GREMLIN Database
UPPS - Tritrans,polycis-undecaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific)
UniProt: Q980W4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 262 (230)
Sequences: 5057 (3266)
Seq/√Len: 215.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
178_D197_Y3.4661.00
33_D77_K3.4581.00
64_L81_V2.7411.00
121_E153_K2.7151.00
236_A245_D2.7001.00
178_D183_K2.5831.00
43_R53_L2.5751.00
146_E149_S2.5051.00
51_L55_D2.4371.00
209_V226_V2.4211.00
105_K136_D2.4101.00
118_D147_K2.3901.00
109_Q140_Y2.3191.00
73_E243_K2.2841.00
121_E152_D2.2171.00
54_N99_I2.1521.00
245_D248_R2.1281.00
170_D199_Y2.1221.00
70_W247_W2.1101.00
206_I229_S2.0671.00
94_Q98_S2.0481.00
63_K66_E2.0351.00
169_L194_F2.0321.00
65_K111_L1.9711.00
129_K170_D1.9701.00
118_D151_Y1.9581.00
138_I142_N1.9451.00
130_L142_N1.8921.00
218_I226_V1.8831.00
72_L153_K1.8771.00
157_T203_L1.8761.00
242_R245_D1.8581.00
232_F249_A1.8541.00
232_F252_S1.8471.00
130_L145_V1.8061.00
71_L246_L1.7941.00
78_N204_Q1.7631.00
132_K161_C1.7511.00
126_A141_L1.7321.00
165_R205_D1.7271.00
78_N203_L1.7131.00
166_Q170_D1.7021.00
48_D237_Y1.6631.00
209_V229_S1.6621.00
185_V188_E1.6591.00
78_N157_T1.6521.00
31_L76_I1.6451.00
74_L247_W1.5941.00
174_R197_Y1.5721.00
66_E243_K1.5671.00
167_E199_Y1.5641.00
166_Q199_Y1.5551.00
135_K139_D1.5461.00
35_V246_L1.5261.00
175_L193_T1.5161.00
59_Y62_K1.5071.00
177_D181_N1.4811.00
172_V194_F1.4751.00
78_N155_K1.4731.00
69_I120_Y1.4641.00
125_S155_K1.4611.00
55_D58_F1.4561.00
121_E151_Y1.4511.00
69_I116_I1.4391.00
37_I67_V1.4121.00
130_L138_I1.3881.00
190_N193_T1.3811.00
165_R191_E1.3581.00
175_L189_I1.3561.00
175_L197_Y1.3551.00
74_L250_I1.3531.00
80_T159_A1.3521.00
142_N146_E1.3031.00
250_I254_Q1.2871.00
143_R147_K1.2851.00
133_L160_I1.2801.00
180_R186_K1.2671.00
37_I79_I1.2571.00
70_W73_E1.2541.00
164_G223_L1.2261.00
176_L179_Y1.2111.00
129_K166_Q1.2091.00
84_L97_L1.2041.00
139_D143_R1.1901.00
127_I200_D1.1851.00
63_K67_V1.1681.00
135_K138_I1.1651.00
252_S255_K1.1561.00
184_I193_T1.1401.00
129_K132_K1.1381.00
195_R205_D1.1371.00
167_E225_H1.1351.00
194_F197_Y1.1341.00
38_I209_V1.1331.00
127_I159_A1.1321.00
208_L249_A1.1311.00
81_V156_L1.1221.00
112_L144_V1.1191.00
176_L189_I1.1171.00
123_K155_K1.1151.00
105_K140_Y1.1131.00
168_I194_F1.1031.00
63_K242_R1.0971.00
80_T222_L1.0961.00
180_R185_V1.0931.00
105_K137_L1.0931.00
84_L89_C1.0811.00
52_S55_D1.0801.00
35_V76_I1.0731.00
192_E196_K1.0721.00
58_F106_R1.0711.00
125_S145_V1.0661.00
104_I160_I1.0611.00
167_E170_D1.0461.00
216_V233_F1.0451.00
