GREMLIN Database
YBFI - Uncharacterized HTH-type transcriptional regulator YbfI
UniProt: O31449 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 275 (240)
Sequences: 32529 (27830)
Seq/√Len: 1796.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
226_K258_V3.2021.00
222_I258_V2.9961.00
233_V241_Q2.9831.00
188_N198_K2.9781.00
211_I219_T2.9661.00
178_E220_I2.9151.00
224_Q227_K2.7881.00
176_F180_H2.7741.00
180_H183_E2.7181.00
219_T257_Q2.6011.00
254_F265_Y2.5781.00
228_L241_Q2.3551.00
225_A250_M2.3161.00
228_L242_T2.0751.00
205_F216_Y2.0721.00
173_V201_L2.0681.00
186_T189_D2.0591.00
47_Y54_E2.0571.00
233_V237_D1.9751.00
177_L217_M1.9331.00
228_L233_V1.9251.00
260_L268_I1.9101.00
176_F193_L1.9011.00
214_N218_E1.8831.00
47_Y56_I1.8701.00
234_R237_D1.8341.00
222_I257_Q1.8071.00
170_V209_K1.8031.00
142_L145_H1.7751.00
49_A54_E1.7721.00
247_Q251_T1.7521.00
187_L202_L1.7391.00
181_Y220_I1.7341.00
45_Q56_I1.7031.00
226_K265_Y1.7011.00
200_H204_S1.6651.00
174_C209_K1.6631.00
224_Q228_L1.6581.00
253_F256_R1.6571.00
145_H149_E1.6301.00
173_V194_T1.6291.00
58_N61_D1.6201.00
236_I247_Q1.6141.00
229_L235_P1.6041.00
198_K202_L1.5961.00
190_L213_P1.5931.00
175_E179_E1.5831.00
49_A72_S1.5561.00
176_F185_V1.5511.00
227_K231_Q1.5511.00
200_H203_R1.5391.00
43_K82_D1.5351.00
42_E84_R1.5341.00
211_I215_S1.5191.00
237_D241_Q1.5141.00
120_T124_Q1.4961.00
36_Y67_P1.4741.00
244_F253_F1.4701.00
236_I240_F1.4621.00
249_H253_F1.4551.00
220_I224_Q1.4471.00
201_L213_P1.4471.00
196_W200_H1.4461.00
260_L264_Q1.4351.00
45_Q58_N1.4341.00
237_D240_F1.4321.00
47_Y74_E1.4291.00
263_K267_K1.4271.00
181_Y224_Q1.4221.00
225_A242_T1.4211.00
248_S251_T1.4001.00
167_S208_Q1.3981.00
213_P217_M1.3961.00
238_A242_T1.3951.00
178_E216_Y1.3701.00
141_E145_H1.3551.00
51_Q69_D1.3451.00
224_Q242_T1.3401.00
173_V190_L1.3381.00
196_W201_L1.3331.00
251_T261_T1.3061.00
66_N69_D1.3031.00
197_S200_H1.2981.00
232_G266_M1.2961.00
188_N192_E1.2941.00
189_D193_L1.2921.00
202_L213_P1.2911.00
219_T223_N1.2891.00
177_L220_I1.2821.00
218_E253_F1.2811.00
174_C178_E1.2811.00
141_E144_L1.2791.00
251_T263_K1.2781.00
182_A241_Q1.2761.00
212_T215_S1.2581.00
199_Y203_R1.2571.00
220_I223_N1.2051.00
43_K59_P1.1851.00
183_E189_D1.1701.00
141_E148_E1.1591.00
42_E82_D1.1521.00
121_A125_E1.1391.00
33_H71_H1.1251.00
121_A124_Q1.1241.00
226_K230_E1.1211.00
191_S198_K1.1161.00
31_H71_H1.1131.00
169_E204_S1.1071.00
148_E152_R1.0891.00
138_R142_L1.0851.00
252_K256_R1.0841.00
204_S207_K1.0771.00
37_V71_H1.0701.00
113_V116_R1.0691.00
149_E153_H1.0681.00
215_S218_E1.0661.00
185_V190_L1.0621.00
264_Q267_K1.0581.00
169_E196_W1.0491.00
