GREMLIN Database
YBCM - Uncharacterized HTH-type transcriptional regulator YbcM
UniProt: P77634 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13629
Length: 265 (231)
Sequences: 36183 (30097)
Seq/√Len: 1980.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
204_V212_D3.2551.00
219_L252_F3.2221.00
172_L213_V3.0411.00
215_L252_F2.9841.00
227_K235_E2.9241.00
170_L174_E2.8091.00
217_N220_S2.7771.00
182_N192_V2.7351.00
212_D251_R2.5991.00
248_F259_I2.5501.00
174_E177_T2.5441.00
167_C195_L2.2521.00
218_A244_F2.2281.00
221_A235_E2.2161.00
199_L209_I2.1911.00
221_A236_N2.0211.00
175_P213_V1.9841.00
180_T183_K1.9691.00
227_K231_E1.9441.00
168_Y202_E1.9261.00
170_L187_Y1.8921.00
167_C188_L1.8271.00
215_L251_R1.8251.00
41_V48_T1.8161.00
171_L210_L1.8131.00
164_I202_E1.7881.00
207_Q211_D1.7831.00
228_P231_E1.7671.00
221_A227_K1.7471.00
241_P245_T1.7201.00
184_V206_F1.6721.00
194_T198_R1.6541.00
41_V50_T1.6501.00
169_N173_S1.6451.00
219_L259_I1.6211.00
43_N48_T1.6131.00
181_A196_H1.5951.00
247_R250_N1.5811.00
138_L141_G1.5781.00
204_V208_S1.5631.00
217_N221_A1.5581.00
220_S224_T1.5581.00
213_V217_N1.5451.00
52_D55_Q1.5451.00
37_Q77_L1.5371.00
230_S241_P1.5271.00
170_L179_W1.5131.00
195_L206_F1.5121.00
243_R247_R1.5091.00
39_K50_T1.4991.00
172_L209_I1.4981.00
36_R79_E1.4961.00
192_V196_H1.4791.00
175_P217_N1.4791.00
222_I229_I1.4771.00
168_Y172_L1.4511.00
231_E235_E1.4511.00
206_F210_L1.4461.00
171_L213_V1.4411.00
194_T197_R1.4371.00
254_I258_E1.4361.00
230_S234_R1.4231.00
231_E234_R1.4101.00
176_G235_E1.4051.00
43_N66_Y1.4041.00
167_C184_V1.4001.00
218_A236_N1.3981.00
190_I194_T1.3921.00
141_G145_S1.3851.00
238_Y247_R1.3811.00
257_R261_K1.3791.00
232_I236_N1.3701.00
30_P61_C1.3691.00
217_N236_N1.3671.00
39_K52_D1.3421.00
212_D216_N1.3321.00
116_I120_E1.3091.00
196_H206_F1.3011.00
182_N186_R1.2931.00
193_S197_R1.2881.00
242_S245_T1.2851.00
205_S208_S1.2831.00
213_V216_N1.2681.00
41_V68_E1.2681.00
45_E63_Y1.2651.00
211_D247_R1.2491.00
183_K187_Y1.2471.00
225_T260_R1.2381.00
177_T183_K1.2341.00
60_P63_Y1.2281.00
137_H144_L1.2241.00
190_I195_L1.2181.00
245_T255_T1.1971.00
137_H140_M1.1891.00
191_S194_T1.1791.00
137_H141_G1.1681.00
245_T257_R1.1631.00
163_L190_I1.1581.00
246_E250_N1.1471.00
105_T108_F1.1321.00
216_N219_L1.1241.00
37_Q53_N1.1181.00
219_L223_Q1.1101.00
227_K232_I1.1041.00
36_R77_L1.0911.00
185_A192_V1.0821.00
176_G217_N1.0771.00
170_L188_L1.0751.00
31_A65_F1.0741.00
181_A206_F1.0711.00
27_P65_F1.0671.00
117_Y121_Q1.0631.00
184_V187_Y1.0361.00
120_E124_T1.0341.00
