GREMLIN Database
YTHB - Putative cytochrome bd menaquinol oxidase subunit II
UniProt: O34505 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 346 (322)
Sequences: 3256 (2065)
Seq/√Len: 115.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
33_F176_L3.7531.00
161_S164_A3.7111.00
126_F172_I3.3231.00
87_L143_F3.3211.00
333_K336_M3.3131.00
317_Y321_F3.1431.00
23_V275_G2.8191.00
130_A172_I2.8041.00
130_A168_I2.7821.00
307_P311_R2.7731.00
176_L202_S2.6371.00
48_D52_R2.5571.00
33_F172_I2.4811.00
12_S16_G2.4331.00
129_P171_A2.3871.00
108_S118_R2.3841.00
154_N157_K2.3471.00
163_N217_I2.3461.00
326_P329_F2.3311.00
93_M131_I2.2771.00
31_A50_A2.2271.00
169_G173_L2.1871.00
46_A194_D2.1651.00
18_V72_L2.1581.00
197_R201_K2.1581.00
16_G20_I2.1241.00
137_P167_F2.0641.00
188_N340_R2.0511.00
315_A319_V2.0331.00
266_K269_L2.0321.00
134_L168_I2.0261.00
122_G126_F2.0111.00
9_I314_F1.9901.00
7_A304_F1.9801.00
75_F313_L1.9741.00
116_T119_Y1.9691.00
329_F333_K1.9651.00
129_P175_T1.9541.00
100_I120_I1.9371.00
50_A183_L1.9061.00
181_L199_Y1.9021.00
165_Y169_G1.9001.00
59_E106_V1.8951.00
119_Y123_I1.8931.00
173_L209_I1.8871.00
124_S128_I1.8861.00
141_G161_S1.8421.00
49_I339_K1.7481.00
292_Y299_T1.7431.00
51_N105_L1.7161.00
146_K152_N1.6941.00
216_C220_T1.6781.00
178_L275_G1.6761.00
192_E267_P1.6551.00
244_I248_I1.6501.00
120_I124_S1.6321.00
97_L124_S1.6271.00
320_A323_I1.6171.00
78_G149_G1.5861.00
210_S281_A1.5831.00
27_M332_W1.5621.00
173_L205_I1.5521.00
241_A287_R1.5391.00
97_L127_I1.5391.00
211_L246_F1.5361.00
94_I132_L1.5351.00
86_V143_F1.5301.00
49_I191_E1.5221.00
14_I71_A1.5171.00
33_F126_F1.4911.00
140_H289_H1.4781.00
82_V294_I1.4751.00
246_F250_G1.4461.00
31_A54_L1.4371.00
105_L117_L1.4291.00
29_F129_P1.4281.00
196_Y200_R1.4281.00
255_L273_A1.4221.00
311_R315_A1.4211.00
131_I160_S1.4101.00
185_D268_R1.4081.00
7_A310_F1.3991.00
27_M57_T1.3931.00
47_T118_R1.3771.00
181_L270_A1.3771.00
180_S199_Y1.3741.00
115_K119_Y1.3731.00
27_M271_L1.3671.00
87_L138_V1.3621.00
258_K266_K1.3601.00
91_G135_V1.3551.00
138_V164_A1.3441.00
36_M122_G1.3371.00
130_A134_L1.3361.00
131_I134_L1.3351.00
314_F318_I1.3341.00
255_L258_K1.3291.00
87_L90_P1.3001.00
32_G125_G1.2920.99
218_M233_M1.2900.99
31_A183_L1.2860.99
10_A75_F1.2860.99
207_G211_L1.2790.99
174_S278_Y1.2790.99
169_G209_I1.2750.99
306_E309_T1.2720.99
19_F279_F1.2630.99
210_S284_A1.2630.99
200_R257_N1.2550.99
17_F20_I1.2530.99
238_W241_A1.2530.99
92_S96_L1.2460.99
208_P212_L1.2380.99
46_A341_Y1.2350.99
20_I325_F1.2350.99
249_A253_L1.2310.99
249_A277_Q1.2300.99
79_A83_L1.1990.99
