PYRB - BACSU - GREMLIN Contacts

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PYRB - Aspartate carbamoyltransferase

UniProt:	P05654	Sequences: MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQTNVKRGEAAYVISH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	304 (285)
Sequences:	6937 (3629)
Seq/√Len:	214.9

ECOLI - YGEW OTC2 OTC1 PYRB
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
234_V	261_S	4.090	1.00
149_T	175_R	3.969	1.00
32_N	35_T	3.512	1.00
149_T	177_L	3.421	1.00
151_S	204_S	3.188	1.00
246_I	258_I	3.135	1.00
198_D	239_R	3.047	1.00
26_K	140_E	2.876	1.00
21_T	286_Q	2.819	1.00
138_I	206_V	2.771	1.00
89_E	114_N	2.704	1.00
205_D	241_K	2.608	1.00
141_E	269_R	2.581	1.00
90_S	272_K	2.575	1.00
245_I	269_R	2.573	1.00
196_S	199_E	2.541	1.00
23_Q	139_Y	2.461	1.00
6_T	126_Q	2.331	1.00
82_Y	108_E	2.313	1.00
20_Q	139_Y	2.284	1.00
40_A	93_V	2.281	1.00
58_E	63_M	2.205	1.00
247_M	269_R	2.177	1.00
16_K	139_Y	2.135	1.00
39_A	58_E	2.105	1.00
23_Q	136_M	2.098	1.00
95_V	285_I	2.054	1.00
131_S	168_V	2.034	1.00
135_L	168_V	1.934	1.00
142_F	243_H	1.934	1.00
179_S	200_A	1.920	1.00
60_K	282_M	1.885	1.00
182_S	195_V	1.868	1.00
201_V	207_V	1.844	1.00
185_Q	195_V	1.834	1.00
169_L	176_V	1.817	1.00
141_E	272_K	1.814	1.00
12_T	16_K	1.814	1.00
90_S	275_K	1.814	1.00
59_K	64_N	1.783	1.00
237_A	244_A	1.775	1.00
253_N	256_V	1.769	1.00
97_V	120_A	1.768	1.00
234_V	238_E	1.768	1.00
11_S	14_E	1.713	1.00
175_R	192_G	1.695	1.00
194_Y	199_E	1.659	1.00
52_F	88_L	1.656	1.00
17_D	287_R	1.654	1.00
142_F	148_L	1.601	1.00
129_T	284_V	1.582	1.00
25_L	286_Q	1.573	1.00
177_L	194_Y	1.573	1.00
69_D	72_S	1.570	1.00
240_M	244_A	1.562	1.00
102_E	105_Y	1.559	1.00
39_A	95_V	1.559	1.00
235_E	238_E	1.548	1.00
18_L	287_R	1.536	1.00
182_S	185_Q	1.519	1.00
244_A	267_K	1.518	1.00
126_Q	167_E	1.517	1.00
165_N	208_M	1.505	1.00
21_T	287_R	1.497	1.00
151_S	179_S	1.484	1.00
184_W	226_Y	1.469	1.00
12_T	171_R	1.465	1.00
12_T	146_K	1.464	1.00
222_S	226_Y	1.459	1.00
206_V	245_I	1.458	1.00
44_F	105_Y	1.446	1.00
95_V	289_L	1.439	1.00
175_R	190_T	1.415	1.00
4_L	132_L	1.404	1.00
151_S	177_L	1.387	1.00
198_D	236_R	1.386	1.00
129_T	281_R	1.384	1.00
180_G	185_Q	1.366	1.00
33_Q	286_Q	1.355	1.00
22_A	136_M	1.352	1.00
208_M	273_Q	1.346	1.00
86_R	264_E	1.335	1.00
153_H	201_V	1.328	1.00
19_L	136_M	1.328	1.00
2_K	14_E	1.327	1.00
203_S	241_K	1.321	1.00
85_I	109_L	1.320	1.00
233_T	259_D	1.288	1.00
8_S	167_E	1.275	1.00
86_R	271_F	1.267	1.00
19_L	139_Y	1.264	1.00
4_L	284_V	1.253	1.00
21_T	24_E	1.252	1.00
197_M	236_R	1.250	1.00
39_A	97_V	1.245	1.00
48_T	84_T	1.231	1.00
7_M	168_V	1.225	1.00
207_V	232_L	1.220	1.00
202_E	239_R	1.215	1.00
