GREMLIN Database
YKUM - Uncharacterized HTH-type transcriptional regulator YkuM
UniProt: O34827 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 293 (278)
Sequences: 79587 (58313)
Seq/√Len: 3497.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
70_D74_E3.5601.00
15_E24_R3.3911.00
157_D284_K2.6761.00
96_A141_V2.5471.00
67_F81_N2.4231.00
225_A232_A2.3691.00
163_H236_S2.2391.00
11_V24_R2.1881.00
161_T261_D2.1761.00
14_E69_N2.1621.00
20_K23_E2.1511.00
158_Y161_T2.1451.00
92_T123_S2.1451.00
92_T121_K2.1011.00
158_Y261_D2.0381.00
222_K242_E2.0371.00
8_M35_R2.0261.00
10_V65_I2.0171.00
94_K123_S2.0091.00
45_T60_A2.0031.00
161_T259_G1.9731.00
168_D251_L1.9681.00
112_T282_V1.9581.00
67_F74_E1.9481.00
226_L247_K1.9311.00
18_M36_L1.9241.00
71_V75_Q1.9161.00
11_V14_E1.9121.00
10_V69_N1.9021.00
8_M32_L1.8971.00
13_A57_V1.8921.00
10_V14_E1.8651.00
11_V15_E1.8571.00
226_L242_E1.8571.00
65_I69_N1.8241.00
165_Y236_S1.7911.00
132_M144_G1.7561.00
49_L56_T1.7421.00
64_I78_I1.7321.00
173_C182_R1.6981.00
63_K81_N1.6771.00
113_Y279_F1.6721.00
185_I230_G1.6621.00
165_Y250_L1.6371.00
14_E24_R1.6361.00
156_K263_W1.6161.00
135_S140_Q1.6151.00
9_L65_I1.6091.00
13_A65_I1.5881.00
8_M27_V1.5801.00
15_E20_K1.5661.00
10_V68_A1.5641.00
113_Y120_A1.5591.00
88_E119_N1.5431.00
19_R29_Q1.5361.00
183_P212_T1.5331.00
59_P62_E1.5321.00
134_K138_E1.5291.00
5_E35_R1.5211.00
155_R268_E1.4851.00
28_S31_A1.4731.00
5_E38_T1.4701.00
5_E42_A1.4671.00
46_K49_L1.4551.00
10_V72_T1.4511.00
194_F198_Q1.4351.00
17_N20_K1.4331.00
67_F70_D1.4131.00
157_D266_G1.4121.00
11_V25_L1.4101.00
146_I265_L1.4071.00
148_G263_W1.3901.00
155_R266_G1.3891.00
71_V78_I1.3861.00
280_V284_K1.3851.00
170_E247_K1.3771.00
67_F77_R1.3751.00
143_I276_V1.3621.00
103_Q219_E1.3581.00
264_L280_V1.3371.00
266_G280_V1.3361.00
112_T116_K1.3341.00
90_H119_N1.3331.00
94_K125_I1.3251.00
136_L144_G1.3211.00
272_E276_V1.3191.00
127_G131_E1.3141.00
42_A79_R1.3081.00
278_A281_Q1.3011.00
242_E247_K1.2981.00
64_I79_R1.2911.00
3_L75_Q1.2771.00
221_C232_A1.2751.00
162_D237_V1.2711.00
143_I264_L1.2701.00
114_V212_T1.2621.00
51_S56_T1.2601.00
135_S141_V1.2571.00
240_Q244_K1.2491.00
62_E66_Q1.2431.00
37_Q41_K1.2311.00
236_S240_Q1.2301.00
74_E77_R1.2281.00
201_W207_T1.2201.00
236_S250_L1.2171.00
223_Q226_L1.2141.00
66_Q70_D1.2101.00
116_K282_V1.2091.00
9_L48_F1.1951.00
63_K66_Q1.1931.00
182_R231_Y1.1931.00
67_F78_I1.1851.00
112_T115_E1.1741.00
111_K115_E1.1731.00
93_L279_F1.1601.00
158_Y263_W1.1541.00
9_L47_I1.1521.00
170_E249_P1.1511.00
156_K265_L1.1491.00
27_V31_A1.1361.00
168_D231_Y1.1351.00
33_S37_Q1.1311.00
7_H76_E1.1291.00
113_Y282_V1.1281.00
9_L13_A1.1281.00
34_Q37_Q1.1181.00
111_K227_H1.1171.00
123_S214_L1.1051.00
12_L21_A1.1021.00
34_Q38_T1.1021.00
215_V221_C1.0961.00
167_V250_L1.0951.00
267_Y270_A1.0921.00
70_D77_R1.0911.00
281_Q284_K1.0891.00
117_Y278_A1.0851.00
18_M55_L1.0841.00
11_V21_A1.0771.00
102_G126_T1.0751.00
71_V74_E1.0631.00
