GREMLIN Database
YDFH - Uncharacterized HTH-type transcriptional regulator YdfH
UniProt: P0ACM2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13820
Length: 228 (205)
Sequences: 23719 (17643)
Seq/√Len: 1232.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
114_E192_Q3.7711.00
99_R200_E3.2961.00
195_D198_A2.9571.00
121_R185_L2.8001.00
24_D29_L2.7301.00
31_A34_T2.6811.00
24_D44_R2.4121.00
92_A96_A2.3251.00
38_E49_R2.2731.00
112_Q142_L2.2331.00
85_N150_Q2.1471.00
91_Q208_Q2.0921.00
18_Y58_K2.0781.00
66_Q76_N2.0541.00
88_F100_R1.9761.00
22_R62_N1.9681.00
17_I47_V1.9651.00
103_S196_G1.9611.00
145_Q153_W1.8181.00
17_I45_F1.8071.00
190_A198_A1.7941.00
110_C192_Q1.7901.00
109_Q148_D1.7511.00
67_I73_S1.7421.00
142_L145_Q1.7391.00
20_I24_D1.7101.00
95_C204_T1.7081.00
106_T109_Q1.6871.00
117_L188_F1.6591.00
183_Q209_E1.6361.00
99_R196_G1.6261.00
128_Q131_D1.6251.00
89_I155_T1.5951.00
200_E204_T1.5891.00
198_A202_A1.5761.00
95_C200_E1.5761.00
96_A99_R1.5601.00
11_Q19_R1.5581.00
23_R27_H1.5371.00
140_H184_H1.5281.00
186_D202_A1.4841.00
144_T156_I1.4421.00
119_Q135_L1.4421.00
109_Q146_I1.4361.00
121_R181_L1.4261.00
98_A199_V1.4211.00
154_D158_N1.4191.00
141_Q157_E1.4131.00
91_Q204_T1.4051.00
114_E188_F1.3931.00
151_L162_T1.3931.00
18_Y62_N1.3861.00
189_S193_K1.3721.00
116_N135_L1.3651.00
39_K43_V1.3571.00
68_R71_R1.3541.00
91_Q211_S1.3531.00
193_K198_A1.3361.00
105_I110_C1.3321.00
85_N151_L1.3081.00
185_L189_S1.2901.00
196_G200_E1.2711.00
114_E118_H1.2531.00
115_Q119_Q1.2471.00
40_E44_R1.2401.00
37_S40_E1.2321.00
35_P74_Y1.2181.00
119_Q138_N1.2151.00
116_N142_L1.2011.00
183_Q206_H1.2001.00
16_Q20_I1.1961.00
91_Q95_C1.1951.00
117_L185_L1.1901.00
41_V52_V1.1871.00
201_R205_Q1.1811.00
20_I23_R1.1691.00
90_R94_E1.1651.00
24_D45_F1.1581.00
84_R215_R1.1551.00
141_Q145_Q1.1531.00
138_N142_L1.1511.00
20_I45_F1.1391.00
68_R74_Y1.1371.00
105_I194_R1.1361.00
95_C99_R1.1301.00
198_A201_R1.1261.00
60_A67_I1.1181.00
204_T208_Q1.1181.00
84_R211_S1.1091.00
105_I146_I1.1071.00
99_R197_D1.1041.00
105_I109_Q1.1031.00
85_N149_C1.0941.00
143_L191_L1.0921.00
116_N138_N1.0891.00
98_A102_A1.0871.00
30_I75_V1.0871.00
136_D140_H1.0861.00
98_A203_M1.0751.00
131_D134_E1.0751.00
142_L146_I1.0691.00
117_L121_R1.0651.00
97_V144_T1.0631.00
110_C188_F1.0611.00
188_F192_Q1.0571.00
189_S192_Q1.0541.00
117_L120_Q1.0431.00
114_E185_L1.0411.00
112_Q145_Q1.0201.00
110_C194_R1.0181.00
88_F149_C1.0171.00
66_Q74_Y1.0111.00
211_S215_R1.0101.00
135_L138_N1.0011.00
155_T158_N0.9931.00
60_A65_I0.9931.00
112_Q115_Q0.9861.00
54_E57_I0.9851.00
118_H121_R0.9841.00
11_Q16_Q0.9841.00
190_A195_D0.9801.00
184_H206_H0.9791.00
140_H206_H0.9721.00
24_D30_I0.9691.00
94_E140_H0.9651.00
96_A200_E0.9551.00
186_D205_Q0.9541.00
100_R104_M0.9511.00
102_A196_G0.9451.00
56_F73_S0.9421.00
147_A153_W0.9421.00
14_N58_K0.9401.00
25_I75_V0.9361.00
112_Q116_N0.9341.00
139_F188_F0.9311.00
182_R186_D0.9301.00
134_E138_N0.9241.00
111_Y115_Q0.9161.00
65_I73_S0.9121.00
38_E53_R0.9111.00
186_D198_A0.9101.00
186_D189_S0.9081.00
79_S82_Q0.9071.00
35_P72_G0.9061.00
153_W157_E0.9061.00
102_A191_L0.8961.00
58_K61_E0.8901.00
68_R72_G0.8881.00
110_C114_E0.8741.00
18_Y22_R0.8741.00
197_D201_R0.8701.00
104_M148_D0.8701.00
71_R74_Y0.8671.00
116_N119_Q0.8631.00
187_I203_M0.8631.00
96_A100_R0.8521.00
22_R64_L0.8511.00
42_S52_V0.8511.00
89_I151_L0.8491.00
109_Q112_Q0.8401.00
