GREMLIN Database
YBGA - Uncharacterized HTH-type transcriptional regulator YbgA
UniProt: O31459 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 235 (193)
Sequences: 22233 (16949)
Seq/√Len: 1220.0

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_Q25_D3.8901.00
15_L20_K3.7591.00
13_I54_E3.2981.00
118_E175_E3.1851.00
15_L36_Q3.1091.00
9_K50_Q2.9701.00
58_K68_S2.7411.00
103_P183_D2.6241.00
8_I39_V2.4771.00
30_E41_R2.4641.00
178_E181_L2.4401.00
60_I63_K2.4261.00
125_R168_I2.3671.00
11_K15_L2.3501.00
59_R65_T2.3341.00
26_Q66_F2.1861.00
14_E18_S2.0961.00
8_I37_Y2.0921.00
9_K54_E2.0591.00
63_K66_F1.9221.00
11_K37_Y1.8741.00
89_G152_E1.8161.00
52_E59_R1.7851.00
9_K13_I1.7411.00
113_K150_A1.7151.00
46_L49_Q1.7031.00
96_V100_V1.6961.00
13_I17_K1.6681.00
107_S179_P1.6491.00
183_D186_I1.6271.00
48_L57_I1.6001.00
32_E36_Q1.5571.00
57_I65_T1.5541.00
13_I56_Y1.5491.00
11_K14_E1.5251.00
183_D187_S1.5161.00
95_K191_L1.4921.00
33_F44_V1.4811.00
52_E57_I1.4771.00
109_A114_M1.4621.00
7_V11_K1.4551.00
130_E133_P1.4551.00
124_V138_T1.4521.00
31_S35_E1.4341.00
15_L21_Y1.4231.00
29_T32_E1.4151.00
49_Q59_R1.4091.00
16_I67_V1.3851.00
114_M175_E1.3791.00
110_E113_K1.3621.00
30_E45_R1.3501.00
166_Y192_T1.3401.00
122_K138_T1.3381.00
108_I140_Y1.3361.00
4_L7_V1.3331.00
39_V44_V1.3201.00
181_L185_T1.3151.00
147_P155_T1.3121.00
93_E128_Y1.3121.00
15_L19_G1.3111.00
181_L197_P1.3101.00
23_A69_A1.2981.00
105_D108_I1.2851.00
95_K99_L1.2801.00
21_Y67_V1.2791.00
184_E188_G1.2561.00
116_E144_K1.2531.00
32_E35_E1.2481.00
144_K147_P1.2411.00
60_I66_F1.2401.00
115_K118_E1.2351.00
58_K66_F1.2221.00
120_V137_H1.1951.00
109_A177_I1.1881.00
49_Q53_L1.1831.00
103_P179_P1.1801.00
49_Q52_E1.1761.00
121_N171_S1.1731.00
136_Y186_I1.1581.00
17_K56_Y1.1491.00
173_G181_L1.1451.00
50_Q53_L1.1311.00
118_E171_S1.1061.00
92_S108_I1.0911.00
123_L140_Y1.0841.00
168_I172_R1.0841.00
160_E164_T1.0801.00
26_Q64_G1.0711.00
5_Y50_Q1.0651.00
171_S175_E1.0611.00
143_W147_P1.0471.00
15_L37_Y1.0441.00
48_L65_T1.0401.00
104_A108_I1.0161.00
149_L155_T1.0091.00
120_V140_Y1.0031.00
101_V119_P0.9991.00
95_K187_S0.9971.00
60_I64_G0.9951.00
50_Q54_E0.9951.00
102_I122_K0.9891.00
99_L183_D0.9891.00
46_L50_Q0.9891.00
103_P180_I0.9741.00
95_K128_Y0.9721.00
21_Y25_D0.9681.00
118_E122_K0.9601.00
138_T142_P0.9571.00
121_N168_I0.9551.00
24_N58_K0.9491.00
193_N196_A0.9321.00
10_F13_I0.9311.00
101_V143_W0.9281.00
114_M171_S0.9251.00
92_S104_A0.9241.00
117_N144_K0.9191.00
122_K125_R0.9051.00
182_T192_T0.8981.00
140_Y144_K0.8951.00
114_M118_E0.8921.00
99_L187_S0.8881.00
90_L130_E0.8881.00
100_V103_P0.8871.00
114_M177_I0.8841.00
187_S191_L0.8841.00
133_P136_Y0.8821.00
109_A148_G0.8821.00
179_P183_D0.8811.00
172_R176_S0.8781.00
127_R137_H0.8751.00
124_V185_T0.8731.00
6_S10_F0.8721.00
109_A113_K0.8701.00
180_I186_I0.8531.00
118_E168_I0.8491.00
102_I186_I0.8481.00
98_E124_V0.8461.00
120_V144_K0.8411.00
119_P123_L0.8411.00
6_S50_Q0.8391.00
83_F87_M0.8361.00
62_G65_T0.8271.00
123_L137_H0.8181.00
4_L43_T0.8161.00
98_E122_K0.8151.00
123_L126_V0.8131.00
84_A87_M0.8121.00
48_L52_E0.8111.00
116_E119_P0.8051.00
123_L127_R0.8041.00
142_P145_A0.7931.00
116_E147_P0.7901.00
40_S43_T0.7901.00
