GREMLIN Database
RLUD - Ribosomal large subunit pseudouridine synthase D
UniProt: P33643 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12098
Length: 326 (285)
Sequences: 9120 (6368)
Seq/√Len: 377.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
87_V145_L3.4791.00
170_E225_R3.4521.00
211_H229_E3.3541.00
48_N63_E3.2811.00
283_M296_E2.8801.00
89_E150_K2.8401.00
85_D97_N2.8261.00
213_R225_R2.8221.00
285_R296_E2.8051.00
172_E282_T2.7881.00
172_E223_R2.7381.00
184_T211_H2.7081.00
183_G212_Y2.6591.00
92_D290_I2.6491.00
92_D151_T2.5841.00
187_E242_H2.4641.00
182_G213_R2.3721.00
97_N299_A2.3531.00
184_T209_V2.2781.00
181_A217_H2.2481.00
168_T227_R2.2471.00
226_L240_M2.2411.00
186_D207_P2.2321.00
186_D209_V2.2271.00
285_R294_E2.2161.00
95_I297_W2.1531.00
170_E283_M2.1041.00
151_T154_A2.0981.00
82_I118_A2.0791.00
287_Y294_E2.0461.00
276_R304_D2.0381.00
283_M298_H2.0261.00
80_Q112_D1.9861.00
214_I222_T1.9681.00
115_V146_M1.9341.00
168_T285_R1.9171.00
209_V229_E1.9171.00
173_A226_L1.9081.00
20_L52_C1.8861.00
170_E227_R1.8721.00
80_Q113_G1.8671.00
215_M225_R1.8591.00
12_S15_Q1.8481.00
143_T280_H1.8421.00
179_M222_T1.8411.00
161_S166_E1.8381.00
210_T226_L1.8031.00
52_C57_E1.8001.00
160_E164_R1.7301.00
47_V57_E1.7041.00
175_A224_L1.6801.00
138_L146_M1.5991.00
282_T298_H1.5961.00
226_L236_I1.5801.00
23_A27_M1.5571.00
95_I145_L1.5531.00
87_V297_W1.5471.00
303_Q307_E1.5421.00
104_V146_M1.5381.00
217_H222_T1.5191.00
90_D288_H1.5181.00
95_I147_V1.5081.00
18_Q26_E1.5081.00
178_H217_H1.5051.00
185_V243_I1.4911.00
211_H227_R1.4841.00
274_F278_A1.4821.00
81_D121_H1.4301.00
278_A305_M1.4291.00
177_G222_T1.4281.00
119_L148_V1.4081.00
141_D277_Q1.4041.00
46_L66_A1.4031.00
201_V242_H1.4011.00
224_L240_M1.3981.00
157_R161_S1.3531.00
100_R143_T1.3521.00
175_A240_M1.3471.00
16_L61_G1.3441.00
172_E225_R1.3061.00
47_V52_C1.2981.00
169_R228_L1.2921.00
15_Q27_M1.2891.00
306_V310_E1.2881.00
172_E301_I1.2831.00
179_M245_H1.2691.00
153_P290_I1.2561.00
189_I238_V1.2551.00
13_E61_G1.2541.00
212_Y240_M1.2511.00
172_E215_M1.2471.00
124_P127_A1.2431.00
214_I217_H1.2351.00
192_H198_H1.2331.00
37_K41_L1.2331.00
103_V110_N1.2301.00
288_H295_M1.2261.00
114_T117_N1.2231.00
206_K232_R1.2211.00
99_P102_L1.2031.00
278_A308_L1.1941.00
162_L167_I1.1881.00
47_V65_V1.1841.00
100_R276_R1.1811.00
90_D93_I1.1671.00
96_I115_V1.1641.00
38_E42_D1.1581.00
160_E163_Q1.1551.00
179_M224_L1.1491.00
18_Q22_Q1.1431.00
190_S202_H1.1371.00
141_D251_P1.1321.00
23_A59_V1.1281.00
92_D154_A1.1261.00
174_V223_R1.1111.00
210_T228_L1.1041.00
155_Q159_V1.0921.00
173_A224_L1.0901.00
303_Q306_V1.0891.00
177_G245_H1.0841.00
157_R160_E1.0831.00
176_I255_G1.0781.00
41_L55_P1.0721.00
195_K198_H1.0721.00
173_A247_L1.0721.00
102_L118_A1.0701.00
35_R39_W1.0631.00
100_R304_D1.0631.00
168_T294_E1.0601.00
49_G66_A1.0551.00
174_V309_I1.0501.00
175_A179_M1.0431.00
228_L236_I1.0431.00
184_T229_E1.0281.00
176_I248_V1.0281.00
107_G110_N1.0251.00
174_V308_L1.0231.00
25_A33_R1.0221.00
93_I154_A1.0191.00
301_I305_M1.0151.00
135_V158_L1.0081.00
24_L36_I1.0051.00
