PYRB - SULSO - GREMLIN Contacts

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PYRB - Aspartate carbamoyltransferase

UniProt:	Q9UX08	Sequences: MRLRHVVSSLDLTRDDYFRIFELADKFYDVKKLNYLSGKVVSLAFFEPSTRTAQSFHTAAIKLGADVIGFASEESTSIAKGENLADTIRMLNNYSNCIVMRHKFDGAALFASEISDIPIINAGDGKHEHPTQAVIDLYTVYKAFGEIDGRTFALLGDLKYARTVNSLLRALTRFKPKKVFLISPSQLKVRREILDELNYPVIETENPYDVIQEIDVLYVTRIQKERFVDEVEYEKVKESYVVDLKLVNMMKKDGIILHPLPRVTEIDRRVDKTVNAKYFYQASLAVPVRMALFYEVLGDREDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	303 (291)
Sequences:	7070 (3725)
Seq/√Len:	218.4

ECOLI - PYRB YGEW OTC1 OTC2
BACSU - PYRB OTC
HALSA - PYRB OTCC
SULSO - PYRB OTC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
244_L	269_R	4.060	1.00
151_T	178_K	3.916	1.00
151_T	180_F	3.405	1.00
34_N	37_S	3.379	1.00
153_A	214_I	3.156	1.00
256_I	266_I	3.107	1.00
208_Y	249_M	2.993	1.00
28_Y	142_K	2.783	1.00
140_V	216_V	2.770	1.00
23_L	294_Y	2.708	1.00
92_N	116_D	2.629	1.00
215_D	251_K	2.593	1.00
93_N	280_Y	2.592	1.00
143_A	277_K	2.535	1.00
255_I	277_K	2.510	1.00
206_N	209_D	2.510	1.00
25_D	141_Y	2.462	1.00
42_S	95_S	2.309	1.00
22_E	141_Y	2.278	1.00
8_S	128_E	2.262	1.00
85_A	110_F	2.236	1.00
60_A	65_A	2.160	1.00
257_L	277_K	2.147	1.00
41_V	60_A	2.098	1.00
25_D	138_Y	2.096	1.00
18_F	141_Y	2.085	1.00
97_C	293_F	2.068	1.00
191_R	195_D	2.043	1.00
133_A	170_A	2.005	1.00
185_S	205_E	1.937	1.00
137_L	170_A	1.905	1.00
182_I	210_V	1.904	1.00
144_F	253_D	1.898	1.00
188_K	205_E	1.893	1.00
211_I	217_L	1.877	1.00
62_K	290_M	1.839	1.00
14_R	18_F	1.831	1.00
244_L	248_N	1.813	1.00
61_I	66_D	1.796	1.00
143_A	280_Y	1.794	1.00
93_N	283_S	1.784	1.00
247_V	254_G	1.783	1.00
171_L	179_V	1.780	1.00
99_V	122_A	1.752	1.00
178_K	202_I	1.718	1.00
13_T	16_D	1.709	1.00
19_R	295_E	1.649	1.00
54_Q	91_L	1.638	1.00
180_F	204_T	1.638	1.00
104_F	107_A	1.627	1.00
250_M	254_G	1.622	1.00
204_T	209_D	1.606	1.00
71_A	75_S	1.596	1.00
27_F	294_Y	1.596	1.00
131_T	292_L	1.562	1.00
144_F	150_R	1.538	1.00
41_V	97_C	1.537	1.00
254_G	275_N	1.532	1.00
245_K	248_N	1.522	1.00
20_I	295_E	1.510	1.00
187_L	236_V	1.506	1.00
178_K	200_P	1.503	1.00
185_S	188_K	1.496	1.00
14_R	173_R	1.481	1.00
167_L	218_Y	1.470	1.00
23_L	295_E	1.468	1.00
46_F	107_A	1.467	1.00
