GREMLIN Database
RSMD - Ribosomal RNA small subunit methyltransferase D
UniProt: P0ADX9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10343
Length: 198 (178)
Sequences: 4174 (3084)
Seq/√Len: 231.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
67_G80_L3.2421.00
68_L95_L2.8691.00
25_P93_K2.7501.00
14_I68_L2.6591.00
19_W100_A2.6121.00
43_L184_Y2.3461.00
158_S185_R2.3461.00
40_R65_A2.3361.00
22_R97_T2.3351.00
55_Q77_G2.2571.00
79_T121_H2.1641.00
85_R107_N2.1231.00
18_Q102_N2.1041.00
148_L152_A2.0581.00
56_C66_L2.0331.00
95_L103_A2.0211.00
71_L103_A1.9401.00
77_G104_R1.8981.00
61_A80_L1.8941.00
71_L78_A1.8561.00
41_E45_N1.8261.00
173_L187_Y1.8151.00
82_E88_S1.8091.00
46_W186_L1.7991.00
88_S105_V1.7741.00
79_T106_V1.7731.00
176_E183_A1.7671.00
122_N149_A1.7601.00
42_T179_A1.7171.00
39_V182_V1.6661.00
95_L105_V1.6611.00
89_Q93_K1.6371.00
57_L121_H1.6301.00
55_Q119_T1.6251.00
32_L87_V1.6101.00
59_C81_I1.5591.00
22_R99_K1.5551.00
178_V183_A1.5421.00
60_F138_T1.4951.00
88_S107_N1.4891.00
85_R89_Q1.4701.00
19_W98_L1.4691.00
13_R37_D1.4581.00
124_V152_A1.4571.00
67_G78_A1.4281.00
42_T45_N1.3721.00
108_S113_F1.3581.00
35_T157_E1.3581.00
131_R159_E1.3541.00
142_L152_A1.3521.00
173_L185_R1.3511.00
51_I54_A1.3471.00
173_L176_E1.3411.00
81_I113_F1.3351.00
93_K96_A1.3331.00
160_V178_V1.3211.00
46_W175_R1.3041.00
56_C70_A1.2841.00
66_L125_F1.2791.00
134_L138_T1.2771.00
77_G119_T1.2751.00
71_L80_L1.2591.00
149_A152_A1.2521.00
89_Q92_I1.2091.00
143_E170_N1.2041.00
43_L66_L1.1931.00
82_E87_V1.1891.00
167_V187_Y1.1871.00
134_L137_E1.1831.00
109_N112_S1.1801.00
86_A89_Q1.1761.00
174_H188_Q1.1721.00
59_C110_A1.1561.00
80_L103_A1.1531.00
124_V142_L1.1421.00
53_D76_A1.1121.00
22_R98_L1.1011.00
61_A91_L1.0991.00
136_E140_N1.0971.00
120_P149_A1.0941.00
153_L174_H1.0891.00
83_M109_N1.0831.00
143_E171_W1.0801.00
176_E185_R1.0681.00
56_C75_A1.0651.00
141_L145_N1.0631.00
120_P146_G1.0561.00
115_A141_L1.0551.00
140_N144_D1.0511.00
137_E140_N1.0471.00
93_K97_T1.0371.00
26_V29_S1.0301.00
56_C123_I1.0281.00
56_C78_A1.0231.00
108_S112_S1.0051.00
159_E181_Q1.0041.00
12_I26_V0.9941.00
18_Q100_A0.9931.00
92_I107_N0.9911.00
15_I41_E0.9831.00
51_I123_I0.9791.00
26_V63_S0.9691.00
39_V42_T0.9571.00
35_T127_D0.9541.00
24_L94_N0.9541.00
88_S91_L0.9531.00
71_L95_L0.9481.00
56_C125_F0.9411.00
27_P90_Q0.9411.00
61_A67_G0.9391.00
51_I75_A0.9371.00
15_I37_D0.9341.00
106_V113_F0.9321.00
172_S188_Q0.9281.00
55_Q120_P0.9201.00
46_W177_K0.9111.00
96_A101_G0.9111.00
81_I108_S0.9071.00
39_V184_Y0.9050.99
79_T113_F0.9040.99
79_T104_R0.9030.99
55_Q149_A0.8920.99
126_V154_I0.8910.99
135_L156_V0.8860.99
28_D86_A0.8850.99
131_R161_E0.8800.99
19_W22_R0.8790.99
126_V156_V0.8760.99
42_T46_W0.8730.99
81_I110_A0.8690.99
44_F70_A0.8680.99
55_Q76_A0.8680.99
55_Q79_T0.8660.99
55_Q121_H0.8620.99
108_S116_Q0.8470.99
159_E162_N0.8450.99
143_E189_R0.8450.99
179_A184_Y0.8320.99
160_V183_A0.8310.99
177_K184_Y0.8290.99
135_L158_S0.8280.99
