GREMLIN Database
Prok_Ub - Prokaryotic Ubiquitin
PFAM: PF14454 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 64 (63)
Sequences: 1687 (1122)
Seq/√Len: 141.4
META: 0.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_L32_Y3.3861.00
20_D23_L2.3651.00
8_V15_E2.3251.00
19_P28_V2.3151.00
24_S27_E2.2281.00
27_E30_D1.9731.00
25_P44_I1.8431.00
8_V53_K1.7611.00
45_E59_V1.7231.00
6_K53_K1.5931.00
31_F35_Q1.5771.00
10_K15_E1.5501.00
29_R58_F1.5081.00
14_I36_Y1.4891.00
49_I54_L1.4891.00
11_Y38_E1.4481.00
46_G56_Y1.4131.00
26_E29_R1.4131.00
47_P56_Y1.3821.00
7_R18_D1.3721.00
15_E53_K1.3571.00
25_P56_Y1.3011.00
9_F18_D1.2911.00
10_K55_V1.2391.00
32_Y36_Y1.2381.00
10_K50_V1.1731.00
59_V62_I1.1480.99
4_T22_S1.1170.99
23_L27_E1.0950.99
59_V64_T1.0890.99
8_V55_V1.0760.99
18_D21_P1.0430.99
48_E54_L1.0290.99
23_L31_F1.0280.99
33_A40_T1.0260.99
19_P31_F1.0030.99
44_I58_F0.9940.98
50_V55_V0.9900.98
29_R43_T0.9890.98
9_F19_P0.9650.98
38_E60_R0.9210.97
10_K57_T0.8840.97
23_L28_V0.8600.96
11_Y60_R0.8450.96
45_E57_T0.8440.96
3_T52_D0.8410.96
43_T59_V0.8130.95
29_R42_A0.7900.94
30_D34_A0.7770.93
5_L49_I0.7630.93
43_T64_T0.7610.93
43_T61_A0.7550.92
33_A36_Y0.7510.92
31_F34_A0.7470.92
20_D28_V0.7410.92
44_I47_P0.7390.91
32_Y58_F0.7350.91
17_P21_P0.6950.89
26_E41_T0.6890.88
31_F40_T0.6850.88
61_A64_T0.6820.88
45_E62_I0.6790.88
42_A58_F0.6680.87
10_K14_I0.6660.87
26_E44_I0.6490.85
26_E30_D0.6440.85
6_K50_V0.6420.85
6_K33_A0.6310.84
25_P39_L0.6290.83
29_R61_A0.6270.83
12_N60_R0.6260.83
16_L36_Y0.6160.82
20_D34_A0.6120.82
16_L39_L0.6100.81
9_F58_F0.6070.81
28_V39_L0.6040.81
44_I56_Y0.6010.80
39_L58_F0.5840.79
29_R60_R0.5760.78
28_V44_I0.5690.77
50_V53_K0.5660.76
22_S50_V0.5600.76
48_E61_A0.5600.76
29_R44_I0.5520.75
14_I34_A0.5510.74
48_E57_T0.5490.74
23_L38_E0.5410.73
18_D28_V0.5310.72
33_A39_L0.5270.71
46_G54_L0.5240.71
29_R39_L0.5170.70
49_I52_D0.5120.69
28_V58_F0.5090.69
29_R38_E0.5000.67
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  
3l7uA 5 0.9375 18.9 0.869 Contact Map
1w7wA 5 1 16.6 0.872 Contact Map
3evoA 5 1 16.1 0.873 Contact Map
2az3A 6 0.9375 15.8 0.873 Contact Map
1iedA 2 0.9219 14.6 0.875 Contact Map
1ehwA 4 0.9375 14 0.876 Contact Map
2dxeA 5 0.9375 13.9 0.876 Contact Map
3ztpA 3 0.9375 12.6 0.879 Contact Map
4dz6A 5 0.9375 12.3 0.879 Contact Map
3q8uA 3 0.9375 11.3 0.881 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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