SYY - HALSA - GREMLIN Contacts

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SYY - Tyrosine--tRNA ligase

UniProt:	Q9HN62	Sequences: MNAYERITRNTAEVVTEEEVRELAEDPEGKRVYVGYEPSGVLHLGHLLTANKLMDLQDAGMEVVVLLADVHAYLNDKGSFEEIRATADQMKAQFLAYGLDEDQTEFVLGSSFQLDEDYELDLHAMQVETSLKRAQRAMAEIQSGETPKVSHVVYPLMQALDIEYLDLDLAIGGMDQRKVHMLAREELPSVGYEKRPVLHTPIIGDLGSGDGKMSSSEGVTISMEDSTADIEEKVTGAFCPQTRDPEGETVNPVLELFQYHVFPRFDEVVVQRPDEYGGDLVYESYEDLADDLESGELHPADAKGALAAALDELIEPGRQRLREIRGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	327 (275)
Sequences:	7144 (3349)
Seq/√Len:	202.0

ECOLI - SYW SYY
BACSU - SYW SYY2 SYY1
HALSA - SYY SYW2
SULSO - SYY SYW

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
226_S	229_D	4.552	1.00
31_R	62_E	3.638	1.00
64_V	105_E	3.005	1.00
315_E	319_Q	2.982	1.00
231_E	235_T	2.758	1.00
289_A	293_E	2.655	1.00
312_E	315_E	2.637	1.00
292_L	305_A	2.594	1.00
33_Y	66_L	2.592	1.00
85_A	89_Q	2.589	1.00
286_E	289_A	2.563	1.00
128_E	152_V	2.462	1.00
286_E	290_D	2.310	1.00
79_S	82_E	2.293	1.00
62_E	105_E	2.271	1.00
287_D	291_D	2.253	1.00
54_M	58_D	2.237	1.00
132_K	152_V	2.139	1.00
229_D	232_E	2.060	1.00
283_E	291_D	2.060	1.00
283_E	287_D	2.057	1.00
227_T	311_D	2.051	1.00
235_T	304_G	1.997	1.00
284_S	287_D	1.946	1.00
59_A	103_Q	1.925	1.00
82_E	85_A	1.913	1.00
225_D	233_K	1.909	1.00
38_P	72_A	1.903	1.00
295_G	301_D	1.873	1.00
87_A	108_L	1.852	1.00
233_K	236_G	1.843	1.00
149_V	153_V	1.829	1.00
117_D	120_L	1.829	1.00
97_Y	317_G	1.800	1.00
33_Y	68_A	1.771	1.00
163_E	187_L	1.750	1.00
290_D	293_E	1.737	1.00
231_E	307_A	1.727	1.00
205_D	219_V	1.715	1.00
187_L	195_R	1.712	1.00
64_V	167_L	1.699	1.00
318_R	322_R	1.681	1.00
93_Q	321_L	1.679	1.00
255_E	258_Q	1.667	1.00
36_Y	94_F	1.665	1.00
300_A	304_G	1.647	1.00
227_T	315_E	1.639	1.00
234_V	310_L	1.624	1.00
31_R	64_V	1.618	1.00
247_G	251_N	1.609	1.00
163_E	190_V	1.600	1.00
30_K	168_D	1.599	1.00
287_D	290_D	1.597	1.00
38_P	67_L	1.580	1.00
230_I	311_D	1.568	1.00
301_D	304_G	1.556	1.00
67_L	91_K	1.554	1.00
285_Y	289_A	1.553	1.00
168_D	199_H	1.544	1.00
131_L	149_V	1.543	1.00
258_Q	288_L	1.508	1.00
53_L	56_L	1.482	1.00
225_D	229_D	1.470	1.00
180_H	197_V	1.450	1.00
284_S	305_A	1.445	1.00
198_L	202_I	1.439	1.00
99_L	104_T	1.438	1.00
290_D	294_S	1.436	1.00
107_V	165_L	1.431	1.00
211_G	217_E	1.418	1.00
307_A	311_D	1.402	1.00
247_G	250_V	1.400	1.00
288_L	292_L	1.393	1.00
70_V	113_Q	1.382	1.00
227_T	318_R	1.374	1.00
222_S	225_D	1.367	1.00
261_V	306_L	1.362	1.00
107_V	111_S	1.357	1.00
50_A	94_F	1.355	1.00
159_A	183_A	1.343	1.00
196_P	202_I	1.340	1.00
231_E	308_A	1.328	1.00
123_H	153_V	1.320	1.00
193_E	198_L	1.317	1.00
247_G	255_E	1.317	1.00
