PYRDB - SULSO - GREMLIN Contacts

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

UniProt:	Q9UX04	Sequences: MITIKNITLNDPLIIASGIIPDVPNYVETICEKYKPSAITTKTVTLNPLEPHKPPTVIKLHDGIYMNAIGLGNPGAKAINEIGVLCPLIVSVGGSSINEIKEVVEVVQSKAKIIEINVSSPNRKGYGESLSKLIGDIIESVKSVTKLPVFVKLGPWDNVIELAGKALEKGADGLTLINTIKGLIIDVETFKPILYYGTGGVSGRCLYPIALRIIKDVYEEYGVDIIGVGGVYDWTDVIGMLAAGAKLVGLGTVLIEKGFSVIEEIRKGLQSYLLEKGLKFEDIIGISVRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (274)
Sequences:	5029 (2926)
Seq/√Len:	176.7

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
234_W	268_G	3.828	1.00
77_K	106_V	3.794	1.00
257_K	264_E	3.665	1.00
3_T	8_T	3.356	1.00
105_E	144_V	3.069	1.00
5_K	150_F	2.919	1.00
135_G	168_E	2.879	1.00
9_L	247_L	2.759	1.00
160_I	220_E	2.603	1.00
135_G	169_K	2.555	1.00
218_Y	246_K	2.502	1.00
210_A	240_M	2.487	1.00
142_K	172_D	2.484	1.00
176_L	217_V	2.416	1.00
232_Y	236_D	2.411	1.00
44_V	79_I	2.393	1.00
207_Y	239_G	2.322	1.00
211_L	240_M	2.229	1.00
150_F	173_G	2.215	1.00
233_D	236_D	2.189	1.00
11_D	37_S	2.158	1.00
142_K	149_V	2.146	1.00
134_I	166_A	2.132	1.00
214_I	225_I	2.086	1.00
279_K	282_D	2.038	1.00
218_Y	225_I	1.981	1.00
207_Y	236_D	1.967	1.00
167_L	223_V	1.937	1.00
11_D	266_R	1.931	1.00
22_D	74_P	1.875	1.00
231_V	248_V	1.852	1.00
89_I	113_I	1.794	1.00
238_I	276_K	1.791	1.00
272_Y	276_K	1.753	1.00
104_V	114_I	1.744	1.00
167_L	222_G	1.725	1.00
175_T	228_V	1.719	1.00
271_S	275_E	1.699	1.00
163_A	217_V	1.683	1.00
250_L	265_I	1.666	1.00
101_K	144_V	1.665	1.00
14_I	40_T	1.662	1.00
207_Y	240_M	1.659	1.00
231_V	240_M	1.638	1.00
28_E	85_L	1.631	1.00
164_G	168_E	1.622	1.00
76_A	106_V	1.603	1.00
237_V	265_I	1.592	1.00
224_D	246_K	1.589	1.00
74_P	78_A	1.565	1.00
235_T	239_G	1.555	1.00
7_I	113_I	1.552	1.00
118_V	134_I	1.547	1.00
158_N	161_E	1.535	1.00
76_A	107_V	1.535	1.00
188_E	276_K	1.526	1.00
235_T	272_Y	1.525	1.00
13_L	266_R	1.489	1.00
177_I	180_I	1.487	1.00
150_F	226_I	1.487	1.00
241_L	280_F	1.478	1.00
92_V	103_V	1.450	1.00
97_I	136_D	1.449	1.00
14_I	38_A	1.437	1.00
45_T	93_G	1.436	1.00
180_I	209_I	1.434	1.00
160_I	216_D	1.428	1.00
108_Q	145_T	1.424	1.00
92_V	104_V	1.420	1.00
174_L	221_Y	1.413	1.00
104_V	141_V	1.410	1.00
182_G	209_I	1.402	1.00
108_Q	146_K	1.401	1.00
214_I	227_G	1.396	1.00
237_V	248_V	1.374	1.00
90_V	111_A	1.354	1.00
131_S	161_E	1.352	1.00
253_V	261_V	1.333	1.00
273_L	278_L	1.328	1.00
101_K	140_S	1.327	1.00
142_K	145_T	1.325	1.00
237_V	269_L	1.324	1.00
13_L	265_I	1.305	1.00
238_I	272_Y	1.298	1.00
132_K	136_D	1.294	1.00
185_I	243_A	1.292	1.00
43_T	93_G	1.291	1.00
270_Q	274_L	1.279	1.00
46_L	95_S	1.277	1.00
