GREMLIN Database
YYBE - Uncharacterized HTH-type transcriptional regulator YybE
UniProt: P37499 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 292 (283)
Sequences: 79635 (58064)
Seq/√Len: 3451.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
70_A74_E3.6081.00
15_M24_S3.3941.00
158_I287_I2.6821.00
96_G141_L2.5631.00
67_R81_E2.4391.00
11_T24_S2.2911.00
231_V238_S2.2551.00
159_K162_S2.2341.00
162_S264_V2.2231.00
92_V123_Q2.2051.00
173_H189_E2.1921.00
164_E242_D2.1761.00
159_K264_V2.1331.00
92_V121_S2.1101.00
20_K23_K2.0961.00
45_V60_Y2.0721.00
182_T185_E2.0601.00
8_Y35_S2.0541.00
162_S262_Q2.0341.00
14_R69_Q2.0311.00
232_A250_K2.0161.00
112_S285_Y2.0121.00
10_Q65_L1.9741.00
67_R74_E1.9731.00
10_Q69_Q1.9651.00
94_S123_Q1.9601.00
10_Q14_R1.9151.00
11_T14_R1.9071.00
11_T15_M1.8861.00
192_I236_G1.8831.00
166_F242_D1.8761.00
8_Y32_L1.8641.00
169_V254_I1.8631.00
71_M75_Y1.8621.00
228_A245_G1.8531.00
13_A57_L1.8461.00
65_L69_Q1.8321.00
18_V36_I1.7481.00
49_D56_S1.7421.00
190_R218_M1.7331.00
64_F78_G1.7041.00
166_F253_K1.6941.00
63_I81_E1.6761.00
157_W266_G1.6701.00
135_R140_D1.6441.00
232_A245_G1.6291.00
13_A65_L1.6081.00
15_M20_K1.5891.00
14_R24_S1.5811.00
113_F282_F1.5801.00
156_Q271_K1.5781.00
10_Q68_V1.5671.00
178_R185_E1.5641.00
9_F65_L1.5441.00
88_P119_N1.5391.00
8_Y27_I1.5281.00
134_E138_S1.5171.00
19_T29_Q1.4831.00
5_Q35_S1.4821.00
5_Q42_H1.4741.00
158_I269_W1.4741.00
113_F120_I1.4721.00
201_R205_D1.4701.00
59_Q62_H1.4651.00
67_R70_A1.4621.00
17_H20_K1.4561.00
46_P49_D1.4541.00
28_T31_A1.4471.00
5_Q38_R1.4461.00
11_T25_L1.4401.00
156_Q269_W1.4071.00
146_L268_A1.3951.00
10_Q72_M1.3911.00
67_R77_E1.3881.00
283_K287_I1.3881.00
103_T225_T1.3781.00
148_S266_G1.3751.00
275_L279_A1.3721.00
171_N250_K1.3681.00
90_Q119_N1.3491.00
71_M78_G1.3471.00
269_W283_K1.3451.00
137_K154_P1.3401.00
94_S125_K1.3361.00
136_L144_C1.3181.00
51_Q56_S1.3161.00
135_R141_L1.3131.00
281_T284_Q1.3121.00
267_I283_K1.3091.00
143_L279_A1.3021.00
112_S116_E1.2991.00
64_F79_K1.2981.00
143_L267_I1.2781.00
42_H79_K1.2781.00
169_V237_I1.2691.00
74_E77_E1.2681.00
189_E237_I1.2531.00
3_W75_Y1.2511.00
114_Q218_M1.2501.00
227_A238_S1.2421.00
66_R70_A1.2411.00
116_E285_Y1.2381.00
229_G232_A1.2321.00
114_Q190_R1.2141.00
67_R78_G1.2131.00
63_I66_R1.2051.00
159_K266_G1.1991.00
37_A41_N1.1971.00
171_N252_T1.1961.00
111_G115_Q1.1891.00
62_H66_R1.1881.00
9_F48_F1.1781.00
242_D253_K1.1721.00
245_G250_K1.1641.00
157_W268_A1.1601.00
27_I31_A1.1591.00
179_E252_T1.1531.00
174_P189_E1.1451.00
111_G233_A1.1411.00
123_Q220_E1.1341.00
34_R38_R1.1281.00
9_F13_A1.1261.00
112_S115_Q1.1241.00
127_N135_R1.1081.00
190_R216_N1.1061.00
180_S257_S1.1051.00
34_R37_A1.1001.00
9_F47_L1.0971.00
192_I227_A1.0931.00
208_F213_I1.0901.00
33_S37_A1.0901.00
284_Q287_I1.0901.00
117_Y281_T1.0891.00
93_V282_F1.0891.00
102_G126_Q1.0831.00
113_F285_Y1.0781.00
70_A77_E1.0771.00
221_G227_A1.0761.00
168_F253_K1.0731.00
18_V55_I1.0681.00
6_L68_V1.0631.00
108_D233_A1.0601.00
