GREMLIN Database
YVBU - Uncharacterized HTH-type transcriptional regulator YvbU
UniProt: O32255 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 292 (279)
Sequences: 79596 (58165)
Seq/√Len: 3482.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
71_E75_G3.5731.00
15_T24_A3.3961.00
157_I286_K2.6731.00
97_G142_I2.5691.00
68_H82_V2.4141.00
228_I235_A2.2871.00
11_K24_A2.2291.00
161_K263_D2.2051.00
163_K239_E2.1941.00
172_H188_E2.1921.00
93_T124_V2.1731.00
158_H161_K2.1661.00
93_T122_E2.0961.00
20_K23_Q2.0941.00
14_E70_R2.0861.00
158_H263_D2.0761.00
181_T184_D2.0401.00
45_V61_T2.0341.00
8_V35_A2.0301.00
161_K261_Y2.0151.00
225_I245_M1.9791.00
113_E284_M1.9791.00
10_V66_L1.9721.00
95_H124_V1.9701.00
68_H75_G1.9621.00
229_R250_H1.9581.00
10_V70_R1.9351.00
11_K14_E1.8941.00
10_V14_E1.8871.00
191_I233_G1.8851.00
72_V76_I1.8781.00
8_V32_V1.8771.00
11_K15_T1.8641.00
13_A58_L1.8571.00
165_A239_E1.8391.00
168_L254_R1.8331.00
229_R245_M1.8331.00
66_L70_R1.8081.00
18_F36_I1.7951.00
49_I57_M1.7251.00
65_I79_V1.7041.00
165_A253_T1.6801.00
189_P215_A1.6761.00
64_Q82_V1.6651.00
156_Y265_Q1.6601.00
136_W141_M1.6211.00
114_F281_F1.6171.00
14_E24_A1.5941.00
13_A66_L1.5861.00
9_F66_L1.5781.00
177_H184_D1.5591.00
10_V69_I1.5571.00
15_T20_K1.5561.00
8_V27_M1.5391.00
155_E270_S1.5171.00
114_F121_L1.5051.00
5_Q35_A1.5001.00
19_T29_Q1.4991.00
135_E139_T1.4811.00
60_D63_K1.4781.00
198_E202_I1.4731.00
28_T31_A1.4671.00
5_Q42_E1.4641.00
89_L120_K1.4641.00
157_I268_V1.4531.00
17_S20_K1.4491.00
5_Q38_A1.4391.00
46_K49_I1.4201.00
68_H71_E1.4181.00
11_K25_L1.4091.00
274_A278_A1.4071.00
10_V73_L1.4021.00
282_I286_K1.3881.00
72_V79_V1.3761.00
155_E268_V1.3751.00
147_L267_A1.3741.00
149_Y265_Q1.3691.00
68_H78_K1.3661.00
91_L120_K1.3371.00
170_D250_H1.3371.00
268_V282_I1.3311.00
104_A222_N1.3301.00
266_L282_I1.3151.00
95_H126_H1.3131.00
137_L145_G1.3101.00
113_E117_K1.3081.00
280_L283_E1.3061.00
144_V278_A1.3021.00
3_I76_I1.2931.00
162_D240_M1.2931.00
136_W142_I1.2791.00
65_I80_E1.2791.00
42_E80_E1.2771.00
144_V266_L1.2671.00
168_L234_L1.2671.00
51_D57_M1.2651.00
115_K215_A1.2561.00
224_S235_A1.2531.00
75_G78_K1.2461.00
245_M250_H1.2451.00
205_F210_A1.2371.00
138_H153_E1.2361.00
188_E234_L1.2211.00
117_K284_M1.2211.00
243_S247_L1.2181.00
67_V71_E1.2111.00
239_E243_S1.2111.00
226_S229_R1.2081.00
68_H79_V1.1941.00
170_D252_V1.1921.00
37_S41_A1.1901.00
63_K67_V1.1861.00
64_Q67_V1.1861.00
9_F48_I1.1821.00
112_S116_Q1.1741.00
115_K189_P1.1731.00
239_E253_T1.1601.00
173_P188_E1.1511.00
158_H265_Q1.1451.00
156_Y267_A1.1451.00
27_M31_A1.1431.00
178_S252_V1.1301.00
113_E116_Q1.1281.00
199_S203_D1.1281.00
9_F13_A1.1251.00
9_F47_L1.1171.00
128_G136_W1.1111.00
34_H38_A1.1111.00
34_H37_S1.1101.00
191_I224_S1.1091.00
94_I281_F1.1061.00
124_V217_T1.1041.00
112_S230_E1.1011.00
33_S37_S1.0961.00
167_V253_T1.0891.00
114_F284_M1.0831.00
283_E286_K1.0831.00
179_A257_D1.0821.00
118_Y280_L1.0811.00
189_P213_H1.0761.00