128_E	169_R	1.451	1.00
216_V	255_I	1.443	1.00
153_A	182_I	1.442	1.00
14_R	148_D	1.418	1.00
232_E	236_V	1.415	1.00
6_V	134_V	1.408	1.00
35_Y	294_Y	1.401	1.00
208_Y	246_L	1.394	1.00
97_C	297_L	1.386	1.00
24_A	138_Y	1.373	1.00
131_T	289_R	1.356	1.00
218_Y	281_Q	1.343	1.00
153_A	180_F	1.335	1.00
4_R	16_D	1.334	1.00
183_S	188_K	1.332	1.00
89_R	272_K	1.327	1.00
21_F	138_Y	1.324	1.00
207_P	246_L	1.323	1.00
213_E	251_K	1.317	1.00
88_I	111_A	1.314	1.00
10_L	196_E	1.313	1.00
217_L	242_V	1.290	1.00
155_L	211_I	1.285	1.00
243_D	267_D	1.279	1.00
21_F	141_Y	1.257	1.00
212_Q	249_M	1.252	1.00
26_K	30_V	1.248	1.00
50_T	87_T	1.243	1.00
23_L	26_K	1.241	1.00
9_S	170_A	1.233	1.00
89_R	279_F	1.233	1.00
10_L	169_R	1.228	1.00
219_V	242_V	1.228	1.00
241_V	267_D	1.227	1.00
41_V	99_V	1.213	1.00
138_Y	288_V	1.209	1.00
287_P	290_M	1.199	1.00
247_V	256_I	1.198	1.00
18_F	174_F	1.194	1.00
6_V	292_L	1.193	1.00
109_L	113_E	1.192	1.00
146_E	150_R	1.191	1.00
53_A	57_H	1.177	1.00
263_V	268_R	1.176	1.00
50_T	81_G	1.169	1.00
85_A	114_I	1.163	1.00
5_H	112_S	1.157	1.00
204_T	210_V	1.151	1.00
194_L	203_E	1.148	1.00
98_I	117_I	1.124	1.00
180_F	202_I	1.121	1.00
247_V	275_N	1.121	1.00
98_I	111_A	1.112	1.00
61_I	67_V	1.109	1.00
50_T	77_S	1.105	1.00
211_I	246_L	1.090	1.00
134_V	292_L	1.075	1.00
171_L	176_P	1.068	1.00
106_G	110_F	1.068	1.00
242_V	256_I	1.067	1.00
150_R	216_V	1.062	1.00
60_A	67_V	1.061	1.00
59_A	293_F	1.059	1.00
144_F	215_D	1.057	1.00
21_F	25_D	1.055	1.00
262_R	272_K	1.054	1.00
283_S	287_P	1.053	1.00
6_V	12_L	1.051	1.00
8_S	11_D	1.051	1.00
18_F	22_E	1.042	1.00
25_D	142_K	1.040	1.00
28_Y	284_L	1.039	1.00
90_M	282_A	1.036	1.00
48_P	79_A	1.028	1.00
168_L	181_L	1.013	1.00
273_T	276_A	1.012	1.00
152_F	171_L	1.010	1.00
144_F	255_I	1.003	1.00
133_A	167_L	0.998	1.00
271_D	278_Y	0.994	1.00
89_R	114_I	0.982	1.00
182_I	204_T	0.982	1.00
152_F	167_L	0.981	1.00
294_Y	298_G	0.974	1.00
62_K	286_V	0.971	1.00
77_S	80_K	0.969	1.00
120_I	292_L	0.968	1.00
57_H	69_G	0.964	1.00
137_L	174_F	0.958	1.00
133_A	163_T	0.954	1.00
17_Y	174_F	0.950	1.00
158_L	183_S	0.945	1.00
41_V	65_A	0.942	1.00
17_Y	173_R	0.939	1.00
54_Q	70_F	0.936	1.00
142_K	284_L	0.934	1.00
108_A	124_D	0.930	0.99
8_S	169_R	0.928	0.99
