.776	1.00
265_C	280_G	1.758	1.00
232_E	236_K	1.749	1.00
10_Q	14_E	1.730	1.00
276_C	279_T	1.721	1.00
178_T	182_H	1.702	1.00
265_C	279_T	1.677	1.00
117_I	314_V	1.671	1.00
203_D	206_H	1.642	1.00
59_A	63_E	1.642	1.00
155_M	250_S	1.639	1.00
176_T	298_A	1.591	1.00
19_A	28_I	1.586	1.00
23_K	27_D	1.586	1.00
78_K	82_E	1.575	1.00
107_R	111_T	1.521	1.00
138_Y	180_E	1.510	1.00
129_E	190_I	1.507	1.00
261_V	285_L	1.502	1.00
51_A	54_R	1.494	1.00
107_R	115_E	1.489	1.00
179_M	188_V	1.486	1.00
115_E	118_E	1.474	1.00
140_N	169_T	1.473	1.00
135_E	177_R	1.452	1.00
120_L	237_K	1.436	1.00
77_E	81_E	1.427	1.00
14_E	18_A	1.420	0.99
9_E	13_L	1.418	0.99
16_V	19_A	1.410	0.99
69_A	73_A	1.408	0.99
200_D	207_S	1.407	0.99
37_G	40_T	1.398	0.99
187_P	219_D	1.397	0.99
207_S	331_Y	1.392	0.99
265_C	275_V	1.392	0.99
26_N	29_R	1.386	0.99
55_P	59_A	1.347	0.99
200_D	208_H	1.347	0.99
49_L	57_M	1.344	0.99
243_R	264_T	1.342	0.99
42_V	61_A	1.338	0.99
162_T	165_T	1.332	0.99
81_E	85_K	1.331	0.99
22_L	80_E	1.328	0.99
9_E	64_V	1.326	0.99
123_G	237_K	1.317	0.99
6_K	9_E	1.308	0.99
312_M	317_I	1.308	0.99
209_Q	331_Y	1.307	0.99
7_Q	10_Q	1.306	0.99
41_E	44_R	1.300	0.99
236_K	241_Q	1.296	0.99
175_Q	290_V	1.284	0.99
22_L	79_L	1.279	0.99
234_V	238_M	1.269	0.99
238_M	317_I	1.261	0.99
47_G	54_R	1.255	0.99
57_M	61_A	1.251	0.99
218_V	295_L	1.248	0.99
68_I	72_I	1.235	0.99
172_S	214_E	1.224	0.98
146_L	170_Q	1.219	0.98
27_D	31_Q	1.211	0.98
146_L	293_N	1.210	0.98
22_L	83_E	1.208	0.98
83_E	86_Q	1.205	0.98
16_V	28_I	1.204	0.98
74_D	78_K	1.204	0.98
248_R	262_D	1.202	0.98
128_V	191_I	1.200	0.98
12_A	32_Y	1.199	0.98
235_A	261_V	1.197	0.98
293_N	297_M	1.195	0.98
129_E	174_V	1.179	0.98
324_I	330_F	1.178	0.98
10_Q	13_L	1.174	0.98
140_N	173_P	1.170	0.98
85_K	89_A	1.166	0.98
43_L	61_A	1.160	0.98
132_P	177_R	1.159	0.98
124_M	233_L	1.158	0.98
264_T	276_C	1.155	0.98
114_I	314_V	1.153	0.98
223_S	226_D	1.153	0.98
143_S	176_T	1.144	0.98
60_L	63_E	1.143	0.98
277_K	280_G	1.138	0.98
266_F	276_C	1.135	0.98
53_E	56_K	1.128	0.97
13_L	17_E	1.126	0.97
138_Y	142_E	1.124	0.97
61_A	64_V	1.123	0.97
200_D	203_D	1.118	0.97
15_Q	32_Y	1.106	0.97
56_K	60_L	1.106	0.97
265_C	277_K	1.104	0.97
230_T	308_F	1.102	0.97
26_N	76_N	1.099	0.97
285_L	312_M	1.093	0.97
265_C	274_S	1.093	0.97
200_D	205_T	1.092	0.97
12_A	68_I	1.091	0.97
284_I	320_L	1.083	0.97
13_L	67_R	1.083	0.97
127_T	182_H	1.083	0.97
266_F	275_V	1.081	0.97
42_V	45_G	1.066	0.96
128_V	193_P	1.062	0.96
113_V	116_E	1.062	0.96
129_E	192_C	1.060	0.96
156_Q	199_R	1.058	0.96
63_E	67_R	1.058	0.96
19_A	25_V	1.055	0.96
232_E	247_L	1.052	0.96
261_V	287_A	1.046	0.96
44_R	47_G	1.038	0.96
191_I	213_I	1.035	0.96
155_M	170_Q	1.034	0.96
