GREMLIN Database
YDEO - HTH-type transcriptional regulator YdeO
UniProt: P76135 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13797
Length: 253 (223)
Sequences: 34216 (29426)
Seq/√Len: 1970.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
191_K223_F3.2331.00
176_T184_D3.1841.00
144_N185_A3.0001.00
187_M223_F2.8521.00
142_I146_K2.7631.00
189_H192_N2.7331.00
154_K164_E2.7121.00
184_D222_H2.5011.00
146_K149_H2.4841.00
219_F230_V2.4791.00
139_V167_L2.2461.00
190_A215_F2.1621.00
193_L206_Q2.1551.00
171_L181_I2.1181.00
147_P185_A2.0131.00
193_L207_C1.9681.00
225_N233_E1.9461.00
152_K155_D1.9441.00
15_N22_D1.8501.00
142_I159_C1.8441.00
179_S183_L1.7981.00
143_V182_L1.7831.00
187_M222_H1.7811.00
139_V160_L1.7701.00
140_R174_E1.7351.00
212_T216_I1.7021.00
199_S202_K1.6911.00
15_N24_A1.6891.00
156_I178_F1.6581.00
191_K230_V1.6541.00
153_L168_K1.6461.00
141_N145_M1.6421.00
17_N22_D1.6241.00
136_S174_E1.6161.00
166_L170_K1.6101.00
110_L113_S1.5771.00
192_N196_V1.5691.00
11_H47_H1.5671.00
218_A221_K1.5641.00
109_L116_S1.5571.00
13_A24_A1.5481.00
189_H193_L1.5471.00
26_S29_E1.5331.00
176_T180_Q1.5261.00
142_I151_W1.5201.00
167_L178_F1.5151.00
201_N212_T1.5101.00
185_A189_H1.4971.00
178_F182_L1.4801.00
109_L113_S1.4771.00
225_N229_R1.4591.00
214_Y218_A1.4521.00
144_N181_I1.4501.00
194_I200_V1.4451.00
147_P189_H1.4401.00
10_I49_K1.4361.00
116_S120_A1.4281.00
228_K232_K1.4231.00
166_L169_K1.4221.00
202_K205_E1.4181.00
164_E168_K1.4131.00
113_S117_I1.4061.00
13_A26_S1.3991.00
201_N205_E1.3911.00
148_A206_Q1.3851.00
143_V185_A1.3831.00
139_V156_I1.3741.00
168_K178_F1.3711.00
190_A207_C1.3571.00
162_I166_L1.3571.00
165_S169_K1.3561.00
112_F116_S1.3501.00
140_R144_N1.3461.00
209_Y218_A1.3411.00
17_N40_H1.3401.00
203_I207_C1.3161.00
184_D188_Q1.3101.00
154_K158_D1.3091.00
202_K206_Q1.3021.00
189_H207_C1.2941.00
197_E231_S1.2891.00
90_N94_A1.2791.00
177_T180_Q1.2681.00
213_S216_I1.2651.00
19_L37_V1.2631.00
155_D159_C1.2611.00
34_D37_V1.2571.00
183_L218_A1.2411.00
149_H155_D1.2401.00
86_T90_N1.2241.00
185_A188_Q1.2021.00
216_I226_S1.1691.00
216_I228_K1.1541.00
163_S166_L1.1521.00
11_H27_D1.1491.00
135_V162_I1.1441.00
217_Y221_K1.1441.00
162_I167_L1.1411.00
191_K195_R1.1411.00
99_E103_H1.1371.00
109_L112_F1.1271.00
188_Q191_K1.1091.00
211_S217_Y1.0991.00
157_C164_E1.0901.00
15_N42_E1.0851.00
142_I160_L1.0821.00
153_L178_F1.0821.00
229_R232_K1.0761.00
91_E95_Y1.0701.00
151_W156_I1.0621.00
