GREMLIN Database
RLUA - Ribosomal large subunit pseudouridine synthase A
UniProt: P0AA37 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12609
Length: 219 (202)
Sequences: 12353 (8249)
Seq/√Len: 580.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
138_E157_I3.2471.00
95_Q153_V3.2271.00
19_Q75_L2.7301.00
110_L138_E2.7061.00
199_M212_T2.6781.00
97_V198_E2.6541.00
154_L168_M2.5661.00
22_H76_T2.4911.00
110_L136_Q2.4621.00
17_L70_V2.4571.00
109_G139_Y2.4571.00
201_T212_T2.4101.00
97_V151_R2.4051.00
140_E153_V2.3231.00
76_T79_A2.2271.00
201_T210_S2.2191.00
113_L170_A2.2061.00
22_H206_A2.1931.00
15_V27_N2.1691.00
112_D136_Q2.1601.00
154_L164_L2.1441.00
95_Q199_M2.1191.00
68_S196_H2.0981.00
203_T210_S2.0361.00
93_K155_K2.0081.00
25_V213_F1.9921.00
100_V152_V1.9921.00
93_K201_T1.9671.00
112_D134_P1.8931.00
107_A144_Y1.8921.00
136_Q157_I1.8511.00
95_Q155_K1.8361.00
108_E140_E1.8311.00
141_V150_A1.8031.00
85_R89_E1.7971.00
98_A154_L1.7271.00
27_N215_A1.7231.00
199_M214_K1.6961.00
86_Q91_E1.6911.00
34_S71_I1.5941.00
138_E155_K1.5841.00
102_G150_A1.5701.00
44_D49_R1.5651.00
142_V153_V1.5451.00
66_A193_L1.5001.00
137_T154_L1.5001.00
104_P150_A1.4901.00
20_D204_H1.4661.00
103_H144_Y1.4571.00
190_A194_L1.4541.00
12_P49_R1.4171.00
25_V72_V1.3901.00
111_V171_L1.3831.00
198_E214_K1.3791.00
97_V153_V1.3731.00
100_V168_M1.3721.00
152_V168_M1.3491.00
46_V71_I1.3181.00
63_L71_I1.3121.00
82_E86_Q1.3111.00
133_K160_R1.3111.00
141_V144_Y1.3031.00
80_E84_K1.3011.00
86_Q203_T1.2991.00
85_R88_R1.2871.00
99_R149_T1.2451.00
30_S68_S1.2431.00
101_W183_S1.2401.00
115_L166_V1.2301.00
25_V70_V1.2181.00
87_F92_P1.1891.00
20_D23_I1.1831.00
203_T208_G1.1741.00
106_P109_G1.1651.00
81_R85_R1.1651.00
60_V83_L1.1451.00
17_L213_F1.1441.00
149_T176_L1.1271.00
45_S48_T1.1271.00
104_P173_H1.1251.00
50_I73_V1.1181.00
156_P164_L1.1131.00
82_E85_R1.1101.00
103_H148_N1.1061.00
102_G173_H1.0981.00
98_A175_I1.0751.00
144_Y150_A1.0661.00
30_S192_R1.0641.00
137_T167_H1.0601.00
93_K210_S1.0571.00
22_H79_A1.0571.00
74_A80_E1.0561.00
104_P141_V1.0381.00
97_V142_V1.0341.00
60_V74_A1.0331.00
29_P32_L1.0331.00
94_K156_P1.0231.00
22_H204_H1.0081.00
153_V198_E1.0041.00
113_L171_L1.0041.00
23_I204_H1.0031.00
101_W149_T0.9931.00
110_L157_I0.9871.00
70_V213_F0.9691.00
118_D124_K0.9691.00
204_H211_M0.9671.00
118_D121_N0.9571.00
77_K81_R0.9571.00
11_E52_R0.9501.00
139_Y168_M0.9461.00
33_L41_E0.9451.00
66_A179_R0.9441.00
116_I131_T0.9411.00
117_C161_S0.9371.00
77_K80_E0.9351.00
196_H215_A0.9181.00
59_S73_V0.9131.00
168_M175_I0.9121.00
121_N124_K0.9111.00
99_R151_R0.9101.00
116_I129_Y0.8941.00
32_L49_R0.8871.00
202_I213_F0.8821.00
145_A148_N0.8821.00
95_Q198_E0.8801.00
26_V46_V0.8771.00
114_P134_P0.8711.00
23_I202_I0.8671.00
57_A73_V0.8631.00
99_R194_L0.8621.00
84_K88_R0.8601.00
143_E151_R0.8591.00
48_T51_Q0.8581.00
104_P152_V0.8571.00
70_V215_A0.8561.00
114_P167_H0.8481.00
27_N196_H0.8441.00
118_D126_K0.8421.00
100_V104_P0.8401.00
78_A82_E0.8371.00
78_A206_A0.8281.00
108_E138_E0.8191.00
46_V73_V0.8181.00
34_S63_L0.8171.00
114_P132_G0.8161.00
137_T156_P0.8151.00
100_V150_A0.8141.00
91_E203_T0.8121.00
98_A152_V0.8111.00
197_A200_L0.8081.00
82_E206_A0.8041.00
74_A79_A0.8011.00
100_V175_I0.7971.00
106_P139_Y0.7971.00
24_M73_V0.7961.00
34_S59_S0.7901.00
103_H150_A0.7881.00
87_F156_P0.7841.00