233_V238_A1.0421.00
232_G238_A1.0371.00
30_N70_T1.0361.00
33_H37_V1.0361.00
261_T264_Q1.0331.00
235_P238_A1.0191.00
182_A224_Q1.0181.00
187_L213_P1.0111.00
138_R145_H1.0041.00
263_K266_M1.0011.00
223_N226_K0.9961.00
49_A74_E0.9821.00
204_S208_Q0.9811.00
246_D252_K0.9771.00
189_D192_E0.9771.00
187_L198_K0.9761.00
168_D172_M0.9661.00
251_T255_K0.9641.00
171_K175_E0.9621.00
199_Y202_L0.9581.00
228_L238_A0.9551.00
176_F190_L0.9481.00
46_R81_L0.9471.00
145_H148_E0.9441.00
184_N245_S0.9331.00
144_L148_E0.9321.00
190_L193_L0.9281.00
50_C53_Q0.9201.00
140_E144_L0.9181.00
174_C216_Y0.9151.00
194_T201_L0.9081.00
249_H252_K0.9051.00
169_E194_T0.9041.00
41_I46_R0.9021.00
253_F257_Q0.8981.00
124_Q128_I0.8961.00
47_Y76_I0.8871.00
214_N249_H0.8801.00
41_I44_G0.8781.00
176_F194_T0.8751.00
226_K254_F0.8741.00
181_Y185_V0.8731.00
264_Q268_I0.8691.00
172_M193_L0.8651.00
170_V173_V0.8571.00
45_Q76_I0.8521.00
215_S257_Q0.8441.00
218_E256_R0.8441.00
118_E121_A0.8401.00
218_E257_Q0.8391.00
117_H121_A0.8351.00
37_V87_N0.8331.00
215_S219_T0.8311.00
81_L85_C0.8291.00
170_V204_S0.8281.00
36_Y64_L0.8251.00
222_I250_M0.8231.00
205_F209_K0.8221.00
177_L213_P0.8211.00
221_R242_T0.8181.00
258_V265_Y0.8141.00
30_N72_S0.8111.00
181_Y217_M0.8051.00
173_V176_F0.7961.00
214_N217_M0.7951.00
184_N189_D0.7891.00
222_I253_F0.7881.00
255_K261_T0.7851.00
190_L201_L0.7821.00
125_E142_L0.7791.00
117_H120_T0.7761.00
196_W204_S0.7741.00
39_G85_C0.7721.00
46_R57_I0.7671.00
229_L266_M0.7641.00
260_L265_Y0.7631.00
172_M175_E0.7601.00
43_K80_T0.7591.00
95_K99_E0.7581.00
180_H189_D0.7541.00
225_A228_L0.7521.00
136_A140_E0.7521.00
125_E129_L0.7511.00
167_S204_S0.7491.00
40_F62_L0.7481.00
216_Y220_I0.7461.00
105_H108_Y0.7461.00
142_L149_E0.7451.00
90_P94_E0.7391.00
171_K174_C0.7361.00
172_M194_T0.7321.00
229_L238_A0.7281.00
127_H131_S0.7271.00
104_G107_P0.7251.00
245_S249_H0.7251.00
170_V174_C0.7241.00
205_F213_P0.7221.00
181_Y242_T0.7211.00
166_P207_K0.7201.00
240_F245_S0.7191.00
185_V189_D0.7191.00
94_E98_K0.7181.00
255_K264_Q0.7181.00
170_V208_Q0.7171.00
239_A247_Q0.7171.00
173_V205_F0.7141.00
57_I63_L0.7131.00
149_E152_R0.7111.00
173_V213_P0.7071.00
234_R238_A0.7061.00
250_M254_F0.6961.00
202_L206_T0.6931.00
246_D249_H0.6901.00
180_H193_L0.6831.00
202_L212_T0.6791.00
82_D85_C0.6761.00
46_R56_I0.6741.00
222_I244_F0.6711.00
118_E122_S0.6711.00
247_Q250_M0.6701.00
138_R148_E0.6681.00
135_Q139_K0.6661.00
125_E128_I0.6651.00
177_L216_Y0.6601.00
49_A52_D0.6591.00
125_E145_H0.6561.00
206_T212_T0.6561.00
137_L141_E0.6531.00
238_A266_M0.6521.00
137_L144_L0.6511.00
118_E125_E0.6461.00
202_L214_N0.6421.00
218_E249_H0.6411.00
