YFCD - ECOLI - GREMLIN Contacts

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YFCD - Uncharacterized Nudix hydrolase YfcD

UniProt:	P65556	Sequences: MEQRRLASTEWVDIVNEENEVIAQASREQMRAQCLRHRATYIVVHDGMGKILVQRRTETKDFLPGMLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWMKRNAKNEAVETETAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14107
Length:	180 (157)
Sequences:	2753 (1899)
Seq/√Len:	151.6

ECOLI - YFCD IDI
HALSA - IDI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_N	20_E	5.907	1.00
46_D	50_K	5.105	1.00
58_E	65_G	4.430	1.00
55_R	137_E	3.829	1.00
47_G	125_H	3.509	1.00
55_R	136_S	2.854	1.00
141_L	146_I	2.821	1.00
42_I	85_A	2.793	1.00
80_Q	83_E	2.674	1.00
58_E	136_S	2.361	1.00
142_T	145_E	2.277	1.00
71_A	89_A	2.229	1.00
11_W	24_Q	2.061	1.00
149_R	153_F	1.936	1.00
81_L	118_A	1.924	1.00
79_E	87_R	1.912	1.00
29_Q	33_Q	1.877	1.00
50_K	142_T	1.811	1.00
15_V	38_R	1.784	1.00
19_N	38_R	1.774	1.00
26_S	29_Q	1.760	1.00
88_E	91_E	1.740	1.00
65_G	136_S	1.738	1.00
25_A	29_Q	1.730	1.00
63_L	155_P	1.719	1.00
52_L	138_V	1.647	1.00
47_G	123_V	1.612	1.00
128_F	138_V	1.592	1.00
67_L	139_C	1.587	1.00
25_A	30_M	1.570	1.00
45_H	51_I	1.568	1.00
31_R	74_V	1.456	1.00
84_S	87_R	1.455	1.00
25_A	35_L	1.446	1.00
139_C	149_R	1.446	1.00
12_V	30_M	1.391	1.00
148_A	152_E	1.375	1.00
55_R	65_G	1.373	1.00
93_L	138_V	1.366	1.00
90_E	96_A	1.358	1.00
130_L	135_V	1.357	1.00
52_L	140_W	1.336	1.00
31_R	37_H	1.332	1.00
31_R	115_V	1.322	1.00
146_I	157_S	1.277	1.00
66_M	154_T	1.260	1.00
44_V	122_C	1.258	1.00
68_D	154_T	1.257	1.00
13_D	77_A	1.236	1.00
54_Q	68_D	1.208	1.00
86_R	90_E	1.203	1.00
95_I	124_S	1.179	1.00
130_L	138_V	1.170	1.00
74_V	115_V	1.157	1.00
44_V	95_I	1.144	1.00
24_Q	77_A	1.136	1.00
81_L	120_F	1.122	0.99
9_T	26_S	1.122	0.99
11_W	26_S	1.117	0.99
42_I	89_A	1.114	0.99
67_L	137_E	1.111	0.99
45_H	123_V	1.107	0.99
100_F	122_C	1.065	0.99
12_V	37_H	1.062	0.99
68_D	72_G	1.041	0.99
86_R	96_A	1.036	0.99
51_I	146_I	1.034	0.99
109_E	114_R	1.033	0.99
14_I	25_A	1.029	0.99
91_E	131_Q	1.025	0.99
53_V	141_L	1.022	0.99
139_C	145_E	1.014	0.99
150_C	161_L	1.001	0.99
145_E	148_A	1.001	0.99
36_R	107_Y	0.996	0.99
104_G	119_L	0.993	0.99
27_R	88_E	0.979	0.99
55_R	67_L	0.976	0.99
10_E	76_Q	0.969	0.99
95_I	128_F	0.967	0.98
93_L	135_V	0.964	0.98
45_H	121_S	0.962	0.98
75_V	84_S	0.953	0.98
69_A	72_G	0.953	0.98
46_D	140_W	0.945	0.98
107_Y	116_W	0.938	0.98
10_E	87_R	0.938	0.98
105_Q	118_A	0.925	0.98
16_N	22_I	0.921	0.98
51_I	70_T	0.918	0.98
143_P	147_T	0.914	0.98
135_V	138_V	0.911	0.98
101_A	121_S	0.907	0.98
10_E	27_R	0.903	0.98
14_I	35_L	0.888	0.97
55_R	58_E	0.882	0.97
40_T	84_S	0.874	0.97
73_G	88_E	0.870	0.97
41_Y	69_A	0.867	0.97
37_H	74_V	0.865	0.97
54_Q	138_V	0.859	0.97
9_T	28_E	0.856	0.97
44_V	89_A	0.848	0.97
12_V	74_V	0.847	0.97
17_E	107_Y	0.841	0.96
13_D	78_D	0.836	0.96
148_A	151_D	0.836	0.96
141_L	149_R	0.830	0.96
109_E	112_N	0.829	0.96
147_T	151_D	0.818	0.96
14_I	23_A	0.814	0.96
19_N	116_W	0.812	0.96
41_Y	115_V	0.806	0.95
54_Q	93_L	0.805	0.95
42_I	122_C	0.804	0.95
99_P	124_S	0.802	0.95
147_T	162_A	0.796	0.95
79_E	84_S	0.781	0.95
82_L	86_R	0.774	0.94
