GREMLIN Database
RNP4 - Ribonuclease P protein component 4
UniProt: Q9HRP7 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 93 (75)
Sequences: 9323 (7912)
Seq/√Len: 913.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
57_D82_D3.9421.00
80_T86_H2.8001.00
27_R30_E2.5361.00
65_G90_P2.5181.00
54_T80_T2.2351.00
61_V86_H2.0251.00
59_D84_G1.9291.00
60_A85_T1.9051.00
80_T84_G1.8801.00
57_D70_V1.8251.00
64_P67_N1.8061.00
17_R20_A1.6941.00
55_C69_R1.6791.00
54_T61_V1.6771.00
64_P89_Y1.6261.00
24_D27_R1.5551.00
58_C73_R1.5221.00
62_L85_T1.4941.00
63_V88_R1.4811.00
56_D70_V1.4801.00
62_L87_A1.4361.00
44_L70_V1.4251.00
63_V67_N1.3601.00
60_A87_A1.3251.00
75_G88_R1.3101.00
69_R73_R1.2491.00
25_D30_E1.2001.00
21_R24_D1.1801.00
30_E34_L1.1751.00
19_A25_D1.1401.00
23_G27_R1.1241.00
18_A21_R1.0991.00
83_C87_A1.0701.00
27_R34_L1.0561.00
37_R41_R1.0501.00
19_A22_T1.0321.00
36_R39_A0.9961.00
18_A24_D0.9891.00
54_T59_D0.9831.00
79_V90_P0.9621.00
26_D33_R0.9541.00
58_C69_R0.9411.00
77_V88_R0.9321.00
20_A24_D0.9281.00
79_V83_C0.9101.00
66_R91_Y0.8991.00
71_R76_H0.8951.00
21_R25_D0.8901.00
17_R24_D0.8791.00
19_A24_D0.8731.00
72_T88_R0.8721.00
40_E43_R0.8691.00
51_R77_V0.8531.00
81_C87_A0.8501.00
79_V86_H0.8301.00
18_A22_T0.8291.00
22_T25_D0.7941.00
25_D28_A0.7761.00
34_L41_R0.7461.00
33_R41_R0.7451.00
17_R21_R0.7441.00
72_T77_V0.7431.00
27_R43_R0.7351.00
75_G78_V0.7321.00
28_A43_R0.7241.00
39_A42_N0.7211.00
23_G26_D0.7191.00
72_T76_H0.7151.00
19_A28_A0.7061.00
55_C73_R0.7041.00
74_S78_V0.7001.00
35_A39_A0.6941.00
30_E40_E0.6921.00
78_V86_H0.6901.00
27_R33_R0.6501.00
19_A23_G0.6481.00
58_C62_L0.6481.00
18_A26_D0.6311.00
28_A56_D0.6301.00
18_A28_A0.6231.00
60_A74_S0.6161.00
21_R27_R0.6141.00
34_L38_L0.6101.00
24_D34_L0.6081.00
27_R40_E0.6071.00
41_R44_L0.6071.00
74_S77_V0.6041.00
26_D29_R0.6041.00
31_Y34_L0.6001.00
55_C58_C0.5991.00
71_R78_V0.5971.00
19_A27_R0.5961.00
71_R75_G0.5871.00
26_D31_Y0.5841.00
21_R26_D0.5811.00
25_D37_R0.5751.00
49_A52_R0.5711.00
43_R47_P0.5701.00
62_L69_R0.5521.00
29_R44_L0.5521.00
33_R36_R0.5421.00
72_T75_G0.5381.00
32_V35_A0.5371.00
36_R40_E0.5341.00
39_A43_R0.5281.00
34_L39_A0.5251.00
25_D34_L0.5231.00
20_A25_D0.5221.00
30_E37_R0.5201.00
34_L40_E0.5141.00
49_A63_V0.5041.00
32_V37_R0.5001.00
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  
3w5kB 1 0.871 99.1 0.413 Contact Map
4r2qA 1 0.7849 98.9 0.44 Contact Map
2dmdA 1 0.828 98.9 0.449 Contact Map
2ee8A 1 0.9247 98.9 0.452 Contact Map
2kmkA 1 0.7527 98.9 0.454 Contact Map
1tf6A 1 0.8065 98.9 0.456 Contact Map
4x9jA 1 0.7742 98.9 0.458 Contact Map
1ej6B 7 0.8387 98.8 0.465 Contact Map
2cshA 1 0.8387 98.8 0.465 Contact Map
2m9aA 1 0.7849 98.8 0.466 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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