GREMLIN Database
YBEF - Uncharacterized HTH-type transcriptional regulator YbeF
UniProt: P30979 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11594
Length: 317 (285)
Sequences: 78787 (57555)
Seq/√Len: 3409.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
98_Q102_S3.7451.00
43_H52_V3.4181.00
39_A52_V2.6361.00
95_Y109_I2.5721.00
182_H314_R2.5551.00
183_V291_D2.4261.00
122_A165_T2.3851.00
73_D88_F2.2741.00
38_E97_S2.2421.00
186_T291_D2.2331.00
183_V186_T2.2181.00
118_T149_R2.2031.00
190_V265_S2.1611.00
197_N212_A2.1521.00
38_E42_V2.1491.00
36_I63_S2.1461.00
95_Y102_S2.1321.00
39_A43_H2.0831.00
118_T147_L2.0801.00
254_V261_A2.0791.00
188_N265_S2.0301.00
186_T289_Q2.0131.00
255_A276_P1.9931.00
120_T149_R1.9821.00
138_A312_V1.9581.00
190_V279_K1.9471.00
41_Y85_P1.9371.00
205_D208_T1.9251.00
39_A42_V1.9171.00
99_G103_I1.9131.00
251_A271_F1.8981.00
36_I60_I1.8901.00
48_N51_K1.8851.00
42_V97_S1.8791.00
93_H97_S1.8661.00
38_E93_H1.8521.00
255_A271_F1.8271.00
215_V259_M1.8131.00
41_Y93_H1.8071.00
181_H293_S1.7591.00
213_A241_N1.7531.00
159_Q164_Q1.7421.00
193_C280_L1.7261.00
91_H109_I1.7211.00
95_Y98_Q1.6851.00
43_H48_N1.6661.00
77_I84_T1.6631.00
92_L106_A1.6031.00
45_G48_N1.6011.00
180_Q298_K1.5791.00
182_H296_Y1.5531.00
33_L70_I1.5441.00
38_E96_I1.5411.00
46_I64_I1.5391.00
156_A168_I1.5311.00
42_V52_V1.5161.00
33_L63_S1.5001.00
129_A248_L1.4951.00
158_N162_Q1.4931.00
33_L66_K1.4931.00
56_T59_A1.4731.00
79_K84_T1.4691.00
296_Y310_I1.4671.00
95_Y105_G1.4641.00
102_S105_G1.4541.00
180_Q296_Y1.4431.00
39_A53_L1.4311.00
170_D295_H1.4131.00
172_M293_S1.4111.00
159_Q165_T1.4071.00
74_P77_I1.4071.00
139_I309_V1.4071.00
30_D33_L1.3961.00
99_G106_A1.3781.00
37_F93_H1.3741.00
47_V57_P1.3671.00
302_R306_L1.3641.00
120_T151_P1.3611.00
224_F228_R1.3581.00
94_E98_Q1.3581.00
294_I310_I1.3501.00
139_I146_L1.3431.00
142_H312_V1.3351.00
36_I55_L1.3331.00
250_I261_A1.3291.00
183_V293_S1.3261.00
271_F276_P1.3211.00
310_I314_R1.3201.00
38_E100_L1.3181.00
92_L107_L1.3171.00
95_Y106_A1.3091.00
87_A90_M1.3061.00
252_A255_A1.3041.00
31_L103_I1.2991.00
187_D266_R1.2961.00
55_L59_A1.2891.00
195_E278_E1.2871.00
167_L294_I1.2781.00
308_G311_D1.2631.00
62_Q66_K1.2591.00
212_A260_L1.2501.00
140_K241_N1.2451.00
167_L306_L1.2451.00
137_R256_N1.2451.00
193_C260_L1.2421.00
116_Q145_Q1.2421.00
195_E276_P1.2261.00
138_A142_H1.2251.00
161_S178_T1.2191.00
91_H94_E1.2151.00
91_H95_Y1.2121.00
137_R141_T1.2001.00
203_E283_P1.1921.00
265_S279_K1.1901.00
140_K213_A1.1801.00
198_P212_A1.1761.00
37_F41_Y1.1751.00
134_V256_N1.1691.00
98_Q105_G1.1641.00
265_S269_N1.1621.00
37_F76_F1.1571.00
90_M94_E1.1571.00
62_Q65_Q1.1511.00
279_K282_F1.1501.00
181_H295_H1.1491.00
34_L96_I1.1221.00
143_Y308_G1.1011.00
252_A256_N1.0991.00
204_D208_T1.0951.00
153_I159_Q1.0951.00
202_L278_E1.0921.00
213_A239_Q1.0921.00
63_S66_K1.0871.00
182_H310_I1.0871.00
65_Q69_V1.0821.00
39_A49_A1.0821.00
99_G102_S1.0771.00
70_I107_L1.0761.00
251_A255_A1.0691.00
151_P159_Q1.0661.00
192_I279_K1.0641.00
46_I83_V1.0501.00
188_N289_Q1.0441.00
