PYRF - ECOLI - GREMLIN Contacts

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PYRF - Orotidine 5'-phosphate decarboxylase

UniProt:	P08244	Sequences: MTLTASSSSRAVTNSPVVVALDYHNRDDALAFVDKIDPRDCRLKVGKEMFTLFGPQFVRELQQRGFDIFLDLKFHDIPNTAAHAVAAAADLGVWMVNVHASGGARMMTAAREALVPFGKDAPLLIAVTVLTSMEASDLVDLGMTLSPADYAERLAALTQKCGLDGVVCSAQEAVRFKQVFGQEFKLVTPGIRPQGSEAGDQRRIMTPEQALSAGVDYMVIGRPVTQSVDPAQTLKAINASLQRSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10809
Length:	245 (224)
Sequences:	2657 (1705)
Seq/√Len:	113.9

ECOLI - PYRF ULAD SGBH
BACSU - PYRF HPS
SULSO - PYRF Q980S5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_D	64_R	3.422	1.00
100_A	126_A	3.251	1.00
25_N	28_D	3.156	1.00
62_Q	94_W	3.071	1.00
229_D	232_Q	3.034	1.00
135_A	147_P	2.438	1.00
134_E	202_R	2.432	1.00
170_A	205_M	2.380	1.00
56_Q	59_R	2.363	1.00
102_G	106_M	2.321	1.00
104_A	140_D	2.269	1.00
107_M	163_L	2.245	1.00
177_K	216_D	2.245	1.00
227_S	233_T	2.217	1.00
104_A	108_T	2.129	1.00
82_A	112_E	2.083	1.00
105_R	202_R	2.075	1.00
30_L	60_E	2.048	1.00
17_V	220_I	2.008	1.00
196_S	223_P	1.981	1.00
111_R	115_V	1.938	1.00
208_E	240_S	1.928	1.00
47_K	51_T	1.875	1.00
26_R	60_E	1.856	1.00
159_Q	181_G	1.848	1.00
205_M	213_A	1.843	1.00
231_A	235_K	1.793	1.00
177_K	186_L	1.789	1.00
135_A	139_V	1.780	1.00
208_E	212_S	1.745	1.00
193_P	196_S	1.738	1.00
193_P	223_P	1.717	1.00
209_Q	212_S	1.690	1.00
23_Y	32_F	1.679	1.00
104_A	160_K	1.663	1.00
152_E	179_V	1.639	1.00
232_Q	236_A	1.639	1.00
74_F	88_A	1.599	1.00
32_F	36_I	1.578	1.00
135_A	146_S	1.575	1.00
138_L	143_M	1.573	1.00
176_F	186_L	1.568	1.00
105_R	108_T	1.568	1.00
215_V	218_M	1.567	1.00
82_A	113_A	1.551	1.00
104_A	161_C	1.543	1.00
105_R	137_D	1.543	1.00
146_S	149_D	1.540	1.00
26_R	53_F	1.494	1.00
18_V	42_R	1.463	1.00
83_H	86_A	1.462	1.00
134_E	137_D	1.456	1.00
49_M	53_F	1.450	1.00
85_V	96_V	1.446	1.00
52_L	87_A	1.435	1.00
39_R	235_K	1.429	1.00
33_V	43_L	1.397	1.00
195_G	236_A	1.388	1.00
209_Q	213_A	1.381	1.00
156_A	179_V	1.374	1.00
168_C	186_L	1.348	1.00
115_V	121_A	1.335	1.00
193_P	237_I	1.333	1.00
170_A	191_I	1.330	1.00
145_L	149_D	1.311	1.00
188_T	215_V	1.298	0.99
104_A	157_L	1.297	0.99
17_V	234_L	1.296	0.99
125_I	163_L	1.296	0.99
67_D	94_W	1.291	0.99
159_Q	180_F	1.287	0.99
123_L	185_K	1.281	0.99
45_V	61_L	1.263	0.99
198_A	204_I	1.262	0.99
145_L	153_R	1.247	0.99
28_D	31_A	1.246	0.99
20_A	221_G	1.229	0.99
186_L	216_D	1.229	0.99
79_N	83_H	1.218	0.99
236_A	240_S	1.211	0.99
121_A	164_D	1.210	0.99
26_R	30_L	1.209	0.99
35_K	229_D	1.202	0.99
97_N	127_V	1.190	0.99
49_M	57_F	1.188	0.99
142_G	153_R	1.172	0.99
173_A	215_V	1.159	0.99
31_A	35_K	1.149	0.99
35_K	230_P	1.148	0.99
129_V	133_M	1.131	0.99
43_L	66_F	1.127	0.99
235_K	239_A	1.124	0.99
174_V	213_A	1.123	0.99
81_A	110_A	1.122	0.99
19_V	225_T	1.116	0.98
133_M	137_D	1.115	0.98
173_A	186_L	1.088	0.98
129_V	150_Y	1.086	0.98
81_A	106_M	1.086	0.98
166_V	184_F	1.085	0.98
