GREMLIN Database
YOFA - HTH-type transcriptional regulator YofA
UniProt: O34685 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 285 (275)
Sequences: 78541 (57150)
Seq/√Len: 3446.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
70_Q74_L3.6561.00
15_E24_M3.4081.00
157_L281_N2.5871.00
95_G140_V2.5451.00
67_Y81_S2.5131.00
11_A24_M2.4371.00
172_G180_Q2.3581.00
222_V229_A2.2431.00
91_P122_S2.2431.00
158_H161_H2.2381.00
161_H258_E2.2311.00
158_H258_E2.2311.00
45_I60_A2.1611.00
8_I35_R2.1091.00
91_P120_D2.1061.00
163_E233_K2.1021.00
10_Q69_D2.0731.00
67_Y74_L2.0531.00
10_Q14_R2.0291.00
20_K23_Q2.0281.00
165_V233_K1.9981.00
161_H256_D1.9871.00
111_S279_E1.9791.00
173_T176_D1.9791.00
93_R122_S1.9761.00
11_A15_E1.9711.00
10_Q65_L1.9441.00
11_A14_R1.9351.00
14_R69_D1.9351.00
168_S248_H1.9311.00
13_A57_L1.8971.00
223_S244_N1.8851.00
8_I32_V1.8811.00
71_V75_L1.8671.00
183_L227_G1.8471.00
65_L69_D1.8401.00
165_V247_I1.7571.00
181_P209_I1.7441.00
49_H56_K1.7161.00
156_Q260_V1.6971.00
13_A65_L1.6941.00
64_L78_A1.6891.00
63_N81_S1.6871.00
18_I36_V1.6771.00
134_Q139_K1.6681.00
15_E20_K1.6521.00
155_R265_K1.5871.00
10_Q68_A1.5581.00
67_Y70_Q1.5551.00
14_R24_M1.5511.00
5_D35_R1.5351.00
168_S172_G1.5331.00
17_S20_K1.5261.00
5_D42_D1.5161.00
157_L263_Y1.5081.00
5_D38_N1.5061.00
133_Q137_D1.5061.00
9_F65_L1.4941.00
112_F276_F1.4931.00
8_I27_Y1.4571.00
11_A25_L1.4551.00
28_V31_N1.4551.00
46_R49_H1.4411.00
19_T29_Q1.4331.00
112_F119_V1.4311.00
102_V216_E1.4301.00
67_Y77_Q1.4261.00
155_R263_Y1.4211.00
87_Q118_E1.4181.00
51_T56_K1.4071.00
145_V262_I1.4061.00
59_A62_E1.3971.00
263_Y277_L1.3971.00
147_G260_V1.3931.00
71_V78_A1.3811.00
134_Q140_V1.3811.00
192_R196_K1.3751.00
93_R124_N1.3751.00
10_Q72_L1.3651.00
74_L77_Q1.3621.00
135_V143_A1.3511.00
269_I273_F1.3441.00
162_D234_S1.3261.00
89_K118_E1.3191.00
64_L79_E1.3121.00
261_F277_L1.3081.00
277_L281_N1.3051.00
170_R244_N1.3001.00
136_L153_A1.3001.00
275_T278_D1.2971.00
180_Q228_T1.2961.00
218_I229_A1.2941.00
66_Q70_Q1.2931.00
142_G261_F1.2901.00
3_S75_L1.2741.00
142_G273_F1.2711.00
220_K223_S1.2631.00
67_Y78_A1.2621.00
170_R246_W1.2581.00
113_L209_I1.2481.00
63_N66_Q1.2431.00
42_D79_E1.2411.00
115_R279_E1.2381.00
158_H260_V1.2371.00
168_S228_T1.2361.00
27_Y31_N1.2341.00
111_S115_R1.2211.00
233_K247_I1.2151.00
9_F48_F1.1961.00
110_A114_R1.1941.00
34_A38_N1.1891.00
110_A224_A1.1881.00
113_L181_P1.1741.00
156_Q262_I1.1701.00
9_F13_A1.1651.00
233_K237_D1.1581.00
126_A134_Q1.1421.00
62_E66_Q1.1401.00
63_N67_Y1.1271.00
107_E224_A1.1271.00
37_H41_E1.1261.00
34_A37_H1.1261.00
237_D241_H1.1191.00
122_S211_E1.1121.00
70_Q77_Q1.1001.00
6_L68_A1.1001.00
116_F275_T1.0991.00
247_I250_L1.0971.00
11_A21_A1.0901.00
18_I55_M1.0901.00
101_A125_T1.0881.00
181_P207_Q1.0741.00
9_F47_L1.0721.00
33_T37_H1.0681.00
220_K224_A1.0591.00
167_I247_I1.0551.00
71_V74_L1.0461.00
111_S114_R1.0421.00
12_V21_A1.0391.00
