PYRE - HALSA - GREMLIN Contacts

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PYRE - Orotate phosphoribosyltransferase

UniProt:	Q9HNG2	Sequences: MSATDDLVSALRAADAVQFGEFELSHGGTSEYYVDKYLFETDPECLSAIAAAFADRIDEDTTLAGVALGGVPLAAATATEAGVPYVIARKQAKEYGTANRIEGRLDDGEEVVVVEDIATTGQSAVDAVDALRDAGATVNRALIVVDREEGGRELLAEHGVEMAALVTASDLLDAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	175 (167)
Sequences:	3459 (1843)
Seq/√Len:	142.6

ECOLI - PYRE
BACSU - PYRE
HALSA - PYRE
SULSO - PYRE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
131_L	136_A	3.676	1.00
148_E	169_S	3.653	1.00
23_E	29_T	3.586	1.00
21_E	29_T	3.525	1.00
110_E	137_T	3.463	1.00
106_D	109_E	2.752	1.00
143_I	164_A	2.545	1.00
51_A	80_E	2.338	1.00
65_G	74_A	2.336	1.00
129_D	133_D	2.177	1.00
57_I	112_V	2.095	1.00
128_V	160_V	2.032	1.00
152_R	156_A	2.018	1.00
74_A	85_Y	1.956	1.00
124_A	141_A	1.887	1.00
18_Q	22_F	1.868	1.00
91_Q	94_E	1.833	1.00
9_S	13_A	1.832	1.00
62_T	109_E	1.824	1.00
54_A	81_A	1.791	1.00
64_A	86_V	1.766	1.00
61_T	109_E	1.764	1.00
52_A	55_D	1.750	1.00
39_F	49_I	1.739	1.00
56_R	163_A	1.710	1.00
129_D	158_H	1.705	1.00
140_R	163_A	1.672	1.00
129_D	132_R	1.659	1.00
118_A	162_M	1.637	1.00
110_E	139_N	1.633	1.00
76_A	79_T	1.631	1.00
105_L	109_E	1.599	1.00
47_S	82_G	1.592	1.00
153_E	157_E	1.591	1.00
50_A	76_A	1.544	1.00
6_D	48_A	1.508	1.00
47_S	80_E	1.505	1.00
132_R	137_T	1.496	1.00
132_R	160_V	1.476	1.00
10_A	48_A	1.470	1.00
24_L	30_S	1.457	1.00
57_I	142_L	1.412	1.00
154_L	157_E	1.386	1.00
105_L	136_A	1.379	1.00
50_A	77_T	1.377	1.00
14_A	45_C	1.374	1.00
115_E	118_A	1.371	1.00
167_T	170_D	1.370	1.00
148_E	167_T	1.348	1.00
10_A	45_C	1.340	1.00
140_R	161_E	1.334	1.00
61_T	110_E	1.319	1.00
62_T	86_V	1.318	1.00
84_P	109_E	1.316	1.00
143_I	162_M	1.313	1.00
67_A	71_V	1.298	1.00
118_A	143_I	1.296	1.00
38_L	104_R	1.295	1.00
61_T	108_G	1.281	1.00
118_A	151_G	1.276	1.00
10_A	13_A	1.195	1.00
125_V	158_H	1.193	1.00
75_A	85_Y	1.192	1.00
141_A	160_V	1.186	1.00
60_D	163_A	1.178	1.00
34_V	145_V	1.176	1.00
100_R	133_D	1.162	1.00
77_T	114_V	1.136	0.99
100_R	130_A	1.130	0.99
113_V	124_A	1.128	0.99
88_A	130_A	1.110	0.99
52_A	165_L	1.100	0.99
146_D	150_G	1.088	0.99
44_E	82_G	1.074	0.99
138_V	160_V	1.069	0.99
53_F	142_L	1.063	0.99
113_V	128_V	1.061	0.99
109_E	136_A	1.058	0.99
19_F	32_Y	1.048	0.99
68_L	71_V	1.040	0.99
112_V	140_R	1.036	0.99
6_D	9_S	1.029	0.99
55_D	59_E	1.026	0.99
36_K	117_I	1.012	0.99
21_E	31_E	1.008	0.99
55_D	58_D	0.987	0.98
155_L	162_M	0.986	0.98
78_A	84_P	0.965	0.98
54_A	58_D	0.962	0.98
78_A	85_Y	0.958	0.98
18_Q	97_T	0.957	0.98
164_A	167_T	0.952	0.98
11_L	39_F	0.950	0.98
128_V	132_R	0.942	0.98
19_F	31_E	0.925	0.98
149_E	153_E	0.920	0.97
125_V	154_L	0.918	0.97
8_V	166_V	0.916	0.97
11_L	34_V	0.912	0.97
113_V	138_V	0.905	0.97
17_V	34_V	0.901	0.97
26_H	119_T	0.901	0.97
6_D	10_A	0.898	0.97
12_R	19_F	0.894	0.97
71_V	87_I	0.885	0.97
132_R	158_H	0.884	0.97
60_D	161_E	0.883	0.97
105_L	111_V	0.878	0.97
56_R	60_D	0.872	0.96
92_A	100_R	0.870	0.96
25_S	94_E	0.859	0.96
54_A	77_T	0.858	0.96
62_T	105_L	0.854	0.96
41_T	84_P	0.852	0.96
76_A	80_E	0.846	0.96
50_A	80_E	0.843	0.96
132_R	138_V	0.843	0.96
53_F	165_L	0.841	0.96
50_A	73_L	0.838	0.96
156_A	161_E	0.826	0.95
125_V	157_E	0.822	0.95
115_E	124_A	0.821	0.95
153_E	156_A	0.815	0.95
69_G	72_P	0.803	0.94
