PYRDB - BACSU - GREMLIN Contacts

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PYRDB - Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit

UniProt:	P25996	Sequences: MLEVKLPGLDLKNPIIPASGCFGFGKEFSRFYDLSCLGAIMIKATTKEPRFGNPTPRVAETGAGMLNAIGLQNPGLDSVLHHELPWLEQFDTPIIANVAGSQVDDYVEVAEHISKAPNVHALELNISCPNVKTGGIAFGTNPEMAADLTKAVKEVSDVPVYVKLSPNVANITEIALAIEEAGADGLTMINTLIGMRLDLKTGKPILANKTGGLSGPAVKPVAIRMVYEVSQMVNIPIIGMGGVQTAEDALEFLLAGASAVAVGTANFVNPFACPEIIEQLPSVLLQYGYQSIEECIGRSWNHEKQPAHHRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	311 (286)
Sequences:	5103 (2986)
Seq/√Len:	176.5

ECOLI - PREA PYRD
BACSU - PYRDB
HALSA - PYRD
SULSO - PYRDB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
246_A	279_Q	3.755	1.00
77_D	112_H	3.626	1.00
5_K	10_D	3.542	1.00
269_N	275_E	3.499	1.00
3_E	10_D	3.009	1.00
111_E	155_V	2.921	1.00
146_A	180_E	2.894	1.00
7_P	161_Y	2.813	1.00
11_L	259_A	2.634	1.00
172_T	232_M	2.563	1.00
146_A	181_A	2.562	1.00
289_Y	295_C	2.480	1.00
222_A	252_F	2.397	1.00
230_S	258_S	2.337	1.00
244_Q	248_D	2.332	1.00
153_K	184_D	2.329	1.00
45_T	79_V	2.324	1.00
188_M	229_V	2.291	1.00
219_K	251_E	2.290	1.00
223_I	252_F	2.223	1.00
161_Y	185_G	2.171	1.00
153_K	160_V	2.159	1.00
145_A	178_I	2.099	1.00
245_T	248_D	2.086	1.00
13_N	38_G	2.063	1.00
226_V	237_I	2.010	1.00
219_K	248_D	1.945	1.00
230_S	237_I	1.904	1.00
179_E	235_I	1.873	1.00
13_N	277_I	1.873	1.00
24_F	74_P	1.856	1.00
291_S	294_E	1.844	1.00
243_V	260_V	1.828	1.00
290_Q	294_E	1.768	1.00
110_A	122_L	1.761	1.00
95_I	121_A	1.761	1.00
293_E	296_I	1.750	1.00
282_S	286_Q	1.730	1.00
283_V	287_Y	1.717	1.00
219_K	252_F	1.689	1.00
187_T	240_M	1.681	1.00
250_L	287_Y	1.670	1.00
179_E	234_N	1.663	1.00
16_I	41_M	1.650	1.00
175_A	229_V	1.633	1.00
262_V	276_I	1.628	1.00
253_L	296_I	1.622	1.00
243_V	252_F	1.606	1.00
76_L	112_H	1.597	1.00
107_V	155_V	1.582	1.00
63_A	216_P	1.582	1.00
176_L	180_E	1.574	1.00
247_E	251_E	1.572	1.00
249_A	276_I	1.562	1.00
9_L	121_A	1.559	1.00
258_S	296_I	1.548	1.00
284_L	295_C	1.548	1.00
126_I	145_A	1.543	1.00
247_E	283_V	1.524	1.00
200_K	287_Y	1.523	1.00
74_P	78_S	1.504	1.00
170_N	173_E	1.501	1.00
142_P	173_E	1.492	1.00
253_L	295_C	1.486	1.00
76_L	113_I	1.471	1.00
98_V	110_A	1.452	1.00
236_P	258_S	1.448	1.00
16_I	39_A	1.433	1.00
192_L	221_V	1.432	1.00
103_V	147_D	1.431	1.00
110_A	152_V	1.428	1.00
15_I	277_I	1.424	1.00
161_Y	238_I	1.423	1.00
172_T	228_E	1.418	1.00
46_T	99_A	1.411	1.00
114_S	156_S	1.409	1.00
189_I	192_L	1.407	1.00
98_V	109_V	1.398	1.00
114_S	157_D	1.390	1.00
253_L	292_I	1.381	1.00
186_L	233_V	1.367	1.00
5_K	8_G	1.354	1.00
249_A	280_L	1.350	1.00
226_V	239_G	1.350	1.00
96_A	119_V	1.347	1.00
146_A	150_K	1.341	1.00
194_G	221_V	1.333	1.00
249_A	260_V	1.323	1.00
78_S	82_H	1.295	1.00
