GREMLIN Database
YYDK - Uncharacterized HTH-type transcriptional regulator YydK
UniProt: Q45591 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 236 (189)
Sequences: 22617 (17821)
Seq/√Len: 1296.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
14_Y19_Q4.2011.00
21_Q24_D4.1591.00
8_A49_L3.5321.00
12_E53_K3.5191.00
14_Y35_Q3.4261.00
57_F67_R3.0821.00
10_E14_Y2.7171.00
178_H181_Q2.6391.00
58_Q64_I2.6201.00
29_L40_K2.5941.00
59_V62_S2.5101.00
7_I38_V2.4661.00
8_A53_K2.3591.00
25_K65_F2.2941.00
7_I36_F2.2251.00
13_T17_E2.1551.00
8_A12_E2.1041.00
62_S65_F2.0721.00
10_E36_F1.9691.00
105_T108_A1.9341.00
45_K48_E1.9121.00
12_E16_E1.8891.00
51_E58_Q1.8831.00
183_N186_E1.8031.00
12_E55_A1.7311.00
30_E34_A1.7141.00
31_T35_Q1.6941.00
127_R135_C1.6831.00
14_Y20_L1.6731.00
113_N175_L1.6411.00
10_E13_T1.6351.00
48_E58_Q1.6251.00
51_E56_I1.5901.00
47_L56_I1.5781.00
183_N187_A1.5691.00
32_L43_I1.5681.00
28_V31_T1.5431.00
56_I64_I1.5361.00
104_P109_A1.5161.00
122_Y138_E1.4781.00
29_L44_T1.4611.00
124_K127_R1.4601.00
15_I66_V1.4421.00
98_E183_N1.3871.00
93_T128_Y1.3831.00
181_Q185_E1.3781.00
14_Y18_H1.3701.00
57_F65_F1.3661.00
22_Q68_K1.3571.00
6_Q10_E1.3471.00
20_L66_V1.3471.00
123_V139_S1.3421.00
59_V65_F1.3411.00
31_T34_A1.3371.00
95_K128_Y1.3101.00
16_E55_A1.3091.00
38_V43_I1.2901.00
108_A140_Y1.2881.00
124_K138_E1.2861.00
166_L192_L1.2811.00
48_E51_E1.2661.00
49_L52_Q1.2641.00
48_E52_Q1.2601.00
173_S181_Q1.2581.00
123_V127_R1.2311.00
171_G175_L1.2291.00
184_E188_E1.2251.00
108_A130_N1.2221.00
109_A114_I1.2151.00
179_V183_N1.2071.00
104_P108_A1.1771.00
136_Y186_E1.1751.00
115_G118_E1.1741.00
14_Y36_F1.1621.00
158_I162_I1.1541.00
102_R122_Y1.1521.00
59_V63_G1.1441.00
168_L172_F1.1361.00
49_L53_K1.1291.00
25_K63_G1.1161.00
160_H164_E1.1161.00
102_R179_V1.1131.00
20_L24_D1.1111.00
150_N153_I1.1091.00
85_K89_D1.0861.00
182_L192_L1.0821.00
47_L64_I1.0651.00
159_F163_R1.0601.00
86_D90_F1.0471.00
136_Y140_Y1.0271.00
83_F87_L1.0271.00
193_E196_L1.0151.00
45_K49_L1.0131.00
101_V143_K1.0081.00
23_G57_F0.9991.00
91_N95_K0.9921.00
9_T12_E0.9891.00
187_A191_G0.9771.00
39_S42_T0.9761.00
98_E122_Y0.9751.00
110_E114_I0.9711.00
157_S160_H0.9651.00
25_K28_V0.9611.00
161_Y166_L0.9341.00
11_I32_L0.9251.00
120_I124_K0.9171.00
126_V138_E0.9101.00
117_D120_I0.9071.00
100_D122_Y0.9031.00
149_L153_I0.9021.00
109_A175_L0.9021.00
133_T144_S0.9011.00
61_G64_I0.8981.00
124_K128_Y0.8961.00
124_K185_E0.8941.00
78_L81_Q0.8791.00
106_P110_E0.8781.00
149_L152_E0.8781.00
109_A112_L0.8771.00
158_I161_Y0.8761.00
5_Q9_T0.8721.00
108_A111_N0.8671.00
47_L51_E0.8591.00
172_F176_F0.8591.00
121_Y125_R0.8581.00
135_C139_S0.8521.00
180_G186_E0.8511.00
97_I101_V0.8461.00
10_E35_Q0.8451.00
7_I43_I0.8401.00
172_F175_L0.8381.00
101_V119_D0.8371.00
93_T131_G0.8321.00
118_E144_S0.8311.00
82_G85_K0.8301.00
104_P177_L0.8251.00
33_M43_I0.8241.00
105_T112_L0.8231.00
85_K132_Q0.8191.00
94_S98_E0.8091.00
29_L58_Q0.8041.00
11_I20_L0.7941.00
22_Q67_R0.7931.00
116_M120_I0.7911.00
26_L56_I0.7881.00
169_K185_E0.7831.00
32_L47_L0.7821.00
181_Q184_E0.7781.00
144_S147_T0.7771.00
151_N154_V0.7741.00
