GREMLIN Database
IOJAP - Ribosomal silencing factor RsfS
UniProt: P54457 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 118 (106)
Sequences: 3242 (2028)
Seq/√Len: 197.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
14_C51_I2.9781.00
14_C19_A2.7871.00
99_N102_K2.4931.00
58_Q61_E2.3471.00
19_A40_C2.2871.00
22_I40_C2.1651.00
9_I62_N2.0761.00
42_G48_V2.0591.00
76_R94_E2.0371.00
54_E58_Q1.7991.00
59_A82_L1.7521.00
66_V82_L1.5761.00
27_M34_A1.5721.00
14_C55_I1.5401.00
76_R91_H1.5341.00
70_E79_L1.5031.00
7_L11_A1.4981.00
9_I13_A1.4851.00
14_C40_C1.4801.00
69_M80_V1.4351.00
15_D22_I1.4351.00
56_K69_M1.4051.00
25_L107_A1.3371.00
72_F78_V1.3351.00
52_A78_V1.3281.00
60_D65_Q1.3271.00
91_H94_E1.3251.00
10_A82_L1.3211.00
57_D61_E1.2941.00
11_A15_D1.2711.00
27_M31_S1.2641.00
6_I59_A1.2331.00
55_I87_V1.2291.00
39_I100_L1.2281.00
7_L38_L1.2231.00
96_S99_N1.2211.00
21_D41_H1.2101.00
10_A87_V1.2091.00
43_N47_Q1.2061.00
24_A38_L1.1981.00
10_A85_V1.1911.00
7_L36_Y1.1911.00
40_C89_V1.1841.00
6_I64_I1.1821.00
17_K54_E1.1791.00
23_L109_L1.1701.00
59_A64_I1.1631.00
67_K83_G1.1601.00
72_F75_A1.1511.00
48_V89_V1.1461.00
53_R72_F1.1331.00
48_V91_H1.1311.00
38_L85_V1.1141.00
20_E43_N1.1081.00
7_L24_A1.0931.00
19_A51_I1.0841.00
75_A78_V1.0771.00
51_I89_V1.0761.00
79_L86_V1.0561.00
49_Q72_F1.0531.00
47_Q50_A1.0511.00
49_Q75_A1.0401.00
10_A38_L1.0351.00
54_E57_D1.0261.00
11_A22_I1.0261.00
5_S8_K1.0231.00
13_A55_I1.0221.00
42_G51_I1.0191.00
24_A36_Y1.0071.00
13_A54_E1.0051.00
52_A89_V1.0021.00
44_S47_Q0.9871.00
11_A24_A0.9861.00
56_K80_V0.9861.00
58_Q62_N0.9780.99
41_H92_K0.9620.99
23_L101_E0.9410.99
6_I85_V0.9350.99
8_K11_A0.9320.99
30_I107_A0.9290.99
16_D54_E0.9190.99
20_E41_H0.9180.99
8_K12_A0.9130.99
13_A58_Q0.8830.99
7_L85_V0.8730.99
92_K96_S0.8700.99
28_E36_Y0.8660.99
34_A86_V0.8610.99
10_A59_A0.8510.99
43_N92_K0.8480.99
26_D108_P0.8450.98
45_D49_Q0.8380.98
48_V78_V0.8370.98
57_D60_D0.8330.98
38_L87_V0.8250.98
101_E104_W0.8030.98
48_V75_A0.7990.98
37_F88_H0.7750.97
20_E92_K0.7700.97
22_I38_L0.7600.97
17_K51_I0.7530.97
45_D91_H0.7440.97
5_S9_I0.7360.96
12_A16_D0.7320.96
59_A85_V0.7280.96
12_A58_Q0.7170.96
56_K72_F0.7150.96
26_D29_G0.7140.96
82_L87_V0.6820.95
9_I58_Q0.6670.94
16_D58_Q0.6610.94
56_K82_L0.6550.93
46_K49_Q0.6540.93
79_L97_Y0.6500.93
9_I12_A0.6490.93
52_A72_F0.6460.93
17_K37_F0.6440.93
35_D84_D0.6390.92
26_D110_A0.6370.92
17_K90_F0.6300.92
29_G108_P0.6300.92
33_V86_V0.6290.92
13_A17_K0.6250.92
25_L39_I0.6120.91
37_F86_V0.6120.91
39_I101_E0.6080.90
17_K50_A0.6020.90
47_Q51_I0.6000.90
17_K47_Q0.5990.90
76_R93_D0.5970.90
25_L105_G0.5970.90
11_A14_C0.5940.89
25_L37_F0.5940.89
33_V88_H0.5830.89
42_G89_V0.5790.88
41_H48_V0.5740.88
41_H46_K0.5730.88
40_C51_I0.5730.88
42_G47_Q0.5640.87
77_W81_D0.5640.87
34_A85_V0.5570.86
35_D70_E0.5570.86
34_A37_F0.5540.86
90_F101_E0.5530.86
25_L30_I0.5500.86
27_M32_L0.5490.85
102_K106_D0.5360.84
66_V69_M0.5360.84
64_I84_D0.5350.84
42_G91_H0.5270.83
41_H91_H0.5140.81
43_N90_F0.5140.81
21_D96_S0.5100.81
6_I10_A0.5080.81
32_L104_W0.5070.81
71_G78_V0.5060.80
9_I64_I0.5060.80
45_D76_R0.5000.80
18_R43_N0.5000.80
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  
2o5aA 2 0.9153 100 0.056 Contact Map
2id1A 1 1 100 0.075 Contact Map
4wcwA 2 0.9661 100 0.075 Contact Map
3upsA 2 0.9153 100 0.092 Contact Map
2qipA 2 0.7542 23.5 0.925 Contact Map
3w34A 2 0.5424 18.5 0.929 Contact Map
4oxxA 1 0.9322 18.4 0.929 Contact Map
1e5dA 2 0.9407 16.2 0.931 Contact Map
2wp4A 2 0.6102 14.6 0.932 Contact Map
2hnaA 1 0.9407 14.1 0.933 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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