GREMLIN Database
UPF0016 - Uncharacterized protein family UPF0016
PFAM: PF01169 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 75 (74)
Sequences: 32477 (16676)
Seq/√Len: 1938.5
META: 0.909

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
62_L65_L3.0471.00
61_R65_L2.8981.00
20_T36_A2.5021.00
53_A57_R2.4611.00
28_R31_P2.4031.00
37_T41_L2.1761.00
59_P62_L2.1311.00
60_P64_R2.1271.00
69_A73_A2.0541.00
62_L66_V2.0491.00
52_A56_R2.0011.00
50_L53_A1.9771.00
65_L69_A1.8881.00
43_A47_A1.8771.00
40_L44_H1.5221.00
68_A72_L1.5221.00
53_A56_R1.4781.00
49_L53_A1.4051.00
30_L34_L1.4011.00
36_A40_L1.3781.00
2_T6_A1.3441.00
31_P35_G1.3261.00
13_G17_Q1.3131.00
5_G9_L1.2961.00
23_L35_G1.2031.00
45_A49_L1.1951.00
11_E14_D1.1151.00
49_L52_A1.1111.00
34_L38_L1.0881.00
8_F12_L1.0881.00
46_L49_L1.0651.00
61_R64_R1.0501.00
63_L67_A1.0461.00
39_A43_A1.0351.00
18_L22_A1.0061.00
67_A70_L1.0021.00
38_L41_L1.0001.00
70_L74_F0.9951.00
38_L42_L0.9751.00
65_L68_A0.9641.00
60_P63_L0.9581.00
66_V70_L0.9581.00
52_A55_A0.9341.00
19_A22_A0.9301.00
66_V69_A0.9301.00
28_R32_V0.9281.00
33_F37_T0.9181.00
12_L15_K0.9081.00
2_T5_G0.8991.00
11_E16_T0.8931.00
5_G8_F0.8861.00
31_P34_L0.8831.00
3_S23_L0.8741.00
50_L54_L0.8691.00
72_L75_G0.8661.00
4_F8_F0.8651.00
12_L21_L0.8491.00
27_Y32_V0.8341.00
3_S7_V0.8051.00
20_T24_A0.7871.00
63_L66_V0.7651.00
42_L45_A0.7561.00
12_L17_Q0.7411.00
55_A59_P0.7261.00
64_R67_A0.7131.00
32_V35_G0.7031.00
23_L32_V0.6891.00
43_A46_L0.6821.00
35_G39_A0.6761.00
32_V36_A0.6661.00
42_L46_L0.6611.00
67_A71_F0.6561.00
29_P33_F0.6481.00
41_L44_H0.6481.00
54_L58_L0.6471.00
30_L33_F0.6401.00
58_L62_L0.6351.00
6_A10_A0.6241.00
24_A27_Y0.6201.00
26_R29_P0.6101.00
55_A63_L0.6051.00
57_R62_L0.6041.00
12_L16_T0.6041.00
54_L57_R0.6001.00
22_A26_R0.5961.00
55_A60_P0.5921.00
17_Q33_F0.5891.00
50_L55_A0.5871.00
46_L50_L0.5871.00
64_R71_F0.5831.00
21_L43_A0.5791.00
48_V52_A0.5771.00
15_K19_A0.5741.00
59_P63_L0.5711.00
23_L26_R0.5591.00
3_S6_A0.5561.00
46_L74_F0.5461.00
71_F74_F0.5451.00
20_T23_L0.5441.00
19_A71_F0.5371.00
47_A50_L0.5361.00
18_L44_H0.5351.00
7_V44_H0.5301.00
4_F7_V0.5241.00
15_K18_L0.5221.00
52_A60_P0.5131.00
15_K24_A0.5101.00
7_V11_E0.5021.00
22_A25_A0.5021.00
20_T40_L0.5011.00
33_F36_A0.5001.00
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  
4ymuD 2 0.7867 3.1 0.882 Contact Map
1q90G 1 0.4 1.1 0.908 Contact Map
4oh3A 2 0.9867 1.1 0.909 Contact Map
1rh1A 1 0.8533 1 0.91 Contact Map
4hlsA 2 0.2267 1 0.911 Contact Map
4j05A 3 1 0.9 0.912 Contact Map
4uvmA 1 0.9867 0.9 0.913 Contact Map
4k0jA 3 0.32 0.9 0.915 Contact Map
4tphA 2 1 0.8 0.916 Contact Map
3tuiA 2 0.7867 0.8 0.916 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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