52_K	56_L	1.314	1.00
166_D	199_H	1.305	1.00
198_L	201_P	1.296	1.00
205_D	217_E	1.283	1.00
291_D	305_A	1.273	1.00
128_E	132_K	1.270	1.00
194_K	197_V	1.244	1.00
232_E	236_G	1.243	1.00
69_D	110_S	1.242	1.00
84_R	88_D	1.236	1.00
115_D	165_L	1.225	1.00
308_A	312_E	1.224	1.00
193_E	196_P	1.224	1.00
305_A	309_A	1.216	1.00
33_Y	167_L	1.215	1.00
91_K	95_L	1.212	1.00
33_Y	64_V	1.200	1.00
82_E	86_T	1.198	1.00
34_V	49_T	1.184	1.00
70_V	116_E	1.178	1.00
264_R	309_A	1.161	1.00
119_E	123_H	1.159	1.00
230_I	314_I	1.147	1.00
235_T	239_C	1.139	1.00
35_G	66_L	1.138	1.00
108_L	111_S	1.135	1.00
69_D	111_S	1.134	1.00
195_R	198_L	1.129	1.00
205_D	211_G	1.119	1.00
194_K	198_L	1.116	1.00
306_L	309_A	1.115	1.00
262_F	288_L	1.110	1.00
100_D	103_Q	1.102	1.00
149_V	156_L	1.101	1.00
113_Q	117_D	1.091	1.00
248_E	255_E	1.090	1.00
32_V	53_L	1.086	1.00
42_L	90_M	1.074	1.00
298_H	301_D	1.058	1.00
235_T	238_F	1.052	1.00
36_Y	49_T	1.051	1.00
231_E	311_D	1.049	1.00
252_P	255_E	1.046	1.00
34_V	171_I	1.034	1.00
49_T	200_T	1.034	1.00
256_L	260_H	1.031	1.00
292_L	302_A	1.029	1.00
36_Y	42_L	1.027	1.00
110_S	114_L	1.022	1.00
30_K	61_M	1.020	1.00
260_H	263_P	1.008	1.00
98_G	101_E	1.006	1.00
196_P	199_H	1.002	1.00
32_V	56_L	1.002	1.00
166_D	191_G	1.001	1.00
309_A	312_E	0.994	1.00
36_Y	50_A	0.993	1.00
93_Q	224_E	0.988	1.00
42_L	94_F	0.987	1.00
81_E	85_A	0.982	1.00
311_D	315_E	0.981	1.00
52_K	313_L	0.975	1.00
163_E	191_G	0.965	0.99
251_N	254_L	0.955	0.99
319_Q	322_R	0.951	0.99
234_V	238_F	0.950	0.99
66_L	107_V	0.947	0.99
238_F	242_T	0.947	0.99
234_V	239_C	0.946	0.99
223_M	314_I	0.945	0.99
78_G	86_T	0.944	0.99
197_V	200_T	0.942	0.99
207_G	211_G	0.939	0.99
46_H	50_A	0.936	0.99
56_L	60_G	0.935	0.99
311_D	318_R	0.931	0.99
128_E	137_A	0.921	0.99
185_E	188_P	0.920	0.99
31_R	167_L	0.917	0.99
226_S	322_R	0.917	0.99
233_K	238_F	0.916	0.99
265_F	269_V	0.913	0.99
316_P	320_R	0.912	0.99
207_G	217_E	0.909	0.99
35_G	68_A	0.909	0.99
292_L	299_P	0.905	0.99
113_Q	116_E	0.904	0.99
85_A	88_D	0.903	0.99
92_A	95_L	0.901	0.99
199_H	202_I	0.900	0.99
188_P	192_Y	0.900	0.99
258_Q	262_F	0.898	0.99
94_F	106_F	0.895	0.99
29_G	62_E	0.895	0.99
75_N	78_G	0.895	0.99
95_L	106_F	0.892	0.99
187_L	191_G	0.889	0.99
69_D	87_A	0.887	0.99
120_L	124_A	0.885	0.99
228_A	231_E	0.881	0.99
30_K	169_L	0.871	0.99
256_L	259_Y	0.869	0.99
233_K	239_C	0.867	0.99
88_D	92_A	0.867	0.99
301_D	305_A	0.865	0.99
62_E	103_Q	0.864	0.99
127_V	130_S	0.864	0.99
36_Y	51_N	0.864	0.99
264_R	313_L	0.864	0.99
91_K	106_F	0.856	0.99
258_Q	285_Y	0.851	0.99
311_D	314_I	0.850	0.99
41_V	222_S	0.840	0.99
224_E	321_L	0.838	0.99
81_E	84_R	0.837	0.99
252_P	258_Q	0.836	0.99
235_T	307_A	0.836	0.99