71_E78_K1.0701.00
7_K77_E1.0701.00
12_I21_A1.0691.00
218_V224_S1.0681.00
6_L69_I1.0671.00
103_S127_E1.0611.00
11_K21_A1.0541.00
279_K283_E1.0521.00
72_V75_G1.0441.00
225_I229_R1.0401.00
110_L285_A1.0401.00
58_L62_G1.0361.00
64_Q68_H1.0351.00
18_F56_L1.0261.00
169_R231_G1.0191.00
109_K230_E1.0191.00
226_S230_E1.0181.00
253_T256_L1.0151.00
4_T7_K1.0141.00
167_V242_M1.0131.00
35_A38_A1.0111.00
180_I184_D1.0091.00
157_I282_I1.0051.00
80_E84_A0.9971.00
163_K261_Y0.9891.00
166_V234_L0.9811.00
8_V25_L0.9691.00
27_M32_V0.9651.00
77_E81_Q0.9621.00
13_A48_I0.9541.00
65_I69_I0.9541.00
77_E80_E0.9541.00
12_I18_F0.9531.00
114_F118_Y0.9531.00
244_G248_P0.9521.00
9_F58_L0.9501.00
153_E270_S0.9461.00
74_K78_K0.9391.00
136_W139_T0.9361.00
218_V227_M0.9351.00
192_V214_P0.9311.00
117_K287_E0.9301.00
21_A32_V0.9251.00
110_L284_M0.9231.00
168_L172_H0.9151.00
275_S278_A0.9151.00
199_S202_I0.9141.00
48_I56_L0.9051.00
172_H175_A0.9051.00
284_M287_E0.9031.00
38_A41_A0.9021.00
9_F39_I0.9001.00
45_V83_A0.8971.00
126_H136_W0.8961.00
172_H189_P0.8931.00
97_G145_G0.8921.00
13_A62_G0.8831.00
64_Q86_E0.8791.00
20_K24_A0.8751.00
142_I145_G0.8711.00
67_V70_R0.8701.00
122_E213_H0.8691.00
176_S189_P0.8601.00
97_G147_L0.8571.00
154_M267_A0.8551.00
19_T23_Q0.8541.00
100_S220_N0.8521.00
149_Y263_D0.8511.00
155_E158_H0.8431.00
242_M245_M0.8421.00
269_P272_K0.8421.00
173_P178_S0.8401.00
190_M212_L0.8391.00
121_L277_A0.8391.00
168_L173_P0.8381.00
204_M208_A0.8361.00
96_I144_V0.8351.00
184_D187_H0.8341.00
167_V235_A0.8311.00
71_E74_K0.8271.00
25_L32_V0.8271.00
134_K138_H0.8271.00
283_E287_E0.8261.00
245_M248_P0.8181.00
61_T86_E0.8141.00
198_E204_M0.8131.00
126_H142_I0.8121.00
92_G277_A0.8081.00
189_P214_P0.8051.00
172_H176_S0.8051.00
9_F65_I0.8001.00
274_A279_K0.7961.00
61_T83_A0.7941.00
163_K255_E0.7931.00
16_G57_M0.7901.00
12_I36_I0.7871.00
37_S46_K0.7861.00
29_Q33_S0.7851.00
16_G63_K0.7851.00
183_K186_D0.7811.00
112_S232_L0.7781.00
169_R232_L0.7781.00
13_A16_G0.7771.00
92_G121_L0.7751.00
12_I48_I0.7711.00
3_I73_L0.7681.00
75_G79_V0.7651.00
4_T35_A0.7631.00
174_L188_E0.7621.00
76_I79_V0.7621.00
171_D175_A0.7601.00
14_E66_L0.7581.00
78_K82_V0.7531.00
138_H154_M0.7491.00
15_T21_A0.7491.00
61_T64_Q0.7461.00
181_T257_D0.7441.00
144_V281_F0.7421.00
115_K232_L0.7411.00
163_K259_Q0.7411.00
76_I80_E0.7411.00
276_L280_L0.7411.00
5_Q8_V0.7321.00
227_M232_L0.7301.00
167_V237_L0.7271.00
204_M207_Q0.7271.00
203_D207_Q0.7241.00
90_E118_Y0.7201.00
117_K280_L0.7191.00
79_V83_A0.7151.00
69_I72_V0.7141.00
7_K11_K0.7131.00
49_I59_T0.7121.00
95_H142_I0.7091.00
57_M63_K0.7051.00
238_S241_S0.7041.00
18_F32_V0.7031.00
201_F205_F0.7031.00
31_A35_A0.7021.00
169_R172_H0.7011.00
114_F280_L0.7001.00
58_L63_K0.6991.00
12_I32_V0.6991.00
168_L252_V0.6971.00
84_A87_K0.6961.00
203_D206_R0.6961.00
98_T103_S0.6881.00
220_N223_T0.6841.00
201_F204_M0.6811.00
40_E45_V0.6811.00
198_E217_T0.6811.00
146_I285_A0.6801.00
175_A252_V0.6791.00