114_E189_S0.8361.00
181_L185_L0.8351.00
90_R207_L0.8341.00
48_S51_P0.8341.00
13_V16_Q0.8331.00
105_I191_L0.8321.00
22_R26_V0.8271.00
82_Q151_L0.8271.00
136_D184_H0.8221.00
197_D200_E0.8221.00
107_E111_Y0.8201.00
119_Q122_I0.8201.00
57_I60_A0.8201.00
102_A194_R0.8151.00
56_F65_I0.8021.00
118_H122_I0.7971.00
123_A131_D0.7961.00
186_D190_A0.7961.00
40_E43_V0.7941.00
151_L155_T0.7931.00
187_I202_A0.7931.00
101_A146_I0.7861.00
122_I126_R0.7831.00
41_V56_F0.7801.00
15_Q58_K0.7721.00
81_A148_D0.7721.00
113_L142_L0.7691.00
88_F211_S0.7631.00
13_V51_P0.7631.00
178_E182_R0.7611.00
12_P15_Q0.7611.00
190_A202_A0.7581.00
121_R125_E0.7571.00
151_L154_D0.7561.00
120_Q132_F0.7561.00
107_E194_R0.7551.00
113_L188_F0.7551.00
102_A199_V0.7541.00
47_V52_V0.7531.00
57_I67_I0.7461.00
88_F104_M0.7441.00
118_H185_L0.7411.00
14_N18_Y0.7401.00
202_A205_Q0.7371.00
100_R103_S0.7341.00
99_R103_S0.7341.00
87_S210_I0.7311.00
81_A85_N0.7271.00
208_Q212_E0.7241.00
141_Q160_K0.7231.00
89_I97_V0.7181.00
89_I152_A0.7091.00
111_Y192_Q0.7021.00
201_R204_T0.7011.00
100_R149_C0.6971.00
11_Q15_Q0.6971.00
112_Q138_N0.6911.00
131_D135_L0.6871.00
111_Y114_E0.6841.00
187_I199_V0.6821.00
141_Q153_W0.6821.00
123_A135_L0.6811.00
119_Q131_D0.6761.00
117_L181_L0.6741.00
205_Q209_E0.6741.00
208_Q211_S0.6711.00
137_D160_K0.6701.00
110_C191_L0.6691.00
51_P55_A0.6661.00
29_L44_R0.6631.00
88_F96_A0.6631.00
109_Q145_Q0.6621.00
119_Q123_A0.6621.00
109_Q142_L0.6591.00
137_D164_D0.6581.00
58_K62_N0.6521.00
209_E213_S0.6501.00
138_N141_Q0.6431.00
115_Q118_H0.6431.00
183_Q186_D0.6421.00
92_A152_A0.6351.00
30_I34_T0.6291.00
187_I206_H0.6261.00
97_V147_A0.6201.00
97_V152_A0.6191.00
89_I93_I0.6161.00
98_A196_G0.6141.00
70_Q73_S0.6101.00
91_Q207_L0.6101.00
14_N54_E0.6061.00
94_E184_H0.6061.00
95_C203_M0.6041.00
101_A105_I0.5981.00
101_A147_A0.5911.00
24_D28_C0.5901.00
120_Q181_L0.5881.00
123_A127_K0.5871.00
154_D162_T0.5861.00
82_Q150_Q0.5811.00
212_E215_R0.5801.00
33_G77_K0.5781.00
108_S112_Q0.5681.00
113_L146_I0.5681.00
93_I156_I0.5671.00
32_P77_K0.5631.00
123_A128_Q0.5631.00
176_P179_M0.5601.00
45_F52_V0.5591.00
132_F180_L0.5591.00
92_A95_C0.5581.00
95_C196_G0.5461.00
57_I61_E0.5451.00
39_K42_S0.5431.00
21_L41_V0.5411.00
74_Y77_K0.5371.00
36_L65_I0.5351.00
99_R204_T0.5351.00
182_R185_L0.5341.00
107_E192_Q0.5301.00
98_A143_L0.5291.00
205_Q208_Q0.5261.00
15_Q19_R0.5251.00
43_V46_N0.5241.00
113_L117_L0.5211.00
89_I92_A0.5201.00
26_V64_L0.5201.00
100_R147_A0.5191.00
187_I190_A0.5181.00
150_Q153_W0.5171.00
84_R88_F0.5171.00
30_I36_L0.5161.00
183_Q205_Q0.5151.00
154_D157_E0.5141.00
165_R169_M0.5121.00
122_I125_E0.5101.00
94_E207_L0.5101.00
101_A143_L0.5101.00
209_E212_E0.5091.00
38_E73_S0.5091.00
144_T160_K0.5081.00
130_D168_Y0.5071.00
203_M207_L0.5071.00
82_Q162_T0.5061.00
88_F91_Q0.5041.00
179_M182_R0.5031.00
24_D27_H0.5021.00
191_L199_V0.5021.00
30_I44_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  
3sxyA 2 0.8772 100 0.141 Contact Map
2hs5A 1 0.9079 100 0.151 Contact Map
3ihuA 1 0.8947 100 0.155 Contact Map
4p96A 2 0.9737 100 0.155 Contact Map
3c7jA 4 0.9781 100 0.163 Contact Map
4p9fA 1 0.9167 100 0.168 Contact Map
1hw1A 2 0.9035 100 0.202 Contact Map
2di3A 2 0.9079 100 0.209 Contact Map
3by6A 2 0.5395 99.8 0.546 Contact Map
3ic7A 2 0.4825 99.8 0.551 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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