223_R309_I1.0001.00
179_M214_I1.0001.00
156_T160_E0.9991.00
240_M247_L0.9951.00
287_Y292_G0.9931.00
92_D288_H0.9901.00
145_L297_W0.9841.00
210_T239_H0.9841.00
135_V149_A0.9831.00
93_I286_L0.9791.00
153_P157_R0.9791.00
94_I119_L0.9731.00
94_I123_Y0.9711.00
178_H219_R0.9651.00
134_I148_V0.9641.00
300_P306_V0.9631.00
57_E63_E0.9601.00
46_L68_N0.9561.00
101_D143_T0.9531.00
35_R38_E0.9531.00
15_Q23_A0.9441.00
34_S37_K0.9411.00
37_K55_P0.9391.00
113_G118_A0.9371.00
190_S204_M0.9341.00
178_H220_V0.9321.00
102_L115_V0.9291.00
189_I199_M0.9291.00
197_T252_V0.9201.00
175_A222_T0.9201.00
31_Y39_W0.9141.00
149_A155_Q0.9071.00
192_H195_K0.9041.00
286_L297_W0.8991.00
174_V305_M0.8971.00
75_A129_V0.8941.00
16_L60_L0.8931.00
60_L63_E0.8881.00
39_W44_R0.8861.00
175_A247_L0.8831.00
40_I45_V0.8821.00
225_R282_T0.8791.00
93_I288_H0.8781.00
87_V300_P0.8751.00
83_P118_A0.8661.00
181_A214_I0.8651.00
185_V240_M0.8591.00
280_H299_A0.8561.00
174_V221_H0.8551.00
94_I148_V0.8531.00
18_Q23_A0.8521.00
157_R292_G0.8511.00
274_F305_M0.8481.00
161_S287_Y0.8421.00
288_H291_S0.8421.00
179_M217_H0.8401.00
145_L299_A0.8401.00
170_E282_T0.8391.00
33_R37_K0.8381.00
54_K57_E0.8361.00
162_L169_R0.8331.00
192_H200_A0.8301.00
149_A154_A0.8291.00
45_V67_I0.8271.00
175_A245_H0.8261.00
84_L118_A0.8241.00
182_G211_H0.8191.00
236_I247_L0.8161.00
187_E243_I0.8131.00
221_H248_V0.8101.00
40_I55_P0.8081.00
152_V155_Q0.8071.00
216_E223_R0.8071.00
104_V138_L0.8071.00
286_L295_M0.8041.00
180_T245_H0.8011.00
274_F308_L0.7981.00
183_G214_I0.7951.00
276_R305_M0.7951.00
278_A304_D0.7941.00
59_V65_V0.7931.00
57_E60_L0.7931.00
44_R68_N0.7901.00
31_Y36_I0.7881.00
157_R290_I0.7871.00
46_L51_V0.7841.00
162_L228_L0.7841.00
116_L134_I0.7831.00
88_Y297_W0.7781.00
117_N120_L0.7781.00
89_E123_Y0.7771.00
20_L40_I0.7761.00
182_G214_I0.7711.00
176_I221_H0.7691.00
24_L45_V0.7611.00
188_P207_P0.7571.00
188_P239_H0.7571.00
43_Q51_V0.7541.00
174_V218_F0.7441.00
190_S200_A0.7401.00
191_R233_T0.7381.00
276_R280_H0.7361.00
178_H222_T0.7351.00
96_I146_M0.7301.00
31_Y35_R0.7271.00
87_V299_A0.7271.00
202_H205_G0.7251.00
106_P114_T0.7241.00
152_V156_T0.7231.00
185_V239_H0.7221.00
15_Q18_Q0.7211.00
287_Y291_S0.7181.00
115_V148_V0.7171.00
84_L96_I0.7161.00
185_V212_Y0.7151.00
103_V109_G0.7151.00
123_Y150_K0.7131.00
208_A232_R0.7121.00
93_I295_M0.7121.00
169_R229_E0.7121.00
274_F304_D0.7081.00
19_R22_Q0.7081.00
28_F36_I0.7071.00
255_G259_P0.7030.99
307_E310_E0.6940.99
104_V134_I0.6940.99
218_F221_H0.6930.99
159_V163_Q0.6910.99
198_H241_A0.6910.99
20_L65_V0.6910.99
116_L132_A0.6890.99
188_P205_G0.6870.99
136_H162_L0.6820.99
17_G61_G0.6810.99
88_Y93_I0.6780.99
28_F31_Y0.6760.99
81_D118_A0.6760.99
213_R227_R0.6710.99
255_G258_R0.6710.99
132_A148_V0.6670.99
305_M309_I0.6590.99
156_T159_V0.6580.99
146_M281_A0.6570.99
168_T283_M0.6550.99
15_Q26_E0.6540.99
277_Q304_D0.6530.99
84_L122_Y0.6500.99
170_E285_R0.6450.99
248_V274_F0.6440.99
22_Q26_E0.6440.99
103_V107_G0.6430.99
201_V238_V0.6430.99
39_W67_I0.6380.99
174_V248_V0.6360.99
89_E122_Y0.6350.99
198_H252_V0.6350.99
