GREMLIN Database
YDCN - Uncharacterized HTH-type transcriptional regulator YdcN
UniProt: P77626 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13757
Length: 178 (167)
Sequences: 5976 (4018)
Seq/√Len: 310.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
131_Q144_N4.0381.00
129_D168_H3.8401.00
133_D140_W3.1221.00
133_D160_R3.0201.00
132_L167_V2.9251.00
133_D142_T2.9151.00
133_D162_G2.8641.00
103_S168_H2.8561.00
131_Q142_T2.7271.00
105_Q166_T2.6281.00
107_A166_T2.3191.00
105_Q168_H2.2591.00
129_D145_C2.1791.00
25_R29_A2.1041.00
24_S28_E2.0801.00
23_L37_L1.9171.00
137_D155_V1.8931.00
135_C140_W1.8891.00
14_Q18_Q1.8621.00
15_L61_V1.8491.00
134_L149_V1.8161.00
26_L59_L1.7821.00
25_R28_E1.7761.00
24_S34_K1.7581.00
111_I160_R1.7431.00
101_H124_H1.7241.00
119_K123_E1.6371.00
125_V171_S1.6331.00
143_L147_E1.6231.00
128_I170_H1.6111.00
135_C160_R1.5901.00
129_D165_Q1.5781.00
123_E157_H1.5501.00
125_V149_V1.5461.00
132_L169_F1.5441.00
135_C158_I1.5261.00
36_M40_I1.5211.00
33_S36_M1.4831.00
101_H172_L1.4811.00
131_Q163_G1.4671.00
21_W29_A1.4661.00
7_F43_N1.4431.00
126_V170_H1.4401.00
32_V51_T1.3761.00
131_Q162_G1.3751.00
142_T162_G1.3531.00
129_D166_T1.3461.00
127_V167_V1.3451.00
40_I47_P1.3411.00
15_L19_R1.3031.00
88_T105_Q1.2921.00
11_T14_Q1.2771.00
119_K157_H1.2751.00
19_R60_N1.2581.00
62_P65_T1.2491.00
75_P78_Y1.2401.00
88_T103_S1.2371.00
122_I150_R1.2231.00
135_C138_G1.2151.00
38_G42_R1.2071.00
136_V155_V1.1891.00
144_N147_E1.1851.00
111_I158_I1.1481.00
163_G167_V1.1481.00
76_S79_D1.1471.00
80_P83_Q1.1341.00
86_V107_A1.1251.00
124_H148_G1.1161.00
21_W26_L1.1111.00
30_T58_G1.1001.00
13_K17_Q1.0971.00
15_L59_L1.0921.00
103_S126_V1.0911.00
120_G154_D1.0891.00
161_N166_T1.0741.00
137_D156_T1.0701.00
82_Q85_M1.0701.00
56_A61_V1.0521.00
32_V36_M1.0501.00
36_M45_S1.0481.00
106_M169_F1.0321.00
26_L58_G1.0301.00
136_V151_F1.0241.00
103_S128_I1.0111.00
56_A66_F1.0051.00
36_M39_Q1.0021.00
127_V132_L1.0021.00
9_S43_N0.9881.00
16_R41_E0.9861.00
108_S165_Q0.9771.00
99_F150_R0.9761.00
21_W25_R0.9751.00
103_S170_H0.9681.00
128_I168_H0.9601.00
10_T14_Q0.9531.00
104_I169_F0.9401.00
74_T78_Y0.9261.00
127_V169_F0.9201.00
36_M51_T0.9031.00
35_A38_G0.9001.00
27_A34_K0.8981.00
108_S166_T0.8891.00
126_V148_G0.8861.00
15_L18_Q0.8781.00
30_T34_K0.8761.00
81_Q85_M0.8741.00
99_F172_L0.8691.00
108_S161_N0.8691.00
97_L150_R0.8631.00
97_L122_I0.8611.00
23_L38_G0.8601.00
8_L52_L0.8571.00
80_P85_M0.8551.00
117_H157_H0.8481.00
32_V37_L0.8471.00
79_D147_E0.8451.00
39_Q44_E0.8331.00
81_Q84_A0.8181.00
80_P84_A0.8151.00
52_L63_F0.8041.00
30_T37_L0.8001.00
117_H159_Y0.7921.00
40_I55_I0.7921.00
53_W57_T0.7901.00
11_T15_L0.7871.00
39_Q45_S0.7841.00
117_H123_E0.7841.00
12_L55_I0.7750.99
101_H150_R0.7750.99
161_N164_E0.7700.99
12_L59_L0.7690.99