255_T258_E1.0331.00
162_S166_R1.0251.00
240_C246_E1.0241.00
178_K183_K1.0231.00
211_D250_N1.0201.00
25_V65_F1.0191.00
198_R201_S1.0111.00
229_I232_I1.0091.00
258_E261_K1.0081.00
165_S169_N1.0051.00
208_S211_D1.0011.00
179_W184_V0.9941.00
117_Y120_E0.9911.00
178_K239_K0.9881.00
168_Y209_I0.9791.00
163_L188_L0.9771.00
105_T109_L0.9731.00
257_R260_R0.9601.00
166_R187_Y0.9551.00
252_F259_I0.9551.00
134_I138_L0.9521.00
183_K186_R0.9511.00
221_A232_I0.9501.00
132_T136_E0.9481.00
163_L198_R0.9441.00
40_K76_Y0.9411.00
171_L206_F0.9401.00
247_R251_R0.9391.00
208_S212_D0.9331.00
245_T249_H0.9321.00
170_L184_V0.9311.00
181_A192_V0.9301.00
136_E140_M0.9231.00
27_P31_A0.9111.00
166_R169_N0.9091.00
193_S196_H0.9081.00
44_W47_H0.9011.00
134_I141_G0.8821.00
243_R246_E0.8801.00
114_E117_Y0.8771.00
188_L195_L0.8771.00
43_N46_T0.8731.00
215_L247_R0.8711.00
219_L248_F0.8671.00
190_I198_R0.8641.00
249_H255_T0.8581.00
164_I198_R0.8511.00
199_L206_F0.8491.00
222_I232_I0.8401.00
35_I40_K0.8351.00
174_E187_Y0.8331.00
140_M144_L0.8321.00
211_D251_R0.8311.00
166_R188_L0.8301.00
209_I213_V0.8281.00
207_Q210_L0.8271.00
175_P210_L0.8261.00
43_N68_E0.8231.00
40_K51_V0.8201.00
175_P179_W0.8201.00
225_T232_I0.8201.00
214_R236_N0.8191.00
165_S168_Y0.8191.00
254_I259_I0.8111.00
168_Y199_L0.8081.00
164_I167_C0.8071.00
215_L244_F0.8021.00
37_Q75_L0.8011.00
40_K50_T0.8011.00
41_V70_Y0.8011.00
133_K136_E0.7981.00
207_Q243_R0.7971.00
218_A221_A0.7931.00
141_G144_L0.7921.00
199_L202_E0.7881.00
30_P58_L0.7851.00
234_R239_K0.7801.00
175_P236_N0.7781.00
160_K201_S0.7781.00
39_K70_Y0.7731.00
208_S251_R0.7691.00
171_L209_I0.7681.00
179_W183_K0.7621.00
164_I168_Y0.7601.00
114_E145_S0.7561.00
167_C170_L0.7521.00
31_A82_Y0.7481.00
196_H200_A0.7471.00
197_R201_S0.7441.00
161_Q198_R0.7441.00
42_I57_I0.7411.00
174_E183_K0.7401.00
144_L148_V0.7391.00
196_H205_S0.7381.00
223_Q259_I0.7371.00
55_Q108_F0.7321.00
244_F248_F0.7301.00
175_P214_R0.7301.00
121_Q125_S0.7301.00
33_C78_A0.7291.00
163_L166_R0.7231.00
167_C199_L0.7231.00
85_I89_E0.7201.00
222_I260_R0.7171.00
196_H207_Q0.7051.00
33_C80_M0.7051.00
167_C206_F0.7031.00
233_A241_P0.7031.00
249_H258_E0.6991.00
35_I38_G0.6981.00
104_K107_F0.6971.00
200_A205_S0.6971.00
111_Q114_E0.6951.00
113_P117_Y0.6931.00
184_V195_L0.6911.00
118_C121_Q0.6881.00
211_D243_R0.6871.00
114_E118_C0.6851.00
239_K243_R0.6781.00
228_P232_I0.6711.00
241_P244_F0.6701.00
34_R56_I0.6691.00
117_Y124_T0.6691.00
59_F65_F0.6591.00
242_S255_T0.6541.00
89_E93_K0.6531.00
248_F254_I0.6531.00
216_N252_F0.6531.00
204_V209_I0.6501.00
