GREMLIN Database
YJBO - Uncharacterized RNA pseudouridine synthase YjbO
UniProt: O31613 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 283 (262)
Sequences: 9613 (6670)
Seq/√Len: 412.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
152_R208_A3.4901.00
194_H212_E3.3591.00
69_L127_I3.0671.00
30_N44_D3.0441.00
71_E132_K2.9051.00
252_H265_R2.8231.00
254_S265_R2.7391.00
196_Y208_A2.7111.00
67_D79_N2.6491.00
154_A251_E2.6301.00
154_A206_S2.6081.00
166_G195_F2.5651.00
167_T194_H2.5361.00
74_H133_H2.4501.00
170_A225_Y2.4301.00
74_H259_L2.4271.00
209_L223_M2.3501.00
165_E196_Y2.2741.00
254_S263_N2.2491.00
150_K210_Q2.2381.00
79_N268_A2.2011.00
164_M200_A2.1501.00
169_D192_V2.1451.00
169_D190_K2.1401.00
167_T192_V2.1391.00
245_R273_D2.1041.00
152_R252_H2.0971.00
77_V266_F2.0801.00
133_H136_A2.0221.00
150_K254_S1.9611.00
256_I263_N1.9541.00
197_V205_T1.9211.00
252_H267_H1.9091.00
97_I128_M1.9021.00
64_V100_G1.9011.00
125_S249_H1.8921.00
192_V212_E1.8821.00
155_A209_L1.8721.00
209_L219_I1.8661.00
152_R210_Q1.8631.00
143_A148_L1.8621.00
157_V207_V1.8171.00
62_E94_S1.8031.00
193_T209_L1.7901.00
198_T208_A1.7871.00
34_V38_Y1.7811.00
161_M205_T1.7341.00
142_S146_N1.6641.00
251_E267_H1.5811.00
77_V129_L1.5341.00
29_I38_Y1.5341.00
62_E95_G1.5301.00
243_I247_A1.5221.00
120_L128_M1.5211.00
86_S128_M1.5171.00
159_G205_T1.5091.00
194_H210_Q1.5081.00
72_D257_H1.4991.00
77_V127_I1.4981.00
13_S18_T1.4821.00
123_D246_Q1.4681.00
69_L266_F1.4461.00
272_Q276_K1.4411.00
247_A274_M1.4171.00
15_R18_T1.3891.00
160_R200_A1.3881.00
14_K18_T1.3781.00
139_I143_A1.3771.00
101_I130_V1.3561.00
28_Q47_I1.3531.00
207_V223_M1.3291.00
168_V226_L1.3241.00
157_V223_M1.3231.00
200_A205_T1.3161.00
14_K20_I1.3151.00
161_M228_H1.3111.00
14_K17_L1.3111.00
172_I221_V1.3091.00
63_P103_D1.3021.00
154_A208_A1.2881.00
82_P125_S1.2861.00
29_I34_V1.2851.00
154_A270_L1.2771.00
96_S99_N1.2441.00
151_R211_L1.2401.00
257_H264_M1.2361.00
159_G228_H1.2161.00
16_L20_I1.2151.00
204_M231_C1.2141.00
95_G100_G1.2101.00
13_S20_I1.2021.00
13_S17_L1.2011.00
85_S92_H1.1811.00
189_Q215_R1.1791.00
195_F223_M1.1741.00
156_V204_M1.1681.00
184_V225_Y1.1651.00
72_D75_V1.1641.00
154_A198_T1.1491.00
193_T222_H1.1471.00
197_V200_A1.1431.00
29_I46_L1.1421.00
144_Q149_V1.1341.00
137_H141_S1.1321.00
12_I20_I1.1231.00
142_S145_K1.1161.00
123_D234_T1.1081.00
135_F259_L1.1011.00
175_H181_E1.0951.00
82_P245_R1.0951.00
81_Q84_V1.0921.00
117_V131_A1.0881.00
163_Q197_V1.0871.00
116_L130_V1.0781.00
17_L20_I1.0731.00
127_I266_F1.0721.00
31_G47_I1.0701.00
158_H238_G1.0621.00
178_S181_E1.0501.00
23_G36_V1.0461.00
84_V100_G1.0421.00
272_Q275_S1.0411.00
12_I17_L1.0381.00
211_L219_I1.0331.00
139_I142_S1.0261.00
117_V140_L1.0241.00
193_T211_L1.0221.00
74_H257_H1.0211.00
155_A207_V1.0171.00
16_L19_D1.0151.00
131_A137_H1.0141.00
