GREMLIN Database
YDES - Uncharacterized HTH-type transcriptional regulator YdeS
UniProt: P96676 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 198 (179)
Sequences: 39995 (31958)
Seq/√Len: 2388.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_D46_K3.9641.00
28_K37_K3.9351.00
23_D41_R3.8171.00
54_S58_A2.8171.00
55_N58_A2.2981.00
25_L33_V2.2811.00
39_A49_I2.1761.00
133_K152_E2.1641.00
14_H62_D2.1161.00
83_D138_K2.0841.00
24_L37_K2.0711.00
15_K66_S2.0461.00
13_T16_A2.0341.00
24_L33_V2.0281.00
27_E41_R2.0231.00
24_L41_R2.0041.00
133_K137_E1.9661.00
79_S82_Q1.9101.00
137_E141_Q1.9051.00
45_S48_T1.8721.00
16_A20_A1.8501.00
24_L28_K1.8251.00
36_D40_E1.7871.00
20_A41_R1.7391.00
15_K19_S1.6941.00
14_H52_W1.6741.00
137_E151_I1.5991.00
137_E140_I1.5961.00
20_A23_D1.5711.00
35_V46_K1.5561.00
34_T37_K1.5311.00
35_V50_Y1.5181.00
62_D65_L1.5161.00
23_D27_E1.4861.00
22_Y66_S1.4761.00
89_T179_R1.4651.00
18_L62_D1.4651.00
21_A25_L1.4561.00
22_Y67_T1.4381.00
138_K142_K1.4221.00
153_V180_D1.4031.00
29_G33_V1.3931.00
37_K41_R1.3851.00
139_G145_L1.3581.00
33_V38_I1.3371.00
66_S70_D1.3361.00
37_K40_E1.3321.00
81_V85_V1.3311.00
29_G32_A1.3061.00
184_N188_G1.2991.00
140_I147_E1.2921.00
35_V49_I1.2891.00
19_S66_S1.2851.00
85_V179_R1.2781.00
61_M65_L1.2751.00
157_L161_P1.2691.00
113_D116_L1.2461.00
45_S51_K1.2451.00
22_Y63_S1.2401.00
48_T51_K1.2301.00
12_G16_A1.2191.00
28_K32_A1.2171.00
85_V89_T1.2101.00
139_G144_E1.2061.00
163_F166_L1.1861.00
21_A59_V1.1811.00
53_W62_D1.1781.00
82_Q86_T1.1771.00
25_L30_F1.1761.00
13_T52_W1.1631.00
46_K50_Y1.1591.00
20_A24_L1.1581.00
38_I59_V1.1531.00
100_G105_E1.1311.00
135_L139_G1.1181.00
61_M119_E1.1171.00
58_A62_D1.1151.00
183_M187_K1.1121.00
129_R156_D1.1041.00
77_T83_D1.1011.00
44_V48_T1.1001.00
129_R133_K1.0961.00
150_D153_V1.0951.00
30_F60_I1.0831.00
18_L63_S1.0811.00
85_V183_M1.0541.00
19_S23_D1.0531.00
12_G15_K1.0511.00
57_A113_D1.0451.00
175_D179_R1.0441.00
86_T89_T1.0351.00
133_K151_I1.0301.00
57_A61_M1.0291.00
58_A61_M1.0231.00
20_A42_A1.0101.00
65_L119_E0.9971.00
131_Q134_G0.9851.00
78_G86_T0.9781.00
49_I59_V0.9781.00
126_Q130_L0.9751.00
79_S144_E0.9731.00
22_Y26_L0.9721.00
65_L69_T0.9681.00
146_R149_L0.9681.00
80_S142_K0.9661.00
11_E15_K0.9581.00
48_T52_W0.9561.00
178_V181_L0.9541.00
129_R152_E0.9471.00
83_D135_L0.9471.00
130_L134_G0.9451.00
31_D109_A0.9431.00
134_G137_E0.9331.00
140_I143_G0.9321.00
10_D51_K0.9311.00
47_A51_K0.9271.00
134_G138_K0.9231.00
28_K41_R0.9231.00
82_Q85_V0.9211.00
152_E156_D0.9181.00
105_E109_A0.9071.00
176_S180_D0.9041.00
13_T44_V0.8891.00
179_R183_M0.8891.00
89_T175_D0.8861.00
67_T70_D0.8811.00
18_L53_W0.8811.00
123_R127_P0.8801.00
108_G112_L0.8771.00
46_K51_K0.8761.00
72_L127_P0.8681.00
140_I151_I0.8661.00
66_S69_T0.8581.00
140_I148_N0.8551.00
93_R175_D0.8531.00
180_D183_M0.8471.00
140_I149_L0.8471.00
62_D66_S0.8451.00
177_Y181_L0.8421.00
30_F56_K0.8421.00
89_T93_R0.8401.00
10_D13_T0.8381.00
