GREMLIN Database
UBN2 - gag-polypeptide of LTR copia-type
PFAM: PF14223 Sequences:
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_K8_D4.1641.00
46_Y76_S3.9211.00
29_K68_D3.1221.00
41_E49_R2.5931.00
54_A69_L2.5821.00
35_L50_F2.1461.00
32_L72_K2.0031.00
86_T109_E1.9571.00
35_L46_Y1.9321.00
8_D12_K1.8111.00
47_L103_I1.8041.00
33_E72_K1.7391.00
35_L49_R1.6351.00
44_D107_L1.5971.00
30_R75_R1.5741.00
37_M78_P1.5731.00
69_L99_L1.5661.00
50_F73_L1.5401.00
42_S45_E1.5331.00
58_A63_K1.5011.00
90_E105_R1.4961.00
11_E15_E1.4811.00
25_K67_E1.4681.00
12_K100_E1.4351.00
47_L73_L1.4241.00
62_E68_D1.4031.00
83_T86_T1.3981.00
43_I106_L1.3951.00
26_L71_L1.3871.00
109_E113_L1.3591.00
50_F69_L1.3461.00
89_E112_R1.3451.00
8_D11_E1.3441.00
31_E56_E1.3351.00
52_K56_E1.3251.00
62_E65_D1.3221.00
70_V102_L1.2891.00
28_L53_I1.2041.00
57_L62_E1.1871.00
33_E68_D1.1841.00
29_K62_E1.1831.00
9_A12_K1.1761.00
51_K103_I1.1671.00
31_E49_R1.1601.00
35_L53_I1.1421.00
38_K41_E1.1251.00
99_L103_I1.1181.00
39_E80_S1.1181.00
43_I47_L1.1001.00
19_R67_E1.0891.00
27_Q31_E1.0801.00
37_M41_E1.0711.00
30_R34_N1.0491.00
50_F54_A1.0451.00
24_R56_E1.0351.00
31_E53_I1.0301.00
98_T101_E1.0271.00
2_T5_E1.0251.00
9_A13_K1.0131.00
81_Y84_F0.9991.00
84_F102_L0.9851.00
25_K60_L0.9851.00
73_L102_L0.9821.00
87_A90_E0.9571.00
62_E67_E0.9521.00
77_L81_Y0.9441.00
83_T87_A0.9271.00
33_E75_R0.9241.00
37_M40_G0.9201.00
92_K105_R0.9101.00
28_L56_E0.9061.00
28_L57_L0.9011.00
49_R53_I0.8971.00
54_A58_A0.8781.00
65_D68_D0.8751.00
82_E112_R0.8691.00
72_K76_S0.8651.00
73_L99_L0.8631.00
28_L31_E0.8621.00
55_N58_A0.8611.00
42_S110_E0.8591.00
37_M43_I0.8531.00
84_F88_L0.8451.00
41_E45_E0.8431.00
109_E112_R0.8271.00
43_I110_E0.8241.00
66_D98_T0.8141.00
50_F72_K0.8121.00
47_L99_L0.8091.00
29_K33_E0.8051.00
7_W11_E0.7961.00
6_A9_A0.7951.00
30_R89_E0.7771.00
26_L75_R0.7761.00
85_V112_R0.7641.00
87_A91_S0.7611.00
32_L64_I0.7591.00
24_R27_Q0.7581.00
111_L114_K0.7561.00
51_K99_L0.7521.00
77_L106_L0.7491.00
79_E82_E0.7431.00
80_S113_L0.7401.00
57_L64_I0.7401.00
10_L14_Y0.7371.00
25_K62_E0.7241.00
82_E113_L0.7191.00
26_L89_E0.7171.00
88_L102_L0.7151.00
24_R28_L0.7101.00
103_I107_L0.6971.00
84_F90_E0.6951.00
29_K64_I0.6821.00
29_K71_L0.6801.00
51_K55_N0.6791.00
25_K57_L0.6491.00
91_S105_R0.6481.00
9_A100_E0.6471.00
5_E9_A0.6431.00
86_T90_E0.6331.00
64_I69_L0.6321.00
58_A69_L0.6281.00
32_L53_I0.6211.00
41_E46_Y0.6151.00
85_V89_E0.6141.00
45_E48_N0.6131.00
101_E104_G0.6121.00
13_K17_K0.6071.00
108_A111_L0.6061.00
54_A66_D0.6051.00
70_V99_L0.6031.00
15_E60_L0.5981.00
92_K95_L0.5971.00
6_A10_L0.5921.00
37_M76_S0.5911.00
92_K101_E0.5871.00
32_L46_Y0.5871.00
28_L60_L0.5831.00
101_E105_R0.5821.00
53_I56_E0.5811.00
34_N75_R0.5811.00
111_L115_K0.5741.00
74_L85_V0.5721.00
89_E105_R0.5701.00
66_D69_L0.5691.00
91_S95_L0.5661.00
72_K75_R0.5631.00
66_D99_L0.5631.00
32_L54_A0.5581.00
64_I68_D0.5541.00
43_I46_Y0.5531.00
88_L91_S0.5511.00
29_K57_L0.5421.00
73_L106_L0.5371.00
30_R85_V0.5361.00
66_D70_V0.5361.00
43_I107_L0.5351.00
55_N59_A0.5321.00
84_F87_A0.5261.00
73_L103_I0.5231.00
44_D48_N0.5201.00
32_L69_L0.5091.00
38_K78_P0.5071.00
53_I60_L0.5041.00
19_R25_K0.5001.00
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  
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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