GREMLIN Database
YBDO - Uncharacterized HTH-type transcriptional regulator YbdO
UniProt: P77746 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13534
Length: 300 (283)
Sequences: 79181 (57618)
Seq/√Len: 3425.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
79_K83_G3.5891.00
24_H33_S3.3891.00
166_M297_N2.6021.00
103_Y149_A2.5081.00
76_H90_I2.3981.00
238_I245_G2.3301.00
172_R249_Y2.2501.00
181_H196_E2.2211.00
20_C33_S2.1891.00
167_P170_T2.1871.00
170_T274_K2.1851.00
99_N131_H2.1701.00
29_K32_E2.1451.00
23_Q78_E2.1381.00
99_N129_E2.1271.00
189_T192_Q2.0771.00
167_P274_K2.0691.00
54_D69_T2.0151.00
19_E74_H2.0101.00
17_I44_S2.0051.00
235_I255_Y1.9871.00
170_T272_S1.9781.00
101_I131_H1.9781.00
239_A260_N1.9721.00
76_H83_G1.9551.00
119_C295_R1.9401.00
177_C264_I1.9121.00
199_T243_L1.9051.00
20_C23_Q1.9021.00
19_E78_E1.9001.00
80_N84_L1.8861.00
17_I41_V1.8841.00
20_C24_H1.8671.00
27_I45_L1.8621.00
22_Y66_P1.8541.00
19_E23_Q1.8521.00
74_H78_E1.8121.00
174_T249_Y1.8121.00
140_A152_V1.8021.00
58_I65_A1.7431.00
239_A255_Y1.7291.00
73_L87_T1.6971.00
197_E225_S1.6971.00
72_N90_I1.6601.00
165_C276_Y1.6531.00
174_T263_E1.6481.00
143_L148_K1.6241.00
23_Q33_S1.6141.00
120_L292_F1.6121.00
18_F74_H1.5901.00
164_I281_K1.5791.00
22_Y74_H1.5781.00
19_E77_L1.5641.00
17_I36_I1.5571.00
24_H29_K1.5531.00
120_L128_I1.5261.00
28_S38_P1.5171.00
68_T71_L1.5111.00
142_E146_H1.5041.00
14_L44_S1.4741.00
55_P58_I1.4521.00
11_D14_L1.4521.00
14_L51_Q1.4521.00
166_M279_Y1.4461.00
37_T40_A1.4421.00
19_E81_L1.4381.00
26_S29_K1.4171.00
20_C34_L1.4131.00
14_L47_R1.4091.00
285_N289_F1.4081.00
208_V212_Q1.4061.00
76_H79_K1.4051.00
179_N260_N1.3891.00
164_I279_Y1.3841.00
154_T278_S1.3801.00
76_H86_Q1.3751.00
80_N87_T1.3651.00
156_M276_Y1.3621.00
12_L84_L1.3471.00
151_L289_F1.3441.00
110_C232_L1.3381.00
97_K127_E1.3231.00
277_I293_I1.3191.00
145_V162_S1.3181.00
101_I133_I1.3091.00
279_Y293_I1.2861.00
51_Q88_I1.2861.00
119_C124_S1.2811.00
143_L149_A1.2781.00
144_L152_V1.2781.00
177_C244_L1.2701.00
73_L88_I1.2651.00
171_I250_E1.2611.00
196_E244_L1.2591.00
121_R225_S1.2571.00
293_I297_N1.2541.00
151_L277_I1.2541.00
234_I245_G1.2481.00
60_S65_A1.2471.00
291_R294_D1.2381.00
46_Q50_A1.2291.00
249_Y253_N1.2271.00
253_N257_D1.2251.00
71_L75_H1.2221.00
215_I220_M1.2211.00
83_G86_Q1.2191.00
236_N239_A1.2121.00
249_Y263_E1.2001.00
75_H79_K1.1981.00
121_R197_E1.1921.00
186_D262_K1.1921.00
72_N75_H1.1891.00
255_Y260_N1.1871.00
76_H87_T1.1821.00
179_N262_K1.1771.00
119_C122_Q1.1731.00
18_F57_F1.1721.00
118_R122_Q1.1641.00
167_P276_Y1.1611.00
182_P196_E1.1561.00
165_C278_S1.1431.00
199_T234_I1.1431.00
100_F292_F1.1391.00
124_S295_R1.1341.00
18_F22_Y1.1241.00
36_I40_A1.1191.00
16_V85_E1.1141.00
18_F56_L1.1131.00
43_Q46_Q1.1131.00
197_E223_K1.1061.00
43_Q47_R1.1011.00
131_H227_R1.0991.00
42_S46_Q1.0951.00
125_S291_R1.0881.00
79_K86_Q1.0831.00
228_G234_I1.0821.00
176_I263_E1.0811.00
27_I64_I1.0811.00
120_L295_R1.0781.00
118_R240_V1.0771.00
15_L77_L1.0761.00
21_I30_A1.0681.00
