GREMLIN Database
TRUB - tRNA pseudouridine synthase B
UniProt: P60340 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11177
Length: 314 (286)
Sequences: 3810 (2735)
Seq/√Len: 161.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
120_E152_P3.9651.00
118_D152_P3.5831.00
87_D94_Q3.4741.00
18_D201_R3.3571.00
105_A109_A3.1351.00
17_L28_A3.0111.00
77_R171_E2.8501.00
16_L54_M2.8141.00
75_R171_E2.7801.00
118_D154_T2.7091.00
134_K138_E2.6661.00
89_S185_D2.6221.00
263_Y268_N2.5361.00
50_L92_D2.5321.00
114_T190_K2.5161.00
75_R173_H2.4311.00
81_R167_E2.3031.00
32_V41_A2.1711.00
161_I171_E2.1411.00
21_Q52_T2.1161.00
129_L151_R2.0901.00
159_L171_E2.0691.00
111_A187_L2.0601.00
104_S107_Q2.0331.00
157_E173_H2.0111.00
80_A184_I1.9951.00
81_R198_I1.9761.00
85_R189_E1.9331.00
257_P260_S1.9151.00
122_I150_A1.9071.00
82_L168_L1.8961.00
32_V57_I1.8681.00
79_I169_E1.8351.00
119_I153_I1.8311.00
52_T201_R1.8061.00
77_R169_E1.8001.00
125_M148_R1.7951.00
184_I197_V1.7731.00
80_A170_L1.7601.00
58_C66_S1.7071.00
38_A59_L1.6981.00
73_D173_H1.6951.00
80_A168_L1.6941.00
115_F190_K1.6941.00
85_R97_E1.6811.00
79_I167_E1.6671.00
89_S182_T1.6661.00
91_A196_H1.6571.00
139_Y144_I1.6541.00
296_E306_R1.6511.00
112_L158_L1.6431.00
78_V170_L1.6221.00
107_Q110_A1.6121.00
251_Y294_M1.6101.00
44_T58_C1.6031.00
17_L219_L1.5941.00
172_I183_I1.5911.00
188_G195_A1.5611.00
113_D116_R1.5421.00
136_L148_R1.5411.00
188_G193_C1.5391.00
112_L160_F1.5351.00
188_G194_G1.5231.00
109_A160_F1.4931.00
264_F283_V1.4671.00
78_V197_V1.4641.00
245_D284_T1.4631.00
85_R96_V1.4421.00
162_R169_E1.4341.00
16_L213_M1.4281.00
18_D52_T1.4121.00
135_K138_E1.4101.00
54_M213_M1.4001.00
134_K139_Y1.3931.00
84_Q98_E1.3931.00
75_R204_A1.3851.00
120_E150_A1.3791.00
26_N33_K1.3521.00
67_Q307_R1.3521.00
86_T196_H1.3471.00
182_T185_D1.3461.00
157_E171_E1.3371.00
217_E220_R1.3341.00
21_Q50_L1.3301.00
256_L264_F1.3281.00
81_R84_Q1.3191.00
215_T218_H1.3181.00
125_M136_L1.3111.00
31_K220_R1.3091.00
173_H204_A1.3021.00
112_L170_L1.3001.00
26_N30_Q1.2991.00
163_H168_L1.2921.00
223_V226_A1.2911.00
105_A163_H1.2901.00
264_F293_G1.2901.00
220_R224_E1.2871.00
130_K135_K1.2751.00
85_R194_G1.2731.00
14_V58_C1.2721.00
134_K142_Q1.2691.00
210_V213_M1.2621.00
109_A116_R1.2601.00
95_I98_E1.2591.00
131_Y148_R1.2461.00
116_R158_L1.2411.00
167_E198_I1.2391.00
80_A195_A1.2361.00
282_R291_F1.2241.00
79_I199_Y1.2051.00
77_R161_I1.2011.00
84_Q95_I1.1931.00
242_M246_S1.1821.00
73_D156_Y1.1811.00
66_S70_L1.1791.00
160_F168_L1.1771.00
50_L197_V1.1631.00
111_A114_T1.1631.00
305_P308_L1.1581.00
79_I198_I1.1401.00
262_V266_N1.1361.00
32_V59_L1.1321.00
75_R203_L1.1201.00
156_Y173_H1.1191.00
87_D126_Y1.1031.00
286_G290_K1.1011.00
12_N61_E1.1001.00
154_T175_S1.1001.00
82_L103_F1.0951.00
36_Y59_L1.0941.00
172_I180_I1.0931.00
31_K34_R1.0921.00
131_Y136_L1.0921.00
293_G308_L1.0891.00
115_F186_D1.0881.00
283_V295_G1.0700.99
125_M146_V1.0630.99
108_L168_L1.0580.99
15_L32_V1.0550.99
201_R210_V1.0550.99
20_P217_E1.0500.99
209_P212_R1.0500.99
44_T66_S1.0480.99
263_Y266_N1.0430.99