226_V229_S1.0321.00
170_D174_R1.0271.00
61_Y107_G1.0201.00
168_I172_V1.0111.00
140_Y143_R1.0081.00
127_I157_T1.0061.00
179_Y184_I0.9961.00
112_L147_K0.9891.00
81_V158_L0.9831.00
174_R177_D0.9791.00
35_V250_I0.9771.00
124_V144_V0.9711.00
137_L140_Y0.9701.00
179_Y182_G0.9611.00
126_A130_L0.9601.00
36_G206_I0.9511.00
113_E147_K0.9481.00
58_F62_K0.9451.00
70_W246_L0.9380.99
251_R254_Q0.9340.99
65_K116_I0.9250.99
246_L250_I0.9220.99
179_Y186_K0.9150.99
175_L184_I0.9110.99
177_D187_S0.9090.99
122_V154_R0.9080.99
226_V231_L0.9060.99
193_T197_Y0.9000.99
86_T163_G0.8890.99
177_D180_R0.8870.99
109_Q143_R0.8820.99
68_L156_L0.8780.99
39_P83_V0.8690.99
134_P137_L0.8680.99
68_L122_V0.8630.99
72_L154_R0.8580.99
67_V70_W0.8540.99
36_G209_V0.8490.99
218_I223_L0.8480.99
232_F245_D0.8400.99
113_E119_K0.8390.99
173_V187_S0.8380.99
125_S157_T0.8360.99
142_N145_V0.8360.99
97_L101_T0.8290.99
131_D138_I0.8170.99
178_D196_K0.8150.99
172_V176_L0.8100.99
35_V71_L0.8090.99
49_N240_E0.8060.98
125_S203_L0.8040.98
234_C249_A0.8020.98
169_L172_V0.7970.98
248_R252_S0.7960.98
79_I154_R0.7950.98
243_K247_W0.7940.98
43_R93_K0.7870.98
74_L246_L0.7840.98
213_S259_N0.7830.98
175_L194_F0.7790.98
247_W251_R0.7760.98
129_K161_C0.7760.98
125_S202_E0.7750.98
76_I250_I0.7750.98
104_I137_L0.7730.98
206_I209_V0.7700.98
31_L254_Q0.7670.98
176_L180_R0.7640.98
169_L189_I0.7620.98
173_V186_K0.7590.98
72_L120_Y0.7580.98
188_E193_T0.7520.98
89_C161_C0.7490.98
184_I188_E0.7490.98
45_W240_E0.7460.97
173_V176_L0.7440.97
237_Y240_E0.7440.97
101_T133_L0.7410.97
163_G220_N0.7410.97
164_G167_E0.7400.97
212_T234_C0.7400.97
213_S216_V0.7380.97
126_A145_V0.7380.97
57_Y96_E0.7370.97
55_D59_Y0.7360.97
95_N98_S0.7350.97
244_I247_W0.7350.97
194_F198_F0.7340.97
66_E242_R0.7330.97
87_E220_N0.7320.97
116_I119_K0.7290.97
164_G221_F0.7290.97
78_N206_I0.7250.97
104_I107_G0.7240.97
66_E69_I0.7230.97
170_D173_V0.7190.97
195_R198_F0.7190.97
31_L250_I0.7160.97
72_L122_V0.7160.97
141_L158_L0.7140.97
169_L173_V0.7120.97
70_W243_K0.7120.97
87_E163_G0.7100.97
177_D186_K0.7070.97
67_V243_K0.7040.96
104_I158_L0.7020.96
172_V175_L0.7000.96
70_W74_L0.6930.96
216_V252_S0.6920.96
126_A158_L0.6920.96
106_R110_D0.6900.96
37_I210_I0.6890.96
141_L160_I0.6870.96
223_L227_A0.6850.96
69_I73_E0.6790.96
59_Y63_K0.6790.96
216_V235_E0.6750.95
80_T127_I0.6710.95
236_A240_E0.6690.95
47_R53_L0.6680.95
193_T196_K0.6660.95
206_I226_V0.6640.95
178_D181_N0.6640.95
130_L141_L0.6560.95
137_L141_L0.6550.95
68_L154_R0.6520.95
82_F220_N0.6480.94
32_P35_V0.6440.94