187_N267_E1.0651.00
13_N16_V1.0621.00
80_N83_G1.0591.00
20_C30_A1.0501.00
109_S134_L1.0491.00
290_S294_D1.0431.00
44_S47_R1.0401.00
66_P70_G1.0291.00
145_V160_S1.0251.00
178_S241_T1.0241.00
188_S192_Q1.0231.00
235_I239_A1.0231.00
175_L244_L1.0201.00
263_E266_L1.0181.00
72_N76_H1.0171.00
190_Y268_H1.0151.00
115_M240_V1.0121.00
236_N240_V1.0011.00
103_Y140_A1.0011.00
85_E89_N0.9911.00
85_E88_I0.9891.00
294_D297_N0.9881.00
88_I92_N0.9831.00
176_I252_Y0.9811.00
17_I34_L0.9801.00
166_M293_I0.9791.00
36_I41_V0.9751.00
172_R272_S0.9741.00
116_L296_L0.9661.00
120_L125_S0.9661.00
22_Y57_F0.9631.00
254_S258_F0.9541.00
18_F66_P0.9491.00
177_C181_H0.9461.00
181_H184_I0.9461.00
143_L146_H0.9421.00
82_R86_Q0.9411.00
116_L295_R0.9401.00
73_L77_L0.9371.00
21_I27_I0.9361.00
286_N289_F0.9321.00
181_H197_E0.9311.00
209_D212_Q0.9271.00
162_S281_K0.9261.00
228_G237_S0.9191.00
18_F48_L0.9191.00
252_Y255_Y0.9181.00
133_I143_L0.9171.00
54_D91_V0.9131.00
200_Q224_I0.9121.00
129_E223_K0.9101.00
22_Y70_G0.9091.00
57_F64_I0.9051.00
30_A41_V0.9001.00
47_R50_A0.8901.00
149_A152_V0.8891.00
72_N94_S0.8851.00
75_H78_E0.8781.00
280_N283_S0.8781.00
128_I288_V0.8771.00
198_F222_R0.8731.00
181_H185_T0.8661.00
29_K33_S0.8661.00
103_Y154_T0.8631.00
106_Q230_S0.8631.00
28_S32_E0.8551.00
163_V278_S0.8541.00
177_C182_P0.8511.00
25_L65_A0.8491.00
176_I245_G0.8431.00
182_P186_D0.8421.00
156_M274_K0.8411.00
185_T197_E0.8381.00
69_T94_S0.8341.00
285_N290_S0.8311.00
13_N44_S0.8271.00
102_I151_L0.8271.00
12_L81_L0.8251.00
79_K82_R0.8221.00
34_L41_V0.8191.00
183_R196_E0.8161.00
214_E218_R0.8161.00
141_E145_V0.8161.00
197_E224_I0.8141.00
256_R259_L0.8131.00
192_Q195_A0.8131.00
60_S63_G0.8091.00
164_I167_P0.8041.00
21_I45_L0.8011.00
98_K128_I0.8001.00
103_Y152_V0.7991.00
255_Y258_F0.7991.00
69_T91_V0.7991.00
46_Q55_P0.7981.00
180_R184_I0.7981.00
18_F73_L0.7961.00
98_K288_V0.7951.00
133_I149_A0.7951.00
25_L71_L0.7921.00
92_N95_E0.7851.00
96_L125_S0.7821.00
118_R242_D0.7821.00
23_Q74_H0.7791.00
139_N142_E0.7781.00
22_Y25_L0.7731.00
191_E194_M0.7731.00
38_P42_S0.7681.00
21_I57_F0.7681.00
178_S242_D0.7651.00
83_G87_T0.7651.00
172_R265_K0.7581.00
237_S242_D0.7541.00
84_L87_T0.7471.00
153_I296_L0.7471.00
208_V227_R0.7461.00
211_I215_I0.7461.00
209_D213_M0.7451.00
151_L292_F0.7441.00
24_H30_A0.7421.00
66_P71_L0.7381.00
145_V163_V0.7381.00
121_R242_D0.7371.00
86_Q90_I0.7361.00
189_T267_E0.7351.00
25_L63_G0.7331.00
287_L291_R0.7281.00
184_I262_K0.7271.00
252_Y256_R0.7271.00
177_C183_R0.7261.00
65_A71_L0.7261.00
176_I247_V0.7261.00
69_T72_N0.7241.00
256_R263_E0.7221.00
14_L17_I0.7211.00
77_L80_N0.7181.00
101_I149_A0.7171.00
248_P251_L0.7161.00
177_C262_K0.7141.00
176_I256_R0.7121.00
120_L291_R0.7101.00
84_L88_I0.7091.00
194_M220_M0.7091.00
172_R270_L0.7051.00
40_A44_S0.7051.00
104_G109_S0.6981.00
16_V20_C0.6971.00
27_I41_V0.6951.00
58_I67_T0.6951.00
195_A223_K0.6951.00
178_S181_H0.6941.00
191_E218_R0.6861.00
214_E217_E0.6841.00
209_D214_E0.6841.00
87_T91_V0.6811.00
