GREMLIN Database
YYBA - Uncharacterized HTH-type transcriptional regulator YybA
UniProt: P37503 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 150 (131)
Sequences: 23486 (17163)
Seq/√Len: 1499.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
77_L89_F3.0191.00
120_E130_R2.8301.00
44_G89_F2.6881.00
46_I85_I2.6501.00
79_D87_K2.6291.00
75_Q89_F2.5061.00
123_T127_L2.3581.00
117_T120_E2.2611.00
78_P86_K2.1531.00
123_T126_A2.1151.00
40_Y98_Y2.0391.00
46_I49_K1.9951.00
32_Q71_Q1.9601.00
40_Y90_P1.9501.00
116_F127_L1.8881.00
115_G134_N1.8701.00
79_D85_I1.8331.00
120_E123_T1.7911.00
69_E76_K1.6171.00
93_K97_V1.6001.00
72_G93_K1.5751.00
32_Q67_K1.5381.00
7_E129_H1.5061.00
47_Q65_I1.4871.00
124_I127_L1.4791.00
97_V100_L1.4781.00
35_Y64_A1.4531.00
66_K70_M1.4421.00
42_N53_M1.4041.00
65_I88_L1.4001.00
120_E126_A1.3961.00
29_T32_Q1.3931.00
7_E132_R1.3871.00
38_R53_M1.3851.00
40_Y95_K1.3581.00
93_K96_K1.3421.00
22_E104_E1.3171.00
127_L130_R1.2751.00
44_G87_K1.2691.00
26_L104_E1.2651.00
76_K86_K1.2531.00
7_E125_S1.2401.00
26_L100_L1.2041.00
120_E127_L1.1791.00
66_K83_K1.1601.00
48_E58_R1.1531.00
47_Q86_K1.1511.00
10_M132_R1.1491.00
35_Y61_A1.1461.00
49_K52_E1.1441.00
56_V60_T1.1441.00
57_D60_T1.1251.00
48_E52_E1.1221.00
20_N24_K1.1141.00
126_A130_R1.1131.00
125_S129_H1.1121.00
42_N45_I1.1051.00
59_T62_A1.1021.00
104_E107_H1.0931.00
11_I132_R1.0831.00
47_Q58_R1.0711.00
73_F97_V1.0621.00
96_K100_L1.0611.00
44_G77_L1.0541.00
121_K125_S1.0461.00
47_Q61_A1.0331.00
22_E107_H1.0131.00
47_Q88_L1.0061.00
26_L101_L1.0011.00
57_D63_R0.9971.00
119_E123_T0.9911.00
90_P94_G0.9861.00
9_G12_A0.9861.00
109_T112_A0.9651.00
31_G64_A0.9611.00
62_A66_K0.9601.00
45_I53_M0.9541.00
39_I74_I0.9531.00
77_L87_K0.9491.00
60_T63_R0.9461.00
71_Q97_V0.9431.00
11_I128_L0.9131.00
56_V61_A0.9041.00
43_P95_K0.8961.00
73_F93_K0.8961.00
92_E95_K0.8941.00
66_K69_E0.8881.00
12_A16_D0.8861.00
40_Y102_R0.8861.00
95_K99_P0.8851.00
45_I49_K0.8781.00
71_Q93_K0.8731.00
49_K53_M0.8711.00
22_E111_V0.8681.00
75_Q91_T0.8651.00
123_T130_R0.8621.00
92_E96_K0.8541.00
18_I108_S0.8501.00
14_A132_R0.8441.00
105_G109_T0.8391.00
82_N85_I0.8301.00
35_Y50_L0.8271.00
25_D104_E0.8241.00
36_L98_Y0.8221.00
63_R66_K0.8211.00
31_G60_T0.8101.00
78_P83_K0.8091.00
33_Y101_L0.8091.00
103_R107_H0.8051.00
27_D71_Q0.8001.00
113_L121_K0.7971.00
67_K70_M0.7931.00
9_G13_R0.7921.00
100_L104_E0.7891.00
118_S122_E0.7771.00
63_R67_K0.7721.00
107_H110_E0.7701.00
90_P95_K0.7701.00
11_I131_V0.7621.00
43_P89_F0.7601.00
51_A61_A0.7531.00
40_Y99_P0.7501.00
111_V114_S0.7481.00
38_R54_I0.7441.00
42_N49_K0.7431.00
129_H133_K0.7381.00
65_I74_I0.7361.00
79_D82_N0.7321.00
117_T121_K0.7301.00
19_S22_E0.7291.00
51_A58_R0.7271.00
13_R17_S0.7251.00
122_E125_S0.7201.00
38_R42_N0.7131.00
8_I12_A0.7101.00
69_E75_Q0.7091.00
116_F131_V0.7091.00
65_I69_E0.7091.00
107_H111_V0.7081.00
34_L54_I0.7001.00
22_E108_S0.6991.00
66_K76_K0.6981.00
33_Y105_G0.6921.00
80_E87_K0.6901.00
69_E74_I0.6891.00
22_E25_D0.6881.00
47_Q62_A0.6751.00
106_E110_E0.6731.00
18_I111_V0.6661.00
38_R45_I0.6641.00
16_D20_N0.6601.00
130_R134_N0.6581.00
38_R50_L0.6491.00
20_N30_R0.6481.00
67_K71_Q0.6451.00
61_A65_I0.6351.00
96_K99_P0.6321.00
76_K88_L0.6241.00
35_Y54_I0.6211.00
39_I90_P0.6201.00
103_R106_E0.6191.00
122_E126_A0.6171.00
32_Q64_A0.6131.00
31_G56_V0.6121.00
116_F121_K0.6121.00
119_E122_E0.6071.00
48_E51_A0.5991.00
100_L103_R0.5921.00
37_V41_E0.5891.00
7_E10_M0.5821.00
8_I11_I0.5751.00
33_Y98_Y0.5701.00
127_L134_N0.5701.00
102_R106_E0.5561.00
68_L73_F0.5511.00
19_S105_G0.5511.00
34_L38_R0.5501.00
108_S111_V0.5501.00
105_G108_S0.5461.00
116_F130_R0.5401.00
39_I45_I0.5391.00
37_V102_R0.5321.00
113_L117_T0.5311.00
126_A129_H0.5311.00
48_E85_I0.5231.00
99_P103_R0.5221.00
98_Y102_R0.5201.00
16_D19_S0.5191.00
30_R34_L0.5181.00
18_I21_I0.5171.00
129_H132_R0.5161.00
117_T130_R0.5141.00
15_L18_I0.5131.00
8_I128_L0.5131.00
46_I79_D0.5081.00
99_P102_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  
4mnuA 2 1 99.9 0.238 Contact Map
4rguA 4 0.94 99.9 0.269 Contact Map
1lj9A 2 0.96 99.9 0.27 Contact Map
3bj6A 2 0.9467 99.9 0.274 Contact Map
3deuA 2 0.8667 99.9 0.274 Contact Map
3cdhA 4 0.88 99.9 0.277 Contact Map
2fbkA 2 0.8667 99.9 0.278 Contact Map
3zplA 2 0.9867 99.9 0.279 Contact Map
4yifA 2 0.9267 99.9 0.279 Contact Map
3cjnA 2 0.92 99.9 0.279 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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