GREMLIN Database
DUF3880 - DUF based on E. rectale Gene description (DUF3880)
PFAM: PF12996 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 78 (77)
Sequences: 7009 (5266)
Seq/√Len: 600.2
META: 0.874

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
21_Y42_H3.0741.00
23_F42_H2.8171.00
25_F46_L2.5931.00
48_A53_H2.4101.00
31_E35_A2.2221.00
23_F44_L2.0941.00
68_S71_S2.0591.00
21_Y40_N2.0351.00
31_E34_R2.0281.00
58_L62_E1.9371.00
24_T29_C1.9341.00
63_R67_G1.8551.00
32_E35_A1.8501.00
27_R43_Y1.7551.00
26_D29_C1.6941.00
30_V34_R1.6201.00
49_D52_I1.5651.00
50_P53_H1.5471.00
30_V41_V1.5471.00
24_T33_L1.4971.00
60_P63_R1.3281.00
65_R68_S1.3251.00
32_E36_L1.3071.00
61_E64_K1.2881.00
25_F77_Y1.2661.00
59_S62_E1.2461.00
3_V46_L1.2261.00
14_E17_P1.1421.00
60_P64_K1.1411.00
62_E66_Y1.0921.00
61_E65_R1.0741.00
25_F43_Y1.0741.00
29_C32_E1.0611.00
38_A41_V1.0481.00
2_F7_L1.0471.00
4_D25_F0.9931.00
16_A36_L0.9891.00
11_Y15_I0.9831.00
3_V8_H0.9691.00
66_Y69_D0.9571.00
62_E65_R0.9441.00
26_D43_Y0.9391.00
8_H11_Y0.9361.00
15_I18_L0.9231.00
5_D24_T0.9021.00
57_E63_R0.8871.00
58_L67_G0.8851.00
7_L12_S0.8831.00
58_L63_R0.8791.00
26_D46_L0.8791.00
59_S63_R0.8771.00
27_R30_V0.8741.00
57_E65_R0.8731.00
24_T30_V0.8701.00
9_F12_S0.8661.00
5_D12_S0.8591.00
8_H12_S0.8341.00
26_D71_S0.8331.00
2_F12_S0.8301.00
4_D12_S0.8191.00
2_F8_H0.8151.00
25_F29_C0.8051.00
24_T41_V0.7901.00
62_E67_G0.7861.00
15_I19_Y0.7841.00
59_S67_G0.7801.00
6_P26_D0.7781.00
50_P54_R0.7771.00
64_K67_G0.7711.00
43_Y48_A0.7611.00
5_D9_F0.7531.00
4_D8_H0.7491.00
34_R40_N0.7451.00
60_P66_Y0.7411.00
22_V25_F0.7311.00
59_S66_Y0.7291.00
26_D48_A0.7271.00
5_D8_H0.6981.00
37_G40_N0.6961.00
1_W47_A0.6901.00
34_R63_R0.6851.00
26_D77_Y0.6831.00
15_I22_V0.6631.00
29_C46_L0.6621.00
3_V7_L0.6591.00
29_C33_L0.6581.00
25_F76_L0.6551.00
46_L49_D0.6511.00
1_W44_L0.6341.00
26_D33_L0.6151.00
49_D53_H0.6081.00
34_R41_V0.5891.00
2_F5_D0.5831.00
58_L66_Y0.5751.00
60_P65_R0.5741.00
18_L39_K0.5651.00
55_P58_L0.5581.00
49_D66_Y0.5440.99
5_D29_C0.5440.99
22_V41_V0.5430.99
3_V43_Y0.5430.99
2_F24_T0.5400.99
39_K42_H0.5390.99
54_R58_L0.5380.99
4_D73_V0.5370.99
59_S65_R0.5320.99
55_P65_R0.5320.99
7_L11_Y0.5220.99
51_E54_R0.5210.99
6_P46_L0.5190.99
20_D77_Y0.5140.99
49_D54_R0.5130.99
16_A20_D0.5090.99
34_R39_K0.5070.99
58_L61_E0.5020.99
28_D31_E0.5000.99
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  
4w6qA 4 0.9231 86.4 0.758 Contact Map
3okpA 1 1 86.4 0.758 Contact Map
2jjmA 4 0.9487 85 0.763 Contact Map
2hy7A 1 0.9231 81.9 0.771 Contact Map
2x0dA 2 0.9487 80.2 0.775 Contact Map
3c48A 2 1 77.7 0.78 Contact Map
4hlnA 1 1 76.7 0.782 Contact Map
3vueA 1 1 75.2 0.785 Contact Map
3oy2A 2 0.9872 74.8 0.786 Contact Map
2r60A 1 1 71.9 0.79 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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