38_A41_A1.0360.99
50_L91_A1.0360.99
111_A190_K1.0340.99
269_P302_R1.0180.99
87_D92_D1.0010.99
105_A162_R0.9930.99
185_D189_E0.9920.99
23_M31_K0.9860.99
126_Y140_A0.9770.99
24_S27_D0.9690.99
218_H221_E0.9690.99
18_D210_V0.9670.99
265_K290_K0.9670.99
158_L170_L0.9640.99
21_Q199_Y0.9590.99
204_A209_P0.9570.99
208_Y246_S0.9460.99
125_M145_E0.9450.99
120_E149_E0.9440.99
84_Q196_H0.9410.99
61_E64_K0.9360.99
72_S206_S0.9310.98
77_R203_L0.9280.98
222_L240_L0.9250.98
223_V237_L0.9150.98
54_M210_V0.9150.98
214_V219_L0.9070.98
71_D176_K0.8960.98
116_R157_E0.8880.98
106_E110_A0.8880.98
256_L260_S0.8870.98
85_R185_D0.8860.98
88_T126_Y0.8760.98
106_E109_A0.8640.97
124_S182_T0.8630.97
253_V282_R0.8590.97
41_A57_I0.8570.97
253_V284_T0.8570.97
183_I187_L0.8560.97
264_F295_G0.8550.97
137_Y140_A0.8530.97
131_Y149_E0.8500.97
158_L183_I0.8470.97
87_D93_G0.8460.97
214_V240_L0.8450.97
51_A129_L0.8430.97
156_Y175_S0.8410.97
82_L191_L0.8410.97
280_L306_R0.8360.97
23_M28_A0.8320.97
14_V247_P0.8310.97
171_E203_L0.8310.97
54_M205_V0.8310.97
158_L172_I0.8290.97
89_S124_S0.8260.97
125_M140_A0.8220.97
78_V184_I0.8220.97
260_S263_Y0.8190.97
99_R189_E0.8180.96
214_V218_H0.8180.96
80_A197_V0.8160.96
148_R182_T0.8100.96
29_L41_A0.8090.96
245_D282_R0.8080.96
14_V65_F0.8070.96
82_L193_C0.8050.96
174_C178_T0.8040.96
158_L187_L0.8030.96
295_G303_V0.8020.96
169_E199_Y0.8010.96
18_D215_T0.7980.96
78_V158_L0.7980.96
135_K139_Y0.7970.96
298_D304_A0.7970.96
32_V219_L0.7970.96
56_P205_V0.7950.96
15_L36_Y0.7940.96
139_Y142_Q0.7910.96
26_N29_L0.7900.96
36_Y219_L0.7810.95
116_R119_I0.7790.95
99_R194_G0.7760.95
110_A113_D0.7750.95
293_G303_V0.7750.95
258_L288_N0.7710.95
264_F292_I0.7680.95
125_M182_T0.7650.95
81_R166_N0.7600.95
161_I169_E0.7590.95
21_Q92_D0.7580.95
86_T95_I0.7570.95
279_G296_E0.7560.95
115_F183_I0.7540.94
97_E189_E0.7530.94
261_S292_I0.7530.94
52_T199_Y0.7520.94
72_S205_V0.7500.94
259_T263_Y0.7490.94
97_E194_G0.7480.94
255_N286_G0.7470.94
261_S286_G0.7460.94
28_A55_L0.7420.94
136_L146_V0.7400.94
252_P279_G0.7400.94
164_E167_E0.7390.94
35_I220_R0.7360.94
82_L195_A0.7350.94
109_A159_L0.7340.94
119_I155_V0.7310.94
64_K67_Q0.7310.94
87_D96_V0.7310.94
108_L163_H0.7300.93
88_T93_G0.7280.93
27_D31_K0.7280.93
41_A59_L0.7270.93
65_F247_P0.7270.93
164_E169_E0.7240.93
69_L72_S0.7230.93
105_A165_G0.7210.93
123_P150_A0.7200.93
88_T92_D0.7200.93
261_S287_E0.7170.93
26_N135_K0.7160.93
101_V193_C0.7140.93
16_L52_T0.7140.93
15_L240_L0.7130.93
160_F163_H0.7110.93
112_L116_R0.7110.93
112_L187_L0.7060.92
258_L287_E0.7010.92
21_Q91_A0.6990.92
255_N287_E0.6970.92
103_F108_L0.6880.91
155_V174_C0.6860.91
125_M139_Y0.6850.91
186_D189_E0.6830.91
246_S249_S0.6830.91
138_E142_Q0.6820.91
67_Q70_L0.6820.91
65_F244_M0.6810.91
271_R302_R0.6810.91
99_R193_C0.6790.91
16_L210_V0.6790.91
105_A160_F0.6760.91
29_L59_L0.6700.90
103_F193_C0.6690.90
280_L294_M0.6690.90
32_V36_Y0.6670.90
256_L261_S0.6630.90
36_Y57_I0.6620.90
67_Q71_D0.6590.89
85_R193_C0.6580.89
121_Q186_D0.6570.89
208_Y247_P0.6550.89
109_A113_D0.6540.89
276_P279_G0.6500.89
