GREMLIN Database
COX4_pro - Prokaryotic Cytochrome C oxidase subunit IV
PFAM: PF03626 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 72 (70)
Sequences: 46999 (28164)
Seq/√Len: 3366.2
META: 0.947

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_A20_L2.6441.00
40_A44_L2.5771.00
27_N31_L2.2001.00
38_K42_V2.0671.00
12_A16_A1.9761.00
27_N30_A1.8761.00
24_G27_N1.7591.00
45_F50_K1.7511.00
5_A9_V1.6631.00
16_A19_Y1.6611.00
4_F8_L1.6601.00
14_T34_I1.6191.00
10_L37_V1.6151.00
3_V41_L1.4751.00
43_V49_L1.4721.00
63_P66_F1.4321.00
25_L28_V1.4291.00
7_L42_V1.4251.00
6_A41_L1.4021.00
17_V30_A1.3911.00
54_R58_L1.3711.00
2_I6_A1.3691.00
26_N30_A1.3231.00
25_L29_V1.2941.00
29_V33_A1.2561.00
52_E56_L1.2511.00
54_R57_R1.2441.00
44_L50_K1.2301.00
38_K46_F1.2301.00
7_L38_K1.2221.00
60_V63_P1.2021.00
40_A61_L1.1861.00
26_N29_V1.1741.00
3_V45_F1.1571.00
15_V19_Y1.1271.00
2_I5_A1.1241.00
10_L34_I1.0921.00
53_S57_R1.0811.00
66_F69_L1.0731.00
66_F70_L1.0661.00
5_A8_L1.0561.00
24_G28_V1.0391.00
6_A10_L1.0371.00
10_L13_L1.0341.00
58_L62_A0.9921.00
13_L34_I0.9881.00
62_A65_V0.9821.00
39_A43_V0.9741.00
65_V69_L0.9731.00
64_L67_L0.9581.00
56_L59_L0.9261.00
63_P67_L0.9241.00
41_L45_F0.8971.00
62_A66_F0.8791.00
28_V32_L0.7981.00
57_R61_L0.7851.00
55_L58_L0.7741.00
26_N31_L0.7721.00
14_T38_K0.7681.00
11_T14_T0.7481.00
56_L63_P0.7461.00
57_R60_V0.7441.00
67_L70_L0.7301.00
67_L71_L0.7101.00
64_L68_L0.7091.00
14_T31_L0.7021.00
65_V68_L0.7011.00
28_V31_L0.7001.00
37_V40_A0.6911.00
23_G26_N0.6811.00
36_V40_A0.6801.00
14_T18_A0.6651.00
9_V12_A0.6491.00
3_V7_L0.6461.00
48_H52_E0.6411.00
20_L23_G0.6381.00
61_L64_L0.6371.00
44_L51_Y0.6331.00
6_A37_V0.6241.00
10_L14_T0.6201.00
19_Y22_L0.6151.00
42_V47_M0.6141.00
49_L60_V0.6071.00
10_L41_L0.6061.00
14_T35_A0.6041.00
48_H51_Y0.6001.00
59_L62_A0.6001.00
57_R64_L0.5971.00
58_L61_L0.5811.00
45_F51_Y0.5671.00
32_L36_V0.5631.00
56_L60_V0.5591.00
56_L66_F0.5531.00
57_R66_F0.5441.00
18_A35_A0.5371.00
56_L67_L0.5371.00
60_V67_L0.5351.00
15_V18_A0.5351.00
11_T38_K0.5341.00
62_A67_L0.5301.00
9_V13_L0.5261.00
55_L59_L0.5171.00
18_A21_D0.5171.00
40_A45_F0.5021.00
57_R62_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  
3c02A 3 0.2639 4.4 0.843 Contact Map
4p02A 1 0.9167 2.6 0.86 Contact Map
3ug9A 2 0.875 2.1 0.866 Contact Map
1z1nX 1 0 1.7 0.873 Contact Map
3rlfG 1 0.2361 1.7 0.873 Contact Map
4fbzA 3 1 1.6 0.874 Contact Map
2e84A 1 0 1.6 0.875 Contact Map
1rz2A 1 0 1.5 0.876 Contact Map
2wswA 3 0.7361 1.4 0.88 Contact Map
3dmkA 2 0.0139 1.3 0.882 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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