GREMLIN Database
YDIP - Uncharacterized HTH-type transcriptional regulator YdiP
UniProt: P77402 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13975
Length: 303 (248)
Sequences: 28668 (24577)
Seq/√Len: 1560.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
238_K271_V3.2061.00
223_I231_Q3.1511.00
234_M271_V3.1041.00
246_L254_R2.9261.00
190_N232_R2.9151.00
236_E239_W2.8321.00
200_E210_V2.8311.00
188_Y192_N2.8221.00
192_N195_E2.7251.00
231_Q270_H2.4821.00
237_A263_F2.3711.00
267_F278_Y2.3611.00
185_I213_I2.2921.00
240_S254_R2.2601.00
217_F228_Y2.1001.00
55_R62_L2.0531.00
193_Y232_R2.0021.00
240_S255_V1.9961.00
273_C281_Q1.9681.00
246_L250_E1.9491.00
198_T201_Q1.9191.00
189_L229_V1.9171.00
234_M270_H1.8791.00
55_R64_V1.8751.00
240_S246_L1.8531.00
182_I221_Y1.8051.00
185_I206_F1.8041.00
226_I230_I1.7901.00
188_Y205_K1.7751.00
186_L221_Y1.7591.00
57_T62_L1.7571.00
53_V64_V1.7291.00
51_K90_T1.7171.00
212_Y216_E1.6901.00
199_L214_C1.6871.00
247_S250_E1.6801.00
187_F191_N1.6791.00
202_L225_P1.6691.00
190_N228_Y1.6371.00
241_L248_Q1.6351.00
50_K92_C1.6131.00
152_A156_T1.5761.00
238_K278_Y1.5721.00
153_F156_T1.5701.00
266_L269_R1.5671.00
225_P229_V1.5621.00
260_V264_A1.5611.00
66_H69_D1.5601.00
189_L232_R1.5581.00
53_V66_H1.5541.00
236_E240_S1.5471.00
232_R236_E1.5401.00
213_I225_P1.5361.00
223_I227_N1.5331.00
239_W243_N1.5311.00
152_A155_Y1.5251.00
188_Y197_I1.5241.00
249_A260_V1.5121.00
249_A253_W1.4941.00
273_C277_D1.4811.00
59_D77_R1.4801.00
262_H266_L1.4711.00
179_D220_E1.4691.00
44_T75_R1.4691.00
152_A159_I1.4671.00
128_K132_N1.4591.00
57_T80_A1.4581.00
193_Y236_E1.4501.00
250_E253_W1.4371.00
250_E254_R1.4361.00
212_Y215_H1.4331.00
276_S280_R1.4241.00
210_V214_C1.4131.00
208_A212_Y1.4021.00
185_I202_L1.4001.00
194_R254_R1.3941.00
200_E204_K1.3911.00
214_C225_P1.3901.00
251_I255_V1.3881.00
237_A255_V1.3811.00
211_S215_H1.3521.00
151_D155_Y1.3491.00
201_Q205_K1.3451.00
257_Y266_L1.3311.00
244_T279_R1.3311.00
55_R82_A1.2961.00
186_L190_N1.2951.00
208_A213_I1.2911.00
261_D264_A1.2801.00
181_L208_A1.2671.00
224_S227_N1.2541.00
264_A274_S1.2331.00
209_S212_Y1.2291.00
236_E255_V1.2251.00
51_K67_A1.2071.00
231_Q235_T1.1971.00
195_E201_Q1.1901.00
264_A276_S1.1811.00
74_E77_R1.1571.00
230_I266_L1.1531.00
50_K90_T1.1521.00
232_R235_T1.1311.00
129_T132_N1.1181.00
246_L251_I1.1051.00
238_K242_T1.1001.00
40_H79_H1.0981.00
129_T133_E1.0951.00
265_K269_R1.0881.00
38_H79_H1.0771.00
155_Y159_I1.0771.00
235_T238_K1.0741.00
277_D280_R1.0671.00
45_E79_H1.0571.00
199_L225_P1.0571.00
216_E219_K1.0531.00
194_R236_E1.0521.00
40_H45_E1.0471.00
37_H78_L1.0421.00
276_S279_R1.0421.00
196_K201_Q1.0371.00
117_V120_A1.0371.00
132_N136_V1.0341.00
188_Y206_F1.0291.00
