GREMLIN Database
YFER - Uncharacterized HTH-type transcriptional regulator YfeR
UniProt: P0ACR7 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14159
Length: 308 (286)
Sequences: 79729 (57780)
Seq/√Len: 3416.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
72_R76_E3.6861.00
17_E26_R3.4431.00
160_E290_R2.7131.00
98_A143_V2.5781.00
69_R83_D2.4901.00
13_T26_R2.4251.00
233_V240_S2.2741.00
161_A164_S2.2651.00
164_S267_Q2.2611.00
94_K125_V2.2421.00
114_E292_Q2.2411.00
175_S191_A2.2191.00
161_A267_Q2.2151.00
47_V62_A2.1521.00
166_P244_A2.1311.00
94_K123_Q2.1171.00
10_V37_S2.0851.00
164_S265_E2.0731.00
22_R25_E2.0681.00
12_V71_E2.0521.00
114_E288_V2.0301.00
184_P187_A2.0291.00
69_R76_E2.0231.00
12_V16_Q2.0071.00
96_R125_V1.9781.00
168_F244_A1.9731.00
16_Q71_E1.9531.00
13_T17_E1.9511.00
12_V67_A1.9431.00
13_T16_Q1.9241.00
194_V238_G1.9011.00
10_V34_V1.8971.00
15_A59_L1.8821.00
73_L77_L1.8661.00
67_A71_E1.8371.00
234_A250_P1.8051.00
230_F250_P1.8041.00
192_K220_V1.7631.00
51_D58_V1.7311.00
66_L80_T1.7051.00
65_Q83_D1.7021.00
159_C269_M1.6901.00
20_F38_V1.6761.00
15_A67_A1.6741.00
137_S142_D1.6711.00
17_E22_R1.6091.00
158_Q274_K1.5901.00
180_E187_A1.5831.00
12_V70_L1.5641.00
16_Q26_R1.5531.00
69_R72_R1.5391.00
115_S285_L1.5191.00
7_Q37_S1.5191.00
136_E140_Q1.5161.00
160_E272_R1.5121.00
19_S22_R1.5021.00
90_Q121_D1.4971.00
11_F67_A1.4951.00
7_Q44_H1.4951.00
10_V29_L1.4901.00
7_Q40_E1.4551.00
115_S122_I1.4541.00
234_A255_L1.4491.00
30_S33_A1.4461.00
286_W290_R1.4461.00
21_S31_Q1.4461.00
48_R51_D1.4401.00
148_V271_V1.4371.00
13_T27_I1.4371.00
203_R207_D1.4311.00
158_Q272_R1.4271.00
69_R79_S1.4111.00
105_A227_A1.4041.00
61_D64_Q1.3971.00
255_L259_R1.3901.00
53_T58_V1.3811.00
272_R286_W1.3801.00
150_D269_M1.3701.00
12_V74_L1.3681.00
4_S7_Q1.3651.00
92_S121_D1.3611.00
278_L282_A1.3591.00
138_I146_G1.3561.00
137_S143_V1.3511.00
284_A287_D1.3461.00
96_R127_H1.3441.00
73_L80_T1.3431.00
76_E79_S1.3391.00
114_E118_R1.3351.00
118_R288_V1.3331.00
165_E245_L1.3231.00
5_L77_L1.3221.00
139_R156_D1.3111.00
270_L286_W1.3061.00
66_L81_L1.3051.00
68_L72_R1.2821.00
171_C239_I1.2741.00
145_F270_L1.2721.00
116_H220_V1.2701.00
229_L240_S1.2551.00
191_A239_I1.2521.00
69_R80_T1.2471.00
231_P234_A1.2441.00
145_F282_A1.2381.00
44_H81_L1.2361.00
116_H192_K1.2231.00
65_Q68_L1.2101.00
113_A117_R1.2091.00
161_A269_M1.2071.00
29_L33_A1.1881.00
11_F50_L1.1851.00
113_A235_A1.1841.00
36_H40_E1.1701.00
159_C271_V1.1591.00
256_V259_R1.1521.00
11_F15_A1.1441.00
256_V260_I1.1401.00
64_Q68_L1.1391.00
39_K43_N1.1371.00
248_P252_G1.1351.00
244_A248_P1.1341.00
176_A191_A1.1341.00
125_V222_E1.1331.00
129_R137_S1.1231.00
168_F258_K1.1211.00
119_Y284_A1.1121.00
36_H39_K1.1111.00
65_Q69_R1.1091.00
114_E117_R1.0991.00
72_R79_S1.0951.00
192_K218_N1.0941.00
288_V292_Q1.0891.00
8_L70_L1.0791.00
110_Q235_A1.0781.00
104_S128_D1.0761.00
287_D290_R1.0741.00
250_P255_L1.0691.00
160_E286_W1.0651.00
183_V187_A1.0601.00
20_F57_V1.0591.00
11_F49_L1.0591.00
35_S39_K1.0581.00
230_F234_A1.0561.00
