GREMLIN Database
YVOA - HTH-type transcriptional repressor YvoA
UniProt: O34817 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 243 (196)
Sequences: 25518 (19306)
Seq/√Len: 1379.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
22_Q27_E3.8101.00
29_Q32_M3.6541.00
16_M57_N3.1541.00
22_Q43_Q3.0201.00
20_K61_E3.0121.00
65_Y75_S2.8231.00
106_D191_T2.5891.00
37_E48_R2.5571.00
18_Q22_Q2.5311.00
15_I46_I2.5251.00
186_E189_A2.4761.00
66_R72_T2.3471.00
67_L70_R2.2301.00
16_M61_E2.1921.00
99_T103_R2.1461.00
33_P73_F2.1171.00
113_T116_L2.1051.00
15_I44_F2.1031.00
21_T25_N2.0991.00
9_I17_E1.8961.00
110_I187_P1.8901.00
18_Q44_F1.8371.00
16_M20_K1.8311.00
59_V66_R1.7901.00
53_Q56_S1.7531.00
116_L138_N1.7341.00
70_R73_F1.7031.00
20_K24_K1.6891.00
135_R143_A1.6871.00
11_I14_Q1.6561.00
38_R42_E1.6491.00
117_A183_Q1.6191.00
14_Q18_Q1.6181.00
191_T195_A1.6041.00
36_S39_E1.5871.00
22_Q28_L1.5711.00
39_E43_Q1.5621.00
191_T194_E1.5521.00
59_V64_L1.5191.00
20_K63_L1.5071.00
92_D140_I1.5031.00
18_Q21_T1.4921.00
112_S117_A1.4301.00
98_M199_G1.4201.00
12_Y57_N1.4181.00
23_I74_V1.4081.00
101_G136_L1.3991.00
37_E52_R1.3901.00
40_Y51_V1.3901.00
67_L73_F1.3861.00
112_S116_L1.3851.00
28_L74_V1.3781.00
57_N60_N1.3671.00
30_P76_K1.3571.00
56_S66_R1.3471.00
55_L64_L1.3421.00
65_Y73_F1.3331.00
131_I147_S1.3141.00
181_A189_A1.3131.00
95_S107_Y1.2971.00
106_D187_P1.2941.00
10_P13_Y1.2931.00
64_L72_T1.2711.00
46_I51_V1.2561.00
39_E42_E1.2451.00
9_I14_Q1.2381.00
102_S195_A1.2381.00
189_A193_E1.2371.00
67_L71_G1.2351.00
56_S60_N1.2281.00
187_P191_T1.2261.00
144_I148_H1.2221.00
132_T135_R1.2211.00
125_P128_I1.2151.00
24_K63_L1.2061.00
103_R136_L1.1971.00
189_A205_P1.1941.00
119_I132_T1.1881.00
123_G126_S1.1791.00
33_P71_G1.1781.00
179_S183_Q1.1641.00
57_N61_E1.1561.00
102_S191_T1.1501.00
130_K146_S1.1501.00
22_Q26_G1.1501.00
116_L148_H1.1491.00
56_S59_V1.1431.00
131_I135_R1.1411.00
98_M195_A1.1331.00
192_T196_N1.1281.00
55_L72_T1.1271.00
96_R145_E1.1201.00
98_M102_S1.1111.00
112_S185_L1.0991.00
122_C126_S1.0841.00
168_D172_R1.0641.00
13_Y17_E1.0481.00
13_Y57_N1.0321.00
167_Y171_E1.0251.00
176_I180_R1.0151.00
143_A147_S1.0131.00
195_A199_G1.0061.00
144_I194_E0.9971.00
132_T136_L0.9951.00
22_Q44_F0.9931.00
28_L32_M0.9871.00
166_I170_I0.9821.00
132_T146_S0.9791.00
109_L127_S0.9741.00
110_I130_K0.9711.00
47_S50_T0.9641.00
174_N200_I0.9611.00
12_Y16_M0.9561.00
134_V146_S0.9421.00
53_Q57_N0.9361.00
109_L151_F0.9311.00
180_R184_E0.9231.00
11_I50_T0.9191.00
9_I13_Y0.9081.00
117_A185_L0.8991.00
103_R106_D0.8981.00
108_Q130_K0.8951.00
114_E118_A0.8931.00
69_G72_T0.8911.00
169_H174_N0.8911.00
117_A179_S0.8891.00
31_D65_Y0.8871.00
201_Q204_A0.8871.00
141_P152_E0.8851.00
31_D76_K0.8841.00
165_S168_D0.8761.00
19_L40_Y0.8711.00
12_Y53_Q0.8691.00
106_D188_S0.8681.00
177_P193_E0.8651.00
86_L89_F0.8641.00
17_E20_K0.8451.00
105_I109_L0.8411.00
112_S136_L0.8391.00
116_L119_I0.8241.00
115_E119_I0.8211.00
37_E66_R0.8131.00
106_D130_K0.8131.00
124_H128_I0.8091.00
189_A192_T0.8081.00
103_R107_Y0.8021.00
105_I194_E0.8011.00
150_P153_L0.7981.00
188_S191_T0.7971.00
120_L132_T0.7911.00
133_R182_K0.7911.00
40_Y55_L0.7911.00
166_I169_H0.7861.00
41_A51_V0.7831.00
152_E155_G0.7831.00