44_A	97_N	1.283	1.00
108_E	112_H	1.279	1.00
44_A	99_A	1.277	1.00
197_L	255_A	1.274	1.00
77_D	81_H	1.258	1.00
107_V	151_A	1.258	1.00
124_L	152_V	1.255	1.00
281_P	285_L	1.253	1.00
32_Y	92_T	1.253	1.00
15_I	276_I	1.252	1.00
64_G	217_A	1.251	1.00
47_K	101_S	1.243	1.00
143_E	147_D	1.235	1.00
274_P	278_E	1.232	1.00
177_A	181_A	1.228	1.00
239_G	252_F	1.227	1.00
250_L	283_V	1.227	1.00
15_I	243_V	1.218	1.00
108_E	111_E	1.213	1.00
6_L	259_A	1.209	1.00
41_M	261_A	1.208	1.00
47_K	109_V	1.201	1.00
42_I	96_A	1.199	1.00
284_L	289_Y	1.190	1.00
58_V	69_I	1.188	1.00
250_L	280_L	1.186	1.00
76_L	109_V	1.185	1.00
152_V	160_V	1.171	1.00
219_K	223_I	1.167	1.00
275_E	279_Q	1.142	1.00
224_R	228_E	1.138	1.00
277_I	281_P	1.133	1.00
149_T	162_V	1.131	1.00
63_A	269_N	1.131	1.00
103_V	151_A	1.129	1.00
103_V	107_V	1.125	1.00
200_K	286_Q	1.124	1.00
113_I	122_L	1.122	1.00
176_L	232_M	1.115	1.00
246_A	250_L	1.110	1.00
240_M	261_A	1.105	1.00
122_L	158_V	1.098	1.00
150_K	181_A	1.097	1.00
102_Q	105_D	1.095	1.00
230_S	297_G	1.093	1.00
250_L	254_L	1.091	1.00
80_L	112_H	1.087	1.00
192_L	218_V	1.076	1.00
12_K	91_D	1.073	1.00
238_I	259_A	1.073	1.00
16_I	261_A	1.064	1.00
42_I	79_V	1.062	1.00
168_V	174_I	1.055	1.00
46_T	50_R	1.051	1.00
246_A	276_I	1.050	1.00
283_V	286_Q	1.050	1.00
199_L	250_L	1.043	1.00
283_V	289_Y	1.037	0.99
244_Q	265_A	1.035	0.99
87_L	120_H	1.033	0.99
278_E	282_S	1.027	0.99
216_P	244_Q	1.023	0.99
226_V	252_F	1.021	0.99
164_L	229_V	1.013	0.99
141_N	144_M	1.000	0.99
247_E	279_Q	0.999	0.99
138_F	170_N	0.991	0.99
223_I	255_A	0.990	0.99
81_H	84_L	0.986	0.99
18_A	263_G	0.983	0.99
151_A	154_E	0.983	0.99
67_N	191_T	0.982	0.99
37_L	273_C	0.980	0.99
69_I	73_N	0.975	0.99
162_V	183_A	0.970	0.99
62_G	201_T	0.969	0.99
7_P	185_G	0.957	0.99
147_D	150_K	0.951	0.99
107_V	111_E	0.943	0.99
171_I	229_V	0.939	0.99
246_A	283_V	0.937	0.99
6_L	161_Y	0.927	0.99
74_P	82_H	0.926	0.99
147_D	151_A	0.922	0.99
71_L	99_A	0.922	0.99
16_I	259_A	0.922	0.99
102_Q	132_K	0.916	0.99
12_K	92_T	0.914	0.99
25_G	79_V	0.912	0.99
9_L	93_P	0.908	0.99
31_F	40_I	0.905	0.99
161_Y	187_T	0.903	0.99
216_P	219_K	0.892	0.98
104_D	108_E	0.891	0.98
191_T	214_S	0.889	0.98
100_G	123_E	0.887	0.98
188_M	225_M	0.885	0.98
114_S	158_V	0.881	0.98
189_I	222_A	0.875	0.98
198_D	201_T	0.874	0.98
29_S	89_Q	0.872	0.98
189_I	218_V	0.864	0.98
6_L	238_I	0.864	0.98
124_L	162_V	0.864	0.98
47_K	108_E	0.864	0.98
202_G	287_Y	0.857	0.98
266_N	273_C	0.854	0.98
62_G	198_D	0.846	0.98
142_P	177_A	0.844	0.98
17_P	37_L	0.840	0.98
282_S	285_L	0.837	0.98
150_K	154_E	0.835	0.98
279_Q	283_V	0.833	0.98
138_F	141_N	0.825	0.97
107_V	154_E	0.825	0.97
41_M	187_T	0.820	0.97
96_A	113_I	0.820	0.97
254_L	287_Y	0.810	0.97
48_E	101_S	0.807	0.97
258_S	297_G	0.807	0.97
