GREMLIN Database
CYOD - Cytochrome bo(3) ubiquinol oxidase subunit 4
UniProt: P0ABJ6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10181
Length: 109 (102)
Sequences: 732 (512)
Seq/√Len: 50.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
15_V19_M3.6691.00
32_P50_I2.7661.00
83_F87_I2.7651.00
25_S61_H2.4971.00
32_P53_M2.2821.00
41_A45_V2.0731.00
41_A46_I2.0071.00
90_I94_G1.9841.00
51_L95_S1.9310.99
58_V61_H1.9260.99
13_G17_T1.9170.99
23_I27_I1.8410.99
19_M23_I1.8400.99
60_V106_M1.8090.99
101_N105_N1.7800.99
34_W38_T1.7300.99
9_G72_S1.7220.99
87_I91_L1.7130.99
102_L105_N1.7040.99
35_M41_A1.6520.98
71_K74_E1.5650.97
94_G102_L1.5470.97
90_I93_V1.5220.97
45_V49_T1.5000.97
17_T64_C1.5000.97
61_H80_A1.4740.96
85_V89_A1.4610.96
34_W74_E1.3770.95
71_K75_G1.3030.93
96_I99_M1.3000.93
33_F66_L1.2970.93
48_G52_A1.2740.92
42_S45_V1.2680.92
94_G99_M1.2460.91
27_I31_I1.2430.91
71_K78_M1.2410.91
78_M86_L1.2310.91
75_G101_N1.2170.90
42_S48_G1.2090.90
94_G101_N1.2030.90
95_S103_N1.2000.89
51_L96_I1.1970.89
76_W90_I1.1960.89
62_L98_I1.1850.89
26_I30_V1.1680.88
23_I68_M1.1590.88
88_I92_V1.1180.86
61_H66_L1.1090.85
11_S17_T1.1010.85
62_L68_M1.0840.84
55_V58_V1.0820.84
82_V85_V1.0450.82
54_A98_I1.0260.81
35_M46_I1.0130.80
99_M102_L1.0120.80
62_L81_F1.0110.80
93_V100_W0.9900.78
91_L95_S0.9730.77
27_I56_V0.9710.77
88_I105_N0.9430.75
46_I50_I0.9360.74
47_L86_L0.9230.73
72_S76_W0.8940.71
31_I53_M0.8750.69
55_V59_L0.8680.68
34_W96_I0.8640.68
83_F90_I0.8630.68
89_A104_Y0.8610.68
24_L84_T0.8600.68
75_G78_M0.8540.67
72_S77_N0.8470.66
51_L92_V0.8430.66
55_V92_V0.8260.64
66_L106_M0.8080.63
69_N72_S0.8030.62
38_T54_A0.8020.62
10_A13_G0.7980.62
97_W103_N0.7970.62
79_T91_L0.7960.62
49_T53_M0.7950.61
36_V39_G0.7910.61
78_M99_M0.7830.60
59_L81_F0.7640.58
35_M40_A0.7600.58
76_W99_M0.7590.58
12_H16_K0.7550.57
87_I90_I0.7480.57
10_A16_K0.7400.56
39_G51_L0.7370.56
49_T54_A0.7320.55
10_A50_I0.7230.54
56_V59_L0.7220.54
39_G97_W0.7220.54
61_H91_L0.7220.54
95_S98_I0.7120.53
17_T27_I0.7080.53
75_G88_I0.7030.52
87_I96_I0.7030.52
96_I100_W0.6950.51
75_G80_A0.6900.51
26_I47_L0.6880.51
88_I102_L0.6870.51
98_I102_L0.6780.50
31_I97_W0.6770.49
22_F64_C0.6750.49
12_H29_T0.6650.48
49_T104_Y0.6640.48
15_V47_L0.6550.47
99_M104_Y0.6510.47
44_A48_G0.6440.46
6_D10_A0.6430.46
79_T87_I0.6420.46
90_I102_L0.6420.46
74_E78_M0.6380.45
25_S54_A0.6350.45
15_V86_L0.6310.45
7_H11_S0.6260.44
13_G25_S0.6250.44
83_F102_L0.6230.44
76_W105_N0.6170.43
100_W104_Y0.6150.43
23_I48_G0.6140.43
63_V105_N0.6110.43
43_P62_L0.6070.42
27_I72_S0.6040.42
34_W40_A0.5990.42
16_K31_I0.5930.41
35_M53_M0.5860.40
51_L77_N0.5820.40
63_V99_M0.5770.39
52_A55_V0.5690.39
17_T43_P0.5680.38
7_H10_A0.5680.38
26_I55_V0.5550.37
101_N104_Y0.5530.37
44_A51_L0.5510.37
32_P97_W0.5480.37
37_M98_I0.5460.36
32_P61_H0.5380.36
42_S69_N0.5370.35
29_T57_Q0.5350.35
14_S85_V0.5340.35
43_P50_I0.5320.35
19_M83_F0.5270.35
6_D11_S0.5260.34
70_T85_V0.5160.34
22_F68_M0.5150.33
81_F84_T0.5140.33
73_D88_I0.5120.33
50_I95_S0.5110.33
86_L89_A0.5010.32
6_D86_L0.5010.32
94_G98_I0.5000.32
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  
2ksrA 1 0.8349 11.9 0.935 Contact Map
2bg9A 1 0.8899 10.9 0.936 Contact Map
4g1uA 2 0.4587 5 0.945 Contact Map
4njnA 4 0.5413 4.2 0.947 Contact Map
2oarA 7 0.789 3.8 0.948 Contact Map
4xtrG 1 0.1927 3.6 0.949 Contact Map
3rlbA 1 0.8532 3.5 0.949 Contact Map
4od4A 1 0.8073 3.3 0.95 Contact Map
2lx0A 1 0.2936 3 0.951 Contact Map
4aq5A 1 0.5413 2.8 0.952 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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