GREMLIN Database
APPY - HTH-type transcriptional regulator AppY
UniProt: P05052 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10050
Length: 249 (229)
Sequences: 36065 (30961)
Seq/√Len: 2046.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
193_K226_Y3.2341.00
178_T186_D3.1761.00
146_S187_T3.0031.00
201_Y209_K2.9661.00
189_M226_Y2.8651.00
156_K166_E2.7231.00
144_I148_N2.7181.00
191_Y194_K2.6311.00
186_D225_Y2.6171.00
222_F233_Y2.5621.00
148_N151_R2.5031.00
141_I169_I2.2591.00
195_L209_K2.2531.00
192_A218_F2.2291.00
173_L183_I2.1421.00
195_L210_C2.0581.00
154_H157_D2.0051.00
228_V236_K1.9801.00
149_I187_T1.9801.00
142_T176_E1.9441.00
201_Y205_V1.9191.00
144_I161_L1.9121.00
181_T185_R1.8631.00
15_D22_V1.8591.00
138_T176_E1.8231.00
145_I184_L1.7881.00
195_L201_Y1.7821.00
141_I162_I1.7811.00
189_M225_Y1.7741.00
202_S205_V1.7321.00
215_T219_I1.7221.00
193_K233_Y1.7031.00
15_D24_S1.7011.00
221_A224_D1.6781.00
17_I22_V1.6581.00
168_L172_R1.6521.00
158_I180_F1.6451.00
155_L170_K1.6441.00
26_K29_S1.6381.00
143_G147_F1.5931.00
178_T182_E1.5841.00
191_Y195_L1.5721.00
112_L115_S1.5531.00
13_S24_S1.5531.00
194_K198_S1.5491.00
166_E170_K1.5421.00
187_T191_Y1.5361.00
204_N215_T1.5351.00
169_I180_F1.5131.00
144_I153_W1.4921.00
228_V232_H1.4771.00
111_R118_A1.4661.00
180_F184_L1.4601.00
149_I191_Y1.4501.00
150_E209_K1.4371.00
168_L171_K1.4351.00
146_S183_I1.4341.00
217_Y221_A1.4331.00
205_V209_K1.4251.00
192_A210_C1.4031.00
196_I203_I1.4021.00
167_S171_K1.3971.00
142_T146_S1.3961.00
204_N208_Q1.3961.00
231_S235_E1.3891.00
205_V208_Q1.3861.00
10_I49_R1.3821.00
13_S26_K1.3701.00
15_D42_P1.3571.00
17_I40_E1.3571.00
170_K180_F1.3561.00
164_T168_L1.3551.00
191_Y210_C1.3481.00
186_D190_R1.3441.00
145_I187_T1.3411.00
185_R221_A1.3401.00
206_V210_C1.3371.00
115_S119_M1.3251.00
141_I158_I1.3191.00
179_S182_E1.3191.00
212_Y221_A1.3061.00
111_R114_I1.3011.00
156_K160_E1.2971.00
19_N37_I1.2841.00
187_T190_R1.2771.00
216_S219_I1.2741.00
157_D161_L1.2551.00
111_R115_S1.2321.00
88_L92_F1.2311.00
34_S37_I1.2111.00
165_S168_L1.1851.00
151_R157_D1.1841.00
199_N234_F1.1711.00
193_K197_T1.1661.00
220_C224_D1.1641.00
219_I229_T1.1591.00
110_E114_I1.1481.00
11_C27_K1.1391.00
164_T169_I1.1381.00
201_Y206_V1.1311.00
137_F164_T1.1171.00
190_R193_K1.1041.00
92_F96_E1.1001.00
150_E191_Y1.0981.00
155_L180_F1.0811.00
219_I231_S1.0771.00
144_I162_I1.0741.00
101_A105_S1.0721.00
159_A166_E1.0661.00
232_H235_E1.0631.00
89_S93_S1.0561.00
172_R175_D1.0561.00
136_T140_K1.0541.00
231_S234_F1.0471.00
229_T232_H1.0431.00
89_S92_F1.0381.00
185_R224_D1.0361.00
214_S220_C1.0181.00
153_W158_I1.0161.00
167_S170_K1.0101.00
203_I206_V0.9921.00
137_F172_R0.9921.00
219_I223_K0.9831.00
195_L206_V0.9811.00
108_L115_S0.9801.00
139_C143_G0.9771.00
142_T183_I0.9741.00
157_D160_E0.9701.00
182_E185_R0.9681.00
137_F162_I0.9681.00
108_L112_L0.9671.00
221_A225_Y0.9641.00
158_I161_L0.9601.00
152_Q213_N0.9571.00
118_A122_K0.9531.00
11_C47_K0.9531.00
193_K222_F0.9481.00
155_L166_E0.9471.00
140_K161_L0.9431.00
114_I118_A0.9361.00
182_E186_D0.9311.00
144_I158_I0.9221.00
152_Q157_D0.9191.00
9_F14_F0.9181.00
148_N161_L0.9161.00
223_K229_T0.9161.00
226_Y233_Y0.9121.00
181_T217_Y0.9101.00
138_T172_R0.9031.00
17_I20_R0.8971.00
232_H236_K0.8931.00
29_S82_A0.8901.00