162_I	183_A	0.835	0.98
55_D	58_D	0.834	0.98
249_T	255_E	0.830	0.98
309_A	313_L	0.830	0.98
248_E	252_P	0.822	0.98
291_D	294_S	0.821	0.98
36_Y	54_M	0.819	0.98
88_D	91_K	0.819	0.98
122_L	156_L	0.819	0.98
252_P	256_L	0.814	0.98
135_Q	139_A	0.814	0.98
129_T	133_R	0.813	0.98
131_L	156_L	0.813	0.98
262_F	285_Y	0.811	0.98
257_F	260_H	0.802	0.98
124_A	150_S	0.802	0.98
113_Q	160_L	0.797	0.98
289_A	292_L	0.790	0.98
126_Q	186_E	0.789	0.98
242_T	251_N	0.788	0.98
236_G	239_C	0.787	0.98
65_V	94_F	0.780	0.98
193_E	197_V	0.779	0.98
258_Q	289_A	0.778	0.98
30_K	60_G	0.776	0.98
285_Y	288_L	0.774	0.98
54_M	94_F	0.773	0.98
315_E	318_R	0.773	0.98
242_T	255_E	0.769	0.97
54_M	65_V	0.768	0.97
64_V	107_V	0.768	0.97
245_P	248_E	0.766	0.97
257_F	289_A	0.764	0.97
257_F	262_F	0.761	0.97
51_N	97_Y	0.759	0.97
153_V	156_L	0.755	0.97
260_H	264_R	0.754	0.97
235_T	300_A	0.754	0.97
129_T	182_L	0.749	0.97
118_Y	160_L	0.747	0.97
41_V	224_E	0.745	0.97
47_L	52_K	0.745	0.97
34_V	54_M	0.744	0.97
217_E	220_T	0.743	0.97
130_S	189_S	0.743	0.97
44_L	264_R	0.741	0.97
118_Y	157_M	0.740	0.97
159_A	182_L	0.739	0.97
316_P	319_Q	0.736	0.97
46_H	49_T	0.735	0.97
196_P	200_T	0.735	0.97
193_E	200_T	0.735	0.97
55_D	59_A	0.735	0.97
255_E	259_Y	0.734	0.97
195_R	200_T	0.731	0.97
231_E	234_V	0.731	0.97
58_D	104_T	0.726	0.96
283_E	286_E	0.725	0.96
231_E	304_G	0.718	0.96
133_R	185_E	0.715	0.96
299_P	302_A	0.713	0.96
105_E	108_L	0.712	0.96
308_A	311_D	0.710	0.96
48_L	203_I	0.709	0.96
89_Q	321_L	0.708	0.96
125_M	186_E	0.708	0.96
304_G	308_A	0.704	0.96
243_R	298_H	0.702	0.96
235_T	241_Q	0.700	0.96
247_G	256_L	0.697	0.95
252_P	257_F	0.696	0.95
257_F	261_V	0.695	0.95
261_V	264_R	0.684	0.95
253_V	306_L	0.683	0.95
223_M	317_G	0.683	0.95
238_F	253_V	0.680	0.95
37_E	75_N	0.678	0.95
83_I	87_A	0.676	0.95
228_A	232_E	0.674	0.95
235_T	242_T	0.672	0.94
123_H	148_K	0.671	0.94
101_E	104_T	0.666	0.94
227_T	231_E	0.666	0.94
221_I	234_V	0.666	0.94
122_L	157_M	0.663	0.94
222_S	233_K	0.663	0.94
143_S	146_T	0.658	0.94
78_G	82_E	0.658	0.94
238_F	241_Q	0.655	0.94
195_R	199_H	0.655	0.94
34_V	46_H	0.654	0.94
95_L	101_E	0.653	0.94
119_E	153_V	0.653	0.94
249_T	252_P	0.652	0.94
206_L	233_K	0.650	0.93
240_P	244_D	0.649	0.93
73_Y	78_G	0.646	0.93
262_F	289_A	0.645	0.93
73_Y	80_F	0.645	0.93
130_S	133_R	0.643	0.93
261_V	302_A	0.641	0.93
245_P	254_L	0.640	0.93
292_L	295_G	0.637	0.93
57_Q	104_T	0.635	0.93
67_L	90_M	0.634	0.93
137_A	181_M	0.632	0.92
80_F	84_R	0.632	0.92
251_N	256_L	0.631	0.92
239_C	243_R	0.631	0.92
286_E	293_E	0.630	0.92
99_L	102_D	0.630	0.92
130_S	185_E	0.627	0.92
90_M	94_F	0.627	0.92
42_L	46_H	0.626	0.92
239_C	242_T	0.625	0.92
261_V	265_F	0.623	0.92
156_L	186_E	0.622	0.92
