GREMLIN Database
YHGD - Uncharacterized HTH-type transcriptional regulator YhgD
UniProt: P32398 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 191 (179)
Sequences: 39960 (31452)
Seq/√Len: 2350.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
28_D38_K3.9071.00
20_F29_L3.8531.00
15_K33_L3.4381.00
46_K50_E2.6841.00
17_F25_T2.3181.00
47_N50_E2.1821.00
129_K147_E2.1041.00
31_A41_I2.0861.00
16_S25_T2.0301.00
16_S29_L2.0131.00
16_S33_L1.9741.00
19_Q33_L1.9261.00
129_K133_E1.9171.00
80_N134_D1.8851.00
8_L12_A1.8801.00
12_A33_L1.8481.00
5_R8_L1.8311.00
7_K58_T1.8301.00
6_K54_E1.8261.00
76_P79_E1.8081.00
16_S20_F1.8031.00
133_E146_P1.7811.00
28_D32_K1.7441.00
133_E137_K1.7231.00
12_A15_K1.7111.00
136_I143_P1.7051.00
37_G40_T1.6891.00
133_E136_I1.6151.00
14_T58_T1.6081.00
27_M42_Y1.5841.00
10_L54_E1.5421.00
27_M38_K1.5121.00
7_K11_E1.4621.00
54_E57_T1.4581.00
13_A17_F1.4421.00
14_T59_L1.4351.00
29_L32_K1.4241.00
15_K19_Q1.4241.00
68_D127_Y1.4111.00
152_V156_L1.3881.00
86_F177_A1.3811.00
14_T55_I1.3751.00
29_L33_L1.3731.00
25_T30_V1.3711.00
134_D138_S1.3701.00
58_T62_E1.3611.00
45_F54_E1.3401.00
148_L179_L1.3361.00
57_T116_V1.3341.00
26_T29_L1.3311.00
13_A51_L1.3281.00
53_D57_T1.3151.00
82_H178_G1.3091.00
135_G141_I1.2931.00
40_T43_T1.2841.00
136_I144_C1.2781.00
135_G140_A1.2521.00
21_G25_T1.2411.00
12_A16_S1.2351.00
11_E58_T1.2291.00
20_F24_A1.2221.00
27_M41_I1.2141.00
53_D116_V1.2011.00
125_L151_F1.1951.00
78_H82_H1.1901.00
36_V40_T1.1761.00
80_N131_K1.1541.00
37_G43_T1.1511.00
97_L100_K1.1461.00
66_K87_A1.1421.00
6_K44_F1.1381.00
49_E53_D1.1351.00
21_G24_A1.1331.00
86_F174_E1.1331.00
50_E54_E1.1331.00
86_F178_G1.1311.00
39_G43_T1.1221.00
79_E83_R1.1151.00
82_H86_F1.1101.00
42_Y47_N1.1001.00
145_D148_L1.0921.00
136_I146_P1.0891.00
102_F105_N1.0871.00
76_P140_A1.0851.00
125_L129_K1.0731.00
22_Y52_F1.0721.00
172_D175_T1.0691.00
10_L45_F1.0661.00
38_K42_Y1.0611.00
83_R86_F1.0451.00
64_K123_S1.0441.00
66_K69_E1.0421.00
70_A87_A1.0401.00
82_H181_E1.0371.00
17_F22_Y1.0371.00
127_Y130_S1.0361.00
12_A34_A1.0271.00
75_L83_R1.0161.00
50_E53_D1.0131.00
10_L55_I1.0131.00
131_K135_G1.0121.00
155_K159_A1.0031.00
148_L175_T1.0031.00
11_E15_K1.0021.00
49_E110_T1.0011.00
77_F138_S1.0011.00
30_V51_L1.0001.00
99_I102_F0.9911.00
14_T18_T0.9891.00
116_V119_K0.9811.00
40_T44_F0.9781.00
15_K97_L0.9631.00
20_F33_L0.9581.00
49_E112_A0.9511.00
91_F95_H0.9461.00
57_T61_K0.9361.00
41_I51_L0.9281.00
74_S80_N0.9261.00
130_S134_D0.9241.00
5_R44_F0.9231.00
79_E82_H0.9221.00
144_C149_T0.9191.00
129_K146_P0.9181.00
54_E58_T0.9171.00
70_A83_R0.9081.00
77_F135_G0.8961.00
126_S130_S0.8941.00
59_L62_E0.8881.00
122_R126_S0.8851.00
134_D137_K0.8841.00
119_K123_S0.8791.00
178_G182_L0.8761.00
130_S133_E0.8751.00
109_G112_A0.8731.00
58_T61_K0.8711.00
31_A38_K0.8681.00
86_F90_E0.8621.00
13_A55_I0.8611.00
125_L147_E0.8611.00
38_K43_T0.8551.00
87_A90_E0.8531.00
147_E151_F0.8401.00
