PYRD - ECOLI - GREMLIN Contacts

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PYRD - Dihydroorotate dehydrogenase (quinone)

UniProt:	P0A7E1	Sequences: MYYPFVRKALFQLDPERAHEFTFQQLRRITGTPFEALVRQKVPAKPVNCMGLTFKNPLGLAAGLDKDGECIDALGAMGFGSIEIGTVTPRPQPGNDKPRLFRLVDAEGLINRMGFNNLGVDNLVENVKKAHYDGVLGINIGKNKDTPVEQGKDDYLICMEKIYAYAGYIAINISSPNTPGLRTLQYGEALDDLLTAIKNKQNDLQAMHHKYVPIAVKIAPDLSEEELIQVADSLVRHNIDGVIATNTTLDRSLVQGMKNCDQTGGLSGRPLQLKSTEIIRRLSLELNGRLPIIGVGGIDSVIAAREKIAAGASLVQIYSGFIFKGPPLIKEIVTHI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10807
Length:	336 (273)
Sequences:	5152 (2921)
Seq/√Len:	176.8

ECOLI - PYRD PREA
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
48_N	53_T	3.837	1.00
121_D	161_K	3.674	1.00
324_K	331_E	3.380	1.00
46_P	53_T	3.134	1.00
160_E	200_K	3.068	1.00
50_M	215_A	3.065	1.00
191_D	236_R	2.835	1.00
54_F	314_L	2.760	1.00
228_I	285_E	2.697	1.00
275_S	307_K	2.557	1.00
283_S	313_S	2.524	1.00
191_D	237_H	2.516	1.00
299_D	303_A	2.511	1.00
244_A	282_L	2.454	1.00
87_V	123_L	2.426	1.00
272_Q	306_E	2.385	1.00
276_T	307_K	2.291	1.00
215_A	241_G	2.267	1.00
198_K	240_D	2.259	1.00
300_S	303_A	2.240	1.00
279_I	292_I	2.206	1.00
56_N	80_G	2.141	1.00
198_K	214_I	2.046	1.00
272_Q	303_A	2.032	1.00
283_S	292_I	2.023	1.00
67_D	118_L	2.010	1.00
235_V	290_L	1.997	1.00
190_L	234_L	1.975	1.00
298_I	315_V	1.890	1.00
137_G	168_Y	1.859	1.00
159_M	169_I	1.854	1.00
56_N	333_V	1.757	1.00
45_K	57_P	1.752	1.00
235_V	289_R	1.749	1.00
243_I	295_V	1.732	1.00
223_S	226_E	1.732	1.00
272_Q	307_K	1.722	1.00
231_A	282_L	1.721	1.00
298_I	307_K	1.689	1.00
302_I	306_E	1.685	1.00
118_L	122_N	1.676	1.00
52_L	168_Y	1.665	1.00
59_G	83_E	1.662	1.00
305_R	309_A	1.657	1.00
120_V	161_K	1.655	1.00
107_E	269_R	1.652	1.00
232_D	236_R	1.638	1.00
156_L	200_K	1.580	1.00
90_R	145_D	1.570	1.00
173_I	190_L	1.542	1.00
187_G	229_Q	1.532	1.00
228_I	281_R	1.517	1.00
291_P	313_S	1.507	1.00
59_G	81_S	1.499	1.00
245_T	248_T	1.493	1.00
88_T	141_G	1.488	1.00
279_I	294_G	1.482	1.00
120_V	162_I	1.479	1.00
304_A	315_V	1.468	1.00
188_E	192_D	1.468	1.00
140_I	158_C	1.465	1.00
163_Y	210_K	1.464	1.00
286_L	290_L	1.455	1.00
131_H	167_G	1.453	1.00
191_D	195_T	1.444	1.00
140_I	159_M	1.444	1.00
215_A	293_I	1.435	1.00
163_Y	211_Y	1.432	1.00
248_T	274_K	1.430	1.00
226_E	229_Q	1.418	1.00
138_I	166_A	1.413	1.00
48_N	51_G	1.409	1.00
86_T	139_N	1.403	1.00
250_D	274_K	1.396	1.00
317_I	332_I	1.387	1.00
121_D	125_E	1.354	1.00
49_C	314_L	1.349	1.00
122_N	126_N	1.347	1.00
242_V	286_L	1.338	1.00
108_G	270_P	1.336	1.00
58_L	333_V	1.329	1.00
304_A	332_I	1.328	1.00
294_G	307_K	1.328	1.00
84_I	138_I	1.301	1.00
157_I	160_E	1.300	1.00