183_K187_F1.0271.00
197_I202_L1.0251.00
116_P119_A1.0231.00
189_L225_P1.0151.00
259_N265_K1.0131.00
159_I163_E1.0101.00
203_S210_V1.0061.00
196_K258_E1.0041.00
181_L216_E0.9981.00
180_V184_D0.9961.00
181_L206_F0.9911.00
184_D205_K0.9841.00
201_Q204_K0.9791.00
230_I269_R0.9711.00
240_S251_I0.9661.00
202_L205_K0.9661.00
248_Q251_I0.9641.00
156_T160_L0.9631.00
244_T251_I0.9611.00
216_E220_E0.9591.00
188_Y202_L0.9561.00
274_S277_D0.9521.00
206_F213_I0.9511.00
54_A65_A0.9491.00
156_T159_I0.9461.00
264_A268_L0.9321.00
234_M266_L0.9291.00
57_T82_A0.9251.00
149_L156_T0.9171.00
69_D119_A0.9151.00
54_A89_A0.9131.00
126_V129_T0.9111.00
226_I262_H0.9111.00
53_V84_D0.9061.00
211_S214_C0.9061.00
186_L228_Y0.9041.00
233_R255_V0.9031.00
208_A216_E0.9021.00
277_D281_Q0.8951.00
266_L270_H0.8931.00
44_T72_V0.8921.00
49_V54_A0.8891.00
227_N231_Q0.8881.00
238_K267_F0.8881.00
45_E95_A0.8881.00
199_L210_V0.8841.00
58_I61_S0.8821.00
148_S152_A0.8781.00
271_V278_Y0.8701.00
56_F71_V0.8671.00
227_N230_I0.8661.00
133_E156_T0.8641.00
148_S155_Y0.8621.00
193_Y229_V0.8581.00
184_D187_F0.8571.00
37_H80_A0.8531.00
241_L251_I0.8471.00
182_I216_E0.8461.00
55_R84_D0.8361.00
148_S151_D0.8291.00
121_G124_K0.8261.00
226_I229_V0.8241.00
184_D206_F0.8191.00
48_Y70_I0.8111.00
230_I270_H0.8101.00
234_M263_F0.8081.00
193_Y197_I0.8081.00
262_H265_K0.8041.00
193_Y255_V0.8021.00
160_L164_N0.8011.00
98_G102_Q0.7991.00
51_K88_P0.7971.00
237_A240_S0.7941.00
178_K219_K0.7911.00
47_I93_T0.7911.00
183_K186_L0.7901.00
268_L277_D0.7891.00
54_A64_V0.7861.00
217_F221_Y0.7861.00
57_T60_S0.7821.00
182_I220_E0.7781.00
189_L228_Y0.7751.00
182_I185_I0.7741.00
214_C224_S0.7681.00
253_W258_E0.7661.00
268_L274_S0.7651.00
217_F225_P0.7641.00
192_N205_K0.7641.00
125_E128_K0.7631.00
202_L213_I0.7631.00
215_H219_K0.7611.00
141_S146_T0.7611.00
149_L153_F0.7601.00
192_N201_Q0.7581.00
241_L279_R0.7571.00
193_Y233_R0.7511.00
146_T150_W0.7451.00
185_I225_P0.7421.00
214_C218_T0.7401.00
227_N270_H0.7361.00
259_N262_H0.7331.00
147_S151_D0.7321.00
150_W154_A0.7321.00
133_E137_I0.7291.00
43_E95_A0.7291.00
65_A71_V0.7291.00
113_H116_P0.7271.00
34_E82_A0.7201.00
261_D274_S0.7181.00
73_I79_H0.7121.00
185_I217_F0.7121.00
185_I188_Y0.7091.00
102_Q106_E0.7091.00
124_K128_K0.7081.00
179_D216_E0.7061.00
242_T278_Y0.7041.00
197_I201_Q0.6981.00
186_L217_F0.6971.00
273_C278_Y0.6941.00
252_S260_V0.6941.00
99_F102_Q0.6921.00
136_V140_Q0.6911.00
49_V52_G0.6911.00
228_Y232_R0.6891.00
126_V133_E0.6881.00
185_I189_L0.6881.00
133_E136_V0.6871.00
181_L184_D0.6831.00
165_F169_Y0.6821.00
267_F273_C0.6811.00
197_I233_R0.6781.00
126_V130_L0.6741.00
133_E153_F0.6731.00
150_W153_F0.6731.00
258_E262_H0.6711.00
182_I213_I0.6701.00
47_I91_T0.6691.00
