GREMLIN Database
YPDC - Uncharacterized HTH-type transcriptional regulator YpdC
UniProt: P77396 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14150
Length: 285 (242)
Sequences: 32516 (27897)
Seq/√Len: 1793.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
224_M232_W3.3051.00
239_R272_F3.2891.00
235_M272_F3.1061.00
247_L255_R3.0961.00
191_Q233_V3.0151.00
237_K240_M2.9301.00
201_E211_P2.8901.00
189_W193_N2.8301.00
193_N196_Q2.6581.00
232_W271_Q2.5761.00
238_A264_F2.3301.00
186_I214_L2.3261.00
241_I255_R2.2751.00
268_F279_Y2.2581.00
218_F229_Y2.1521.00
247_L251_E2.0411.00
199_T202_S2.0111.00
241_I256_C1.9951.00
194_Y233_V1.9891.00
190_V230_V1.9271.00
60_G67_Q1.9241.00
235_M271_Q1.8951.00
183_Y222_G1.8721.00
189_W206_F1.8601.00
186_I207_F1.8381.00
187_C222_G1.8301.00
227_I231_R1.8161.00
241_I247_L1.7981.00
60_G69_R1.7891.00
56_R93_M1.7531.00
248_S251_E1.7381.00
188_N192_D1.7251.00
203_V226_F1.7181.00
62_L67_Q1.7061.00
261_S265_C1.6611.00
200_R215_S1.6561.00
213_H217_L1.6461.00
267_V270_R1.6231.00
191_Q229_Y1.6041.00
156_L159_S1.5901.00
242_L249_I1.5881.00
58_E69_R1.5871.00
224_M228_E1.5841.00
239_R279_Y1.5761.00
226_F230_V1.5671.00
233_V237_K1.5531.00
237_K241_I1.5511.00
71_V74_E1.5491.00
189_W198_L1.5451.00
240_M244_K1.5441.00
214_L226_F1.5441.00
250_H261_S1.5361.00
194_Y237_K1.5121.00
58_E71_V1.5041.00
263_Y267_V1.5021.00
55_L95_L1.5011.00
180_D221_H1.4941.00
274_L278_E1.4551.00
190_V233_V1.4441.00
155_P159_S1.4411.00
195_A255_R1.4411.00
211_P215_S1.4371.00
277_G281_A1.4371.00
209_I213_H1.4371.00
251_E254_Q1.4331.00
250_H254_Q1.4291.00
49_P80_A1.4261.00
155_P162_H1.4191.00
251_E255_R1.4131.00
238_A256_C1.4041.00
258_F267_V1.4011.00
62_L85_L1.3961.00
134_E138_T1.3831.00
201_E205_Q1.3831.00
252_V256_C1.3791.00
213_H216_K1.3651.00
215_S226_F1.3591.00
212_N216_K1.3471.00
186_I203_V1.3471.00
64_E82_A1.3451.00
60_G87_V1.3451.00
187_C191_Q1.3361.00
196_Q202_S1.3281.00
262_D265_C1.3241.00
245_Y280_S1.3091.00
237_K256_C1.3091.00
202_S206_F1.3001.00
209_I214_L1.2781.00
232_W236_A1.2721.00
225_R228_E1.2671.00
231_R267_V1.2421.00
265_C275_T1.2251.00
46_I84_N1.2221.00
159_S163_L1.2171.00
182_L209_I1.2171.00
265_C277_G1.2031.00
210_T213_H1.1931.00
233_V236_A1.1831.00
79_P82_A1.1781.00
56_R72_E1.1761.00
239_R243_Q1.1591.00
266_R270_R1.1581.00
44_L84_N1.1531.00
50_R84_N1.1461.00
155_P158_L1.1371.00
197_P259_P1.1291.00
236_A239_R1.1271.00
55_L93_M1.1141.00
135_A138_T1.1131.00
195_A237_K1.1031.00
200_R226_F1.1001.00
247_L252_V1.0871.00
135_A139_A1.0861.00
154_Q158_L1.0821.00
162_H166_S1.0771.00
158_L162_H1.0621.00
189_W207_F1.0591.00
217_L220_Q1.0551.00
198_L203_V1.0531.00
59_Y92_V1.0461.00
