GREMLIN Database
RLME - Ribosomal RNA large subunit methyltransferase E
UniProt: Q9HN40 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 259 (201)
Sequences: 1229 (665)
Seq/√Len: 46.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
29_D58_R5.1191.00
150_V191_V4.6331.00
15_E23_Y3.9721.00
107_D144_D3.4271.00
52_L82_L3.2781.00
135_A149_F2.9061.00
28_L34_V2.8551.00
28_L176_H2.8521.00
87_G94_T2.8391.00
171_A194_N2.6381.00
176_H191_V2.5761.00
55_A110_V2.5051.00
143_L170_F2.4901.00
30_D58_R2.4711.00
56_A82_L2.3081.00
11_K15_E2.2821.00
42_V106_A2.2501.00
143_L147_G2.2451.00
136_L166_I2.2381.00
52_L67_G2.2181.00
117_M154_F2.1541.00
52_L84_T2.1141.00
177_S181_S2.0871.00
89_M138_T1.9540.99
22_A54_V1.9150.99
41_V59_A1.8670.99
50_G189_Y1.8630.99
125_H156_G1.7860.99
32_F176_H1.7770.99
171_A196_I1.7760.99
34_V148_H1.7420.98
17_Y23_Y1.7130.98
174_A193_K1.6150.97
102_A106_A1.6060.97
59_A65_V1.6040.97
41_V55_A1.5930.97
42_V98_V1.5690.97
96_Q100_D1.5560.97
180_A189_Y1.5350.96
97_R100_D1.5200.96
32_F193_K1.5130.96
172_F193_K1.5020.96
8_Y179_D1.5010.96
46_A73_I1.5010.96
45_G113_M1.4730.95
148_H193_K1.4520.95
32_F174_A1.4230.94
34_V108_V1.4180.94
28_L191_V1.3980.94
66_V106_A1.3850.94
83_E101_A1.3770.93
67_G73_I1.3740.93
125_H159_F1.3500.93
70_F116_D1.3390.92
120_E123_L1.3360.92
60_G63_G1.3240.92
140_R169_E1.3210.92
26_Q54_V1.3090.92
19_S189_Y1.2940.91
97_R101_A1.2610.90
147_G170_F1.2520.90
92_D96_Q1.2420.89
17_Y57_E1.2420.89
87_G97_R1.2370.89
146_G162_L1.2340.89
166_I190_V1.2210.88
76_F82_L1.2200.88
33_D36_F1.2180.88
46_A67_G1.2090.88
160_Q164_A1.1950.87
87_G93_E1.1850.87
55_A108_V1.1820.87
114_A189_Y1.1610.86
125_H129_V1.1530.85
99_R141_E1.1510.85
128_S186_S1.1410.85
38_G108_V1.1390.85
95_R141_E1.1150.83
146_G183_D1.1110.83
29_D35_L1.1100.83
90_T115_P1.1050.83
166_I173_V1.1030.83
140_R165_D1.1000.82
19_S50_G1.0960.82
18_R53_Q1.0910.82
64_K83_E1.0860.82
150_V176_H1.0710.81
18_R73_I1.0640.80
166_I192_G1.0580.80
163_L175_T1.0410.79
163_L190_V1.0320.78
54_V90_T1.0250.78
71_Q116_D1.0140.77
46_A52_L1.0120.77
18_R75_Q1.0070.76
4_R9_Y0.9980.76
72_S86_R0.9910.75
38_G63_G0.9850.75
148_H194_N0.9820.75
67_G82_L0.9720.74
44_L143_L0.9650.73
32_F36_F0.9430.72
133_R165_D0.9420.72
155_D188_L0.9390.71
67_G84_T0.9230.70
26_Q58_R0.9170.69
3_N184_A0.9150.69
2_G9_Y0.9100.69
95_R99_R0.9080.69
29_D184_A0.9040.68
105_S139_A0.8940.67
26_Q57_E0.8930.67
32_F191_V0.8920.67
44_L135_A0.8890.67
70_F73_I0.8850.67
42_V190_V0.8850.67
153_V190_V0.8850.67
110_V150_V0.8810.66
106_A142_L0.8760.66
18_R114_A0.8710.65
11_K14_Q0.8690.65
44_L109_V0.8650.65
5_K9_Y0.8630.65
118_T164_A0.8590.64
26_Q30_D0.8570.64
65_V69_D0.8500.64
111_S135_A0.8460.63
22_A53_Q0.8460.63
66_V98_V0.8450.63
169_E198_A0.8430.63
67_G125_H0.8400.63
9_Y13_K0.8400.63
17_Y81_G0.8310.62
59_A67_G0.8310.62
27_Q142_L0.8280.61
4_R7_H0.8260.61
10_N14_Q0.8220.61
98_V140_R0.8150.60
15_E57_E0.8110.60
98_V102_A0.8080.60
65_V82_L0.8060.59
69_D185_S0.8040.59
87_G191_V0.8020.59
93_E97_R0.8020.59
21_A147_G0.7930.58
35_L58_R0.7870.58
94_T98_V0.7830.57
111_S132_A0.7800.57
9_Y27_Q0.7750.56
128_S155_D0.7720.56
23_Y26_Q0.7700.56
162_L166_I0.7680.56
40_S104_G0.7660.56
42_V142_L0.7640.55
38_G59_A0.7590.55
5_K174_A0.7530.54
158_D161_D0.7520.54
198_A203_G0.7510.54
174_A196_I0.7510.54
