GREMLIN Database
UBN2_3 - gag-polypeptide of LTR copia-type
PFAM: PF14244 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 152 (128)
Sequences: 4846 (3786)
Seq/√Len: 334.6
META: 0.377

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
85_K89_D6.3911.00
119_L127_K3.8581.00
33_N57_R3.1561.00
59_D84_A3.1481.00
18_Y92_K3.1281.00
30_R60_S2.7771.00
63_L87_I2.7631.00
70_L78_V2.4471.00
135_D138_A1.9811.00
14_D71_S1.9681.00
120_S123_E1.9541.00
52_Y56_K1.8271.00
33_N53_E1.7911.00
89_D92_K1.7631.00
44_K56_K1.7231.00
26_K82_E1.7221.00
27_I67_L1.6631.00
74_I95_F1.6161.00
83_T86_E1.5891.00
26_K35_L1.5861.00
22_K92_K1.5771.00
114_L128_L1.5661.00
29_L38_V1.5461.00
30_R56_K1.5331.00
35_L38_V1.5131.00
37_F58_C1.4791.00
25_M66_I1.4661.00
81_C87_I1.4591.00
106_Q110_E1.4571.00
18_Y22_K1.4531.00
55_W59_D1.4181.00
119_L123_E1.4061.00
44_K52_Y1.3781.00
24_Q72_P1.3741.00
59_D83_T1.3621.00
24_Q75_L1.3601.00
78_V87_I1.3571.00
36_G40_G1.3461.00
46_P49_D1.3421.00
22_K26_K1.3141.00
13_L17_N1.2851.00
26_K30_R1.2801.00
37_F42_I1.2641.00
54_A58_C1.2621.00
31_A61_M1.2391.00
35_L39_D1.1971.00
110_E115_K1.1951.00
47_E52_Y1.1931.00
105_F109_R1.1821.00
23_R67_L1.1801.00
30_R63_L1.1801.00
89_D93_E1.1771.00
20_L75_L1.1761.00
82_E86_E1.1471.00
121_V124_Y1.1371.00
110_E114_L1.1241.00
36_G42_I1.0571.00
81_C86_E1.0541.00
42_I58_C1.0531.00
110_E127_K1.0471.00
90_A94_R1.0461.00
77_S94_R1.0301.00
111_L131_L1.0001.00
25_M65_W0.9931.00
11_V72_P0.9611.00
108_K112_A0.9591.00
22_K96_S0.9511.00
23_R82_E0.9451.00
128_L132_W0.9421.00
67_L87_I0.9371.00
107_L131_L0.9221.00
20_L79_L0.9191.00
30_R35_L0.9171.00
33_N54_A0.9151.00
20_L76_S0.9011.00
120_S124_Y0.8741.00
90_A93_E0.8741.00
121_V125_F0.8681.00
92_K96_S0.8641.00
90_A129_K0.8571.00
101_G106_Q0.8461.00
44_K47_E0.8431.00
76_S130_S0.8411.00
81_C90_A0.8371.00
123_E127_K0.8351.00
33_N58_C0.8281.00
18_Y88_W0.8151.00
62_V65_W0.8111.00
37_F59_D0.8111.00
33_N61_M0.8031.00
129_K135_D0.8001.00
50_P54_A0.8001.00
18_Y91_L0.7881.00
66_I87_I0.7871.00
23_R27_I0.7851.00
67_L75_L0.7761.00
66_I70_L0.7671.00
63_L81_C0.7561.00
44_K55_W0.7490.99
124_Y127_K0.7470.99
31_A64_S0.7460.99
116_Q119_L0.7440.99
101_G110_E0.7400.99
27_I63_L0.7370.99
111_L114_L0.7350.99
32_K65_W0.7310.99
25_M88_W0.7200.99
36_G41_T0.7180.99
29_L62_V0.7180.99
45_P48_T0.7080.99
53_E56_K0.7060.99
124_Y128_L0.7000.99
122_S129_K0.6990.99
37_F40_G0.6970.99
107_L110_E0.6940.99
114_L127_K0.6930.99
18_Y21_W0.6900.99
109_R112_A0.6880.99
27_I79_L0.6850.99
102_A106_Q0.6850.99
103_R107_L0.6800.99
28_A32_K0.6790.99
36_G53_E0.6790.99
109_R114_L0.6780.99
30_R33_N0.6780.99
110_E113_T0.6760.99
26_K63_L0.6750.99
70_L91_L0.6710.99
34_L37_F0.6710.99
25_M69_S0.6680.99
56_K59_D0.6600.99
26_K92_K0.6500.99
19_L79_L0.6490.99
49_D52_Y0.6470.99
20_L72_P0.6440.98
97_Q102_A0.6410.98
78_V81_C0.6340.98
23_R80_Y0.6280.98
29_L37_F0.6260.98
38_V84_A0.6250.98
48_T52_Y0.6210.98
63_L67_L0.6200.98
122_S126_T0.6170.98
46_P50_P0.6140.98
104_I108_K0.6090.98
58_C61_M0.6060.98
73_E123_E0.6030.98
38_V62_V0.6020.98
104_I107_L0.6010.98
30_R53_E0.6000.98
116_Q121_V0.5980.98
40_G44_K0.5950.97
109_R113_T0.5880.97
70_L74_I0.5850.97
43_P85_K0.5830.97
54_A57_R0.5810.97
95_F98_S0.5790.97
46_P52_Y0.5780.97
103_R106_Q0.5780.97
74_I94_R0.5750.97
107_L111_L0.5640.97
108_K115_K0.5630.96
58_C62_V0.5610.96
36_G39_D0.5610.96
25_M38_V0.5580.96
45_P49_D0.5580.96
111_L132_W0.5540.96
119_L124_Y0.5460.96
40_G55_W0.5460.96
40_G43_P0.5450.96
117_G124_Y0.5440.96
24_Q68_N0.5440.96
85_K92_K0.5430.96
37_F84_A0.5410.96
23_R63_L0.5380.95
79_L87_I0.5370.95
62_V84_A0.5310.95
103_R110_E0.5240.95
34_L65_W0.5210.95
57_R61_M0.5190.95
61_M65_W0.5180.94
52_Y120_S0.5130.94
36_G57_R0.5120.94
24_Q79_L0.5120.94
56_K60_S0.5100.94
38_V85_K0.5100.94
13_L87_I0.5090.94
113_T128_L0.5050.94
74_I79_L0.5020.93
25_M29_L0.5010.93
45_P50_P0.5000.93
22_K88_W0.5000.93
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  
3cxbA 1 0.4934 6.3 0.932 Contact Map
4zcfC 1 0 5.7 0.934 Contact Map
2o2cA 2 0.4737 4.4 0.938 Contact Map
1lwuB 1 0.4539 3.1 0.942 Contact Map
2m7cA 1 0.1316 3 0.942 Contact Map
3mzoA 5 0.9408 3 0.942 Contact Map
3w92A 3 0.2039 2.9 0.943 Contact Map
1i1rB 1 0.3092 2.8 0.943 Contact Map
3a11A 4 0.4737 2.7 0.943 Contact Map
1xx7A 5 0.7829 2.6 0.944 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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