86_V105_Q0.7690.99
49_V52_L0.7640.99
61_V66_F0.7630.99
108_S163_G0.7620.99
23_L30_T0.7580.99
12_L56_A0.7570.99
124_H172_L0.7490.99
23_L34_K0.7460.99
100_E173_I0.7450.99
151_F157_H0.7400.99
35_A39_Q0.7390.99
123_E153_A0.7360.99
136_V141_Q0.7350.99
29_A58_G0.7340.99
91_F101_H0.7290.99
40_I46_S0.7140.99
141_Q149_V0.7130.99
11_T69_P0.7080.99
151_F159_Y0.7030.99
127_V144_N0.7010.99
87_I91_F0.6970.99
116_P158_I0.6970.99
73_A139_E0.6920.99
109_G164_E0.6890.99
106_M167_V0.6880.99
7_F10_T0.6780.99
99_F124_H0.6770.99
106_M132_L0.6740.99
46_S50_A0.6600.98
37_L55_I0.6570.98
29_A60_N0.6550.98
53_W63_F0.6540.98
12_L38_G0.6500.98
131_Q145_C0.6500.98
30_T59_L0.6490.98
122_I152_A0.6480.98
63_F67_I0.6450.98
22_S34_K0.6440.98
106_M110_A0.6420.98
34_K51_T0.6420.98
45_S49_V0.6410.98
108_S164_E0.6400.98
64_S100_E0.6390.98
38_G67_I0.6390.98
159_Y171_S0.6370.98
47_P51_T0.6310.98
30_T54_K0.6300.98
22_S25_R0.6280.98
101_H126_V0.6260.98
153_A157_H0.6250.98
10_T13_K0.6170.97
104_I171_S0.6130.97
45_S48_T0.6100.97
108_S162_G0.6090.97
83_Q86_V0.6080.97
124_H150_R0.6050.97
60_N65_T0.6050.97
11_T66_F0.6040.97
55_I59_L0.6040.97
109_G161_N0.6040.97
64_S124_H0.6030.97
143_L149_V0.5920.97
42_R45_S0.5910.97
121_V153_A0.5890.97
98_C122_I0.5880.97
23_L33_S0.5870.97
124_H151_F0.5870.97
99_F122_I0.5840.96
142_T164_E0.5840.96
33_S51_T0.5820.96
140_W162_G0.5800.96
36_M48_T0.5790.96
65_T68_S0.5750.96
37_L125_V0.5740.96
23_L27_A0.5720.96
87_I102_F0.5700.96
117_H154_D0.5660.96
91_F150_R0.5650.96
139_E155_V0.5650.96
27_A37_L0.5640.96
114_S117_H0.5600.96
117_H120_G0.5580.95
33_S45_S0.5570.95
14_Q17_Q0.5550.95
46_S51_T0.5530.95
119_K154_D0.5490.95
51_T54_K0.5480.95
50_A100_E0.5460.95
49_V63_F0.5440.95
115_T156_T0.5400.95
23_L42_R0.5400.95
134_L169_F0.5380.94
21_W59_L0.5370.94
52_L66_F0.5350.94
32_V54_K0.5340.94
132_L159_Y0.5310.94
32_V58_G0.5310.94
127_V143_L0.5290.94
134_L159_Y0.5270.94
32_V47_P0.5270.94
94_D150_R0.5270.94
97_L100_E0.5270.94
10_T144_N0.5260.94
19_R59_L0.5250.94
81_Q86_V0.5220.94
48_T85_M0.5180.93
53_W159_Y0.5170.93
9_S16_R0.5170.93
33_S39_Q0.5160.93
140_W160_R0.5160.93
101_H170_H0.5150.93
63_F114_S0.5140.93
10_T17_Q0.5130.93
90_L170_H0.5110.93
117_H153_A0.5100.93
40_I45_S0.5070.93
125_V132_L0.5050.92
93_Y97_L0.5010.92
46_S56_A0.5000.92
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  
1y9qA 1 0.9775 100 0.315 Contact Map
2bnmA 3 0.9607 100 0.356 Contact Map
4yarA 2 0.9831 100 0.366 Contact Map
4b29A 1 0.9494 100 0.434 Contact Map
4qm9A 1 0.764 100 0.454 Contact Map
2p5tA 2 0.5337 99.9 0.481 Contact Map
4lukA 2 0.8146 99.9 0.512 Contact Map
1j58A 5 0.8202 99.9 0.52 Contact Map
4e2qA 6 0.7247 99.9 0.533 Contact Map
3bu7A 3 0.8483 99.8 0.613 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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