277_Q281_Q1.0611.00
57_V61_G1.0581.00
6_L68_A1.0581.00
169_T228_G1.0441.00
127_G135_S1.0421.00
250_L253_M1.0421.00
35_R38_T1.0401.00
4_Q7_H1.0391.00
222_K226_L1.0341.00
109_V283_I1.0331.00
195_Q198_Q1.0331.00
185_I221_C1.0291.00
8_M25_L1.0201.00
63_K67_F1.0151.00
108_K227_H1.0111.00
223_Q227_H1.0081.00
76_E80_E1.0071.00
167_V239_L0.9971.00
114_V183_P0.9931.00
27_V32_L0.9931.00
116_K285_D0.9891.00
79_R83_D0.9841.00
76_E79_R0.9811.00
13_A48_F0.9731.00
168_D174_I0.9701.00
137_Y154_G0.9691.00
163_H259_G0.9681.00
179_H249_P0.9671.00
157_D280_V0.9661.00
241_N245_V0.9651.00
9_L57_V0.9611.00
135_S138_E0.9581.00
113_Y117_Y0.9561.00
183_P210_K0.9531.00
64_I68_A0.9491.00
109_V282_V0.9471.00
166_L231_Y0.9441.00
12_L18_M0.9431.00
13_A61_G0.9421.00
73_L77_R0.9381.00
45_T82_I0.9351.00
137_Y152_W0.9341.00
215_V224_M0.9331.00
48_F55_L0.9321.00
125_I135_S0.9261.00
273_L276_V0.9231.00
9_L39_I0.9201.00
96_A146_I0.9171.00
282_V285_D0.9161.00
21_A32_L0.9071.00
131_E134_K0.9031.00
141_V144_G0.9011.00
38_T41_K0.8951.00
173_C183_P0.8841.00
66_Q69_N0.8761.00
121_K210_K0.8741.00
195_Q199_H0.8711.00
20_K24_R0.8711.00
239_L242_E0.8681.00
19_R23_E0.8651.00
120_A275_Q0.8621.00
155_R158_Y0.8601.00
96_A132_M0.8591.00
148_G261_D0.8551.00
281_Q285_D0.8551.00
167_V232_A0.8511.00
95_L143_I0.8511.00
16_L56_T0.8481.00
51_S54_G0.8481.00
242_E245_V0.8481.00
99_S217_Q0.8441.00
12_L36_L0.8411.00
186_Q211_Q0.8401.00
25_L32_L0.8361.00
175_E249_P0.8321.00
125_I141_V0.8281.00
70_D73_L0.8211.00
96_A144_G0.8181.00
173_C177_I0.8161.00
9_L64_I0.8101.00
89_I117_Y0.8081.00
60_A82_I0.8061.00
16_L62_E0.8031.00
37_Q46_K0.8021.00
91_G275_Q0.7961.00
13_A16_L0.7951.00
12_L48_F0.7931.00
169_T229_I0.7931.00
29_Q33_S0.7921.00
111_K229_I0.7871.00
74_E78_I0.7821.00
197_I201_W0.7781.00
194_F214_L0.7771.00
133_L137_Y0.7711.00
14_E65_I0.7701.00
154_G268_E0.7681.00
168_D249_P0.7671.00
75_Q78_I0.7671.00
91_G120_A0.7651.00
143_I279_F0.7641.00
224_M229_I0.7611.00
167_V234_L0.7561.00
63_K85_L0.7541.00
184_F209_P0.7541.00
60_A85_L0.7541.00
171_I175_E0.7531.00
163_H252_D0.7531.00
145_I283_I0.7531.00
3_L72_T0.7531.00
15_E21_A0.7521.00
83_D86_E0.7521.00
57_V62_E0.7511.00
274_K278_A0.7511.00
183_P211_Q0.7511.00
116_K278_A0.7491.00
174_I177_I0.7461.00
4_Q35_R0.7431.00
31_A35_R0.7431.00
163_H257_P0.7411.00
77_R81_N0.7391.00
56_T62_E0.7361.00
16_L54_G0.7361.00
199_H203_Q0.7351.00
235_P238_T0.7301.00
60_A63_K0.7291.00
114_V229_I0.7281.00
5_E8_M0.7281.00
94_K141_V0.7271.00
12_L32_L0.7261.00
194_F200_W0.7251.00
198_Q202_H0.7231.00
68_A71_V0.7221.00
78_I82_I0.7201.00
174_I182_R0.7191.00
127_G132_M0.7181.00
113_Y278_A0.7181.00
75_Q79_R0.7181.00
49_L58_T0.7131.00
49_L54_G0.7111.00
7_H11_V0.7051.00
18_M54_G0.7041.00
18_M32_L0.7011.00
196_E200_W0.7001.00
270_A273_L0.6971.00
40_E45_T0.6951.00
173_C178_A0.6931.00
97_V106_L0.6931.00
97_V102_G0.6921.00
112_T285_D0.6901.00
142_H276_V0.6891.00
217_Q220_T0.6891.00
60_A64_I0.6831.00