264_R267_F1.0381.00
157_L277_L1.0361.00
238_G242_R1.0341.00
274_Q278_D1.0331.00
35_R38_N1.0321.00
92_L276_F1.0321.00
169_S225_G1.0301.00
199_L204_I1.0301.00
212_F218_I1.0271.00
79_E83_R1.0241.00
112_F279_E1.0201.00
136_L151_H1.0181.00
124_N134_Q1.0101.00
183_L218_I1.0071.00
4_G7_K1.0061.00
57_L61_G0.9941.00
163_E256_D0.9941.00
73_S77_Q0.9911.00
64_L68_A0.9891.00
167_I236_V0.9851.00
12_V18_I0.9841.00
278_D281_N0.9821.00
7_K76_D0.9821.00
184_F208_K0.9761.00
38_N41_E0.9741.00
219_I223_S0.9721.00
193_D196_K0.9711.00
27_Y32_V0.9701.00
8_I25_L0.9691.00
112_F116_F0.9691.00
108_H280_I0.9691.00
21_A32_V0.9551.00
13_A48_F0.9531.00
76_D79_E0.9491.00
166_L228_T0.9441.00
174_A252_P0.9391.00
134_Q137_D0.9331.00
20_K24_M0.9311.00
9_F57_L0.9281.00
76_D80_K0.9261.00
9_F39_L0.9221.00
70_Q73_S0.9221.00
212_F221_G0.9201.00
108_H279_E0.9201.00
270_T273_F0.9161.00
98_E214_T0.9021.00
45_I82_T0.8941.00
48_F55_M0.8911.00
95_G143_A0.8901.00
140_V143_A0.8831.00
16_G56_K0.8831.00
240_E243_T0.8821.00
95_G145_V0.8811.00
75_L79_E0.8761.00
147_G258_E0.8751.00
169_S172_G0.8711.00
195_V199_L0.8661.00
19_T23_Q0.8591.00
66_Q69_D0.8581.00
63_N84_M0.8511.00
51_T54_G0.8491.00
132_I136_L0.8481.00
25_L32_V0.8471.00
110_A226_M0.8471.00
193_D197_R0.8421.00
90_G272_A0.8421.00
155_R158_H0.8411.00
198_L202_A0.8391.00
120_D207_Q0.8391.00
172_G181_P0.8361.00
124_N140_V0.8351.00
182_M206_N0.8351.00
13_A61_G0.8331.00
60_A63_N0.8321.00
60_A82_T0.8301.00
181_P208_K0.8291.00
13_A16_G0.8251.00
94_I142_G0.8241.00
119_V272_A0.8231.00
154_V262_I0.8201.00
75_L78_A0.8171.00
29_Q33_T0.8151.00
9_F64_L0.8151.00
175_E178_L0.8131.00
77_Q81_S0.8101.00
169_S226_M0.8091.00
269_I274_Q0.8061.00
14_R65_L0.8051.00
168_S246_W0.8041.00
3_S72_L0.8031.00
113_L226_M0.8031.00
271_S275_T0.8031.00
173_T251_P0.8021.00
16_G62_E0.8021.00
167_I229_A0.8011.00
15_E21_A0.7971.00
74_L78_A0.7961.00
16_G54_G0.7941.00
37_H46_R0.7851.00
7_K11_A0.7821.00
4_G35_R0.7811.00
12_V48_F0.7721.00
5_D8_I0.7671.00
221_G226_M0.7651.00
90_G119_V0.7641.00
78_A82_T0.7641.00
153_A265_K0.7591.00
163_E249_Q0.7581.00
12_V36_V0.7581.00
68_A71_V0.7521.00
69_D73_S0.7471.00
62_E65_L0.7461.00
96_S101_A0.7461.00
49_H58_T0.7451.00
223_S242_R0.7441.00
195_V198_L0.7441.00
167_I231_L0.7401.00
12_V32_V0.7381.00
136_L154_V0.7321.00
142_G276_F0.7311.00
18_I32_V0.7301.00
138_H264_R0.7291.00
267_F270_T0.7291.00
214_T217_A0.7291.00
194_R198_L0.7241.00
112_F275_T0.7221.00
178_L204_I0.7191.00
232_P235_A0.7191.00
198_L201_E0.7181.00
88_P116_F0.7161.00
240_E247_I0.7141.00
60_A64_L0.7101.00
176_D179_Q0.7081.00
196_K200_E0.7071.00
197_R201_E0.7031.00
7_K10_Q0.7011.00
167_I240_E0.6991.00
171_E225_G0.6971.00
275_T279_E0.6961.00
59_A63_N0.6941.00
57_L62_E0.6931.00
31_N35_R0.6911.00
93_R140_V0.6861.00
115_R275_T0.6831.00
93_R141_D0.6821.00
186_G211_E0.6791.00
64_L82_T0.6791.00
56_K62_E0.6761.00
141_D273_F0.6741.00
175_E202_A0.6731.00
