GREMLIN Database
YBAM - Uncharacterized protein YbaM
UniProt: P45807 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12830
Length: 53 (48)
Sequences: 110 (62)
Seq/√Len: 8.9

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_V22_E3.5760.96
35_D38_K3.4410.95
8_D11_K2.3710.76
9_D32_R2.2610.72
30_V41_Y1.8740.57
28_S32_R1.8330.55
43_K46_T1.7270.51
25_I30_V1.5640.44
8_D29_T1.5570.43
27_A45_L1.5450.43
1_M39_R1.3030.33
11_K30_V1.2470.31
2_S31_L1.1900.29
18_V35_D1.1770.28
18_V30_V1.1480.27
8_D42_E1.1430.27
22_E42_E1.0640.25
23_N41_Y1.0360.24
39_R42_E1.0210.23
9_D25_I1.0180.23
43_K47_R1.0150.23
18_V23_N1.0050.23
5_N28_S0.9430.21
10_V30_V0.9420.21
10_V41_Y0.9380.21
32_R42_E0.9300.21
7_P28_S0.9070.20
38_K47_R0.8940.20
22_E29_T0.8930.19
8_D23_N0.8720.19
9_D29_T0.8650.19
6_A42_E0.8610.19
1_M10_V0.8560.19
38_K42_E0.8510.18
7_P41_Y0.8440.18
39_R43_K0.8300.18
39_R46_T0.8200.18
35_D46_T0.8020.17
39_R48_D0.7990.17
18_V38_K0.7970.17
24_Q48_D0.7960.17
25_I35_D0.7950.17
28_S48_D0.7940.17
26_P41_Y0.7920.17
10_V31_L0.7840.17
22_E30_V0.7800.17
25_I46_T0.7470.16
5_N35_D0.7420.16
32_R43_K0.7380.16
18_V27_A0.7200.15
9_D36_I0.7140.15
24_Q28_S0.6930.15
25_I37_V0.6930.15
18_V24_Q0.6840.14
5_N42_E0.6800.14
25_I45_L0.6750.14
3_L10_V0.6720.14
43_K48_D0.6670.14
42_E45_L0.6640.14
11_K18_V0.6410.14
24_Q42_E0.6110.13
7_P10_V0.6090.13
7_P42_E0.6090.13
23_N47_R0.6010.13
27_A38_K0.5840.12
8_D39_R0.5820.12
2_S10_V0.5640.12
2_S39_R0.5500.12
20_L45_L0.5340.12
6_A37_V0.5150.11
29_T48_D0.5040.11
27_A31_L0.5000.11
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  
2mmpA 1 0.5094 25.6 0.869 Contact Map
2j7nA 2 1 9.2 0.893 Contact Map
4pxjA 2 0.5849 8.4 0.895 Contact Map
1tlqA 4 0.8868 8 0.896 Contact Map
4bndA 2 0.4151 6.4 0.901 Contact Map
3g7pA 2 0.3585 6.1 0.902 Contact Map
2a1dD 1 0.3396 6.1 0.902 Contact Map
1nu7D 1 0.3585 5.9 0.902 Contact Map
2zu6B 1 1 5.6 0.903 Contact Map
2ionA 1 1 5.5 0.904 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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