GREMLIN Database
YVDT - Uncharacterized HTH-type transcriptional regulator YvdT
UniProt: O07001 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 194 (178)
Sequences: 42860 (33896)
Seq/√Len: 2540.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
31_S41_Q4.0071.00
23_K32_D3.8451.00
18_E36_K3.5341.00
49_S53_A2.7081.00
20_I28_A2.3791.00
50_S53_A2.1921.00
34_V44_F2.0621.00
19_V32_D2.0571.00
130_E149_K2.0301.00
9_Y57_A2.0101.00
19_V36_K1.9911.00
10_E61_N1.9531.00
22_E36_K1.9411.00
19_V28_A1.9381.00
11_K15_A1.8881.00
15_A36_K1.8861.00
130_E134_N1.8801.00
83_V135_K1.8731.00
8_K11_K1.8661.00
79_D82_T1.7971.00
19_V23_K1.7911.00
31_S35_K1.7541.00
15_A18_E1.6641.00
134_N148_S1.6561.00
17_I61_N1.6461.00
40_A43_T1.6411.00
13_L57_A1.5931.00
10_E14_Q1.5891.00
134_N138_A1.5801.00
30_I45_Y1.5651.00
134_N137_I1.5451.00
137_I145_G1.5361.00
17_I62_L1.5101.00
16_A20_I1.4781.00
30_I41_Q1.4721.00
18_E22_E1.4661.00
57_A60_E1.4631.00
28_A33_I1.4571.00
29_S32_D1.4471.00
32_D35_K1.4321.00
150_W182_E1.4271.00
32_D36_K1.3941.00
85_D181_K1.3921.00
154_T158_L1.3911.00
135_K139_N1.3901.00
136_A142_V1.3631.00
9_Y47_Y1.3561.00
16_A54_L1.3471.00
43_T46_L1.3451.00
17_I58_I1.3401.00
71_K128_W1.3271.00
30_I44_F1.3261.00
61_N65_H1.3201.00
24_G28_A1.3151.00
136_A141_E1.3001.00
24_G27_K1.2991.00
48_F57_A1.2971.00
7_G11_K1.2961.00
15_A19_V1.2781.00
89_D180_K1.2731.00
89_D177_E1.2411.00
14_Q61_N1.2111.00
89_D181_K1.2101.00
85_D89_D1.2061.00
107_S111_I1.2041.00
23_K27_K1.1991.00
81_W85_D1.1891.00
69_Q90_E1.1741.00
41_Q45_Y1.1721.00
56_P60_E1.1711.00
39_T43_T1.1511.00
42_G46_L1.1331.00
82_T86_I1.1241.00
126_Y153_R1.1241.00
20_I25_L1.1191.00
40_A46_L1.1171.00
52_N56_P1.1061.00
137_I146_I1.1041.00
132_I136_A1.0911.00
8_K47_Y1.0831.00
53_A57_A1.0781.00
126_Y130_E1.0771.00
13_L58_I1.0581.00
15_A37_A1.0541.00
83_V132_I1.0531.00
175_N178_V1.0521.00
147_N150_W1.0481.00
45_Y50_S1.0401.00
86_I89_D1.0391.00
53_A56_P1.0361.00
25_L55_I1.0341.00
14_Q18_E1.0341.00
78_E86_I1.0281.00
7_G10_E1.0151.00
85_D184_F1.0131.00
33_I54_L1.0121.00
17_I21_S1.0091.00
128_W131_K1.0061.00
137_I148_S1.0021.00
130_E148_S0.9901.00
157_N161_N0.9901.00
67_L124_P0.9891.00
102_I105_C0.9871.00
13_L48_F0.9861.00
79_D141_E0.9841.00
112_D115_M0.9791.00
150_W178_V0.9771.00
69_Q72_G0.9751.00
143_T146_I0.9731.00
73_R90_E0.9701.00
43_T47_Y0.9631.00
123_Q127_S0.9561.00
44_F54_L0.9551.00
23_K36_K0.9461.00
103_V107_S0.9421.00
57_A61_N0.9371.00
172_Q175_N0.9311.00
8_K39_T0.9251.00
181_K185_T0.9251.00
166_F169_G0.9201.00
131_K134_N0.9191.00
131_K135_K0.9181.00
62_L65_H0.9121.00
90_E93_L0.9101.00
16_A58_I0.9031.00
6_S10_E0.9001.00
77_D83_V0.9001.00
103_V106_Y0.8971.00
82_T85_D0.8951.00
60_E64_T0.8911.00
178_V182_E0.8871.00
120_T124_P0.8861.00
80_F139_N0.8851.00
34_V41_Q0.8851.00
89_D93_L0.8741.00
86_I90_E0.8741.00
94_I98_H0.8691.00
182_E185_T0.8631.00
177_E181_K0.8591.00
126_Y149_K0.8591.00
52_N114_S0.8581.00
127_S131_K0.8561.00