196_R	199_L	0.805	0.97
101_S	109_V	0.804	0.97
80_L	113_I	0.803	0.97
15_I	262_V	0.803	0.97
118_N	158_V	0.802	0.97
228_E	232_M	0.802	0.97
18_A	261_A	0.800	0.97
175_A	233_V	0.800	0.97
220_P	224_R	0.796	0.97
128_C	131_V	0.796	0.97
172_T	229_V	0.795	0.97
278_E	281_P	0.793	0.97
17_P	273_C	0.793	0.97
226_V	255_A	0.792	0.97
58_V	65_M	0.789	0.97
41_M	97_N	0.789	0.97
144_M	147_D	0.787	0.97
202_G	254_L	0.784	0.97
74_P	79_V	0.783	0.97
78_S	81_H	0.781	0.96
221_V	224_R	0.780	0.96
143_E	146_A	0.776	0.96
65_M	264_T	0.774	0.96
129_P	212_G	0.772	0.96
178_I	186_L	0.767	0.96
222_A	239_G	0.764	0.96
15_I	260_V	0.764	0.96
50_R	101_S	0.762	0.96
176_L	179_E	0.760	0.96
69_I	72_Q	0.743	0.95
172_T	176_L	0.742	0.95
83_E	87_L	0.741	0.95
98_V	124_L	0.740	0.95
52_G	75_G	0.740	0.95
4_V	258_S	0.735	0.95
113_I	118_N	0.731	0.95
141_N	170_N	0.730	0.95
171_I	225_M	0.729	0.95
186_L	229_V	0.729	0.95
115_K	118_N	0.728	0.95
250_L	279_Q	0.728	0.95
128_C	137_A	0.723	0.95
194_G	197_L	0.720	0.94
179_E	233_V	0.720	0.94
254_L	283_V	0.720	0.94
289_Y	292_I	0.719	0.94
196_R	251_E	0.717	0.94
11_L	39_A	0.717	0.94
136_I	140_T	0.713	0.94
210_T	227_Y	0.710	0.94
27_E	31_F	0.709	0.94
61_T	213_L	0.709	0.94
44_A	98_V	0.706	0.94
164_L	186_L	0.706	0.94
169_A	172_T	0.705	0.94
15_I	249_A	0.704	0.94
292_I	296_I	0.702	0.94
53_N	57_R	0.702	0.94
224_R	227_Y	0.701	0.94
249_A	279_Q	0.700	0.94
132_K	135_G	0.700	0.94
47_K	105_D	0.700	0.94
189_I	225_M	0.699	0.94
262_V	265_A	0.699	0.94
27_E	30_R	0.698	0.94
283_V	295_C	0.698	0.94
250_L	295_C	0.693	0.93
26_K	83_E	0.693	0.93
151_A	155_V	0.693	0.93
26_K	78_S	0.693	0.93
76_L	80_L	0.690	0.93
193_I	228_E	0.688	0.93
186_L	237_I	0.682	0.93
93_P	120_H	0.682	0.93
191_T	212_G	0.678	0.93
153_K	181_A	0.676	0.92
281_P	284_L	0.675	0.92
85_P	88_E	0.674	0.92
11_L	121_A	0.672	0.92
104_D	107_V	0.670	0.92
284_L	292_I	0.667	0.92
173_E	177_A	0.665	0.92
121_A	261_A	0.664	0.92
107_V	152_V	0.664	0.92
230_S	234_N	0.663	0.92
164_L	225_M	0.663	0.92
197_L	200_K	0.662	0.92
219_K	226_V	0.660	0.91
216_P	248_D	0.660	0.91
110_A	148_L	0.659	0.91
126_I	162_V	0.659	0.91
171_I	232_M	0.655	0.91
187_T	261_A	0.651	0.91
35_S	91_D	0.648	0.91
229_V	233_V	0.648	0.91
253_L	260_V	0.647	0.91
178_I	237_I	0.647	0.91
39_A	261_A	0.645	0.91
11_L	16_I	0.644	0.90
50_R	99_A	0.644	0.90
77_D	108_E	0.642	0.90
7_P	121_A	0.639	0.90
253_L	297_G	0.637	0.90
6_L	236_P	0.634	0.90
119_V	122_L	0.633	0.90
19_S	43_K	0.632	0.90
249_A	253_L	0.628	0.89
160_V	184_D	0.627	0.89
48_E	108_E	0.627	0.89
186_L	235_I	0.625	0.89
26_K	74_P	0.623	0.89
37_L	277_I	0.621	0.89
110_A	155_V	0.621	0.89
79_V	113_I	0.620	0.89
67_N	212_G	0.617	0.89
21_C	267_F	0.617	0.89
6_L	258_S	0.614	0.88
142_P	146_A	0.611	0.88
46_T	73_N	0.610	0.88
23_G	43_K	0.607	0.88
88_E	120_H	0.604	0.87
6_L	11_L	0.602	0.87
