GREMLIN Database
RL28 - 50S ribosomal protein L28
UniProt: P37807 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 62 (61)
Sequences: 653 (286)
Seq/√Len: 36.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_I47_V3.4661.00
18_R24_A2.8751.00
16_N26_K2.6501.00
8_T53_A2.3120.99
33_L48_Y2.3110.99
50_S53_A2.2710.99
8_T50_S2.2500.99
12_T28_T2.1970.99
52_R55_K2.1970.99
18_R22_M2.0900.99
6_V48_Y2.0790.99
14_A26_K1.9140.98
35_K46_K1.5480.93
4_K11_K1.5300.93
17_N25_S1.4920.92
25_S34_Q1.4700.91
39_L44_P1.4310.90
12_T30_G1.3790.88
6_V47_V1.3010.85
10_K31_A1.2480.82
34_Q51_A1.1690.78
49_V54_L1.1490.77
16_N22_M1.1200.75
12_T31_A1.1160.75
19_S23_N1.1080.74
23_N26_K1.0980.73
16_N24_A1.0400.69
35_K48_Y1.0170.67
39_L43_K0.9990.66
56_S59_V0.9960.66
40_V44_P0.9770.64
34_Q46_K0.9580.63
40_V43_K0.9360.61
36_V39_L0.9260.60
17_N23_N0.9180.59
19_S22_M0.9090.59
20_H23_N0.9080.59
3_R30_G0.8970.58
11_K26_K0.8690.55
33_L61_R0.8130.50
37_R46_K0.8030.49
9_G34_Q0.7980.49
9_G51_A0.7970.49
6_V33_L0.7930.49
4_K54_L0.7800.47
19_S25_S0.7530.45
38_I49_V0.7460.44
36_V54_L0.7060.41
52_R56_S0.6860.39
39_L49_V0.6800.39
36_V58_K0.6780.39
12_T60_E0.6710.38
37_R49_V0.6700.38
4_K9_G0.6530.37
2_A48_Y0.6490.36
4_K48_Y0.6480.36
7_I47_V0.6470.36
20_H25_S0.6380.35
7_I10_K0.6330.35
7_I55_K0.6320.35
25_S60_E0.6310.35
6_V38_I0.6250.34
17_N21_A0.6070.33
2_A38_I0.6000.32
35_K44_P0.5990.32
34_Q54_L0.5920.32
10_K53_A0.5880.31
1_M4_K0.5880.31
19_S24_A0.5860.31
9_G14_A0.5850.31
27_R30_G0.5850.31
31_A35_K0.5760.31
13_T25_S0.5750.31
54_L61_R0.5740.30
49_V57_G0.5700.30
6_V31_A0.5680.30
8_T51_A0.5640.30
12_T34_Q0.5610.29
17_N29_W0.5570.29
36_V57_G0.5550.29
45_K58_K0.5540.29
35_K58_K0.5470.28
29_W43_K0.5470.28
44_P56_S0.5440.28
7_I35_K0.5350.28
21_A33_L0.5240.27
46_K60_E0.5230.27
3_R9_G0.5190.27
15_G29_W0.5110.26
2_A47_V0.5100.26
2_A12_T0.5070.26
28_T36_V0.5000.25
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  
2jz6A 1 1 99.9 0.182 Contact Map
2zjrU 1 0.8871 99.9 0.242 Contact Map
4rb61 1 0.9839 99.9 0.25 Contact Map
3bboY 1 0.9677 99.9 0.287 Contact Map
4tp9X 1 0.9839 99.8 0.306 Contact Map
1vw4S 1 1 99.8 0.361 Contact Map
3j7yX 1 0.9839 99.8 0.368 Contact Map
1w4rA 3 0.6935 46.5 0.88 Contact Map
2orvA 3 0.6935 38.4 0.886 Contact Map
2orwA 3 0.7419 28.2 0.893 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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