31_C	86_C	1.275	1.00
116_I	141_V	1.271	1.00
102_E	106_V	1.270	1.00
135_G	139_E	1.268	1.00
43_T	91_S	1.262	1.00
227_G	240_M	1.251	1.00
102_E	105_E	1.251	1.00
40_T	249_G	1.247	1.00
141_V	149_V	1.246	1.00
165_K	169_K	1.245	1.00
238_I	269_L	1.237	1.00
46_L	103_V	1.233	1.00
4_I	247_L	1.231	1.00
207_Y	211_L	1.225	1.00
41_T	90_V	1.223	1.00
107_V	114_I	1.210	1.00
57_V	69_I	1.199	1.00
82_I	85_L	1.198	1.00
76_A	103_V	1.195	1.00
97_I	101_K	1.179	1.00
263_E	267_K	1.178	1.00
212_R	216_D	1.177	1.00
238_I	242_A	1.166	1.00
13_L	231_V	1.159	1.00
264_E	268_G	1.157	1.00
188_E	275_E	1.153	1.00
234_W	238_I	1.144	1.00
164_G	220_E	1.139	1.00
228_V	249_G	1.134	1.00
97_I	140_S	1.127	1.00
266_R	270_Q	1.123	1.00
138_I	151_V	1.121	1.00
74_P	81_E	1.103	1.00
114_I	147_L	1.103	1.00
14_I	249_G	1.099	1.00
233_D	261_V	1.093	1.00
45_T	49_L	1.088	1.00
226_I	247_L	1.077	1.00
104_V	145_T	1.076	1.00
3_T	6_N	1.074	1.00
96_S	99_E	1.072	1.00
60_L	63_G	1.071	1.00
272_Y	275_E	1.071	1.00
272_Y	278_L	1.068	1.00
151_V	171_A	1.067	1.00
204_R	232_Y	1.064	1.00
180_I	206_L	1.063	1.00
41_T	79_I	1.062	1.00
16_A	251_G	1.051	1.00
63_G	189_T	1.048	1.00
120_S	123_R	1.044	1.00
36_P	262_I	1.043	1.00
101_K	105_E	1.027	0.99
139_E	169_K	1.021	0.99
187_V	238_I	1.021	0.99
232_Y	253_V	1.010	0.99
153_L	217_V	1.003	0.99
80_N	83_G	1.000	0.99
211_L	243_A	1.000	0.99
214_I	240_M	0.998	0.99
235_T	268_G	0.998	0.99
23_V	79_I	0.996	0.99
234_W	265_I	0.993	0.99
26_Y	30_I	0.992	0.99
267_K	271_S	0.991	0.99
140_S	143_S	0.989	0.99
5_K	173_G	0.985	0.99
69_I	73_N	0.983	0.99
234_W	272_Y	0.976	0.99
30_I	39_I	0.970	0.99
260_S	264_E	0.970	0.99
136_D	139_E	0.965	0.99
136_D	140_S	0.958	0.99
159_V	217_V	0.955	0.99
14_I	247_L	0.949	0.99
250_L	261_V	0.942	0.99
7_I	87_P	0.941	0.99
150_F	175_T	0.940	0.99
10_N	86_C	0.936	0.99
108_Q	147_L	0.935	0.99
67_N	179_T	0.926	0.99
179_T	202_S	0.924	0.99
94_G	115_E	0.920	0.99
177_I	210_A	0.919	0.99
176_L	213_I	0.917	0.99
4_I	150_F	0.911	0.99
65_Y	252_T	0.907	0.99
268_G	272_Y	0.906	0.99
63_G	186_D	0.902	0.99
139_E	143_S	0.898	0.99
71_L	93_G	0.896	0.99
116_I	151_V	0.888	0.98
90_V	107_V	0.887	0.98
271_S	274_L	0.886	0.98
204_R	207_Y	0.884	0.98
133_L	136_D	0.874	0.98
16_A	249_G	0.869	0.98
177_I	206_L	0.867	0.98
35_K	267_K	0.867	0.98
98_N	102_E	0.849	0.98
242_A	276_K	0.844	0.98
15_I	36_P	0.843	0.98
4_I	226_I	0.841	0.98
74_P	79_I	0.834	0.98
46_L	102_E	0.831	0.98
15_I	262_I	0.822	0.97
267_K	270_Q	0.819	0.97
163_A	221_Y	0.817	0.97
208_P	212_R	0.816	0.97
209_I	212_R	0.816	0.97
101_K	143_S	0.815	0.97
166_A	174_L	0.814	0.97
35_K	263_E	0.807	0.97
145_T	149_V	0.802	0.97