197_E203_I1.0581.00
148_A189_H1.0521.00
134_S138_K1.0491.00
200_V203_I1.0421.00
29_E80_R1.0421.00
183_L221_K1.0281.00
106_F113_S1.0241.00
170_K173_Q1.0231.00
156_I159_C1.0221.00
135_V160_L1.0151.00
228_K231_S1.0151.00
226_S229_R1.0081.00
193_L203_I1.0061.00
137_G141_N0.9901.00
10_I47_H0.9841.00
180_Q183_L0.9821.00
216_I220_R0.9781.00
87_G90_N0.9761.00
138_K159_C0.9741.00
95_Y99_E0.9701.00
150_P155_D0.9691.00
155_D158_D0.9691.00
135_V170_K0.9681.00
140_R181_I0.9661.00
81_A85_P0.9631.00
150_P210_A0.9601.00
218_A222_H0.9371.00
191_K219_F0.9331.00
108_E112_F0.9321.00
180_Q184_D0.9281.00
165_S168_K0.9201.00
143_V178_F0.9161.00
9_F14_F0.9141.00
142_I156_I0.9061.00
87_G91_E0.9041.00
105_N109_L0.9011.00
106_F110_L0.8951.00
18_I21_K0.8921.00
153_L164_E0.8921.00
17_N20_D0.8891.00
147_P151_W0.8881.00
223_F230_V0.8851.00
160_L167_L0.8841.00
136_S170_K0.8781.00
186_R207_C0.8751.00
187_M218_A0.8741.00
171_L178_F0.8671.00
179_S214_Y0.8641.00
138_K141_N0.8641.00
138_K160_L0.8551.00
75_P78_F0.8541.00
113_S116_S0.8501.00
183_L222_H0.8481.00
229_R233_E0.8471.00
214_Y217_Y0.8451.00
14_F25_F0.8371.00
162_I170_K0.8321.00
137_G140_R0.8311.00
179_S182_L0.8201.00
33_V39_T0.8181.00
147_P182_L0.8171.00
146_K159_C0.8081.00
220_R226_S0.8061.00
136_S139_V0.8041.00
105_N108_E0.8031.00
194_I203_I0.7951.00
14_F24_A0.7911.00
91_E94_A0.7911.00
195_R230_V0.7891.00
140_R171_L0.7861.00
194_I231_S0.7861.00
16_A31_L0.7841.00
55_E59_K0.7781.00
168_K177_T0.7771.00
180_Q222_H0.7761.00
187_M215_F0.7731.00
78_F81_A0.7701.00
205_E210_A0.7691.00
181_I185_A0.7661.00
146_K155_D0.7601.00
139_V142_I0.7591.00
168_K172_K0.7571.00
135_V138_K0.7551.00
77_K80_R0.7541.00
143_V181_I0.7541.00
190_A193_L0.7541.00
171_L174_E0.7521.00
100_E103_H0.7501.00
105_N116_S0.7491.00
133_L170_K0.7481.00
147_P207_C0.7471.00
225_N230_V0.7461.00
88_L91_E0.7421.00
8_I30_I0.7421.00
130_N133_L0.7371.00
156_I167_L0.7331.00
13_A44_Y0.7321.00
147_P186_R0.7271.00
106_F116_S0.7261.00
220_R229_R0.7261.00
88_L96_L0.7231.00
136_S140_R0.7231.00
78_F85_P0.7181.00
139_V171_L0.7121.00
210_A214_Y0.7121.00
88_L95_Y0.7021.00
82_S85_P0.7011.00
169_K173_Q0.7001.00
99_E102_N0.6971.00
139_V178_F0.6961.00
94_A98_S0.6951.00
7_V50_E0.6941.00
204_A212_T0.6911.00
14_F41_F0.6891.00
212_T215_F0.6891.00
106_F109_L0.6881.00
15_N44_Y0.6851.00
168_K179_S0.6781.00
211_S214_Y0.6771.00
106_F120_A0.6771.00
213_S226_S0.6731.00
176_T181_I0.6711.00
203_I231_S0.6631.00
43_P46_R0.6611.00
25_F31_L0.6591.00
