GREMLIN Database
CYDB - Cytochrome bd ubiquinol oxidase subunit 2
UniProt: P94365 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 338 (322)
Sequences: 3257 (2011)
Seq/√Len: 112.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
159_N162_S3.4371.00
31_M174_F3.4221.00
125_L170_T3.2101.00
324_Y327_R3.0671.00
83_Y142_M3.0241.00
308_A312_L2.8311.00
232_L272_I2.8251.00
239_C261_A2.7371.00
42_E192_R2.6671.00
129_F170_T2.6301.00
298_D302_K2.6001.00
129_F166_G2.5741.00
21_F260_G2.5441.00
161_Y215_S2.5331.00
174_F200_I2.4751.00
195_K199_K2.4301.00
171_L207_A2.4181.00
44_R48_N2.3591.00
31_M170_T2.2741.00
10_I14_V2.2181.00
104_R117_D2.2131.00
89_I130_V2.1571.00
198_Q248_R2.1501.00
179_M197_A2.1461.00
29_V46_L2.1331.00
251_K254_W2.1181.00
128_P169_V2.1021.00
45_V330_V2.1001.00
186_I331_S2.0791.00
317_G320_I2.0691.00
14_V18_G2.0331.00
5_H295_S2.0301.00
16_F68_I2.0281.00
171_L203_V1.9901.00
133_V166_G1.9691.00
306_I310_T1.9671.00
197_A247_I1.9551.00
194_R198_Q1.9511.00
167_V171_L1.9491.00
136_T165_G1.9221.00
153_H156_D1.9081.00
221_M224_R1.8941.00
46_L181_I1.8861.00
71_A304_M1.8831.00
163_I167_V1.8681.00
121_F125_L1.8661.00
320_I324_Y1.8601.00
128_P173_C1.8411.00
7_L305_S1.7991.00
118_W122_F1.7781.00
96_G119_V1.7741.00
178_L197_A1.7621.00
209_L237_V1.7421.00
55_D102_E1.7351.00
277_R290_T1.7331.00
115_V118_W1.7301.00
140_R159_N1.7101.00
246_F258_M1.6951.00
123_G127_P1.6941.00
40_E113_V1.6761.00
238_I242_L1.6661.00
240_F262_G1.6501.00
220_D223_T1.6131.00
167_V207_A1.5981.00
47_I101_F1.5861.00
241_M245_V1.5591.00
208_V269_M1.5491.00
208_V266_T1.5311.00
190_Q252_D1.5291.00
119_V123_G1.5181.00
90_V131_L1.5111.00
176_H260_G1.5101.00
82_G142_M1.4941.00
168_T207_A1.4721.00
130_V158_I1.4711.00
311_L314_F1.4641.00
25_F323_Y1.4471.00
93_A123_G1.4431.00
12_V67_A1.4351.00
206_V210_A1.4231.00
27_F128_P1.4121.00
239_C258_M1.4091.00
139_F274_L1.4071.00
239_C265_L1.4051.00
229_T272_I1.4021.00
242_L258_M1.4011.00
31_M125_L1.3981.00
202_G206_V1.3721.00
229_T233_A1.3701.00
214_L218_Q1.3691.00
302_K306_I1.3571.00
172_L263_L1.3531.00
29_V50_I1.3461.00
305_S309_L1.3441.00
235_L265_L1.3331.00
182_T190_Q1.3281.00
233_A269_M1.3251.00
145_D151_H1.3131.00
87_F134_L1.3101.00
43_R117_D1.2970.99
93_A126_I1.2870.99
78_T279_M1.2850.99
188_D191_N1.2830.99
137_T162_S1.2810.99
130_V133_V1.2780.99
221_M225_R1.2740.99
45_V189_L1.2710.99
5_H301_L1.2700.99
25_F53_F1.2620.99
220_D224_R1.2500.99
101_F116_W1.2470.99
83_Y86_P1.2450.99
213_A217_Y1.2440.99
136_T211_F1.2430.99
201_M243_A1.2430.99
183_L253_G1.2380.99
34_R121_F1.2290.99