57_L124_V0.8170.99
79_T119_T0.8080.99
113_F117_K0.8080.99
38_R41_E0.8040.99
88_S92_I0.7960.99
124_V148_L0.7910.99
48_A73_R0.7890.99
110_A138_T0.7890.99
43_L155_Y0.7860.99
158_S162_N0.7840.99
90_Q94_N0.7810.99
92_I96_A0.7810.99
104_R119_T0.7770.98
133_G136_E0.7690.98
114_L141_L0.7470.98
29_S32_L0.7470.98
57_L79_T0.7460.98
44_F125_F0.7450.98
165_P168_P0.7450.98
14_I95_L0.7420.98
60_F134_L0.7370.98
61_A82_E0.7370.98
36_T39_V0.7370.98
31_G84_D0.7330.98
112_S115_A0.7330.98
139_I154_I0.7230.98
46_W184_Y0.7200.97
150_D189_R0.7190.97
68_L103_A0.7180.97
48_A51_I0.7160.97
158_S183_A0.7140.97
125_F155_Y0.7130.97
14_I40_R0.7120.97
24_L98_L0.7090.97
111_M137_E0.7060.97
80_L95_L0.6820.97
47_L155_Y0.6800.96
36_T182_V0.6800.96
25_P90_Q0.6800.96
141_L144_D0.6770.96
49_P54_A0.6730.96
82_E91_L0.6700.96
120_P147_W0.6690.96
151_E188_Q0.6680.96
175_R186_L0.6650.96
66_L155_Y0.6640.96
117_K147_W0.6500.95
50_V54_A0.6480.95
25_P97_T0.6450.95
59_C126_V0.6440.95
36_T179_A0.6430.95
155_Y184_Y0.6370.95
85_R88_S0.6370.95
161_E181_Q0.6340.95
29_S87_V0.6320.95
59_C114_L0.6290.95
37_D41_E0.6290.95
132_R162_N0.6260.94
54_A75_A0.6220.94
43_L125_F0.6170.94
16_G73_R0.6080.94
143_E169_A0.6060.93
35_T39_V0.6040.93
166_T173_L0.6040.93
16_G40_R0.6030.93
19_W71_L0.6030.93
29_S84_D0.6010.93
68_L98_L0.5990.93
114_L147_W0.5990.93
137_E141_L0.5970.93
170_N189_R0.5950.93
42_T184_Y0.5940.93
78_A103_A0.5930.93
19_W102_N0.5900.93
126_V138_T0.5890.92
40_R66_L0.5890.92
26_V32_L0.5820.92
155_Y186_L0.5810.92
135_L162_N0.5800.92
100_A103_A0.5770.92
115_A145_N0.5750.92
136_E166_T0.5740.91
110_A114_L0.5700.91
54_A122_N0.5690.91
157_E182_V0.5690.91
49_P52_V0.5680.91
165_P187_Y0.5680.91
38_R42_T0.5630.91
84_D87_V0.5630.91
32_L90_Q0.5620.91
135_L159_E0.5600.90
135_L139_I0.5580.90
146_G189_R0.5570.90
111_M138_T0.5570.90
23_K97_T0.5570.90
66_L186_L0.5530.90
35_T65_A0.5480.89
138_T142_L0.5470.89
94_N97_T0.5430.89
126_V135_L0.5420.89
171_W189_R0.5420.89
43_L186_L0.5390.89
143_E172_S0.5390.89
60_F109_N0.5370.89
81_I106_V0.5370.89
111_M134_L0.5350.88
133_G162_N0.5340.88
106_V116_Q0.5310.88
75_A123_I0.5270.88
26_V90_Q0.5250.87
130_F182_V0.5240.87
60_F110_A0.5230.87
27_P88_S0.5200.87
18_Q74_Y0.5190.87
66_L70_A0.5190.87
83_M107_N0.5180.87
68_L94_N0.5170.87
21_G177_K0.5170.87
13_R23_K0.5160.87
35_T41_E0.5140.86
155_Y179_A0.5120.86
17_G72_S0.5100.86
114_L145_N0.5050.85
121_H124_V0.5030.85
48_A52_V0.5020.85
46_W155_Y0.5000.85
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  
2fpoA 1 0.9192 100 0.561 Contact Map
1ws6A 1 0.8434 100 0.567 Contact Map
2iftA 1 0.8838 100 0.588 Contact Map
2fhpA 1 0.9091 100 0.6 Contact Map
4bluA 2 0.904 99.9 0.624 Contact Map
3x0dA 1 0.9596 99.9 0.638 Contact Map
3p9nA 1 0.8939 99.9 0.642 Contact Map
2oo3A 1 0.9242 99.9 0.642 Contact Map
2esrA 2 0.803 99.9 0.645 Contact Map
4dcmA 1 0.904 99.8 0.684 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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