GREMLIN Database
YLYB - Uncharacterized RNA pseudouridine synthase YlyB
UniProt: Q45480 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 303 (278)
Sequences: 9189 (6375)
Seq/√Len: 382.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
169_K225_E3.5031.00
83_Y144_L3.4691.00
211_H229_E3.4151.00
45_N59_D3.2361.00
270_V283_E2.9251.00
85_E149_K2.8961.00
213_H225_E2.8551.00
272_G283_E2.8041.00
171_T223_L2.7941.00
171_T269_G2.7641.00
81_D93_N2.7161.00
184_T211_H2.7031.00
88_D277_R2.6541.00
183_G212_F2.5911.00
88_D150_N2.5641.00
187_A242_Y2.5431.00
93_N286_A2.3831.00
182_D213_H2.2981.00
186_D209_V2.2831.00
226_C240_M2.2731.00
181_D217_R2.2531.00
167_T227_Q2.2491.00
272_G281_Y2.2411.00
186_D207_N2.2401.00
184_T209_V2.2101.00
91_V284_F2.1341.00
169_K270_V2.0921.00
263_G291_D2.0871.00
150_N153_A2.0511.00
78_M114_G2.0461.00
76_E108_T2.0441.00
274_D281_Y2.0391.00
270_V285_E1.9881.00
214_V222_T1.9851.00
111_L145_L1.9701.00
169_K227_Q1.9611.00
209_V229_E1.9381.00
172_A226_C1.9211.00
167_T272_G1.9071.00
49_V53_Y1.8561.00
17_I49_V1.8431.00
215_L225_E1.8391.00
160_Q165_T1.8281.00
142_S267_H1.8061.00
178_I222_T1.8031.00
210_T226_C1.7971.00
174_V224_V1.7521.00
76_E109_G1.7481.00
159_N163_N1.7151.00
226_C236_I1.6491.00
269_G285_E1.6201.00
44_V53_Y1.5901.00
137_I145_L1.5841.00
100_V145_L1.5641.00
91_V144_L1.5621.00
91_V146_M1.5541.00
261_F265_A1.5511.00
15_E23_S1.5411.00
176_G222_T1.5401.00
83_Y284_F1.5151.00
20_F24_T1.4971.00
290_E294_E1.4911.00
86_D275_H1.4691.00
217_R222_T1.4611.00
77_P117_A1.4501.00
211_H227_Q1.4341.00
265_A292_M1.4311.00
140_D264_Q1.4311.00
185_I243_I1.4171.00
177_L217_R1.4131.00
156_S160_Q1.3991.00
224_V240_M1.3891.00
115_L147_V1.3791.00
43_V62_T1.3671.00
12_Q24_T1.3341.00
96_R142_S1.3341.00
171_T225_E1.3171.00
174_V240_M1.3081.00
44_V49_V1.3061.00
201_V242_Y1.3021.00
13_K57_P1.2941.00
189_I238_V1.2741.00
212_F240_M1.2651.00
171_T288_L1.2631.00
99_V106_H1.2571.00
168_R228_L1.2471.00
171_T215_L1.2411.00
221_F248_A1.2331.00
206_K232_R1.2331.00
275_H282_V1.2301.00
110_T113_N1.2291.00
178_I245_F1.2291.00
109_G114_G1.2221.00
192_D198_S1.2211.00
34_Q38_K1.2051.00
152_M277_R1.1961.00
173_V221_F1.1941.00
86_D89_V1.1931.00
214_V217_R1.1881.00
15_E19_K1.1771.00
95_P98_M1.1661.00
265_A295_L1.1621.00
96_R263_G1.1551.00
44_V61_V1.1481.00
161_L166_V1.1461.00
159_N162_V1.1361.00
35_Q39_D1.1351.00
210_T228_L1.1341.00
98_M114_G1.1301.00
140_D251_P1.1301.00
154_H158_V1.1281.00
92_V111_L1.1201.00
20_F55_I1.1131.00
32_Q36_W1.1111.00
178_I224_V1.1011.00
195_D198_S1.0971.00
190_G202_T1.0941.00
172_A224_V1.0921.00
176_G245_F1.0871.00
38_K51_A1.0841.00
175_H255_P1.0831.00
22_A30_R1.0721.00
156_S159_N1.0711.00
173_V223_L1.0701.00
210_T239_H1.0691.00
228_L236_I1.0591.00
174_V178_I1.0581.00
290_E293_A1.0561.00
88_D153_A1.0561.00
172_A247_L1.0531.00
46_G62_T1.0481.00
167_T281_Y1.0471.00
177_L220_D1.0391.00
223_L296_I1.0341.00
134_V157_L1.0281.00
173_V295_L1.0251.00
173_V296_I1.0231.00
96_R291_D1.0201.00
155_E159_N1.0091.00