18_Q	38_L	0.800	0.94
63_L	74_A	0.795	0.94
125_V	128_V	0.795	0.94
47_S	51_A	0.790	0.94
28_G	149_E	0.789	0.94
57_I	77_T	0.783	0.94
145_V	171_L	0.782	0.94
25_S	122_Q	0.782	0.94
70_G	87_I	0.782	0.94
24_L	119_T	0.779	0.94
127_A	130_A	0.761	0.93
122_Q	126_D	0.757	0.93
11_L	36_K	0.754	0.92
16_A	39_F	0.754	0.92
133_D	137_T	0.754	0.92
49_I	165_L	0.746	0.92
17_V	32_Y	0.745	0.92
50_A	79_T	0.739	0.92
50_A	54_A	0.738	0.92
7_L	44_E	0.734	0.91
66_V	69_G	0.730	0.91
51_A	54_A	0.727	0.91
18_Q	66_V	0.722	0.91
113_V	131_L	0.716	0.90
39_F	144_V	0.714	0.90
61_T	83_V	0.713	0.90
62_T	136_A	0.713	0.90
65_G	85_Y	0.708	0.90
99_N	102_E	0.704	0.90
53_F	77_T	0.696	0.89
115_E	143_I	0.695	0.89
107_D	135_G	0.691	0.89
47_S	79_T	0.689	0.89
70_G	86_V	0.684	0.88
73_L	114_V	0.683	0.88
11_L	16_A	0.678	0.88
142_L	163_A	0.677	0.88
124_A	155_L	0.676	0.88
144_V	165_L	0.675	0.88
24_L	147_R	0.675	0.88
51_A	55_D	0.672	0.87
56_R	59_E	0.669	0.87
107_D	134_A	0.669	0.87
10_A	14_A	0.666	0.87
66_V	127_A	0.664	0.87
155_L	161_E	0.663	0.87
15_D	18_Q	0.662	0.86
126_D	129_D	0.657	0.86
105_L	131_L	0.656	0.86
54_A	80_E	0.655	0.86
45_C	48_A	0.655	0.86
88_A	131_L	0.655	0.86
108_G	135_G	0.651	0.86
40_E	76_A	0.649	0.85
112_V	139_N	0.640	0.85
151_G	162_M	0.640	0.85
132_R	159_G	0.636	0.84
56_R	165_L	0.634	0.84
86_V	136_A	0.627	0.83
117_I	145_V	0.623	0.83
62_T	111_V	0.623	0.83
70_G	74_A	0.623	0.83
128_V	141_A	0.616	0.82
146_D	167_T	0.614	0.82
13_A	45_C	0.610	0.82
146_D	152_R	0.610	0.82
7_L	166_V	0.607	0.81
123_S	128_V	0.605	0.81
37_Y	68_L	0.604	0.81
52_A	56_R	0.602	0.81
68_L	87_I	0.599	0.81
139_N	161_E	0.599	0.81
58_D	81_A	0.598	0.80
67_A	90_K	0.596	0.80
94_E	133_D	0.594	0.80
128_V	138_V	0.592	0.80
107_D	137_T	0.591	0.80
77_T	142_L	0.588	0.79
89_R	102_E	0.587	0.79
72_P	89_R	0.587	0.79
47_S	76_A	0.585	0.79
53_F	73_L	0.584	0.79
7_L	49_I	0.582	0.79
112_V	142_L	0.580	0.78
25_S	123_S	0.573	0.78
111_V	131_L	0.570	0.77
99_N	103_G	0.569	0.77
48_A	51_A	0.569	0.77
49_I	144_V	0.567	0.77
156_A	159_G	0.565	0.77
149_E	152_R	0.562	0.76
25_S	66_V	0.560	0.76
41_T	86_V	0.556	0.75
26_H	30_S	0.553	0.75
34_V	117_I	0.552	0.75
91_Q	126_D	0.551	0.75
72_P	75_A	0.549	0.75
141_A	155_L	0.548	0.74
25_S	95_Y	0.548	0.74
92_A	98_A	0.548	0.74
67_A	70_G	0.546	0.74
69_G	88_A	0.544	0.74
5_D	9_S	0.542	0.74
115_E	127_A	0.541	0.73
32_Y	168_A	0.540	0.73
86_V	105_L	0.539	0.73
43_P	84_P	0.536	0.73
25_S	124_A	0.531	0.72
63_L	112_V	0.529	0.72
37_Y	102_E	0.529	0.72
9_S	166_V	0.523	0.71
166_V	170_D	0.522	0.71
64_A	131_L	0.522	0.71
88_A	127_A	0.521	0.71
20_G	147_R	0.518	0.70
28_G	122_Q	0.517	0.70
64_A	88_A	0.515	0.70
120_T	123_S	0.515	0.70
35_D	66_V	0.514	0.70
104_R	109_E	0.514	0.70
8_V	12_R	0.512	0.69
65_G	68_L	0.512	0.69
115_E	165_L	0.506	0.68
36_K	144_V	0.502	0.68
74_A	114_V	0.501	0.68
150_G	153_E	0.500	0.68

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
3qw4B	4	0.9714	100	0.301	Contact Map
3mjdA	2	0.9543	100	0.316	Contact Map
3n2lA	4	0.9429	100	0.322	Contact Map
2wnsA	2	0.9886	100	0.333	Contact Map
4fymA	4	0.9486	100	0.335	Contact Map
3m3hA	2	0.9314	100	0.343	Contact Map
2ps1A	2	0.9943	100	0.346	Contact Map
1lh0A	2	0.9886	100	0.347	Contact Map
3dezA	2	0.9543	100	0.357	Contact Map
4ohcA	5	1	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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