GREMLIN Database
NDUF_B12 - NADH-ubiquinone oxidoreductase B12 subunit family
PFAM: PF08122 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 56 (54)
Sequences: 541 (402)
Seq/√Len: 54.7
META: 0.392

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
30_F34_F3.7021.00
2_D8_E2.8551.00
35_V39_V2.5841.00
41_V45_Y2.0651.00
43_Y47_F1.9721.00
34_F37_F1.8340.99
33_G38_A1.8020.99
28_P40_Y1.7090.99
38_A42_A1.6990.99
32_I36_A1.6890.99
43_Y48_L1.6320.99
33_G37_F1.6110.98
8_E11_R1.5050.97
17_S21_R1.4530.97
34_F38_A1.4380.97
41_V44_E1.4350.97
31_G35_V1.4200.96
37_F44_E1.3780.96
44_E47_F1.3600.95
52_H55_G1.3320.95
48_L51_K1.2830.94
51_K55_G1.2800.94
23_K26_F1.2230.92
42_A47_F1.1630.90
8_E13_H1.1280.88
19_W23_K1.0820.86
29_G33_G1.0220.83
38_A41_V0.9950.81
12_Y32_I0.9870.81
9_A16_F0.9490.78
39_V44_E0.9410.77
28_P37_F0.9350.77
49_K52_H0.9270.76
18_R22_F0.8850.73
16_F22_F0.8030.65
51_K54_H0.7820.63
28_P35_V0.7710.62
6_R12_Y0.7680.62
37_F40_Y0.7580.61
50_D55_G0.7570.61
7_N40_Y0.7480.60
15_P18_R0.7390.59
20_N25_A0.7360.59
16_F30_F0.7220.57
20_N23_K0.7160.56
7_N28_P0.7130.56
4_W7_N0.7050.55
5_A53_H0.7020.55
8_E12_Y0.7010.55
40_Y44_E0.6990.55
13_H55_G0.6870.53
47_F50_D0.6760.52
17_S20_N0.6720.52
39_V42_A0.6630.51
26_F51_K0.6520.50
1_R6_R0.6490.49
21_R25_A0.6290.47
18_R21_R0.6220.46
25_A51_K0.6220.46
50_D54_H0.6000.44
18_R48_L0.5970.44
50_D53_H0.5750.42
32_I35_V0.5730.41
6_R24_G0.5700.41
46_L49_K0.5660.41
37_F41_V0.5590.40
28_P34_F0.5570.40
30_F33_G0.5540.39
1_R7_N0.5520.39
12_Y21_R0.5500.39
5_A25_A0.5470.39
31_G52_H0.5450.38
20_N55_G0.5410.38
5_A37_F0.5360.38
21_R24_G0.5280.37
14_G26_F0.5270.37
17_S23_K0.5200.36
1_R18_R0.5120.35
18_R24_G0.5110.35
2_D29_G0.5090.35
20_N46_L0.5000.34
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  
3okzA 1 0.9643 33.6 0.843 Contact Map
4k6mA 2 0.375 24.5 0.853 Contact Map
1pc2A 1 0.9464 23.6 0.854 Contact Map
3e2vA 1 0.8393 19.8 0.859 Contact Map
2kxtA 1 0.8036 17.6 0.863 Contact Map
4tnwA 3 0.6786 17.2 0.863 Contact Map
3dh4A 3 0.6786 14.2 0.868 Contact Map
2jneA 1 0 13.6 0.869 Contact Map
3mi9A 1 0.6071 12.7 0.871 Contact Map
3tlkA 1 0.875 12.4 0.872 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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