42_E332_H1.2250.99
15_L18_G1.2240.99
8_W71_A1.2240.99
129_F133_V1.2230.99
114_K118_W1.2230.99
39_N42_E1.2130.99
6_D292_A1.2100.99
25_F256_F1.2030.99
75_W79_M1.1950.99
297_G300_S1.1910.99
164_L214_L1.1850.99
227_E231_P1.1820.99
83_Y137_T1.1820.99
30_G124_S1.1770.99
41_L332_H1.1770.99
194_R250_K1.1750.99
88_V92_L1.1740.99
175_Q201_M1.1660.99
205_F240_F1.1570.99
29_V181_I1.1570.99
172_L266_T1.1550.99
86_P133_V1.1350.99
107_V112_W1.1300.99
243_A258_M1.1280.98
235_L239_C1.1240.98
45_V48_N1.1230.98
18_G316_I1.1210.98
32_A178_L1.1190.98
298_D301_L1.1060.98
299_Y302_K1.1030.98
68_I75_W1.0970.98
115_V119_V1.0950.98
169_V173_C1.0790.98
299_Y303_V1.0730.98
17_V264_A1.0720.98
209_L213_A1.0470.98
65_A80_L1.0440.97
83_Y279_M1.0430.97
179_M255_T1.0390.97
15_L63_T1.0360.97
75_W278_V1.0340.97
222_F225_R1.0320.97
196_M199_K1.0310.97
53_F180_F1.0230.97
142_M279_M1.0220.97
229_T232_L1.0130.97
205_F244_A1.0110.97
41_L45_V1.0070.97
131_L173_C1.0050.97
122_F126_I1.0000.97
17_V267_V0.9920.97
245_V249_K0.9910.97
39_N332_H0.9890.97
190_Q194_R0.9890.97
179_M259_T0.9820.96
74_N148_M0.9700.96
175_Q197_A0.9680.96
205_F209_L0.9660.96
137_T157_Y0.9620.96
175_Q179_M0.9620.96
176_H259_T0.9610.96
11_L66_G0.9600.96
31_M121_F0.9600.96
45_V185_T0.9590.96
234_V238_I0.9570.96
182_T194_R0.9490.96
33_T121_F0.9290.95
33_T47_I0.9250.95
9_F13_A0.9240.95
44_R105_G0.9240.95
45_V332_H0.9200.95
205_F237_V0.9130.95
44_R47_I0.9110.95
14_V66_G0.9090.94
246_F254_W0.9080.94
196_M200_I0.9070.94
126_I130_V0.9060.94
220_D225_R0.9040.94
232_L235_L0.9030.94
188_D192_R0.9020.94
107_V110_L0.9020.94
23_E27_F0.8970.94
125_L129_F0.8970.94
277_R281_S0.8920.94
201_M244_A0.8910.94
143_P282_S0.8850.94
270_I274_L0.8840.94
56_A322_S0.8820.94
150_I156_D0.8800.93
65_A76_Y0.8720.93
15_L66_G0.8640.93
8_W304_M0.8640.93
253_G257_G0.8630.93
86_P157_Y0.8610.93
36_L46_L0.8600.93
228_I272_I0.8550.92
202_G244_A0.8540.92
191_N194_R0.8530.92
105_G113_V0.8510.92
119_V122_F0.8470.92
219_T223_T0.8420.92
20_F319_Q0.8410.92
180_F327_R0.8390.92
133_V163_I0.8360.92
78_T144_I0.8350.92
79_M142_M0.8310.91
14_V312_L0.8310.91
11_L14_V0.8290.91
20_F131_L0.8260.91
164_L210_A0.8260.91
232_L269_M0.8250.91
30_G128_P0.8240.91
290_T293_N0.8220.91
138_L279_M0.8210.91
90_V130_V0.8190.91
296_S300_S0.8180.91
80_L87_F0.8170.91
310_T314_F0.8160.91
203_V206_V0.8150.91
175_Q259_T0.8130.90
195_K198_Q0.8120.90
93_A127_P0.8090.90
36_L193_A0.8090.90
191_N250_K0.8080.90
189_L193_A0.8060.90
157_Y160_V0.8050.90
108_D115_V0.8050.90
128_P131_L0.7990.90
25_F184_R0.7970.90
95_M295_S0.7940.89
233_A240_F0.7930.89
