GREMLIN Database
Q9HQN6 - Menaquinone biosynthesis
UniProt: Q9HQN6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 311 (273)
Sequences: 8792 (6342)
Seq/√Len: 383.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
67_Y93_P3.5741.00
70_A93_P3.4681.00
60_A104_F2.9951.00
94_A98_Q2.8511.00
232_R236_L2.7991.00
92_R95_R2.6831.00
172_A188_P2.6781.00
13_W17_A2.4641.00
67_Y97_K2.4611.00
273_S277_T2.2491.00
79_R82_F2.2141.00
214_K218_E2.1831.00
294_T298_L2.1491.00
233_F236_L2.0991.00
12_A90_L2.0811.00
33_T47_A2.0731.00
293_R297_L2.0731.00
120_V124_V2.0431.00
215_D218_E2.0361.00
291_L294_T2.0021.00
63_F103_T1.9921.00
293_R296_Q1.9701.00
68_Y138_G1.8881.00
72_R222_K1.8661.00
22_L55_A1.8661.00
101_Y105_A1.8361.00
15_M90_L1.8131.00
236_L240_G1.8131.00
49_A110_D1.8091.00
291_L295_G1.8081.00
271_A274_V1.7971.00
56_L106_A1.7911.00
57_I107_A1.7731.00
188_P191_A1.7591.00
260_S264_P1.7481.00
121_P125_I1.7471.00
98_Q102_V1.7411.00
276_K280_E1.7341.00
298_L302_S1.7271.00
261_V265_L1.7151.00
292_S296_Q1.7091.00
229_F233_F1.6951.00
297_L301_Y1.6791.00
283_E286_A1.6771.00
14_L17_A1.6371.00
11_R15_M1.6231.00
49_A113_Y1.6131.00
295_G298_L1.6111.00
270_L273_S1.6061.00
91_I96_V1.5991.00
218_E227_V1.5971.00
272_V276_K1.5921.00
43_A46_P1.5891.00
287_L291_L1.5661.00
63_F99_A1.5651.00
275_T279_F1.5411.00
125_I129_S1.5361.00
214_K231_Y1.5261.00
272_V275_T1.5201.00
13_W95_R1.5071.00
294_T297_L1.4491.00
268_L271_A1.4401.00
246_Y267_T1.4381.00
243_V247_A1.4341.00
290_A293_R1.4331.00
293_R298_L1.4311.00
291_L298_L1.4281.00
30_V51_L1.4271.00
295_G299_A1.4081.00
292_S295_G1.3991.00
74_A87_A1.3841.00
119_G122_I1.3801.00
59_I103_T1.3781.00
298_L301_Y1.3671.00
296_Q299_A1.3651.00
214_K227_V1.3581.00
121_P124_V1.3421.00
24_A205_I1.3391.00
13_W99_A1.3361.00
67_Y96_V1.3311.00
264_P267_T1.3301.00
56_L103_T1.3221.00
226_A234_S1.3201.00
147_G228_R1.3151.00
163_T195_S1.3081.00
56_L107_A1.3041.00
93_P97_K1.2981.00
274_V277_T1.2891.00
143_L146_H1.2741.00
269_P273_S1.2681.00
166_Y170_A1.2591.00
233_F237_E1.2551.00
109_L113_Y1.2501.00
271_A275_T1.2461.00
75_D220_T1.2451.00
290_A294_T1.2411.00
121_P129_S1.2371.00
64_A100_M1.2321.00
33_T169_Q1.2241.00
270_L274_V1.2101.00
211_I234_S1.2011.00
288_N292_S1.1941.00
286_A289_P1.1731.00
112_V123_L1.1651.00
237_E241_L1.1521.00
32_G36_A1.1521.00
17_A103_T1.1441.00
124_V128_A1.1391.00
270_L277_T1.1311.00
276_K279_F1.1251.00
223_R228_R1.1051.00
97_K101_Y1.1031.00
94_A97_K1.0961.00
261_V264_P1.0871.00
294_T302_S1.0871.00
144_G222_K1.0731.00
294_T301_Y1.0711.00
258_G261_V1.0701.00
126_G129_S1.0641.00
26_A30_V1.0531.00
296_Q302_S1.0491.00
260_S263_L1.0481.00
63_F100_M1.0441.00
200_A241_L1.0421.00
17_A63_F1.0381.00
52_V110_D1.0381.00
291_L297_L1.0381.00
99_A103_T1.0341.00
274_V279_F1.0331.00
296_Q304_L1.0311.00
48_V52_V1.0271.00
289_P292_S1.0271.00
187_V192_V1.0261.00
70_A74_A1.0251.00
275_T278_V1.0231.00
132_S156_F1.0221.00
290_A297_L1.0171.00
10_Q14_L1.0141.00