111_N114_I0.7731.00
138_E142_T0.7681.00
7_I10_E0.7621.00
86_D89_D0.7481.00
98_E102_R0.7471.00
119_D143_K0.7461.00
20_L26_L0.7431.00
186_E189_Y0.7401.00
23_G68_K0.7311.00
36_F43_I0.7271.00
14_Y17_E0.7261.00
176_F181_Q0.7251.00
106_P109_A0.7251.00
97_I100_D0.7231.00
34_A37_E0.7211.00
9_T13_T0.7181.00
109_A177_L0.7171.00
163_R169_K0.7151.00
168_L171_G0.7101.00
122_Y125_R0.7051.00
98_E124_K0.7021.00
185_E188_E0.6981.00
143_K147_T0.6951.00
27_P35_Q0.6951.00
104_P112_L0.6921.00
142_T145_I0.6911.00
111_N115_G0.6881.00
30_E33_M0.6831.00
184_E187_A0.6811.00
103_K119_D0.6781.00
19_Q35_Q0.6771.00
93_T100_D0.6751.00
98_E179_V0.6751.00
94_S97_I0.6731.00
108_A112_L0.6701.00
125_R174_D0.6701.00
170_I186_E0.6671.00
128_Y131_G0.6641.00
32_L36_F0.6591.00
92_V97_I0.6561.00
107_E111_N0.6511.00
186_E190_L0.6501.00
84_K88_E0.6501.00
120_I123_V0.6491.00
118_E122_Y0.6441.00
129_I134_L0.6391.00
180_G184_E0.6341.00
95_K98_E0.6331.00
5_Q8_A0.6331.00
41_S45_K0.6291.00
192_L196_L0.6281.00
182_L196_L0.6261.00
51_E64_I0.6241.00
152_E155_S0.6161.00
121_Y171_G0.6121.00
188_E192_L0.6071.00
8_A46_S0.6061.00
122_Y167_G0.6051.00
88_E92_V0.6051.00
43_I56_I0.6001.00
42_T46_S0.6001.00
93_T97_I0.6001.00
104_P128_Y0.5991.00
60_R63_G0.5991.00
169_K172_F0.5981.00
96_V100_D0.5971.00
82_G86_D0.5961.00
160_H163_R0.5951.00
101_V121_Y0.5931.00
182_L186_E0.5901.00
161_Y164_E0.5891.00
145_I148_Y0.5881.00
137_E140_Y0.5871.00
123_V142_T0.5871.00
87_L129_I0.5861.00
180_G183_N0.5861.00
113_N171_G0.5851.00
107_E110_E0.5841.00
133_T136_Y0.5781.00
88_E103_K0.5771.00
129_I135_C0.5771.00
33_M36_F0.5761.00
47_L58_Q0.5761.00
182_L195_G0.5711.00
28_V43_I0.5661.00
25_K62_S0.5661.00
91_N94_S0.5641.00
138_E186_E0.5641.00
20_L27_P0.5621.00
182_L187_A0.5581.00
181_Q196_L0.5581.00
104_P114_I0.5571.00
85_K88_E0.5551.00
42_T45_K0.5551.00
157_S161_Y0.5541.00
109_A113_N0.5541.00
187_A195_G0.5531.00
185_E189_Y0.5511.00
105_T109_A0.5481.00
124_K136_Y0.5461.00
112_L115_G0.5461.00
157_S162_I0.5461.00
104_P118_E0.5431.00
33_M40_K0.5431.00
103_K108_A0.5421.00
43_I46_S0.5401.00
126_V133_T0.5351.00
33_M41_S0.5351.00
169_K181_Q0.5351.00
84_K87_L0.5321.00
95_K99_L0.5311.00
97_I126_V0.5301.00
111_N124_K0.5241.00
122_Y140_Y0.5221.00
5_Q49_L0.5211.00
102_R108_A0.5201.00
70_K73_G0.5181.00
70_K74_Y0.5171.00
81_Q84_K0.5171.00
13_T16_E0.5161.00
95_K126_V0.5141.00
181_Q195_G0.5101.00
182_L190_L0.5101.00
163_R168_L0.5101.00
116_M119_D0.5091.00
104_P120_I0.5091.00
26_L43_I0.5081.00
127_R137_E0.5081.00
54_G67_R0.5051.00
7_I46_S0.5031.00
139_S142_T0.5031.00
30_E40_K0.5021.00
84_K90_F0.5021.00
70_K178_H0.5001.00
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 0.9831 100 0.122 Contact Map
3bwgA 2 0.9746 100 0.128 Contact Map
3edpA 2 0.928 100 0.148 Contact Map
3f8mA 2 0.9619 100 0.155 Contact Map
2ra5A 2 0.6271 100 0.159 Contact Map
3eetA 2 0.9661 100 0.171 Contact Map
3f8lA 2 0.678 99.9 0.453 Contact Map
1hw1A 2 0.8305 99.9 0.468 Contact Map
2di3A 2 0.8517 99.9 0.485 Contact Map
4p96A 2 0.8729 99.9 0.487 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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