247_A277_L1.0121.00
74_H136_A1.0111.00
160_R203_D1.0101.00
155_A230_L1.0101.00
161_M207_V1.0021.00
138_S142_S1.0001.00
256_I261_Q0.9961.00
150_K263_N0.9951.00
78_I97_I0.9911.00
173_G185_T0.9891.00
157_V161_M0.9831.00
15_R19_D0.9731.00
156_V206_S0.9731.00
255_F266_F0.9671.00
82_P273_D0.9591.00
270_L274_M0.9581.00
167_T212_E0.9581.00
38_Y44_D0.9521.00
143_A256_I0.9511.00
161_M197_V0.9501.00
75_V255_F0.9441.00
269_P275_S0.9441.00
15_R20_I0.9431.00
156_V277_L0.9301.00
75_V257_H0.9241.00
158_H204_M0.9241.00
238_G242_E0.9171.00
157_V205_T0.9171.00
223_M230_L0.9081.00
75_V136_A0.9041.00
175_H178_S0.9021.00
158_H231_C0.8901.00
208_A251_E0.8811.00
131_A136_A0.8801.00
89_S92_H0.8771.00
86_S120_L0.8761.00
35_T38_Y0.8751.00
13_S16_L0.8721.00
127_I268_A0.8691.00
171_P222_H0.8681.00
160_R202_D0.8651.00
163_Q166_G0.8641.00
76_L105_Y0.8631.00
173_G187_D0.8601.00
135_F139_I0.8591.00
199_C206_S0.8591.00
18_T23_G0.8581.00
156_V274_M0.8521.00
152_R251_E0.8521.00
84_V97_I0.8511.00
257_H260_T0.8501.00
168_V222_H0.8431.00
157_V230_L0.8381.00
12_I16_L0.8371.00
243_I274_M0.8331.00
76_L130_V0.8301.00
38_Y41_K0.8301.00
174_R216_T0.8301.00
165_E194_H0.8271.00
25_G33_H0.8261.00
28_Q49_K0.8211.00
12_I18_T0.8201.00
219_I230_L0.8171.00
172_I182_R0.8121.00
66_L100_G0.8091.00
41_K44_D0.8071.00
56_S111_R0.8051.00
161_M200_A0.8051.00
157_V228_H0.8031.00
165_E197_V0.8031.00
27_L48_V0.8031.00
249_H268_A0.8021.00
168_V223_M0.8011.00
255_F264_M0.8001.00
22_F36_V0.8001.00
170_A226_L0.7971.00
134_R137_H0.7941.00
97_I130_V0.7921.00
83_Y125_S0.7911.00
118_T128_M0.7871.00
160_R205_T0.7841.00
144_Q211_L0.7831.00
70_Y266_F0.7821.00
76_L101_I0.7801.00
245_R249_H0.7791.00
243_I277_L0.7781.00
28_Q33_H0.7751.00
40_L46_L0.7661.00
98_A116_L0.7641.00
26_D49_K0.7631.00
69_L269_P0.7611.00
171_P190_K0.7561.00
71_E105_Y0.7561.00
180_I235_L0.7521.00
245_R274_M0.7511.00
134_R138_S0.7511.00
139_I259_L0.7511.00
196_Y210_Q0.7511.00
171_P188_G0.7481.00
70_Y75_V0.7471.00
162_A228_H0.7421.00
247_A273_D0.7411.00
243_I246_Q0.7391.00
66_L104_H0.7361.00
56_S59_L0.7351.00
175_H183_T0.7321.00
256_I260_T0.7311.00
166_G197_V0.7281.00
151_R212_E0.7261.00
173_G183_T0.7241.00
144_Q151_R0.7181.00
250_S253_L0.7151.00
158_H241_Q0.7121.00
141_S145_K0.7051.00
193_T219_I0.7051.00
105_Y132_K0.7031.00
14_K19_D0.7001.00
88_P96_S0.7001.00
163_Q195_F0.6981.00
71_E104_H0.6961.00
86_S116_L0.6941.00
66_L78_I0.6931.00
22_F27_L0.6881.00
18_T36_V0.6861.00
65_P100_G0.6851.00
118_T144_Q0.6811.00
99_N102_I0.6801.00
22_F34_V0.6761.00
166_G209_L0.6751.00
76_L132_K0.6740.99
138_S141_S0.6730.99
168_V195_F0.6700.99
170_A222_H0.6660.99
98_A114_V0.6630.99
191_A215_R0.6550.99
75_V264_M0.6500.99
243_I273_D0.6490.99
114_V130_V0.6480.99
76_L104_H0.6460.99
166_G223_M0.6450.99
234_T238_G0.6430.99
158_H242_E0.6420.99
129_L253_L0.6400.99
