GREMLIN Database
NEP1 - Ribosomal RNA small subunit methyltransferase Nep1
UniProt: Q97WJ0 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 218 (189)
Sequences: 374 (248)
Seq/√Len: 18.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
106_R109_G5.0331.00
68_A204_L4.5261.00
45_L105_L4.2121.00
77_V212_N3.5361.00
69_L82_I3.1890.99
75_D78_I3.1630.99
74_T102_K3.0380.99
136_L139_I3.0150.99
40_L108_I2.9910.99
174_F179_F2.9710.99
84_I94_V2.6480.97
119_K127_T2.5280.97
105_L108_I2.2790.94
38_D116_K2.2210.93
73_L78_I2.1960.92
173_A176_H2.1930.92
172_G177_G2.0340.89
104_Y108_I1.9720.88
83_F142_R1.9650.87
144_D189_K1.8740.85
32_R49_A1.8080.83
84_I92_I1.7770.81
74_T199_E1.7610.81
194_S198_L1.7170.79
159_E165_E1.7070.79
68_A72_I1.6830.78
94_V129_M1.6800.78
65_L82_I1.6690.77
84_I100_P1.6270.75
49_A60_G1.6220.75
178_D190_I1.5820.73
96_P200_T1.5260.70
194_S206_R1.5120.69
160_I188_K1.5060.69
204_L208_F1.4760.68
129_M217_W1.4440.66
37_E40_L1.4290.65
134_L145_L1.4240.65
58_K120_I1.4220.65
193_I198_L1.4130.64
104_Y127_T1.3990.63
29_A34_K1.3950.63
102_K106_R1.3830.62
206_R213_S1.3730.62
89_S143_Y1.3500.60
41_L62_P1.3460.60
42_D45_L1.3350.60
67_Q201_Q1.3260.59
70_L74_T1.3170.58
146_I156_N1.3140.58
29_A32_R1.3100.58
52_Y111_M1.2960.57
52_Y116_K1.2920.57
30_K33_N1.2900.57
73_L94_V1.2740.56
29_A33_N1.2700.56
144_D165_E1.2680.56
63_D66_H1.2380.54
93_K132_T1.2330.53
78_I201_Q1.2150.52
68_A200_T1.2070.52
83_F91_I1.1980.51
76_P206_R1.1940.51
202_Q205_C1.1740.50
171_I204_L1.1740.50
153_E189_K1.1640.49
114_L129_M1.1500.48
140_V182_K1.1490.48
106_R110_L1.1440.48
75_D102_K1.1360.47
91_I134_L1.1350.47
45_L108_I1.1340.47
43_I47_Y1.1340.47
157_P165_E1.1250.47
53_L59_R1.0930.45
91_I140_V1.0910.45
47_Y58_K1.0840.44
93_K134_L1.0770.44
102_K109_G1.0760.44
61_R64_I1.0740.44
72_I204_L1.0670.43
163_L203_V1.0650.43
114_L120_I1.0570.43
93_K130_E1.0560.43
27_K30_K1.0510.42
75_D199_E1.0460.42
106_R114_L1.0410.42
154_K195_G1.0380.41
192_S195_G1.0370.41
34_K112_E1.0230.41
49_A59_R1.0230.41
50_M53_L1.0230.41
66_H70_L1.0070.40
50_M55_N0.9970.39
36_P171_I0.9940.39
146_I169_L0.9930.39
83_F92_I0.9860.38
147_L169_L0.9830.38
46_H63_D0.9740.38
88_Q136_L0.9680.37
135_T138_N0.9650.37
158_E181_D0.9590.37
81_D93_K0.9550.37
75_D96_P0.9510.36
153_E163_L0.9470.36
160_I191_Y0.9440.36
73_L106_R0.9410.36
149_S178_D0.9370.36
206_R212_N0.9370.36
69_L94_V0.9350.35
135_T141_N0.9350.35
53_L216_G0.9300.35
27_K170_G0.9230.35
94_V119_K0.9220.35
147_L207_I0.9200.35
92_I129_M0.9130.34
28_N45_L0.9080.34
73_L79_K0.8890.33
171_I200_T0.8830.33
72_I134_L0.8730.32
154_K176_H0.8720.32
109_G120_I0.8710.32
64_I84_I0.8650.32
89_S98_M0.8640.32
59_R65_L0.8610.31
124_G180_S0.8590.31
94_V98_M0.8580.31
30_K35_K0.8530.31
65_L157_P0.8520.31
118_G133_N0.8510.31
61_R66_H0.8420.30
114_L176_H0.8260.30
40_L65_L0.8230.29
44_S106_R0.8130.29
82_I196_F0.8110.29
94_V198_L0.8080.29
98_M109_G0.8070.29
98_M106_R0.8020.28
126_E146_I0.8010.28
54_E120_I0.7980.28
35_K171_I0.7950.28
85_H125_D0.7900.28
92_I114_L0.7870.28
60_G179_F0.7700.27
150_E172_G0.7680.27
90_K140_V0.7630.26
120_I164_D0.7610.26
111_M131_V0.7590.26
163_L189_K0.7580.26
73_L76_P0.7530.26
