GREMLIN Database
YTQB - Putative rRNA methylase YtqB
UniProt: O34614 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 194 (181)
Sequences: 828 (702)
Seq/√Len: 52.2

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_M50_A4.0791.00
79_S118_S3.5791.00
55_E59_A3.4941.00
47_H74_T3.3581.00
100_F122_A3.3131.00
113_T146_E3.0721.00
78_K86_S3.0111.00
18_A24_V2.9911.00
84_A125_Q2.7791.00
22_D96_A2.7171.00
96_A131_K2.6391.00
29_M61_T2.6091.00
78_K82_K2.5871.00
98_A126_L2.5811.00
49_Y76_F2.4561.00
102_L119_T2.3431.00
163_Q176_Q1.9611.00
58_V75_L1.9391.00
69_Y72_R1.9200.99
76_F86_S1.9180.99
36_Q68_M1.8740.99
137_V183_I1.8360.99
23_I49_Y1.8300.99
13_L185_A1.8230.99
166_A186_I1.8020.99
99_V137_V1.7490.99
14_L97_A1.6750.99
18_A41_L1.6680.98
169_L173_F1.6620.98
35_T48_V1.6610.98
126_L136_I1.6580.98
140_V184_V1.6160.98
63_E67_D1.5480.98
81_D118_S1.5470.98
151_K182_F1.5060.97
123_I157_F1.4860.97
146_E149_A1.4810.97
162_D165_T1.4710.97
123_I154_V1.4480.96
14_L99_V1.4360.96
121_K125_Q1.4280.96
31_N60_N1.4150.96
123_I136_I1.3950.95
84_A128_S1.3750.95
142_H151_K1.3680.95
155_L182_F1.3490.94
82_K85_E1.3440.94
163_Q178_N1.3440.94
27_A98_A1.3390.94
33_H64_R1.3330.94
127_L161_L1.3320.94
55_E77_H1.3250.94
64_R68_M1.3220.94
7_L171_Y1.3200.94
21_G46_G1.2980.93
95_V98_A1.2950.93
81_D121_K1.2860.93
42_V46_G1.2830.93
21_G43_G1.2720.93
25_V126_L1.2350.91
161_L168_V1.2150.91
49_Y87_L1.2100.91
137_V185_A1.2070.90
36_Q69_Y1.2050.90
39_A72_R1.1970.90
140_V151_K1.1940.90
29_M58_V1.1720.89
36_Q40_E1.1470.88
43_G46_G1.1420.88
39_A69_Y1.1250.87
140_V182_F1.1190.87
158_C186_I1.1070.86
9_Y171_Y1.1040.86
50_A76_F1.0970.86
61_T75_L1.0750.84
61_T65_L1.0700.84
155_L170_T1.0680.84
176_Q180_P1.0670.84
35_T61_T1.0630.84
167_R189_K1.0490.83
21_G42_V1.0490.83
113_T116_G1.0370.82
102_L138_L1.0360.82
163_Q180_P1.0260.82
83_I98_A1.0170.81
158_C184_V1.0090.80
87_L129_I1.0080.80
39_A73_T1.0000.80
83_I126_L0.9940.79
29_M35_T0.9920.79
163_Q177_Q0.9910.79
119_T154_V0.9840.79
121_K124_E0.9830.79
65_L75_L0.9770.78
6_I139_V0.9560.77
40_E68_M0.9490.76
142_H182_F0.9420.76
17_A96_A0.9400.75
9_Y13_L0.9400.75
56_S60_N0.9360.75
113_T144_H0.9360.75
50_A61_T0.9310.75
25_V95_V0.9300.75
62_K66_G0.9110.73
35_T50_A0.9110.73
53_I108_G0.9000.72
17_A135_L0.8970.72
154_V158_C0.8950.72
15_K37_F0.8880.71
55_E62_K0.8810.71
124_E157_F0.8720.70
27_A100_F0.8700.70
5_K183_I0.8690.70
113_T148_K0.8690.70
88_P94_K0.8690.70
65_L73_T0.8690.70
10_S183_I0.8640.69
19_G96_A0.8580.69
155_L184_V0.8570.69
42_V48_V0.8560.68
142_H146_E0.8560.68
15_K41_L0.8540.68
36_Q64_R0.8530.68
171_Y185_A0.8500.68
87_L94_K0.8490.68
94_K131_K0.8490.68
151_K155_L0.8450.67
6_I182_F0.8410.67
19_G22_D0.8260.66
161_L166_A0.8230.65
123_I126_L0.8190.65
35_T75_L0.8050.64
79_S82_K0.8030.63
127_L166_A0.8020.63
29_M75_L0.7910.62
148_K179_D0.7880.62
88_P93_G0.7840.62
44_E72_R0.7830.61
119_T138_L0.7800.61
5_K8_P0.7700.60
13_L171_Y0.7700.60
59_A62_K0.7680.60
59_A63_E0.7650.60
116_G153_D0.7650.60
171_Y182_F0.7580.59