151_T290_I0.6330.99
104_V115_V0.6320.99
301_I309_I0.6310.99
222_T245_H0.6300.99
210_T236_I0.6300.99
13_E16_L0.6290.99
274_F277_Q0.6270.99
133_G155_Q0.6260.99
39_W69_A0.6260.99
201_V205_G0.6250.99
187_E201_V0.6240.99
82_I102_L0.6230.99
105_H114_T0.6230.99
147_V162_L0.6210.99
47_V63_E0.6200.99
145_L284_L0.6180.99
49_G64_Q0.6170.99
176_I259_P0.6160.99
94_I150_K0.6140.99
218_F309_I0.6140.99
183_G243_I0.6130.99
281_A284_L0.6130.99
92_D153_P0.6060.98
218_F223_R0.6040.98
248_V278_A0.6040.98
71_I74_E0.6010.98
20_L47_V0.6010.98
118_A121_H0.6000.98
94_I122_Y0.5950.98
215_M223_R0.5950.98
107_G197_T0.5940.98
196_R199_M0.5920.98
147_V284_L0.5920.98
176_I258_R0.5920.98
136_H281_A0.5910.98
47_V59_V0.5900.98
79_P120_L0.5890.98
120_L132_A0.5880.98
113_G117_N0.5840.98
251_P255_G0.5830.98
135_V155_Q0.5800.98
248_V258_R0.5790.98
154_A290_I0.5790.98
161_S167_I0.5770.98
120_L124_P0.5770.98
86_I94_I0.5770.98
212_Y226_L0.5760.98
183_G240_M0.5760.98
85_D99_P0.5760.98
158_L161_S0.5750.98
115_V122_Y0.5720.98
23_A65_V0.5710.98
100_R275_D0.5710.98
183_G226_L0.5710.98
136_H146_M0.5700.98
176_I254_G0.5700.98
86_I89_E0.5700.98
149_A158_L0.5700.98
85_D88_Y0.5700.98
176_I256_R0.5680.98
119_L123_Y0.5670.98
187_E239_H0.5660.98
179_M240_M0.5650.98
20_L57_E0.5620.98
168_T296_E0.5620.98
39_W45_V0.5600.97
112_D117_N0.5600.97
188_P204_M0.5590.97
301_I306_V0.5580.97
91_E150_K0.5550.97
97_N143_T0.5530.97
127_A155_Q0.5520.97
192_H196_R0.5500.97
17_G58_K0.5490.97
191_R196_R0.5470.97
282_T300_P0.5470.97
34_S38_E0.5450.97
101_D141_D0.5450.97
135_V162_L0.5450.97
179_M183_G0.5440.97
22_Q33_R0.5440.97
96_I119_L0.5430.97
122_Y126_I0.5420.97
179_M212_Y0.5400.97
133_G152_V0.5380.97
174_V278_A0.5380.97
153_P156_T0.5360.97
96_I148_V0.5360.97
21_D25_A0.5330.97
166_E287_Y0.5330.97
25_A36_I0.5310.97
138_L165_R0.5310.97
110_N113_G0.5310.97
93_I158_L0.5300.97
29_P36_I0.5290.96
143_T276_R0.5290.96
119_L126_I0.5280.96
28_F67_I0.5270.96
165_R168_T0.5260.96
117_N121_H0.5230.96
89_E94_I0.5230.96
84_L102_L0.5210.96
208_A238_V0.5210.96
24_L28_F0.5200.96
32_S39_W0.5190.96
88_Y295_M0.5190.96
70_E73_E0.5180.96
44_R51_V0.5180.96
103_V134_I0.5180.96
94_I145_L0.5170.96
238_V242_H0.5160.96
74_E77_F0.5150.96
124_P130_P0.5150.96
249_G278_A0.5150.96
165_R229_E0.5140.96
154_A157_R0.5140.96
259_P272_R0.5110.96
91_E290_I0.5090.96
80_Q84_L0.5090.96
304_D308_L0.5090.96
225_R283_M0.5080.96
93_I297_W0.5070.96
128_D152_V0.5040.95
129_V132_A0.5040.95
161_S290_I0.5040.95
32_S35_R0.5030.95
97_N280_H0.5020.95
14_N27_M0.5010.95
92_D291_S0.5010.95
173_A240_M0.5000.95
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  
1v9fA 1 0.7669 100 0.172 Contact Map
1v9kA 1 0.6871 100 0.356 Contact Map
2i82A 1 0.6534 100 0.381 Contact Map
4lgtA 1 0.7362 100 0.463 Contact Map
1vioA 2 0.7025 100 0.467 Contact Map
1kskA 1 0.7117 100 0.475 Contact Map
3dh3A 1 0.7393 100 0.476 Contact Map
2olwA 1 0.5031 100 0.526 Contact Map
2omlA 1 0.5123 100 0.534 Contact Map
2gmlA 1 0.5245 100 0.589 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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