237_A	246_I	1.214	1.00
231_G	259_D	1.213	1.00
209_L	232_L	1.212	1.00
48_T	78_G	1.209	1.00
51_R	55_E	1.205	1.00
136_M	280_I	1.195	1.00
144_T	148_L	1.192	1.00
16_K	172_L	1.190	1.00
279_F	282_M	1.186	1.00
255_G	260_D	1.177	1.00
169_L	174_A	1.171	1.00
132_L	284_V	1.150	1.00
48_T	74_S	1.144	1.00
194_Y	200_A	1.140	1.00
148_L	206_V	1.139	1.00
82_Y	112_Q	1.133	1.00
252_V	263_V	1.128	1.00
3_H	110_V	1.128	1.00
59_K	65_V	1.126	1.00
254_R	264_E	1.105	1.00
96_C	115_I	1.102	1.00
201_V	236_R	1.099	1.00
142_F	205_D	1.098	1.00
237_A	267_K	1.095	1.00
275_K	279_F	1.088	1.00
177_L	192_G	1.087	1.00
23_Q	140_E	1.075	1.00
107_E	111_S	1.073	1.00
232_L	246_I	1.068	1.00
96_C	109_L	1.055	1.00
142_F	245_I	1.048	1.00
87_T	274_M	1.046	1.00
58_E	65_V	1.045	1.00
6_T	9_E	1.044	1.00
26_K	276_N	1.043	1.00
166_A	178_F	1.042	1.00
265_S	268_S	1.038	1.00
57_A	285_I	1.031	1.00
46_P	76_Q	1.021	1.00
4_L	10_L	1.019	1.00
179_S	194_Y	1.014	1.00
104_E	108_E	1.008	1.00
16_K	20_Q	1.007	1.00
19_L	23_Q	1.006	1.00
286_Q	290_Q	1.005	1.00
131_S	165_N	0.998	1.00
156_I	180_G	0.991	1.00
15_I	172_L	0.982	1.00
150_V	169_L	0.978	1.00
263_V	270_I	0.976	1.00
150_V	165_N	0.971	1.00
60_K	278_V	0.971	1.00
195_V	230_Y	0.968	1.00
6_T	167_E	0.963	1.00
55_E	67_N	0.962	1.00
19_L	280_I	0.959	1.00
39_A	63_M	0.955	1.00
131_S	161_V	0.952	1.00
86_R	112_Q	0.951	1.00
118_L	284_V	0.946	1.00
226_Y	229_K	0.932	0.99
89_E	115_I	0.931	0.99
52_F	68_L	0.931	0.99
26_K	136_M	0.930	0.99
55_E	59_K	0.922	0.99
135_L	172_L	0.919	0.99
98_I	109_L	0.917	0.99
186_D	193_T	0.916	0.99
138_I	148_L	0.916	0.99
100_H	122_D	0.911	0.99
140_E	276_N	0.908	0.99
222_S	225_G	0.906	0.99
15_I	171_R	0.904	0.99
149_T	203_S	0.903	0.99
95_V	118_L	0.903	0.99
82_Y	264_E	0.894	0.99
144_T	147_G	0.888	0.99
74_S	77_K	0.888	0.99
106_Y	122_D	0.887	0.99
234_V	265_S	0.887	0.99
38_F	64_N	0.886	0.99
103_D	107_E	0.882	0.99
74_S	84_T	0.880	0.99
177_L	204_S	0.879	0.99
199_E	202_E	0.877	0.99
179_S	204_S	0.876	0.99
3_H	89_E	0.875	0.99
7_M	131_S	0.869	0.99
3_H	113_V	0.869	0.99
20_Q	24_E	0.864	0.99
32_N	62_G	0.864	0.99
38_F	60_K	0.858	0.99
136_M	140_E	0.855	0.99
272_K	275_K	0.855	0.99
126_Q	164_S	0.853	0.99
142_F	269_R	0.850	0.99
82_Y	86_R	0.845	0.99
153_H	207_V	0.843	0.99
145_F	172_L	0.838	0.99
132_L	280_I	0.837	0.99
237_A	262_L	0.835	0.99
58_E	285_I	0.835	0.99
254_R	263_V	0.835	0.99
55_E	65_V	0.834	0.99
192_G	199_E	0.828	0.99
235_E	239_R	0.822	0.99
177_L	203_S	0.815	0.99
260_D	264_E	0.813	0.99
74_S	78_G	0.811	0.99
54_F	129_T	0.811	0.99
125_G	187_E	0.805	0.98
138_I	145_F	0.796	0.98
166_A	176_V	0.790	0.98
98_I	105_Y	0.789	0.98
283_A	287_R	0.789	0.98
179_S	197_M	0.783	0.98
200_A	204_S	0.782	0.98
