GREMLIN Database
Complex1_LYR - Complex 1 protein (LYR family)
PFAM: PF05347 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 59 (57)
Sequences: 4541 (3311)
Seq/√Len: 438.6
META: 0.407

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
35_R38_R2.6581.00
40_V45_K2.6441.00
40_V49_L2.4351.00
6_L53_G2.2041.00
31_R35_R2.1971.00
10_L30_I2.1821.00
33_E36_K2.0701.00
29_R33_E1.7151.00
5_S9_R1.6631.00
52_K56_E1.6201.00
37_N49_L1.5681.00
27_R31_R1.5231.00
18_P21_N1.2911.00
9_R54_E1.2901.00
45_K48_E1.2851.00
29_R32_E1.2701.00
17_F21_N1.2531.00
42_D45_K1.2491.00
8_R12_R1.2381.00
51_R55_K1.2341.00
43_P47_E1.1711.00
11_L30_I1.1511.00
25_Y29_R1.1411.00
2_R54_E1.1351.00
50_L54_E1.1001.00
13_A16_K1.0901.00
37_N40_V1.0721.00
3_V50_L1.0651.00
48_E51_R1.0501.00
14_A26_F1.0461.00
48_E52_K1.0441.00
11_L27_R1.0241.00
46_I50_L1.0141.00
50_L53_G1.0111.00
14_A30_I0.9651.00
32_E36_K0.9641.00
26_F29_R0.9201.00
7_Y31_R0.9121.00
28_R32_E0.9111.00
47_E51_R0.9041.00
40_V43_P0.8701.00
25_Y28_R0.8701.00
33_E52_K0.8631.00
17_F26_F0.8531.00
13_A57_L0.8301.00
23_R26_F0.8181.00
24_E28_R0.8161.00
22_F25_Y0.8081.00
49_L53_G0.7921.00
3_V34_F0.7911.00
16_K20_Y0.7821.00
6_L10_L0.7791.00
53_G56_E0.7751.00
23_R27_R0.7561.00
14_A27_R0.7551.00
22_F26_F0.7451.00
28_R35_R0.7061.00
49_L52_K0.7031.00
30_I56_E0.6841.00
19_D22_F0.6791.00
52_K55_K0.6711.00
17_F22_F0.6651.00
17_F25_Y0.6631.00
45_K49_L0.6500.99
15_R27_R0.6390.99
10_L14_A0.6390.99
33_E56_E0.6330.99
8_R15_R0.6320.99
44_E48_E0.6310.99
42_D47_E0.6230.99
9_R13_A0.5900.99
34_F50_L0.5890.99
51_R54_E0.5730.99
43_P46_I0.5730.99
14_A19_D0.5640.99
41_T46_I0.5610.98
17_F20_Y0.5390.98
42_D46_I0.5350.98
44_E47_E0.5320.98
54_E58_E0.5130.97
6_L34_F0.5110.97
2_R5_S0.5080.97
11_L14_A0.5060.97
10_L56_E0.5040.97
19_D23_R0.5020.97
13_A17_F0.5000.97
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  
2ld7A 1 0.9492 9.5 0.814 Contact Map
2qr4A 2 0.8305 8 0.82 Contact Map
3fvbA 6 0.9492 5.1 0.836 Contact Map
3ce2A 1 0.8305 5 0.837 Contact Map
1s94A 1 0.5763 5 0.837 Contact Map
4cvrA 2 0.9492 4.4 0.84 Contact Map
4ynvA 1 0.6441 4.3 0.841 Contact Map
2cqnA 1 0.9831 4.2 0.842 Contact Map
4tofA 6 0.9492 4.2 0.842 Contact Map
3gvyA 5 0.9492 4 0.844 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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