288_L292_M1.0031.00
32_Q35_Q1.0031.00
240_M247_L0.9921.00
175_H248_A0.9901.00
88_D275_H0.9871.00
174_V222_T0.9841.00
152_M156_S0.9831.00
89_V273_F0.9801.00
184_T229_E0.9781.00
178_I214_V0.9741.00
53_Y59_D0.9701.00
90_L119_C0.9661.00
133_I147_V0.9661.00
287_P293_A0.9591.00
103_A106_H0.9591.00
12_Q20_F0.9551.00
21_L33_V0.9541.00
180_H183_G0.9541.00
134_V148_A0.9501.00
274_D279_G0.9501.00
148_A154_H0.9471.00
144_L284_F0.9431.00
98_M111_L0.9411.00
31_T34_Q0.9331.00
89_V153_A0.9311.00
90_L115_L0.9271.00
192_D195_D0.9181.00
190_G204_D0.9161.00
175_H221_F0.9121.00
56_Q59_D0.9091.00
174_V247_L0.8961.00
37_V51_A0.8931.00
41_Q64_T0.8851.00
13_K56_Q0.8841.00
34_Q51_A0.8831.00
89_V275_H0.8821.00
50_K53_Y0.8821.00
43_V64_T0.8791.00
273_F284_F0.8731.00
180_H212_F0.8721.00
225_E269_G0.8691.00
189_I199_M0.8681.00
178_I217_R0.8671.00
173_V292_M0.8641.00
177_L219_Q0.8621.00
180_H214_V0.8621.00
71_L128_V0.8601.00
261_F292_M0.8581.00
144_L286_A0.8571.00
97_G142_S0.8521.00
28_W36_W0.8491.00
255_P258_T0.8481.00
151_D154_H0.8461.00
185_I240_M0.8461.00
160_Q274_D0.8431.00
181_D214_V0.8371.00
148_A153_A0.8361.00
36_W41_Q0.8351.00
197_Q252_K0.8301.00
169_K269_G0.8291.00
216_E223_L0.8291.00
15_E20_F0.8271.00
100_V137_I0.8261.00
267_H286_A0.8211.00
79_D114_G0.8181.00
90_L147_V0.8161.00
236_I247_L0.8151.00
40_G48_A0.8111.00
174_V245_F0.7971.00
28_W33_V0.7971.00
156_S279_G0.7961.00
261_F295_L0.7961.00
177_L222_T0.7961.00
84_Y284_F0.7931.00
187_A243_I0.7911.00
43_V48_A0.7911.00
161_L168_R0.7901.00
190_G200_T0.7891.00
265_A291_D0.7871.00
183_G214_V0.7851.00
263_G292_M0.7821.00
42_V63_V0.7821.00
156_S277_R0.7751.00
80_L114_G0.7741.00
274_D278_T0.7721.00
37_V42_V0.7691.00
55_I61_V0.7641.00
53_Y56_Q0.7641.00
182_D211_H0.7641.00
21_L42_V0.7601.00
161_L228_L0.7601.00
151_D155_E0.7581.00
188_P239_H0.7501.00
113_N116_M0.7481.00
83_Y287_P0.7471.00
273_F282_V0.7471.00
187_A201_V0.7461.00
261_F264_Q0.7451.00
213_H227_Q0.7391.00
179_S245_F0.7361.00
158_V162_V0.7351.00
30_R34_Q0.7331.00
89_V282_V0.7291.00
182_D214_V0.7281.00
192_D200_T0.7271.00
131_P147_V0.7191.00
84_Y89_V0.7181.00
85_E119_C0.7171.00
263_G267_H0.7161.00
201_V205_G0.7161.00
188_P205_G0.7161.00
16_R19_K0.7111.00
111_L147_V0.7111.00
275_H278_T0.7101.00
185_I239_H0.7101.00
12_Q23_S0.7091.00
109_G113_N0.7041.00
188_P207_N0.7031.00
112_V133_I0.7021.00
12_Q15_E0.7000.99
145_L268_A0.7000.99
102_P110_T0.6990.99
119_C149_K0.6970.99
292_M296_I0.6960.99
92_V145_L0.6920.99
191_R233_T0.6900.99
100_V133_I0.6900.99
80_L92_V0.6880.99
17_I37_V0.6870.99
173_V218_F0.6860.99
112_V131_P0.6840.99
175_H258_T0.6840.99
261_F291_D0.6810.99
28_W32_Q0.6780.99
185_I212_F0.6780.99
168_R229_E0.6770.99
155_E158_V0.6770.99
25_E33_V0.6760.99
198_S241_K0.6750.99
80_L118_H0.6720.99
90_L149_K0.6710.99
210_T236_I0.6710.99
255_P259_I0.6660.99
175_H259_I0.6650.99
135_H145_L0.6610.99
25_E28_W0.6550.99
83_Y286_A0.6530.99
135_H161_L0.6520.99
268_A271_L0.6520.99
208_A232_R0.6470.99
99_V105_G0.6450.99
74_L77_P0.6450.99