167_C187_Y0.6491.00
170_L183_K0.6471.00
35_I78_A0.6451.00
240_C243_R0.6441.00
104_K108_F0.6431.00
121_Q141_G0.6421.00
172_L217_N0.6421.00
114_E121_Q0.6411.00
113_P116_I0.6401.00
221_A224_T0.6381.00
104_K109_L0.6361.00
121_Q138_L0.6331.00
211_D215_L0.6321.00
29_M82_Y0.6311.00
121_Q124_T0.6311.00
51_V57_I0.6261.00
160_K163_L0.6241.00
131_S135_Q0.6181.00
86_D89_E0.6181.00
181_A207_Q0.6171.00
127_S131_S0.6161.00
138_L145_S0.6151.00
76_Y80_M0.6141.00
145_S148_V0.6101.00
118_C122_L0.6051.00
26_K64_E0.6041.00
186_R189_Y0.6041.00
218_A232_I0.6011.00
185_A188_L0.5971.00
219_L254_I0.5971.00
161_Q165_S0.5961.00
164_I195_L0.5941.00
167_C171_L0.5941.00
134_I137_H0.5931.00
215_L238_Y0.5921.00
179_W214_R0.5901.00
35_I51_V0.5861.00
242_S246_E0.5841.00
244_F256_P0.5841.00
90_S94_L0.5811.00
133_K137_H0.5801.00
35_I76_Y0.5791.00
210_L213_V0.5791.00
216_N251_R0.5771.00
222_I259_I0.5771.00
184_V188_L0.5731.00
220_S223_Q0.5711.00
107_F110_P0.5711.00
33_C42_I0.5701.00
202_E209_I0.5691.00
112_N116_I0.5691.00
158_Y161_Q0.5671.00
45_E64_E0.5671.00
109_L112_N0.5671.00
33_C57_I0.5661.00
169_N172_L0.5641.00
210_L214_R0.5631.00
36_R120_E0.5601.00
248_F252_F0.5601.00
232_I260_R0.5571.00
44_W59_F0.5571.00
181_A193_S0.5551.00
208_S250_N0.5541.00
240_C250_N0.5521.00
171_L179_W0.5511.00
90_S93_K0.5501.00
72_E75_L0.5481.00
167_C198_R0.5451.00
184_V214_R0.5451.00
106_S109_L0.5441.00
33_C59_F0.5421.00
195_L202_E0.5421.00
79_E82_Y0.5381.00
28_L84_P0.5381.00
179_W210_L0.5371.00
40_K67_I0.5361.00
229_I257_R0.5361.00
30_P60_P0.5351.00
134_I148_V0.5321.00
87_L90_S0.5321.00
134_I144_L0.5321.00
217_N235_E0.5311.00
69_N76_Y0.5291.00
238_Y243_R0.5281.00
160_K194_T0.5261.00
105_T110_P0.5261.00
35_I53_N0.5231.00
131_S134_I0.5221.00
238_Y244_F0.5211.00
34_R119_W0.5201.00
107_F111_Q0.5201.00
39_K71_P0.5191.00
111_Q116_I0.5181.00
133_K140_M0.5171.00
174_E179_W0.5171.00
30_P33_C0.5151.00
138_L142_V0.5131.00
216_N220_S0.5121.00
164_I188_L0.5121.00
224_T227_K0.5121.00
32_L56_I0.5081.00
247_R252_F0.5041.00
188_L192_V0.5001.00
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 0.9547 100 0.208 Contact Map
3mklA 1 0.4151 100 0.455 Contact Map
1bl0A 1 0.4 100 0.46 Contact Map
3oouA 1 0.3925 100 0.463 Contact Map
3oioA 1 0.4113 100 0.464 Contact Map
3w6vA 1 0.3962 100 0.469 Contact Map
3mn2A 1 0.3962 100 0.469 Contact Map
2k9sA 1 0.3962 99.9 0.476 Contact Map
3lsgA 2 0.3811 99.9 0.49 Contact Map
1d5yA 1 0.4 99.9 0.49 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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