171_I	197_I	1.299	1.00
86_T	141_G	1.295	1.00
100_L	113_M	1.287	1.00
301_V	305_R	1.282	1.00
75_G	134_G	1.281	1.00
83_E	316_Q	1.276	1.00
61_A	318_Y	1.276	1.00
106_A	257_M	1.275	1.00
58_L	298_I	1.274	1.00
159_M	197_I	1.268	1.00
89_P	143_N	1.264	1.00
157_I	161_K	1.256	1.00
197_I	214_I	1.255	1.00
320_G	328_L	1.237	1.00
233_S	237_H	1.236	1.00
272_Q	276_T	1.231	1.00
156_L	196_A	1.223	1.00
277_E	281_R	1.217	1.00
152_K	156_L	1.210	1.00
107_E	324_K	1.203	1.00
120_V	158_C	1.189	1.00
195_T	237_H	1.183	1.00
89_P	158_C	1.179	1.00
293_I	314_L	1.177	1.00
84_I	123_L	1.163	1.00
222_L	230_V	1.160	1.00
59_G	316_Q	1.154	1.00
186_Y	189_A	1.151	1.00
232_D	285_E	1.147	1.00
295_V	316_Q	1.135	1.00
58_L	332_I	1.133	1.00
248_T	271_L	1.127	1.00
300_S	328_L	1.121	1.00
299_D	320_G	1.117	1.00
162_I	169_I	1.111	1.00
124_V	161_K	1.109	1.00
55_K	133_D	1.108	1.00
72_D	130_A	1.097	1.00
330_K	334_T	1.088	1.00
169_I	212_V	1.085	1.00
196_A	199_N	1.085	1.00
50_M	241_G	1.085	1.00
125_E	128_K	1.077	1.00
106_A	254_V	1.069	1.00
279_I	307_K	1.066	1.00
269_R	299_D	1.063	1.00
194_L	216_V	1.060	1.00
276_T	310_A	1.059	1.00
317_I	328_L	1.058	1.00
218_I	282_L	1.053	1.00
88_T	92_Q	1.050	1.00
227_L	282_L	1.049	1.00
183_T	226_E	1.045	1.00
152_K	196_A	1.032	0.99
111_N	247_T	1.020	0.99
327_P	331_E	1.019	0.99
192_D	196_A	1.015	0.99
156_L	160_E	1.014	0.99
52_L	135_V	1.013	0.99
216_V	239_I	1.006	0.99
115_F	141_G	0.995	0.99
103_L	106_A	0.990	0.99
163_Y	212_V	0.990	0.99
144_K	154_D	0.987	0.99
55_K	134_G	0.981	0.99
118_L	126_N	0.978	0.99
47_V	313_S	0.975	0.99
192_D	195_T	0.973	0.99
195_T	199_N	0.969	0.99
305_R	308_I	0.966	0.99
74_L	82_I	0.957	0.99
49_C	215_A	0.956	0.99
79_F	329_I	0.952	0.99
244_A	278_I	0.948	0.99
188_E	191_D	0.947	0.99
269_R	272_Q	0.945	0.99
153_D	157_I	0.943	0.99
124_V	165_Y	0.938	0.99
250_D	253_L	0.930	0.99
215_A	243_I	0.926	0.99
152_K	192_D	0.925	0.99
245_T	275_S	0.925	0.99
59_G	314_L	0.910	0.99
301_V	332_I	0.907	0.99
105_D	257_M	0.906	0.99
49_C	293_I	0.903	0.99
175_S	182_R	0.899	0.99
183_T	186_Y	0.896	0.99
68_G	123_L	0.894	0.98
113_M	117_N	0.893	0.98
245_T	271_L	0.890	0.98
109_L	319_S	0.883	0.98
253_L	256_G	0.872	0.98
247_T	267_S	0.869	0.98
273_L	277_E	0.867	0.98
58_L	304_A	0.865	0.98
92_Q	143_N	0.864	0.98
144_K	179_P	0.862	0.98
60_L	79_F	0.855	0.98
43_P	46_P	0.848	0.98
187_G	233_S	0.845	0.98
175_S	178_T	0.842	0.98
142_K	170_A	0.841	0.98
187_G	191_D	0.838	0.98
171_I	216_V	0.836	0.98
83_E	243_I	0.831	0.98
86_T	140_I	0.828	0.98
89_P	157_I	0.824	0.97
122_N	125_E	0.820	0.97
283_S	289_R	0.818	0.97
228_I	282_L	0.814	0.97
143_N	158_C	0.812	0.97
228_I	232_D	0.810	0.97
254_V	305_R	0.807	0.97
234_L	242_V	0.803	0.97
