GREMLIN Database
YDHB - Uncharacterized HTH-type transcriptional regulator YdhB
UniProt: P0ACR2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12140
Length: 310 (281)
Sequences: 79753 (57657)
Seq/√Len: 3439.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
71_S75_K3.5201.00
16_N25_E3.2931.00
161_R289_G2.5821.00
97_A142_V2.4231.00
68_E82_Q2.4021.00
12_A25_E2.3081.00
176_H193_W2.1841.00
231_I238_G2.1691.00
165_M267_A2.1671.00
93_Q124_L2.1531.00
162_D165_M2.1481.00
113_D291_S2.1461.00
162_D267_A2.1321.00
167_S242_T2.0691.00
46_V61_A2.0621.00
9_V36_T2.0381.00
93_Q122_E2.0331.00
165_M265_D1.9981.00
21_A24_Q1.9911.00
11_D70_R1.9841.00
186_S189_T1.9641.00
68_E75_K1.9591.00
232_S253_K1.9541.00
113_D287_Y1.9421.00
11_D15_R1.9201.00
15_R70_R1.9151.00
95_A124_L1.9151.00
169_S242_T1.8961.00
12_A15_R1.8881.00
11_D66_L1.8871.00
12_A16_N1.8841.00
228_A248_W1.8541.00
14_A58_L1.8361.00
9_V33_V1.8311.00
72_V76_M1.8231.00
172_V257_L1.8161.00
196_L236_C1.8141.00
66_L70_R1.7821.00
232_S248_W1.7081.00
169_S256_A1.6931.00
50_E57_E1.6861.00
194_P218_R1.6751.00
19_F37_V1.6631.00
160_F269_C1.6611.00
65_F79_T1.6581.00
64_W82_Q1.6491.00
133_V145_A1.6321.00
136_A141_R1.6241.00
14_A66_L1.6141.00
16_N21_A1.5771.00
11_D69_G1.5381.00
159_A274_Q1.5231.00
15_R25_E1.5231.00
114_F284_L1.4981.00
68_E71_S1.4901.00
6_S36_T1.4881.00
135_D139_D1.4871.00
6_S43_W1.4731.00
161_R272_W1.4711.00
10_V66_L1.4661.00
205_L208_R1.4661.00
9_V28_R1.4591.00
18_S21_A1.4571.00
6_S39_Q1.4441.00
89_G120_D1.4351.00
47_P50_E1.4261.00
114_F121_V1.4241.00
285_L289_G1.4241.00
20_S30_P1.4161.00
29_V32_A1.4111.00
181_M189_T1.3961.00
159_A272_W1.3941.00
277_M281_L1.3921.00
12_A26_L1.3911.00
272_W285_L1.3891.00
147_G271_T1.3841.00
60_A63_A1.3771.00
68_E78_I1.3761.00
149_T269_C1.3761.00
104_P225_E1.3621.00
52_R57_E1.3401.00
72_V79_T1.3391.00
11_D73_V1.3371.00
95_A126_F1.3251.00
136_A142_V1.3221.00
91_R120_D1.3221.00
283_W286_E1.3171.00
75_K78_I1.3121.00
137_L145_A1.3081.00
270_L285_L1.2981.00
117_H287_Y1.2971.00
113_D117_H1.2941.00
138_S157_R1.2891.00
65_F80_R1.2851.00
166_L243_H1.2831.00
174_S253_K1.2811.00
3_S6_S1.2761.00
144_L270_L1.2711.00
4_E76_M1.2621.00
193_W237_I1.2591.00
172_V237_I1.2551.00
67_K71_S1.2501.00
227_S238_G1.2401.00
144_L281_L1.2281.00
229_T232_S1.2181.00
115_Y218_R1.2171.00
43_W80_R1.2131.00
68_E79_T1.2111.00
174_S255_V1.1971.00
162_D269_C1.1941.00
64_W67_K1.1871.00
242_T246_K1.1861.00
10_V49_F1.1861.00
28_R32_A1.1821.00
112_V116_R1.1791.00
242_T256_A1.1771.00
115_Y194_P1.1681.00
248_W253_K1.1511.00
176_H179_A1.1491.00
112_V233_A1.1421.00
160_F271_T1.1391.00
10_V14_A1.1361.00
35_Y39_Q1.1341.00
38_R42_E1.1311.00
63_A67_K1.1271.00
183_G255_V1.1251.00
172_V176_H1.1161.00
246_K250_N1.1151.00
35_Y38_R1.1041.00
124_L220_V1.0981.00
64_W68_E1.0931.00
113_D116_R1.0911.00
204_T207_K1.0871.00
184_P260_E1.0841.00
71_S78_I1.0831.00
194_P216_Q1.0801.00
118_F283_W1.0791.00
273_Q276_D1.0751.00
138_S155_G1.0751.00
171_V256_A1.0721.00
