GREMLIN Database
Cys_rich_VLP - Cysteine-rich VLP
PFAM: PF14194 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 57 (56)
Sequences: 748 (383)
Seq/√Len: 51.2
META: 0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
15_L56_L5.2651.00
17_A48_Y3.8211.00
48_Y52_A2.4851.00
5_R9_R2.4851.00
40_S43_S2.1541.00
7_A57_D2.0651.00
36_P40_S2.0501.00
3_A6_R1.6630.98
48_Y56_L1.6380.98
5_R41_W1.5320.97
34_V38_L1.3470.94
15_L50_R1.3310.94
17_A52_A1.3130.93
2_P10_K1.2210.90
20_D25_L1.2190.90
2_P5_R1.1920.89
30_G35_C1.1890.89
11_L49_F1.1580.88
16_C19_Y1.1570.88
36_P43_S1.1390.87
37_Q40_S1.1170.86
36_P45_L1.0980.85
27_L37_Q1.0260.81
49_F54_L1.0090.80
2_P6_R1.0020.79
2_P14_K0.9220.73
26_L33_C0.9180.73
19_Y38_L0.9170.73
42_Y45_L0.9150.73
53_V57_D0.8760.69
45_L50_R0.8760.69
18_N33_C0.8750.69
52_A55_P0.8740.69
48_Y53_V0.8740.69
37_Q44_L0.8700.69
36_P44_L0.8670.69
12_V38_L0.8600.68
2_P13_R0.8480.67
11_L57_D0.8410.66
10_K14_K0.8330.66
5_R8_I0.8250.65
29_D32_E0.8230.65
18_N25_L0.8140.64
22_G37_Q0.8130.64
34_V42_Y0.8120.64
47_K50_R0.8110.63
27_L47_K0.8030.63
6_R10_K0.7420.57
39_I42_Y0.7390.56
5_R51_N0.7360.56
14_K21_E0.7260.55
14_K51_N0.7210.54
18_N26_L0.7200.54
35_C47_K0.6750.50
3_A14_K0.6590.48
15_L48_Y0.6440.46
9_R20_D0.6380.46
37_Q50_R0.6340.45
34_V39_I0.6330.45
14_K56_L0.6320.45
26_L36_P0.6250.45
5_R12_V0.6250.45
3_A7_A0.6250.45
27_L30_G0.6240.44
2_P7_A0.6170.44
29_D33_C0.6090.43
10_K13_R0.5940.41
27_L36_P0.5920.41
6_R41_W0.5910.41
5_R42_Y0.5670.39
23_N37_Q0.5590.38
4_Q40_S0.5560.38
22_G44_L0.5540.37
24_C47_K0.5470.37
22_G56_L0.5470.37
32_E36_P0.5440.36
7_A49_F0.5400.36
4_Q37_Q0.5370.36
42_Y47_K0.5350.36
22_G47_K0.5280.35
6_R13_R0.5240.35
50_R53_V0.5150.34
30_G33_C0.5080.33
52_A56_L0.5000.32
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  
1vw4R 1 0.6491 14.9 0.865 Contact Map
4o6iA 2 0.8421 11.8 0.871 Contact Map
1lbaA 1 0.9123 7.1 0.883 Contact Map
2e2dC 1 0.8421 5 0.891 Contact Map
1uapA 1 0.3684 4.9 0.891 Contact Map
3itfA 2 0.4561 4.5 0.894 Contact Map
4lu2A 2 0.8246 4.4 0.894 Contact Map
3ghgC 2 0.6667 4.3 0.894 Contact Map
3q7cA 1 0.8421 4 0.896 Contact Map
4k7eA 2 0.7193 3.9 0.897 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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