118_L	123_L	0.800	0.97
175_S	181_L	0.800	0.97
49_C	291_P	0.797	0.97
124_V	162_I	0.797	0.97
242_V	282_L	0.797	0.97
281_R	285_E	0.793	0.97
274_K	277_E	0.789	0.97
227_L	278_I	0.788	0.97
176_P	265_G	0.786	0.97
90_R	143_N	0.785	0.97
232_D	235_V	0.784	0.97
163_Y	169_I	0.782	0.97
189_A	192_D	0.781	0.96
162_I	165_Y	0.780	0.96
58_L	317_I	0.779	0.96
61_A	316_Q	0.778	0.96
231_A	286_L	0.777	0.96
317_I	320_G	0.774	0.96
304_A	308_I	0.768	0.96
140_I	171_I	0.767	0.96
120_V	124_V	0.759	0.96
245_T	278_I	0.758	0.96
89_P	154_D	0.757	0.96
196_A	200_K	0.756	0.96
275_S	294_G	0.753	0.96
186_Y	226_E	0.753	0.96
198_K	237_H	0.749	0.96
269_R	303_A	0.747	0.95
58_L	315_V	0.745	0.95
263_T	280_R	0.744	0.95
279_I	310_A	0.739	0.95
235_V	286_L	0.739	0.95
54_F	168_Y	0.737	0.95
94_G	119_G	0.733	0.95
70_C	74_L	0.733	0.95
277_E	280_R	0.731	0.95
218_I	242_V	0.731	0.95
104_V	107_E	0.731	0.95
249_L	281_R	0.730	0.95
81_S	316_Q	0.730	0.95
83_E	139_N	0.729	0.95
70_C	73_A	0.727	0.95
127_V	130_A	0.726	0.95
45_K	305_R	0.725	0.95
324_K	327_P	0.724	0.95
135_V	167_G	0.722	0.95
95_N	99_R	0.722	0.95
168_Y	316_Q	0.721	0.95
282_L	286_L	0.718	0.94
166_A	169_I	0.717	0.94
54_F	81_S	0.714	0.94
62_A	85_G	0.710	0.94
173_I	216_V	0.704	0.94
100_L	109_L	0.699	0.94
229_Q	233_S	0.697	0.93
218_I	278_I	0.696	0.93
214_I	240_D	0.692	0.93
121_D	157_I	0.692	0.93
153_D	156_L	0.692	0.93
156_L	199_N	0.690	0.93
88_T	117_N	0.688	0.93
247_T	265_G	0.687	0.93
50_M	168_Y	0.687	0.93
54_F	59_G	0.686	0.93
49_C	313_S	0.685	0.93
321_F	329_I	0.683	0.93
47_V	57_P	0.681	0.93
43_P	57_P	0.681	0.93
257_M	309_A	0.679	0.93
227_L	285_E	0.678	0.93
242_V	292_I	0.677	0.92
328_L	332_I	0.676	0.92
243_I	316_Q	0.675	0.92
190_L	193_L	0.673	0.92
272_Q	279_I	0.673	0.92
281_R	284_L	0.670	0.92
152_K	189_A	0.669	0.92
161_K	164_A	0.666	0.92
92_Q	141_G	0.665	0.92
128_K	131_H	0.665	0.92
49_C	54_F	0.661	0.92
159_M	163_Y	0.658	0.91
129_K	132_Y	0.655	0.91
65_D	71_I	0.655	0.91
114_G	117_N	0.654	0.91
156_L	197_I	0.653	0.91
298_I	304_A	0.651	0.91
78_G	330_K	0.647	0.91
234_L	292_I	0.642	0.90
252_S	272_Q	0.642	0.90
103_L	108_G	0.640	0.90
138_I	162_I	0.639	0.90
111_N	265_G	0.637	0.90
327_P	330_K	0.637	0.90
128_K	164_A	0.635	0.90
168_Y	243_I	0.634	0.90
123_L	162_I	0.634	0.90
90_R	157_I	0.633	0.90
113_M	116_N	0.632	0.90
280_R	284_L	0.631	0.90
124_V	128_K	0.631	0.90
156_L	193_L	0.631	0.90
308_I	315_V	0.630	0.90
159_M	193_L	0.630	0.90
103_L	266_L	0.627	0.89
46_P	55_K	0.626	0.89
86_T	168_Y	0.624	0.89
272_Q	275_S	0.623	0.89
159_M	200_K	0.621	0.89
87_V	138_I	0.619	0.89
60_L	329_I	0.618	0.89
69_E	118_L	0.617	0.89
190_L	194_L	0.616	0.88
81_S	135_V	0.616	0.88
259_N	264_G	0.615	0.88
139_N	170_A	0.614	0.88