176_L184_I0.6400.94
200_D225_H0.6400.94
140_Y144_V0.6390.94
189_I193_T0.6390.94
196_K202_E0.6370.94
102_T136_D0.6370.94
184_I189_I0.6360.94
155_K203_L0.6360.94
183_K197_Y0.6350.94
164_G168_I0.6340.94
195_R202_E0.6310.94
30_P254_Q0.6290.93
208_L232_F0.6230.93
179_Y185_V0.6220.93
215_E259_N0.6200.93
101_T134_P0.6180.93
186_K193_T0.6160.93
77_K155_K0.6160.93
164_G218_I0.6130.93
62_K110_D0.6070.92
127_I222_L0.6060.92
31_L75_G0.6040.92
71_L79_I0.6040.92
131_D161_C0.6010.92
83_V158_L0.6000.92
57_Y103_Y0.5990.92
36_G221_F0.5970.92
171_A194_F0.5970.92
48_D240_E0.5960.92
244_I248_R0.5950.91
82_F167_E0.5910.91
68_L79_I0.5910.91
210_I241_F0.5900.91
35_V210_I0.5890.91
175_L178_D0.5860.91
173_V177_D0.5840.91
256_R259_N0.5840.91
98_S102_T0.5820.91
234_C245_D0.5800.90
176_L186_K0.5790.90
186_K190_N0.5780.90
241_F249_A0.5770.90
49_N53_L0.5770.90
111_L116_I0.5700.90
230_E258_R0.5690.90
108_I112_L0.5680.89
234_C241_F0.5680.89
67_V246_L0.5670.89
107_G166_Q0.5670.89
102_T106_R0.5660.89
63_K70_W0.5640.89
230_E256_R0.5620.89
213_S237_Y0.5590.89
212_T233_F0.5590.89
238_W241_F0.5570.89
109_Q113_E0.5550.88
104_I108_I0.5540.88
210_I249_A0.5530.88
31_L74_L0.5520.88
59_Y66_E0.5520.88
112_L140_Y0.5510.88
116_I120_Y0.5480.88
218_I231_L0.5470.88
70_W242_R0.5420.87
139_D142_N0.5410.87
59_Y240_E0.5410.87
66_E70_W0.5380.87
242_R248_R0.5370.87
118_D150_N0.5360.87
228_Y258_R0.5360.87
169_L191_E0.5350.87
57_Y100_I0.5340.86
232_F248_R0.5340.86
87_E228_Y0.5320.86
29_G254_Q0.5310.86
124_V158_L0.5300.86
69_I72_L0.5280.86
234_C252_S0.5260.86
180_R183_K0.5260.86
104_I133_L0.5240.85
86_T220_N0.5210.85
85_S163_G0.5210.85
191_E195_R0.5200.85
183_K186_K0.5200.85
105_K109_Q0.5190.85
32_P254_Q0.5180.85
124_V156_L0.5170.85
82_F218_I0.5140.84
53_L93_K0.5140.84
207_D260_F0.5130.84
102_T105_K0.5120.84
209_V231_L0.5110.84
68_L72_L0.5100.84
49_N52_S0.5090.84
136_D139_D0.5080.84
68_L111_L0.5080.84
151_Y154_R0.5020.83
117_V156_L0.5020.83
112_L118_D0.5010.83
105_K134_P0.5010.83
43_R54_N0.5000.83
87_E191_E0.5000.83
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  
1f75A 2 0.8282 100 0.115 Contact Map
2vg3A 2 0.9847 100 0.119 Contact Map
3sgvB 2 0.8702 100 0.12 Contact Map
4q9mA 2 0.8626 100 0.124 Contact Map
4h8eA 2 0.8931 100 0.131 Contact Map
2d2rA 2 0.8282 100 0.138 Contact Map
3ugsB 2 0.7939 100 0.151 Contact Map
2vg0A 2 0.8473 100 0.156 Contact Map
3wqlA 2 0.9008 98.2 0.9 Contact Map
2qw5A 3 0.9008 15.7 0.97 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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