101_W176_L0.7821.00
32_L46_V0.7811.00
192_R196_H0.7801.00
18_Y23_I0.7801.00
111_V168_M0.7771.00
83_L86_Q0.7751.00
47_M59_S0.7701.00
116_I126_K0.7641.00
24_M75_L0.7631.00
67_T193_L0.7611.00
61_H71_I0.7601.00
36_P45_S0.7601.00
107_A141_V0.7571.00
23_I83_L0.7531.00
145_A149_T0.7521.00
33_L37_G0.7511.00
27_N68_S0.7511.00
82_E208_G0.7511.00
26_V73_V0.7461.00
72_V200_L0.7451.00
23_I79_A0.7411.00
48_T52_R0.7411.00
58_E77_K0.7401.00
74_A83_L0.7381.00
44_D48_T0.7371.00
105_S173_H0.7351.00
127_V170_A0.7331.00
19_Q54_Y0.7221.00
37_G41_E0.7181.00
43_K48_T0.7171.00
109_G154_L0.7161.00
111_V167_H0.7141.00
58_E80_E0.7061.00
109_G171_L0.7031.00
104_P144_Y0.7011.00
100_V173_H0.6951.00
61_H87_F0.6941.00
113_L167_H0.6861.00
61_H197_A0.6841.00
24_M50_I0.6831.00
103_H146_A0.6821.00
26_V71_I0.6761.00
35_V59_S0.6761.00
15_V29_P0.6751.00
135_A160_R0.6721.00
87_F94_K0.6711.00
81_R84_K0.6691.00
140_E155_K0.6651.00
108_E141_V0.6611.00
203_T207_Y0.6571.00
35_V80_E0.6561.00
33_L65_M0.6501.00
184_P188_A0.6471.00
51_Q57_A0.6461.00
126_K129_Y0.6411.00
95_Q201_T0.6401.00
31_G66_A0.6401.00
144_Y148_N0.6391.00
164_L175_I0.6371.00
179_R183_S0.6351.00
17_L27_N0.6351.00
47_M57_A0.6351.00
41_E44_D0.6331.00
153_V199_M0.6311.00
204_H207_Y0.6291.00
79_A206_A0.6291.00
117_C122_R0.6261.00
94_K157_I0.6241.00
14_L49_R0.6241.00
150_A173_H0.6231.00
26_V50_I0.6211.00
42_H45_S0.6201.00
14_L26_V0.6191.00
123_P180_F0.6161.00
47_M51_Q0.6151.00
183_S187_R0.6111.00
127_V132_G0.6081.00
78_A81_R0.6021.00
106_P141_V0.6011.00
72_V202_I0.5971.00
190_A193_L0.5951.00
86_Q92_P0.5911.00
177_G194_L0.5891.00
118_D122_R0.5881.00
93_K199_M0.5841.00
98_A168_M0.5841.00
202_I211_M0.5821.00
137_T164_L0.5811.00
31_G68_S0.5781.00
19_Q53_D0.5771.00
111_V139_Y0.5771.00
115_L125_Q0.5751.00
79_A82_E0.5751.00
166_V170_A0.5741.00
101_W184_P0.5731.00
121_N125_Q0.5711.00
94_K162_H0.5711.00
101_W182_A0.5681.00
38_R41_E0.5660.99
60_V80_E0.5660.99
129_Y132_G0.5650.99
16_I24_M0.5620.99
87_F90_R0.5600.99
17_L215_A0.5540.99
55_P58_E0.5480.99
120_P124_K0.5470.99
167_H171_L0.5470.99
55_P75_L0.5470.99
90_R157_I0.5420.99
67_T161_S0.5410.99
61_H200_L0.5380.99
135_A166_V0.5370.99
146_A149_T0.5360.99
42_H49_R0.5350.99
101_W148_N0.5350.99
176_L194_L0.5350.99
60_V87_F0.5350.99
21_D206_A0.5350.99
86_Q202_I0.5350.99
71_I197_A0.5340.99
50_I57_A0.5340.99
113_L127_V0.5320.99
92_P202_I0.5310.99
109_G141_V0.5310.99
51_Q56_Q0.5310.99
139_Y154_L0.5300.99
31_G65_M0.5270.99
16_I19_Q0.5230.99
187_R190_A0.5220.99
185_E188_A0.5210.99
114_P127_V0.5200.99
177_G190_A0.5190.99
50_I54_Y0.5180.99
30_S191_P0.5160.99
18_Y213_F0.5150.99
184_P189_M0.5140.99
45_S49_R0.5120.99
97_V101_W0.5090.99
125_Q133_K0.5090.99
83_L202_I0.5070.99
120_P123_P0.5040.99
142_V151_R0.5040.99
67_T197_A0.5030.99
36_P48_T0.5020.99
49_R52_R0.5000.99
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  
2i82A 1 0.9863 100 0.124 Contact Map
1v9fA 1 0.9543 100 0.143 Contact Map
1v9kA 1 0.9269 100 0.149 Contact Map
2olwA 1 0.8037 100 0.353 Contact Map
2omlA 1 0.7671 100 0.367 Contact Map
4lgtA 1 0.8995 100 0.403 Contact Map
1vioA 2 0.8311 100 0.423 Contact Map
3dh3A 1 0.8356 100 0.437 Contact Map
1kskA 1 0.8584 100 0.446 Contact Map
2gmlA 1 0.7534 100 0.45 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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