UBN2_2 - PFAM28P - GREMLIN Contacts

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UBN2_2 - gag-polypeptide of LTR copia-type

PFAM:	PF14227	Sequences: CKTAKEAWDALEKKYEGKSLANKLQLKRQLYNLKMKEGESIDEHLNRFTKIANELAALGVKIDDEDLVLKLLRSLPESYETFVTALEESKDLETLTLEELISRLLAEELRLKKREESSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (113)
Sequences:	11747 (7956)
Seq/√Len:	748.4
META:	0.691

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_K	9_D	4.436	1.00
44_H	74_S	3.974	1.00
27_K	66_D	3.586	1.00
52_A	67_L	2.785	1.00
39_E	47_R	2.480	1.00
30_L	70_K	2.077	1.00
33_L	48_F	2.033	1.00
9_D	13_K	1.843	1.00
33_L	44_H	1.777	1.00
28_R	73_R	1.767	1.00
10_A	13_K	1.758	1.00
12_E	16_E	1.754	1.00
45_L	101_I	1.736	1.00
23_K	65_E	1.640	1.00
40_S	43_E	1.635	1.00
84_T	107_E	1.595	1.00
35_M	76_P	1.592	1.00
56_A	61_K	1.555	1.00
42_D	105_L	1.531	1.00
31_Y	70_K	1.527	1.00
67_L	97_L	1.511	1.00
13_K	98_E	1.507	1.00
49_T	101_I	1.490	1.00
48_F	67_L	1.472	1.00
107_E	111_L	1.465	1.00
9_D	12_E	1.461	1.00
68_V	100_L	1.454	1.00
3_T	6_E	1.442	1.00
60_V	66_D	1.422	1.00
48_F	71_L	1.409	1.00
80_E	114_R	1.361	1.00
33_L	47_R	1.348	1.00
81_T	84_T	1.343	1.00
60_V	63_D	1.337	1.00
31_Y	66_D	1.323	1.00
41_I	104_L	1.289	1.00
96_T	99_E	1.274	1.00
29_Q	47_R	1.274	1.00
50_K	54_E	1.262	1.00
36_K	39_E	1.236	1.00
45_L	71_L	1.230	1.00
10_A	14_K	1.229	1.00
29_Q	54_E	1.227	1.00
48_F	52_A	1.218	1.00
91_D	94_T	1.204	1.00
20_L	65_E	1.147	1.00
55_L	60_V	1.147	1.00
33_L	51_I	1.140	1.00
37_E	78_S	1.136	1.00
8_W	12_E	1.121	1.00
71_L	97_L	1.107	1.00
97_L	101_I	1.102	1.00
41_I	45_L	1.098	1.00
29_Q	51_I	1.088	1.00
82_F	100_L	1.069	1.00
88_E	103_R	1.058	1.00
24_L	69_L	1.053	1.00
40_S	108_E	1.046	1.00
27_K	31_Y	1.035	1.00
35_M	39_E	1.004	1.00
60_V	65_E	1.000	1.00
47_R	51_I	0.986	1.00
26_L	51_I	0.974	1.00
75_L	104_L	0.953	1.00
109_L	112_K	0.949	1.00
19_S	22_N	0.935	1.00
80_E	110_R	0.917	1.00
7_A	10_A	0.917	1.00
101_I	105_L	0.908	1.00
49_T	97_L	0.906	1.00
70_K	74_S	0.902	1.00
6_E	10_A	0.895	1.00
27_K	60_V	0.886	1.00
82_F	88_E	0.885	1.00
25_Q	29_Q	0.885	1.00
41_I	44_H	0.882	1.00
28_R	32_N	0.878	1.00
107_E	110_R	0.875	1.00
71_L	100_L	0.870	1.00
22_N	26_L	0.843	1.00
39_E	43_E	0.831	1.00
81_T	85_A	0.828	1.00
35_M	38_G	0.826	1.00
2_K	6_E	0.822	1.00
31_Y	73_R	0.818	1.00
87_E	110_R	0.817	1.00
79_Y	82_F	0.807	1.00