65_F248_A0.6490.89
264_F303_V0.6480.89
155_V183_I0.6480.89
51_A205_V0.6480.89
65_F293_G0.6470.89
248_A291_F0.6470.89
259_T262_V0.6450.88
131_Y147_P0.6450.88
31_K35_I0.6430.88
144_I148_R0.6410.88
16_L212_R0.6360.88
248_A251_Y0.6350.88
79_I168_L0.6340.88
136_L139_Y0.6340.88
244_M247_P0.6340.88
184_I195_A0.6330.88
61_E307_R0.6320.87
155_V172_I0.6320.87
107_Q111_A0.6320.87
27_D34_R0.6310.87
204_A207_K0.6310.87
35_I215_T0.6290.87
62_A243_P0.6250.87
135_K146_V0.6250.87
108_L191_L0.6200.86
284_T291_F0.6170.86
260_S270_V0.6170.86
32_V35_I0.6170.86
253_V289_G0.6140.86
212_R242_M0.6090.85
261_S265_K0.6080.85
15_L59_L0.6080.85
35_I223_V0.6060.85
148_R185_D0.6040.85
59_L241_L0.6000.85
35_I219_L0.5990.85
131_Y135_K0.5980.84
12_N60_G0.5980.84
221_E225_Q0.5950.84
119_I154_T0.5940.84
254_V260_S0.5930.84
258_L261_S0.5910.84
149_E153_I0.5890.84
78_V180_I0.5880.83
92_D196_H0.5850.83
122_I149_E0.5850.83
255_N284_T0.5840.83
283_V292_I0.5840.83
237_L240_L0.5830.83
126_Y135_K0.5820.83
34_R37_N0.5810.83
16_L201_R0.5810.83
89_S188_G0.5790.83
122_I125_M0.5780.82
116_R159_L0.5780.82
64_K308_L0.5750.82
243_P246_S0.5730.82
78_V199_Y0.5730.82
111_A191_L0.5710.82
44_T69_L0.5660.81
256_L283_V0.5650.81
46_A197_V0.5640.81
81_R196_H0.5630.81
123_P148_R0.5590.80
270_V297_I0.5580.80
163_H166_N0.5580.80
262_V265_K0.5580.80
269_P304_A0.5570.80
110_A114_T0.5540.80
23_M216_L0.5530.80
176_K205_V0.5530.80
139_Y146_V0.5520.79
80_A188_G0.5510.79
264_F308_L0.5510.79
49_P137_Y0.5480.79
124_S140_A0.5460.79
248_A253_V0.5420.78
70_L73_D0.5420.78
145_E148_R0.5420.78
158_L180_I0.5400.78
20_P40_R0.5390.78
99_R103_F0.5370.78
168_L187_L0.5370.78
86_T96_V0.5360.77
222_L225_Q0.5330.77
155_V178_T0.5330.77
122_I148_R0.5290.77
178_T183_I0.5280.76
22_G92_D0.5280.76
184_I188_G0.5280.76
297_I301_G0.5280.76
31_K216_L0.5270.76
297_I303_V0.5270.76
245_D291_F0.5260.76
64_K307_R0.5260.76
281_V284_T0.5260.76
271_R274_G0.5250.76
260_S268_N0.5250.76
38_A64_K0.5240.76
25_S55_L0.5230.76
12_N40_R0.5220.76
128_A141_R0.5210.75
129_L148_R0.5190.75
16_L208_Y0.5180.75
28_A216_L0.5170.75
170_L180_I0.5170.75
23_M27_D0.5170.75
263_Y274_G0.5170.75
123_P151_R0.5150.75
70_L129_L0.5150.75
248_A282_R0.5140.75
15_L219_L0.5140.75
85_R89_S0.5140.75
20_P23_M0.5130.74
88_T137_Y0.5100.74
147_P150_A0.5090.74
208_Y213_M0.5080.74
68_Y294_M0.5060.73
121_Q153_I0.5060.73
86_T93_G0.5060.73
124_S248_A0.5050.73
42_G45_G0.5040.73
296_E304_A0.5040.73
26_N38_A0.5030.73
30_Q34_R0.5030.73
155_V180_I0.5030.73
255_N289_G0.5010.73
82_L194_G0.5010.73
103_F107_Q0.5000.72
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  
1k8wA 1 0.965 100 0.095 Contact Map
1r3eA 1 0.914 100 0.114 Contact Map
1sgvA 1 0.8344 100 0.122 Contact Map
3u28A 1 0.8694 100 0.289 Contact Map
2apoA 1 0.8471 100 0.295 Contact Map
2ausC 1 0.8439 100 0.299 Contact Map
2v9kA 1 0.5541 100 0.741 Contact Map
1kskA 1 0.5541 99.8 0.815 Contact Map
4lgtA 1 0.5764 98.9 0.885 Contact Map
3dh3A 1 0.5701 98.7 0.895 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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