215_F219_F0.6581.00
151_W186_R0.6571.00
117_I121_C0.6571.00
9_F48_F0.6501.00
59_K63_Q0.6501.00
79_L85_P0.6471.00
16_A39_T0.6461.00
215_F227_P0.6421.00
151_W155_D0.6401.00
183_L214_Y0.6371.00
41_F48_F0.6351.00
153_L179_S0.6331.00
172_K177_T0.6321.00
57_T60_K0.6281.00
56_N59_K0.6281.00
18_I33_V0.6261.00
136_S167_L0.6231.00
188_Q223_F0.6221.00
193_L196_V0.6221.00
96_L99_E0.6221.00
144_N189_H0.6191.00
7_V16_A0.6181.00
187_M209_Y0.6161.00
190_A203_I0.6161.00
194_I230_V0.6141.00
213_S217_Y0.6131.00
41_F50_E0.6121.00
183_L187_M0.6111.00
7_V48_F0.6101.00
9_F25_F0.6091.00
198_G203_I0.6081.00
7_V33_V0.6051.00
42_E45_E0.6031.00
76_A80_R0.6001.00
60_K63_Q0.5991.00
107_S110_L0.5991.00
117_I120_A0.5981.00
199_S203_I0.5981.00
139_V159_C0.5961.00
219_F225_N0.5951.00
188_Q222_H0.5951.00
115_L118_F0.5931.00
156_I160_L0.5931.00
92_M96_L0.5921.00
139_V143_V0.5871.00
151_W182_L0.5871.00
157_C160_L0.5861.00
81_A84_V0.5851.00
211_S221_K0.5851.00
158_D161_Y0.5841.00
74_V77_K0.5821.00
7_V31_L0.5801.00
92_M95_Y0.5791.00
16_A41_F0.5761.00
142_I155_D0.5751.00
74_V81_A0.5741.00
132_V173_Q0.5681.00
167_L174_E0.5671.00
47_H50_E0.5631.00
94_A97_N0.5591.00
153_L165_S0.5561.00
80_R85_P0.5541.00
143_V151_W0.5531.00
174_E181_I0.5521.00
192_N195_R0.5501.00
141_N144_N0.5471.00
200_V228_K0.5461.00
73_P77_K0.5451.00
209_Y214_Y0.5421.00
213_S220_R0.5401.00
146_K151_W0.5401.00
191_K225_N0.5391.00
183_L209_Y0.5381.00
109_L118_F0.5351.00
107_S118_F0.5351.00
93_I96_L0.5341.00
83_N86_T0.5341.00
87_G94_A0.5321.00
139_V170_K0.5311.00
182_L186_R0.5311.00
219_F223_F0.5301.00
105_N112_F0.5291.00
182_L185_A0.5271.00
10_I90_N0.5241.00
180_Q221_K0.5241.00
111_L115_L0.5231.00
143_V156_I0.5211.00
48_F52_G0.5211.00
194_I197_E0.5201.00
107_S111_L0.5191.00
16_A33_V0.5181.00
156_I186_R0.5181.00
101_R104_H0.5131.00
35_N40_H0.5081.00
201_N213_S0.5061.00
88_L117_I0.5041.00
188_Q192_N0.5021.00
136_S160_L0.5021.00
113_S120_A0.5001.00
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  
3gbgA 1 0.9051 100 0.237 Contact Map
3mklA 1 0.4348 99.9 0.47 Contact Map
3oouA 1 0.4071 99.9 0.474 Contact Map
3mn2A 1 0.4111 99.9 0.476 Contact Map
1bl0A 1 0.4506 99.9 0.476 Contact Map
3w6vA 1 0.4308 99.9 0.482 Contact Map
3oioA 1 0.4348 99.9 0.483 Contact Map
2k9sA 1 0.4111 99.9 0.487 Contact Map
3lsgA 2 0.3953 99.9 0.495 Contact Map
4fe7A 2 0.8775 99.9 0.505 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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