153_V159_F0.7510.54
35_L148_H0.7490.54
46_A50_G0.7460.54
95_R138_T0.7430.53
196_I200_I0.7370.53
109_V143_L0.7290.52
129_V132_A0.7240.51
6_D22_A0.7220.51
42_V66_V0.7160.51
45_G111_S0.7150.50
75_Q81_G0.7150.50
40_S144_D0.7130.50
91_E137_E0.7130.50
117_M128_S0.7070.50
153_V188_L0.7020.49
37_G108_V0.6970.49
81_G85_V0.6960.49
20_R43_D0.6950.48
90_T134_Q0.6890.48
76_F91_E0.6890.48
27_Q180_A0.6850.47
3_N9_Y0.6830.47
14_Q154_F0.6810.47
64_K103_N0.6800.47
76_F86_R0.6800.47
133_R162_L0.6800.47
116_D121_Y0.6790.47
41_V111_S0.6790.47
109_V139_A0.6780.47
41_V75_Q0.6770.47
82_L85_V0.6770.47
98_V104_G0.6770.47
34_V145_A0.6760.47
33_D167_E0.6730.46
38_G41_V0.6720.46
40_S66_V0.6630.45
197_V202_E0.6630.45
51_W124_D0.6620.45
81_G145_A0.6610.45
124_D135_A0.6610.45
137_E141_E0.6580.45
159_F175_T0.6580.45
51_W69_D0.6570.45
140_R171_A0.6530.44
158_D175_T0.6520.44
105_S145_A0.6520.44
11_K23_Y0.6490.44
124_D185_S0.6470.44
139_A145_A0.6460.44
55_A172_F0.6450.44
110_V166_I0.6410.43
156_G159_F0.6380.43
105_S142_L0.6370.43
45_G89_M0.6360.43
21_A167_E0.6350.43
9_Y138_T0.6350.43
85_V97_R0.6320.42
52_L56_A0.6290.42
134_Q137_E0.6280.42
145_A199_P0.6270.42
108_V148_H0.6260.42
132_A153_V0.6240.42
109_V150_V0.6230.41
63_G156_G0.6200.41
19_S154_F0.6160.41
62_R198_A0.6160.41
159_F190_V0.6120.40
27_Q121_Y0.6050.40
38_G60_G0.6040.40
89_M95_R0.6040.40
160_Q172_F0.5970.39
101_A106_A0.5970.39
22_A50_G0.5950.39
54_V162_L0.5950.39
87_G138_T0.5910.38
13_K162_L0.5900.38
106_A198_A0.5900.38
37_G63_G0.5870.38
145_A197_V0.5850.38
38_G55_A0.5820.38
69_D75_Q0.5810.37
38_G45_G0.5800.37
2_G7_H0.5800.37
44_L154_F0.5790.37
105_S110_V0.5770.37
9_Y128_S0.5720.37
39_A80_A0.5670.36
36_F39_A0.5670.36
98_V144_D0.5660.36
113_M135_A0.5620.36
11_K70_F0.5610.36
101_A108_V0.5600.36
68_V94_T0.5600.36
127_R192_G0.5590.35
18_R47_A0.5590.35
125_H158_D0.5540.35
28_L50_G0.5530.35
64_K144_D0.5520.35
151_V162_L0.5490.35
104_G138_T0.5460.34
21_A138_T0.5450.34
157_R162_L0.5440.34
34_V96_Q0.5430.34
200_I203_G0.5420.34
96_Q167_E0.5410.34
50_G169_E0.5410.34
44_L86_R0.5370.33
34_V139_A0.5360.33
2_G184_A0.5350.33
20_R25_L0.5340.33
42_V130_H0.5340.33
111_S156_G0.5330.33
9_Y89_M0.5320.33
132_A173_V0.5310.33
9_Y133_R0.5300.33
103_N109_V0.5290.33
153_V162_L0.5290.33
112_D187_E0.5280.33
42_V109_V0.5250.32
55_A125_H0.5250.32
5_K21_A0.5230.32
117_M184_A0.5230.32
29_D55_A0.5230.32
53_Q76_F0.5220.32
76_F84_T0.5200.32
37_G196_I0.5190.32
36_F192_G0.5180.32
132_A186_S0.5170.32
132_A179_D0.5160.32
154_F184_A0.5130.31
122_D186_S0.5120.31
91_E171_A0.5110.31
45_G48_P0.5090.31
50_G103_N0.5080.31
128_S189_Y0.5080.31
62_R101_A0.5070.31
109_V135_A0.5070.31
201_A204_D0.5060.31
92_D201_A0.5050.31
117_M186_S0.5050.31
12_S115_P0.5040.31
163_L168_D0.5010.30
50_G71_Q0.5000.30
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  
3r24A 1 0.8919 100 0.439 Contact Map
4v0qA 2 0.9305 100 0.453 Contact Map
4n49A 1 0.9923 100 0.489 Contact Map
2xyqA 1 0.8958 100 0.495 Contact Map
4k6mA 2 0.9151 100 0.516 Contact Map
2px2A 1 0.8494 100 0.531 Contact Map
3lkzA 1 0.8069 100 0.544 Contact Map
4r8rA 1 0.8301 100 0.566 Contact Map
1ej0A 1 0.6911 100 0.604 Contact Map
2nyuA 1 0.6718 100 0.629 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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