GREMLIN Database
YBAO - Uncharacterized HTH-type transcriptional regulator YbaO
UniProt: P0ACJ5 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13218
Length: 152 (139)
Sequences: 13537 (8837)
Seq/√Len: 749.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
43_E51_K2.9361.00
12_L27_A2.8591.00
95_G108_R2.6421.00
102_E135_T2.5971.00
71_K133_D2.4311.00
21_L39_L2.3301.00
112_A116_R2.2981.00
58_E115_K2.2121.00
6_D38_R2.1161.00
49_I56_D2.1001.00
12_L19_L2.0861.00
41_R45_D1.9571.00
73_Q132_S1.8941.00
79_W82_R1.8891.00
67_F97_W1.8161.00
49_I54_L1.8071.00
90_M120_F1.7741.00
65_T108_R1.7691.00
40_K44_D1.7571.00
12_L15_Q1.6871.00
94_L110_Q1.6841.00
30_L34_P1.6671.00
5_I30_L1.6631.00
22_Q26_E1.6291.00
23_A26_E1.6261.00
119_E123_R1.6111.00
116_R119_E1.5941.00
19_L27_A1.5671.00
113_D116_R1.5351.00
83_F87_V1.5161.00
9_L24_L1.5121.00
69_L137_S1.4791.00
92_E116_R1.4691.00
86_V89_E1.4611.00
22_Q32_T1.4351.00
21_L36_W1.4331.00
30_L35_C1.4291.00
31_T34_P1.4211.00
86_V128_V1.4101.00
18_T51_K1.4041.00
28_V35_C1.4011.00
68_V109_V1.3681.00
81_C85_T1.3581.00
84_V88_T1.3481.00
70_I107_M1.3241.00
71_K102_E1.3151.00
19_L24_L1.2781.00
15_Q27_A1.2781.00
62_L112_A1.2761.00
118_D141_E1.2701.00
23_A27_A1.2621.00
69_L103_Y1.2461.00
13_L39_L1.2421.00
4_K8_K1.2231.00
20_S23_A1.2221.00
72_T83_F1.2091.00
40_K43_E1.2061.00
84_V141_E1.1731.00
64_L114_M1.1561.00
16_D27_A1.1471.00
3_D38_R1.1381.00
5_I8_K1.1321.00
69_L135_T1.1291.00
71_K132_S1.1171.00
12_L24_L1.0811.00
8_K11_A1.0641.00
21_L25_A1.0551.00
5_I28_V1.0461.00
56_D59_K1.0441.00
96_F107_M1.0301.00
63_G113_D1.0291.00
11_A15_Q1.0231.00
93_V109_V1.0161.00
67_F106_L1.0131.00
111_V116_R1.0121.00
82_R86_V0.9871.00
50_G54_L0.9751.00
8_K12_L0.9711.00
17_C51_K0.9671.00
25_A35_C0.9661.00
99_M106_L0.9601.00
90_M123_R0.9561.00
84_V105_Y0.9541.00
118_D122_K0.9421.00
32_T36_W0.9411.00
65_T110_Q0.9401.00
109_V120_F0.9401.00
21_L32_T0.9401.00
19_L23_A0.9271.00
67_F108_R0.9221.00
18_T43_E0.9101.00
85_T89_E0.9091.00
85_T88_T0.9091.00
25_A30_L0.9011.00
111_V120_F0.9001.00
24_L39_L0.8971.00
111_V117_Y0.8951.00
97_W108_R0.8951.00
98_R122_K0.8851.00
67_F139_A0.8831.00
42_L47_I0.8781.00
2_L7_R0.8781.00
57_P110_Q0.8741.00
36_W40_K0.8731.00
17_C53_A0.8241.00
97_W142_Q0.8211.00
93_V107_M0.8101.00
22_Q36_W0.8091.00
93_V96_F0.8031.00
97_W139_A0.8011.00
82_R85_T0.7961.00
