GREMLIN Database
YDHC - Uncharacterized HTH-type transcriptional regulator YdhC
UniProt: O05494 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 224 (203)
Sequences: 23625 (17424)
Seq/√Len: 1222.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
113_E192_K3.7781.00
98_E200_K3.2961.00
195_N198_A2.9161.00
120_E185_R2.7891.00
23_M28_T2.7171.00
30_K33_E2.6871.00
23_M43_S2.3901.00
91_P95_L2.2991.00
37_E48_R2.2321.00
111_I142_L2.2141.00
84_E150_R2.1881.00
90_I208_N2.0931.00
17_Y57_L2.0731.00
65_K75_T2.0191.00
21_K61_D1.9621.00
16_F46_V1.9561.00
87_K99_L1.9521.00
102_D196_K1.9491.00
66_A72_F1.8281.00
145_D153_K1.8211.00
109_L192_K1.7971.00
16_F44_F1.7911.00
190_E198_A1.7831.00
108_E148_H1.7381.00
142_L145_D1.7221.00
105_D108_E1.7121.00
19_Q23_M1.6791.00
94_Q204_L1.6631.00
116_L188_F1.6531.00
183_E209_H1.6071.00
98_E196_K1.6071.00
88_I155_L1.5871.00
200_K204_L1.5871.00
128_E131_E1.5771.00
198_A202_H1.5581.00
22_K26_N1.5551.00
10_T18_N1.5531.00
94_Q200_K1.5431.00
140_H184_H1.5421.00
95_L98_E1.5361.00
186_R202_H1.4761.00
144_V156_L1.4341.00
120_E181_L1.4171.00
118_E135_L1.4171.00
141_E157_E1.4161.00
154_N158_H1.4061.00
97_V199_A1.3981.00
189_E193_K1.3961.00
151_H162_L1.3951.00
90_I204_L1.3941.00
67_D70_N1.3891.00
17_Y61_D1.3881.00
115_Q135_L1.3721.00
108_E146_F1.3711.00
113_E188_F1.3661.00
193_K198_A1.3631.00
90_I211_C1.3601.00
38_T42_K1.3351.00
84_E151_H1.3121.00
185_R189_E1.3071.00
104_A109_L1.3061.00
196_K200_K1.2701.00
118_E138_K1.2591.00
113_E117_E1.2581.00
114_K118_E1.2521.00
39_Q43_S1.2301.00
36_N39_Q1.2041.00
40_L51_I1.2001.00
90_I94_Q1.1971.00
115_Q142_L1.1971.00
34_R73_S1.1941.00
116_L185_R1.1911.00
15_Q19_Q1.1821.00
19_Q22_K1.1821.00
183_E206_H1.1811.00
201_Q205_A1.1791.00
67_D73_S1.1641.00
204_L208_N1.1441.00
23_M44_F1.1421.00
89_R93_E1.1401.00
59_E66_A1.1391.00
104_A194_K1.1381.00
138_K142_L1.1381.00
19_Q44_F1.1331.00
141_E145_D1.1311.00
198_A201_Q1.1311.00
84_E149_N1.1191.00
104_A146_F1.1191.00
97_V101_I1.1051.00
143_L191_V1.1021.00
98_E197_E1.0911.00
94_Q98_E1.0911.00
136_N140_H1.0901.00
142_L146_F1.0741.00
97_V203_V1.0701.00
116_L119_T1.0691.00
131_E134_R1.0691.00
115_Q138_K1.0641.00
109_L188_F1.0621.00
189_E192_K1.0621.00
104_A108_E1.0561.00
29_F74_I1.0541.00
113_E185_R1.0521.00
188_F192_K1.0481.00
111_I145_D1.0351.00
96_A144_V1.0331.00
87_K149_N1.0301.00
116_L120_E1.0171.00
184_H206_H1.0111.00
83_D211_C1.0091.00
117_E120_E1.0051.00
109_L194_K1.0021.00
65_K73_S0.9971.00
135_L138_K0.9871.00
190_E195_N0.9751.00
53_E56_R0.9731.00
111_I114_K0.9721.00
140_H206_H0.9701.00
155_L158_H0.9681.00
59_E64_L0.9671.00
10_T15_Q0.9671.00
99_L103_E0.9591.00
182_R186_R0.9591.00
95_L200_K0.9501.00
55_M72_F0.9481.00
24_I74_I0.9471.00
121_K125_N0.9471.00
110_T114_K0.9471.00
147_S153_K0.9461.00
67_D71_G0.9411.00
186_R205_A0.9401.00
101_I196_K0.9371.00
23_M29_F0.9291.00
139_F188_F0.9261.00
134_R138_K0.9241.00
13_Y57_L0.9231.00
93_E140_H0.9221.00
186_R198_A0.9201.00
111_I115_Q0.9161.00
64_L72_F0.9041.00
153_K157_E0.9021.00
78_T81_D0.9001.00
186_R189_E0.9001.00
197_E201_Q0.8961.00
34_R71_G0.8921.00
37_E52_R0.8861.00
17_Y21_K0.8841.00
101_I191_V0.8811.00
57_L60_K0.8771.00
109_L113_E0.8761.00
187_I203_V0.8751.00
88_I151_H0.8671.00
103_E148_H0.8641.00
70_N73_S0.8631.00
104_A191_V0.8571.00
41_A51_I0.8551.00
115_Q118_E0.8551.00
81_D151_H0.8551.00
21_K63_L0.8471.00