273_C	277_I	0.602	0.87
228_E	231_Q	0.599	0.87
265_A	272_A	0.598	0.87
121_A	187_T	0.598	0.87
84_L	88_E	0.597	0.87
149_T	183_A	0.595	0.87
70_G	73_N	0.595	0.87
276_I	279_Q	0.594	0.87
3_E	12_K	0.592	0.86
127_S	212_G	0.591	0.86
93_P	121_A	0.591	0.86
227_Y	231_Q	0.591	0.86
62_G	200_K	0.590	0.86
173_E	176_L	0.589	0.86
165_S	168_V	0.589	0.86
17_P	31_F	0.589	0.86
123_E	187_T	0.587	0.86
22_F	28_F	0.587	0.86
48_E	77_D	0.586	0.86
80_L	84_L	0.586	0.86
66_L	194_G	0.585	0.86
272_A	275_E	0.584	0.86
196_R	219_K	0.583	0.86
287_Y	295_C	0.583	0.86
67_N	73_N	0.580	0.85
223_I	239_G	0.579	0.85
61_T	64_G	0.579	0.85
52_G	70_G	0.578	0.85
193_I	210_T	0.578	0.85
184_D	236_P	0.571	0.84
156_S	160_V	0.570	0.84
39_A	93_P	0.569	0.84
253_L	284_L	0.569	0.84
79_V	96_A	0.567	0.84
137_A	140_T	0.566	0.84
223_I	226_V	0.566	0.84
8_G	159_P	0.565	0.84
280_L	284_L	0.562	0.83
107_V	148_L	0.561	0.83
67_N	127_S	0.559	0.83
85_P	89_Q	0.558	0.83
84_L	87_L	0.558	0.83
110_A	158_V	0.556	0.83
28_F	266_N	0.555	0.83
127_S	130_N	0.555	0.83
40_I	92_T	0.554	0.83
164_L	188_M	0.553	0.82
44_A	121_A	0.552	0.82
243_V	249_A	0.549	0.82
124_L	149_T	0.548	0.82
65_M	267_F	0.547	0.82
166_P	190_N	0.547	0.82
67_N	71_L	0.545	0.82
153_K	183_A	0.545	0.82
68_A	208_N	0.544	0.81
219_K	222_A	0.540	0.81
32_Y	40_I	0.540	0.81
69_I	264_T	0.539	0.81
39_A	259_A	0.539	0.81
200_K	247_E	0.539	0.81
20_G	263_G	0.538	0.81
70_G	125_N	0.538	0.81
83_E	96_A	0.537	0.81
97_N	123_E	0.536	0.81
136_I	139_G	0.534	0.80
284_L	296_I	0.531	0.80
225_M	229_V	0.530	0.80
223_I	227_Y	0.530	0.80
262_V	273_C	0.530	0.80
145_A	149_T	0.528	0.80
70_G	212_G	0.528	0.80
102_Q	128_C	0.528	0.80
121_A	161_Y	0.527	0.79
131_V	136_I	0.526	0.79
68_A	72_Q	0.523	0.79
110_A	114_S	0.522	0.79
42_I	45_T	0.518	0.78
174_I	178_I	0.517	0.78
28_F	83_E	0.517	0.78
76_L	79_V	0.517	0.78
84_L	118_N	0.516	0.78
146_A	177_A	0.516	0.78
71_L	128_C	0.516	0.78
45_T	96_A	0.515	0.78
110_A	156_S	0.514	0.78
7_P	236_P	0.513	0.78
11_L	93_P	0.512	0.77
227_Y	251_E	0.511	0.77
128_C	136_I	0.509	0.77
17_P	22_F	0.509	0.77
41_M	240_M	0.506	0.77
203_K	209_K	0.505	0.76
140_T	168_V	0.504	0.76
81_H	85_P	0.503	0.76
103_V	144_M	0.503	0.76
145_A	148_L	0.502	0.76
124_L	160_V	0.502	0.76
29_S	33_D	0.500	0.76

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
4cq8A	1	0.9357	100	0.386	Contact Map
4ef8A	2	0.9614	100	0.389	Contact Map
1tv5A	3	0.9325	100	0.394	Contact Map
1ep3A	2	0.9743	100	0.402	Contact Map
4oqvA	1	0.9132	100	0.426	Contact Map
1jubA	2	0.9582	100	0.442	Contact Map
2e6fA	2	0.9614	100	0.449	Contact Map
1gteA	4	0.9904	100	0.461	Contact Map
3oixA	3	0.9421	100	0.464	Contact Map
1f76A	1	0.8682	100	0.519	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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