53_G110_D1.0091.00
262_F265_L1.0081.00
297_L300_A1.0081.00
260_S267_T1.0021.00
111_G114_L0.9971.00
241_L245_A0.9951.00
17_A59_I0.9951.00
236_L239_A0.9921.00
197_P248_A0.9911.00
166_Y191_A0.9901.00
286_A290_A0.9861.00
295_G306_A0.9801.00
69_D145_Y0.9781.00
16_A96_V0.9751.00
76_T216_E0.9731.00
290_A301_Y0.9721.00
289_P293_R0.9651.00
42_L47_A0.9611.00
244_V248_A0.9581.00
29_V54_A0.9581.00
192_V196_L0.9521.00
225_L229_F0.9511.00
301_Y306_A0.9511.00
238_Y242_L0.9501.00
158_G202_S0.9471.00
245_A249_P0.9461.00
135_T152_F0.9451.00
301_Y304_L0.9451.00
189_L192_V0.9441.00
123_L127_L0.9431.00
297_L304_L0.9421.00
290_A296_Q0.9421.00
296_Q300_A0.9391.00
290_A298_L0.9391.00
112_V120_V0.9391.00
297_L302_S0.9381.00
143_L152_F0.9361.00
45_W49_A0.9331.00
295_G302_S0.9251.00
294_T300_A0.9231.00
86_T96_V0.9221.00
285_A289_P0.9211.00
284_G287_L0.9201.00
295_G301_Y0.9161.00
279_F282_T0.9101.00
296_Q301_Y0.9081.00
268_L272_V0.9071.00
26_A51_L0.9061.00
288_N291_L0.8971.00
67_Y100_M0.8971.00
213_D217_D0.8931.00
239_A243_V0.8911.00
122_I125_I0.8871.00
258_G262_F0.8871.00
215_D219_T0.8791.00
214_K226_A0.8771.00
69_D72_R0.8761.00
187_V191_A0.8681.00
70_A86_T0.8671.00
120_V123_L0.8651.00
240_G244_V0.8651.00
284_G288_N0.8641.00
248_A252_F0.8641.00
207_V237_E0.8631.00
273_S276_K0.8621.00
231_Y235_R0.8621.00
287_L294_T0.8561.00
275_T280_E0.8561.00
287_L290_A0.8541.00
29_V50_A0.8531.00
122_I167_Y0.8511.00
104_F130_V0.8491.00
278_V281_R0.8481.00
95_R98_Q0.8471.00
135_T143_L0.8461.00
111_G126_G0.8461.00
17_A99_A0.8391.00
134_I138_G0.8351.00
188_P192_V0.8331.00
49_A114_L0.8311.00
301_Y305_F0.8301.00
16_A63_F0.8281.00
143_L147_G0.8251.00
237_E240_G0.8221.00
292_S298_L0.8211.00
283_E287_L0.8191.00
105_A109_L0.8121.00
272_V279_F0.8001.00
71_V75_D0.7991.00
263_L267_T0.7941.00
108_I112_V0.7941.00
110_D114_L0.7921.00
266_V269_P0.7901.00
81_G84_R0.7891.00
297_L303_A0.7881.00
210_N226_A0.7861.00
172_A190_A0.7831.00
292_S299_A0.7821.00
232_R235_R0.7811.00
127_L131_A0.7781.00
235_R238_Y0.7771.00
296_Q303_A0.7721.00
294_T299_A0.7721.00
241_L244_V0.7711.00
63_F91_I0.7681.00
211_I233_F0.7681.00
274_V278_V0.7681.00
63_F96_V0.7651.00
44_V48_V0.7651.00
61_T133_G0.7621.00
91_I99_A0.7611.00
215_D231_Y0.7611.00
250_L254_A0.7611.00
25_A58_Q0.7601.00
13_W16_A0.7601.00
204_N241_L0.7561.00
286_A293_R0.7521.00
34_A306_A0.7491.00
153_V206_I0.7451.00
137_T145_Y0.7431.00
102_V106_A0.7401.00
265_L269_P0.7381.00
158_G198_V0.7361.00
293_R300_A0.7361.00
299_A303_A0.7331.00
196_L248_A0.7321.00
293_R299_A0.7311.00
72_R145_Y0.7291.00
64_A68_Y0.7281.00
198_V202_S0.7281.00
72_R220_T0.7281.00
295_G304_L0.7271.00
159_V195_S0.7251.00
196_L200_A0.7241.00
71_V93_P0.7241.00
126_G130_V0.7241.00
247_A251_W0.7201.00
293_R303_A0.7181.00
156_F195_S0.7171.00
269_P276_K0.7171.00
52_V56_L0.7131.00
253_Y262_F0.7131.00
131_A135_T0.7071.00
211_I231_Y0.7061.00
292_S297_L0.7021.00
211_I235_R0.6960.99
291_L302_S0.6940.99
150_D210_N0.6930.99
285_A288_N0.6930.99