269_N273_R1.0431.00
107_L111_G1.0401.00
149_R243_T1.0301.00
194_R257_S1.0271.00
270_L274_C1.0271.00
61_S65_Q1.0241.00
119_I309_V1.0221.00
101_E105_G1.0111.00
307_H311_D1.0051.00
128_G152_P1.0031.00
215_V250_I1.0001.00
216_L240_I0.9991.00
32_N35_T0.9911.00
40_V49_A0.9891.00
138_A141_T0.9881.00
37_F75_L0.9841.00
103_I107_L0.9801.00
139_I143_Y0.9801.00
139_I312_V0.9791.00
225_S228_R0.9781.00
92_L96_I0.9721.00
91_H113_Y0.9711.00
135_I313_I0.9691.00
35_T104_L0.9671.00
66_K69_V0.9541.00
85_P89_A0.9531.00
49_A60_I0.9531.00
40_V46_I0.9511.00
98_Q101_E0.9451.00
161_S176_N0.9451.00
244_S250_I0.9411.00
55_L60_I0.9301.00
48_N52_V0.9291.00
41_Y76_F0.9241.00
44_K84_T0.9221.00
88_F91_H0.9221.00
104_L107_L0.9211.00
191_L260_L0.9201.00
192_I268_Y0.9201.00
37_F67_L0.9191.00
311_D314_R0.9191.00
160_L168_I0.9181.00
225_S229_Q0.9151.00
137_R258_D0.9081.00
231_V236_P0.9071.00
193_C197_N0.9041.00
159_Q162_Q0.9011.00
36_I53_L0.9011.00
135_I312_V0.8971.00
303_D306_L0.8921.00
125_P246_N0.8891.00
180_Q183_V0.8871.00
122_A170_D0.8821.00
37_F85_P0.8811.00
172_M291_D0.8781.00
244_S253_L0.8781.00
32_N63_S0.8771.00
94_E97_S0.8691.00
206_R284_S0.8681.00
88_F113_Y0.8681.00
103_I106_A0.8661.00
197_N200_L0.8661.00
73_D110_E0.8651.00
47_V51_K0.8641.00
105_G109_I0.8631.00
104_L108_D0.8531.00
304_P308_G0.8501.00
140_K258_D0.8481.00
29_I70_I0.8481.00
271_F274_C0.8461.00
102_S106_A0.8461.00
35_T39_A0.8441.00
117_R305_I0.8431.00
76_F83_V0.8401.00
42_V93_H0.8401.00
197_N201_S0.8341.00
43_H49_A0.8311.00
88_F110_E0.8301.00
155_D158_N0.8261.00
40_V76_F0.8241.00
199_L212_A0.8231.00
302_R307_H0.8211.00
79_K82_G0.8211.00
44_K82_G0.8201.00
41_Y44_K0.8201.00
297_N300_S0.8141.00
200_L278_E0.8101.00
213_A240_I0.8091.00
146_L305_I0.8091.00
122_A168_I0.8041.00
227_L231_V0.8021.00
53_L60_I0.8011.00
90_M93_H0.8011.00
230_R234_M0.8001.00
121_I167_L0.7991.00
253_L258_D0.7981.00
57_P61_S0.7981.00
163_F297_N0.7951.00
165_T168_I0.7911.00
35_T38_E0.7891.00
157_E161_S0.7891.00
207_E210_D0.7881.00
205_D283_P0.7881.00
40_V60_I0.7851.00
193_C198_P0.7791.00
106_A110_E0.7791.00
196_G257_S0.7781.00
246_N249_T0.7761.00
151_P165_T0.7731.00
268_Y271_F0.7731.00
188_N287_E0.7721.00
147_L239_Q0.7711.00
97_S101_E0.7711.00
31_L100_L0.7691.00
40_V64_I0.7671.00
155_D159_Q0.7661.00
194_R258_D0.7641.00
96_I99_G0.7621.00
179_V295_H0.7611.00
41_Y89_A0.7591.00
201_S213_A0.7531.00
46_I60_I0.7511.00
37_F92_L0.7511.00
123_T128_G0.7501.00
198_P202_L0.7491.00
44_K90_M0.7451.00
33_L36_I0.7431.00
65_Q74_P0.7411.00
194_R197_N0.7401.00
77_I86_T0.7361.00
268_Y272_S0.7341.00
139_I308_G0.7341.00
192_I263_I0.7321.00
230_R233_E0.7321.00
166_D306_L0.7281.00
192_I261_A0.7261.00
87_A91_H0.7251.00
210_D236_P0.7241.00
188_N281_P0.7221.00
214_H238_R0.7211.00
218_L243_T0.7211.00
161_S179_V0.7181.00
115_K143_Y0.7111.00
208_T211_N0.7081.00
129_A252_A0.7041.00
193_C278_E0.7041.00
308_G312_V0.7021.00
226_G230_R0.7021.00
111_G114_D0.7011.00
192_I272_S0.7011.00
35_T100_L0.7011.00
85_P90_M0.7001.00
196_G200_L0.6981.00
95_Y99_G0.6961.00
226_G229_Q0.6961.00
228_R232_Q0.6951.00
