GREMLIN Database
RL35 - 50S ribosomal protein L35
UniProt: P55874 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 66 (63)
Sequences: 1209 (575)
Seq/√Len: 72.4

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_R11_A3.7641.00
32_L35_N3.1871.00
10_S14_F2.3801.00
54_D57_R2.2391.00
29_T45_R2.1371.00
16_K22_L1.8361.00
26_H48_A1.7561.00
51_S54_D1.7171.00
39_K43_K1.6250.99
4_M63_A1.5810.99
7_H61_M1.5180.99
22_L58_I1.5130.99
50_V58_I1.3980.98
23_K49_V1.3750.98
21_K49_V1.3700.98
15_K23_K1.3060.97
37_S41_K1.2180.96
16_K59_K1.2170.96
58_I61_M1.1850.96
27_A54_D1.1830.95
25_S45_R1.1580.95
55_F59_K1.1490.95
10_S61_M1.1330.94
17_T49_V1.1260.94
26_H29_T1.1090.94
6_T11_A1.1070.94
52_A55_F1.1070.94
23_K47_S1.0850.93
38_Q41_K1.0670.92
17_T21_K1.0630.92
22_L59_K1.0620.92
40_Q44_L1.0610.92
25_S29_T1.0500.92
25_S30_S1.0390.91
9_G34_A1.0190.90
28_Y40_Q1.0100.90
22_L62_L0.9880.89
32_L40_Q0.9660.88
35_N40_Q0.9500.87
17_T23_K0.9490.87
37_S40_Q0.9450.87
18_G49_V0.9420.87
24_R50_V0.9420.87
42_R45_R0.9280.86
57_R60_Q0.8740.82
34_A38_Q0.8660.82
24_R27_A0.8580.81
57_R61_M0.8490.80
24_R48_A0.8300.79
4_M41_K0.8090.77
53_G56_K0.7950.76
10_S33_F0.7930.76
29_T33_F0.7800.74
30_S40_Q0.7690.73
19_S49_V0.7680.73
33_F41_K0.7660.73
7_H34_A0.7660.73
7_H10_S0.7640.73
22_L50_V0.7490.71
34_A40_Q0.7470.71
30_S43_K0.7470.71
6_T62_L0.7420.71
42_R46_K0.7370.70
26_H46_K0.7350.70
22_L55_F0.7140.68
18_G21_K0.7030.66
37_S43_K0.7020.66
4_M8_R0.6640.62
43_K46_K0.6630.62
32_L39_K0.6480.60
56_K60_Q0.6400.59
38_Q45_R0.6370.59
21_K57_R0.6330.58
26_H43_K0.6280.58
24_R46_K0.6240.57
51_S60_Q0.6210.57
22_L63_A0.6160.56
51_S55_F0.6130.56
18_G22_L0.5860.53
52_A56_K0.5730.51
52_A63_A0.5570.49
35_N38_Q0.5560.49
26_H44_L0.5550.49
33_F40_Q0.5540.49
36_K63_A0.5510.48
45_R63_A0.5510.48
33_F63_A0.5490.48
38_Q44_L0.5440.48
2_P33_F0.5360.47
6_T13_R0.5250.45
15_K41_K0.5220.45
8_R38_Q0.5160.44
44_L61_M0.5130.44
11_A16_K0.5000.42
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  
3bbo5 1 0.9394 99.9 0.102 Contact Map
2zjr3 1 0.9545 99.9 0.104 Contact Map
4rb68 1 0.9697 99.9 0.109 Contact Map
1vw4Z 1 0.9394 99.9 0.137 Contact Map
4tp93 1 0.9697 99.9 0.145 Contact Map
3j7y3 1 1 99.9 0.174 Contact Map
3ivrA 2 0 4.6 0.92 Contact Map
4xbaA 2 0.3182 4 0.923 Contact Map
3rixA 1 0 3.4 0.925 Contact Map
4o30A 1 0.1364 3.4 0.925 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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