13_T23_A1.0541.00
73_L76_E1.0531.00
194_V229_L1.0531.00
210_L215_I1.0511.00
231_P235_A1.0501.00
283_E287_D1.0491.00
139_R154_V1.0451.00
6_K9_K1.0441.00
37_S40_E1.0441.00
115_S288_V1.0431.00
273_R276_R1.0391.00
223_I229_L1.0331.00
171_C258_K1.0291.00
95_V285_L1.0281.00
14_V23_A1.0251.00
172_H236_G1.0251.00
111_C289_V1.0241.00
166_P265_E1.0111.00
181_D257_V1.0091.00
81_L85_G1.0081.00
204_P207_D1.0011.00
75_D79_S0.9901.00
9_K78_N0.9871.00
249_L253_S0.9871.00
288_V291_D0.9801.00
173_R254_P0.9771.00
127_H137_S0.9701.00
170_L247_L0.9691.00
29_L34_V0.9661.00
66_L70_L0.9641.00
59_L63_G0.9631.00
195_L219_I0.9631.00
15_A50_L0.9571.00
14_V20_F0.9561.00
10_V27_I0.9501.00
169_L239_I0.9501.00
204_P208_A0.9491.00
40_E43_N0.9481.00
78_N81_L0.9471.00
223_I232_M0.9461.00
115_S119_Y0.9421.00
78_N82_R0.9351.00
171_C175_S0.9331.00
11_F59_L0.9271.00
23_A34_V0.9181.00
173_R256_V0.9161.00
137_S140_Q0.9161.00
22_R26_R0.9071.00
65_Q87_M0.9051.00
118_R291_D0.9041.00
175_S178_A0.9031.00
279_S282_A0.9021.00
11_F41_L0.9011.00
98_A146_G0.8981.00
72_R75_D0.8961.00
111_C288_V0.8891.00
101_Q225_H0.8801.00
50_L57_V0.8721.00
68_L71_E0.8691.00
18_K58_V0.8661.00
47_V84_T0.8601.00
6_K37_S0.8561.00
123_Q218_N0.8541.00
143_V146_G0.8481.00
176_A181_D0.8481.00
179_V192_K0.8471.00
98_A148_V0.8461.00
193_L217_A0.8451.00
21_S25_E0.8441.00
150_D267_Q0.8421.00
27_I34_V0.8401.00
15_A63_G0.8391.00
53_T56_E0.8381.00
171_C176_A0.8371.00
97_V145_F0.8341.00
158_Q161_A0.8331.00
62_A87_M0.8331.00
122_I281_A0.8311.00
177_L191_A0.8311.00
192_K219_I0.8301.00
135_M139_R0.8261.00
175_S179_V0.8251.00
93_G281_A0.8251.00
113_A237_I0.8251.00
187_A190_G0.8241.00
77_L81_L0.8241.00
175_S192_K0.8161.00
209_A213_N0.8091.00
157_L271_V0.8091.00
5_L74_L0.8071.00
127_H143_V0.8041.00
62_A65_Q0.8041.00
15_A18_K0.8031.00
116_H237_I0.8001.00
234_A254_P0.7991.00
31_Q35_S0.7981.00
111_C292_Q0.7961.00
79_S83_D0.7941.00
244_A258_K0.7931.00
287_D291_D0.7921.00
18_K64_Q0.7921.00
62_A84_T0.7921.00
170_L240_S0.7921.00
11_F66_L0.7871.00
278_L283_E0.7841.00
18_K56_E0.7821.00
16_Q67_A0.7781.00
77_L80_T0.7751.00
17_E23_A0.7751.00
280_T284_A0.7721.00
186_Q189_Q0.7721.00
172_H237_I0.7711.00
166_P263_V0.7691.00
39_K48_R0.7681.00
76_E80_T0.7631.00
156_D274_K0.7631.00
14_V50_L0.7631.00
166_P259_R0.7611.00
9_K13_T0.7531.00
7_Q10_V0.7501.00
250_P253_S0.7501.00
251_E254_P0.7441.00
145_F285_L0.7421.00
232_M237_I0.7411.00
93_G122_I0.7401.00
99_A104_S0.7381.00
174_D178_A0.7331.00
80_T84_T0.7321.00
115_S284_A0.7321.00
206_I210_L0.7271.00
71_E75_D0.7231.00
70_L73_L0.7221.00
170_L242_L0.7211.00
209_A212_R0.7211.00
14_V38_V0.7201.00
172_H175_S0.7201.00
114_E291_D0.7201.00
118_R284_A0.7171.00
51_D60_T0.7171.00
85_G88_G0.7161.00
20_F34_V0.7161.00
205_L209_A0.7151.00
14_V34_V0.7141.00
225_H228_T0.7141.00
64_Q67_A0.7131.00
185_W261_T0.7101.00
91_L119_Y0.7031.00
139_R157_L0.6981.00
254_P260_I0.6951.00
284_A288_V0.6931.00
170_L251_E0.6921.00
184_P261_T0.6911.00
170_L257_V0.6911.00
249_L252_G0.6901.00
171_C177_L0.6851.00
243_P246_A0.6851.00
189_Q215_I0.6851.00