210_A	227_G	0.801	0.97
254_L	262_I	0.801	0.97
96_S	124_K	0.796	0.97
160_I	217_V	0.793	0.97
216_D	220_E	0.790	0.97
257_K	260_S	0.790	0.97
238_I	268_G	0.789	0.97
13_L	250_L	0.787	0.97
25_N	81_E	0.786	0.97
108_Q	114_I	0.780	0.96
95_S	103_V	0.779	0.96
242_A	272_Y	0.779	0.96
214_I	243_A	0.775	0.96
70_G	73_N	0.771	0.96
69_I	72_G	0.769	0.96
47_N	95_S	0.767	0.96
157_D	160_I	0.765	0.96
159_V	213_I	0.764	0.96
40_T	175_T	0.763	0.96
164_G	167_L	0.762	0.96
120_S	127_G	0.761	0.96
40_T	91_S	0.760	0.96
261_V	265_I	0.759	0.96
78_A	81_E	0.757	0.96
49_L	95_S	0.755	0.96
186_D	189_T	0.753	0.96
174_L	217_V	0.752	0.96
51_P	75_G	0.747	0.95
132_K	135_G	0.747	0.95
160_I	164_G	0.744	0.95
13_L	248_V	0.742	0.95
273_L	280_F	0.736	0.95
198_T	215_K	0.733	0.95
123_R	127_G	0.732	0.95
140_S	144_V	0.731	0.95
131_S	165_K	0.727	0.95
250_L	253_V	0.727	0.95
4_I	246_K	0.726	0.95
43_T	92_V	0.723	0.95
186_D	193_I	0.722	0.95
270_Q	273_L	0.716	0.94
153_L	174_L	0.715	0.94
167_L	221_Y	0.714	0.94
110_K	147_L	0.709	0.94
184_I	187_V	0.706	0.94
161_E	165_K	0.705	0.94
218_Y	222_G	0.705	0.94
87_P	112_K	0.704	0.94
130_L	158_N	0.703	0.94
49_L	93_G	0.702	0.94
107_V	110_K	0.699	0.94
174_L	225_I	0.696	0.93
179_T	200_G	0.693	0.93
13_L	237_V	0.691	0.93
182_G	185_I	0.690	0.93
204_R	236_D	0.688	0.93
177_I	213_I	0.688	0.93
212_R	215_K	0.687	0.93
237_V	268_G	0.683	0.93
9_L	38_A	0.683	0.93
46_L	99_E	0.683	0.93
57_V	65_Y	0.680	0.93
17_S	42_K	0.679	0.93
92_V	116_I	0.679	0.93
104_V	108_Q	0.679	0.93
237_V	241_L	0.678	0.93
181_K	216_D	0.677	0.92
77_K	80_N	0.675	0.92
9_L	113_I	0.674	0.92
159_V	220_E	0.666	0.92
67_N	71_L	0.663	0.92
47_N	102_E	0.662	0.92
118_V	151_V	0.659	0.91
83_G	109_S	0.657	0.91
98_N	101_K	0.655	0.91
121_P	200_G	0.654	0.91
9_L	14_I	0.650	0.91
217_V	221_Y	0.649	0.91
26_Y	29_T	0.645	0.91
80_N	84_V	0.644	0.91
79_I	107_V	0.644	0.91
166_A	225_I	0.642	0.90
101_K	141_V	0.639	0.90
257_K	261_V	0.639	0.90
113_I	249_G	0.639	0.90
25_N	74_P	0.638	0.90
104_V	144_V	0.636	0.90
38_A	249_G	0.635	0.90
142_K	169_K	0.635	0.90
63_G	188_E	0.634	0.90
4_I	9_L	0.633	0.90
129_S	154_G	0.633	0.90
104_V	137_I	0.630	0.90
207_Y	214_I	0.630	0.90
120_S	126_Y	0.629	0.89
22_D	25_N	0.629	0.89
81_E	85_L	0.626	0.89
216_D	219_E	0.623	0.89
175_T	249_G	0.621	0.89
189_T	193_I	0.621	0.89
149_V	172_D	0.620	0.89
52_H	56_T	0.620	0.89
153_L	213_I	0.618	0.89
19_I	255_I	0.616	0.88
82_I	88_L	0.615	0.88
241_L	273_L	0.614	0.88
101_K	137_I	0.613	0.88
211_L	214_I	0.612	0.88
215_K	219_E	0.610	0.88
111_A	114_I	0.608	0.88
5_K	113_I	0.607	0.88
260_S	263_E	0.604	0.87
67_N	73_N	0.598	0.87
269_L	273_L	0.597	0.87
31_C	39_I	0.597	0.87