34_W180_S1.1980.99
116_T120_I1.1920.99
190_A194_D1.1870.99
8_L301_M1.1860.99
72_L79_A1.1810.99
42_E114_R1.1770.99
90_P134_L1.1750.99
255_L259_S1.1720.99
145_E296_P1.1670.99
190_A193_Q1.1550.99
17_F67_A1.1510.99
307_P310_F1.1510.99
171_A175_T1.1460.99
38_Y50_A1.1380.99
204_L208_P1.1300.99
174_S281_A1.1270.99
308_A311_R1.1260.99
251_I254_F1.1210.99
193_Q196_Y1.1100.98
16_G70_V1.0990.98
230_S234_N1.0910.98
235_D239_I1.0900.98
242_S245_T1.0890.98
132_L175_T1.0890.98
123_I127_I1.0880.98
308_A312_A1.0840.98
159_F162_P1.0810.98
79_A293_M1.0750.98
69_V84_G1.0750.98
33_F122_G1.0720.98
151_Y157_K1.0670.98
39_L46_A1.0650.98
127_I131_I1.0620.98
139_T294_I1.0620.98
49_I187_S1.0430.98
242_S284_A1.0390.98
250_G254_F1.0370.98
35_S51_N1.0360.98
235_D238_W1.0340.98
35_S122_G1.0330.98
82_V145_E1.0300.97
49_I52_R1.0270.97
177_F181_L1.0240.97
19_F282_S1.0230.97
57_T182_L1.0220.97
13_I16_G1.0200.97
193_Q197_R1.0180.97
109_N114_R1.0130.97
41_K45_K1.0100.97
170_F209_I1.0060.97
166_S216_C0.9980.97
268_R272_V0.9920.97
11_I15_W0.9880.97
198_A201_K0.9810.97
48_D51_N0.9800.97
277_Q281_A0.9730.96
83_L143_F0.9720.96
48_D109_N0.9640.96
126_F130_A0.9590.96
87_L294_I0.9590.96
143_F294_I0.9550.96
245_T248_I0.9540.96
189_V193_Q0.9540.96
138_V159_F0.9530.96
178_L274_I0.9510.96
181_L274_I0.9460.96
60_V331_F0.9460.96
184_A196_Y0.9450.96
184_A192_E0.9400.96
254_F258_K0.9360.96
252_A256_P0.9340.96
214_A284_A0.9320.95
279_F283_Y0.9310.95
292_Y297_D0.9310.95
215_V219_V0.9300.95
69_V80_T0.9270.95
25_A29_F0.9220.95
13_I70_V0.9210.95
97_L128_I0.9150.95
84_G91_G0.9080.95
41_K341_Y0.9070.95
173_L206_T0.9070.95
182_L336_M0.9030.95
248_I280_L0.8980.94
17_F70_V0.8960.94
119_Y122_G0.8950.94
177_F199_Y0.8930.94
237_S287_R0.8910.94
32_G129_P0.8890.94
146_K150_I0.8860.94
195_A198_A0.8860.94
285_Y289_H0.8800.94
305_T309_T0.8790.94
22_A328_F0.8750.94
312_A316_T0.8720.94
134_L165_Y0.8700.94
10_A313_L0.8690.93
252_A255_L0.8650.93
27_M186_F0.8630.93
109_N112_K0.8580.93
70_V321_F0.8570.93
16_G321_F0.8570.93
192_E338_D0.8570.93
94_I131_I0.8530.93
49_I341_Y0.8510.93
136_L285_Y0.8470.93
129_P132_L0.8430.92
211_L215_V0.8420.92
177_F274_I0.8380.92
205_I208_P0.8340.92
238_W287_R0.8320.92
298_V302_S0.8320.92
102_S105_L0.8310.92
85_T88_L0.8300.92
299_T302_S0.8300.92
41_K46_A0.8230.91
126_F276_I0.8210.91
18_V68_I0.8200.91
253_L256_P0.8170.91
319_V323_I0.8140.91
52_R55_S0.8140.91
192_E196_Y0.8100.91
117_L120_I0.8070.91
22_A132_L0.8050.91
114_R118_R0.8030.90
256_P259_S0.8020.90
228_L231_G0.8010.90
126_F129_P0.7970.90
227_W230_S0.7970.90
79_A82_V0.7960.90
