GREMLIN Database
YOED - Uncharacterized protein YoeD
UniProt: O34555 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 76 (76)
Sequences: 109 (81)
Seq/√Len: 9.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
8_T39_I2.5150.82
15_S20_K2.5020.81
28_I39_I2.4560.80
26_G32_H2.3110.75
54_Y62_L2.2980.75
6_E16_E2.2180.72
42_E45_K2.0000.64
24_L32_H1.9600.62
57_L61_I1.9250.61
23_V35_E1.9110.60
18_Y27_K1.8340.57
5_I39_I1.8320.57
37_F47_H1.7750.54
3_L8_T1.7240.52
23_V30_A1.6800.50
37_F60_E1.4580.41
16_E25_E1.4380.40
19_I48_L1.4250.39
21_S32_H1.4100.38
19_I66_I1.4050.38
3_L39_I1.3990.38
3_L29_R1.3760.37
5_I32_H1.3360.35
54_Y58_V1.2850.33
31_V66_I1.2680.33
41_K49_E1.2470.32
3_L41_K1.1920.30
48_L51_L1.1910.30
14_L18_Y1.1570.29
35_E51_L1.1440.28
36_Q49_E1.1400.28
23_V42_E1.1170.27
11_Y27_K1.1160.27
58_V61_I1.1130.27
5_I35_E1.0750.26
10_E53_N1.0500.25
29_R46_T1.0280.24
32_H36_Q1.0250.24
6_E23_V1.0160.24
11_Y64_E1.0030.23
53_N64_E0.9870.23
54_Y57_L0.9710.22
19_I46_T0.9610.22
8_T26_G0.9550.22
32_H56_A0.9300.21
41_K53_N0.9150.21
41_K47_H0.9120.21
18_Y31_V0.9090.21
40_Y58_V0.9050.20
30_A37_F0.9010.20
3_L53_N0.8860.20
14_L70_I0.8840.20
14_L49_E0.8740.20
59_Q62_L0.8600.19
51_L61_I0.8520.19
14_L19_I0.8470.19
33_D69_D0.8430.19
15_S27_K0.8390.19
3_L42_E0.8170.18
22_L68_E0.7950.17
4_T15_S0.7930.17
57_L63_N0.7920.17
55_K59_Q0.7890.17
14_L51_L0.7770.17
4_T11_Y0.7720.17
13_N21_S0.7710.17
5_I21_S0.7580.16
9_A29_R0.7490.16
13_N61_I0.7490.16
31_V53_N0.7450.16
35_E40_Y0.7310.16
49_E61_I0.7300.16
45_K53_N0.7270.16
36_Q69_D0.7170.16
22_L54_Y0.7110.15
16_E68_E0.7080.15
18_Y70_I0.7050.15
26_G61_I0.7020.15
10_E54_Y0.7020.15
6_E13_N0.6900.15
12_T37_F0.6830.15
51_L57_L0.6730.15
45_K56_A0.6700.14
39_I72_V0.6550.14
20_K31_V0.6550.14
57_L60_E0.6460.14
18_Y49_E0.6300.14
63_N68_E0.6300.14
1_M52_E0.6160.13
14_L32_H0.6140.13
8_T59_Q0.6130.13
16_E56_A0.6130.13
26_G49_E0.6070.13
54_Y61_I0.5990.13
11_Y60_E0.5960.13
8_T52_E0.5920.13
63_N72_V0.5820.13
55_K63_N0.5800.13
46_T58_V0.5780.13
24_L42_E0.5750.13
32_H37_F0.5650.12
10_E64_E0.5640.12
6_E42_E0.5580.12
15_S25_E0.5530.12
17_D55_K0.5510.12
3_L64_E0.5510.12
25_E35_E0.5500.12
41_K45_K0.5420.12
47_H61_I0.5400.12
11_Y40_Y0.5350.12
6_E45_K0.5290.12
30_A73_K0.5210.11
6_E26_G0.5140.11
22_L72_V0.5000.11
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  
1y6uA 1 0.6711 98.1 0.764 Contact Map
2og0A 1 0.6184 98.1 0.768 Contact Map
2kfsA 1 0.9868 96.8 0.818 Contact Map
4j2nA 4 0.6711 96.4 0.824 Contact Map
1z4hA 1 0.75 94.7 0.845 Contact Map
1j9iA 2 0.7763 94.7 0.846 Contact Map
4ua1A 2 0.8421 88.7 0.87 Contact Map
2jmlA 1 0.8553 88.6 0.87 Contact Map
1r8dA 2 0.9474 88.3 0.871 Contact Map
1pm6A 1 0.8684 86.7 0.874 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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