71_M74_E1.0591.00
12_L21_A1.0571.00
63_I67_R1.0551.00
246_L249_S1.0551.00
11_T21_A1.0551.00
270_I273_R1.0531.00
280_E284_Q1.0491.00
137_K152_E1.0451.00
7_E76_T1.0421.00
181_I185_E1.0411.00
253_K256_V1.0381.00
35_S38_R1.0281.00
229_G233_A1.0271.00
158_I283_K1.0271.00
228_A232_A1.0261.00
170_P234_G1.0251.00
4_E7_E1.0181.00
79_K83_Q1.0121.00
183_L258_W1.0091.00
57_L61_G1.0071.00
109_L286_V1.0071.00
202_M205_D1.0011.00
244_K248_Q0.9991.00
167_V237_I0.9991.00
163_E243_L0.9861.00
164_E262_Q0.9801.00
76_T80_E0.9801.00
76_T79_K0.9751.00
27_I32_L0.9701.00
13_A48_F0.9651.00
64_F68_V0.9651.00
8_Y25_L0.9641.00
73_K77_E0.9621.00
12_L18_V0.9581.00
202_M206_E0.9541.00
193_L217_I0.9511.00
135_R138_S0.9381.00
169_V173_H0.9381.00
125_K135_R0.9381.00
113_F117_Y0.9371.00
9_F57_L0.9351.00
173_H176_A0.9311.00
109_L285_Y0.9271.00
116_E288_S0.9221.00
21_A32_L0.9221.00
221_G230_F0.9201.00
38_R41_N0.9191.00
276_S279_A0.9181.00
9_F39_L0.9121.00
96_G144_C0.9071.00
48_F55_I0.9041.00
20_K24_S0.9011.00
63_I85_L0.8991.00
177_S190_R0.8971.00
45_V82_I0.8941.00
121_S216_N0.8911.00
285_Y288_S0.8861.00
173_H190_R0.8851.00
141_L144_C0.8791.00
66_R69_Q0.8741.00
13_A61_G0.8651.00
120_I278_V0.8631.00
70_A73_K0.8631.00
154_P271_K0.8611.00
16_Q56_S0.8601.00
99_H223_E0.8551.00
96_G146_L0.8531.00
174_P179_E0.8511.00
169_V174_P0.8481.00
133_L137_K0.8481.00
19_T23_K0.8471.00
190_R217_I0.8431.00
51_Q54_S0.8421.00
155_I268_A0.8371.00
25_L32_L0.8341.00
185_E188_G0.8331.00
148_S264_V0.8321.00
95_L143_L0.8261.00
245_G248_Q0.8201.00
168_F238_S0.8201.00
60_Y85_L0.8191.00
125_K141_L0.8181.00
156_Q159_K0.8151.00
284_Q288_S0.8121.00
9_F64_F0.8091.00
91_G278_V0.8071.00
207_L211_A0.8071.00
275_L280_E0.8061.00
191_F215_P0.8061.00
184_N187_A0.8031.00
60_Y82_I0.8021.00
111_G235_L0.7931.00
16_Q62_H0.7931.00
13_A16_Q0.7911.00
204_V208_F0.7891.00
4_E35_S0.7871.00
172_D176_A0.7851.00
175_L189_E0.7851.00
37_A46_P0.7831.00
29_Q33_S0.7801.00
75_Y79_K0.7781.00
14_R65_L0.7761.00
164_E260_E0.7731.00
60_Y63_I0.7711.00
74_E78_G0.7711.00
75_Y78_G0.7691.00
3_W72_M0.7691.00
77_E81_E0.7691.00
114_Q235_L0.7691.00
16_Q54_S0.7621.00
182_T257_S0.7611.00
277_P281_T0.7611.00
164_E255_R0.7581.00
12_L36_I0.7551.00
15_M21_A0.7551.00
12_L48_F0.7551.00
170_P235_L0.7541.00
89_D117_Y0.7531.00
91_G120_I0.7521.00
143_L282_F0.7511.00
232_A248_Q0.7481.00
230_F235_L0.7451.00
116_E281_T0.7431.00
5_Q8_Y0.7361.00
207_L210_K0.7351.00
7_E11_T0.7331.00
83_Q86_L0.7321.00
206_E210_K0.7301.00
68_V71_M0.7261.00
137_K155_I0.7241.00
113_F281_T0.7191.00
56_S62_H0.7171.00
170_P173_H0.7161.00
168_F240_L0.7161.00
78_G82_I0.7151.00
18_V32_L0.7131.00
49_D58_N0.7131.00
173_H177_S0.7121.00
31_A35_S0.7111.00
244_K247_D0.7091.00
57_L62_H0.7091.00
97_F102_G0.7081.00
69_Q73_K0.7081.00
223_E226_T0.7071.00
94_S141_L0.7051.00
12_L32_L0.7001.00
184_N211_A0.6961.00
273_R276_S0.6961.00
60_Y64_F0.6941.00
176_A252_T0.6941.00
203_T207_L0.6921.00
187_A213_I0.6911.00
169_V252_T0.6891.00
139_G270_I0.6811.00
62_H65_L0.6811.00