92_N	117_I	0.924	0.99
21_F	288_V	0.918	0.99
209_D	212_Q	0.917	0.99
165_N	193_I	0.916	0.99
102_H	124_D	0.911	0.99
205_E	240_Y	0.909	0.99
77_S	81_G	0.908	0.99
140_V	150_R	0.905	0.99
85_A	89_R	0.903	0.99
245_K	249_M	0.903	0.99
146_E	149_G	0.902	0.99
97_C	120_I	0.901	0.99
236_V	239_S	0.900	0.99
28_Y	138_Y	0.900	0.99
85_A	272_K	0.898	0.99
208_Y	212_Q	0.891	0.99
5_H	92_N	0.889	0.99
30_V	33_L	0.889	0.99
40_V	66_D	0.886	0.99
144_F	277_K	0.881	0.99
151_T	213_E	0.876	0.99
34_N	64_G	0.876	0.99
232_E	235_K	0.875	0.99
57_H	67_V	0.873	0.99
128_E	166_S	0.871	0.99
3_L	295_E	0.870	0.99
180_F	214_I	0.869	0.99
105_D	109_L	0.869	0.99
77_S	87_T	0.866	0.99
100_M	111_A	0.865	0.99
40_V	62_K	0.862	0.99
244_L	273_T	0.861	0.99
5_H	115_S	0.860	0.99
57_H	61_I	0.860	0.99
147_I	174_F	0.860	0.99
9_S	133_A	0.854	0.99
22_E	26_K	0.851	0.99
134_V	288_V	0.848	0.99
280_Y	283_S	0.848	0.99
189_V	203_E	0.846	0.99
182_I	214_I	0.845	0.99
138_Y	142_K	0.845	0.99
262_R	271_D	0.843	0.99
60_A	293_F	0.842	0.99
158_L	164_V	0.837	0.99
180_F	213_E	0.836	0.99
234_E	264_T	0.834	0.99
168_L	197_L	0.823	0.99
56_F	131_T	0.819	0.99
25_D	29_D	0.815	0.99
3_L	296_V	0.809	0.99
182_I	207_P	0.808	0.99
26_K	29_D	0.808	0.99
127_H	190_R	0.807	0.99
247_V	270_V	0.803	0.99
88_I	115_S	0.801	0.98
268_R	272_K	0.799	0.98
19_R	23_L	0.799	0.98
202_I	209_D	0.797	0.98
100_M	107_A	0.797	0.98
46_F	78_I	0.795	0.98
109_L	112_S	0.791	0.98
140_V	147_I	0.787	0.98
155_L	217_L	0.786	0.98
208_Y	245_K	0.784	0.98
139_T	277_K	0.782	0.98
72_S	75_S	0.781	0.98
39_K	96_N	0.781	0.98
247_V	250_M	0.776	0.98
270_V	273_T	0.775	0.98
168_L	179_V	0.768	0.98
7_V	112_S	0.763	0.98
155_L	246_L	0.763	0.98
85_A	268_R	0.758	0.98
76_T	81_G	0.758	0.98
110_F	114_I	0.757	0.98
20_I	288_V	0.756	0.98
140_V	144_F	0.756	0.98
151_T	214_I	0.753	0.98
210_V	214_I	0.753	0.98
17_Y	170_A	0.751	0.98
55_S	94_Y	0.750	0.98
40_V	58_T	0.744	0.98
24_A	291_A	0.742	0.98
268_R	271_D	0.737	0.97
243_D	246_L	0.737	0.97
164_V	181_L	0.737	0.97
89_R	92_N	0.733	0.97
168_L	189_V	0.732	0.97
9_S	17_Y	0.731	0.97
231_V	234_E	0.731	0.97
76_T	80_K	0.730	0.97
194_L	201_V	0.729	0.97
12_L	20_I	0.722	0.97
144_F	216_V	0.718	0.97
217_L	254_G	0.717	0.97
36_L	97_C	0.716	0.97
291_A	295_E	0.716	0.97