10_V48_L1.0701.00
109_Q233_A1.0681.00
7_L69_G1.0641.00
5_Y8_E1.0611.00
287_Y291_S1.0611.00
286_E289_G1.0601.00
19_F56_V1.0581.00
12_A22_A1.0571.00
256_A259_L1.0521.00
161_R285_L1.0511.00
36_T39_Q1.0501.00
34_S38_R1.0501.00
204_T208_R1.0481.00
110_M288_L1.0441.00
72_V75_K1.0421.00
185_F189_T1.0391.00
94_L284_L1.0381.00
282_T286_E1.0331.00
13_V22_A1.0301.00
228_A232_S1.0301.00
229_T233_A1.0261.00
114_F287_Y1.0251.00
221_V227_S1.0251.00
196_L227_S1.0061.00
80_R84_Q1.0031.00
167_S265_D1.0001.00
8_E77_Q0.9951.00
173_A234_G0.9931.00
247_P251_E0.9831.00
187_D261_N0.9791.00
74_K78_I0.9781.00
126_F136_A0.9741.00
287_Y290_D0.9721.00
28_R33_V0.9631.00
58_L62_G0.9621.00
197_V217_K0.9561.00
77_Q80_R0.9541.00
13_V19_F0.9511.00
171_V245_A0.9501.00
114_F118_F0.9461.00
9_V26_L0.9451.00
14_A49_F0.9421.00
65_F69_G0.9391.00
39_Q42_E0.9391.00
170_C237_I0.9321.00
77_Q81_Q0.9251.00
10_V58_L0.9221.00
10_V40_L0.9211.00
22_A33_V0.9201.00
172_V178_L0.9181.00
136_A139_D0.9131.00
221_V230_C0.9131.00
97_A133_V0.9091.00
117_H290_D0.9081.00
278_S281_L0.9051.00
100_N223_D0.9011.00
21_A25_E0.9001.00
64_W86_I0.8961.00
49_F56_V0.8911.00
110_M287_Y0.8821.00
142_V145_A0.8751.00
5_Y36_T0.8741.00
46_V83_C0.8741.00
71_S74_K0.8721.00
149_T267_A0.8701.00
97_A147_G0.8671.00
67_K70_R0.8641.00
17_G57_E0.8611.00
159_A162_D0.8581.00
122_E216_Q0.8541.00
14_A62_G0.8511.00
20_S24_Q0.8471.00
189_T192_N0.8371.00
194_P217_K0.8331.00
96_I144_L0.8321.00
121_V280_A0.8271.00
134_W138_S0.8271.00
61_A86_I0.8261.00
76_M80_R0.8201.00
52_R55_D0.8201.00
112_V235_L0.8161.00
26_L33_V0.8141.00
171_V238_G0.8131.00
158_Y271_T0.8111.00
126_F142_V0.8111.00
157_R274_Q0.8111.00
175_H179_A0.8091.00
61_A83_C0.8031.00
179_A255_V0.8011.00
10_V65_F0.8001.00
277_M282_T0.7991.00
245_A248_W0.7981.00
92_G280_A0.7981.00
61_A64_W0.7961.00
97_A145_A0.7961.00
30_P34_S0.7941.00
14_A17_G0.7931.00
38_R47_P0.7911.00
248_W251_E0.7911.00
15_R66_L0.7901.00
78_I82_Q0.7891.00
286_E290_D0.7871.00
17_G63_A0.7861.00
75_K79_T0.7851.00
4_E73_V0.7841.00
16_N22_A0.7831.00
173_A176_H0.7831.00
208_R213_L0.7831.00
188_D191_R0.7821.00
17_G55_D0.7811.00
173_A235_L0.7811.00
110_M291_S0.7771.00
76_M79_T0.7761.00
115_Y235_L0.7721.00
176_H194_P0.7701.00
13_V49_F0.7651.00
6_S9_V0.7651.00
167_S258_E0.7571.00
132_G135_D0.7561.00
8_E12_A0.7561.00
249_L252_G0.7501.00
230_C235_L0.7491.00
279_P283_W0.7491.00
186_S260_E0.7451.00
144_L284_L0.7451.00
13_V37_V0.7441.00
178_L183_G0.7431.00
92_G121_V0.7421.00
70_R74_K0.7401.00
245_A249_L0.7381.00
19_F33_V0.7351.00
79_T83_C0.7331.00
178_L193_W0.7331.00
138_S158_Y0.7291.00
171_V240_V0.7281.00
50_E59_T0.7241.00
13_V33_V0.7231.00
117_H283_W0.7231.00
98_V103_R0.7201.00
114_F283_W0.7171.00
203_R206_P0.7161.00
69_G72_V0.7141.00
113_D290_D0.7131.00
90_W118_F0.7111.00
172_V255_V0.7091.00
140_G273_Q0.7081.00
63_A66_L0.7081.00
84_Q87_A0.7071.00
171_V249_L0.7051.00
241_P244_F0.7041.00
232_S251_E0.7031.00
283_W287_Y0.7001.00
143_E281_L0.6991.00
184_P258_E0.6881.00