44_F	75_V	0.779	0.98
156_I	162_A	0.778	0.98
198_D	202_E	0.777	0.98
107_E	110_V	0.772	0.98
53_S	91_I	0.772	0.98
137_T	269_R	0.769	0.98
23_Q	27_S	0.767	0.98
5_T	110_V	0.766	0.98
108_E	112_Q	0.764	0.98
37_K	94_D	0.764	0.98
38_F	56_V	0.762	0.98
198_D	235_E	0.760	0.98
17_D	21_T	0.760	0.98
18_L	280_I	0.759	0.98
7_M	15_I	0.758	0.98
166_A	186_D	0.757	0.98
153_H	236_R	0.756	0.98
82_Y	260_D	0.752	0.98
137_T	276_N	0.752	0.98
237_A	240_M	0.750	0.98
85_I	113_V	0.749	0.98
32_N	36_G	0.746	0.97
4_L	288_A	0.746	0.97
224_E	256_V	0.745	0.97
138_I	142_F	0.740	0.97
24_E	27_S	0.737	0.97
15_I	168_V	0.733	0.97
149_T	204_S	0.725	0.97
262_L	265_S	0.723	0.97
162_A	178_F	0.722	0.97
142_F	206_V	0.720	0.97
78_G	84_T	0.719	0.97
221_V	224_E	0.719	0.97
22_A	283_A	0.719	0.97
260_D	263_V	0.718	0.97
165_N	169_L	0.718	0.97
233_T	236_R	0.717	0.97
86_R	89_E	0.715	0.97
254_R	260_D	0.713	0.97
93_V	115_I	0.712	0.97
269_R	272_K	0.712	0.97
100_H	105_Y	0.711	0.97
207_V	244_A	0.710	0.97
18_L	283_A	0.709	0.97
53_S	281_R	0.708	0.97
21_T	25_L	0.707	0.96
143_N	147_G	0.705	0.96
10_L	18_L	0.705	0.96
153_H	197_M	0.704	0.96
22_A	280_I	0.700	0.96
232_L	258_I	0.697	0.96
30_T	33_Q	0.692	0.96
95_V	288_A	0.691	0.96
2_K	287_R	0.691	0.96
34_L	63_M	0.691	0.96
185_Q	188_E	0.686	0.96
40_A	96_C	0.683	0.96
34_L	95_V	0.681	0.96
57_A	281_R	0.679	0.96
73_T	78_G	0.679	0.96
138_I	169_L	0.677	0.96
60_K	94_D	0.676	0.95
138_I	245_I	0.673	0.95
102_E	123_G	0.667	0.95
234_V	259_D	0.666	0.95
252_V	258_I	0.665	0.95
141_E	245_I	0.665	0.95
170_T	189_N	0.665	0.95
7_M	10_L	0.664	0.95
228_N	231_G	0.659	0.95
41_N	58_E	0.658	0.95
48_T	77_K	0.657	0.95
237_A	258_I	0.656	0.95
39_A	285_I	0.655	0.95
13_E	16_K	0.653	0.95
220_A	223_Q	0.652	0.95
225_G	228_N	0.651	0.94
104_E	107_E	0.651	0.94
238_E	267_K	0.651	0.94
15_I	132_L	0.650	0.94
108_E	111_S	0.645	0.94
41_N	67_N	0.643	0.94
211_R	215_E	0.642	0.94
236_R	239_R	0.642	0.94
30_T	35_T	0.642	0.94
56_V	66_L	0.640	0.94
211_R	253_N	0.637	0.94
41_N	65_V	0.635	0.94
73_T	77_K	0.634	0.94
246_I	262_L	0.634	0.94
135_L	139_Y	0.633	0.94
151_S	200_A	0.632	0.94
201_V	239_R	0.632	0.94
7_M	126_Q	0.630	0.93
265_S	270_I	0.630	0.93
219_S	222_S	0.629	0.93
81_L	105_Y	0.629	0.93
80_T	264_E	0.627	0.93
218_Q	221_V	0.625	0.93
150_V	208_M	0.624	0.93
138_I	150_V	0.620	0.93
152_I	159_S	0.618	0.93
122_D	125_G	0.618	0.93
208_M	211_R	0.617	0.93
153_H	209_L	0.615	0.93
197_M	201_V	0.615	0.93
234_V	267_K	0.614	0.93
53_S	129_T	0.613	0.93
208_M	247_M	0.612	0.92
89_E	113_V	0.612	0.92
13_E	17_D	0.610	0.92
54_F	281_R	0.609	0.92
213_Q	221_V	0.608	0.92
48_T	73_T	0.605	0.92
131_S	273_Q	0.604	0.92
135_L	145_F	0.604	0.92
38_F	59_K	0.602	0.92
