GREMLIN Database
YDEE - Uncharacterized HTH-type transcriptional regulator YdeE
UniProt: P96662 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 290 (274)
Sequences: 2950 (2224)
Seq/√Len: 134.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
17_N20_N6.7181.00
62_A88_F4.9141.00
65_E80_Y4.0531.00
65_E79_K3.9121.00
13_Y17_N3.6651.00
25_Q35_E3.5801.00
137_A222_E3.4951.00
71_V79_K3.1431.00
139_R220_R3.0501.00
72_K75_D2.9041.00
10_A38_F2.9041.00
71_V76_I2.8781.00
66_L73_V2.8751.00
234_I280_K2.7361.00
23_D26_E2.6871.00
134_E227_T2.6841.00
14_I54_I2.5731.00
232_E282_E2.5701.00
74_I78_I2.5421.00
26_E29_K2.4831.00
84_S87_S2.3841.00
42_F53_Y2.2971.00
137_A225_A2.2501.00
69_S104_R2.2351.00
59_L95_L2.2271.00
139_R222_E2.1921.00
89_A99_N2.1741.00
233_S244_V2.1571.00
76_I104_R2.1011.00
144_K203_D2.0941.00
231_F248_I2.0711.00
74_I85_P2.0641.00
227_T258_Y2.0501.00
15_E57_R2.0341.00
85_P89_A2.0231.00
10_A30_L1.9881.00
65_E71_V1.9571.00
157_E160_S1.9131.00
247_R251_E1.8981.00
226_S261_I1.8291.00
232_E280_K1.7921.00
69_S76_I1.7911.00
252_W256_S1.7701.00
19_T61_L1.7521.00
124_G128_M1.7391.00
53_Y57_R1.7121.00
48_I56_R1.6941.00
145_K164_S1.6881.00
229_A252_W1.6721.00
253_F256_S1.6711.00
15_E53_Y1.6511.00
18_L61_L1.6341.00
18_L57_R1.6301.00
14_I22_I1.5991.00
144_K219_S1.5221.00
19_T79_K1.5141.00
27_A30_L1.4811.00
13_Y30_L1.4711.00
163_E167_E1.4501.00
249_Y260_Q1.4461.00
245_W283_I1.4451.00
140_I205_Y1.4311.00
10_A27_A1.4201.00
266_I284_W1.4191.00
186_S204_H1.4041.00
129_N232_E1.3991.00
215_P218_F1.3821.00
268_W282_E1.3791.00
24_F39_K1.3691.00
83_N87_S1.3501.00
102_K106_N1.3351.00
272_K279_F1.3301.00
130_Y231_F1.3271.00
102_K105_F1.3221.00
230_V284_W1.3191.00
6_S32_F1.3161.00
78_I85_P1.3141.00
87_S91_A1.2941.00
134_E225_A1.2631.00
138_F223_V1.2631.00
6_S9_R1.2611.00
71_V75_D1.2541.00
131_R230_V1.2481.00
142_G205_Y1.2371.00
50_L54_I1.2251.00
43_S49_S1.2171.00
7_M46_A1.1840.99
205_Y210_T1.1750.99
186_S269_N1.1720.99
59_L96_H1.1650.99
52_E56_R1.1590.99
9_R30_L1.1580.99
246_G250_S1.1540.99
63_A103_A1.1470.99
31_A38_F1.1380.99
73_V101_S1.1260.99
192_S201_E1.1030.99
51_S54_I1.1030.99
274_V279_F1.0790.99
146_R201_E1.0780.99
74_I86_D1.0600.99
168_K171_N1.0520.99
240_T243_E1.0510.99
226_S263_G1.0460.99
125_G128_M1.0390.99
160_S163_E1.0330.99
136_E225_A1.0290.98
37_H40_R1.0270.98
93_Q99_N1.0270.98
142_G221_L1.0250.98
183_G268_W1.0220.98
25_Q29_K1.0220.98
234_I278_S1.0190.98
36_Y40_R1.0170.98
37_H41_M1.0110.98
251_E287_I1.0110.98
165_L169_A1.0090.98
276_S279_F1.0090.98
85_P101_S1.0080.98
61_L80_Y1.0040.98
270_E280_K0.9950.98
123_K128_M0.9920.98
88_F92_F0.9900.98
133_E230_V0.9890.98
161_M165_L0.9850.98
75_D78_I0.9840.98
253_F260_Q0.9830.98
39_K51_S0.9830.98
275_T278_S0.9800.98
141_V218_F0.9720.98
89_A100_P0.9700.98
56_R60_T0.9580.98
186_S267_L0.9580.98
26_E30_L0.9550.98
20_N26_E0.9550.98
135_K138_F0.9550.98
243_E247_R0.9540.98
92_F100_P0.9530.98
