UBN2 - PFAM28P - GREMLIN Contacts

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UBN2 - gag-polypeptide of LTR copia-type

PFAM:	PF14223	Sequences: KTAKEAWDALEKKYEGKSRVKEARKLQLKRELENLKMKEGESIDEYLNRFKKIANELAALGEKIDDEDLVLKLLRSLPESYETFVTALEESKDLLTLTLEELIGRLLAEELRLKKREEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (110)
Sequences:	12459 (8586)
Seq/√Len:	818.6
META:	0.679

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_K	8_D	4.164	1.00
46_Y	76_S	3.921	1.00
29_K	68_D	3.122	1.00
41_E	49_R	2.593	1.00
54_A	69_L	2.582	1.00
35_L	50_F	2.146	1.00
32_L	72_K	2.003	1.00
86_T	109_E	1.957	1.00
35_L	46_Y	1.932	1.00
8_D	12_K	1.811	1.00
47_L	103_I	1.804	1.00
33_E	72_K	1.739	1.00
35_L	49_R	1.635	1.00
44_D	107_L	1.597	1.00
30_R	75_R	1.574	1.00
37_M	78_P	1.573	1.00
69_L	99_L	1.566	1.00
50_F	73_L	1.540	1.00
42_S	45_E	1.533	1.00
58_A	63_K	1.501	1.00
90_E	105_R	1.496	1.00
11_E	15_E	1.481	1.00
25_K	67_E	1.468	1.00
12_K	100_E	1.435	1.00
47_L	73_L	1.424	1.00
62_E	68_D	1.403	1.00
83_T	86_T	1.398	1.00
43_I	106_L	1.395	1.00
26_L	71_L	1.387	1.00
109_E	113_L	1.359	1.00
50_F	69_L	1.346	1.00
89_E	112_R	1.345	1.00
8_D	11_E	1.344	1.00
31_E	56_E	1.335	1.00
52_K	56_E	1.325	1.00
62_E	65_D	1.322	1.00
70_V	102_L	1.289	1.00
28_L	53_I	1.204	1.00
57_L	62_E	1.187	1.00
33_E	68_D	1.184	1.00
29_K	62_E	1.183	1.00
9_A	12_K	1.176	1.00
51_K	103_I	1.167	1.00
31_E	49_R	1.160	1.00
35_L	53_I	1.142	1.00
38_K	41_E	1.125	1.00
99_L	103_I	1.118	1.00
39_E	80_S	1.118	1.00
43_I	47_L	1.100	1.00
19_R	67_E	1.089	1.00
27_Q	31_E	1.080	1.00
37_M	41_E	1.071	1.00
30_R	34_N	1.049	1.00
50_F	54_A	1.045	1.00
24_R	56_E	1.035	1.00
31_E	53_I	1.030	1.00
98_T	101_E	1.027	1.00
2_T	5_E	1.025	1.00
9_A	13_K	1.013	1.00
81_Y	84_F	0.999	1.00
84_F	102_L	0.985	1.00
25_K	60_L	0.985	1.00
73_L	102_L	0.982	1.00
87_A	90_E	0.957	1.00
62_E	67_E	0.952	1.00
77_L	81_Y	0.944	1.00
83_T	87_A	0.927	1.00
33_E	75_R	0.924	1.00
37_M	40_G	0.920	1.00
92_K	105_R	0.910	1.00
28_L	56_E	0.906	1.00
28_L	57_L	0.901	1.00
49_R	53_I	0.897	1.00
54_A	58_A	0.878	1.00
65_D	68_D	0.875	1.00
82_E	112_R	0.869	1.00
72_K	76_S	0.865	1.00
73_L	99_L	0.863	1.00
28_L	31_E	0.862	1.00
55_N	58_A	0.861	1.00
42_S	110_E	0.859	1.00
37_M	43_I	0.853	1.00
84_F	88_L	0.845	1.00
41_E	45_E	0.843	1.00
109_E	112_R	0.827	1.00
