PYRF - BACSU - GREMLIN Contacts

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PYRF - Orotidine 5'-phosphate decarboxylase

UniProt:	P25971	Sequences: MKNNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKERNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEGLEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAEESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAIAREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEGIKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	239 (224)
Sequences:	2663 (1702)
Seq/√Len:	113.7

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
23_A	53_R	3.435	1.00
89_A	118_A	3.224	1.00
14_S	17_E	3.131	1.00
222_D	225_K	3.073	1.00
51_K	83_D	3.060	1.00
127_E	140_L	2.464	1.00
126_S	195_V	2.429	1.00
163_V	198_A	2.367	1.00
91_G	95_M	2.359	1.00
45_S	48_K	2.334	1.00
93_K	133_E	2.269	1.00
220_A	226_A	2.185	1.00
170_Y	209_S	2.144	1.00
93_K	97_Q	2.118	1.00
71_N	101_E	2.116	1.00
94_K	195_V	2.039	1.00
19_L	49_Q	2.034	1.00
6_P	213_V	2.017	1.00
100_L	104_E	1.971	1.00
189_D	216_S	1.952	1.00
201_A	233_E	1.941	1.00
96_M	156_L	1.879	1.00
36_M	40_Y	1.856	1.00
198_A	206_K	1.842	1.00
15_A	49_Q	1.811	1.00
170_Y	179_T	1.807	1.00
224_V	228_K	1.802	1.00
127_E	131_K	1.799	1.00
201_A	205_E	1.776	1.00
152_E	174_S	1.745	1.00
186_M	216_S	1.712	1.00
186_M	189_D	1.701	1.00
93_K	153_E	1.684	1.00
202_I	205_E	1.675	1.00
145_V	172_A	1.670	1.00
12_F	21_F	1.666	1.00
225_K	229_A	1.634	1.00
63_L	77_L	1.589	1.00
21_F	25_F	1.575	1.00
130_M	136_I	1.562	1.00
208_S	211_I	1.560	1.00
127_E	139_S	1.559	1.00
94_K	97_Q	1.558	1.00
94_K	129_I	1.550	1.00
71_N	102_G	1.549	1.00
169_I	179_T	1.549	1.00
139_S	142_D	1.544	1.00
28_E	228_K	1.532	1.00
93_K	154_S	1.526	1.00
15_A	42_E	1.467	1.00
149_K	172_A	1.454	1.00
126_S	129_I	1.447	1.00
7_I	31_F	1.447	1.00
74_M	85_V	1.445	1.00
38_L	42_E	1.423	1.00
72_K	75_K	1.416	1.00
104_E	113_R	1.403	1.00
22_L	32_V	1.391	1.00
202_I	206_K	1.384	1.00
41_Q	76_R	1.378	1.00
188_E	229_A	1.361	1.00
113_R	157_D	1.359	1.00
186_M	230_V	1.339	1.00
161_C	179_T	1.327	1.00
115_S	178_L	1.314	1.00
163_V	184_I	1.310	1.00
9_A	214_G	1.301	1.00
152_E	173_V	1.294	0.99
56_E	83_D	1.293	0.99
6_P	227_Y	1.292	0.99
93_K	150_Q	1.288	0.99
181_T	208_S	1.275	0.99
117_I	156_L	1.267	0.99
17_E	20_A	1.261	0.99
229_A	233_E	1.253	0.99
138_K	146_H	1.253	0.99
34_V	50_L	1.240	0.99
68_T	72_K	1.237	0.99
138_K	142_D	1.232	0.99
179_T	209_S	1.212	0.99
191_A	197_V	1.207	0.99
75_K	105_E	1.203	0.99
15_A	19_L	1.194	0.99
38_L	46_I	1.192	0.99
86_N	119_V	1.190	0.99
24_P	222_D	1.172	0.99
166_A	208_S	1.172	0.99
20_A	24_P	1.166	0.99
115_S	157_D	1.163	0.99
70_V	99_A	1.129	0.99
121_Q	125_T	1.128	0.99
24_P	223_P	1.120	0.98
125_T	129_I	1.119	0.98
135_L	146_H	1.114	0.98
166_A	179_T	1.106	0.98
8_I	218_T	1.106	0.98
167_K	206_K	1.098	0.98
90_A	147_Y	1.093	0.98
40_Y	63_L	1.088	0.98
228_K	232_L	1.077	0.98