301_D	304_E	1.031	0.96
252_F	260_E	1.027	0.96
73_A	77_E	1.027	0.96
87_K	91_Q	1.024	0.95
231_L	261_V	1.023	0.95
114_I	118_E	1.011	0.95
143_S	298_A	1.011	0.95
179_M	300_F	1.010	0.95
118_E	128_V	1.009	0.95
172_S	175_Q	1.009	0.95
236_K	242_D	1.009	0.95
83_E	87_K	1.007	0.95
161_I	166_L	1.007	0.95
274_S	279_T	1.000	0.95
113_V	318_A	0.994	0.95
190_I	216_L	0.994	0.95
66_E	70_N	0.988	0.94
118_E	191_I	0.988	0.94
39_I	64_V	0.987	0.94
146_L	160_Y	0.987	0.94
73_A	76_N	0.985	0.94
138_Y	297_M	0.976	0.94
42_V	57_M	0.972	0.94
24_V	27_D	0.970	0.94
275_V	319_M	0.970	0.94
21_S	83_E	0.968	0.94
66_E	69_A	0.966	0.94
327_I	330_F	0.951	0.93
51_A	55_P	0.951	0.93
26_N	30_V	0.950	0.93
217_V	230_T	0.947	0.93
137_D	156_Q	0.945	0.93
14_E	17_E	0.945	0.93
38_P	41_E	0.943	0.93
86_Q	89_A	0.939	0.93
233_L	237_K	0.936	0.93
218_V	306_Q	0.933	0.93
315_E	330_F	0.932	0.93
84_M	88_L	0.927	0.92
89_A	92_T	0.920	0.92
113_V	238_M	0.915	0.92
30_V	34_G	0.910	0.92
200_D	206_H	0.906	0.92
144_L	176_T	0.902	0.91
88_L	91_Q	0.897	0.91
245_I	261_V	0.889	0.91
264_T	279_T	0.888	0.91
113_V	322_Y	0.888	0.91
82_E	85_K	0.885	0.91
337_F	341_F	0.883	0.90
148_K	164_E	0.882	0.90
291_H	298_A	0.878	0.90
39_I	68_I	0.877	0.90
295_L	300_F	0.874	0.90
112_V	322_Y	0.871	0.90
170_Q	173_P	0.870	0.90
143_S	180_E	0.870	0.90
111_T	115_E	0.866	0.90
46_M	57_M	0.862	0.89
174_V	192_C	0.856	0.89
6_K	60_L	0.856	0.89
38_P	42_V	0.855	0.89
57_M	60_L	0.853	0.89
75_K	82_E	0.852	0.89
62_N	65_R	0.852	0.89
41_E	45_G	0.849	0.89
266_F	274_S	0.849	0.89
131_G	174_V	0.847	0.89
318_A	322_Y	0.846	0.88
211_M	315_E	0.834	0.88
251_F	291_H	0.830	0.88
40_T	43_L	0.829	0.87
146_L	156_Q	0.828	0.87
133_E	197_Y	0.824	0.87
135_E	173_P	0.822	0.87
12_A	19_A	0.822	0.87
117_I	191_I	0.816	0.87
109_P	112_V	0.815	0.87
265_C	278_G	0.815	0.87
213_I	315_E	0.812	0.86
152_A	156_Q	0.811	0.86
11_E	14_E	0.807	0.86
110_L	211_M	0.803	0.86
266_F	282_I	0.803	0.86
207_S	332_T	0.803	0.86
180_E	298_A	0.802	0.86
182_H	186_G	0.799	0.85
221_N	304_E	0.798	0.85
266_F	279_T	0.793	0.85
23_K	83_E	0.791	0.85
29_R	76_N	0.784	0.84
155_M	251_F	0.784	0.84
67_R	71_A	0.783	0.84
126_Y	308_F	0.779	0.84
40_T	44_R	0.776	0.84
250_S	262_D	0.774	0.84
329_H	332_T	0.774	0.84
71_A	74_D	0.774	0.84
248_R	260_E	0.772	0.83
166_L	169_T	0.771	0.83
182_H	185_K	0.768	0.83
224_M	289_M	0.768	0.83
219_D	305_Y	0.765	0.83
47_G	51_A	0.764	0.83
222_I	226_D	0.759	0.82
274_S	280_G	0.758	0.82
325_D	329_H	0.756	0.82
291_H	296_K	0.751	0.82
178_T	188_V	0.749	0.82
170_Q	199_R	0.747	0.81
84_M	87_K	0.746	0.81
179_M	216_L	0.745	0.81
129_E	178_T	0.745	0.81
337_F	340_Q	0.744	0.81
46_M	49_L	0.743	0.81
327_I	331_Y	0.740	0.81
115_E	119_D	0.739	0.81