118_E149_E0.6411.00
230_E265_Y0.6411.00
38_I62_L0.6391.00
167_S171_K0.6391.00
83_Y86_I0.6381.00
116_R120_T0.6371.00
96_A99_E0.6361.00
39_G65_F0.6321.00
48_L63_L0.6311.00
128_I132_E0.6291.00
169_E172_M0.6281.00
129_L133_E0.6241.00
95_K98_K0.6241.00
138_R141_E0.6221.00
178_E224_Q0.6211.00
235_P263_K0.6191.00
211_I216_Y0.6171.00
85_C88_V0.6161.00
41_I57_I0.6141.00
138_R152_R0.6131.00
150_L154_Y0.6131.00
39_G83_Y0.6131.00
228_L231_Q0.6121.00
41_I83_Y0.6121.00
65_F71_H0.6101.00
187_L214_N0.6081.00
97_V100_I0.6031.00
51_Q70_T0.6031.00
32_F70_T0.6021.00
137_L140_E0.6021.00
223_N257_Q0.6021.00
239_A244_F0.6011.00
191_S194_T0.6001.00
115_F118_E0.5991.00
46_R73_C0.5971.00
122_S125_E0.5971.00
121_A128_I0.5951.00
89_M92_I0.5931.00
122_S126_L0.5931.00
217_M221_R0.5921.00
38_I64_L0.5901.00
185_V221_R0.5881.00
203_R207_K0.5881.00
209_K216_Y0.5871.00
173_V193_L0.5871.00
173_V177_L0.5851.00
137_L148_E0.5841.00
113_V117_H0.5821.00
254_F260_L0.5771.00
248_S261_T0.5711.00
225_A238_A0.5701.00
170_V201_L0.5701.00
118_E128_I0.5681.00
96_A101_T0.5671.00
111_Q115_F0.5671.00
223_N258_V0.5671.00
97_V101_T0.5631.00
40_F123_L0.5621.00
250_M262_P0.5621.00
190_L194_T0.5611.00
143_F150_L0.5611.00
166_P169_E0.5611.00
146_L149_E0.5591.00
244_F249_H0.5571.00
217_M220_I0.5551.00
45_Q77_D0.5551.00
185_V217_M0.5551.00
73_C83_Y0.5541.00
177_L185_V0.5511.00
127_H130_I0.5471.00
164_P167_S0.5461.00
126_L129_L0.5451.00
96_A100_I0.5431.00
254_F258_V0.5411.00
194_T198_K0.5401.00
166_P200_H0.5381.00
61_D110_S0.5351.00
181_Y221_R0.5341.00
39_G63_L0.5301.00
34_D89_M0.5291.00
192_E195_G0.5271.00
248_S252_K0.5251.00
111_Q114_L0.5241.00
54_E74_E0.5241.00
152_R156_D0.5231.00
143_F147_L0.5221.00
176_F189_D0.5201.00
41_I81_L0.5201.00
139_K142_L0.5191.00
174_C205_F0.5181.00
180_H185_V0.5171.00
146_L150_L0.5171.00
84_R87_N0.5161.00
138_R149_E0.5151.00
155_S159_F0.5141.00
175_E178_E0.5131.00
147_L150_L0.5111.00
201_L204_S0.5081.00
34_D68_R0.5081.00
145_H152_R0.5071.00
206_T209_K0.5071.00
39_G48_L0.5071.00
122_S142_L0.5051.00
35_Y87_N0.5051.00
168_D171_K0.5051.00
114_L118_E0.5031.00
166_P208_Q0.5021.00
103_S106_L0.5001.00
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 0.8909 100 0.24 Contact Map
1bl0A 1 0.4 100 0.477 Contact Map
3oouA 1 0.3782 100 0.481 Contact Map
3mn2A 1 0.3818 100 0.482 Contact Map
3oioA 1 0.4036 100 0.484 Contact Map
3w6vA 1 0.3964 99.9 0.491 Contact Map
3mklA 1 0.4 99.9 0.492 Contact Map
2k9sA 1 0.3818 99.9 0.493 Contact Map
3lsgA 2 0.3673 99.9 0.502 Contact Map
1d5yA 1 0.4 99.9 0.509 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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