43_I	110_E	0.824	1.00
66_D	98_T	0.814	1.00
50_F	72_K	0.812	1.00
47_L	99_L	0.809	1.00
29_K	33_E	0.805	1.00
7_W	11_E	0.796	1.00
6_A	9_A	0.795	1.00
30_R	89_E	0.777	1.00
26_L	75_R	0.776	1.00
85_V	112_R	0.764	1.00
87_A	91_S	0.761	1.00
32_L	64_I	0.759	1.00
24_R	27_Q	0.758	1.00
111_L	114_K	0.756	1.00
51_K	99_L	0.752	1.00
77_L	106_L	0.749	1.00
79_E	82_E	0.743	1.00
80_S	113_L	0.740	1.00
57_L	64_I	0.740	1.00
10_L	14_Y	0.737	1.00
25_K	62_E	0.724	1.00
82_E	113_L	0.719	1.00
26_L	89_E	0.717	1.00
88_L	102_L	0.715	1.00
24_R	28_L	0.710	1.00
103_I	107_L	0.697	1.00
84_F	90_E	0.695	1.00
29_K	64_I	0.682	1.00
29_K	71_L	0.680	1.00
51_K	55_N	0.679	1.00
25_K	57_L	0.649	1.00
91_S	105_R	0.648	1.00
9_A	100_E	0.647	1.00
5_E	9_A	0.643	1.00
86_T	90_E	0.633	1.00
64_I	69_L	0.632	1.00
58_A	69_L	0.628	1.00
32_L	53_I	0.621	1.00
41_E	46_Y	0.615	1.00
85_V	89_E	0.614	1.00
45_E	48_N	0.613	1.00
101_E	104_G	0.612	1.00
13_K	17_K	0.607	1.00
108_A	111_L	0.606	1.00
54_A	66_D	0.605	1.00
70_V	99_L	0.603	1.00
15_E	60_L	0.598	1.00
92_K	95_L	0.597	1.00
6_A	10_L	0.592	1.00
37_M	76_S	0.591	1.00
92_K	101_E	0.587	1.00
32_L	46_Y	0.587	1.00
28_L	60_L	0.583	1.00
101_E	105_R	0.582	1.00
53_I	56_E	0.581	1.00
34_N	75_R	0.581	1.00
111_L	115_K	0.574	1.00
74_L	85_V	0.572	1.00
89_E	105_R	0.570	1.00
66_D	69_L	0.569	1.00
91_S	95_L	0.566	1.00
72_K	75_R	0.563	1.00
66_D	99_L	0.563	1.00
32_L	54_A	0.558	1.00
64_I	68_D	0.554	1.00
43_I	46_Y	0.553	1.00
88_L	91_S	0.551	1.00
29_K	57_L	0.542	1.00
73_L	106_L	0.537	1.00
30_R	85_V	0.536	1.00
66_D	70_V	0.536	1.00
43_I	107_L	0.535	1.00
55_N	59_A	0.532	1.00
84_F	87_A	0.526	1.00
73_L	103_I	0.523	1.00
44_D	48_N	0.520	1.00
32_L	69_L	0.509	1.00
38_K	78_P	0.507	1.00
53_I	60_L	0.504	1.00
19_R	25_K	0.500	1.00

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
3tirA	3	0.7479	36.1	0.836	Contact Map
1d1dA	1	0.7059	33.9	0.839	Contact Map
4bhxA	2	0.7395	29.2	0.844	Contact Map
4e6sA	2	0.6807	20.7	0.854	Contact Map
1ez3A	1	0.6807	19.2	0.857	Contact Map
1vr8A	1	0.4454	15.7	0.862	Contact Map
3g21A	2	0.6471	11.8	0.869	Contact Map
4i4tE	1	0.395	11.4	0.871	Contact Map
1bm4A	1	0.2689	11.1	0.871	Contact Map
3g1gA	2	0.5546	10.5	0.873	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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