235_A	317_I	0.738	0.81
275_V	279_T	0.737	0.81
79_L	83_E	0.736	0.80
289_M	308_F	0.734	0.80
13_L	16_V	0.732	0.80
137_D	152_A	0.732	0.80
220_K	305_Y	0.729	0.80
295_L	302_P	0.729	0.80
80_E	83_E	0.727	0.80
264_T	280_G	0.727	0.80
71_A	75_K	0.725	0.79
49_L	53_E	0.723	0.79
235_A	284_I	0.719	0.79
137_D	155_M	0.712	0.78
17_E	78_K	0.712	0.78
119_D	123_G	0.710	0.78
179_M	298_A	0.710	0.78
211_M	331_Y	0.709	0.78
221_N	306_Q	0.709	0.78
44_R	61_A	0.707	0.78
37_G	55_P	0.703	0.77
45_G	57_M	0.702	0.77
107_R	112_V	0.702	0.77
235_A	285_L	0.696	0.77
35_K	40_T	0.692	0.76
171_T	214_E	0.691	0.76
295_L	298_A	0.690	0.76
12_A	16_V	0.690	0.76
155_M	169_T	0.688	0.76
117_I	312_M	0.686	0.76
142_E	156_Q	0.685	0.75
43_L	65_R	0.684	0.75
70_N	73_A	0.682	0.75
335_V	339_S	0.682	0.75
43_L	47_G	0.680	0.75
146_L	152_A	0.677	0.75
255_T	260_E	0.675	0.74
178_T	190_I	0.673	0.74
161_I	164_E	0.671	0.74
15_Q	18_A	0.671	0.74
43_L	46_M	0.666	0.73
174_V	178_T	0.665	0.73
205_T	319_M	0.665	0.73
205_T	224_M	0.664	0.73
160_Y	199_R	0.663	0.73
155_M	201_N	0.662	0.73
75_K	79_L	0.661	0.73
289_M	295_L	0.661	0.73
7_Q	27_D	0.659	0.73
119_D	122_I	0.659	0.73
259_V	310_F	0.657	0.72
275_V	280_G	0.657	0.72
185_K	304_E	0.657	0.72
82_E	90_G	0.655	0.72
16_V	72_I	0.652	0.72
243_R	266_F	0.651	0.72
203_D	208_H	0.651	0.72
274_S	277_K	0.650	0.72
103_A	339_S	0.649	0.71
179_M	218_V	0.649	0.71
182_H	188_V	0.646	0.71
176_T	297_M	0.640	0.70
21_S	25_V	0.638	0.70
219_D	226_D	0.638	0.70
188_V	216_L	0.638	0.70
290_V	307_G	0.637	0.70
9_E	63_E	0.636	0.70
22_L	26_N	0.635	0.70
121_F	234_V	0.634	0.70
110_L	209_Q	0.633	0.70
42_V	64_V	0.633	0.70
188_V	300_F	0.633	0.70
23_K	30_V	0.633	0.70
220_K	302_P	0.632	0.69
204_A	207_S	0.631	0.69
250_S	260_E	0.630	0.69
233_L	236_K	0.630	0.69
63_E	66_E	0.628	0.69
42_V	46_M	0.628	0.69
7_Q	20_S	0.628	0.69
77_E	80_E	0.626	0.69
16_V	29_R	0.626	0.69
186_G	300_F	0.625	0.69
12_A	28_I	0.624	0.69
252_F	283_E	0.622	0.68
250_S	261_V	0.622	0.68
106_G	112_V	0.620	0.68
18_A	24_V	0.620	0.68
200_D	255_T	0.619	0.68
122_I	128_V	0.617	0.68
137_D	146_L	0.615	0.67
147_P	154_D	0.612	0.67
228_K	287_A	0.605	0.66
189_K	247_L	0.604	0.66
22_L	76_N	0.604	0.66
46_M	61_A	0.602	0.66
136_T	165_T	0.600	0.66
129_E	182_H	0.598	0.65
208_H	332_T	0.596	0.65
10_Q	20_S	0.595	0.65
228_K	310_F	0.595	0.65
33_L	69_A	0.595	0.65
138_Y	298_A	0.593	0.65
275_V	282_I	0.591	0.64
200_D	258_S	0.591	0.64
201_N	209_Q	0.591	0.64
64_V	67_R	0.589	0.64
156_Q	250_S	0.589	0.64
110_L	207_S	0.588	0.64
190_I	290_V	0.588	0.64
135_E	140_N	0.586	0.64
172_S	179_M	0.585	0.64
208_H	327_I	0.584	0.63
36_K	40_T	0.584	0.63
39_I	42_V	0.583	0.63
203_D	207_S	0.582	0.63
330_F	337_F	0.582	0.63
