Retrotrans_gag - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

Retrotrans_gag - Retrotransposon gag protein

PFAM:	PF03732	Sequences: KLAPFSLKGAALTWWRSLPAGSITAIITWEEFKKAFLKRFFPPDRTEKLRRELLNLKQGNESVREYIERFRELARRCPDGLDEEELVSRFLRGLND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (93)
Sequences:	18786 (12621)
Seq/√Len:	1308.8
META:	0.721

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_I	90_F	4.221	1.00
56_L	69_R	2.894	1.00
61_E	69_R	2.618	1.00
66_Y	93_G	2.587	1.00
74_A	86_L	2.186	1.00
54_L	92_R	2.175	1.00
58_Q	95_N	2.023	1.00
33_K	37_L	2.011	1.00
29_W	33_K	1.945	1.00
62_S	65_E	1.882	1.00
45_R	49_L	1.858	1.00
54_L	89_R	1.855	1.00
70_F	90_F	1.827	1.00
3_A	32_F	1.748	1.00
67_I	71_R	1.717	1.00
4_P	15_W	1.682	1.00
56_L	61_E	1.656	1.00
54_L	88_S	1.648	1.00
50_R	85_E	1.575	1.00
51_R	92_R	1.575	1.00
81_L	85_E	1.565	1.00
28_T	31_E	1.557	1.00
37_L	41_F	1.522	1.00
82_D	85_E	1.482	1.00
18_L	22_S	1.437	1.00
52_E	73_L	1.430	1.00
47_E	88_S	1.411	1.00
69_R	72_E	1.408	1.00
56_L	73_L	1.387	1.00
49_L	76_R	1.385	1.00
56_L	70_F	1.377	1.00
48_K	52_E	1.370	1.00
34_K	38_K	1.331	1.00
83_E	86_L	1.318	1.00
61_E	65_E	1.303	1.00
63_V	67_I	1.255	1.00
70_F	74_A	1.223	1.00
53_L	89_R	1.222	1.00
87_V	91_L	1.183	1.00
12_L	16_R	1.160	1.00
50_R	88_S	1.156	1.00
35_A	38_K	1.115	1.00
39_R	68_E	1.108	1.00
56_L	66_Y	1.052	1.00
89_R	92_R	1.014	1.00
18_L	35_A	1.008	1.00
22_S	25_A	1.006	1.00
35_A	39_R	0.996	1.00
14_W	35_A	0.983	1.00
30_E	34_K	0.953	1.00
10_A	68_E	0.950	1.00
51_R	55_N	0.938	1.00
13_T	72_E	0.923	1.00
31_E	34_K	0.914	1.00
81_L	89_R	0.912	1.00
84_E	88_S	0.905	1.00
52_E	69_R	0.875	1.00
63_V	94_L	0.874	1.00
3_A	36_F	0.871	1.00
7_L	36_F	0.851	1.00
19_P	22_S	0.843	1.00
53_L	74_A	0.841	1.00
46_T	50_R	0.841	1.00
46_T	84_E	0.834	1.00
51_R	54_L	0.828	1.00
55_N	92_R	0.828	1.00
15_W	18_L	0.822	1.00
36_F	40_F	0.810	1.00
3_A	6_S	0.808	1.00
85_E	88_S	0.796	1.00
58_Q	62_S	0.794	1.00
26_I	30_E	0.794	1.00
30_E	33_K	0.782	1.00
27_I	31_E	0.775	1.00
49_L	52_E	0.774	1.00
79_D	82_D	0.763	1.00
69_R	73_L	0.760	1.00
18_L	21_G	0.744	1.00
50_R	54_L	0.740	1.00
15_W	32_F	0.729	1.00
79_D	85_E	0.702	1.00
48_K	51_R	0.701	1.00
41_F	45_R	0.697	1.00
18_L	23_I	0.696	1.00
10_A	13_T	0.695	1.00
15_W	19_P	0.690	1.00
21_G	24_T	0.685	1.00
85_E	89_R	0.681	1.00
46_T	49_L	0.673	1.00
72_E	76_R	0.664	1.00
17_S	75_R	0.661	1.00
81_L	91_L	0.655	1.00
10_A	40_F	0.649	1.00
13_T	16_R	0.649	1.00
49_L	77_C	0.636	1.00
54_L	85_E	0.634	1.00
14_W	36_F	0.630	1.00
81_L	86_L	0.626	1.00
13_T	75_R	0.626	1.00
60_N	95_N	0.624	1.00
71_R	74_A	0.620	1.00
31_E	35_A	0.618	1.00
71_R	75_R	0.615	1.00
4_P	32_F	0.613	1.00
88_S	92_R	0.607	1.00
45_R	48_K	0.605	1.00
7_L	15_W	0.605	1.00
53_L	73_L	0.604	1.00
5_F	12_L	0.600	1.00
63_V	90_F	0.599	1.00
34_K	37_L	0.599	1.00
21_G	25_A	0.599	1.00
79_D	84_E	0.590	1.00
32_F	36_F	0.590	1.00
70_F	89_R	0.585	1.00
53_L	77_C	0.576	1.00
39_R	71_R	0.568	1.00
67_I	70_F	0.565	1.00
3_A	7_L	0.565	1.00
42_P	45_R	0.561	1.00
46_T	78_P	0.555	1.00
36_F	41_F	0.553	1.00
41_F	46_T	0.544	1.00
44_D	48_K	0.537	1.00
22_S	27_I	0.534	1.00
65_E	69_R	0.534	1.00
8_K	11_A	0.534	1.00
67_I	74_A	0.531	1.00
47_E	50_R	0.528	1.00
7_L	14_W	0.524	1.00
66_Y	70_F	0.523	1.00
44_D	47_E	0.522	1.00
59_G	95_N	0.522	1.00
83_E	87_V	0.521	1.00
49_L	53_L	0.519	1.00
43_P	47_E	0.518	1.00
19_P	23_I	0.515	1.00
43_P	49_L	0.503	1.00
27_I	35_A	0.502	1.00
57_K	60_N	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
4x3iA	1	0.3958	44.6	0.814	Contact Map
4x3xA	1	0.5417	30.9	0.83	Contact Map
3g1gA	2	0.4792	21.7	0.842	Contact Map
3g21A	2	0.4896	18.4	0.847	Contact Map
1y6zA	2	0.9688	13.1	0.857	Contact Map
2gq0A	1	0.9688	13	0.857	Contact Map
2uvaG	3	0.9375	12.2	0.859	Contact Map
4bhxA	2	0.5729	10.8	0.862	Contact Map
1y4sA	2	0.9688	10.1	0.864	Contact Map
4e6sA	2	0.5729	9.1	0.867	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.

Page generated in 0.0052 seconds.