61_N64_T0.8481.00
85_D185_T0.8471.00
108_G111_I0.8431.00
80_F136_A0.8421.00
146_I151_T0.8211.00
71_K75_H0.8171.00
73_R86_I0.8091.00
41_Q46_L0.8081.00
18_E100_D0.8061.00
19_V22_E0.8021.00
35_K41_Q0.8011.00
137_I140_H0.7901.00
130_E152_A0.7831.00
135_K138_A0.7811.00
64_T68_D0.7781.00
78_E82_T0.7781.00
132_I135_K0.7751.00
68_D72_G0.7721.00
149_K153_R0.7701.00
12_I44_F0.7681.00
11_K14_Q0.7661.00
11_K37_A0.7641.00
165_R168_I0.7601.00
180_K184_F0.7581.00
88_I155_I0.7551.00
13_L61_N0.7411.00
67_L71_K0.7401.00
124_P128_W0.7361.00
52_N112_D0.7281.00
25_L51_K0.7281.00
101_I104_L0.7231.00
119_E123_Q0.7161.00
104_L108_G0.7121.00
65_H68_D0.7121.00
177_E180_K0.7101.00
89_D184_F0.7071.00
104_L107_S0.7071.00
77_D82_T0.7051.00
113_H116_E0.7021.00
26_D111_I0.6921.00
23_K28_A0.6841.00
108_G112_D0.6811.00
133_I155_I0.6721.00
31_S45_Y0.6681.00
182_E186_F0.6681.00
136_A140_H0.6671.00
26_D108_G0.6661.00
12_I37_A0.6581.00
127_S130_E0.6571.00
133_I148_S0.6551.00
76_G86_I0.6501.00
14_Q17_I0.6501.00
180_K183_I0.6461.00
137_I142_V0.6451.00
93_L177_E0.6441.00
124_P127_S0.6421.00
85_D88_I0.6421.00
67_L128_W0.6381.00
148_S152_A0.6331.00
73_R76_G0.6331.00
96_E176_V0.6311.00
79_D83_V0.6301.00
8_K40_A0.6291.00
119_E122_Y0.6271.00
37_A40_A0.6261.00
77_D86_I0.6251.00
179_Y183_I0.6191.00
30_I34_V0.6191.00
150_W154_T0.6171.00
157_N160_E0.6171.00
102_I106_Y0.6151.00
154_T157_N0.6151.00
122_Y126_Y0.6141.00
25_L52_N0.6101.00
8_K43_T0.6091.00
176_V180_K0.6081.00
22_E32_D0.6071.00
13_L17_I0.6061.00
93_L176_V0.6041.00
133_I137_I0.6041.00
137_I143_T0.6031.00
72_G90_E0.6021.00
165_R169_G0.5981.00
80_F141_E0.5941.00
150_W153_R0.5931.00
91_T95_T0.5891.00
107_S110_A0.5831.00
114_S117_K0.5831.00
68_D71_K0.5801.00
12_I47_Y0.5781.00
121_I125_Y0.5701.00
60_E121_I0.5701.00
64_T121_I0.5691.00
34_V39_T0.5681.00
20_I55_I0.5661.00
174_E177_E0.5641.00
158_L183_I0.5601.00
133_I151_T0.5571.00
174_E178_V0.5571.00
134_N149_K0.5471.00
94_I97_R0.5441.00
6_S9_Y0.5441.00
83_V136_A0.5381.00
93_L180_K0.5361.00
178_V181_K0.5331.00
112_D116_E0.5311.00
179_Y182_E0.5291.00
160_E164_E0.5291.00
41_Q44_F0.5291.00
93_L97_R0.5251.00
142_V147_N0.5211.00
39_T47_Y0.5211.00
8_K12_I0.5211.00
72_G76_G0.5211.00
121_I124_P0.5191.00
56_P114_S0.5171.00
145_G148_S0.5131.00
65_H69_Q0.5121.00
19_V29_S0.5101.00
151_T154_T0.5091.00
30_I51_K0.5051.00
161_N164_E0.5031.00
122_Y125_Y0.5021.00
69_Q94_I0.5011.00
81_W141_E0.5001.00
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  
2f07A 2 1 100 0.19 Contact Map
2iaiA 2 0.9639 100 0.201 Contact Map
2ibdA 2 0.9742 100 0.204 Contact Map
3npiA 2 0.9794 100 0.207 Contact Map
3g1oA 2 0.9794 100 0.21 Contact Map
4udsA 2 0.9433 100 0.213 Contact Map
3ppbA 2 0.9639 100 0.219 Contact Map
2xdnA 2 0.9948 100 0.222 Contact Map
3nrgA 2 1 100 0.222 Contact Map
3q0wA 2 0.9794 100 0.222 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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