199_L226_I0.6651.00
47_I73_I0.6641.00
135_S139_P0.6611.00
137_I163_E0.6601.00
261_D265_K0.6591.00
125_E129_T0.6551.00
214_C226_I0.6541.00
247_S251_I0.6471.00
251_I279_R0.6471.00
54_A81_V0.6461.00
166_K170_R0.6451.00
126_V160_L0.6441.00
182_I186_L0.6421.00
223_I228_Y0.6361.00
45_E73_I0.6311.00
185_I205_K0.6301.00
53_V87_D0.6291.00
49_V89_A0.6271.00
49_V65_A0.6261.00
245_E251_I0.6251.00
147_S150_W0.6231.00
129_T136_V0.6201.00
56_F73_I0.6191.00
263_F275_P0.6191.00
248_Q276_S0.6191.00
178_K181_L0.6191.00
150_W156_T0.6181.00
190_N236_E0.6181.00
123_G126_V0.6171.00
130_L134_L0.6161.00
49_V91_T0.6151.00
138_L141_S0.6131.00
218_T224_S0.6121.00
229_V233_R0.6111.00
46_L70_I0.6101.00
58_I73_I0.6091.00
48_Y131_F0.6091.00
149_L152_A0.5981.00
178_K220_E0.5971.00
47_I71_V0.5971.00
149_L159_I0.5961.00
48_Y124_K0.5951.00
140_Q143_N0.5921.00
59_D78_L0.5921.00
189_L197_I0.5911.00
203_S206_F0.5901.00
230_I234_M0.5891.00
116_P120_A0.5891.00
127_I130_L0.5871.00
234_M257_Y0.5831.00
229_V232_R0.5801.00
204_K207_R0.5791.00
164_N168_A0.5791.00
160_L163_E0.5791.00
81_V93_T0.5771.00
39_V78_L0.5751.00
260_V263_F0.5711.00
202_L206_F0.5681.00
230_I262_H0.5671.00
230_I257_Y0.5661.00
130_L133_E0.5661.00
176_I179_D0.5641.00
100_Q103_G0.5621.00
89_A93_T0.5621.00
188_Y193_Y0.5611.00
47_I56_F0.5611.00
46_L72_V0.5561.00
162_Y166_K0.5551.00
187_F190_N0.5541.00
259_N269_R0.5501.00
163_E167_N0.5491.00
132_N135_S0.5461.00
103_G106_E0.5451.00
143_N146_T0.5451.00
98_G101_F0.5441.00
148_S156_T0.5441.00
34_E80_A0.5431.00
126_V136_V0.5411.00
161_Y165_F0.5391.00
243_N246_L0.5381.00
237_A251_I0.5371.00
114_S117_V0.5371.00
182_I206_F0.5351.00
213_I221_Y0.5341.00
235_T271_V0.5321.00
145_Q149_L0.5321.00
206_F210_V0.5291.00
110_L114_S0.5291.00
197_I229_V0.5271.00
235_T270_H0.5251.00
145_Q148_S0.5201.00
263_F267_F0.5201.00
92_C95_A0.5171.00
221_Y228_Y0.5151.00
218_T221_Y0.5141.00
185_I216_E0.5141.00
62_L82_A0.5141.00
39_V76_G0.5131.00
99_F103_G0.5131.00
239_W242_T0.5121.00
56_F81_V0.5121.00
179_D183_K0.5111.00
196_K233_R0.5091.00
227_N269_R0.5091.00
202_L233_R0.5081.00
180_V220_E0.5071.00
44_T47_I0.5071.00
45_E93_T0.5061.00
252_S257_Y0.5051.00
188_Y201_Q0.5051.00
213_I216_E0.5051.00
134_L137_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  
3gbgA 1 0.8449 100 0.305 Contact Map
3oioA 1 0.3696 100 0.525 Contact Map
3oouA 1 0.3465 100 0.525 Contact Map
3mn2A 1 0.3498 100 0.531 Contact Map
1bl0A 1 0.3828 100 0.531 Contact Map
3mklA 1 0.3663 100 0.533 Contact Map
3w6vA 1 0.3663 100 0.536 Contact Map
2k9sA 1 0.3498 100 0.537 Contact Map
3lsgA 2 0.3366 100 0.544 Contact Map
1d5yA 1 0.4158 99.9 0.554 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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