GREMLIN Database
DUF2129 - Uncharacterized protein conserved in bacteria (DUF2129)
PFAM: PF09902 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 70 (70)
Sequences: 885 (592)
Seq/√Len: 70.8
META: 0.429

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
2_Q39_Q3.4391.00
38_N41_D3.3321.00
23_V33_V3.2291.00
7_W59_E3.0551.00
41_D44_E3.0381.00
62_Y65_E2.6301.00
46_I60_P2.3811.00
5_I34_V2.2811.00
8_L33_V2.1151.00
67_K70_F2.0841.00
46_I50_K2.0411.00
42_V46_I1.8811.00
27_S30_M1.7851.00
20_Y52_L1.5020.99
2_Q64_P1.4530.99
37_V45_T1.4230.98
9_Y56_K1.3900.98
8_L14_A1.3710.98
11_L33_V1.2900.97
13_Q16_Q1.2550.97
39_Q65_E1.2130.96
44_E47_K1.1700.95
8_L13_Q1.1650.95
4_L46_I1.1260.94
37_V42_V1.1240.94
40_D43_E1.1150.93
4_L37_V1.1140.93
10_S18_R1.0640.92
4_L42_V1.0540.91
34_V38_N1.0150.90
7_W22_N0.9990.89
44_E50_K0.9730.88
2_Q65_E0.9620.87
63_R68_T0.9570.87
3_G24_H0.9490.86
61_S66_I0.9400.86
3_G62_Y0.9330.85
10_S13_Q0.8900.83
4_L58_V0.8620.81
2_Q5_I0.8490.80
14_A26_V0.8460.79
8_L26_V0.8350.78
18_R23_V0.8330.78
25_Y31_K0.8210.77
20_Y44_E0.8130.77
45_T49_L0.8030.76
42_V45_T0.8000.75
4_L35_L0.7960.75
11_L26_V0.7840.74
12_K26_V0.7830.74
15_K52_L0.7820.74
12_K21_G0.7500.71
46_I49_L0.7500.71
28_K43_E0.7480.70
16_Q20_Y0.7250.68
9_Y70_F0.7140.67
25_Y39_Q0.7070.66
10_S51_K0.7010.65
46_I69_E0.6920.64
31_K49_L0.6860.64
3_G34_V0.6710.62
64_P68_T0.6700.62
33_V63_R0.6630.61
12_K15_K0.6500.60
25_Y30_M0.6490.59
28_K61_S0.6490.59
15_K31_K0.6410.58
14_A18_R0.6390.58
39_Q48_K0.6320.57
6_V58_V0.6250.57
20_Y45_T0.6240.56
44_E48_K0.6210.56
6_V35_L0.6190.56
39_Q42_V0.6150.55
7_W53_P0.6050.54
5_I52_L0.6000.54
18_R56_K0.5970.53
16_Q54_F0.5940.53
20_Y48_K0.5900.52
66_I70_F0.5880.52
40_D55_V0.5880.52
2_Q42_V0.5820.51
27_S54_F0.5730.50
1_R6_V0.5690.50
26_V29_K0.5680.50
47_K50_K0.5650.49
48_K51_K0.5650.49
39_Q64_P0.5640.49
11_L53_P0.5630.49
18_R64_P0.5610.49
10_S31_K0.5580.48
15_K59_E0.5570.48
21_G52_L0.5560.48
23_V50_K0.5470.47
9_Y67_K0.5440.47
22_N37_V0.5390.46
59_E62_Y0.5370.46
43_E58_V0.5340.45
11_L14_A0.5220.44
19_K25_Y0.5180.44
49_L52_L0.5150.43
4_L21_G0.5090.42
53_P66_I0.5030.42
6_V47_K0.5030.42
4_L48_K0.5000.41
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  
3wiuA 2 0.9429 22.8 0.875 Contact Map
3whiA 2 0.9429 16.6 0.882 Contact Map
2x4jA 3 0.5429 16.1 0.883 Contact Map
1r6vA 1 1 14.8 0.885 Contact Map
3afgA 1 1 14.8 0.885 Contact Map
1u0sA 1 0.9 12.4 0.888 Contact Map
1q5yA 4 0.9571 8.3 0.897 Contact Map
4n8nA 1 0.6286 8.1 0.898 Contact Map
2c5sA 2 0.9429 7.5 0.899 Contact Map
2hzaA 3 0.9286 6.3 0.902 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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