GREMLIN Database
RLUB - Ribosomal large subunit pseudouridine synthase B
UniProt: P35159 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 244 (218)
Sequences: 15108 (10186)
Seq/√Len: 689.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
31_N46_D3.9581.00
131_T179_Q3.7821.00
165_K179_Q3.1221.00
163_K183_H2.9831.00
133_V177_I2.9001.00
29_K49_E2.8991.00
27_K51_N2.7101.00
35_V40_V2.6721.00
58_E113_N2.6131.00
129_D181_T2.5601.00
61_V114_D2.3971.00
131_T181_T2.3151.00
167_L179_Q2.2271.00
180_L194_F2.1591.00
135_K177_I2.0051.00
7_V42_V1.9871.00
133_V179_Q1.9861.00
21_E25_E1.9161.00
134_A180_L1.8901.00
114_D117_F1.8891.00
18_K21_E1.8161.00
7_V11_A1.7971.00
14_A19_A1.7851.00
65_L87_F1.7711.00
71_V87_F1.7651.00
73_S109_L1.7461.00
84_V109_L1.7391.00
139_I169_L1.7391.00
124_P127_E1.7231.00
69_R106_S1.7071.00
30_V40_V1.7061.00
140_P176_S1.6961.00
106_S203_K1.6481.00
161_P183_H1.6431.00
218_H221_D1.6361.00
166_L176_S1.6121.00
4_L35_V1.5991.00
163_K181_T1.5911.00
131_T208_E1.5771.00
8_I19_A1.5691.00
146_R150_R1.5401.00
178_I194_F1.5281.00
29_K34_V1.4961.00
101_L109_L1.4881.00
136_V194_F1.4771.00
136_V178_I1.4721.00
96_Y118_A1.4421.00
180_L190_V1.4121.00
118_A122_M1.3921.00
168_S177_I1.3881.00
64_L108_L1.3851.00
106_S219_T1.3611.00
106_S205_K1.3591.00
134_A178_I1.3541.00
189_Q193_M1.3491.00
30_V35_V1.3451.00
22_L50_V1.3381.00
120_K124_P1.3331.00
162_A180_L1.3281.00
24_K38_L1.3151.00
18_K22_L1.3071.00
138_G176_S1.3041.00
170_D173_K1.3031.00
134_A201_V1.2871.00
5_Q20_E1.2841.00
135_K175_T1.2781.00
37_E40_V1.2671.00
64_L110_L1.2661.00
188_R191_R1.2631.00
133_V220_G1.2541.00
144_L199_H1.2531.00
30_V48_I1.2521.00
137_K200_E1.2511.00
88_F111_L1.2491.00
32_G49_E1.2321.00
43_T46_D1.2181.00
146_R149_E1.2181.00
116_E120_K1.2161.00
14_A22_L1.2141.00
140_P199_H1.2081.00
47_Q54_K1.2031.00
169_L176_S1.2021.00
143_E169_L1.2001.00
138_G199_H1.1961.00
166_L169_L1.1901.00
75_A85_T1.1811.00
83_V86_D1.1811.00
20_E24_K1.1691.00
73_S97_P1.1591.00
63_F222_A1.1591.00
119_N123_H1.1321.00
151_G154_L1.1091.00
112_T118_A1.1081.00
59_E62_Y1.0981.00
68_P71_V1.0981.00
130_K182_I1.0981.00
135_K203_K1.0981.00
82_K87_F1.0961.00
62_Y117_F1.0921.00
22_L27_K1.0901.00
133_V167_L1.0841.00
159_T162_A1.0821.00
148_L151_G1.0821.00
164_A194_F1.0771.00
85_T97_P1.0721.00
147_K150_R1.0721.00
65_L88_F1.0711.00
136_V176_S1.0711.00
140_P178_I1.0641.00