185_I	188_E	0.597	0.87
60_L	201_V	0.594	0.87
36_P	266_R	0.593	0.87
15_I	30_I	0.591	0.86
4_I	224_D	0.591	0.86
66_M	194_L	0.591	0.86
21_P	42_K	0.591	0.86
77_K	102_E	0.590	0.86
28_E	32_E	0.590	0.86
47_N	77_K	0.589	0.86
138_I	171_A	0.585	0.86
241_L	248_V	0.585	0.86
114_I	145_T	0.584	0.86
211_L	227_G	0.581	0.85
194_L	199_G	0.581	0.85
113_I	175_T	0.580	0.85
70_G	121_P	0.580	0.85
188_E	235_T	0.578	0.85
172_D	224_D	0.577	0.85
184_I	207_Y	0.577	0.85
123_R	126_Y	0.576	0.85
262_I	266_R	0.575	0.85
20_I	27_V	0.575	0.85
87_P	113_I	0.572	0.85
67_N	200_G	0.572	0.85
119_S	200_G	0.571	0.84
124_K	127_G	0.570	0.84
91_S	115_E	0.569	0.84
83_G	110_K	0.567	0.84
174_L	223_V	0.567	0.84
273_L	281_E	0.566	0.84
45_T	73_N	0.565	0.84
104_V	147_L	0.564	0.84
161_E	164_G	0.561	0.83
65_Y	255_I	0.558	0.83
181_K	198_T	0.558	0.83
96_S	120_S	0.556	0.83
38_A	87_P	0.556	0.83
6_N	148_P	0.554	0.83
115_E	175_T	0.553	0.83
38_A	247_L	0.553	0.83
85_L	88_L	0.551	0.82
25_N	78_A	0.551	0.82
70_G	117_N	0.551	0.82
231_V	237_V	0.550	0.82
265_I	268_G	0.546	0.82
68_A	72_G	0.546	0.82
242_A	278_L	0.544	0.82
119_S	122_N	0.544	0.82
215_K	239_G	0.542	0.81
213_I	217_V	0.540	0.81
15_I	20_I	0.538	0.81
184_I	239_G	0.538	0.81
67_N	72_G	0.538	0.81
127_G	154_G	0.536	0.81
106_V	109_S	0.533	0.80
278_L	282_D	0.532	0.80
142_K	171_A	0.531	0.80
134_I	138_I	0.530	0.80
153_L	176_L	0.528	0.80
184_I	193_I	0.527	0.79
71_L	126_Y	0.525	0.79
76_A	79_I	0.524	0.79
162_L	166_A	0.524	0.79
39_I	86_C	0.524	0.79
155_P	178_N	0.523	0.79
27_V	85_L	0.522	0.79
43_T	113_I	0.521	0.79
41_T	44_V	0.520	0.79
232_Y	257_K	0.515	0.78
211_L	215_K	0.514	0.78
79_I	90_V	0.513	0.78
134_I	137_I	0.513	0.78
9_L	87_P	0.513	0.78
269_L	272_Y	0.512	0.77
97_I	133_L	0.511	0.77
60_L	66_M	0.511	0.77
66_M	182_G	0.509	0.77
68_A	197_G	0.507	0.77
73_N	79_I	0.507	0.77
250_L	262_I	0.507	0.77
52_H	73_N	0.507	0.77
113_I	150_F	0.506	0.77
51_P	70_G	0.505	0.77
200_G	203_G	0.504	0.76
40_T	228_V	0.504	0.76
31_C	262_I	0.503	0.76
157_D	162_L	0.502	0.76
207_Y	210_A	0.502	0.76
18_G	251_G	0.502	0.76
43_T	71_L	0.502	0.76
14_I	89_I	0.501	0.76
120_S	200_G	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	0.9724	100	0.383	Contact Map
1tv5A	3	0.969	100	0.397	Contact Map
4ef8A	2	0.9931	100	0.417	Contact Map
4oqvA	1	0.9517	100	0.423	Contact Map
1ep3A	2	0.9897	100	0.434	Contact Map
1jubA	2	0.9931	100	0.466	Contact Map
2e6fA	2	0.9931	100	0.468	Contact Map
3oixA	3	0.9724	100	0.481	Contact Map
1gteA	4	0.9931	100	0.494	Contact Map
1f76A	1	0.9103	100	0.509	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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