82_H182_L0.8401.00
83_R87_A0.8391.00
131_K134_D0.8341.00
175_T179_L0.8271.00
179_L182_L0.8241.00
174_E178_G0.8201.00
16_S19_Q0.8191.00
169_P172_D0.8091.00
100_K104_E0.7921.00
148_L152_V0.7911.00
10_L58_T0.7901.00
115_E119_K0.7891.00
18_T97_L0.7891.00
75_L79_E0.7871.00
9_I41_I0.7831.00
8_L34_A0.7801.00
61_K65_Q0.7801.00
32_K38_K0.7751.00
5_R36_V0.7741.00
85_L153_M0.7621.00
111_M115_E0.7601.00
177_A181_E0.7591.00
64_K68_D0.7561.00
129_K150_A0.7521.00
86_F181_E0.7521.00
126_S129_K0.7511.00
177_A180_L0.7461.00
123_S127_Y0.7381.00
136_I139_G0.7361.00
93_K173_K0.7341.00
164_W167_Q0.7321.00
62_E65_Q0.7311.00
64_K127_Y0.7291.00
65_Q69_E0.7261.00
114_Q118_Q0.7201.00
132_I146_P0.7131.00
116_V120_M0.7081.00
132_I136_I0.7051.00
101_I105_N0.7041.00
97_L101_I0.6991.00
118_Q122_R0.6991.00
90_E174_E0.6981.00
9_I34_A0.6941.00
179_L183_Y0.6941.00
155_K158_I0.6921.00
8_L11_E0.6921.00
57_T119_K0.6831.00
146_P150_A0.6801.00
132_I153_M0.6801.00
20_F25_T0.6801.00
123_S126_S0.6771.00
5_R37_G0.6771.00
11_E14_T0.6741.00
136_I141_I0.6731.00
97_L105_N0.6711.00
90_E177_A0.6691.00
74_S79_E0.6651.00
76_P80_N0.6651.00
17_F52_F0.6591.00
19_Q29_L0.6561.00
22_Y48_K0.6511.00
148_L151_F0.6511.00
77_F140_A0.6491.00
5_R40_T0.6461.00
57_T120_M0.6441.00
118_Q121_E0.6431.00
69_E87_A0.6421.00
174_E177_A0.6381.00
22_Y49_E0.6351.00
82_H85_L0.6301.00
152_V155_K0.6231.00
111_M114_Q0.6221.00
10_L14_T0.6191.00
136_I142_K0.6181.00
34_A37_G0.6171.00
95_H98_T0.6161.00
27_M31_A0.6151.00
90_E94_T0.6121.00
28_D42_Y0.6111.00
90_E173_K0.6101.00
99_I103_Q0.6091.00
74_S83_R0.6091.00
163_D167_Q0.6061.00
156_L180_L0.5991.00
98_T101_I0.5941.00
171_L175_T0.5931.00
36_V44_F0.5841.00
100_K105_N0.5831.00
88_I92_R0.5801.00
176_I180_L0.5761.00
100_K103_Q0.5691.00
23_K108_I0.5681.00
73_P83_R0.5651.00
143_P149_T0.5611.00
132_I149_T0.5601.00
31_A36_V0.5601.00
173_K176_I0.5571.00
9_I44_F0.5551.00
71_M127_Y0.5551.00
65_Q68_D0.5481.00
61_K120_M0.5481.00
173_K177_A0.5451.00
78_H140_A0.5441.00
171_L174_E0.5441.00
60_L120_M0.5411.00
176_I179_L0.5371.00
145_D179_L0.5371.00
85_L88_I0.5371.00
23_K105_N0.5361.00
38_K41_I0.5341.00
175_T178_G0.5331.00
163_D166_K0.5321.00
16_S26_T0.5251.00
62_E66_K0.5141.00
98_T104_E0.5141.00
5_R43_T0.5121.00
27_M48_K0.5121.00
22_Y25_T0.5111.00
87_A91_F0.5111.00
80_N135_G0.5111.00
121_E125_L0.5101.00
178_G181_E0.5091.00
119_K122_R0.5041.00
155_K163_D0.5021.00
104_E108_I0.5011.00
53_D115_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  
2ibdA 2 0.9948 100 0.216 Contact Map
4udsA 2 0.9634 100 0.22 Contact Map
1vi0A 2 0.9843 100 0.224 Contact Map
3himA 2 0.9948 100 0.226 Contact Map
4jykA 2 0.9948 100 0.229 Contact Map
3ppbA 2 0.9843 100 0.229 Contact Map
3dcfA 2 0.9581 100 0.23 Contact Map
2genA 2 0.9791 100 0.23 Contact Map
3npiA 2 0.9948 100 0.23 Contact Map
3dewA 2 0.9738 100 0.231 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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