81_S84_Y0.7920.89
31_M124_S0.7900.89
69_F76_Y0.7850.89
191_N195_K0.7790.88
38_H42_E0.7770.88
129_F163_I0.7770.88
171_L200_I0.7740.88
23_E184_R0.7720.88
48_N51_G0.7720.88
226_G229_T0.7710.88
98_G101_F0.7700.88
264_A268_G0.7690.88
171_L204_V0.7680.88
321_W325_V0.7620.87
13_A271_F0.7610.87
236_I240_F0.7610.87
118_W121_F0.7550.87
168_T208_V0.7520.87
135_F270_I0.7510.87
232_L265_L0.7490.86
75_W78_T0.7460.86
289_L293_N0.7450.86
66_G312_L0.7430.86
16_F64_G0.7350.85
65_A304_M0.7340.85
144_I279_M0.7330.85
175_Q243_A0.7330.85
17_V21_F0.7310.85
257_G261_A0.7260.85
212_A269_M0.7220.84
144_I148_M0.7170.84
125_L128_P0.7160.84
219_T222_F0.7130.84
183_L256_F0.7130.84
116_W119_V0.7120.84
32_A174_F0.7050.83
74_N294_A0.7050.83
185_T329_R0.7040.83
110_L113_V0.7040.83
165_G211_F0.7030.83
49_T180_F0.7020.83
190_Q329_R0.7000.82
82_G86_P0.6970.82
200_I203_V0.6970.82
11_L312_L0.6950.82
179_M243_A0.6940.82
89_I126_I0.6930.82
11_L308_A0.6910.82
38_H192_R0.6900.82
245_V248_R0.6860.81
53_F322_S0.6850.81
241_M244_A0.6850.81
199_K202_G0.6820.81
21_F264_A0.6810.81
289_L294_A0.6780.80
303_V307_A0.6780.80
233_A237_V0.6780.80
178_L182_T0.6780.80
319_Q322_S0.6770.80
48_N106_K0.6760.80
54_W76_Y0.6760.80
19_F27_F0.6750.80
48_N105_G0.6740.80
46_L107_V0.6740.80
98_G269_M0.6730.80
232_L268_G0.6730.80
181_I193_A0.6730.80
123_G128_P0.6710.80
27_F98_G0.6710.80
85_I89_I0.6710.80
55_D318_S0.6700.80
100_A119_V0.6700.80
305_S329_R0.6700.80
67_A70_A0.6690.80
12_V307_A0.6690.80
109_H112_W0.6690.80
216_A230_I0.6690.80
217_Y250_K0.6680.79
243_A262_G0.6680.79
108_D112_W0.6670.79
219_T225_R0.6670.79
182_T247_I0.6660.79
305_S308_A0.6650.79
198_Q201_M0.6640.79
207_A211_F0.6630.79
226_G230_I0.6610.79
261_A265_L0.6610.79
320_I327_R0.6570.78
231_P236_I0.6560.78
129_F167_V0.6560.78
192_R195_K0.6560.78
105_G108_D0.6550.78
268_G272_I0.6540.78
178_L196_M0.6500.78
20_F173_C0.6480.77
237_V242_L0.6460.77
312_L317_G0.6430.77
242_L246_F0.6430.77
231_P238_I0.6420.77
42_E45_V0.6420.77
122_F331_S0.6410.77
198_Q202_G0.6410.77
26_D29_V0.6410.77
35_F196_M0.6400.77
144_I281_S0.6390.76
37_G42_E0.6350.76
194_R197_A0.6330.76
113_V117_D0.6330.76
27_F94_L0.6310.76
132_G166_G0.6300.75
14_V308_A0.6240.75
216_A225_R0.6240.75
154_V157_Y0.6190.74
37_G46_L0.6180.74
9_F291_V0.6180.74
265_L272_I0.6170.74
95_M100_A0.6150.74
32_A181_I0.6140.74
47_I105_G0.6100.73
55_D58_E0.6070.73
236_I239_C0.6070.73
46_L189_L0.6070.73
234_V248_R0.6060.73
49_T331_S0.6050.72
29_V33_T0.6040.72
134_L208_V0.6000.72
275_F301_L0.5990.72
110_L114_K0.5990.72
6_D275_F0.5970.71
317_G322_S0.5970.71
15_L67_A0.5970.71