202_L207_G0.9520.98
271_H279_F0.9480.97
56_R95_L0.9460.97
52_E55_R0.9450.97
73_V76_I0.9420.97
248_I285_I0.9400.97
12_K16_E0.9370.97
273_D276_S0.9350.97
4_L8_N0.9300.97
154_I159_A0.9250.97
196_T199_N0.9220.97
24_F35_E0.9190.97
86_D89_A0.9150.97
11_L53_Y0.9120.97
178_N211_T0.9120.97
5_K9_R0.9110.97
186_S202_L0.9110.97
143_I169_A0.9040.97
236_P239_D0.9010.97
9_R12_K0.9000.96
168_K218_F0.8980.96
200_G204_H0.8890.96
188_S202_L0.8850.96
164_S168_K0.8800.96
236_P240_T0.8800.96
126_N129_N0.8790.96
200_G207_G0.8770.96
9_R31_A0.8730.96
190_N201_E0.8640.96
258_Y287_I0.8620.96
10_A31_A0.8590.95
53_Y60_T0.8520.95
23_D82_Y0.8500.95
175_E178_N0.8410.95
51_S55_R0.8370.95
11_L15_E0.8350.95
143_I161_M0.8220.94
165_L184_L0.8130.94
248_I283_I0.8130.94
74_I84_S0.8120.94
93_Q102_K0.8120.94
143_I164_S0.8120.94
36_Y127_E0.8100.94
158_I162_W0.8050.94
224_P263_G0.8020.93
204_H207_G0.8000.93
244_V283_I0.7990.93
245_W285_I0.7990.93
141_V210_T0.7880.93
274_V278_S0.7860.93
137_A224_P0.7860.93
22_I26_E0.7840.93
275_T287_I0.7820.93
130_Y229_A0.7790.92
13_Y22_I0.7770.92
48_I113_Y0.7710.92
171_N175_E0.7690.92
236_P276_S0.7660.92
245_W281_S0.7660.92
135_K284_W0.7660.92
245_W265_E0.7640.92
73_V104_R0.7630.92
92_F103_A0.7630.92
162_W269_N0.7620.92
98_I103_A0.7600.91
233_S281_S0.7520.91
18_L54_I0.7510.91
177_S180_A0.7500.91
14_I17_N0.7490.91
140_I187_A0.7480.91
159_A162_W0.7480.91
11_L46_A0.7440.91
144_K205_Y0.7430.91
160_S164_S0.7380.90
270_E281_S0.7330.90
241_L252_W0.7310.90
252_W258_Y0.7210.89
205_Y219_S0.7190.89
62_A181_P0.7150.89
271_H276_S0.7130.89
57_R80_Y0.7130.89
33_C38_F0.7130.89
254_P257_N0.7110.89
251_E255_S0.7110.89
84_S90_R0.7110.89
239_D243_E0.7080.88
171_N174_K0.7060.88
273_D279_F0.7050.88
260_Q265_E0.7040.88
55_R91_A0.7020.88
14_I50_L0.7010.88
93_Q119_Q0.7000.88
36_Y91_A0.6980.88
11_L42_F0.6980.88
25_Q78_I0.6960.87
162_W186_S0.6960.87
82_Y113_Y0.6960.87
155_N242_Q0.6890.87
9_R16_E0.6880.87
241_L245_W0.6880.87
13_Y27_A0.6830.87
165_L185_I0.6790.86
61_L65_E0.6780.86
84_S108_H0.6780.86
38_F101_S0.6770.86
185_I188_S0.6760.86
12_K115_R0.6700.85
27_A31_A0.6700.85
86_D90_R0.6680.85
237_F241_L0.6670.85
133_E284_W0.6660.85
162_W166_D0.6650.85
143_I165_L0.6630.85
213_R220_R0.6600.85
142_G219_S0.6590.85
33_C41_M0.6590.85
47_G246_G0.6580.84
83_N86_D0.6560.84
142_G207_G0.6550.84
58_R80_Y0.6540.84
111_K116_M0.6530.84
67_K107_G0.6530.84
103_A110_L0.6500.84
72_K89_A0.6490.84
231_F247_R0.6480.84
39_K49_S0.6460.83
26_E54_I0.6440.83
82_Y87_S0.6410.83
63_A92_F0.6400.83
233_S241_L0.6390.83
55_R60_T0.6370.82
235_G241_L0.6370.82
189_T192_S0.6350.82
61_L64_F0.6350.82
9_R275_T0.6350.82
235_G281_S0.6340.82
123_K127_E0.6340.82
145_K161_M0.6330.82
96_H111_K0.6320.82
15_E110_L0.6310.82
162_W204_H0.6310.82
22_I28_A0.6310.82
185_I209_A0.6300.82
31_A37_H0.6280.82
45_L250_S0.6270.81
6_S27_A0.6270.81
37_H248_I0.6260.81
147_V158_I0.6250.81
132_I229_A0.6250.81
167_E170_I0.6230.81