43_S83_A1.0411.00
278_E281_A1.0341.00
185_S206_F1.0261.00
181_F185_S1.0241.00
231_R270_R1.0231.00
217_L221_H1.0201.00
275_T278_E1.0181.00
260_D266_R1.0161.00
182_L217_L1.0151.00
184_H188_N1.0051.00
277_G280_S1.0021.00
203_V206_F0.9931.00
202_S205_Q0.9911.00
204_A211_P0.9911.00
138_T142_H0.9881.00
152_I159_S0.9791.00
241_I252_V0.9701.00
187_C229_Y0.9691.00
182_L207_F0.9651.00
190_V226_F0.9581.00
159_S162_H0.9491.00
265_C269_R0.9491.00
197_P202_S0.9391.00
267_V271_Q0.9381.00
245_Y252_V0.9351.00
235_M267_V0.9321.00
62_L65_A0.9241.00
54_V59_Y0.9241.00
228_E231_R0.9241.00
272_F279_Y0.9211.00
249_I252_V0.9191.00
189_W203_V0.9131.00
207_F214_L0.9091.00
131_G135_A0.9001.00
59_Y70_L0.8921.00
127_S130_R0.8911.00
234_R256_C0.8881.00
200_R211_P0.8811.00
209_I217_L0.8741.00
63_L66_K0.8731.00
194_Y198_L0.8731.00
152_I156_L0.8721.00
126_P130_R0.8711.00
227_I263_Y0.8701.00
62_L87_V0.8701.00
185_S188_N0.8661.00
228_E232_W0.8631.00
239_R268_F0.8591.00
194_Y230_V0.8571.00
212_N215_S0.8541.00
231_R271_Q0.8411.00
269_R275_T0.8381.00
183_Y217_L0.8321.00
218_F226_F0.8311.00
263_Y266_R0.8271.00
238_A241_I0.8261.00
46_I50_R0.8231.00
126_P129_Q0.8231.00
185_S207_F0.8231.00
179_G220_Q0.8201.00
118_H121_R0.8191.00
49_P77_F0.8191.00
184_H187_C0.8181.00
132_E135_A0.8151.00
227_I230_V0.8141.00
101_P105_G0.8111.00
242_L252_V0.8101.00
183_Y186_I0.8051.00
183_Y221_H0.8051.00
56_R91_P0.8031.00
59_Y69_R0.8011.00
235_M264_F0.7961.00
218_F222_G0.7921.00
61_N76_L0.7891.00
140_L143_L0.7881.00
193_N206_F0.7841.00
52_D96_S0.7811.00
215_S225_R0.7781.00
151_N158_L0.7761.00
254_Q259_P0.7761.00
194_Y256_C0.7751.00
130_R134_E0.7721.00
194_Y234_R0.7601.00
228_E271_Q0.7581.00
151_N155_P0.7581.00
132_E139_A0.7561.00
242_L280_S0.7541.00
53_I75_M0.7531.00
186_I189_W0.7521.00
43_S85_L0.7501.00
229_Y233_V0.7491.00
216_K220_Q0.7491.00
187_C218_F0.7451.00
78_I84_N0.7441.00
253_A261_S0.7411.00
190_V229_Y0.7391.00
243_Q279_Y0.7371.00
150_Q154_Q0.7371.00
193_N202_S0.7361.00
262_D275_T0.7341.00
186_I226_F0.7281.00
215_S219_A0.7231.00
269_R278_E0.7181.00
131_G134_E0.7171.00
141_T145_R0.7161.00
70_L76_L0.7131.00
125_L128_L0.7121.00
50_R98_V0.7121.00
260_D263_Y0.7081.00
142_H146_S0.6991.00
183_Y187_C0.6971.00
132_E163_L0.6951.00
92_V96_S0.6931.00
139_A156_L0.6931.00
274_L279_Y0.6931.00
203_V214_L0.6931.00
54_V94_L0.6861.00
186_I218_F0.6851.00
117_L120_A0.6821.00
163_L166_S0.6801.00
252_V280_S0.6761.00
48_F98_V0.6741.00
259_P263_Y0.6741.00
215_S227_I0.6721.00
198_L202_S0.6681.00
180_D217_L0.6641.00
182_L185_S0.6601.00
224_M229_Y0.6601.00
191_Q237_K0.6581.00
163_L167_V0.6561.00
144_S147_P0.6511.00
219_A225_R0.6511.00
186_I206_F0.6501.00
52_D94_L0.6451.00