204_R	211_I	1.077	0.98
70_V	95_M	1.073	0.98
121_Q	143_T	1.071	0.98
32_V	55_C	1.067	0.98
86_N	117_I	1.055	0.98
159_V	177_F	1.053	0.98
188_E	192_N	1.051	0.98
72_K	76_R	1.051	0.98
7_I	210_A	1.051	0.98
84_L	115_S	1.046	0.98
15_A	46_I	1.043	0.98
31_F	56_E	1.042	0.98
192_N	219_K	1.041	0.98
169_I	173_V	1.040	0.98
48_K	52_E	1.037	0.98
19_L	23_A	1.032	0.97
131_K	138_K	1.028	0.97
100_L	157_D	1.027	0.97
87_V	96_M	1.025	0.97
225_K	228_K	1.020	0.97
59_L	82_V	1.018	0.97
100_L	113_R	1.017	0.97
178_L	209_S	1.008	0.97
50_L	55_C	1.006	0.97
143_T	147_Y	0.995	0.97
30_L	55_C	0.988	0.97
131_K	137_E	0.983	0.97
129_I	133_E	0.982	0.97
84_L	117_I	0.980	0.96
141_I	168_A	0.978	0.96
229_A	232_L	0.977	0.96
87_V	116_L	0.976	0.96
29_P	227_Y	0.970	0.96
86_N	96_M	0.969	0.96
70_V	91_G	0.968	0.96
6_P	234_W	0.967	0.96
90_A	143_T	0.966	0.96
98_A	101_E	0.960	0.96
97_Q	101_E	0.959	0.96
90_A	121_Q	0.957	0.96
13_A	17_E	0.951	0.96
72_K	219_K	0.950	0.96
204_R	234_W	0.950	0.96
74_M	103_L	0.949	0.96
98_A	102_G	0.946	0.96
161_C	169_I	0.945	0.96
31_F	84_L	0.943	0.96
168_A	172_A	0.932	0.95
63_L	70_V	0.930	0.95
192_N	216_S	0.926	0.95
145_V	168_A	0.918	0.95
8_I	29_P	0.907	0.95
37_E	72_K	0.901	0.94
226_A	229_A	0.895	0.94
159_V	179_T	0.888	0.94
167_K	171_Q	0.884	0.94
94_K	98_A	0.881	0.94
39_F	61_L	0.878	0.94
135_L	138_K	0.877	0.94
145_V	149_K	0.869	0.93
71_N	75_K	0.868	0.93
96_M	154_S	0.867	0.93
47_V	80_L	0.865	0.93
118_A	156_L	0.856	0.93
24_P	224_V	0.855	0.93
198_A	202_I	0.850	0.92
187_S	233_E	0.850	0.92
49_Q	52_E	0.845	0.92
90_A	125_T	0.843	0.92
149_K	173_V	0.837	0.92
30_L	227_Y	0.835	0.92
6_P	231_R	0.833	0.92
89_A	151_A	0.833	0.92
41_Q	79_S	0.830	0.92
37_E	218_T	0.826	0.91
117_I	180_V	0.823	0.91
63_L	73_A	0.822	0.91
100_L	116_L	0.818	0.91
36_M	73_A	0.817	0.91
211_I	234_W	0.817	0.91
39_F	44_P	0.812	0.91
47_V	57_L	0.812	0.91
34_V	38_L	0.811	0.91
149_K	153_E	0.805	0.90
42_E	46_I	0.805	0.90
4_N	56_E	0.801	0.90
40_Y	77_L	0.798	0.90
18_T	38_L	0.796	0.90
85_V	103_L	0.795	0.90
12_F	18_T	0.784	0.89
164_H	198_A	0.783	0.89
118_A	151_A	0.777	0.89
28_E	224_V	0.776	0.89
162_S	165_E	0.775	0.89
5_L	204_R	0.771	0.88
50_L	53_R	0.771	0.88
57_L	82_V	0.769	0.88
191_A	195_V	0.763	0.88
93_K	96_M	0.763	0.88
120_T	159_V	0.760	0.88
89_A	144_V	0.759	0.88
136_I	143_T	0.759	0.88
32_V	50_L	0.757	0.87
74_M	99_A	0.757	0.87
224_V	227_Y	0.753	0.87
76_R	79_S	0.751	0.87
49_Q	53_R	0.747	0.87
216_S	230_V	0.742	0.86
119_V	122_L	0.742	0.86
217_I	227_Y	0.741	0.86
84_L	210_A	0.737	0.86
31_F	83_D	0.732	0.86
8_I	21_F	0.732	0.86
12_F	218_T	0.731	0.85
64_H	125_T	0.725	0.85
19_L	22_L	0.719	0.85
19_L	53_R	0.711	0.84
227_Y	231_R	0.709	0.84
4_N	30_L	0.709	0.84
151_A	156_L	0.706	0.83
21_F	32_V	0.700	0.83
10_L	22_L	0.700	0.83
26_Q	32_V	0.694	0.82
28_E	231_R	0.693	0.82
89_A	147_Y	0.693	0.82
15_A	45_S	0.689	0.82
10_L	34_V	0.689	0.82
46_I	49_Q	0.684	0.81
200_P	211_I	0.683	0.81
138_K	143_T	0.681	0.81