195_K220_E0.6781.00
94_S142_D0.6781.00
188_G216_N0.6701.00
59_Q63_I0.6691.00
49_D54_S0.6671.00
206_E209_E0.6671.00
281_T285_Y0.6661.00
40_E45_V0.6651.00
205_D209_E0.6651.00
180_S255_R0.6631.00
172_D175_L0.6631.00
112_S288_S0.6601.00
168_F246_L0.6591.00
64_F82_I0.6571.00
142_D279_A0.6561.00
73_K76_T0.6561.00
201_R220_E0.6561.00
219_F230_F0.6551.00
145_L286_V0.6531.00
246_L253_K0.6511.00
169_V175_L0.6501.00
77_E80_E0.6471.00
97_F106_V0.6451.00
204_V207_L0.6431.00
172_D234_G0.6431.00
7_E10_Q0.6421.00
194_L227_A0.6401.00
172_D252_T0.6381.00
93_V278_V0.6381.00
68_V72_M0.6371.00
191_F237_I0.6361.00
40_E50_R0.6341.00
23_K26_S0.6331.00
103_T229_G0.6311.00
182_T258_W0.6281.00
67_R71_M0.6261.00
121_S220_E0.6261.00
36_I40_E0.6251.00
99_H128_H0.6221.00
167_V186_I0.6201.00
171_N249_S0.6191.00
126_Q222_E0.6171.00
161_W265_I0.6141.00
21_A25_L0.6131.00
136_L268_A0.6111.00
18_V54_S0.6101.00
90_Q121_S0.6101.00
277_P280_E0.6091.00
4_E38_R0.6041.00
208_F215_P0.6021.00
202_M207_L0.6011.00
12_L17_H0.6011.00
245_G249_S0.6001.00
106_V109_L0.5991.00
80_E84_A0.5951.00
93_V143_L0.5941.00
282_F286_V0.5901.00
195_K222_E0.5891.00
63_I82_I0.5891.00
108_D111_G0.5841.00
203_T206_E0.5831.00
143_L283_K0.5821.00
156_Q272_G0.5811.00
7_E72_M0.5801.00
147_A263_R0.5791.00
31_A34_R0.5791.00
200_L204_V0.5791.00
96_G127_N0.5761.00
48_F57_L0.5721.00
221_G226_T0.5701.00
167_V239_I0.5681.00
269_W280_E0.5681.00
57_L65_L0.5681.00
30_P34_R0.5681.00
230_F236_G0.5671.00
43_L64_F0.5671.00
4_E8_Y0.5671.00
108_D112_S0.5641.00
167_V191_F0.5641.00
45_V49_D0.5641.00
43_L82_I0.5631.00
136_L155_I0.5631.00
227_A231_V0.5621.00
165_L239_I0.5611.00
126_Q223_E0.5611.00
163_E263_R0.5581.00
175_L181_I0.5551.00
110_I122_F0.5541.00
28_T34_R0.5491.00
175_L178_R0.5461.00
101_L105_L0.5461.00
96_G125_K0.5461.00
174_P178_R0.5451.00
205_D208_F0.5451.00
117_Y120_I0.5431.00
9_F61_G0.5431.00
201_R207_L0.5411.00
72_M76_T0.5401.00
173_H237_I0.5361.00
196_K220_E0.5361.00
160_L267_I0.5341.00
43_L46_P0.5321.00
8_Y36_I0.5301.00
201_R204_V0.5291.00
66_R81_E0.5281.00
18_V29_Q0.5271.00
180_S185_E0.5251.00
91_G119_N0.5251.00
115_Q176_A0.5221.00
84_A89_D0.5221.00
72_M75_Y0.5221.00
224_A241_P0.5201.00
103_T223_E0.5201.00
184_N213_I0.5171.00
46_P60_Y0.5151.00
244_K249_S0.5151.00
169_V176_A0.5151.00
27_I35_S0.5131.00
8_Y21_A0.5111.00
105_L109_L0.5101.00
279_A283_K0.5091.00
16_Q55_I0.5081.00
145_L267_I0.5071.00
148_S157_W0.5051.00
67_R82_I0.5041.00
13_A62_H0.5011.00
80_E83_Q0.5001.00
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  
1ixcA 4 0.9966 100 0.074 Contact Map
2h98A 2 0.6918 100 0.075 Contact Map
1al3A 1 0.7089 100 0.075 Contact Map
2esnA 3 0.9932 100 0.076 Contact Map
1uthA 2 0.7534 100 0.079 Contact Map
2h9bA 2 0.6918 100 0.08 Contact Map
3fxqA 3 0.9897 100 0.081 Contact Map
4x6gA 4 1 100 0.081 Contact Map
3fzvA 4 0.9726 100 0.083 Contact Map
3szpA 3 0.9829 100 0.103 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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