183_E	225_G	0.601	0.92
185_Q	193_T	0.601	0.92
28_G	31_D	0.598	0.92
46_P	74_S	0.594	0.91
151_S	194_Y	0.594	0.91
121_G	160_R	0.593	0.91
85_I	96_C	0.587	0.91
25_L	33_Q	0.587	0.91
151_S	207_V	0.586	0.91
46_P	78_G	0.586	0.91
118_L	288_A	0.584	0.91
96_C	113_V	0.584	0.91
118_L	285_I	0.583	0.91
5_T	107_E	0.582	0.90
45_E	216_R	0.577	0.90
263_V	268_S	0.577	0.90
201_V	240_M	0.576	0.90
207_V	237_A	0.575	0.90
54_F	97_V	0.575	0.90
131_S	135_L	0.574	0.90
53_S	87_T	0.573	0.90
227_L	259_D	0.573	0.90
168_V	172_L	0.571	0.90
44_F	100_H	0.569	0.89
175_R	189_N	0.567	0.89
43_F	47_S	0.566	0.89
140_E	272_K	0.566	0.89
139_Y	144_T	0.564	0.89
8_S	126_Q	0.562	0.89
232_L	237_A	0.562	0.89
104_E	122_D	0.559	0.89
206_V	247_M	0.559	0.89
47_S	50_T	0.558	0.89
104_E	125_G	0.557	0.89
18_L	284_V	0.557	0.89
87_T	90_S	0.555	0.88
161_V	208_M	0.553	0.88
195_V	199_E	0.553	0.88
170_T	176_V	0.552	0.88
145_F	174_A	0.550	0.88
150_V	174_A	0.546	0.88
54_F	120_A	0.545	0.87
263_V	271_F	0.545	0.87
14_E	287_R	0.544	0.87
180_G	186_D	0.544	0.87
56_V	278_V	0.544	0.87
56_V	60_K	0.544	0.87
170_T	190_T	0.543	0.87
20_Q	23_Q	0.539	0.87
46_P	72_S	0.539	0.87
25_L	30_T	0.538	0.87
148_L	205_D	0.538	0.87
152_I	208_M	0.537	0.87
285_I	289_L	0.536	0.87
84_T	88_L	0.535	0.86
69_D	73_T	0.534	0.86
265_S	269_R	0.534	0.86
17_D	20_Q	0.533	0.86
25_L	29_K	0.532	0.86
223_Q	227_L	0.532	0.86
31_D	35_T	0.531	0.86
255_G	261_S	0.530	0.86
4_L	15_I	0.528	0.86
19_L	22_A	0.528	0.86
85_I	117_I	0.528	0.86
45_E	215_E	0.526	0.86
179_S	201_V	0.524	0.85
87_T	271_F	0.524	0.85
21_T	283_A	0.524	0.85
180_G	195_V	0.523	0.85
31_D	36_G	0.522	0.85
14_E	17_D	0.519	0.85
183_E	226_Y	0.518	0.85
101_S	105_Y	0.518	0.85
250_A	271_F	0.517	0.85
259_D	262_L	0.517	0.85
143_N	245_I	0.516	0.84
43_F	50_T	0.515	0.84
177_L	200_A	0.515	0.84
26_K	279_F	0.514	0.84
6_T	107_E	0.513	0.84
87_T	91_I	0.512	0.84
79_E	83_D	0.511	0.84
161_V	165_N	0.511	0.84
81_L	98_I	0.510	0.84
121_G	215_E	0.509	0.84
47_S	51_R	0.509	0.84
77_K	253_N	0.506	0.83
3_H	114_N	0.504	0.83
8_S	171_R	0.503	0.83
30_T	61_L	0.502	0.83
206_V	269_R	0.501	0.83
221_V	256_V	0.501	0.83
246_I	268_S	0.500	0.83
217_H	220_A	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
3r7fA	3	0.9572	100	0.036	Contact Map
4nf2A	3	0.9441	100	0.041	Contact Map
2i6uA	3	0.9507	100	0.048	Contact Map
3gd5A	4	0.8816	100	0.048	Contact Map
4oh7A	3	0.9441	100	0.049	Contact Map
1pvvA	6	0.9507	100	0.051	Contact Map
1ml4A	3	0.9507	100	0.055	Contact Map
3tpfA	3	0.9474	100	0.056	Contact Map
1pg5A	4	0.9243	100	0.056	Contact Map
3grfA	3	0.8947	100	0.059	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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