GREMLIN Database
RNP4 - Ribonuclease P protein component 4
UniProt: Q97WJ1 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 106 (84)
Sequences: 3028 (2638)
Seq/√Len: 287.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
59_K85_I3.5821.00
58_R84_L3.1961.00
29_L32_E2.7621.00
60_C75_R2.0371.00
17_L20_N2.0321.00
67_G93_V2.0131.00
85_I94_L1.9671.00
92_Y95_S1.9581.00
60_C71_R1.9561.00
63_P89_Q1.8611.00
83_C86_C1.8451.00
56_F82_T1.7931.00
28_E31_R1.7931.00
59_K72_R1.6651.00
57_C60_C1.6431.00
61_Y87_N1.6101.00
82_T87_N1.5901.00
91_R95_S1.5861.00
71_R75_R1.5791.00
57_C71_R1.5751.00
15_I18_A1.5701.00
29_L33_Y1.5371.00
17_L21_T1.4401.00
82_T89_Q1.4371.00
62_T90_R1.4331.00
69_T97_N1.4221.00
57_C75_R1.3721.00
55_M60_C1.2761.00
45_K49_P1.2201.00
58_R72_R1.2191.00
60_C64_L1.2101.00
14_L17_L1.1921.00
86_C90_R1.1531.00
93_V97_N1.1491.00
57_C64_L1.1421.00
76_S79_L1.1221.00
82_T85_I1.1001.00
18_A21_T1.0451.00
21_T27_L1.0431.00
73_R80_I1.0321.00
27_L30_A1.0231.00
69_T72_R1.0151.00
36_L42_R0.9871.00
23_K29_L0.9831.00
14_L18_A0.9811.00
18_A23_K0.9771.00
77_K80_I0.9641.00
22_A25_G0.9611.00
42_R46_V0.9291.00
86_C96_G0.9211.00
15_I19_Y0.8831.00
14_L25_G0.8751.00
15_I20_N0.8691.00
15_I21_T0.8651.00
32_E35_K0.8641.00
30_A35_K0.8591.00
83_C90_R0.8521.00
16_E20_N0.8511.00
81_R93_V0.8501.00
16_E21_T0.8471.00
54_R65_I0.8401.00
73_R78_I0.8371.00
32_E42_R0.8341.00
25_G28_E0.8341.00
25_G34_V0.8191.00
42_R45_K0.8020.99
19_Y22_A0.7970.99
56_F63_P0.7880.99
79_L88_W0.7750.99
18_A24_S0.7730.99
15_I22_A0.7690.99
35_K38_E0.7540.99
24_S31_R0.7500.99
36_L40_Y0.7480.99
22_A28_E0.7450.99
27_L37_A0.7320.99
84_L89_Q0.7270.99
17_L22_A0.7170.99
29_L38_E0.7040.99
33_Y36_L0.7040.99
62_T76_S0.7000.99
18_A22_A0.6980.99
62_T71_R0.6960.98
73_R77_K0.6910.98
19_Y27_L0.6690.98
28_E32_E0.6680.98
74_M91_R0.6660.98
72_R82_T0.6630.98
79_L95_S0.6610.98
91_R94_L0.6420.97
20_N25_G0.6300.97
24_S27_L0.6290.97
46_V49_P0.6190.97
37_A42_R0.6140.97
66_I95_S0.6030.96
37_A43_K0.5970.96
66_I70_E0.5900.96
64_L75_R0.5880.96
26_N29_L0.5860.96
16_E49_P0.5850.96
94_L97_N0.5820.95
62_T88_W0.5820.95
30_A33_Y0.5740.95
16_E25_G0.5720.95
67_G77_K0.5700.95
26_N31_R0.5680.95
39_M43_K0.5670.95
36_L44_G0.5630.95
30_A36_L0.5610.95
64_L88_W0.5600.94
78_I90_R0.5600.94
18_A27_L0.5570.94
46_V61_Y0.5530.94
20_N27_L0.5500.94
89_Q92_Y0.5490.94
32_E36_L0.5490.94
71_R76_S0.5490.94
20_N23_K0.5360.93
76_S81_R0.5290.93
23_K37_A0.5270.93
29_L43_K0.5230.92
43_K47_E0.5190.92
76_S80_I0.5170.92
26_N36_L0.5130.91
56_F59_K0.5120.91
72_R85_I0.5000.90
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  
2kmkA 1 0.7547 99.2 0.417 Contact Map
4x9jA 1 0.7736 99.2 0.422 Contact Map
2ee8A 1 0.9151 99.2 0.422 Contact Map
2dmdA 1 0.8302 99.2 0.424 Contact Map
3w5kB 1 0.8868 99.2 0.426 Contact Map
2m9aA 1 0.7925 99.2 0.432 Contact Map
1x6hA 1 0.6321 99.2 0.434 Contact Map
2lv2A 1 0.7547 99.2 0.434 Contact Map
2ctdA 1 0.8019 99.2 0.435 Contact Map
2n25A 1 0.2736 99.2 0.441 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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