7_I	180_V	0.675	0.81
73_A	76_R	0.675	0.81
86_N	177_F	0.670	0.80
134_L	143_T	0.667	0.80
16_E	20_A	0.666	0.80
186_M	233_E	0.664	0.80
145_V	173_V	0.663	0.79
90_A	136_I	0.660	0.79
74_M	102_G	0.656	0.79
25_F	224_V	0.652	0.78
16_E	19_L	0.650	0.78
10_L	50_L	0.648	0.78
170_Y	210_A	0.647	0.78
121_Q	147_Y	0.646	0.78
23_A	27_Q	0.644	0.77
143_T	146_H	0.644	0.77
67_P	95_M	0.643	0.77
63_L	74_M	0.639	0.77
178_L	210_A	0.638	0.77
44_P	80_L	0.635	0.76
166_A	181_T	0.634	0.76
71_N	98_A	0.633	0.76
230_V	233_E	0.633	0.76
189_D	192_N	0.632	0.76
116_L	156_L	0.632	0.76
179_T	210_A	0.627	0.76
29_P	231_R	0.626	0.75
168_A	171_Q	0.626	0.75
47_V	51_K	0.624	0.75
99_A	102_G	0.622	0.75
8_I	217_I	0.620	0.75
34_V	46_I	0.618	0.75
117_I	160_V	0.615	0.74
84_L	160_V	0.614	0.74
159_V	169_I	0.613	0.74
74_M	116_L	0.611	0.74
27_Q	224_V	0.608	0.73
22_L	50_L	0.607	0.73
222_D	226_A	0.604	0.73
213_V	230_V	0.603	0.73
22_L	42_E	0.600	0.72
84_L	180_V	0.600	0.72
159_V	173_V	0.592	0.71
36_M	77_L	0.591	0.71
8_I	30_L	0.590	0.71
25_F	227_Y	0.589	0.71
10_L	18_T	0.587	0.71
152_E	177_F	0.587	0.71
45_S	52_E	0.582	0.70
37_E	69_T	0.582	0.70
103_L	116_L	0.581	0.70
96_M	151_A	0.574	0.69
18_T	46_I	0.574	0.69
174_S	177_F	0.572	0.69
125_T	147_Y	0.572	0.69
21_F	24_P	0.569	0.68
81_G	114_P	0.569	0.68
39_F	76_R	0.566	0.68
26_Q	55_C	0.565	0.68
200_P	230_V	0.559	0.67
65_D	69_T	0.559	0.67
21_F	223_P	0.558	0.67
188_E	233_E	0.558	0.67
100_L	156_L	0.556	0.67
31_F	55_C	0.553	0.66
134_L	138_K	0.552	0.66
68_T	71_N	0.550	0.66
19_L	46_I	0.549	0.66
129_I	195_V	0.546	0.65
59_L	77_L	0.546	0.65
125_T	143_T	0.543	0.65
103_L	114_P	0.543	0.65
36_M	63_L	0.542	0.65
78_A	81_G	0.541	0.65
64_H	90_A	0.540	0.64
143_T	169_I	0.539	0.64
173_V	177_F	0.539	0.64
164_H	197_V	0.537	0.64
29_P	55_C	0.535	0.64
133_E	150_Q	0.534	0.64
42_E	45_S	0.531	0.63
130_M	140_L	0.531	0.63
37_E	75_K	0.529	0.63
162_S	196_R	0.527	0.63
51_K	81_G	0.526	0.62
187_S	201_A	0.525	0.62
152_E	176_S	0.525	0.62
46_I	50_L	0.520	0.62
95_M	122_L	0.520	0.62
141_I	164_H	0.519	0.61
26_Q	29_P	0.519	0.61
188_E	191_A	0.518	0.61
29_P	32_V	0.518	0.61
75_K	98_A	0.516	0.61
101_E	105_E	0.515	0.61
214_G	218_T	0.514	0.61
22_L	53_R	0.513	0.60
9_A	218_T	0.510	0.60
189_D	233_E	0.509	0.60
20_A	23_A	0.509	0.60
101_E	104_E	0.504	0.59
180_V	212_V	0.503	0.59
7_I	84_L	0.503	0.59
189_D	226_A	0.501	0.59
78_A	103_L	0.500	0.59
145_V	171_Q	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	0.9289	100	0.313	Contact Map
3ldvA	2	0.9665	100	0.329	Contact Map
1dbtA	2	0.9916	100	0.334	Contact Map
3tr2A	2	0.9289	100	0.338	Contact Map
1eixA	2	0.9707	100	0.338	Contact Map
2yyuA	2	0.9582	100	0.344	Contact Map
3qw4B	4	0.9079	100	0.345	Contact Map
3tfxA	2	0.9456	100	0.346	Contact Map
3v75A	2	0.9205	100	0.362	Contact Map
3r89A	2	0.9331	100	0.363	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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