GREMLIN Database
RLUF - Ribosomal large subunit pseudouridine synthase F
UniProt: P32684 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11921
Length: 290 (226)
Sequences: 8250 (5557)
Seq/√Len: 369.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_N50_D5.1221.00
32_N55_N4.0331.00
34_F53_K3.6231.00
136_E178_R3.2391.00
170_K178_R3.1941.00
40_A44_D2.7211.00
72_L93_F2.5301.00
136_E207_R2.4661.00
12_Y46_V2.3831.00
19_C24_A2.3211.00
138_L176_V2.2611.00
140_T176_V2.2061.00
26_R30_Q2.1561.00
138_L178_R2.1021.00
111_Q202_K2.0871.00
134_E180_T2.0691.00
149_F198_Y2.0531.00
217_P220_E1.9721.00
111_Q204_E1.9711.00
78_I93_F1.9701.00
51_V58_L1.9591.00
34_F39_R1.9471.00
136_E180_T1.9271.00
23_E26_R1.8891.00
27_Y54_V1.8821.00
151_R155_A1.8571.00
70_I223_D1.8441.00
87_R108_K1.8171.00
13_I24_A1.8161.00
111_Q218_L1.8151.00
101_F123_V1.7981.00
10_N25_D1.7911.00
226_D230_I1.7841.00
187_R190_R1.7491.00
151_R154_S1.7461.00
222_R228_E1.7371.00
62_R113_L1.7271.00
7_V15_E1.7171.00
76_V111_Q1.6991.00
188_Q192_M1.6951.00
177_F193_C1.6391.00
53_K58_L1.5941.00
71_A211_V1.5831.00
164_T167_C1.5791.00
35_L44_D1.5691.00
139_V177_F1.5651.00
82_T91_V1.5641.00
142_D199_E1.5611.00
6_S45_Q1.5311.00
179_I193_C1.5261.00
134_E182_V1.5141.00
7_V12_Y1.4711.00
159_I191_R1.4691.00
164_T169_V1.4681.00
158_P163_V1.4491.00
90_I114_I1.4471.00
12_Y16_S1.4451.00
145_I175_F1.4351.00
146_T149_F1.4081.00
134_E207_R1.3951.00
123_V127_L1.3941.00
60_E73_N1.3841.00
140_T202_K1.3751.00
70_I221_W1.3501.00
207_R212_S1.3311.00
68_V119_H1.3211.00
143_K175_F1.2681.00
210_N231_D1.2641.00
67_L118_N1.2591.00
9_L40_A1.2521.00
71_A113_L1.2521.00
194_E199_E1.2511.00
144_P175_F1.2431.00
33_V54_V1.2431.00
165_K169_V1.2371.00
159_I162_T1.2221.00
26_R29_E1.2041.00
138_L206_T1.1921.00
72_L94_V1.1911.00
80_S114_I1.1891.00
166_K169_V1.1721.00
68_V223_D1.1701.00
80_S102_P1.1681.00
19_C27_Y1.1591.00
150_I154_S1.1511.00
82_T102_P1.1461.00
153_M196_F1.1391.00
141_V198_Y1.1281.00
152_G196_F1.1221.00
127_L208_I1.1221.00
168_K182_V1.1221.00
143_K198_Y1.1211.00
12_Y52_V1.1161.00
65_E118_N1.1141.00
142_D198_Y1.1051.00
81_T89_N1.0991.00
76_V202_K1.0981.00
149_F196_F1.0961.00
141_V193_C1.0961.00
91_V102_P1.0931.00
47_K50_D1.0881.00
6_S47_K1.0871.00
69_L122_L1.0851.00
139_V200_V1.0811.00
121_D125_K1.0651.00
29_E42_I1.0641.00
126_I208_I1.0641.00
55_N87_R1.0491.00
181_L188_Q1.0411.00
125_K131_N1.0331.00
7_V45_Q1.0271.00
77_G108_K1.0271.00
13_I19_C1.0261.00
141_V175_F1.0221.00
