GREMLIN Database
UBN2_2 - gag-polypeptide of LTR copia-type
PFAM: PF14227 Sequences:
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_K9_D4.4361.00
44_H74_S3.9741.00
27_K66_D3.5861.00
52_A67_L2.7851.00
39_E47_R2.4801.00
30_L70_K2.0771.00
33_L48_F2.0331.00
9_D13_K1.8431.00
33_L44_H1.7771.00
28_R73_R1.7671.00
10_A13_K1.7581.00
12_E16_E1.7541.00
45_L101_I1.7361.00
23_K65_E1.6401.00
40_S43_E1.6351.00
84_T107_E1.5951.00
35_M76_P1.5921.00
56_A61_K1.5551.00
42_D105_L1.5311.00
31_Y70_K1.5271.00
67_L97_L1.5111.00
13_K98_E1.5071.00
49_T101_I1.4901.00
48_F67_L1.4721.00
107_E111_L1.4651.00
9_D12_E1.4611.00
68_V100_L1.4541.00
3_T6_E1.4421.00
60_V66_D1.4221.00
48_F71_L1.4091.00
80_E114_R1.3611.00
33_L47_R1.3481.00
81_T84_T1.3431.00
60_V63_D1.3371.00
31_Y66_D1.3231.00
41_I104_L1.2891.00
96_T99_E1.2741.00
29_Q47_R1.2741.00
50_K54_E1.2621.00
36_K39_E1.2361.00
45_L71_L1.2301.00
10_A14_K1.2291.00
29_Q54_E1.2271.00
48_F52_A1.2181.00
91_D94_T1.2041.00
20_L65_E1.1471.00
55_L60_V1.1471.00
33_L51_I1.1401.00
37_E78_S1.1361.00
8_W12_E1.1211.00
71_L97_L1.1071.00
97_L101_I1.1021.00
41_I45_L1.0981.00
29_Q51_I1.0881.00
82_F100_L1.0691.00
88_E103_R1.0581.00
24_L69_L1.0531.00
40_S108_E1.0461.00
27_K31_Y1.0351.00
35_M39_E1.0041.00
60_V65_E1.0001.00
47_R51_I0.9861.00
26_L51_I0.9741.00
75_L104_L0.9531.00
109_L112_K0.9491.00
19_S22_N0.9351.00
80_E110_R0.9171.00
7_A10_A0.9171.00
101_I105_L0.9081.00
49_T97_L0.9061.00
70_K74_S0.9021.00
6_E10_A0.8951.00
27_K60_V0.8861.00
82_F88_E0.8851.00
25_Q29_Q0.8851.00
41_I44_H0.8821.00
28_R32_N0.8781.00
107_E110_R0.8751.00
71_L100_L0.8701.00
22_N26_L0.8431.00
39_E43_E0.8311.00
81_T85_A0.8281.00
35_M38_G0.8261.00
2_K6_E0.8221.00
31_Y73_R0.8181.00
87_E110_R0.8171.00
79_Y82_F0.8071.00
83_V110_R0.8061.00
55_L62_I0.7911.00
48_F70_K0.7891.00
90_K103_R0.7781.00
64_D96_T0.7771.00
52_A56_A0.7711.00
28_R83_V0.7701.00
99_E102_S0.7511.00
21_A25_Q0.7471.00
10_A98_E0.7461.00
22_N25_Q0.7421.00
35_M41_I0.7401.00
85_A88_E0.7371.00
26_L54_E0.7311.00
11_L15_Y0.7311.00
77_E80_E0.7311.00
77_E114_R0.7281.00
22_N54_E0.7261.00
106_A109_L0.7151.00
108_E112_K0.7141.00
49_T53_N0.7071.00
53_N56_A0.7061.00
78_S111_L0.7051.00
19_S23_K0.6971.00
68_V97_L0.6951.00
44_H47_R0.6811.00
41_I108_E0.6791.00
24_L73_R0.6771.00
56_A67_L0.6711.00
16_E58_L0.6641.00
45_L97_L0.6541.00
26_L58_L0.6531.00
53_N57_A0.6491.00
103_R107_E0.6491.00
27_K69_L0.6491.00
95_L100_L0.6481.00
39_E44_H0.6471.00
12_E18_K0.6451.00
90_K93_E0.6451.00
99_E103_R0.6391.00
6_E9_D0.6361.00
23_K58_L0.6351.00
14_K18_K0.6341.00
68_V95_L0.6321.00
43_E46_N0.6261.00
86_L89_S0.6241.00
35_M74_S0.6201.00
35_M79_Y0.6171.00
70_K73_R0.6151.00
35_M44_H0.6151.00
42_D46_N0.6131.00
14_K17_G0.6121.00
63_D66_D0.6001.00
30_L52_A0.6001.00
54_E57_A0.5991.00
62_I67_L0.5951.00
29_Q113_K0.5891.00
80_E111_L0.5831.00
23_K69_L0.5821.00
41_I79_Y0.5771.00
41_I105_L0.5771.00
52_A64_D0.5751.00
68_V71_L0.5641.00
17_G22_N0.5581.00
66_D69_L0.5441.00
47_R50_K0.5421.00
49_T67_L0.5401.00
32_N73_R0.5401.00
14_K98_E0.5361.00
30_L44_H0.5331.00
30_L62_I0.5301.00
26_L29_Q0.5281.00
72_L83_V0.5261.00
24_L28_R0.5251.00
83_V87_E0.5251.00
7_A11_L0.5201.00
87_E90_K0.5111.00
27_K62_I0.5081.00
48_F74_S0.5071.00
71_L104_L0.5041.00
71_L101_I0.5021.00
109_L113_K0.5021.00
43_E47_R0.5001.00
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  
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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