GREMLIN Database
YHCT - Uncharacterized RNA pseudouridine synthase YhcT
UniProt: P54604 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 302 (278)
Sequences: 9289 (6474)
Seq/√Len: 388.3

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_T227_E3.6051.00
86_L144_A3.3611.00
211_H231_E3.3441.00
48_N62_D3.3111.00
88_E149_K2.9321.00
213_K227_E2.9201.00
84_D96_N2.8441.00
271_K284_V2.8121.00
273_Q284_V2.8091.00
183_G212_F2.6771.00
171_T225_L2.6761.00
171_T270_N2.6731.00
184_T211_H2.6501.00
91_H278_I2.5861.00
91_H150_H2.5181.00
187_S244_S2.4521.00
182_K213_K2.3921.00
228_L242_L2.3691.00
181_K217_S2.3501.00
264_R292_D2.3031.00
96_N287_A2.2671.00
79_E111_T2.2591.00
167_K229_E2.2581.00
186_N207_T2.2091.00
273_Q282_L2.1401.00
184_T209_V2.1381.00
186_N209_V2.1171.00
94_I285_A2.1041.00
114_L145_I2.1001.00
81_G117_L2.0741.00
169_T271_K2.0651.00
150_H153_A2.0431.00
214_V224_S2.0321.00
271_K286_E1.9911.00
167_K273_Q1.9201.00
275_V282_L1.8921.00
160_Q165_T1.8821.00
172_A228_L1.8701.00
209_V231_E1.8411.00
178_L224_S1.8261.00
79_E112_G1.8231.00
21_L52_V1.8041.00
210_T228_L1.8011.00
142_S268_H1.7931.00
215_M227_E1.7931.00
52_V56_M1.7891.00
169_T229_E1.7781.00
174_A226_V1.7661.00
228_L238_I1.7361.00
159_Q163_K1.7071.00
137_L145_I1.6951.00
47_V56_M1.6851.00
94_I146_V1.6431.00
94_I144_A1.6121.00
176_G224_S1.5671.00
262_L266_A1.5521.00
103_T145_I1.5511.00
270_N286_E1.5411.00
89_D276_H1.5311.00
266_A293_M1.5281.00
86_L285_A1.5131.00
211_H229_E1.4751.00
140_D265_Q1.4531.00
118_I147_F1.4501.00
19_Q27_T1.4461.00
80_Y120_Y1.4451.00
226_V242_L1.4351.00
201_V244_S1.4341.00
217_S224_S1.4281.00
291_A295_N1.4241.00
24_V28_A1.4091.00
168_R230_L1.4031.00
112_G117_L1.3741.00
185_I245_L1.3681.00
177_K217_S1.3651.00
46_K65_F1.3601.00
174_A242_L1.3311.00
156_I160_Q1.3271.00
99_A142_S1.3201.00
223_L250_T1.3131.00
276_H283_I1.2941.00
171_T227_E1.2841.00
212_F242_L1.2831.00
178_L247_H1.2741.00
189_I240_V1.2591.00
47_V52_V1.2551.00
192_D198_R1.2511.00
102_A109_G1.2501.00
173_I223_L1.2321.00
16_Q28_A1.2311.00
17_D60_K1.2231.00
113_T116_N1.2221.00
171_T289_F1.2201.00
37_Q41_S1.2141.00
89_D92_M1.2111.00
210_T230_L1.1811.00
206_Q234_R1.1791.00
98_P101_I1.1591.00
99_A264_R1.1561.00
161_L166_L1.1491.00
214_V217_S1.1381.00
266_A296_L1.1331.00
171_T215_M1.1331.00
230_L238_I1.1331.00
172_A226_V1.1251.00
154_H158_D1.1191.00
140_D253_S1.1141.00
152_L278_I1.1141.00
95_I114_L1.1121.00
190_G202_S1.1091.00
176_G247_H1.1071.00
19_Q23_S1.1041.00
47_V64_V1.1031.00
159_Q162_E1.1001.00
24_V58_V1.0951.00
178_L226_V1.0821.00
173_I225_L1.0811.00
91_H153_A1.0771.00
101_I117_L1.0721.00
26_K33_K1.0711.00
99_A292_D1.0701.00
174_A178_L1.0671.00
156_I159_Q1.0591.00
49_H65_F1.0541.00
291_A294_K1.0531.00
35_V39_W1.0451.00
91_H276_H1.0371.00
173_I296_L1.0351.00
38_D42_H1.0351.00
184_T231_E1.0351.00
175_E257_G1.0311.00
134_V148_A1.0281.00
177_K222_R1.0201.00
167_K282_L1.0091.00
134_V157_L1.0021.00
210_T241_H1.0011.00
133_H147_F0.9991.00
180_T214_V0.9981.00
218_N221_E0.9931.00
