GREMLIN Database
DUF3040 - Protein of unknown function (DUF3040)
PFAM: PF11239 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 84 (83)
Sequences: 7321 (4873)
Seq/√Len: 534.9
META: 0.865

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
6_H10_L3.9581.00
51_G81_G3.5741.00
17_A21_E2.4001.00
22_D25_F2.3971.00
25_F29_V2.3051.00
10_L13_E2.2541.00
25_F28_R2.2201.00
12_E16_R2.1251.00
13_E17_A2.0001.00
11_L15_E1.9471.00
69_L72_V1.6491.00
8_Q12_E1.6421.00
14_I17_A1.5721.00
36_R39_R1.4861.00
75_F78_M1.4751.00
79_L83_V1.4691.00
6_H9_R1.4201.00
45_L48_A1.4051.00
52_F59_L1.3231.00
33_R37_R1.3201.00
57_A61_A1.3121.00
2_P5_E1.2991.00
17_A20_A1.2831.00
10_L14_I1.2811.00
4_S7_E1.2481.00
45_L49_A1.2131.00
71_G75_F1.1631.00
68_V72_V1.1561.00
10_L17_A1.1551.00
19_Y26_A1.1461.00
64_A67_L1.1421.00
58_L62_G1.1281.00
41_A44_R1.1241.00
70_L75_F1.1101.00
13_E16_R1.0931.00
72_V76_V1.0861.00
63_V66_S1.0511.00
33_R36_R1.0441.00
75_F79_L1.0341.00
49_A53_V1.0271.00
61_A65_T1.0241.00
78_M82_A1.0141.00
2_P10_L1.0141.00
14_I26_A1.0071.00
12_E19_Y0.9991.00
32_T35_R0.9951.00
62_G70_L0.9741.00
11_L14_I0.9611.00
5_E13_E0.9611.00
40_S43_R0.9601.00
62_G65_T0.9561.00
71_G78_M0.9551.00
59_L79_L0.9451.00
27_S31_G0.9371.00
37_R40_S0.9331.00
55_G81_G0.9201.00
48_A52_F0.9141.00
69_L73_A0.8891.00
11_L29_V0.8801.00
34_P37_R0.8781.00
30_R33_R0.8711.00
70_L73_A0.8691.00
26_A29_V0.8311.00
63_V67_L0.8291.00
77_V81_G0.8241.00
16_R20_A0.8211.00
68_V71_G0.8121.00
11_L25_F0.8071.00
55_G59_L0.7841.00
32_T37_R0.7831.00
18_L25_F0.7811.00
76_V80_A0.7791.00
34_P39_R0.7601.00
14_I47_L0.7561.00
15_E18_L0.7431.00
63_V71_G0.7361.00
47_L51_G0.7321.00
71_G74_G0.7221.00
58_L77_V0.7211.00
74_G77_V0.7101.00
53_V57_A0.7071.00
46_V50_L0.6981.00
72_V75_F0.6881.00
55_G77_V0.6871.00
12_E21_E0.6841.00
36_R41_A0.6811.00
33_R38_R0.6761.00
5_E9_R0.6721.00
24_K28_R0.6711.00
18_L50_L0.6661.00
46_V49_A0.6401.00
47_L50_L0.6371.00
23_P29_V0.6341.00
28_R31_G0.6341.00
5_E8_Q0.6321.00
1_M4_S0.6291.00
65_T68_V0.6151.00
31_G34_P0.6081.00
70_L80_A0.6071.00
2_P6_H0.5951.00
8_Q14_I0.5830.99
21_E28_R0.5830.99
59_L78_M0.5790.99
2_P7_E0.5780.99
50_L54_V0.5760.99
69_L75_F0.5680.99
8_Q19_Y0.5670.99
55_G58_L0.5650.99
48_A53_V0.5630.99
73_A77_V0.5600.99
19_Y83_V0.5570.99
14_I18_L0.5450.99
52_F60_V0.5450.99
9_R12_E0.5430.99
58_L73_A0.5410.99
77_V80_A0.5400.99
21_E26_A0.5390.99
36_R46_V0.5320.99
67_L72_V0.5290.99
46_V52_F0.5110.99
70_L74_G0.5040.98
23_P27_S0.5030.98
37_R41_A0.5020.98
36_R43_R0.5000.98
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  
2ypfA 1 0 15 0.843 Contact Map
3pe5A 1 0 13.9 0.846 Contact Map
4q3mA 2 0.3333 12 0.85 Contact Map
1y6jA 2 0.3214 9.5 0.856 Contact Map
4cl3A 4 0.3333 9.4 0.856 Contact Map
3b3dA 1 0.3333 9.2 0.857 Contact Map
1hyeA 2 0.3333 8.9 0.859 Contact Map
1mzrA 1 0.3333 8.7 0.859 Contact Map
3up8A 1 0.369 8.2 0.86 Contact Map
4av3A 2 0.8571 8.1 0.861 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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