18_V	217_Y	1.084	0.98
30_L	34_D	1.083	0.98
101_S	154_L	1.081	0.98
211_L	218_M	1.077	0.98
111_R	121_A	1.074	0.98
51_T	74_F	1.074	0.98
97_N	125_I	1.064	0.98
195_G	199_G	1.063	0.98
83_H	87_A	1.054	0.98
123_L	164_D	1.054	0.98
59_R	63_Q	1.052	0.98
61_L	66_F	1.045	0.98
26_R	57_F	1.044	0.98
199_G	226_Q	1.043	0.98
98_V	107_M	1.042	0.98
137_D	140_D	1.042	0.98
95_M	123_L	1.040	0.98
176_F	180_F	1.034	0.97
70_L	93_V	1.029	0.97
185_K	216_D	1.028	0.97
42_R	67_D	1.017	0.97
150_Y	154_L	1.016	0.97
139_V	144_T	1.001	0.97
139_V	145_L	0.994	0.97
41_C	66_F	0.985	0.97
232_Q	235_K	0.984	0.97
19_V	40_D	0.983	0.97
40_D	234_L	0.980	0.97
95_M	125_I	0.979	0.96
148_A	175_R	0.976	0.96
97_N	107_M	0.976	0.96
24_H	28_D	0.970	0.96
236_A	239_A	0.966	0.96
108_T	112_E	0.964	0.96
199_G	223_P	0.963	0.96
83_H	226_Q	0.958	0.96
109_A	113_A	0.956	0.96
109_A	112_E	0.956	0.96
81_A	102_G	0.955	0.96
17_V	241_L	0.954	0.96
101_S	150_Y	0.953	0.96
42_R	95_M	0.948	0.96
101_S	129_V	0.947	0.96
98_V	124_L	0.929	0.95
168_C	176_F	0.926	0.95
156_A	180_F	0.923	0.95
74_F	81_A	0.921	0.95
111_R	164_D	0.920	0.95
211_L	241_L	0.917	0.95
60_E	63_Q	0.904	0.95
85_V	114_L	0.903	0.94
233_T	236_A	0.899	0.94
48_E	83_H	0.899	0.94
152_E	175_R	0.895	0.94
166_V	186_L	0.888	0.94
52_L	90_D	0.887	0.94
82_A	86_A	0.882	0.94
58_V	91_L	0.880	0.94
105_R	109_A	0.868	0.93
205_M	209_Q	0.868	0.93
58_V	68_I	0.867	0.93
152_E	156_A	0.864	0.93
50_F	72_L	0.862	0.93
100_A	158_T	0.853	0.93
218_M	241_L	0.853	0.93
101_S	133_M	0.852	0.93
17_V	238_N	0.848	0.92
111_R	124_L	0.846	0.92
35_K	231_A	0.843	0.92
142_G	145_L	0.835	0.92
74_F	84_A	0.834	0.92
48_E	225_T	0.832	0.92
39_R	231_A	0.828	0.92
41_C	234_L	0.821	0.91
107_M	161_C	0.814	0.91
171_Q	205_M	0.812	0.91
47_K	84_A	0.811	0.91
126_A	163_L	0.810	0.91
50_F	55_P	0.807	0.90
68_I	93_V	0.805	0.90
174_V	178_Q	0.801	0.90
119_K	122_P	0.801	0.90
53_F	57_F	0.797	0.90
45_V	49_M	0.796	0.90
125_I	187_V	0.795	0.90
126_A	158_T	0.794	0.90
198_A	202_R	0.789	0.89
194_Q	240_S	0.789	0.89
104_A	107_M	0.789	0.89
51_T	88_A	0.787	0.89
29_A	49_M	0.782	0.89
175_R	179_V	0.778	0.89
156_A	160_K	0.777	0.89
15_S	41_C	0.776	0.89
96_V	114_L	0.776	0.89
16_P	211_L	0.771	0.88
100_A	151_A	0.770	0.88
19_V	32_F	0.765	0.88
224_V	234_L	0.760	0.88
95_M	217_Y	0.757	0.87
42_R	94_W	0.752	0.87
87_A	90_D	0.751	0.87
231_A	234_L	0.750	0.87
23_Y	29_A	0.750	0.87
43_L	61_L	0.744	0.87
127_V	130_L	0.743	0.86
15_S	67_D	0.740	0.86
169_S	172_E	0.738	0.86
37_D	43_L	0.737	0.86
85_V	110_A	0.734	0.86
223_P	237_I	0.728	0.85
75_H	133_M	0.726	0.85
128_T	166_V	0.725	0.85
158_T	163_L	0.725	0.85
23_Y	225_T	0.723	0.85
21_L	45_V	0.722	0.85
30_L	33_V	0.721	0.85
143_M	150_Y	0.710	0.84
100_A	154_L	0.705	0.83
39_R	238_N	0.703	0.83
141_L	150_Y	0.700	0.83
180_F	184_F	0.698	0.83
21_L	33_V	0.698	0.83
26_R	56_Q	0.695	0.83
234_L	238_N	0.692	0.82
152_E	180_F	0.692	0.82
145_L	150_Y	0.689	0.82
207_P	218_M	0.689	0.82
32_F	43_L	0.685	0.82