129_D183_H1.0621.00
175_T202_I1.0601.00
136_V199_H1.0521.00
208_E213_N1.0441.00
142_K166_L1.0431.00
9_A16_R1.0391.00
162_A193_M1.0381.00
26_G34_V1.0361.00
28_V50_V1.0351.00
147_K151_G1.0351.00
60_P113_N1.0251.00
215_R218_H1.0101.00
23_I38_L0.9951.00
144_L165_K0.9921.00
70_G103_Y0.9871.00
133_V207_E0.9761.00
137_K202_I0.9721.00
141_P144_L0.9661.00
139_I176_S0.9631.00
195_E200_E0.9601.00
69_R203_K0.9581.00
72_I79_K0.9541.00
63_F88_F0.9531.00
219_T222_A0.9501.00
23_I28_V0.9451.00
148_L152_I0.9441.00
162_A182_I0.9421.00
64_L212_L0.9261.00
120_K123_H0.9241.00
95_I111_L0.9211.00
129_D208_E0.9191.00
153_R158_K0.9171.00
170_D174_Q0.9161.00
75_A83_V0.9101.00
98_I112_T0.9091.00
139_I174_Q0.9041.00
137_K209_Y0.8991.00
17_R20_E0.8991.00
104_D205_K0.8981.00
145_L149_E0.8961.00
150_R154_L0.8951.00
154_L192_R0.8891.00
16_R20_E0.8801.00
75_A97_P0.8791.00
63_F111_L0.8771.00
42_V48_I0.8731.00
61_V117_F0.8711.00
84_V111_L0.8671.00
104_D191_R0.8671.00
112_T117_F0.8641.00
8_I11_A0.8611.00
119_N122_M0.8601.00
182_I189_Q0.8551.00
149_E152_I0.8551.00
218_H222_A0.8541.00
33_K40_V0.8481.00
182_I190_V0.8461.00
21_E24_K0.8431.00
40_V46_D0.8421.00
137_K199_H0.8411.00
136_V140_P0.8411.00
137_K175_T0.8401.00
49_E54_K0.8401.00
157_G186_R0.8361.00
20_E38_L0.8181.00
117_F121_L0.8161.00
105_T134_A0.8081.00
135_K170_D0.8061.00
165_K181_T0.8031.00
136_V201_V0.8021.00
97_P111_L0.7871.00
141_P199_H0.7851.00
144_L197_I0.7831.00
115_G119_N0.7831.00
179_Q207_E0.7801.00
145_L151_G0.7781.00
194_F201_V0.7751.00
40_V43_T0.7741.00
65_L84_V0.7741.00
160_A183_H0.7661.00
8_I28_V0.7641.00
85_T111_L0.7621.00
158_K186_R0.7601.00
74_A83_V0.7601.00
192_R195_E0.7601.00
161_P164_A0.7581.00
80_G103_Y0.7491.00
8_I14_A0.7481.00
98_I121_L0.7461.00
139_I173_K0.7431.00
73_S101_L0.7371.00
153_R157_G0.7311.00
76_Q79_K0.7271.00
147_K197_I0.7261.00
115_G118_A0.7241.00
209_Y212_L0.7231.00
137_K174_Q0.7231.00
6_K10_H0.7151.00
153_R196_A0.7151.00
170_D175_T0.7141.00
105_T191_R0.7111.00
7_V48_I0.7101.00
131_T221_D0.7091.00
212_L216_G0.7071.00
140_P166_L0.6971.00
144_L164_A0.6911.00
130_K189_Q0.6901.00
157_G160_A0.6891.00
29_K52_G0.6861.00
86_D89_K0.6841.00
145_L148_L0.6841.00
29_K51_N0.6791.00
32_G47_Q0.6771.00
3_R41_K0.6761.00
100_R185_G0.6751.00
164_A180_L0.6741.00
52_G55_V0.6721.00
148_L206_R0.6601.00
79_K82_K0.6531.00
14_A18_K0.6531.00
73_S85_T0.6521.00
120_K126_Y0.6521.00