25_L36_I0.9901.00
289_F293_M0.9901.00
101_I114_L0.9871.00
175_E250_T0.9831.00
195_H198_R0.9821.00
155_A159_Q0.9811.00
106_N109_G0.9791.00
144_A285_A0.9741.00
92_M274_A0.9731.00
92_M276_H0.9651.00
178_L217_S0.9601.00
172_A249_L0.9581.00
275_V280_D0.9581.00
238_I249_L0.9521.00
144_A287_A0.9391.00
56_M62_D0.9371.00
93_L122_Y0.9361.00
92_M153_A0.9351.00
242_L249_L0.9311.00
178_L214_V0.9301.00
197_T254_L0.9291.00
262_L293_M0.9221.00
35_V38_D0.9201.00
148_A154_H0.9161.00
180_T183_G0.9161.00
174_A224_S0.9161.00
175_E223_L0.9141.00
31_A39_W0.9131.00
173_I293_M0.9121.00
16_Q24_V0.9031.00
288_P294_K0.8981.00
74_S128_T0.8971.00
174_A249_L0.8931.00
46_K67_D0.8911.00
34_P37_Q0.8891.00
192_D195_H0.8871.00
151_R154_H0.8841.00
274_A285_A0.8811.00
189_I199_R0.8811.00
276_H279_T0.8791.00
152_L156_I0.8751.00
160_Q275_V0.8741.00
180_T212_F0.8731.00
93_L118_I0.8721.00
31_A36_I0.8661.00
93_L147_F0.8661.00
103_T137_L0.8601.00
58_V64_V0.8581.00
86_L288_P0.8571.00
161_L168_R0.8551.00
174_A247_H0.8511.00
185_I241_H0.8481.00
83_L117_L0.8471.00
216_A225_L0.8441.00
169_T270_N0.8441.00
268_H287_A0.8391.00
218_N222_R0.8381.00
177_K221_E0.8331.00
182_K211_H0.8281.00
25_L45_I0.8251.00
161_L230_L0.8241.00
264_R293_M0.8221.00
190_G204_G0.8221.00
17_D59_K0.8211.00
266_A292_D0.8211.00
274_A283_I0.8191.00
45_I66_I0.8181.00
227_E270_N0.8151.00
44_Q67_D0.8151.00
53_L56_M0.8081.00
264_R268_H0.8061.00
181_K214_V0.8051.00
192_D200_R0.8051.00
100_G142_S0.8051.00
183_G214_V0.8041.00
262_L296_L0.8031.00
82_E117_L0.8031.00
182_K214_V0.8011.00
19_Q24_V0.7991.00
39_W44_Q0.7971.00
179_R247_H0.7971.00
33_K37_Q0.7891.00
257_G261_L0.7861.00
148_A153_A0.7801.00
56_M59_K0.7791.00
43_Q51_S0.7771.00
262_L292_D0.7771.00
190_G200_R0.7721.00
177_K224_S0.7701.00
168_R231_E0.7681.00
115_A133_H0.7651.00
187_S245_L0.7631.00
114_L147_F0.7581.00
87_F92_M0.7551.00
185_I242_L0.7551.00
213_K229_E0.7541.00
188_P241_H0.7491.00
59_K62_D0.7491.00
105_P113_T0.7481.00
210_T238_I0.7471.00
188_P207_T0.7451.00
31_A35_V0.7441.00
87_F285_A0.7401.00
46_K51_S0.7351.00
156_I278_I0.7351.00
262_L265_Q0.7291.00
198_R243_A0.7281.00
131_V147_F0.7251.00
191_R235_T0.7231.00
103_T114_L0.7171.00
115_A131_V0.7151.00
188_P205_G0.7151.00
275_V279_T0.7141.00
95_I145_I0.7141.00
20_W23_S0.7101.00
40_M45_I0.7061.00
83_L95_I0.7061.00
156_I280_D0.7061.00
103_T133_H0.7031.00
29_L36_I0.7011.00
16_Q27_T0.7001.00
151_R155_A0.6951.00
122_Y149_K0.6951.00
135_H269_A0.6951.00
135_H145_I0.6930.99
145_I269_A0.6930.99
135_H161_L0.6920.99
116_N119_A0.6910.99
92_M283_I0.6840.99
185_I212_F0.6830.99
253_S257_G0.6800.99
41_S54_N0.6800.99
112_G116_N0.6780.99
269_A272_V0.6740.99
18_G60_K0.6720.99
158_D162_E0.6720.99
86_L287_A0.6700.99
102_A108_D0.6680.99
39_W68_L0.6670.99
265_Q292_D0.6660.99
187_S201_V0.6620.99
106_N197_T0.6610.99
132_R154_H0.6590.99
104_H113_T0.6590.99
88_E122_Y0.6560.99
201_V205_G0.6540.99
83_L121_H0.6540.99
111_T116_N0.6540.99
39_W66_I0.6530.99
88_E121_H0.6460.99
80_Y117_L0.6460.99
40_M54_N0.6390.99