12_I33_F0.7871.00
144_K148_G0.7841.00
161_L166_Y0.7781.00
30_E59_R0.7771.00
8_I44_V0.7721.00
136_Y140_Y0.7711.00
145_A174_T0.7651.00
8_I11_K0.7631.00
169_E185_T0.7601.00
109_A174_T0.7591.00
102_I106_H0.7581.00
80_I83_F0.7521.00
142_P167_N0.7501.00
33_F48_L0.7501.00
181_L184_E0.7421.00
23_A68_S0.7371.00
116_E120_V0.7351.00
12_I21_Y0.7351.00
99_L103_P0.7351.00
102_I108_I0.7321.00
96_V154_C0.7321.00
48_L59_R0.7291.00
26_Q29_T0.7271.00
172_R175_E0.7221.00
161_L165_K0.7091.00
192_T196_A0.7081.00
109_A117_N0.7061.00
141_I171_S0.7061.00
122_K140_Y0.7001.00
34_C44_V0.6981.00
121_N125_R0.6971.00
118_E144_K0.6941.00
10_F14_E0.6911.00
100_V183_D0.6901.00
111_L177_I0.6901.00
21_Y27_L0.6861.00
100_V104_A0.6821.00
170_I186_I0.6761.00
24_N69_A0.6741.00
143_W156_G0.6731.00
176_S181_L0.6661.00
27_L57_I0.6661.00
89_G92_S0.6661.00
73_Q77_P0.6651.00
93_E153_E0.6641.00
94_S127_R0.6611.00
35_E38_D0.6611.00
166_Y189_H0.6571.00
5_Y9_K0.6571.00
95_K194_V0.6551.00
180_I183_D0.6541.00
184_E187_S0.6521.00
185_T188_G0.6491.00
186_I189_H0.6471.00
104_A109_A0.6441.00
137_H140_Y0.6421.00
122_K126_V0.6401.00
11_K36_Q0.6381.00
131_G134_L0.6331.00
37_Y44_V0.6331.00
104_A120_V0.6321.00
120_V123_L0.6291.00
126_V133_P0.6261.00
93_E131_G0.6251.00
28_P36_Q0.6231.00
102_I105_D0.6231.00
103_P106_H0.6201.00
20_K36_Q0.6171.00
170_I185_T0.6141.00
180_I184_E0.6061.00
26_Q63_K0.6021.00
113_K148_G0.5981.00
87_M129_A0.5951.00
113_K116_E0.5951.00
182_T196_A0.5871.00
96_V99_L0.5851.00
101_V146_A0.5831.00
150_A153_E0.5831.00
99_L150_A0.5811.00
31_S34_C0.5791.00
15_L18_S0.5791.00
125_R129_A0.5761.00
115_K119_P0.5711.00
103_P119_P0.5711.00
93_E97_L0.5651.00
182_T195_G0.5651.00
168_I171_S0.5641.00
44_V47_A0.5631.00
106_H179_P0.5621.00
117_N120_V0.5611.00
182_T187_S0.5601.00
181_L196_A0.5601.00
105_D148_G0.5601.00
97_L126_V0.5591.00
21_Y28_P0.5571.00
42_T46_L0.5571.00
82_S86_Q0.5561.00
123_L133_P0.5561.00
9_K47_A0.5531.00
185_T189_H0.5521.00
138_T186_I0.5501.00
5_Y46_L0.5501.00
33_F37_Y0.5461.00
44_V57_I0.5451.00
14_E17_K0.5451.00
117_N148_G0.5451.00
159_F163_R0.5441.00
43_T47_A0.5441.00
34_C37_Y0.5421.00
71_K75_P0.5421.00
136_Y189_H0.5351.00
105_D109_A0.5331.00
34_C42_T0.5321.00
61_Q64_G0.5321.00
29_T44_V0.5311.00
111_L115_K0.5311.00
102_I140_Y0.5301.00
79_K82_S0.5301.00
81_T85_E0.5261.00
186_I190_L0.5251.00
124_V136_Y0.5221.00
95_K190_L0.5211.00
81_T84_A0.5191.00
108_I112_L0.5161.00
52_E65_T0.5151.00
187_S195_G0.5121.00
103_P107_S0.5111.00
106_H116_E0.5061.00
188_G192_T0.5061.00
105_D140_Y0.5051.00
140_Y143_W0.5031.00
173_G178_E0.5021.00
169_E181_L0.5011.00
119_P143_W0.5001.00
99_L102_I0.5001.00
101_V121_N0.5001.00
146_A149_L0.5001.00
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 0.9915 100 0.124 Contact Map
3bwgA 2 0.9745 100 0.142 Contact Map
3edpA 2 0.9362 100 0.145 Contact Map
3f8mA 2 0.966 100 0.151 Contact Map
2ra5A 2 0.6298 100 0.161 Contact Map
3eetA 2 0.9745 100 0.181 Contact Map
3f8lA 2 0.6809 100 0.437 Contact Map
2di3A 2 0.8468 99.9 0.504 Contact Map
1hw1A 2 0.8298 99.9 0.506 Contact Map
4p96A 2 0.9021 99.9 0.518 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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