171_T	175_Q	0.582	0.63
250_S	255_T	0.581	0.63
239_F	254_F	0.581	0.63
211_M	312_M	0.580	0.63
67_R	70_N	0.580	0.63
213_I	314_V	0.579	0.63
77_E	82_E	0.578	0.63
43_L	57_M	0.578	0.63
110_L	201_N	0.577	0.63
250_S	279_T	0.576	0.62
17_E	71_A	0.576	0.62
20_S	23_K	0.575	0.62
175_Q	214_E	0.575	0.62
247_L	259_V	0.574	0.62
204_A	274_S	0.573	0.62
246_R	281_W	0.572	0.62
186_G	298_A	0.572	0.62
236_K	244_E	0.572	0.62
243_R	263_V	0.572	0.62
319_M	323_G	0.571	0.62
37_G	62_N	0.571	0.62
320_L	327_I	0.571	0.62
195_K	201_N	0.570	0.62
8_L	11_E	0.570	0.62
291_H	295_L	0.563	0.61
45_G	50_S	0.561	0.60
114_I	211_M	0.561	0.60
178_T	181_K	0.560	0.60
327_I	332_T	0.559	0.60
282_I	318_A	0.559	0.60
18_A	78_K	0.558	0.60
50_S	56_K	0.558	0.60
10_Q	41_E	0.557	0.60
178_T	186_G	0.555	0.60
246_R	262_D	0.554	0.59
116_E	120_L	0.553	0.59
114_I	170_Q	0.550	0.59
122_I	189_K	0.550	0.59
129_E	181_K	0.547	0.58
206_H	327_I	0.546	0.58
23_K	26_N	0.546	0.58
146_L	149_E	0.544	0.58
149_E	282_I	0.541	0.58
132_P	135_E	0.540	0.57
43_L	62_N	0.539	0.57
232_E	244_E	0.538	0.57
172_S	193_P	0.537	0.57
110_L	315_E	0.535	0.57
126_Y	189_K	0.532	0.56
263_V	266_F	0.532	0.56
132_P	174_V	0.532	0.56
199_R	208_H	0.532	0.56
286_G	313_G	0.531	0.56
116_E	237_K	0.531	0.56
172_S	290_V	0.530	0.56
174_V	287_A	0.529	0.56
158_S	300_F	0.529	0.56
126_Y	217_V	0.527	0.56
179_M	295_L	0.527	0.56
33_L	68_I	0.526	0.56
193_P	214_E	0.525	0.55
155_M	199_R	0.524	0.55
224_M	338_I	0.523	0.55
315_E	331_Y	0.522	0.55
218_V	298_A	0.522	0.55
189_K	219_D	0.521	0.55
126_Y	341_F	0.521	0.55
43_L	54_R	0.521	0.55
289_M	306_Q	0.521	0.55
142_E	155_M	0.520	0.55
160_Y	200_D	0.519	0.55
224_M	282_I	0.518	0.54
112_V	116_E	0.517	0.54
133_E	195_K	0.517	0.54
7_Q	14_E	0.515	0.54
222_I	229_G	0.514	0.54
224_M	251_F	0.514	0.54
174_V	177_R	0.513	0.54
333_N	338_I	0.513	0.54
188_V	217_V	0.512	0.54
208_H	211_M	0.511	0.53
16_V	68_I	0.510	0.53
329_H	337_F	0.509	0.53
12_A	15_Q	0.509	0.53
50_S	57_M	0.509	0.53
33_L	62_N	0.508	0.53
215_G	312_M	0.507	0.53
333_N	337_F	0.505	0.53
277_K	282_I	0.505	0.53
228_K	284_I	0.504	0.52
235_A	245_I	0.504	0.52
250_S	258_S	0.501	0.52
28_I	31_Q	0.500	0.52
301_D	305_Y	0.500	0.52

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
4p72C	2	0.7122	100	0.332	Contact Map
1b7yA	2	0.6977	100	0.366	Contact Map
3pcoA	2	0.939	100	0.397	Contact Map
3l4gA	2	0.9593	100	0.511	Contact Map
3cmqA	1	0.7442	100	0.557	Contact Map
2rhqA	2	0.7703	100	0.566	Contact Map
2du3A	4	0.782	100	0.591	Contact Map
2du7A	7	0.7384	100	0.623	Contact Map
2odrC	4	0.7267	100	0.631	Contact Map
2odrA	4	0.7267	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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