71_V84_V0.6521.00
65_L71_V0.6511.00
140_P144_L0.6511.00
145_L150_R0.6511.00
190_V201_V0.6501.00
19_A22_L0.6461.00
82_K86_D0.6451.00
217_L221_D0.6421.00
153_R156_E0.6391.00
121_L209_Y0.6391.00
15_S18_K0.6381.00
169_L174_Q0.6341.00
30_V46_D0.6281.00
81_R86_D0.6271.00
5_Q39_G0.6251.00
86_D90_N0.6201.00
4_L23_I0.6181.00
157_G192_R0.6151.00
124_P128_I0.6151.00
130_K183_H0.6121.00
212_L215_R0.6111.00
87_F90_N0.6091.00
99_G109_L0.6091.00
57_R60_P0.6051.00
91_I95_I0.6031.00
85_T95_I0.6011.00
119_N125_K0.6001.00
122_M209_Y0.5961.00
152_I196_A0.5941.00
154_L157_G0.5921.00
213_N216_G0.5911.00
89_K92_P0.5901.00
138_G200_E0.5891.00
176_S199_H0.5891.00
12_G19_A0.5871.00
148_L154_L0.5871.00
140_P194_F0.5851.00
4_L48_I0.5831.00
8_I55_V0.5731.00
216_G219_T0.5721.00
166_L178_I0.5701.00
135_K202_I0.5701.00
140_P169_L0.5701.00
133_V203_K0.5691.00
117_F120_K0.5681.00
98_I118_A0.5671.00
72_I76_Q0.5671.00
150_R153_R0.5661.00
70_G106_S0.5631.00
129_D163_K0.5581.00
167_L177_I0.5571.00
72_I103_Y0.5561.00
66_Y219_T0.5551.00
184_E189_Q0.5541.00
105_T190_V0.5531.00
145_L152_I0.5531.00
30_V42_V0.5531.00
209_Y213_N0.5531.00
162_A183_H0.5511.00
219_T223_R0.5491.00
157_G162_A0.5461.00
130_K185_G0.5441.00
73_S84_V0.5441.00
4_L30_V0.5411.00
177_I203_K0.5411.00
13_V22_L0.5411.00
143_E166_L0.5411.00
215_R222_A0.5411.00
193_M197_I0.5401.00
4_L40_V0.5371.00
162_A189_Q0.5371.00
155_E192_R0.5351.00
71_V82_K0.5341.00
72_I77_D0.5331.00
72_I78_D0.5331.00
63_F113_N0.5321.00
170_D177_I0.5241.00
98_I110_L0.5201.00
13_V50_V0.5191.00
215_R219_T0.5170.99
169_L173_K0.5160.99
31_N48_I0.5150.99
144_L166_L0.5150.99
66_Y218_H0.5110.99
23_I35_V0.5110.99
139_I143_E0.5110.99
146_R151_G0.5110.99
70_G104_D0.5090.99
208_E211_F0.5070.99
77_D80_G0.5070.99
163_K166_L0.5060.99
17_R21_E0.5060.99
63_F66_Y0.5050.99
62_Y114_D0.5020.99
129_D223_R0.5010.99
142_K169_L0.5000.99
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  
1vioA 2 0.9303 100 0.204 Contact Map
1v9fA 1 0.7664 100 0.211 Contact Map
4lgtA 1 0.9754 100 0.24 Contact Map
1kskA 1 0.9385 100 0.244 Contact Map
3dh3A 1 0.959 100 0.245 Contact Map
2omlA 1 0.6926 100 0.333 Contact Map
2olwA 1 0.6885 100 0.335 Contact Map
2i82A 1 0.8115 100 0.356 Contact Map
2gmlA 1 0.7172 100 0.357 Contact Map
1v9kA 1 0.7746 100 0.357 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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