6_D291_V0.5930.71
50_I101_F0.5910.71
5_H298_D0.5900.71
63_T307_A0.5900.71
80_L304_M0.5880.70
262_G266_T0.5870.70
205_F229_T0.5840.70
224_R228_I0.5830.70
27_F30_G0.5810.69
30_G35_F0.5800.69
12_V196_M0.5800.69
242_L254_W0.5780.69
19_F326_F0.5780.69
246_F251_K0.5770.69
87_F263_L0.5760.69
9_F77_A0.5760.69
198_Q249_K0.5760.69
106_K319_Q0.5760.69
175_Q200_I0.5720.68
64_G68_I0.5710.68
20_F267_V0.5710.68
233_A236_I0.5710.68
230_I237_V0.5700.68
182_T252_D0.5700.68
195_K238_I0.5690.68
12_V75_W0.5680.68
13_A296_S0.5660.67
31_M93_A0.5660.67
306_I309_L0.5650.67
42_E46_L0.5620.67
98_G103_F0.5610.67
65_A87_F0.5600.67
89_I92_L0.5590.66
151_H155_S0.5560.66
63_T67_A0.5560.66
312_L316_I0.5550.66
17_V268_G0.5520.65
15_L304_M0.5520.65
167_V192_R0.5490.65
90_V172_L0.5490.65
11_L15_L0.5480.65
193_A197_A0.5470.65
143_P156_D0.5470.65
137_T159_N0.5450.65
109_H115_V0.5450.65
17_V260_G0.5450.65
136_T328_K0.5450.65
101_F269_M0.5430.64
40_E117_D0.5420.64
181_I185_T0.5410.64
143_P152_A0.5400.64
14_V62_L0.5400.64
160_V214_L0.5370.63
120_V124_S0.5370.63
174_F178_L0.5370.63
145_D149_N0.5360.63
42_E188_D0.5360.63
167_V202_G0.5350.63
52_P308_A0.5340.63
278_V291_V0.5330.63
43_R104_R0.5310.63
9_F304_M0.5300.62
243_A247_I0.5300.62
80_L84_Y0.5290.62
263_L266_T0.5290.62
179_M247_I0.5290.62
216_A227_E0.5290.62
210_A214_L0.5290.62
145_D148_M0.5290.62
43_R113_V0.5280.62
51_G71_A0.5280.62
269_M296_S0.5260.62
239_C242_L0.5260.62
125_L174_F0.5250.62
206_V238_I0.5250.62
156_D162_S0.5240.62
289_L295_S0.5220.61
54_W97_R0.5200.61
97_R124_S0.5190.61
128_P138_L0.5180.61
39_N188_D0.5180.61
10_I309_L0.5180.61
161_Y273_S0.5170.60
34_R118_W0.5170.60
152_A155_S0.5170.60
229_T236_I0.5160.60
194_R252_D0.5160.60
137_T160_V0.5160.60
158_I162_S0.5150.60
176_H256_F0.5110.60
57_N60_W0.5110.60
258_M261_A0.5100.59
52_P94_L0.5090.59
49_T53_F0.5070.59
128_P170_T0.5060.59
240_F244_A0.5060.59
175_Q204_V0.5050.59
39_N206_V0.5050.59
314_F321_W0.5040.59
31_M128_P0.5030.58
129_F136_T0.5010.58
269_M273_S0.5010.58
237_V240_F0.5000.58
125_L261_A0.5000.58
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  
4tphA 2 0.8491 18.8 0.969 Contact Map
3wdoA 1 0.8787 18.7 0.969 Contact Map
3wajA 1 0.6716 16.4 0.97 Contact Map
2mgyA 1 0.497 13.9 0.971 Contact Map
2mfrA 1 0.1568 13.7 0.971 Contact Map
3j1zP 8 0.4201 7.9 0.974 Contact Map
4nv5A 1 0.6036 7.6 0.974 Contact Map
2m20A 2 0.1213 7.5 0.974 Contact Map
1fftB 1 0.1568 7 0.974 Contact Map
1fftC 1 0.4201 6.2 0.975 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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