275_T279_F0.6230.81
240_T244_V0.6230.81
82_Y103_A0.6220.81
117_T120_L0.6180.81
147_V191_F0.6170.80
244_V248_I0.6160.80
103_A130_Y0.6150.80
59_L91_A0.6120.80
255_S287_I0.6110.80
43_S102_K0.6110.80
170_I174_K0.6100.80
66_L76_I0.6090.80
60_T96_H0.6080.79
14_I27_A0.6060.79
51_S85_P0.6060.79
57_R60_T0.6030.79
53_Y82_Y0.6020.79
27_A61_L0.6020.79
59_L248_I0.6000.79
82_Y93_Q0.6000.79
76_I121_T0.5990.78
146_R149_I0.5980.78
112_A115_R0.5960.78
24_F50_L0.5960.78
13_Y68_D0.5950.78
135_K228_W0.5950.78
177_S181_P0.5950.78
278_S281_S0.5940.78
82_Y96_H0.5940.78
189_T221_L0.5940.78
57_R142_G0.5930.78
9_R117_T0.5920.78
39_K249_Y0.5920.78
60_T64_F0.5920.78
101_S105_F0.5890.77
261_I286_P0.5890.77
132_I258_Y0.5870.77
230_V282_E0.5860.77
146_R203_D0.5850.77
185_I207_G0.5830.77
154_I183_G0.5810.76
67_K106_N0.5810.76
73_V260_Q0.5790.76
21_D81_G0.5790.76
65_E96_H0.5730.75
51_S86_D0.5690.75
159_A166_D0.5690.75
245_W286_P0.5690.75
120_L123_K0.5680.75
22_I27_A0.5670.75
17_N22_I0.5670.75
189_T205_Y0.5660.74
156_P160_S0.5650.74
6_S33_C0.5650.74
245_W249_Y0.5630.74
33_C265_E0.5620.74
214_C220_R0.5620.74
158_I186_S0.5600.74
35_E39_K0.5580.73
63_A112_A0.5570.73
17_N149_I0.5570.73
259_E283_I0.5570.73
190_N203_D0.5560.73
191_F201_E0.5550.73
36_Y39_K0.5550.73
158_I204_H0.5550.73
231_F244_V0.5540.73
34_S40_R0.5540.73
78_I86_D0.5540.73
212_K216_D0.5520.73
55_R96_H0.5520.73
165_L206_I0.5510.73
132_I227_T0.5490.72
24_F27_A0.5490.72
155_N158_I0.5480.72
191_F198_E0.5460.72
188_S267_L0.5460.72
138_F183_G0.5440.72
7_M33_C0.5420.71
27_A232_E0.5400.71
202_L206_I0.5390.71
134_E278_S0.5380.71
37_H249_Y0.5370.71
187_A221_L0.5360.70
29_K122_I0.5360.70
24_F38_F0.5340.70
233_S283_I0.5340.70
39_K90_R0.5330.70
147_V253_F0.5320.70
156_P159_A0.5310.70
119_Q123_K0.5300.70
130_Y252_W0.5290.69
31_A41_M0.5290.69
216_D219_S0.5280.69
124_G251_E0.5260.69
159_A186_S0.5260.69
274_V281_S0.5240.69
180_A217_N0.5240.69
27_A54_I0.5210.68
174_K177_S0.5200.68
237_F281_S0.5190.68
191_F265_E0.5190.68
59_L74_I0.5170.68
164_S256_S0.5170.68
202_L241_L0.5170.68
64_F68_D0.5160.68
45_L94_N0.5150.67
64_F67_K0.5140.67
271_H281_S0.5140.67
204_H269_N0.5130.67
268_W284_W0.5130.67
55_R94_N0.5120.67
158_I164_S0.5110.67
132_I287_I0.5110.67
130_Y256_S0.5100.67
203_D212_K0.5100.67
55_R59_L0.5080.66
34_S37_H0.5080.66
253_F285_I0.5060.66
66_L104_R0.5060.66
43_S103_A0.5030.66
67_K255_S0.5000.65
168_K176_L0.5000.65
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  
1d5yA 1 0.9517 100 0.301 Contact Map
3gbgA 1 0.3759 100 0.559 Contact Map
4fe7A 2 0.3759 100 0.574 Contact Map
3oioA 1 0.3828 100 0.58 Contact Map
1bl0A 1 0.4 100 0.58 Contact Map
3mn2A 1 0.3655 100 0.582 Contact Map
3w6vA 1 0.3828 100 0.582 Contact Map
2k9sA 1 0.3655 100 0.583 Contact Map
3oouA 1 0.3621 100 0.587 Contact Map
3lsgA 2 0.3517 99.9 0.59 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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