GIDE - PFAM28P - GREMLIN Contacts

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GIDE - E3 Ubiquitin ligase

PFAM:	PF12483	Sequences: EETYTDRDGRRTRTESGWETVASGTSSVPFYLEDDTGRVLVVDDPEGAELDLETVFDRFEPLYYSGPDGALGGSSGRREGTKGYRFTEEILPPGDPLYVLGEAREDGDGALEIAKPKDGGPPFIISTKSEEELLSSLGSSARLLLIGGIVLGVAGLVLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	159 (148)
Sequences:	1847 (1543)
Seq/√Len:	126.8
META:	0.775

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_V	90_I	4.444	1.00
99_V	125_I	3.350	1.00
18_W	85_R	3.255	1.00
31_Y	38_R	3.234	1.00
98_Y	130_E	3.082	1.00
101_G	113_I	2.911	1.00
146_I	150_V	2.840	1.00
143_L	147_G	2.721	1.00
45_P	48_A	2.715	1.00
129_S	132_E	2.663	1.00
32_L	97_L	2.402	1.00
53_E	92_P	2.359	1.00
20_T	23_S	2.309	1.00
33_E	38_R	2.281	1.00
30_F	45_P	2.276	1.00
139_S	143_L	2.169	1.00
70_A	73_G	2.127	1.00
148_G	152_G	2.029	1.00
67_P	71_L	1.942	1.00
102_E	116_P	1.858	1.00
31_Y	40_L	1.800	1.00
45_P	125_I	1.752	1.00
54_T	57_D	1.744	1.00
34_D	37_G	1.721	1.00
140_S	143_L	1.668	1.00
81_T	84_Y	1.649	1.00
72_G	76_G	1.556	1.00
91_L	97_L	1.549	1.00
47_G	115_K	1.508	1.00
39_V	113_I	1.488	1.00
71_L	75_S	1.433	1.00
70_A	76_G	1.429	1.00
70_A	74_S	1.407	1.00
99_V	113_I	1.394	1.00
147_G	150_V	1.386	1.00
95_D	127_T	1.363	1.00
57_D	87_T	1.359	1.00
40_L	44_D	1.349	1.00
98_Y	128_K	1.335	1.00
59_F	83_G	1.322	1.00
39_V	111_L	1.311	1.00
52_L	127_T	1.298	1.00
142_R	146_I	1.295	1.00
21_V	84_Y	1.281	1.00
92_P	95_D	1.280	1.00
145_L	148_G	1.260	1.00
118_D	121_P	1.249	1.00
138_G	142_R	1.249	1.00
63_Y	66_G	1.240	1.00
66_G	78_R	1.234	1.00
66_G	73_G	1.234	1.00
106_D	111_L	1.224	0.99
147_G	151_L	1.221	0.99
52_L	89_E	1.203	0.99
140_S	147_G	1.186	0.99
73_G	78_R	1.178	0.99
16_S	19_E	1.167	0.99
18_W	116_P	1.129	0.99
91_L	127_T	1.124	0.99
67_P	75_S	1.083	0.99
66_G	70_A	1.072	0.99
29_P	44_D	1.063	0.99
72_G	75_S	1.063	0.99
73_G	77_R	1.062	0.99
7_R	10_R	1.059	0.98
65_S	74_S	1.057	0.98
143_L	146_I	1.057	0.98
147_G	154_A	1.041	0.98
69_G	76_G	1.035	0.98
66_G	74_S	1.031	0.98
74_S	78_R	1.024	0.98
50_L	152_G	1.014	0.98
30_F	125_I	1.010	0.98
63_Y	78_R	1.009	0.98
67_P	74_S	1.005	0.98
7_R	11_R	1.002	0.98
128_K	132_E	1.001	0.98
12_T	15_E	0.997	0.98
97_L	127_T	0.971	0.97
9_G	12_T	0.955	0.97
104_R	111_L	0.955	0.97
104_R	112_E	0.944	0.97
104_R	114_A	0.938	0.97
64_Y	70_A	0.934	0.97
32_L	127_T	0.915	0.96
23_S	94_G	0.908	0.96
145_L	149_I	0.902	0.96
71_L	76_G	0.897	0.96
40_L	112_E	0.874	0.95
142_R	148_G	0.870	0.95
53_E	95_D	0.866	0.95
138_G	141_A	0.859	0.95
75_S	78_R	0.859	0.95
54_T	89_E	0.857	0.95
13_R	32_L	0.855	0.95
72_G	77_R	0.855	0.95
73_G	76_G	0.837	0.94
103_A	113_I	0.822	0.93
106_D	109_G	0.821	0.93
11_R	15_E	0.812	0.93
135_S	139_S	0.811	0.93
40_L	45_P	0.808	0.93
146_I	154_A	0.802	0.92
45_P	49_E	0.801	0.92
102_E	118_D	0.800	0.92
150_V	154_A	0.792	0.92
97_L	122_P	0.789	0.92
41_V	99_V	0.788	0.92
68_D	72_G	0.783	0.91
70_A	75_S	0.778	0.91
67_P	78_R	0.776	0.91
64_Y	78_R	0.763	0.90