188_D211_W0.6861.00
57_E63_A0.6861.00
60_A64_W0.6851.00
61_A65_F0.6841.00
223_D226_S0.6831.00
58_L63_A0.6811.00
186_S261_N0.6791.00
8_E11_D0.6791.00
95_A142_V0.6761.00
50_E55_D0.6731.00
175_H234_G0.6701.00
191_R213_L0.6681.00
249_L256_A0.6681.00
198_R227_S0.6661.00
32_A36_T0.6661.00
181_M194_P0.6641.00
199_E220_V0.6591.00
176_H181_M0.6581.00
167_S263_F0.6571.00
195_S237_I0.6541.00
5_Y39_Q0.6531.00
65_F83_C0.6531.00
95_A143_E0.6521.00
74_K77_Q0.6491.00
41_E46_V0.6481.00
104_P229_T0.6481.00
24_Q27_H0.6451.00
78_I81_Q0.6441.00
68_E72_V0.6421.00
219_V230_C0.6421.00
122_E220_V0.6391.00
41_E51_R0.6371.00
247_P250_N0.6351.00
170_C239_M0.6341.00
192_N216_Q0.6311.00
103_R130_F0.6311.00
98_V107_T0.6291.00
175_H255_V0.6251.00
170_C190_L0.6221.00
94_L280_A0.6221.00
69_G73_V0.6171.00
37_V41_E0.6161.00
279_P282_T0.6161.00
148_A266_S0.6151.00
109_Q112_V0.6091.00
132_G136_A0.6091.00
109_Q113_D0.6061.00
13_V18_S0.6031.00
181_M184_P0.6001.00
22_A26_L0.5981.00
81_Q85_Q0.5981.00
199_E222_P0.5971.00
8_E73_V0.5971.00
10_V62_G0.5921.00
107_T110_M0.5911.00
5_Y9_V0.5911.00
174_S252_G0.5901.00
178_L181_M0.5881.00
64_W83_C0.5871.00
44_L83_C0.5871.00
144_L285_L0.5871.00
137_L271_T0.5871.00
94_L144_L0.5861.00
195_S215_N0.5861.00
44_L65_F0.5811.00
172_V179_A0.5781.00
272_W282_T0.5781.00
227_S231_I0.5741.00
32_A35_Y0.5721.00
284_L288_L0.5721.00
166_L266_S0.5711.00
3_S39_Q0.5701.00
91_R122_E0.5701.00
102_V106_R0.5701.00
146_I288_L0.5701.00
164_G268_C0.5701.00
170_C195_S0.5661.00
200_D220_V0.5651.00
19_F55_D0.5651.00
31_S35_Y0.5641.00
168_W239_M0.5641.00
221_V226_S0.5601.00
137_L158_Y0.5601.00
73_V77_Q0.5601.00
46_V50_E0.5601.00
58_L66_L0.5591.00
49_F58_L0.5571.00
230_C236_C0.5551.00
29_V35_Y0.5511.00
118_F121_V0.5501.00
149_T160_F0.5501.00
85_Q90_W0.5501.00
163_M270_L0.5471.00
159_A275_N0.5461.00
19_F30_P0.5441.00
44_L47_P0.5431.00
176_H237_I0.5421.00
240_V245_A0.5391.00
111_I123_L0.5381.00
14_A63_A0.5381.00
224_W241_P0.5381.00
97_A126_F0.5381.00
259_L262_P0.5351.00
135_D141_R0.5331.00
92_G120_D0.5331.00
9_V37_V0.5321.00
104_P223_D0.5281.00
180_L183_G0.5261.00
81_Q84_Q0.5261.00
133_V140_G0.5231.00
67_K82_Q0.5211.00
28_R36_T0.5211.00
73_V76_M0.5191.00
272_W277_M0.5151.00
184_P189_T0.5151.00
99_D102_V0.5141.00
19_F51_R0.5121.00
17_G56_V0.5111.00
109_Q229_T0.5111.00
106_R110_M0.5111.00
9_V22_A0.5111.00
47_P61_A0.5101.00
281_L285_L0.5051.00
138_S141_R0.5041.00
82_Q85_Q0.5041.00
68_E83_C0.5031.00
98_V125_V0.5011.00
72_V80_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  
3fxqA 3 0.9355 100 0.129 Contact Map
3fzvA 4 0.9161 100 0.135 Contact Map
2esnA 3 0.9355 100 0.136 Contact Map
1ixcA 4 0.929 100 0.137 Contact Map
1uthA 2 0.7161 100 0.145 Contact Map
2h9bA 2 0.6613 100 0.15 Contact Map
2h98A 2 0.6742 100 0.15 Contact Map
1al3A 1 0.7129 100 0.153 Contact Map
4x6gA 4 0.9613 100 0.155 Contact Map
3szpA 3 0.9226 100 0.162 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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