200_W203_Q0.6801.00
213_I224_M0.6781.00
272_E277_Q0.6771.00
93_L275_Q0.6771.00
68_A72_T0.6771.00
168_D175_E0.6751.00
73_L76_E0.6711.00
94_K142_H0.6671.00
180_T207_T0.6671.00
40_E50_R0.6661.00
196_E199_H0.6661.00
170_E246_N0.6651.00
204_K207_T0.6641.00
69_N73_L0.6591.00
136_L265_L0.6591.00
12_L17_N0.6591.00
62_E65_I0.6551.00
59_P63_K0.6551.00
200_W204_K0.6531.00
21_A25_L0.6511.00
77_R80_E0.6511.00
121_K214_L0.6501.00
241_N244_K0.6501.00
23_E26_F0.6481.00
177_I183_P0.6431.00
160_M262_T0.6431.00
64_I82_I0.6431.00
278_A282_V0.6431.00
174_I179_H0.6401.00
199_H202_H0.6401.00
181_E210_K0.6391.00
139_D267_Y0.6391.00
36_L40_E0.6371.00
168_D173_C0.6361.00
171_I249_P0.6321.00
197_I200_W0.6321.00
63_K82_I0.6301.00
90_H121_K0.6291.00
179_H254_K0.6241.00
201_W209_P0.6221.00
126_T216_D0.6201.00
126_T217_Q0.6181.00
224_M230_G0.6181.00
279_F283_I0.6161.00
171_I228_G0.6141.00
7_H10_V0.6131.00
103_Q223_Q0.6121.00
67_F71_V0.6121.00
155_R269_P0.6091.00
4_Q38_T0.6091.00
93_L143_I0.6071.00
131_E135_S0.6071.00
80_E84_E0.6041.00
221_C225_A0.6011.00
57_V65_I0.6011.00
143_I280_V0.6011.00
166_L233_I0.5991.00
195_Q200_W0.5981.00
106_L109_V0.5961.00
28_S34_Q0.5921.00
188_K214_L0.5851.00
31_A34_Q0.5851.00
193_Y197_I0.5841.00
30_P34_Q0.5841.00
274_K277_Q0.5821.00
45_T49_L0.5771.00
4_Q8_M0.5771.00
110_L122_I0.5741.00
43_W82_I0.5741.00
187_F221_C0.5711.00
36_L48_F0.5691.00
215_V220_T0.5681.00
189_S214_L0.5671.00
48_F57_V0.5661.00
101_I105_W0.5641.00
164_L233_I0.5631.00
162_D260_R0.5621.00
43_W64_I0.5591.00
108_K111_K0.5591.00
147_R260_R0.5581.00
8_M36_L0.5571.00
184_F187_F0.5561.00
198_Q201_W0.5561.00
72_T75_Q0.5561.00
193_Y196_E0.5551.00
174_I178_A0.5551.00
66_Q81_N0.5531.00
91_G117_Y0.5531.00
173_C176_D0.5511.00
68_A75_Q0.5501.00
234_L239_L0.5501.00
91_G119_N0.5501.00
108_K112_T0.5451.00
266_G277_Q0.5431.00
43_W46_K0.5431.00
7_H72_T0.5411.00
67_F82_I0.5391.00
72_T76_E0.5381.00
176_D179_H0.5371.00
103_Q217_Q0.5361.00
18_M29_Q0.5351.00
166_L184_F0.5341.00
18_M50_R0.5341.00
96_A127_G0.5341.00
96_A125_I0.5341.00
218_I235_P0.5331.00
6_L64_I0.5301.00
145_I264_L0.5301.00
46_K60_A0.5281.00
8_M21_A0.5251.00
27_V35_R0.5201.00
192_T195_Q0.5191.00
117_Y120_A0.5191.00
71_V79_R0.5191.00
184_F231_Y0.5171.00
16_L55_L0.5151.00
150_P153_K0.5121.00
148_G156_K0.5091.00
148_G152_W0.5091.00
276_V280_V0.5081.00
105_W109_V0.5061.00
97_V124_L0.5051.00
16_L57_V0.5021.00
159_L264_L0.5011.00
242_E246_N0.5001.00
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 0.9795 100 0.099 Contact Map
2esnA 3 0.9795 100 0.099 Contact Map
1ixcA 4 0.9727 100 0.11 Contact Map
1al3A 1 0.7031 100 0.11 Contact Map
1uthA 2 0.7543 100 0.112 Contact Map
2h98A 2 0.6826 100 0.113 Contact Map
3fzvA 4 0.9556 100 0.114 Contact Map
2h9bA 2 0.6826 100 0.116 Contact Map
4x6gA 4 0.9966 100 0.118 Contact Map
3szpA 3 0.9659 100 0.131 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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