152_R254_S0.6390.99
139_I261_Q0.6390.99
19_D24_G0.6380.99
170_A184_V0.6350.99
195_F209_L0.6340.99
117_V144_Q0.6310.99
115_H137_H0.6280.99
128_M250_S0.6270.99
117_V137_H0.6270.99
184_V188_G0.6270.99
181_E224_S0.6260.99
205_T228_H0.6230.99
102_I114_V0.6210.99
131_A140_L0.6200.99
78_I128_M0.6190.99
174_R179_I0.6190.99
231_C247_A0.6140.99
95_G99_N0.6140.99
69_L268_A0.6130.99
102_I106_Q0.6120.99
208_A252_H0.6110.99
246_Q273_D0.6110.99
118_T250_S0.6110.99
148_L256_I0.6100.99
185_T188_G0.6010.99
156_V247_A0.5990.99
140_L143_A0.5970.99
86_S97_I0.5960.99
85_S89_S0.5960.99
100_G103_D0.5950.99
158_H239_T0.5930.99
150_K252_H0.5920.99
136_A259_L0.5910.99
164_M205_T0.5900.99
198_T206_S0.5870.99
29_I40_L0.5870.99
143_A149_V0.5860.99
158_H237_G0.5820.99
180_I183_T0.5820.99
79_N125_S0.5800.99
133_H259_L0.5780.98
143_A259_L0.5770.98
85_S91_E0.5750.98
83_Y123_D0.5750.98
52_E55_V0.5720.98
155_A223_M0.5710.98
64_V84_V0.5690.98
176_P183_T0.5680.98
68_I76_L0.5640.98
68_I71_E0.5640.98
60_L63_P0.5620.98
53_E56_S0.5620.98
171_P187_D0.5620.98
67_D81_Q0.5620.98
164_M197_V0.5610.98
19_D23_G0.5590.98
166_G226_L0.5580.98
200_A203_D0.5580.98
75_V266_F0.5570.98
79_N249_H0.5550.98
201_N204_M0.5550.98
232_G247_A0.5540.98
20_I24_G0.5520.98
127_I253_L0.5520.98
99_N103_D0.5510.98
29_I44_D0.5490.98
97_I104_H0.5490.98
94_S99_N0.5470.98
26_D33_H0.5470.98
270_L275_S0.5460.98
221_V225_Y0.5450.98
238_G241_Q0.5450.98
75_V140_L0.5440.98
110_V134_R0.5430.98
67_D70_Y0.5420.98
78_I101_I0.5410.98
82_P244_G0.5390.98
92_H95_G0.5380.98
120_L127_I0.5380.98
98_A115_H0.5350.97
25_G28_Q0.5330.97
26_D51_P0.5320.97
78_I130_V0.5310.97
60_L94_S0.5290.97
182_R216_T0.5290.97
20_I50_F0.5290.97
177_D180_I0.5280.97
161_M223_M0.5270.97
201_N206_S0.5260.97
115_H134_R0.5250.97
150_K265_R0.5250.97
85_S122_R0.5250.97
74_H135_F0.5250.97
195_F226_L0.5240.97
156_V231_C0.5230.97
231_C241_Q0.5230.97
70_Y264_M0.5220.97
231_C243_I0.5210.97
69_L79_N0.5210.97
63_P100_G0.5200.97
103_D106_Q0.5200.97
177_D181_E0.5180.97
20_I26_D0.5170.97
50_F53_E0.5160.97
89_S235_L0.5140.97
161_M166_G0.5140.97
129_L144_Q0.5120.97
101_I114_V0.5100.97
251_E269_P0.5090.97
31_G45_L0.5090.97
124_T216_T0.5080.97
125_S245_R0.5080.97
191_A221_V0.5060.96
20_I48_V0.5050.96
206_S274_M0.5040.96
174_R183_T0.5040.96
79_N269_P0.5020.96
101_I105_Y0.5020.96
74_H260_T0.5000.96
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 0.7915 100 0.163 Contact Map
1v9kA 1 0.7562 100 0.281 Contact Map
2i82A 1 0.7491 100 0.311 Contact Map
4lgtA 1 0.8198 100 0.434 Contact Map
1vioA 2 0.7951 100 0.436 Contact Map
3dh3A 1 0.8163 100 0.443 Contact Map
1kskA 1 0.8021 100 0.459 Contact Map
2olwA 1 0.5795 100 0.469 Contact Map
2omlA 1 0.5866 100 0.481 Contact Map
2gmlA 1 0.6184 100 0.546 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.

Page generated in 0.0091 seconds.