39_A46_K0.8351.00
40_E46_K0.8331.00
101_T104_K0.8251.00
24_L27_E0.8191.00
119_E123_R0.8161.00
50_Y55_N0.8161.00
21_A63_S0.8161.00
138_K141_Q0.8161.00
101_T105_E0.8161.00
69_T73_P0.7981.00
78_G82_Q0.7931.00
90_N93_R0.7931.00
57_A115_K0.7911.00
80_S139_G0.7831.00
136_L151_I0.7831.00
28_K33_V0.7791.00
9_R12_G0.7771.00
153_V156_D0.7701.00
140_I145_L0.7641.00
31_D112_L0.7601.00
8_P12_G0.7561.00
86_T90_N0.7551.00
177_Y180_D0.7451.00
16_A19_S0.7411.00
16_A42_A0.7361.00
9_R13_T0.7311.00
181_L185_A0.7261.00
100_G103_I0.7201.00
79_S83_D0.7121.00
113_D117_A0.7041.00
149_L154_S0.7031.00
109_A113_D0.6981.00
178_V182_V0.6961.00
65_L123_R0.6961.00
23_D101_T0.6951.00
165_R168_I0.6941.00
153_V157_L0.6891.00
17_I42_A0.6891.00
80_S144_E0.6841.00
115_K118_E0.6801.00
94_F99_E0.6801.00
13_T48_T0.6791.00
17_I49_I0.6771.00
133_K155_I0.6621.00
36_D50_Y0.6551.00
72_L131_Q0.6551.00
70_D73_P0.6541.00
118_E121_R0.6511.00
127_P131_Q0.6501.00
114_E117_A0.6491.00
130_L133_K0.6461.00
182_V186_F0.6451.00
175_D178_V0.6441.00
135_L138_K0.6421.00
93_R97_S0.6411.00
30_F57_A0.6411.00
127_P130_L0.6401.00
18_L22_Y0.6381.00
150_D180_D0.6371.00
81_V186_F0.6361.00
109_A112_L0.6361.00
103_I106_L0.6351.00
42_A45_S0.6321.00
185_A188_G0.6321.00
117_A121_R0.6311.00
17_I52_W0.6281.00
176_S179_R0.6281.00
113_D120_Y0.6281.00
115_K119_E0.6201.00
35_V39_A0.6161.00
158_I185_A0.6131.00
74_V78_G0.6131.00
100_G104_K0.6121.00
88_A158_I0.6121.00
136_L140_I0.6121.00
77_T82_Q0.6121.00
26_L101_T0.6111.00
179_R182_V0.6081.00
174_N177_Y0.6051.00
25_L60_I0.6011.00
11_E14_H0.6001.00
8_P11_E0.5981.00
117_A120_Y0.5971.00
164_Y169_T0.5961.00
180_D184_N0.5931.00
85_V186_F0.5921.00
46_K49_I0.5901.00
146_R187_K0.5871.00
164_Y168_I0.5861.00
77_T86_T0.5841.00
113_D121_R0.5801.00
10_D52_W0.5731.00
80_S83_D0.5711.00
85_V88_A0.5661.00
13_T45_S0.5661.00
136_L158_I0.5651.00
78_G83_D0.5621.00
85_V182_V0.5591.00
27_E37_K0.5531.00
19_S22_Y0.5521.00
36_D45_S0.5491.00
90_N94_F0.5441.00
81_V183_M0.5401.00
89_T178_V0.5361.00
106_L109_A0.5341.00
88_A91_L0.5341.00
93_R96_T0.5341.00
104_K108_G0.5331.00
13_T17_I0.5331.00
137_E152_E0.5251.00
166_L169_T0.5241.00
139_G143_G0.5221.00
140_I146_R0.5211.00
10_D14_H0.5211.00
30_F33_V0.5201.00
163_F168_I0.5181.00
169_T173_V0.5181.00
157_L160_G0.5171.00
156_D160_G0.5161.00
89_T182_V0.5161.00
145_L150_D0.5131.00
91_L95_L0.5111.00
94_F97_S0.5111.00
39_A42_A0.5041.00
65_L124_F0.5031.00
14_H53_W0.5001.00
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  
2fq4A 2 0.9293 100 0.22 Contact Map
2zb9A 2 0.9444 100 0.232 Contact Map
2id3A 4 0.9596 100 0.244 Contact Map
3npiA 2 0.9495 100 0.263 Contact Map
2ibdA 2 0.9192 100 0.267 Contact Map
3g1oA 2 0.9192 100 0.268 Contact Map
2qwtA 1 0.8232 100 0.279 Contact Map
3nrgA 2 0.9646 100 0.28 Contact Map
3s5rA 2 0.9141 100 0.281 Contact Map
3q0wA 2 0.9141 100 0.288 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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