45_K49_I0.7950.90
145_E294_I0.7880.90
93_M127_I0.7850.89
185_D271_L0.7840.89
73_F80_T0.7820.89
290_L310_F0.7710.89
15_W286_G0.7700.89
33_F125_G0.7700.89
198_A202_S0.7700.89
39_L42_E0.7690.88
177_F202_S0.7690.88
298_V303_G0.7660.88
69_V160_S0.7650.88
180_S184_A0.7650.88
170_F210_S0.7640.88
19_F23_V0.7590.88
25_A186_F0.7530.87
22_A282_S0.7480.87
243_F246_F0.7480.87
240_I243_F0.7470.87
144_I157_K0.7460.87
113_E116_T0.7450.87
52_R110_T0.7440.87
130_A165_Y0.7430.87
276_I280_L0.7420.87
91_G278_Y0.7410.87
199_Y256_P0.7400.87
58_W80_T0.7370.86
187_S338_D0.7370.86
292_Y296_P0.7350.86
238_W245_T0.7330.86
120_I123_I0.7320.86
330_F334_M0.7310.86
39_L50_A0.7310.86
210_S214_A0.7290.86
246_F249_A0.7290.86
226_N229_Y0.7280.86
197_R200_R0.7270.86
130_A169_G0.7220.85
69_V313_L0.7220.85
243_F247_V0.7180.85
280_L287_R0.7180.85
59_E327_G0.7170.85
328_F331_F0.7140.85
207_G215_V0.7140.85
34_W176_L0.7120.84
14_I316_T0.7110.84
13_I321_F0.7110.84
99_A304_F0.7100.84
86_V90_P0.7100.84
51_N109_N0.7080.84
169_G194_D0.7060.84
180_S198_A0.7060.84
34_W183_L0.7040.84
152_N156_S0.7040.84
13_I317_Y0.7030.84
78_G303_G0.7000.83
57_T331_F0.6980.83
29_F102_S0.6970.83
50_A191_E0.6960.83
71_A74_S0.6960.83
52_R109_N0.6950.83
237_S243_F0.6930.83
22_A175_T0.6920.83
196_Y267_P0.6910.83
329_F336_M0.6900.82
269_L272_V0.6860.82
183_L187_S0.6850.82
166_S212_L0.6850.82
253_L257_N0.6820.82
196_Y199_Y0.6800.82
94_I174_S0.6780.81
104_F120_I0.6760.81
183_L195_A0.6750.81
244_I250_G0.6750.81
69_V91_G0.6720.81
102_S284_A0.6700.81
90_P159_F0.6690.80
31_A35_S0.6680.80
112_K116_T0.6680.80
124_S129_P0.6680.80
28_D31_A0.6680.80
21_Y29_F0.6660.80
194_D198_A0.6640.80
38_Y195_A0.6640.80
50_A111_A0.6630.80
272_V276_I0.6630.80
23_V279_F0.6590.79
251_I255_L0.6570.79
203_A207_G0.6540.79
11_I300_V0.6530.79
291_P300_V0.6530.79
8_L300_V0.6490.78
53_F340_R0.6430.78
292_Y295_Y0.6420.78
238_W242_S0.6380.77
21_Y335_F0.6350.77
67_A71_A0.6320.77
217_I220_T0.6320.77
14_I79_A0.6300.76
187_S271_L0.6280.76
19_F275_G0.6280.76
326_P331_F0.6240.76
241_A252_A0.6210.75
29_F98_L0.6190.75
53_F182_L0.6190.75
130_A137_P0.6190.75
191_E195_A0.6180.75
280_L284_A0.6180.75
241_A244_I0.6170.75
282_S285_Y0.6120.74
110_T328_F0.6120.74
39_L194_D0.6120.74
133_I168_I0.6110.74
321_F325_F0.6080.74
200_R204_L0.6080.74
145_E149_G0.6070.74
248_I273_A0.6070.74
36_M119_Y0.6050.73
102_S107_F0.6040.73
99_A104_F0.6030.73
29_F32_G0.6030.73
84_G313_L0.6020.73
244_I247_V0.6000.73
138_V162_P0.6000.73
45_K341_Y0.6000.73
323_I330_F0.5990.73
137_P213_F0.5970.72
19_F283_Y0.5970.72
228_L288_A0.5970.72
89_I93_M0.5960.72