8_K28_V0.7881.00
87_V96_F0.7771.00
70_I83_F0.7721.00
9_L19_L0.7701.00
7_R11_A0.7671.00
102_E133_D0.7651.00
24_L35_C0.7591.00
6_D41_R0.7581.00
81_C84_V0.7571.00
83_F105_Y0.7521.00
17_C23_A0.7481.00
121_Y136_S0.7421.00
47_I59_K0.7321.00
80_Y105_Y0.7311.00
100_A138_F0.7211.00
69_L106_L0.7211.00
115_K118_D0.7151.00
126_N134_V0.7121.00
114_M138_F0.7031.00
66_A117_Y0.6971.00
73_Q79_W0.6961.00
33_T37_K0.6961.00
86_V90_M0.6921.00
68_V134_V0.6891.00
73_Q130_G0.6881.00
4_K7_R0.6781.00
16_D19_L0.6741.00
120_F125_V0.6741.00
71_K103_Y0.6631.00
62_L110_Q0.6611.00
66_A136_S0.6611.00
103_Y135_T0.6601.00
17_C50_G0.6591.00
69_L102_E0.6551.00
70_I131_L0.6541.00
84_V143_I0.6501.00
66_A138_F0.6471.00
37_K40_K0.6451.00
9_L12_L0.6441.00
3_D6_D0.6381.00
9_L35_C0.6361.00
87_V107_M0.6341.00
62_L92_E0.6291.00
116_R120_F0.6281.00
12_L16_D0.6261.00
68_V107_M0.6241.00
21_L35_C0.6211.00
98_R105_Y0.6201.00
65_T97_W0.6191.00
65_T139_A0.6171.00
46_G49_I0.6151.00
92_E120_F0.6141.00
9_L42_L0.6091.00
81_C122_K0.6071.00
37_K41_R0.6071.00
55_L60_I0.6041.00
6_D42_L0.5981.00
99_M103_Y0.5961.00
90_M128_V0.5901.00
9_L38_R0.5901.00
69_L99_M0.5881.00
38_R42_L0.5871.00
121_Y134_V0.5861.00
120_F123_R0.5861.00
10_L42_L0.5851.00
25_A32_T0.5801.00
115_K119_E0.5781.00
48_L51_K0.5701.00
99_M139_A0.5681.00
117_Y138_F0.5661.00
22_Q25_A0.5641.00
33_T36_W0.5631.00
65_T142_Q0.5621.00
119_E122_K0.5581.00
82_R130_G0.5571.00
70_I134_V0.5571.00
16_D23_A0.5551.00
9_L39_L0.5491.00
72_T104_D0.5471.00
56_D60_I0.5451.00
78_E82_R0.5451.00
92_E112_A0.5391.00
94_L108_R0.5381.00
86_V130_G0.5371.00
96_F143_I0.5351.00
114_M140_M0.5351.00
28_V34_P0.5331.00
20_S25_A0.5311.00
14_Q52_V0.5291.00
102_E137_S0.5261.00
126_N133_D0.5261.00
90_M93_V0.5251.00
92_E111_V0.5241.00
121_Y140_M0.5231.00
98_R104_D0.5171.00
7_R14_Q0.5151.00
99_M137_S0.5001.00
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  
4ch7A 1 0.8947 100 0.131 Contact Map
4un1A 1 0.9342 100 0.18 Contact Map
2e1cA 1 0.9671 100 0.183 Contact Map
4pcqA 2 0.9737 100 0.185 Contact Map
2p5vA 5 0.9934 100 0.193 Contact Map
4un1B 1 0.9737 100 0.195 Contact Map
3i4pA 5 0.9868 100 0.202 Contact Map
2ia0A 2 0.9539 100 0.228 Contact Map
2pn6A 5 0.9671 100 0.229 Contact Map
2cg4A 6 0.9737 100 0.234 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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