34_K49_A0.7530.26
78_I96_P0.7520.26
111_M159_E0.7500.26
79_K209_S0.7470.26
129_M207_I0.7460.26
49_A57_H0.7410.25
203_V216_G0.7380.25
155_I159_E0.7370.25
75_D201_Q0.7360.25
29_A36_P0.7350.25
106_R120_I0.7330.25
71_V157_P0.7330.25
158_E165_E0.7290.25
164_D216_G0.7290.25
85_H142_R0.7280.25
52_Y142_R0.7270.25
46_H172_G0.7250.25
50_M59_R0.7210.24
79_K82_I0.7200.24
42_D60_G0.7190.24
71_V205_C0.7150.24
47_Y60_G0.7150.24
90_K131_V0.7130.24
65_L98_M0.7110.24
101_P128_L0.7090.24
193_I209_S0.7040.24
75_D212_N0.7010.24
170_G183_I0.6970.23
154_K207_I0.6960.23
65_L163_L0.6900.23
57_H175_P0.6840.23
109_G177_G0.6800.23
81_D146_I0.6770.23
172_G175_P0.6750.22
94_V196_F0.6710.22
146_I192_S0.6690.22
60_G174_F0.6680.22
62_P172_G0.6670.22
58_K136_L0.6650.22
97_N160_I0.6580.22
57_H60_G0.6560.22
142_R165_E0.6560.22
68_A206_R0.6530.22
80_G194_S0.6510.21
134_L142_R0.6500.21
151_K154_K0.6490.21
50_M54_E0.6470.21
113_Q168_L0.6470.21
93_K217_W0.6430.21
103_N121_P0.6410.21
86_T89_S0.6410.21
161_C192_S0.6330.21
94_V130_E0.6330.21
121_P127_T0.6290.21
169_L214_I0.6280.20
115_L196_F0.6280.20
139_I142_R0.6260.20
113_Q122_I0.6250.20
146_I159_E0.6190.20
54_E59_R0.6180.20
78_I100_P0.6170.20
36_P136_L0.6170.20
35_K122_I0.6160.20
133_N137_D0.6110.20
145_L204_L0.6070.20
87_I216_G0.6060.20
208_F211_C0.6060.20
194_S201_Q0.6050.20
147_L190_I0.6030.20
44_S103_N0.6030.20
41_L46_H0.6020.19
73_L82_I0.6010.19
121_P125_D0.5930.19
32_R35_K0.5930.19
36_P108_I0.5900.19
147_L187_A0.5820.19
160_I195_G0.5800.19
175_P216_G0.5790.19
145_L188_K0.5770.19
166_K182_K0.5760.18
46_H175_P0.5760.18
97_N111_M0.5760.18
72_I206_R0.5750.18
188_K193_I0.5730.18
97_N123_N0.5690.18
90_K115_L0.5680.18
94_V159_E0.5660.18
77_V211_C0.5630.18
50_M176_H0.5590.18
72_I81_D0.5580.18
108_I139_I0.5570.18
160_I189_K0.5550.18
76_P106_R0.5540.18
69_L75_D0.5530.18
94_V134_L0.5530.18
91_I132_T0.5520.18
108_I112_E0.5520.18
134_L139_I0.5520.18
98_M148_L0.5520.18
45_L103_N0.5520.18
49_A112_E0.5480.17
146_I164_D0.5450.17
119_K153_E0.5420.17
27_K147_L0.5410.17
122_I127_T0.5400.17
89_S95_N0.5390.17
149_S161_C0.5390.17
55_N87_I0.5360.17
78_I102_K0.5360.17
110_L113_Q0.5350.17
129_M157_P0.5350.17
48_H84_I0.5340.17
135_T199_E0.5320.17
44_S199_E0.5320.17
173_A208_F0.5310.17
154_K159_E0.5300.17
205_C208_F0.5290.17
41_L140_V0.5260.17
92_I112_E0.5220.17
54_E58_K0.5210.17
137_D159_E0.5200.16
79_K120_I0.5170.16
60_G203_V0.5160.16
160_I202_Q0.5140.16
104_Y205_C0.5130.16
39_T194_S0.5120.16
55_N59_R0.5090.16
143_Y160_I0.5090.16
64_I69_L0.5080.16
105_L149_S0.5080.16
126_E167_W0.5080.16
73_L102_K0.5070.16
91_I206_R0.5060.16
35_K38_D0.5000.16
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  
3o7bA 2 0.9817 100 0.09 Contact Map
3bbdA 2 0.9037 100 0.184 Contact Map
3oiiA 2 0.8945 100 0.205 Contact Map
3aiaA 2 0.7248 100 0.568 Contact Map
2qmmA 2 0.8073 100 0.649 Contact Map
2qwvA 2 0.789 99.9 0.734 Contact Map
1ns5A 2 0.578 95.8 0.921 Contact Map
1o6dA 2 0.5734 95.5 0.923 Contact Map
1to0A 2 0.5596 94.8 0.926 Contact Map
4fakA 2 0.5963 92.5 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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