95_L99_L0.8391.00
181_L185_R0.8361.00
113_E189_E0.8351.00
197_E200_K0.8341.00
21_K25_F0.8251.00
101_I194_K0.8251.00
89_R207_F0.8251.00
106_E110_T0.8251.00
47_S50_P0.8241.00
118_E121_K0.8171.00
122_A131_E0.8161.00
56_R59_E0.8141.00
39_Q42_K0.8141.00
100_V146_F0.8021.00
108_E111_I0.8001.00
117_E121_K0.7951.00
55_M64_L0.7921.00
12_Y15_Q0.7911.00
187_I202_H0.7881.00
80_K148_H0.7841.00
136_N184_H0.7831.00
46_V51_I0.7811.00
112_L142_L0.7771.00
186_R190_E0.7761.00
56_R66_A0.7761.00
190_E202_H0.7721.00
11_P14_L0.7721.00
151_H155_L0.7711.00
14_L57_L0.7711.00
100_V104_A0.7701.00
87_K211_C0.7641.00
112_L188_F0.7631.00
106_E194_K0.7631.00
40_L55_M0.7581.00
12_Y50_P0.7561.00
178_E182_R0.7491.00
13_Y17_Y0.7481.00
119_T132_I0.7481.00
117_E185_R0.7451.00
101_I199_A0.7411.00
151_H154_N0.7351.00
98_E102_D0.7321.00
80_K84_E0.7311.00
141_E160_N0.7301.00
88_I152_L0.7301.00
202_H205_A0.7231.00
87_K103_E0.7181.00
99_L102_D0.7181.00
131_E135_L0.7161.00
208_N212_E0.7131.00
118_E131_E0.7101.00
86_Y210_D0.7091.00
110_T192_K0.7071.00
201_Q204_L0.7061.00
122_A135_L0.6981.00
99_L149_N0.6961.00
137_Q160_N0.6941.00
111_I138_K0.6931.00
110_T113_E0.6921.00
141_E153_K0.6901.00
116_L181_L0.6861.00
88_I96_A0.6771.00
28_T43_S0.6761.00
137_Q164_H0.6721.00
187_I199_A0.6721.00
100_V147_S0.6601.00
109_L191_V0.6601.00
114_K117_E0.6591.00
205_A209_H0.6571.00
57_L61_D0.6561.00
10_T14_L0.6561.00
108_E142_L0.6511.00
118_E122_A0.6491.00
50_P54_A0.6471.00
108_E145_D0.6451.00
208_N211_C0.6431.00
81_D150_R0.6421.00
138_K141_E0.6381.00
209_H213_H0.6381.00
120_E124_H0.6341.00
91_P152_L0.6331.00
183_E186_R0.6301.00
29_F33_E0.6281.00
87_K95_L0.6231.00
69_R72_F0.6221.00
97_V196_K0.6221.00
88_I92_L0.6161.00
90_I207_F0.6151.00
187_I206_H0.6101.00
96_A147_S0.6041.00
93_E184_H0.6011.00
96_A152_L0.5971.00
125_N128_E0.5951.00
122_A128_E0.5941.00
13_Y53_E0.5931.00
132_I180_I0.5921.00
23_M27_G0.5901.00
94_Q203_V0.5841.00
154_N162_L0.5741.00
32_G76_S0.5731.00
94_Q196_K0.5711.00
107_E111_I0.5681.00
119_T181_L0.5681.00
44_F51_I0.5661.00
80_K83_D0.5611.00
31_P76_S0.5561.00
100_V143_L0.5491.00
92_L156_L0.5461.00
91_P94_Q0.5431.00
112_L116_L0.5411.00
38_T41_A0.5411.00
20_L40_L0.5391.00
80_K150_R0.5391.00
112_L146_F0.5381.00
56_R60_K0.5361.00
106_E192_K0.5351.00
42_K45_G0.5341.00
73_S76_S0.5321.00
179_T182_R0.5291.00
14_L18_N0.5271.00
98_E204_L0.5251.00
176_R179_T0.5211.00
29_F35_I0.5201.00
203_V207_F0.5191.00
88_I91_P0.5191.00
97_V143_L0.5181.00
165_F169_L0.5171.00
182_R185_R0.5161.00
130_T168_I0.5151.00
150_R153_K0.5151.00
35_I64_L0.5141.00
137_Q141_E0.5111.00
112_L115_Q0.5111.00
87_K90_I0.5101.00
205_A208_N0.5101.00
209_H212_E0.5071.00
95_L152_L0.5051.00
81_D162_L0.5051.00
68_D71_G0.5041.00
175_H178_E0.5041.00
154_N157_E0.5031.00
199_A203_V0.5031.00
23_M26_N0.5021.00
121_K124_H0.5011.00
94_Q97_V0.5001.00
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  
3sxyA 2 0.8929 100 0.133 Contact Map
2hs5A 1 0.9241 100 0.138 Contact Map
3ihuA 1 0.9107 100 0.147 Contact Map
3c7jA 4 0.9821 100 0.148 Contact Map
4p9fA 1 0.933 100 0.156 Contact Map
4p96A 2 0.9777 100 0.171 Contact Map
2di3A 2 0.9241 100 0.196 Contact Map
1hw1A 2 0.9196 100 0.216 Contact Map
3by6A 2 0.5491 99.8 0.537 Contact Map
4r1hA 2 0.5045 99.8 0.54 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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