124_Q128_L0.6441.00
129_Q132_E0.6371.00
246_H252_V0.6321.00
268_F274_L0.6311.00
231_R235_M0.6311.00
54_V57_G0.6301.00
152_I155_P0.6281.00
59_Y86_P0.6281.00
198_L234_R0.6281.00
235_M258_F0.6261.00
200_R227_I0.6261.00
151_N154_Q0.6261.00
262_D266_R0.6251.00
139_A159_S0.6241.00
230_V234_R0.6211.00
152_I162_H0.6211.00
203_V207_F0.6181.00
52_D78_I0.6131.00
179_G182_L0.6111.00
127_S131_G0.6101.00
119_P122_Q0.6081.00
177_P180_D0.6081.00
125_L130_R0.6031.00
236_A272_F0.6021.00
105_G109_Y0.5991.00
149_E153_I0.5991.00
179_G221_H0.5981.00
139_A142_H0.5971.00
58_E90_K0.5961.00
242_L279_Y0.5931.00
186_I190_V0.5921.00
236_A271_Q0.5901.00
261_S264_F0.5901.00
51_L75_M0.5891.00
183_Y214_L0.5871.00
165_R169_N0.5861.00
231_R258_F0.5861.00
260_D270_R0.5861.00
45_C83_A0.5841.00
135_A142_H0.5831.00
204_A207_F0.5821.00
125_L129_Q0.5821.00
189_W202_S0.5811.00
230_V233_V0.5781.00
241_I244_K0.5781.00
264_F276_P0.5771.00
249_I277_G0.5771.00
222_G229_Y0.5731.00
132_E136_M0.5711.00
219_A222_G0.5711.00
52_D61_N0.5691.00
181_F221_H0.5691.00
248_S252_V0.5681.00
166_S170_M0.5661.00
133_G136_M0.5621.00
214_L222_G0.5611.00
188_N191_Q0.5611.00
47_D100_A0.5601.00
54_V92_V0.5601.00
54_V70_L0.5571.00
180_D184_H0.5571.00
231_R263_Y0.5561.00
64_E83_A0.5551.00
143_L146_S0.5541.00
205_Q208_N0.5521.00
61_N86_P0.5521.00
63_L78_I0.5511.00
118_H122_Q0.5481.00
197_P234_R0.5481.00
136_M140_L0.5481.00
152_I166_S0.5481.00
200_R212_N0.5471.00
158_L161_L0.5431.00
240_M243_Q0.5421.00
198_L230_V0.5421.00
162_H165_R0.5421.00
74_E124_Q0.5381.00
115_S118_H0.5381.00
139_A143_L0.5371.00
136_M139_A0.5361.00
52_D76_L0.5351.00
190_V198_L0.5321.00
237_K255_R0.5321.00
193_N198_L0.5311.00
102_T105_G0.5301.00
153_I157_V0.5281.00
238_A252_V0.5281.00
103_W106_L0.5261.00
203_V234_R0.5241.00
128_L132_E0.5231.00
61_N78_I0.5221.00
100_A103_W0.5201.00
40_P87_V0.5201.00
186_I217_L0.5171.00
53_I137_L0.5161.00
264_F268_F0.5161.00
86_P94_L0.5131.00
244_K247_L0.5111.00
114_T118_H0.5101.00
143_L166_S0.5101.00
159_S166_S0.5091.00
184_H221_H0.5091.00
138_T141_T0.5091.00
53_I130_R0.5081.00
183_Y207_F0.5061.00
258_F263_Y0.5041.00
253_A258_F0.5021.00
267_V272_F0.5011.00
149_E166_S0.5001.00
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  
3gbgA 1 0.8667 100 0.243 Contact Map
3oouA 1 0.3684 100 0.471 Contact Map
1bl0A 1 0.3754 100 0.471 Contact Map
3oioA 1 0.386 100 0.473 Contact Map
3w6vA 1 0.3719 100 0.479 Contact Map
3mn2A 1 0.3719 100 0.48 Contact Map
3mklA 1 0.386 100 0.48 Contact Map
2k9sA 1 0.3719 100 0.484 Contact Map
3lsgA 2 0.3579 100 0.494 Contact Map
1d5yA 1 0.3754 99.9 0.499 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.

Page generated in 0.009 seconds.