249_P252_F0.6880.99
284_G291_L0.6870.99
64_A134_I0.6870.99
290_A295_G0.6850.99
79_R83_T0.6820.99
246_Y249_P0.6780.99
289_P297_L0.6760.99
14_L19_P0.6750.99
111_G123_L0.6740.99
150_D224_T0.6740.99
295_G305_F0.6720.99
24_A28_P0.6720.99
45_W48_V0.6710.99
205_I209_N0.6680.99
95_R99_A0.6670.99
297_L305_F0.6660.99
234_S238_Y0.6640.99
85_V90_L0.6630.99
97_K100_M0.6630.99
284_G289_P0.6590.99
91_I95_R0.6590.99
291_L301_Y0.6580.99
264_P268_L0.6580.99
242_L245_A0.6570.99
235_R239_A0.6560.99
299_A302_S0.6540.99
144_G150_D0.6540.99
165_T168_V0.6500.99
13_W18_R0.6500.99
270_L276_K0.6490.99
154_F159_V0.6490.99
56_L110_D0.6460.99
271_A278_V0.6460.99
267_T270_L0.6380.99
148_L229_F0.6350.99
157_F202_S0.6340.99
269_P272_V0.6330.99
69_D137_T0.6330.99
300_A305_F0.6300.99
296_Q306_A0.6280.99
293_R301_Y0.6270.99
100_M104_F0.6230.99
84_R87_A0.6220.99
272_V277_T0.6210.99
282_T285_A0.6210.99
283_E291_L0.6200.99
271_A276_K0.6170.99
163_T191_A0.6160.99
204_N242_L0.6160.99
250_L253_Y0.6120.99
59_I63_F0.6100.99
292_S301_Y0.6090.99
190_A255_T0.6070.99
201_I245_A0.6030.99
289_P294_T0.6020.99
287_L295_G0.6000.98
60_A103_T0.6000.98
67_Y86_T0.6000.98
89_G95_R0.5980.98
271_A277_T0.5980.98
86_T91_I0.5970.98
31_V194_A0.5930.98
266_V270_L0.5900.98
298_L305_F0.5890.98
206_I209_N0.5880.98
60_A100_M0.5880.98
238_Y245_A0.5880.98
84_R89_G0.5870.98
68_Y137_T0.5860.98
197_P249_P0.5850.98
203_T241_L0.5840.98
286_A291_L0.5780.98
253_Y256_G0.5770.98
12_A17_A0.5740.98
46_P114_L0.5730.98
261_V267_T0.5710.98
291_L299_A0.5700.98
35_L166_Y0.5700.98
87_A90_L0.5660.98
272_V280_E0.5650.98
60_A107_A0.5650.98
270_L275_T0.5630.98
87_A96_V0.5630.98
34_A37_V0.5560.98
79_R215_D0.5550.97
104_F107_A0.5520.97
124_V127_L0.5510.97
69_D222_K0.5510.97
33_T50_A0.5490.97
85_V89_G0.5470.97
158_G199_A0.5460.97
31_V198_V0.5420.97
32_G165_T0.5410.97
59_I99_A0.5350.97
292_S304_L0.5350.97
273_S280_E0.5340.97
57_I133_G0.5290.97
217_D224_T0.5290.97
291_L304_L0.5290.97
83_T90_L0.5290.97
288_N295_G0.5280.97
128_A132_S0.5250.96
21_T62_N0.5210.96
67_Y70_A0.5160.96
281_R286_A0.5150.96
125_I128_A0.5140.96
58_Q62_N0.5140.96
27_A302_S0.5090.96
302_S306_A0.5080.96
222_K227_V0.5080.96
33_T37_V0.5070.96
166_Y188_P0.5060.96
33_T42_L0.5060.96
50_A169_Q0.5050.96
193_V252_F0.5050.96
229_F237_E0.5040.96
287_L292_S0.5040.96
298_L304_L0.5030.96
129_S132_S0.5020.96
36_A169_Q0.5010.95
108_I123_L0.5010.95
45_W113_Y0.5010.95
60_A134_I0.5000.95
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  
4od4A 1 0.8714 100 0.34 Contact Map
4tq3A 1 0.881 100 0.342 Contact Map
2onkC 2 0.2315 8.7 0.955 Contact Map
2xq2A 2 0.7524 6.3 0.958 Contact Map
3tx3A 2 0.5981 6.1 0.958 Contact Map
3o7qA 1 0.8135 4.9 0.96 Contact Map
2kogA 1 0.1286 4.4 0.961 Contact Map
2cfqA 1 0.4759 4.3 0.961 Contact Map
1pw4A 1 0.8296 3.4 0.963 Contact Map
1m56D 1 0.1158 2.9 0.964 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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