128_K	136_S	0.757	0.90
52_L	55_V	0.755	0.90
145_L	152_G	0.750	0.90
111_L	115_K	0.739	0.89
32_L	113_I	0.737	0.89
34_D	130_E	0.736	0.89
60_E	150_V	0.733	0.89
67_P	70_A	0.730	0.88
100_L	133_L	0.729	0.88
111_L	114_A	0.719	0.88
110_A	114_A	0.717	0.87
146_I	149_I	0.704	0.87
138_G	149_I	0.701	0.86
128_K	133_L	0.701	0.86
39_V	98_Y	0.699	0.86
63_Y	68_D	0.697	0.86
36_T	141_A	0.697	0.86
48_A	51_D	0.696	0.86
67_P	73_G	0.692	0.86
90_I	103_A	0.688	0.85
10_R	14_T	0.683	0.85
13_R	17_G	0.682	0.85
9_G	13_R	0.674	0.84
44_D	48_A	0.670	0.84
144_L	149_I	0.666	0.83
52_L	91_L	0.662	0.83
132_E	155_G	0.657	0.83
109_G	129_S	0.653	0.82
62_L	67_P	0.651	0.82
126_S	153_V	0.651	0.82
15_E	19_E	0.650	0.82
111_L	123_F	0.646	0.81
134_L	138_G	0.645	0.81
40_L	110_A	0.643	0.81
61_P	64_Y	0.642	0.81
98_Y	103_A	0.637	0.81
118_D	142_R	0.637	0.81
67_P	72_G	0.637	0.81
18_W	24_G	0.637	0.81
148_G	154_A	0.636	0.80
68_D	71_L	0.634	0.80
13_R	91_L	0.630	0.80
105_E	110_A	0.630	0.80
52_L	58_R	0.629	0.80
18_W	21_V	0.624	0.79
142_R	149_I	0.624	0.79
142_R	152_G	0.621	0.79
60_E	63_Y	0.620	0.79
111_L	119_G	0.618	0.79
8_D	13_R	0.616	0.78
139_S	147_G	0.611	0.78
68_D	77_R	0.610	0.78
94_G	97_L	0.609	0.78
21_V	94_G	0.608	0.77
99_V	107_G	0.601	0.77
65_S	68_D	0.600	0.76
148_G	151_L	0.598	0.76
39_V	44_D	0.592	0.76
69_G	77_R	0.591	0.75
55_V	92_P	0.591	0.75
144_L	148_G	0.589	0.75
102_E	117_K	0.584	0.75
140_S	144_L	0.584	0.75
65_S	75_S	0.583	0.74
60_E	64_Y	0.580	0.74
142_R	150_V	0.579	0.74
59_F	82_K	0.576	0.74
153_V	156_L	0.571	0.73
103_A	115_K	0.570	0.73
32_L	39_V	0.568	0.73
66_G	71_L	0.563	0.72
65_S	78_R	0.560	0.71
75_S	79_E	0.558	0.71
51_D	124_I	0.558	0.71
120_G	136_S	0.555	0.71
95_D	120_G	0.555	0.71
86_F	103_A	0.554	0.71
30_F	41_V	0.554	0.71
29_P	40_L	0.553	0.71
31_Y	110_A	0.550	0.70
98_Y	123_F	0.547	0.70
72_G	78_R	0.547	0.70
50_L	93_P	0.547	0.70
57_D	85_R	0.542	0.69
14_T	18_W	0.540	0.69
77_R	146_I	0.537	0.68
62_L	66_G	0.536	0.68
143_L	148_G	0.534	0.68
52_L	56_F	0.534	0.68
14_T	19_E	0.533	0.68
106_D	110_A	0.532	0.68
19_E	117_K	0.529	0.67
49_E	156_L	0.528	0.67
34_D	126_S	0.528	0.67
118_D	141_A	0.527	0.67
10_R	13_R	0.526	0.67
65_S	70_A	0.521	0.66
69_G	72_G	0.521	0.66
45_P	51_D	0.520	0.66
68_D	73_G	0.518	0.66
12_T	41_V	0.516	0.65
41_V	112_E	0.515	0.65
61_P	74_S	0.514	0.65
103_A	111_L	0.514	0.65
137_L	141_A	0.512	0.65
69_G	74_S	0.512	0.65
100_L	112_E	0.508	0.64
106_D	112_E	0.502	0.63
16_S	83_G	0.501	0.63
137_L	140_S	0.500	0.63

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
3kdfD	2	0.6289	5.8	0.927	Contact Map
4wl1A	3	0	4.4	0.931	Contact Map
2jxxA	1	0.478	2.8	0.937	Contact Map
4joiA	1	0.7421	2.6	0.938	Contact Map
1i17A	1	0.2327	2.5	0.939	Contact Map
3aqlA	2	0.5472	2.4	0.94	Contact Map
2pi2A	1	0.6478	2.4	0.94	Contact Map
2lk9A	1	0.1069	2.3	0.94	Contact Map
1afoA	2	0.1824	2.1	0.942	Contact Map
3wfpA	2	0.478	2	0.942	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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