13_I59_I1.0141.00
35_L52_V1.0141.00
225_T228_E1.0131.00
141_V177_F1.0121.00
37_G53_K1.0101.00
178_R206_T1.0071.00
57_Q93_F1.0041.00
41_T44_D0.9871.00
80_S91_V0.9871.00
110_S190_R0.9841.00
100_V116_L0.9811.00
139_V179_I0.9791.00
153_M169_V0.9751.00
91_V116_L0.9731.00
140_T174_P0.9711.00
110_S139_V0.9701.00
28_I33_V0.9661.00
94_V116_L0.9621.00
158_P162_T0.9411.00
109_D190_R0.9351.00
134_E168_K0.9341.00
165_K182_V0.9271.00
122_L126_I0.9211.00
153_M156_G0.9151.00
211_V214_S0.9091.00
23_E27_Y0.9031.00
27_Y32_N0.9011.00
162_T167_C0.8981.00
142_D201_K0.8931.00
158_P195_H0.8911.00
124_N128_R0.8871.00
55_N88_D0.8831.00
124_N127_L0.8821.00
163_V167_C0.8761.00
152_G155_A0.8751.00
70_I94_V0.8711.00
110_S189_I0.8641.00
38_K44_D0.8641.00
7_V11_K0.8571.00
138_L202_K0.8501.00
191_R194_E0.8501.00
8_R45_Q0.8451.00
25_D29_E0.8411.00
129_A132_D0.8401.00
157_V196_F0.8321.00
28_I42_I0.8311.00
46_V52_V0.8261.00
117_T123_V0.8241.00
18_I54_V0.8231.00
145_I149_F0.8171.00
145_I198_Y0.8131.00
9_L52_V0.8131.00
119_H122_L0.8111.00
170_K180_T0.8091.00
72_L78_I0.8091.00
106_L114_I0.8051.00
31_G39_R0.8021.00
171_K174_P0.7991.00
145_I177_F0.7991.00
179_I189_I0.7981.00
31_G41_T0.7961.00
154_S168_K0.7921.00
173_A176_V0.7851.00
162_T185_L0.7801.00
19_C23_E0.7791.00
150_I169_V0.7781.00
169_V179_I0.7701.00
135_K181_L0.7671.00
25_D42_I0.7641.00
90_I116_L0.7611.00
227_D231_D0.7591.00
13_I33_V0.7591.00
224_L228_E0.7571.00
79_V86_E0.7561.00
161_G191_R0.7551.00
9_L28_I0.7541.00
159_I164_T0.7531.00
69_L119_H0.7501.00
89_N92_D0.7431.00
10_N43_G0.7401.00
227_D230_I0.7391.00
73_N218_L0.7391.00
79_V87_R0.7361.00
82_T89_N0.7361.00
147_E151_R0.7351.00
157_V195_H0.7341.00
152_G156_G0.7291.00
105_R184_G0.7251.00
34_F56_G0.7161.00
138_L219_G0.7141.00
132_D165_K0.7141.00
18_I27_Y0.7131.00
224_L229_L0.7100.99
73_N217_P0.7090.99
135_K188_Q0.7080.99
149_F152_G0.7070.99
167_C181_L0.7060.99
71_A214_S0.7050.99
78_I88_D0.7050.99
144_P172_E0.7030.99
81_T85_G0.6980.99
214_S222_R0.6960.99
153_M192_M0.6950.99
73_N204_E0.6950.99
150_I153_M0.6930.99
7_V48_P0.6900.99
35_L40_A0.6860.99
174_P201_K0.6840.99
79_V84_D0.6820.99
167_C188_Q0.6820.99
81_T87_R0.6810.99
56_G96_H0.6810.99
183_Q188_Q0.6780.99
113_L213_L0.6760.99
71_A222_R0.6700.99
143_K199_E0.6690.99
164_T188_Q0.6660.99
144_P173_A0.6650.99
68_V118_N0.6650.99
141_V145_I0.6630.99
122_L232_L0.6620.99
72_L90_I0.6580.99
167_C182_V0.6570.99
158_P164_T0.6560.99
13_I16_S0.6560.99
180_T207_R0.6530.99