60_L	74_L	0.613	0.88
301_V	331_E	0.612	0.88
249_L	263_T	0.610	0.88
109_L	322_I	0.610	0.88
127_V	165_Y	0.610	0.88
128_K	132_Y	0.610	0.88
159_M	212_V	0.609	0.88
64_L	322_I	0.604	0.88
255_Q	302_I	0.603	0.87
123_L	138_I	0.602	0.87
44_A	47_V	0.598	0.87
71_I	321_F	0.597	0.87
276_T	294_G	0.596	0.87
111_N	174_S	0.592	0.86
179_P	182_R	0.592	0.86
174_S	177_N	0.591	0.86
127_V	136_L	0.590	0.86
128_K	165_Y	0.589	0.86
210_K	214_I	0.589	0.86
69_E	122_N	0.586	0.86
191_D	233_S	0.584	0.86
178_T	181_L	0.584	0.86
59_G	137_G	0.581	0.85
276_T	279_I	0.581	0.85
111_N	115_F	0.580	0.85
230_V	234_L	0.579	0.85
278_I	282_L	0.576	0.85
242_V	290_L	0.576	0.85
229_Q	232_D	0.575	0.85
132_Y	167_G	0.575	0.85
170_A	243_I	0.575	0.85
280_R	306_E	0.575	0.85
90_R	121_D	0.574	0.85
135_V	168_Y	0.573	0.85
324_K	328_L	0.572	0.85
299_D	324_K	0.572	0.85
294_G	310_A	0.571	0.84
194_L	239_I	0.570	0.84
75_G	82_I	0.569	0.84
178_T	182_R	0.568	0.84
301_V	328_L	0.568	0.84
168_Y	215_A	0.565	0.84
252_S	306_E	0.565	0.84
276_T	280_R	0.562	0.84
193_L	196_A	0.559	0.83
115_F	175_S	0.554	0.83
240_D	291_P	0.554	0.83
111_N	117_N	0.552	0.82
50_M	291_P	0.552	0.82
65_D	85_G	0.551	0.82
218_I	244_A	0.549	0.82
54_F	135_V	0.548	0.82
71_I	127_V	0.548	0.82
174_S	265_G	0.546	0.82
60_L	65_D	0.543	0.81
181_L	185_Q	0.543	0.81
159_M	210_K	0.542	0.81
171_I	214_I	0.542	0.81
81_S	314_L	0.542	0.81
115_F	181_L	0.541	0.81
108_G	271_L	0.541	0.81
120_V	123_L	0.540	0.81
220_P	246_N	0.540	0.81
198_K	239_I	0.539	0.81
110_I	250_D	0.539	0.81
69_E	129_K	0.537	0.81
219_A	222_L	0.537	0.81
187_G	232_D	0.533	0.80
112_R	261_D	0.532	0.80
329_I	333_V	0.532	0.80
51_G	213_P	0.532	0.80
71_I	84_I	0.530	0.80
144_K	175_S	0.527	0.79
114_G	172_N	0.525	0.79
72_D	76_A	0.523	0.79
71_I	82_I	0.521	0.79
114_G	265_G	0.520	0.79
115_F	178_T	0.520	0.79
265_G	268_G	0.519	0.78
223_S	227_L	0.519	0.78
99_R	102_R	0.518	0.78
59_G	293_I	0.515	0.78
328_L	331_E	0.513	0.78
218_I	230_V	0.513	0.78
45_K	333_V	0.512	0.78
84_I	87_V	0.509	0.77
112_R	262_Q	0.508	0.77
83_E	137_G	0.505	0.77
301_V	315_V	0.504	0.76
50_M	314_L	0.503	0.76
234_L	237_H	0.503	0.76
80_G	291_P	0.501	0.76
52_L	167_G	0.501	0.76
47_V	314_L	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	0.9792	100	0.312	Contact Map
1tv5A	3	0.9702	100	0.324	Contact Map
4oqvA	1	0.9524	100	0.362	Contact Map
1f76A	1	0.997	100	0.392	Contact Map
4ef8A	2	0.8244	100	0.468	Contact Map
1ep3A	2	0.8185	100	0.515	Contact Map
2e6fA	2	0.8185	100	0.529	Contact Map
1jubA	2	0.8185	100	0.532	Contact Map
1gteA	4	0.9435	100	0.532	Contact Map
3oixA	3	0.7976	100	0.545	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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