59_E62_N0.5930.72
247_V250_G0.5930.72
148_D152_N0.5930.72
11_I81_F0.5920.72
297_D302_S0.5920.72
204_L210_S0.5910.72
17_F313_L0.5910.72
321_F326_P0.5900.72
50_A190_A0.5890.71
67_A316_T0.5890.71
244_I257_N0.5890.71
56_P317_Y0.5880.71
8_L12_S0.5870.71
184_A199_Y0.5860.71
7_A307_P0.5850.71
251_I273_A0.5830.71
137_P164_A0.5830.71
58_W101_R0.5820.71
17_F71_A0.5820.71
200_R256_P0.5800.70
314_F338_D0.5800.70
242_S246_F0.5780.70
14_I286_G0.5770.70
215_V218_M0.5770.70
145_E298_V0.5770.70
278_Y281_A0.5760.70
50_A53_F0.5730.69
251_I276_I0.5720.69
236_F245_T0.5720.69
54_L105_L0.5700.69
32_G37_I0.5680.69
191_E194_D0.5650.68
174_S277_Q0.5630.68
129_P172_I0.5630.68
248_I287_R0.5620.68
7_A301_M0.5590.68
241_A284_A0.5560.67
111_A114_R0.5560.67
314_F317_Y0.5550.67
138_V161_S0.5510.66
232_M288_A0.5510.66
16_G317_Y0.5510.66
160_S164_A0.5500.66
207_G214_A0.5500.66
84_G88_L0.5500.66
177_F203_A0.5490.66
200_R203_A0.5470.66
283_Y287_R0.5470.66
15_W305_T0.5450.66
219_V229_Y0.5440.65
21_Y72_L0.5410.65
81_F139_T0.5410.65
236_F246_F0.5410.65
212_L220_T0.5400.65
46_A50_A0.5400.65
69_V327_G0.5390.65
219_V250_G0.5390.65
290_L300_V0.5380.65
68_I72_L0.5370.64
184_A267_P0.5360.64
121_S125_G0.5360.64
101_R125_G0.5360.64
231_G234_N0.5340.64
152_N155_M0.5340.64
273_A276_I0.5340.64
38_Y41_K0.5300.63
170_F213_F0.5300.63
234_N237_S0.5290.63
177_F206_T0.5290.63
129_P139_T0.5280.63
184_A270_A0.5270.63
269_L273_A0.5250.63
11_I313_L0.5250.63
163_N288_A0.5240.63
53_F65_I0.5240.63
153_L157_K0.5230.62
267_P270_A0.5220.62
281_A320_A0.5210.62
74_S85_T0.5200.62
198_A209_I0.5190.62
176_L180_S0.5180.62
9_I12_S0.5150.61
56_P98_L0.5150.61
140_H285_Y0.5140.61
184_A256_P0.5130.61
172_I209_I0.5130.61
170_F281_A0.5130.61
239_I243_F0.5130.61
232_M242_S0.5120.61
212_L244_I0.5110.61
238_W248_I0.5110.61
239_I242_S0.5110.61
93_M96_L0.5110.61
51_N121_S0.5070.60
10_A71_A0.5060.60
322_I327_G0.5040.60
197_R219_V0.5030.59
12_S318_I0.5030.59
170_F320_A0.5020.59
32_G36_M0.5010.59
7_A300_V0.5010.59
53_F57_T0.5010.59
114_R183_L0.5000.59
187_S191_E0.5000.59
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  
1zzaA 1 0.1474 31.1 0.966 Contact Map
2mfrA 1 0.1503 24.5 0.967 Contact Map
4wgvA 2 0.5578 19.9 0.969 Contact Map
2kncA 1 0.1387 19.7 0.969 Contact Map
2l8sA 1 0.1329 18.6 0.969 Contact Map
2yevB 1 0.1474 9.2 0.973 Contact Map
2m3eA 1 0.1387 8.5 0.973 Contact Map
4tphA 2 0.8237 8.3 0.974 Contact Map
4x5mA 2 0.2717 7.7 0.974 Contact Map
2m20A 2 0.1098 7.6 0.974 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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