119_A131_V0.6380.99
218_N223_L0.6360.99
16_Q19_Q0.6350.99
187_S241_H0.6340.99
155_A158_D0.6320.99
123_Q129_C0.6310.99
257_G260_K0.6310.99
144_A272_V0.6280.99
81_G101_I0.6260.99
169_T273_Q0.6250.99
208_A234_R0.6170.99
116_N120_Y0.6160.99
21_L40_M0.6140.99
167_K271_K0.6120.99
215_M225_L0.6090.99
173_I266_A0.6080.99
217_S222_R0.6080.99
93_L149_K0.6070.99
150_H278_I0.6030.99
250_T260_K0.6020.99
250_T266_A0.5990.99
183_G242_L0.5980.99
202_S205_G0.5980.99
148_A157_L0.5980.99
85_I88_E0.5970.98
173_I250_T0.5970.98
30_K36_I0.5960.98
102_A106_N0.5960.98
183_G245_L0.5930.98
146_V272_V0.5920.98
224_S247_H0.5910.98
201_V240_V0.5890.98
160_Q166_L0.5870.98
40_M52_V0.5860.98
175_E260_K0.5850.98
191_R196_P0.5790.98
23_S27_T0.5780.98
212_F228_L0.5760.98
118_I122_Y0.5750.98
212_F245_L0.5750.98
134_V161_L0.5730.98
109_G112_G0.5720.98
39_W45_I0.5720.98
146_V161_L0.5710.98
21_L64_V0.5690.98
91_H152_L0.5690.98
95_I147_F0.5690.98
127_E151_R0.5680.98
160_Q278_I0.5680.98
250_T262_L0.5660.98
175_E261_L0.5660.98
117_L120_Y0.5650.98
198_R254_L0.5650.98
119_A123_Q0.5640.98
153_A278_I0.5620.98
25_L29_L0.5620.98
188_P204_G0.5610.98
178_L242_L0.5610.98
175_E258_G0.5610.98
270_N288_P0.5600.98
37_Q54_N0.5600.98
192_D196_P0.5600.98
100_G140_D0.5580.98
142_S264_R0.5580.98
217_S221_E0.5570.98
78_P119_A0.5570.98
175_E256_G0.5530.98
26_K36_I0.5520.97
134_V154_H0.5510.97
90_N149_K0.5500.97
73_A76_V0.5490.97
223_L296_L0.5480.97
78_P120_Y0.5480.97
168_R208_A0.5480.97
178_L212_F0.5470.97
114_L121_H0.5460.97
183_G228_L0.5450.97
165_T275_V0.5450.97
96_N142_S0.5440.97
92_M285_A0.5430.97
32_S39_W0.5430.97
173_I218_N0.5430.97
132_R151_R0.5430.97
164_K167_K0.5420.97
172_A242_L0.5420.97
289_F294_K0.5410.97
21_L47_V0.5400.97
137_L164_K0.5400.97
157_L160_Q0.5400.97
22_F26_K0.5390.97
70_E73_A0.5380.97
118_I131_V0.5380.97
168_R211_H0.5340.97
102_A133_H0.5340.97
93_L121_H0.5330.97
95_I118_I0.5310.97
193_R202_S0.5310.97
87_F283_I0.5300.97
240_V244_S0.5300.97
21_L56_M0.5290.97
167_K284_V0.5270.97
137_L144_A0.5260.97
18_G57_I0.5250.97
227_E271_K0.5250.97
199_R206_Q0.5250.97
218_N225_L0.5240.97
48_N52_V0.5220.97
228_L249_L0.5180.96
178_L181_K0.5170.96
226_V249_L0.5150.96
47_V62_D0.5150.96
92_M157_L0.5130.96
23_S33_K0.5120.96
85_I93_L0.5120.96
47_V58_V0.5110.96
188_P201_V0.5100.96
209_V232_T0.5090.96
34_P38_D0.5080.96
99_A263_N0.5070.96
120_Y123_Q0.5070.96
90_N278_I0.5050.96
15_K28_A0.5040.96
115_A132_R0.5030.96
32_S37_Q0.5030.96
208_A240_V0.5020.96
196_P200_R0.5000.96
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 0.7417 100 0.165 Contact Map
1v9kA 1 0.7086 100 0.321 Contact Map
2i82A 1 0.6987 100 0.343 Contact Map
4lgtA 1 0.7815 100 0.433 Contact Map
1vioA 2 0.7517 100 0.435 Contact Map
3dh3A 1 0.7781 100 0.448 Contact Map
1kskA 1 0.7649 100 0.455 Contact Map
2olwA 1 0.553 100 0.493 Contact Map
2omlA 1 0.5563 100 0.508 Contact Map
2gmlA 1 0.5695 100 0.57 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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