21_I41_V0.6801.00
124_S291_R0.6801.00
187_N265_K0.6791.00
58_I63_G0.6771.00
230_S233_T0.6771.00
226_F237_S0.6751.00
69_T73_L0.6741.00
49_R54_D0.6721.00
239_A258_F0.6691.00
104_G113_N0.6691.00
82_R85_E0.6691.00
213_M217_E0.6681.00
101_I150_D0.6671.00
77_L81_L0.6651.00
211_I214_E0.6641.00
78_E82_R0.6631.00
201_L234_I0.6631.00
254_S257_D0.6621.00
212_Q216_D0.6611.00
100_F288_V0.6611.00
86_Q89_N0.6571.00
202_I227_R0.6531.00
213_M216_D0.6531.00
175_L193_I0.6521.00
73_L91_V0.6511.00
129_E227_R0.6501.00
68_T72_N0.6481.00
150_D289_F0.6461.00
144_L278_S0.6461.00
71_L74_H0.6451.00
180_R262_K0.6441.00
180_R183_R0.6441.00
27_I63_G0.6401.00
45_L49_R0.6381.00
49_R59_R0.6361.00
30_A34_L0.6351.00
32_E35_Y0.6321.00
147_R280_N0.6281.00
97_K129_E0.6281.00
13_N47_R0.6261.00
189_T268_H0.6171.00
169_H275_L0.6121.00
215_I222_R0.6111.00
180_R241_T0.6111.00
21_I26_S0.6091.00
76_H80_N0.6081.00
134_L229_S0.6071.00
164_I282_S0.6071.00
16_V19_E0.6071.00
110_C236_N0.6051.00
198_F244_L0.6051.00
179_N259_L0.6051.00
113_N116_L0.6011.00
283_S286_N0.6001.00
291_R295_R0.5991.00
212_Q215_I0.5951.00
292_F296_L0.5931.00
182_P185_T0.5921.00
187_N192_Q0.5921.00
134_L230_S0.5911.00
183_R188_S0.5901.00
66_P74_H0.5901.00
72_N91_V0.5891.00
98_K125_S0.5881.00
89_N93_K0.5871.00
144_L163_V0.5871.00
175_L198_F0.5861.00
210_D214_E0.5861.00
234_I238_I0.5861.00
287_L290_S0.5861.00
100_F151_L0.5841.00
237_S243_L0.5801.00
52_F91_V0.5791.00
151_L293_I0.5761.00
173_N246_I0.5751.00
98_K127_E0.5741.00
208_V214_E0.5731.00
171_I273_I0.5711.00
175_L246_I0.5701.00
210_D213_M0.5701.00
54_D58_I0.5691.00
117_I130_C0.5671.00
39_S43_Q0.5661.00
139_N143_L0.5631.00
57_F66_P0.5591.00
52_F73_L0.5581.00
202_I229_S0.5561.00
13_N17_I0.5531.00
75_H90_I0.5521.00
140_A147_R0.5511.00
40_A43_Q0.5511.00
155_Q273_I0.5491.00
16_V81_L0.5491.00
37_T43_Q0.5491.00
228_G233_T0.5491.00
108_I112_N0.5431.00
81_L84_L0.5421.00
45_L57_F0.5401.00
181_H244_L0.5391.00
279_Y290_S0.5391.00
115_M118_R0.5361.00
247_V252_Y0.5361.00
194_M221_N0.5351.00
266_L269_P0.5351.00
115_M119_C0.5351.00
52_F55_P0.5331.00
125_S128_I0.5311.00
203_S227_R0.5311.00
77_L84_L0.5301.00
81_L85_E0.5301.00
11_D51_Q0.5291.00
177_C184_I0.5261.00
153_I277_I0.5251.00
17_I45_L0.5221.00
142_E148_K0.5221.00
103_Y133_I0.5201.00
289_F293_I0.5181.00
168_L277_I0.5181.00
76_H91_V0.5181.00
231_L248_P0.5141.00
156_M165_C0.5111.00
110_C230_S0.5101.00
93_K96_L0.5101.00
122_Q184_I0.5101.00
80_N88_I0.5051.00
91_V94_S0.5041.00
27_I38_P0.5041.00
27_I59_R0.5001.00
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  
2esnA 3 0.9833 100 0.083 Contact Map
1uthA 2 0.73 100 0.087 Contact Map
3fxqA 3 0.9667 100 0.103 Contact Map
3fzvA 4 0.9467 100 0.109 Contact Map
2h98A 2 0.6667 100 0.119 Contact Map
1al3A 1 0.68 100 0.12 Contact Map
1ixcA 4 0.9567 100 0.12 Contact Map
4x6gA 4 0.98 100 0.122 Contact Map
2h9bA 2 0.6667 100 0.123 Contact Map
3szpA 3 0.9533 100 0.128 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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