GREMLIN Database
Cmc1 - Cytochrome c oxidase biogenesis protein Cmc1 like
PFAM: PF08583 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 69 (68)
Sequences: 1045 (784)
Seq/√Len: 95.0
META: 0.33

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
18_K22_E2.7171.00
30_K33_G2.5011.00
22_E26_E2.1751.00
27_R30_K1.9941.00
21_A24_H1.9411.00
37_D41_A1.9381.00
6_K10_H1.7691.00
57_N60_K1.7611.00
64_L67_R1.7221.00
15_E19_A1.6931.00
59_E62_E1.6921.00
41_A44_K1.6291.00
56_K59_E1.6171.00
58_R62_E1.6071.00
63_Y66_E1.5491.00
59_E63_Y1.5451.00
19_A41_A1.5211.00
40_R44_K1.4431.00
14_A18_K1.3930.99
22_E25_K1.3750.99
60_K63_Y1.3700.99
20_L24_H1.2770.99
43_N50_R1.2630.99
39_K43_N1.2370.99
2_H5_L1.2330.99
1_M4_D1.2310.99
61_A65_R1.2300.99
56_K60_K1.1990.98
57_N61_A1.1760.98
4_D8_K1.1760.98
54_R58_R1.1720.98
27_R34_A1.1620.98
29_L32_V1.0850.97
24_H36_N1.0820.97
53_E56_K1.0620.96
65_R68_L1.0510.96
26_E30_K1.0480.96
6_K9_A1.0350.96
24_H39_K1.0340.96
53_E57_N1.0330.96
10_H49_E1.0270.95
3_P7_E1.0120.95
1_M5_L1.0050.95
58_R61_A0.9830.94
18_K21_A0.9530.93
47_R54_R0.9480.93
20_L39_K0.9310.92
12_K49_E0.9100.92
46_L50_R0.8830.90
63_Y67_R0.8690.90
16_E38_E0.8650.89
27_R33_G0.8610.89
51_T55_F0.8390.88
43_N46_L0.8190.87
36_N39_K0.8130.86
55_F59_E0.8070.86
34_A41_A0.7890.85
61_A64_L0.7850.84
28_G32_V0.7770.84
47_R50_R0.7730.83
38_E41_A0.7540.82
60_K67_R0.7380.80
24_H33_G0.7240.79
60_K64_L0.7150.78
36_N46_L0.7140.78
23_C45_C0.7140.78
13_C23_C0.7130.78
44_K48_K0.7070.77
23_C35_C0.6990.77
33_G36_N0.6910.76
25_K51_T0.6590.72
52_D55_F0.6510.71
52_D56_K0.6510.71
28_G33_G0.6460.71
15_E25_K0.6460.71
35_C45_C0.6390.70
13_C35_C0.6310.69
13_C45_C0.6250.68
17_I42_L0.6240.68
22_E29_L0.6230.68
20_L42_L0.6090.66
16_E19_A0.6020.66
17_I32_V0.5960.65
64_L68_L0.5880.64
15_E18_K0.5820.63
20_L50_R0.5810.63
41_A48_K0.5720.62
37_D44_K0.5600.60
26_E32_V0.5480.58
12_K62_E0.5460.58
24_H31_V0.5380.57
32_V39_K0.5340.56
11_E14_A0.5330.56
12_K52_D0.5290.56
60_K66_E0.5290.56
5_L46_L0.5230.55
17_I47_R0.5230.55
33_G39_K0.5220.55
26_E34_A0.5180.54
21_A65_R0.5110.53
44_K47_R0.5070.53
17_I24_H0.5000.52
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  
5aj3m 1 0.9565 32.3 0.794 Contact Map
4xhrN 1 0.9275 26.7 0.802 Contact Map
2l0yB 1 0.3043 18.3 0.817 Contact Map
1ei0A 1 0.5507 17.4 0.818 Contact Map
2lqtA 1 0.8406 7.3 0.847 Contact Map
4xizM 1 0.913 7.3 0.847 Contact Map
3cx5F 1 0.8551 6.3 0.852 Contact Map
1u96A 1 0.5072 5.6 0.855 Contact Map
2lqlA 1 0.7681 5 0.858 Contact Map
4d6tH 1 0.8551 3.7 0.867 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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