277_K	280_Y	0.715	0.97
110_F	113_E	0.715	0.97
139_T	284_L	0.713	0.97
242_V	266_I	0.710	0.97
92_N	115_S	0.707	0.97
262_R	268_R	0.706	0.97
140_V	171_L	0.706	0.97
167_L	171_L	0.704	0.97
23_L	27_F	0.700	0.96
102_H	107_A	0.696	0.96
20_I	291_A	0.693	0.96
59_A	289_R	0.692	0.96
42_S	98_I	0.691	0.96
55_S	289_R	0.690	0.96
145_G	149_G	0.690	0.96
15_D	18_F	0.688	0.96
6_V	296_V	0.687	0.96
50_T	80_K	0.685	0.96
244_L	267_D	0.685	0.96
81_G	87_T	0.684	0.96
34_N	38_G	0.684	0.96
235_K	238_E	0.682	0.96
4_R	295_E	0.681	0.96
247_V	266_I	0.681	0.96
143_A	255_I	0.680	0.96
95_S	117_I	0.678	0.96
106_G	109_L	0.674	0.96
176_P	179_V	0.673	0.96
188_K	191_R	0.671	0.96
211_I	249_M	0.670	0.95
140_V	255_I	0.670	0.95
193_I	197_L	0.670	0.95
84_L	107_A	0.670	0.95
221_R	225_E	0.669	0.95
43_L	60_A	0.669	0.95
152_F	218_Y	0.667	0.95
238_E	241_V	0.667	0.95
9_S	12_L	0.667	0.95
189_V	194_L	0.666	0.95
36_L	65_A	0.664	0.95
223_Q	231_V	0.662	0.95
24_A	288_V	0.661	0.95
41_V	293_F	0.659	0.95
246_L	249_M	0.658	0.95
48_P	77_S	0.657	0.95
153_A	210_V	0.657	0.95
27_F	35_Y	0.653	0.95
273_T	278_Y	0.651	0.95
155_L	207_P	0.647	0.95
207_P	211_I	0.647	0.95
105_D	126_K	0.643	0.94
137_L	141_Y	0.642	0.94
256_I	270_V	0.640	0.94
62_K	96_N	0.638	0.94
48_P	81_G	0.637	0.94
43_L	67_V	0.635	0.94
140_V	152_F	0.635	0.94
228_V	231_V	0.634	0.94
17_Y	134_V	0.632	0.94
27_F	30_V	0.632	0.94
104_F	126_K	0.632	0.94
97_C	296_V	0.631	0.94
43_L	69_G	0.630	0.94
120_I	296_V	0.626	0.94
154_L	159_K	0.625	0.93
188_K	203_E	0.624	0.93
218_Y	221_R	0.621	0.93
56_F	289_R	0.618	0.93
218_Y	257_L	0.618	0.93
248_N	275_N	0.617	0.93
230_E	233_Y	0.616	0.93
40_V	61_I	0.611	0.93
47_E	226_R	0.610	0.93
55_S	131_T	0.610	0.93
244_L	275_N	0.610	0.93
83_N	272_K	0.608	0.93
20_I	292_L	0.606	0.92
58_T	68_I	0.606	0.92
50_T	76_T	0.601	0.92
48_P	75_S	0.600	0.92
217_L	247_V	0.600	0.92
263_V	269_R	0.598	0.92
133_A	281_Q	0.597	0.92
155_L	219_V	0.597	0.92
183_S	189_V	0.596	0.92
148_D	175_K	0.593	0.92
170_A	174_F	0.592	0.92
120_I	293_F	0.591	0.91
172_T	199_Y	0.589	0.91
7_V	109_L	0.587	0.91
124_D	127_H	0.585	0.91
45_F	49_S	0.584	0.91
237_K	267_D	0.584	0.91
49_S	52_T	0.582	0.91
9_S	128_E	0.581	0.91
231_V	264_T	0.577	0.90
271_D	276_A	0.577	0.90
46_F	102_H	0.576	0.90