236_V240_E0.6711.00
60_A84_M0.6691.00
49_H54_G0.6681.00
173_T252_P0.6651.00
67_Y71_V0.6621.00
102_V220_K0.6581.00
40_E50_R0.6561.00
197_R200_E0.6551.00
172_G228_T0.6541.00
171_E246_W0.6531.00
23_Q26_N0.6521.00
40_E45_I0.6481.00
193_D198_L0.6471.00
125_T213_G0.6461.00
166_L230_L0.6451.00
73_S76_D0.6411.00
77_Q80_K0.6391.00
238_G241_H0.6371.00
107_E110_A0.6351.00
36_V40_E0.6341.00
179_Q207_Q0.6341.00
7_K72_L0.6331.00
120_D211_E0.6321.00
196_K199_L0.6311.00
4_G38_N0.6311.00
194_R197_R0.6301.00
210_I221_G0.6301.00
192_R211_E0.6291.00
96_S105_L0.6261.00
271_S274_Q0.6251.00
163_E253_S0.6241.00
9_F61_G0.6221.00
68_A72_L0.6191.00
185_F218_I0.6171.00
166_L177_M0.6171.00
146_Y257_L0.6161.00
182_M228_T0.6161.00
105_L108_H0.6141.00
12_V17_S0.6121.00
92_L272_A0.5991.00
142_G277_L0.5981.00
43_L64_L0.5971.00
92_L142_G0.5971.00
170_R243_T0.5951.00
72_L76_D0.5941.00
4_G8_I0.5931.00
21_A25_L0.5921.00
199_L206_N0.5871.00
212_F217_A0.5861.00
191_H195_V0.5851.00
162_D257_L0.5851.00
98_E127_D0.5821.00
135_V262_I0.5811.00
43_L82_T0.5781.00
107_E111_S0.5771.00
276_F280_I0.5761.00
63_N82_T0.5731.00
89_K120_D0.5731.00
186_G213_G0.5721.00
160_S259_I0.5721.00
45_I49_H0.5721.00
48_F57_L0.5721.00
116_F119_V0.5701.00
13_A62_E0.5691.00
90_G118_E0.5691.00
95_G124_N0.5681.00
31_N34_A0.5681.00
135_V154_V0.5681.00
218_I222_V0.5651.00
263_Y274_Q0.5631.00
95_G126_A0.5611.00
166_L182_M0.5591.00
125_T214_T0.5571.00
28_V34_A0.5571.00
164_L230_L0.5561.00
159_V261_F0.5541.00
30_S34_A0.5531.00
84_M87_Q0.5521.00
18_I54_G0.5511.00
18_I29_Q0.5491.00
144_F280_I0.5491.00
221_G227_G0.5481.00
104_H108_H0.5471.00
57_L65_L0.5441.00
100_M104_H0.5441.00
43_L46_R0.5421.00
155_R266_D0.5391.00
8_I36_V0.5371.00
66_Q81_S0.5361.00
147_G156_Q0.5351.00
27_Y35_R0.5341.00
102_V214_T0.5331.00
16_G55_M0.5331.00
177_M180_Q0.5321.00
46_R60_A0.5321.00
250_L253_S0.5241.00
175_E204_I0.5221.00
107_E220_K0.5221.00
272_A275_T0.5201.00
215_L232_P0.5191.00
45_I85_S0.5171.00
106_P110_A0.5161.00
231_L236_V0.5161.00
78_A81_S0.5161.00
96_S123_V0.5151.00
80_K83_R0.5141.00
273_F277_L0.5131.00
109_A121_L0.5121.00
136_L139_K0.5121.00
8_I21_A0.5101.00
190_S193_D0.5081.00
43_L79_E0.5081.00
187_A211_E0.5081.00
191_H194_R0.5071.00
244_N247_I0.5071.00
110_A113_L0.5071.00
192_R198_L0.5061.00
163_E254_Y0.5051.00
18_I50_R0.5041.00
178_L205_H0.5031.00
72_L75_L0.5011.00
120_D209_I0.5011.00
67_Y82_T0.5001.00
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  
3fxqA 3 1 100 0.092 Contact Map
1uthA 2 0.7509 100 0.092 Contact Map
2esnA 3 0.9965 100 0.093 Contact Map
1ixcA 4 0.9895 100 0.104 Contact Map
2h98A 2 0.6807 100 0.106 Contact Map
3fzvA 4 0.9719 100 0.108 Contact Map
4x6gA 4 1 100 0.109 Contact Map
2h9bA 2 0.6807 100 0.11 Contact Map
1al3A 1 0.6982 100 0.11 Contact Map
3szpA 3 0.986 100 0.128 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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