14_S57_P0.6420.99
264_Q291_D0.6400.99
85_E118_H0.6400.99
218_F296_I0.6380.99
167_T270_V0.6370.99
132_G154_H0.6350.99
191_R196_R0.6340.99
116_M131_P0.6290.99
169_K272_G0.6240.99
88_D152_M0.6110.99
135_H268_A0.6110.99
218_F223_L0.6100.99
36_W65_V0.6100.99
115_L119_C0.6090.99
19_K23_S0.6080.99
99_V103_A0.6050.99
36_W63_V0.6050.99
103_A197_Q0.6020.98
288_L296_I0.6010.98
20_F61_V0.6000.98
100_V111_L0.5990.98
146_M271_L0.5980.98
222_T245_F0.5980.98
144_L271_L0.5960.98
248_A265_A0.5960.98
183_G243_I0.5940.98
173_V265_A0.5940.98
218_F221_F0.5940.98
148_A157_L0.5920.98
77_P114_G0.5890.98
215_L223_L0.5840.98
17_I61_V0.5810.98
197_Q200_T0.5800.98
93_N142_S0.5770.98
212_F226_C0.5760.98
137_I164_K0.5760.98
173_V248_A0.5760.98
217_R220_D0.5740.98
251_P255_P0.5720.98
160_Q166_V0.5680.98
160_Q277_R0.5670.98
82_I90_L0.5660.98
134_V154_H0.5660.98
183_G240_M0.5660.98
134_V161_L0.5650.98
17_I53_Y0.5610.98
44_V55_I0.5590.98
92_V147_V0.5580.98
198_S201_V0.5580.98
150_N277_R0.5570.98
35_Q38_K0.5570.98
256_R259_I0.5570.98
175_H254_G0.5570.98
188_P204_D0.5560.97
146_M161_L0.5550.97
117_A120_T0.5550.97
101_H110_T0.5550.97
269_G287_P0.5540.97
132_G151_D0.5530.97
113_N117_A0.5530.97
165_T274_D0.5520.97
256_R260_D0.5520.97
67_E70_A0.5500.97
257_K260_D0.5500.97
188_P202_T0.5490.97
248_A261_F0.5480.97
175_H220_D0.5480.97
108_T113_N0.5480.97
14_S54_K0.5470.97
198_S252_K0.5460.97
202_T205_G0.5450.97
90_L118_H0.5440.97
78_M98_M0.5410.97
81_D95_P0.5400.97
106_H109_G0.5390.97
221_F295_L0.5370.97
183_G226_C0.5370.97
116_M120_T0.5360.97
201_V238_V0.5360.97
45_N49_V0.5350.97
31_T35_Q0.5340.97
157_L160_Q0.5340.97
87_Q149_K0.5340.97
21_L25_E0.5320.97
77_P80_L0.5320.97
187_A239_H0.5310.97
41_Q66_P0.5310.97
153_A277_R0.5300.97
127_G151_D0.5300.97
288_L293_A0.5300.97
17_I44_V0.5300.97
194_K198_S0.5300.97
46_G60_Q0.5290.97
188_P201_V0.5280.97
248_A258_T0.5280.97
167_T283_E0.5260.96
74_L108_T0.5260.96
68_P71_L0.5250.96
89_V284_F0.5250.96
137_I144_L0.5250.96
44_V59_D0.5240.96
225_E270_V0.5240.96
178_I212_F0.5240.96
291_D295_L0.5220.96
96_R262_N0.5220.96
178_I240_M0.5200.96
82_I85_E0.5170.96
34_Q37_V0.5170.96
120_T129_M0.5160.96
75_A109_G0.5160.96
238_V242_Y0.5140.96
189_I205_G0.5130.96
249_G265_A0.5120.96
181_D213_H0.5120.96
43_V47_S0.5120.96
55_I59_D0.5110.96
164_K167_T0.5100.96
36_W42_V0.5090.96
37_V49_V0.5080.96
115_L131_P0.5060.96
93_N267_H0.5040.96
89_V157_L0.5020.95
66_P69_E0.5020.95
54_K57_P0.5010.95
97_G140_D0.5010.95
84_Y282_V0.5000.95
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 0.7492 100 0.154 Contact Map
1v9kA 1 0.7162 100 0.306 Contact Map
2i82A 1 0.703 100 0.342 Contact Map
4lgtA 1 0.7723 100 0.43 Contact Map
1vioA 2 0.7525 100 0.434 Contact Map
3dh3A 1 0.7855 100 0.436 Contact Map
1kskA 1 0.7624 100 0.456 Contact Map
2olwA 1 0.5446 100 0.495 Contact Map
2omlA 1 0.5479 100 0.508 Contact Map
2gmlA 1 0.5776 100 0.564 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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