104_L134_V0.7791.00
190_A200_I0.7741.00
33_P36_S0.7731.00
121_G124_H0.7611.00
30_P75_S0.7601.00
17_E21_T0.7541.00
188_S194_E0.7481.00
102_S106_D0.7471.00
116_L136_L0.7441.00
18_Q43_Q0.7441.00
34_L64_L0.7411.00
35_P43_Q0.7401.00
121_G125_P0.7401.00
22_Q25_N0.7371.00
145_E148_H0.7351.00
180_R183_Q0.7331.00
130_K175_S0.7311.00
101_G139_D0.7301.00
119_I135_R0.7261.00
177_P180_R0.7241.00
114_E117_A0.7201.00
111_D127_S0.7191.00
171_E177_P0.7091.00
146_S150_P0.7081.00
137_A143_A0.7041.00
154_A158_N0.6981.00
158_N161_H0.6981.00
129_H133_R0.6951.00
132_T193_E0.6941.00
44_F51_V0.6931.00
141_P144_I0.6921.00
55_L59_V0.6921.00
97_G101_G0.6911.00
200_I204_A0.6911.00
188_S192_T0.6891.00
126_S152_E0.6811.00
127_S151_F0.6811.00
109_L182_K0.6801.00
106_D110_I0.6791.00
38_R41_A0.6761.00
154_A157_L0.6761.00
105_I190_A0.6751.00
41_A44_F0.6731.00
190_A195_A0.6701.00
193_E196_N0.6661.00
192_T195_A0.6661.00
184_E189_A0.6651.00
28_L34_L0.6631.00
124_H127_S0.6631.00
176_I179_S0.6611.00
91_E94_K0.6601.00
16_M54_A0.6551.00
105_I134_V0.6521.00
103_R191_T0.6511.00
102_S105_I0.6511.00
114_E185_L0.6491.00
98_M202_K0.6481.00
59_V72_T0.6461.00
27_E43_Q0.6431.00
19_L28_L0.6411.00
50_T54_A0.6391.00
181_A186_E0.6341.00
151_F155_G0.6321.00
15_I51_V0.6301.00
194_E197_I0.6281.00
128_I132_T0.6281.00
91_E95_S0.6241.00
136_L139_D0.6241.00
131_I150_P0.6181.00
51_V64_L0.6181.00
55_L66_R0.6131.00
129_H179_S0.6121.00
196_N200_I0.6121.00
178_I194_E0.6041.00
8_P14_Q0.6041.00
112_S182_K0.6011.00
37_E72_T0.6001.00
15_I18_Q0.5981.00
21_T24_K0.5971.00
94_K201_Q0.5941.00
165_S170_I0.5931.00
93_M137_A0.5911.00
169_H172_R0.5911.00
137_A142_M0.5861.00
165_S169_H0.5851.00
115_E118_A0.5841.00
42_E45_G0.5741.00
78_K81_Q0.5731.00
41_A48_R0.5721.00
88_S92_D0.5711.00
15_I19_L0.5691.00
109_L187_P0.5661.00
50_T53_Q0.5631.00
36_S69_G0.5621.00
178_I193_E0.5621.00
150_P154_A0.5611.00
116_L135_R0.5611.00
38_R48_R0.5601.00
95_S111_D0.5591.00
109_L185_L0.5581.00
193_E197_I0.5581.00
92_D96_R0.5481.00
131_I143_A0.5471.00
84_Q92_D0.5421.00
94_K100_P0.5421.00
40_Y44_F0.5401.00
109_L129_H0.5391.00
15_I54_A0.5371.00
155_G158_N0.5361.00
14_Q17_E0.5351.00
134_V150_P0.5331.00
28_L35_P0.5321.00
190_A204_A0.5311.00
107_Y110_I0.5311.00
130_K148_H0.5311.00
107_Y111_D0.5291.00
83_L202_K0.5291.00
94_K97_G0.5251.00
13_Y16_M0.5241.00
157_L161_H0.5231.00
147_S150_P0.5231.00
21_T27_E0.5211.00
157_L160_S0.5201.00
117_A182_K0.5191.00
141_P145_E0.5181.00
123_G127_S0.5171.00
127_S154_A0.5161.00
58_L64_L0.5151.00
68_K71_G0.5131.00
177_P189_A0.5121.00
80_E83_L0.5091.00
174_N197_I0.5051.00
78_K82_A0.5051.00
153_L156_E0.5041.00
190_A198_L0.5031.00
96_R100_P0.5031.00
129_H151_F0.5011.00
73_F76_K0.5011.00
8_P13_Y0.5001.00
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  
4u0wA 2 0.9959 100 0.127 Contact Map
2ra5A 2 0.6091 100 0.175 Contact Map
3f8mA 2 0.9424 100 0.186 Contact Map
3edpA 2 0.9053 100 0.206 Contact Map
3eetA 2 0.9465 100 0.213 Contact Map
3bwgA 2 0.9383 100 0.222 Contact Map
3sxyA 2 0.7654 100 0.417 Contact Map
1hw1A 2 0.8354 100 0.428 Contact Map
3c7jA 4 0.8477 100 0.431 Contact Map
4p96A 2 0.8848 100 0.432 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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