61_T65_I0.6781.00
143_D278_A0.6761.00
113_E287_E0.6751.00
70_R74_K0.6691.00
95_H143_D0.6651.00
193_C224_S0.6611.00
194_D217_T0.6601.00
199_S204_M0.6591.00
202_I206_R0.6581.00
187_H213_H0.6571.00
200_P203_D0.6561.00
171_D174_L0.6541.00
63_K66_L0.6531.00
98_T107_M0.6511.00
280_L284_M0.6511.00
168_L174_L0.6501.00
74_K77_E0.6491.00
60_D64_Q0.6481.00
170_D249_E0.6451.00
216_F227_M0.6431.00
140_R269_P0.6431.00
40_E50_R0.6391.00
94_I277_A0.6381.00
78_K81_Q0.6371.00
200_P204_M0.6361.00
244_G247_L0.6341.00
65_I83_A0.6341.00
69_I73_L0.6341.00
186_D210_A0.6321.00
179_A255_E0.6311.00
36_I40_E0.6301.00
23_Q26_N0.6301.00
122_E217_T0.6291.00
171_D252_V0.6221.00
7_K10_V0.6221.00
171_D231_G0.6211.00
12_I17_S0.6211.00
104_A226_S0.6171.00
127_E219_Y0.6161.00
100_S129_T0.6151.00
137_L267_A0.6141.00
21_A25_L0.6141.00
174_L177_H0.6091.00
4_T38_A0.6091.00
190_M234_L0.6081.00
183_K208_A0.6081.00
199_S205_F0.6071.00
68_H72_V0.6061.00
276_L279_K0.5971.00
64_Q83_A0.5971.00
166_V185_L0.5971.00
194_D219_Y0.5931.00
272_K275_S0.5921.00
166_V236_I0.5911.00
107_M110_L0.5901.00
30_P34_H0.5851.00
144_V282_I0.5851.00
127_E220_N0.5851.00
160_K264_V0.5841.00
81_Q85_A0.5821.00
227_M233_G0.5801.00
137_L154_M0.5781.00
281_F285_A0.5771.00
94_I144_V0.5741.00
224_S228_I0.5711.00
174_L180_I0.5711.00
148_L262_R0.5701.00
91_L122_E0.5701.00
166_V190_M0.5701.00
4_T8_V0.5691.00
28_T34_H0.5681.00
58_L66_L0.5681.00
202_I205_F0.5671.00
31_A34_H0.5671.00
155_E271_L0.5671.00
97_G128_G0.5631.00
111_I123_L0.5621.00
177_H180_I0.5611.00
48_I58_L0.5611.00
109_K112_S0.5561.00
43_L65_I0.5551.00
7_K73_L0.5531.00
164_M236_I0.5511.00
162_D262_R0.5511.00
43_L83_A0.5481.00
268_V279_K0.5471.00
205_F212_L0.5431.00
218_V223_T0.5391.00
97_G126_H0.5391.00
173_P177_H0.5381.00
109_K113_E0.5381.00
45_V49_I0.5381.00
92_G120_K0.5351.00
43_L46_K0.5301.00
73_L77_E0.5291.00
102_A106_F0.5291.00
237_L242_M0.5291.00
85_A90_E0.5261.00
195_G217_T0.5241.00
8_V36_I0.5231.00
179_A184_D0.5221.00
73_L76_I0.5211.00
186_D211_T0.5201.00
221_I238_S0.5201.00
36_I48_I0.5201.00
9_F62_G0.5191.00
118_Y121_L0.5181.00
67_V82_V0.5181.00
198_E203_D0.5171.00
104_A220_N0.5161.00
68_H83_A0.5141.00
172_H234_L0.5141.00
149_Y156_Y0.5131.00
173_P176_S0.5121.00
146_I266_L0.5111.00
116_Q175_A0.5101.00
198_E205_F0.5081.00
46_K61_T0.5071.00
18_F29_Q0.5071.00
168_L175_A0.5061.00
18_F50_R0.5031.00
92_G118_Y0.5021.00
16_G56_L0.5011.00
135_E141_M0.5001.00
159_L266_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  
2esnA 3 0.9863 100 0.087 Contact Map
1uthA 2 0.75 100 0.091 Contact Map
1al3A 1 0.7021 100 0.092 Contact Map
3fxqA 3 0.9829 100 0.092 Contact Map
1ixcA 4 0.9829 100 0.094 Contact Map
3fzvA 4 0.9692 100 0.096 Contact Map
2h98A 2 0.6815 100 0.1 Contact Map
2h9bA 2 0.6815 100 0.103 Contact Map
4x6gA 4 0.9966 100 0.106 Contact Map
3szpA 3 0.9795 100 0.107 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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