GREMLIN Database
RNA_bind_2 - Predicted RNA-binding protein
PFAM: PF10133 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 61 (59)
Sequences: 4862 (3079)
Seq/√Len: 400.9
META: 0.949

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_D40_E2.6441.00
17_L20_E2.3861.00
31_G43_E2.2551.00
32_V60_L2.0831.00
26_E33_R1.8791.00
31_G45_K1.8511.00
5_N17_L1.7961.00
52_D55_D1.6991.00
28_E33_R1.6941.00
7_Y17_L1.6631.00
5_N20_E1.6371.00
6_V34_L1.6191.00
10_K16_E1.6161.00
26_E50_E1.5721.00
24_R35_V1.5021.00
33_R41_Q1.4661.00
3_E23_D1.4321.00
4_A56_H1.4291.00
24_R50_E1.4051.00
46_G60_L1.4011.00
33_R43_E1.3661.00
4_A53_L1.3601.00
30_D45_K1.3161.00
25_I58_I1.2631.00
14_E57_K1.2431.00
28_E31_G1.2111.00
3_E56_H1.1981.00
19_M42_K1.1641.00
25_I53_L1.1581.00
27_P32_V1.1051.00
48_I51_I1.0641.00
25_I48_I1.0451.00
35_V41_Q1.0341.00
18_I44_V1.0181.00
4_A58_I1.0091.00
10_K13_K0.9701.00
23_D54_V0.9311.00
19_M22_V0.9121.00
8_L18_I0.9011.00
9_L59_I0.8841.00
53_L58_I0.8811.00
53_L56_H0.8701.00
22_V34_L0.8641.00
36_D39_G0.8571.00
13_K16_E0.8321.00
23_D37_I0.7951.00
50_E59_I0.7801.00
28_E43_E0.7781.00
51_I56_H0.7601.00
8_L60_L0.7571.00
6_V22_V0.7501.00
32_V46_G0.7481.00
9_L14_E0.7361.00
9_L12_G0.7171.00
21_D56_H0.7091.00
48_I60_L0.7001.00
34_L44_V0.6810.99
3_E57_K0.6270.99
21_D37_I0.6260.99
9_L49_K0.6200.99
3_E21_D0.6140.99
48_I58_I0.6100.99
21_D52_D0.6080.99
8_L16_E0.6050.99
24_R52_D0.5950.99
4_A46_G0.5940.99
25_I32_V0.5940.99
48_I52_D0.5900.99
27_P48_I0.5830.98
4_A7_Y0.5790.98
20_E38_F0.5770.98
19_M34_L0.5750.98
49_K59_I0.5740.98
23_D52_D0.5730.98
37_I41_Q0.5710.98
14_E17_L0.5640.98
27_P31_G0.5570.98
19_M36_D0.5550.98
3_E36_D0.5530.98
50_E57_K0.5440.98
26_E35_V0.5280.97
3_E39_G0.5260.97
6_V60_L0.5210.97
21_D38_F0.5190.97
1_M52_D0.5100.96
3_E37_I0.5100.96
32_V48_I0.5010.96
4_A21_D0.5000.96
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  
2l55A 1 0.3443 9.8 0.848 Contact Map
1b25A 3 0.3443 5.7 0.863 Contact Map
1aorA 2 0.3443 5.4 0.865 Contact Map
2pc6A 2 0.918 4.1 0.872 Contact Map
2f1fA 4 0.918 3.9 0.874 Contact Map
4z3xA 2 0.3607 3.3 0.879 Contact Map
2qcpX 1 0.4426 3.1 0.879 Contact Map
3j3wU 1 0.5902 2.9 0.882 Contact Map
3be6A 2 0.541 2.7 0.883 Contact Map
2ra2A 3 0.9016 2.5 0.885 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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