GREMLIN Database
RALF - Rapid ALkalinization Factor (RALF)
PFAM: PF05498 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 64 (62)
Sequences: 511 (310)
Seq/√Len: 39.3
META: 0.088

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
6_D10_S4.4221.00
33_C43_C2.6561.00
27_R30_R2.3051.00
5_M8_E2.2831.00
38_A45_P1.9620.99
41_Y60_T1.8330.98
5_M10_S1.7780.97
24_G27_R1.6750.96
28_R45_P1.6740.96
8_E11_R1.6180.95
37_G40_Y1.5940.95
38_A46_G1.4290.91
30_R36_R1.4100.91
54_R59_I1.3820.90
11_R14_L1.3700.90
35_R59_I1.3520.89
7_S10_S1.3310.88
25_A57_S1.3290.88
53_S63_R1.2780.86
26_L29_N1.2770.86
49_A55_G1.2570.85
29_N39_S1.2300.84
32_P41_Y1.2220.83
40_Y43_C1.2000.82
9_I15_A1.1820.81
15_A35_R1.1750.81
10_S49_A1.1200.78
60_T64_R1.0660.74
33_C40_Y1.0650.74
57_S64_R1.0520.73
19_R23_Y1.0250.71
22_S57_S1.0100.70
12_R43_C1.0020.69
21_I29_N0.9850.68
23_Y26_L0.9670.66
24_G30_R0.9630.66
4_E61_R0.9360.64
51_P54_R0.8940.60
22_S28_R0.8930.60
17_T21_I0.8860.60
17_T48_P0.8840.59
10_S18_R0.8620.57
18_R44_R0.8620.57
32_P60_T0.8610.57
41_Y52_Y0.8430.56
17_T30_R0.8290.54
25_A41_Y0.8220.54
33_C56_C0.8050.52
32_P42_N0.8040.52
43_C56_C0.7880.51
21_I26_L0.7710.49
23_Y32_P0.7670.49
42_N57_S0.7530.48
24_G34_S0.7440.47
23_Y40_Y0.7430.47
32_P52_Y0.7340.46
26_L37_G0.7330.46
4_E7_S0.7310.46
38_A47_A0.7240.45
22_S51_P0.7220.45
34_S42_N0.7180.44
50_N63_R0.7050.43
49_A64_R0.6950.42
10_S15_A0.6920.42
3_F47_A0.6740.40
13_I59_I0.6680.40
18_R58_A0.6620.39
48_P61_R0.6600.39
52_Y55_G0.6560.39
6_D9_I0.6450.38
37_G41_Y0.6440.38
31_V41_Y0.6400.38
15_A27_R0.6250.36
30_R38_A0.6250.36
41_Y59_I0.6240.36
32_P39_S0.6240.36
56_C62_C0.6210.36
50_N55_G0.6150.35
20_Y32_P0.6030.34
21_I58_A0.5830.33
23_Y31_V0.5820.33
19_R58_A0.5790.33
24_G36_R0.5750.32
22_S43_C0.5740.32
28_R52_Y0.5720.32
20_Y63_R0.5570.31
23_Y28_R0.5570.31
57_S60_T0.5550.31
19_R36_R0.5420.30
30_R44_R0.5270.28
30_R58_A0.5180.28
39_S43_C0.5080.27
39_S42_N0.5000.27
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  
2dunA 1 0.7344 3 0.913 Contact Map
3sqgC 1 0.8594 2 0.922 Contact Map
2e1zA 2 0.2656 1.8 0.923 Contact Map
2y9yB 1 0.2969 1.8 0.923 Contact Map
1e6yC 1 0.8594 1.7 0.924 Contact Map
1hbnC 1 0.8594 1.7 0.924 Contact Map
1e6vC 1 0.8594 1.7 0.925 Contact Map
1d8hA 2 0.3594 1.6 0.925 Contact Map
3u3zA 1 0.3438 1.4 0.928 Contact Map
3ef1A 1 0.3438 1.3 0.929 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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