227_L230_R0.6941.00
167_L309_V0.6901.00
120_T166_D0.6861.00
191_L262_I0.6821.00
37_F89_A0.6821.00
117_R146_L0.6751.00
32_N66_K0.6751.00
205_D284_S0.6741.00
203_E281_P0.6721.00
134_V137_R0.6721.00
92_L110_E0.6681.00
147_L243_T0.6651.00
264_P267_F0.6641.00
59_A63_S0.6641.00
229_Q233_E0.6641.00
122_A156_A0.6641.00
77_I82_G0.6631.00
300_S303_D0.6631.00
88_F92_L0.6621.00
272_S275_W0.6621.00
178_T298_K0.6601.00
255_A274_C0.6581.00
51_K54_N0.6561.00
272_S279_K0.6521.00
193_C199_L0.6511.00
225_S230_R0.6501.00
41_Y90_M0.6471.00
217_L250_I0.6471.00
84_T90_M0.6451.00
304_P307_H0.6431.00
214_H260_L0.6411.00
224_F230_R0.6381.00
142_H308_G0.6351.00
105_G108_D0.6311.00
120_T165_T0.6301.00
242_F253_L0.6281.00
197_N213_A0.6251.00
71_F92_L0.6251.00
171_N290_I0.6191.00
132_L135_I0.6171.00
100_L104_L0.6151.00
207_E234_M0.6151.00
167_L310_I0.6091.00
68_R78_R0.6061.00
218_L245_Y0.6041.00
244_S249_T0.6011.00
158_N161_S0.6001.00
196_G199_L0.6001.00
228_R231_V0.6001.00
152_P245_Y0.5971.00
224_F243_T0.5961.00
101_E104_L0.5941.00
191_L209_I0.5851.00
153_I156_A0.5831.00
40_V45_G0.5821.00
229_Q232_Q0.5821.00
29_I107_L0.5811.00
32_N36_I0.5791.00
195_E275_W0.5771.00
123_T132_L0.5771.00
270_L273_R0.5741.00
49_A53_L0.5741.00
91_H110_E0.5731.00
134_V138_A0.5721.00
119_I167_L0.5691.00
133_P137_R0.5691.00
117_R145_Q0.5681.00
73_D77_I0.5671.00
71_F74_P0.5651.00
309_V313_I0.5651.00
197_N260_L0.5651.00
189_M262_I0.5631.00
161_S164_Q0.5601.00
305_I308_G0.5541.00
172_M181_H0.5541.00
211_N239_Q0.5541.00
108_D112_S0.5541.00
184_L294_I0.5531.00
116_Q147_L0.5511.00
109_I112_S0.5501.00
296_Y307_H0.5501.00
30_D70_I0.5481.00
76_F85_P0.5451.00
64_I68_R0.5441.00
71_F110_E0.5421.00
96_I100_L0.5421.00
131_V135_I0.5421.00
46_I57_P0.5411.00
160_L179_V0.5391.00
187_D290_I0.5371.00
143_Y146_L0.5361.00
196_G278_E0.5361.00
158_N164_Q0.5341.00
137_R140_K0.5331.00
231_V238_R0.5311.00
122_A151_P0.5311.00
44_K83_V0.5301.00
250_I254_V0.5281.00
191_L214_H0.5271.00
74_P88_F0.5261.00
296_Y302_R0.5251.00
129_A246_N0.5231.00
199_L204_D0.5231.00
263_I268_Y0.5231.00
198_P201_S0.5221.00
30_D66_K0.5201.00
58_S62_Q0.5201.00
108_D111_G0.5201.00
59_A62_Q0.5191.00
281_P284_S0.5181.00
127_V131_V0.5181.00
99_G107_L0.5161.00
187_D264_P0.5151.00
306_L310_I0.5151.00
106_A109_I0.5141.00
207_E236_P0.5101.00
85_P93_H0.5101.00
56_T62_Q0.5091.00
38_E104_L0.5081.00
247_I264_P0.5071.00
36_I64_I0.5071.00
34_L92_L0.5061.00
66_K70_I0.5051.00
248_L252_A0.5051.00
134_V252_A0.5051.00
58_S61_S0.5031.00
276_P279_K0.5021.00
119_I305_I0.5001.00
307_H310_I0.5001.00
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  
1uthA 2 0.6845 100 0.165 Contact Map
2esnA 3 0.9243 100 0.165 Contact Map
3fxqA 3 0.9085 100 0.183 Contact Map
3fzvA 4 0.8896 100 0.19 Contact Map
4x6gA 4 0.9211 100 0.194 Contact Map
1al3A 1 0.6372 100 0.194 Contact Map
1ixcA 4 0.8991 100 0.194 Contact Map
2h98A 2 0.6246 100 0.195 Contact Map
3szpA 3 0.9022 100 0.197 Contact Map
2h9bA 2 0.6246 100 0.198 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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