GREMLIN Database
Retrotrans_gag - Retrotransposon gag protein
PFAM: PF03732 Sequences:
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_I90_F4.2211.00
56_L69_R2.8941.00
61_E69_R2.6181.00
66_Y93_G2.5871.00
74_A86_L2.1861.00
54_L92_R2.1751.00
58_Q95_N2.0231.00
33_K37_L2.0111.00
29_W33_K1.9451.00
62_S65_E1.8821.00
45_R49_L1.8581.00
54_L89_R1.8551.00
70_F90_F1.8271.00
3_A32_F1.7481.00
67_I71_R1.7171.00
4_P15_W1.6821.00
56_L61_E1.6561.00
54_L88_S1.6481.00
50_R85_E1.5751.00
51_R92_R1.5751.00
81_L85_E1.5651.00
28_T31_E1.5571.00
37_L41_F1.5221.00
82_D85_E1.4821.00
18_L22_S1.4371.00
52_E73_L1.4301.00
47_E88_S1.4111.00
69_R72_E1.4081.00
56_L73_L1.3871.00
49_L76_R1.3851.00
56_L70_F1.3771.00
48_K52_E1.3701.00
34_K38_K1.3311.00
83_E86_L1.3181.00
61_E65_E1.3031.00
63_V67_I1.2551.00
70_F74_A1.2231.00
53_L89_R1.2221.00
87_V91_L1.1831.00
12_L16_R1.1601.00
50_R88_S1.1561.00
35_A38_K1.1151.00
39_R68_E1.1081.00
56_L66_Y1.0521.00
89_R92_R1.0141.00
18_L35_A1.0081.00
22_S25_A1.0061.00
35_A39_R0.9961.00
14_W35_A0.9831.00
30_E34_K0.9531.00
10_A68_E0.9501.00
51_R55_N0.9381.00
13_T72_E0.9231.00
31_E34_K0.9141.00
81_L89_R0.9121.00
84_E88_S0.9051.00
52_E69_R0.8751.00
63_V94_L0.8741.00
3_A36_F0.8711.00
7_L36_F0.8511.00
19_P22_S0.8431.00
53_L74_A0.8411.00
46_T50_R0.8411.00
46_T84_E0.8341.00
51_R54_L0.8281.00
55_N92_R0.8281.00
15_W18_L0.8221.00
36_F40_F0.8101.00
3_A6_S0.8081.00
85_E88_S0.7961.00
58_Q62_S0.7941.00
26_I30_E0.7941.00
30_E33_K0.7821.00
27_I31_E0.7751.00
49_L52_E0.7741.00
79_D82_D0.7631.00
69_R73_L0.7601.00
18_L21_G0.7441.00
50_R54_L0.7401.00
15_W32_F0.7291.00
79_D85_E0.7021.00
48_K51_R0.7011.00
41_F45_R0.6971.00
18_L23_I0.6961.00
10_A13_T0.6951.00
15_W19_P0.6901.00
21_G24_T0.6851.00
85_E89_R0.6811.00
46_T49_L0.6731.00
72_E76_R0.6641.00
17_S75_R0.6611.00
81_L91_L0.6551.00
10_A40_F0.6491.00
13_T16_R0.6491.00
49_L77_C0.6361.00
54_L85_E0.6341.00
14_W36_F0.6301.00
81_L86_L0.6261.00
13_T75_R0.6261.00
60_N95_N0.6241.00
71_R74_A0.6201.00
31_E35_A0.6181.00
71_R75_R0.6151.00
4_P32_F0.6131.00
88_S92_R0.6071.00
45_R48_K0.6051.00
7_L15_W0.6051.00
53_L73_L0.6041.00
5_F12_L0.6001.00
63_V90_F0.5991.00
34_K37_L0.5991.00
21_G25_A0.5991.00
79_D84_E0.5901.00
32_F36_F0.5901.00
70_F89_R0.5851.00
53_L77_C0.5761.00
39_R71_R0.5681.00
67_I70_F0.5651.00
3_A7_L0.5651.00
42_P45_R0.5611.00
46_T78_P0.5551.00
36_F41_F0.5531.00
41_F46_T0.5441.00
44_D48_K0.5371.00
22_S27_I0.5341.00
65_E69_R0.5341.00
8_K11_A0.5341.00
67_I74_A0.5311.00
47_E50_R0.5281.00
7_L14_W0.5241.00
66_Y70_F0.5231.00
44_D47_E0.5221.00
59_G95_N0.5221.00
83_E87_V0.5211.00
49_L53_L0.5191.00
43_P47_E0.5181.00
19_P23_I0.5151.00
43_P49_L0.5031.00
27_I35_A0.5021.00
57_K60_N0.5001.00
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

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.

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