38_P	231_A	0.683	0.81
84_A	87_A	0.680	0.81
97_N	184_F	0.678	0.81
101_S	143_M	0.675	0.81
57_F	60_E	0.674	0.81
18_V	187_V	0.671	0.80
78_P	106_M	0.663	0.80
36_I	231_A	0.662	0.79
129_V	154_L	0.658	0.79
186_L	217_Y	0.656	0.79
193_P	240_S	0.655	0.79
85_V	113_A	0.653	0.78
150_Y	153_R	0.652	0.78
110_A	113_A	0.652	0.78
27_D	31_A	0.648	0.78
82_A	109_A	0.648	0.78
27_D	30_L	0.646	0.78
36_I	234_L	0.644	0.78
175_R	178_Q	0.644	0.78
74_F	85_V	0.640	0.77
32_F	230_P	0.640	0.77
21_L	61_L	0.636	0.77
37_D	66_F	0.633	0.76
85_V	124_L	0.631	0.76
40_D	238_N	0.629	0.76
229_D	233_T	0.626	0.76
185_K	217_Y	0.625	0.75
47_K	88_A	0.624	0.75
177_K	217_Y	0.623	0.75
33_V	53_F	0.622	0.75
34_D	38_P	0.613	0.74
125_I	167_V	0.607	0.73
45_V	57_F	0.602	0.73
19_V	224_V	0.601	0.73
30_L	64_R	0.601	0.73
220_I	237_I	0.600	0.72
95_M	187_V	0.599	0.72
237_I	240_S	0.599	0.72
19_V	41_C	0.596	0.72
48_E	80_T	0.594	0.72
55_P	91_L	0.592	0.71
140_D	157_L	0.589	0.71
60_E	64_R	0.583	0.70
166_V	180_F	0.583	0.70
173_A	188_T	0.581	0.70
58_V	62_Q	0.578	0.70
107_M	158_T	0.577	0.70
148_A	171_Q	0.575	0.69
50_F	87_A	0.574	0.69
21_L	29_A	0.572	0.69
29_A	57_F	0.572	0.69
86_A	109_A	0.570	0.69
133_M	154_L	0.569	0.68
95_M	167_V	0.568	0.68
115_V	119_K	0.567	0.68
196_S	199_G	0.566	0.68
166_V	176_F	0.561	0.67
195_G	240_S	0.561	0.67
42_R	66_F	0.559	0.67
137_D	202_R	0.559	0.67
48_E	86_A	0.558	0.67
55_P	58_V	0.557	0.67
32_F	35_K	0.557	0.67
152_E	178_Q	0.553	0.66
114_L	124_L	0.552	0.66
70_L	88_A	0.550	0.66
47_K	74_F	0.550	0.66
207_P	237_I	0.548	0.66
171_Q	204_I	0.548	0.66
37_D	40_D	0.547	0.65
138_L	147_P	0.546	0.65
57_F	61_L	0.546	0.65
33_V	61_L	0.545	0.65
159_Q	184_F	0.544	0.65
111_R	163_L	0.544	0.65
76_D	80_T	0.542	0.65
133_M	150_Y	0.541	0.65
40_D	43_L	0.540	0.64
79_N	82_A	0.540	0.64
17_V	170_A	0.537	0.64
159_Q	183_E	0.535	0.64
75_H	101_S	0.534	0.64
89_A	92_G	0.532	0.63
124_L	163_L	0.530	0.63
86_A	113_A	0.529	0.63
106_M	130_L	0.528	0.63
56_Q	63_Q	0.528	0.63
18_V	95_M	0.527	0.63
100_A	107_M	0.525	0.62
163_L	166_V	0.520	0.62
103_G	154_L	0.520	0.62
53_F	56_Q	0.520	0.62
169_S	203_R	0.519	0.61
136_S	140_D	0.518	0.61
150_Y	176_F	0.517	0.61
45_V	50_F	0.516	0.61
24_H	83_H	0.515	0.61
30_L	57_F	0.514	0.61
195_G	198_A	0.510	0.60
51_T	87_A	0.508	0.60
62_Q	92_G	0.506	0.59
31_A	34_D	0.506	0.59
108_T	160_K	0.504	0.59
220_I	234_L	0.502	0.59
228_V	232_Q	0.501	0.59
49_M	52_L	0.500	0.59
112_E	115_V	0.500	0.59

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
3gdmA	2	0.9469	100	0.316	Contact Map
1eixA	2	0.9469	100	0.343	Contact Map
3tr2A	2	0.9061	100	0.345	Contact Map
3ldvA	2	0.9469	100	0.347	Contact Map
3qw4B	4	0.9143	100	0.364	Contact Map
3g3dA	2	0.9347	100	0.365	Contact Map
3r89A	2	0.9429	100	0.367	Contact Map
3v75A	2	0.9306	100	0.372	Contact Map
3ewwA	2	0.9347	100	0.373	Contact Map
3qw3A	2	0.902	100	0.376	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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