237_A	240_P	0.621	0.92
181_M	184_R	0.619	0.92
304_G	307_A	0.618	0.92
252_P	262_F	0.617	0.92
305_A	308_A	0.614	0.91
254_L	257_F	0.613	0.91
144_G	147_P	0.613	0.91
261_V	305_A	0.612	0.91
314_I	318_R	0.611	0.91
250_V	254_L	0.610	0.91
57_Q	63_V	0.607	0.91
166_D	193_E	0.606	0.91
61_M	169_L	0.606	0.91
51_N	55_D	0.604	0.91
259_Y	262_F	0.604	0.91
84_R	87_A	0.603	0.91
159_A	163_E	0.602	0.91
283_E	288_L	0.601	0.90
99_L	106_F	0.600	0.90
284_S	309_A	0.599	0.90
229_D	233_K	0.598	0.90
37_E	90_M	0.598	0.90
69_D	108_L	0.597	0.90
227_T	314_I	0.596	0.90
261_V	309_A	0.595	0.90
260_H	265_F	0.595	0.90
118_Y	121_D	0.592	0.90
248_E	251_N	0.592	0.90
36_Y	46_H	0.591	0.90
238_F	243_R	0.591	0.90
92_A	321_L	0.589	0.90
263_P	266_D	0.588	0.90
70_V	121_D	0.587	0.89
291_D	302_A	0.586	0.89
255_E	261_V	0.585	0.89
234_V	306_L	0.584	0.89
255_E	285_Y	0.582	0.89
310_L	313_L	0.581	0.89
163_E	186_E	0.580	0.89
123_H	156_L	0.580	0.89
295_G	298_H	0.579	0.89
123_H	149_V	0.577	0.89
80_F	83_I	0.576	0.89
313_L	317_G	0.573	0.88
63_V	104_T	0.573	0.88
41_V	86_T	0.573	0.88
50_A	54_M	0.568	0.88
258_Q	261_V	0.566	0.88
188_P	200_T	0.565	0.88
53_L	65_V	0.565	0.88
251_N	255_E	0.556	0.87
49_T	171_I	0.556	0.87
119_E	149_V	0.554	0.87
248_E	254_L	0.553	0.87
205_D	218_G	0.552	0.86
223_M	313_L	0.551	0.86
249_T	253_V	0.550	0.86
31_R	168_D	0.550	0.86
34_V	65_V	0.546	0.86
194_K	202_I	0.544	0.86
39_S	43_H	0.544	0.86
130_S	146_T	0.543	0.86
204_G	263_P	0.542	0.85
318_R	321_L	0.540	0.85
262_F	266_D	0.540	0.85
234_V	240_P	0.540	0.85
31_R	166_D	0.539	0.85
250_V	256_L	0.538	0.85
225_D	230_I	0.538	0.85
93_Q	318_R	0.530	0.84
133_R	137_A	0.526	0.84
197_V	202_I	0.526	0.84
158_Q	183_A	0.526	0.84
83_I	86_T	0.525	0.84
228_A	300_A	0.521	0.83
44_L	310_L	0.521	0.83
259_Y	292_L	0.521	0.83
137_A	141_I	0.520	0.83
56_L	169_L	0.519	0.83
47_L	313_L	0.513	0.82
170_A	180_H	0.513	0.82
128_E	189_S	0.510	0.82
142_Q	146_T	0.508	0.82
98_G	102_D	0.508	0.82
235_T	243_R	0.508	0.82
41_V	89_Q	0.506	0.81
50_A	99_L	0.505	0.81
115_D	164_Y	0.505	0.81
163_E	195_R	0.504	0.81
182_L	186_E	0.503	0.81
127_V	148_K	0.500	0.81
251_N	258_Q	0.500	0.81
107_V	112_F	0.500	0.81

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
3vgjA	2	0.9878	100	0.158	Contact Map
2cycA	2	0.9878	100	0.168	Contact Map
2dlcX	2	0.9541	100	0.175	Contact Map
2cyaA	2	0.945	100	0.179	Contact Map
1n3lA	2	0.9511	100	0.181	Contact Map
3p0jA	1	0.9817	100	0.19	Contact Map
2zp1A	2	0.9388	100	0.192	Contact Map
3jxeA	2	0.896	100	0.208	Contact Map
3i05A	2	0.844	100	0.227	Contact Map
3prhA	2	0.8196	100	0.229	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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