83_V	110_R	0.806	1.00
55_L	62_I	0.791	1.00
48_F	70_K	0.789	1.00
90_K	103_R	0.778	1.00
64_D	96_T	0.777	1.00
52_A	56_A	0.771	1.00
28_R	83_V	0.770	1.00
99_E	102_S	0.751	1.00
21_A	25_Q	0.747	1.00
10_A	98_E	0.746	1.00
22_N	25_Q	0.742	1.00
35_M	41_I	0.740	1.00
85_A	88_E	0.737	1.00
26_L	54_E	0.731	1.00
11_L	15_Y	0.731	1.00
77_E	80_E	0.731	1.00
77_E	114_R	0.728	1.00
22_N	54_E	0.726	1.00
106_A	109_L	0.715	1.00
108_E	112_K	0.714	1.00
49_T	53_N	0.707	1.00
53_N	56_A	0.706	1.00
78_S	111_L	0.705	1.00
19_S	23_K	0.697	1.00
68_V	97_L	0.695	1.00
44_H	47_R	0.681	1.00
41_I	108_E	0.679	1.00
24_L	73_R	0.677	1.00
56_A	67_L	0.671	1.00
16_E	58_L	0.664	1.00
45_L	97_L	0.654	1.00
26_L	58_L	0.653	1.00
53_N	57_A	0.649	1.00
103_R	107_E	0.649	1.00
27_K	69_L	0.649	1.00
95_L	100_L	0.648	1.00
39_E	44_H	0.647	1.00
12_E	18_K	0.645	1.00
90_K	93_E	0.645	1.00
99_E	103_R	0.639	1.00
6_E	9_D	0.636	1.00
23_K	58_L	0.635	1.00
14_K	18_K	0.634	1.00
68_V	95_L	0.632	1.00
43_E	46_N	0.626	1.00
86_L	89_S	0.624	1.00
35_M	74_S	0.620	1.00
35_M	79_Y	0.617	1.00
70_K	73_R	0.615	1.00
35_M	44_H	0.615	1.00
42_D	46_N	0.613	1.00
14_K	17_G	0.612	1.00
63_D	66_D	0.600	1.00
30_L	52_A	0.600	1.00
54_E	57_A	0.599	1.00
62_I	67_L	0.595	1.00
29_Q	113_K	0.589	1.00
80_E	111_L	0.583	1.00
23_K	69_L	0.582	1.00
41_I	79_Y	0.577	1.00
41_I	105_L	0.577	1.00
52_A	64_D	0.575	1.00
68_V	71_L	0.564	1.00
17_G	22_N	0.558	1.00
66_D	69_L	0.544	1.00
47_R	50_K	0.542	1.00
49_T	67_L	0.540	1.00
32_N	73_R	0.540	1.00
14_K	98_E	0.536	1.00
30_L	44_H	0.533	1.00
30_L	62_I	0.530	1.00
26_L	29_Q	0.528	1.00
72_L	83_V	0.526	1.00
24_L	28_R	0.525	1.00
83_V	87_E	0.525	1.00
7_A	11_L	0.520	1.00
87_E	90_K	0.511	1.00
27_K	62_I	0.508	1.00
48_F	74_S	0.507	1.00
71_L	104_L	0.504	1.00
71_L	101_I	0.502	1.00
109_L	113_K	0.502	1.00
43_E	47_R	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
4bhxA	2	0.7395	19.6	0.866	Contact Map
4e6sA	2	0.6807	19	0.867	Contact Map
3tirA	3	0.6723	15.4	0.872	Contact Map
2lh0A	2	0.4706	12.9	0.877	Contact Map
3ahnA	1	0.4958	11.6	0.879	Contact Map
3sksA	1	0.4958	9.7	0.883	Contact Map
1xkpA	1	0.4706	9.4	0.884	Contact Map
3ce2A	1	0.4874	8.8	0.885	Contact Map
4rgkA	2	0.4622	8.8	0.885	Contact Map
1d1dA	1	0.7143	8.8	0.885	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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