19_N	81_L	0.767	0.94
117_G	160_A	0.765	0.94
96_A	99_P	0.762	0.94
60_K	134_E	0.760	0.94
153_F	157_S	0.757	0.94
19_N	105_Q	0.753	0.93
10_E	88_E	0.747	0.93
31_R	113_C	0.744	0.93
124_S	128_F	0.742	0.93
41_Y	68_D	0.740	0.93
102_E	105_Q	0.737	0.93
160_A	164_W	0.731	0.92
149_R	152_E	0.722	0.92
41_Y	117_G	0.721	0.92
89_A	97_G	0.716	0.92
41_Y	156_D	0.712	0.91
50_K	145_E	0.708	0.91
105_Q	116_W	0.706	0.91
75_V	88_E	0.705	0.91
159_K	163_L	0.704	0.91
43_V	160_A	0.692	0.90
82_L	85_A	0.690	0.90
12_V	76_Q	0.687	0.90
30_M	74_V	0.683	0.90
106_F	160_A	0.682	0.90
56_R	60_K	0.680	0.89
51_I	143_P	0.669	0.89
63_L	66_M	0.665	0.88
104_G	160_A	0.656	0.88
39_A	113_C	0.655	0.88
19_N	118_A	0.652	0.87
27_R	61_D	0.651	0.87
54_Q	71_A	0.650	0.87
71_A	93_L	0.646	0.87
10_E	73_G	0.642	0.87
13_D	52_L	0.641	0.86
27_R	75_V	0.640	0.86
76_Q	79_E	0.637	0.86
59_T	132_E	0.632	0.86
17_E	109_E	0.631	0.86
40_T	85_A	0.630	0.86
30_M	35_L	0.625	0.85
53_V	153_F	0.625	0.85
101_A	129_A	0.623	0.85
21_V	77_A	0.622	0.85
30_M	73_G	0.621	0.85
15_V	19_N	0.613	0.84
19_N	22_I	0.607	0.83
41_Y	72_G	0.606	0.83
21_V	24_Q	0.605	0.83
49_G	123_V	0.604	0.83
46_D	123_V	0.599	0.83
26_S	30_M	0.598	0.82
90_E	99_P	0.598	0.82
85_A	120_F	0.594	0.82
72_G	75_V	0.593	0.82
25_A	33_Q	0.587	0.81
59_T	133_D	0.578	0.80
32_A	35_L	0.577	0.80
147_T	161_L	0.576	0.80
37_H	115_V	0.575	0.80
27_R	76_Q	0.574	0.80
121_S	164_W	0.571	0.79
103_H	121_S	0.569	0.79
41_Y	54_Q	0.568	0.79
158_L	162_A	0.567	0.79
41_Y	74_V	0.567	0.79
49_G	143_P	0.565	0.79
11_W	77_A	0.564	0.79
13_D	21_V	0.563	0.79
43_V	89_A	0.563	0.79
151_D	158_L	0.562	0.78
74_V	113_C	0.561	0.78
50_K	144_E	0.559	0.78
72_G	88_E	0.556	0.78
39_A	74_V	0.556	0.78
108_F	117_G	0.556	0.78
106_F	110_D	0.555	0.78
83_E	86_R	0.554	0.77
12_V	61_D	0.553	0.77
70_T	93_L	0.549	0.77
72_G	113_C	0.549	0.77
98_V	122_C	0.546	0.76
15_V	36_R	0.544	0.76
141_L	153_F	0.543	0.76
82_L	148_A	0.539	0.75
36_R	114_R	0.539	0.75
43_V	157_S	0.538	0.75
95_I	98_V	0.536	0.75
46_D	125_H	0.535	0.75
104_G	118_A	0.533	0.75
31_R	35_L	0.532	0.75
69_A	113_C	0.531	0.74
154_T	157_S	0.528	0.74
40_T	75_V	0.527	0.74
11_W	129_A	0.526	0.74
69_A	156_D	0.525	0.74
43_V	51_I	0.521	0.73
27_R	62_F	0.519	0.73
130_L	133_D	0.518	0.73
146_I	153_F	0.517	0.72
143_P	146_I	0.516	0.72
41_Y	113_C	0.516	0.72
19_N	107_Y	0.515	0.72
92_E	134_E	0.514	0.72
27_R	91_E	0.513	0.72
53_V	139_C	0.512	0.72
52_L	128_F	0.509	0.71
26_S	62_F	0.508	0.71
12_V	27_R	0.506	0.71
104_G	164_W	0.505	0.71
38_R	75_V	0.503	0.70
33_Q	140_W	0.503	0.70
31_R	39_A	0.503	0.70
13_D	19_N	0.501	0.70
101_A	123_V	0.500	0.70
143_P	157_S	0.500	0.70

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
2dhoA	1	0.9833	100	0.339	Contact Map
2pnyA	1	1	100	0.339	Contact Map
2fkbA	1	0.9278	100	0.445	Contact Map
1hztA	1	0.7944	100	0.454	Contact Map
3dupA	2	1	100	0.468	Contact Map
1q27A	1	0.9389	100	0.492	Contact Map
3e57A	2	0.8722	99.9	0.607	Contact Map
2xsqA	2	0.8333	99.9	0.611	Contact Map
1sjyA	2	0.8111	99.8	0.645	Contact Map
3grnA	2	0.7611	99.8	0.646	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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