153_A	204_T	0.574	0.90
88_I	98_I	0.573	0.90
106_G	127_H	0.573	0.90
56_F	99_V	0.570	0.90
141_Y	146_E	0.570	0.90
58_T	286_V	0.569	0.90
163_T	218_Y	0.569	0.90
56_F	122_A	0.568	0.90
271_D	279_F	0.566	0.90
87_T	91_L	0.565	0.90
90_M	93_N	0.565	0.90
137_L	147_I	0.565	0.90
153_A	217_L	0.565	0.90
58_T	62_K	0.564	0.89
11_D	173_R	0.563	0.89
55_S	90_M	0.562	0.89
70_F	76_T	0.561	0.89
45_F	52_T	0.559	0.89
229_D	232_E	0.559	0.89
152_F	176_P	0.558	0.89
15_D	19_R	0.558	0.89
175_K	200_P	0.557	0.89
133_A	137_L	0.557	0.89
169_R	196_E	0.557	0.89
142_K	280_Y	0.555	0.89
84_L	100_M	0.554	0.89
22_E	25_D	0.553	0.89
106_G	124_D	0.552	0.88
6_V	17_Y	0.550	0.88
147_I	176_P	0.549	0.88
216_V	257_L	0.548	0.88
175_K	178_K	0.545	0.88
90_M	279_F	0.543	0.88
159_K	187_L	0.540	0.87
145_G	255_I	0.538	0.87
16_D	19_R	0.538	0.87
33_L	37_S	0.536	0.87
172_T	179_V	0.536	0.87
182_I	211_I	0.536	0.87
49_S	53_A	0.534	0.87
123_G	225_E	0.533	0.87
186_Q	236_V	0.532	0.87
163_T	167_L	0.532	0.87
21_F	24_A	0.530	0.86
19_R	22_E	0.529	0.86
47_E	225_E	0.529	0.86
82_E	86_D	0.529	0.86
293_F	297_L	0.528	0.86
242_V	247_V	0.527	0.86
256_I	276_A	0.527	0.86
36_L	293_F	0.524	0.86
150_R	215_D	0.521	0.85
28_Y	287_P	0.519	0.85
10_L	128_E	0.519	0.85
178_K	199_Y	0.519	0.85
273_T	277_K	0.519	0.85
23_L	291_A	0.517	0.85
8_S	109_L	0.516	0.85
17_Y	21_F	0.516	0.85
234_E	238_E	0.512	0.84
90_M	94_Y	0.512	0.84
75_S	79_A	0.511	0.84
186_Q	235_K	0.511	0.84
33_L	64_G	0.511	0.84
227_F	230_E	0.509	0.84
260_L	279_F	0.509	0.84
154_L	218_Y	0.507	0.84
233_Y	237_K	0.507	0.84
255_I	275_N	0.506	0.84
205_E	209_D	0.505	0.84
48_P	69_G	0.503	0.83
98_I	115_S	0.502	0.83
242_V	246_L	0.501	0.83
285_A	289_R	0.501	0.83
211_I	250_M	0.500	0.83

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
1ml4A	3	0.9868	100	0.017	Contact Map
1pg5A	4	0.9538	100	0.024	Contact Map
3csuA	3	0.9934	100	0.026	Contact Map
4iv5A	4	0.934	100	0.028	Contact Map
4nf2A	3	0.9703	100	0.032	Contact Map
3gd5A	4	0.901	100	0.041	Contact Map
4oh7A	3	0.967	100	0.043	Contact Map
2i6uA	3	0.9736	100	0.045	Contact Map
4eknB	5	0.9736	100	0.045	Contact Map
1pvvA	6	0.9769	100	0.047	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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