11_K176_Q0.7580.59
12_E16_M0.7580.59
108_G145_P0.7560.59
102_L154_V0.7490.58
51_F78_K0.7470.58
139_V185_A0.7460.58
51_F86_S0.7410.57
60_N63_E0.7400.57
9_Y169_L0.7390.57
16_M135_L0.7370.57
108_G112_I0.7370.57
7_L142_H0.7360.57
63_E159_R0.7360.57
126_L130_M0.7300.56
139_V183_I0.7210.55
37_F97_A0.7170.55
9_Y183_I0.7170.55
6_I142_H0.7070.54
11_K99_V0.7060.54
168_V175_N0.7040.53
60_N99_V0.6900.52
83_I129_I0.6870.52
24_V42_V0.6850.51
98_A136_I0.6830.51
78_K85_E0.6790.51
73_T77_H0.6740.50
22_D42_V0.6720.50
110_K144_H0.6710.50
10_S99_V0.6670.50
116_G146_E0.6640.49
37_F99_V0.6610.49
110_K171_Y0.6600.49
25_V87_L0.6600.49
136_I186_I0.6550.48
25_V98_A0.6520.48
154_V184_V0.6500.48
94_K160_D0.6500.48
130_M136_I0.6460.47
35_T38_L0.6430.47
21_G41_L0.6420.47
45_N55_E0.6370.46
113_T149_A0.6340.46
130_M134_G0.6340.46
148_K152_N0.6320.46
38_L48_V0.6320.46
82_K86_S0.6280.45
181_P186_I0.6210.45
5_K11_K0.6180.44
158_C161_L0.6180.44
23_I93_G0.6180.44
107_G133_E0.6170.44
59_A66_G0.6150.44
172_G182_F0.6140.44
60_N107_G0.6120.44
23_I95_V0.6120.44
52_D57_A0.6110.44
6_I173_F0.6100.44
116_G142_H0.6060.43
27_A116_G0.6020.43
127_L136_I0.6010.43
145_P148_K0.6000.43
173_F176_Q0.6000.43
138_L158_C0.5990.42
33_H107_G0.5940.42
53_I70_Q0.5920.42
158_C168_V0.5920.42
152_N155_L0.5910.42
7_L11_K0.5870.41
9_Y139_V0.5860.41
121_K136_I0.5820.41
31_N107_G0.5810.41
136_I166_A0.5780.40
120_I153_D0.5770.40
49_Y74_T0.5750.40
80_H122_A0.5700.40
63_E128_S0.5670.39
153_D156_E0.5670.39
142_H180_P0.5640.39
57_A119_T0.5640.39
108_G146_E0.5630.39
51_F79_S0.5630.39
48_V75_L0.5550.38
99_V135_L0.5540.38
53_I145_P0.5530.38
76_F85_E0.5510.38
140_V154_V0.5500.38
27_A119_T0.5500.38
43_G72_R0.5490.37
24_V97_A0.5470.37
48_V97_A0.5450.37
102_L140_V0.5450.37
21_G24_V0.5450.37
13_L135_L0.5450.37
47_H71_A0.5450.37
37_F41_L0.5440.37
62_K71_A0.5430.37
12_E15_K0.5410.37
169_L176_Q0.5400.37
66_G70_Q0.5360.36
104_Y119_T0.5360.36
24_V102_L0.5350.36
144_H171_Y0.5340.36
99_V139_V0.5320.36
115_N160_D0.5310.36
101_N141_Y0.5290.36
39_A70_Q0.5290.36
101_N106_P0.5240.35
14_L41_L0.5230.35
78_K81_D0.5230.35
108_G111_S0.5220.35
37_F123_I0.5220.35
24_V119_T0.5190.35
13_L137_V0.5190.35
57_A105_L0.5170.34
169_L175_N0.5160.34
76_F88_P0.5150.34
11_K37_F0.5150.34
130_M166_A0.5140.34
49_Y99_V0.5110.34
5_K167_R0.5100.34
77_H188_K0.5090.34
87_L93_G0.5090.34
139_V171_Y0.5080.34
110_K133_E0.5050.33
10_S185_A0.5030.33
69_Y138_L0.5000.33
62_K156_E0.5000.33
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  
3eeyA 3 0.9794 100 0.632 Contact Map
3mtiA 2 0.9278 99.9 0.676 Contact Map
4ponA 2 0.8918 99.9 0.681 Contact Map
1wg8A 1 0.8866 99.5 0.796 Contact Map
3evzA 1 0.8247 99.4 0.807 Contact Map
1g8aA 1 0.8918 99.4 0.81 Contact Map
3lpmA 2 0.8454 99.4 0.814 Contact Map
3duwA 2 0.9072 99.3 0.817 Contact Map
3r3hA 2 0.8814 99.3 0.817 Contact Map
2ipxA 1 0.8969 99.3 0.82 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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