217_P223_D0.6520.99
147_E171_K0.6510.99
37_G51_V0.6500.99
11_K15_E0.6470.99
136_E206_T0.6460.99
223_D226_D0.6370.99
143_K174_P0.6360.99
140_T201_K0.6350.99
193_C196_F0.6330.99
82_T90_I0.6310.99
138_L204_E0.6290.99
171_K175_F0.6270.99
88_D108_K0.6190.99
153_M157_V0.6170.99
226_D229_L0.6160.99
186_N190_R0.6150.99
154_S157_V0.6150.99
105_R190_R0.6140.99
222_R225_T0.6140.99
9_L35_L0.6130.98
153_M193_C0.6130.98
113_L208_I0.6120.98
142_D173_A0.6120.98
70_I116_L0.6100.98
13_I18_I0.6100.98
106_L131_N0.6080.98
135_K208_I0.6070.98
24_A27_Y0.6060.98
157_V164_T0.6050.98
83_E86_E0.6030.98
16_S19_C0.6030.98
168_K180_T0.6020.98
146_T198_Y0.5990.98
68_V98_K0.5980.98
148_E152_G0.5950.98
169_V177_F0.5940.98
169_V193_C0.5870.98
111_Q190_R0.5810.98
14_S21_R0.5790.98
176_V202_K0.5790.98
32_N54_V0.5790.98
216_I220_E0.5780.98
96_H221_W0.5760.98
124_N130_G0.5750.98
213_L216_I0.5730.98
107_D184_G0.5720.98
107_D190_R0.5720.98
10_N42_I0.5710.98
25_D43_G0.5680.98
25_D28_I0.5660.97
120_G123_V0.5620.97
144_P174_P0.5610.97
65_E223_D0.5600.97
145_I193_C0.5560.97
163_V169_V0.5490.97
84_D87_R0.5480.97
68_V100_V0.5470.97
217_P226_D0.5450.97
76_V218_L0.5440.97
166_K192_M0.5440.97
88_D92_D0.5430.97
207_R210_N0.5430.97
79_V108_K0.5420.97
160_L163_V0.5420.97
103_I114_I0.5400.97
162_T169_V0.5400.97
162_T191_R0.5390.97
42_I45_Q0.5390.97
210_N232_L0.5390.97
76_V109_D0.5390.97
160_L191_R0.5370.97
217_P221_W0.5360.97
69_L224_L0.5340.96
135_K182_V0.5320.96
24_A28_I0.5320.96
162_T165_K0.5310.96
163_V185_L0.5290.96
82_T101_F0.5290.96
167_C192_M0.5270.96
79_V85_G0.5260.96
22_R25_D0.5260.96
14_S24_A0.5240.96
9_L44_D0.5230.96
56_G59_I0.5210.96
103_I117_T0.5210.96
69_L229_L0.5170.96
137_Y184_G0.5150.96
155_A166_K0.5150.96
12_Y44_D0.5100.95
128_R131_N0.5090.95
76_V190_R0.5080.95
185_L188_Q0.5080.95
22_R26_R0.5070.95
158_P161_G0.5060.95
72_L114_I0.5050.95
186_N191_R0.5020.95
110_S187_R0.5010.95
77_G111_Q0.5000.95
90_I93_F0.5000.95
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  
3dh3A 1 0.831 100 0.178 Contact Map
1vioA 2 0.769 100 0.25 Contact Map
4lgtA 1 0.8138 100 0.258 Contact Map
1kskA 1 0.7862 100 0.273 Contact Map
1v9fA 1 0.7034 100 0.312 Contact Map
2gmlA 1 0.6034 100 0.319 Contact Map
2olwA 1 0.5552 100 0.382 Contact Map
2omlA 1 0.5586 100 0.39 Contact Map
2i82A 1 0.6586 100 0.453 Contact Map
1v9kA 1 0.669 100 0.458 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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