174_D236_G0.6851.00
208_A212_R0.6821.00
58_V64_Q0.6811.00
62_A66_L0.6801.00
276_R279_S0.6791.00
141_G273_R0.6781.00
61_D65_Q0.6771.00
96_R143_V0.6771.00
9_K12_V0.6721.00
33_A37_S0.6701.00
59_L64_Q0.6701.00
197_D222_E0.6691.00
186_Q213_N0.6681.00
144_D282_A0.6671.00
96_R144_D0.6661.00
51_D56_E0.6551.00
171_C259_R0.6521.00
105_A231_P0.6521.00
66_L84_T0.6501.00
193_L239_I0.6491.00
174_D177_L0.6481.00
196_Q229_L0.6471.00
42_E47_V0.6431.00
168_F257_V0.6421.00
247_L250_P0.6411.00
6_K40_E0.6391.00
25_E28_G0.6361.00
202_S206_I0.6361.00
207_D211_A0.6351.00
221_Q232_M0.6341.00
79_S82_R0.6331.00
205_L208_A0.6331.00
69_R73_L0.6331.00
203_R222_E0.6321.00
206_I209_A0.6301.00
123_Q222_E0.6281.00
190_G218_N0.6271.00
42_E52_R0.6271.00
169_L241_I0.6261.00
75_D78_N0.6261.00
255_L260_I0.6191.00
208_A211_A0.6161.00
128_D224_G0.6091.00
38_V42_E0.6061.00
110_Q113_A0.6051.00
99_A108_I0.6041.00
169_L188_L0.6041.00
280_T283_E0.6041.00
110_Q114_E0.6021.00
197_D224_G0.6011.00
9_K74_L0.5981.00
70_L74_L0.5971.00
14_V19_S0.5971.00
254_P258_K0.5921.00
149_I266_R0.5901.00
95_V281_A0.5891.00
145_F286_W0.5881.00
11_F63_G0.5861.00
108_I111_C0.5841.00
23_A27_I0.5811.00
272_R283_E0.5811.00
82_R86_R0.5801.00
92_S123_Q0.5791.00
6_K10_V0.5781.00
177_L183_V0.5731.00
65_Q84_T0.5721.00
45_T66_L0.5711.00
285_L289_V0.5691.00
74_L78_N0.5691.00
128_D225_H0.5671.00
101_Q130_P0.5671.00
251_E255_L0.5671.00
98_A129_R0.5661.00
229_L233_V0.5641.00
147_I289_V0.5641.00
95_V145_F0.5621.00
138_I157_L0.5581.00
45_T84_T0.5571.00
223_I228_T0.5571.00
50_L59_L0.5561.00
47_V51_D0.5561.00
210_L217_A0.5541.00
33_A36_H0.5531.00
20_F56_E0.5521.00
167_F241_I0.5501.00
98_A127_H0.5491.00
204_P209_A0.5481.00
119_Y122_I0.5471.00
242_L247_L0.5461.00
32_S36_H0.5451.00
251_E258_K0.5431.00
93_G121_D0.5421.00
169_L193_L0.5421.00
59_L67_A0.5411.00
162_I270_L0.5401.00
163_L268_L0.5391.00
180_E183_V0.5371.00
177_L180_E0.5351.00
165_E266_R0.5341.00
202_S205_L0.5331.00
15_A64_Q0.5321.00
198_Y222_E0.5301.00
232_M238_G0.5301.00
175_S239_I0.5281.00
138_I271_V0.5271.00
158_Q275_N0.5261.00
150_D159_C0.5261.00
30_S36_H0.5251.00
45_T48_R0.5221.00
176_A179_V0.5191.00
176_A180_E0.5191.00
20_F31_Q0.5161.00
105_A225_H0.5141.00
226_P243_P0.5131.00
171_C178_A0.5111.00
10_V38_V0.5111.00
48_R62_A0.5101.00
29_L37_S0.5101.00
112_I124_F0.5091.00
207_D210_L0.5081.00
247_L251_E0.5071.00
103_I107_L0.5061.00
110_Q231_P0.5061.00
82_R85_G0.5051.00
86_R91_L0.5051.00
107_L111_C0.5041.00
86_R89_Q0.5031.00
18_K57_V0.5011.00
10_V23_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  
3fzvA 4 0.9318 100 0.108 Contact Map
2esnA 3 0.9513 100 0.115 Contact Map
1ixcA 4 0.9448 100 0.117 Contact Map
1uthA 2 0.7305 100 0.122 Contact Map
2h98A 2 0.6851 100 0.122 Contact Map
1al3A 1 0.7175 100 0.125 Contact Map
4x6gA 4 0.9773 100 0.127 Contact Map
3fxqA 3 0.9448 100 0.131 Contact Map
2h9bA 2 0.6883 100 0.133 Contact Map
3hhgA 3 0.9513 100 0.137 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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