18_I21_R0.8791.00
217_Y220_C0.8791.00
139_C142_T0.8781.00
145_I180_F0.8751.00
149_I184_L0.8751.00
77_K80_Y0.8721.00
140_K143_G0.8691.00
149_I153_W0.8691.00
185_R225_Y0.8621.00
93_S97_G0.8611.00
199_N206_V0.8571.00
189_M221_A0.8571.00
140_K162_I0.8511.00
162_I169_I0.8501.00
86_P89_S0.8481.00
196_I206_V0.8481.00
15_D44_C0.8441.00
14_F25_F0.8371.00
173_L180_F0.8361.00
138_T141_I0.8361.00
173_L176_E0.8361.00
13_S44_C0.8351.00
164_T172_R0.8341.00
196_I234_F0.8321.00
86_P119_M0.8291.00
115_S118_A0.8291.00
189_M218_F0.8271.00
183_I187_T0.8251.00
181_T184_L0.8121.00
17_I42_P0.8071.00
142_T173_L0.8061.00
188_R210_C0.7971.00
182_E225_Y0.7961.00
228_V233_Y0.7931.00
137_F140_K0.7831.00
170_K174_R0.7821.00
141_I173_L0.7821.00
55_K59_L0.7781.00
132_T135_N0.7781.00
208_Q213_N0.7751.00
223_K232_H0.7711.00
197_T233_Y0.7691.00
149_I210_C0.7681.00
86_P90_L0.7651.00
138_T142_T0.7651.00
79_G82_A0.7621.00
48_L52_D0.7611.00
148_N157_D0.7611.00
192_A195_L0.7611.00
78_N82_A0.7601.00
218_F222_F0.7481.00
141_I144_I0.7381.00
8_V30_L0.7381.00
153_W157_D0.7371.00
16_L31_F0.7331.00
14_F24_S0.7321.00
33_V39_R0.7301.00
95_F99_K0.7281.00
145_I183_I0.7281.00
135_N172_R0.7271.00
170_K181_T0.7251.00
119_M123_R0.7251.00
108_L118_A0.7201.00
119_M122_K0.7191.00
55_K58_C0.7171.00
207_A215_T0.7111.00
86_P93_S0.7051.00
222_F228_V0.7041.00
171_K175_D0.7001.00
215_T218_F0.6991.00
149_I188_R0.6981.00
170_K179_S0.6971.00
93_S112_L0.6941.00
97_G101_A0.6921.00
25_F31_F0.6911.00
107_W110_E0.6901.00
185_R217_Y0.6901.00
214_S217_Y0.6871.00
80_Y83_E0.6811.00
90_L93_S0.6801.00
213_N217_Y0.6751.00
106_L110_E0.6741.00
7_V50_I0.6701.00
141_I180_F0.6671.00
174_R179_S0.6621.00
178_T183_I0.6611.00
202_S206_V0.6611.00
49_R52_D0.6531.00
158_I169_I0.6491.00
9_F25_F0.6491.00
146_S191_Y0.6471.00
16_L39_R0.6391.00
7_V33_V0.6371.00
192_A206_V0.6361.00
49_R55_K0.6351.00
14_F41_L0.6351.00
141_I145_I0.6341.00
189_M212_Y0.6341.00
176_E183_I0.6331.00
144_I157_D0.6321.00
216_S229_T0.6271.00
93_S115_S0.6261.00
108_L122_K0.6221.00
7_V16_L0.6221.00
153_W188_R0.6151.00
76_D79_G0.6141.00
79_G83_E0.6141.00
159_A162_I0.6141.00
190_R225_Y0.6131.00
9_F48_L0.6091.00
107_W111_R0.6091.00
216_S220_C0.6061.00
59_L63_I0.6061.00
218_F230_P0.6021.00
158_I162_I0.6011.00
155_L167_S0.5951.00
93_S96_E0.5951.00
190_R226_Y0.5941.00
195_L198_S0.5931.00
193_K228_V0.5931.00
155_L181_T0.5921.00
196_I233_Y0.5841.00
57_T60_S0.5841.00
194_K197_T0.5761.00
185_R189_M0.5761.00
206_V234_F0.5751.00
18_I33_V0.5741.00
109_K112_L0.5741.00
108_L111_R0.5731.00
90_L112_L0.5721.00
214_S224_D0.5721.00
160_E163_Y0.5691.00
134_I175_D0.5691.00
54_D57_T0.5671.00
7_V48_L0.5671.00
116_L120_F0.5661.00
8_V91_V0.5641.00
138_T169_I0.5621.00
143_G146_S0.5581.00
141_I172_R0.5571.00
19_N38_R0.5561.00
107_W118_A0.5561.00
141_I161_L0.5561.00
87_P95_F0.5551.00
90_L94_L0.5541.00
98_I101_A0.5541.00
108_L119_M0.5521.00
96_E100_I0.5511.00
10_I92_F0.5511.00
216_S223_K0.5511.00
7_V31_F0.5511.00
182_E224_D0.5501.00
184_L187_T0.5481.00
221_A226_Y0.5481.00
198_S201_Y0.5451.00
212_Y217_Y0.5441.00
94_L97_G0.5431.00
162_I166_E0.5431.00
222_F226_Y0.5431.00
13_S45_P0.5431.00
60_S63_I0.5401.00
89_S96_E0.5391.00
169_I176_E0.5391.00
95_F98_I0.5301.00
30_L33_V0.5291.00
207_A212_Y0.5271.00
101_A104_H0.5261.00
148_N153_W0.5261.00
190_R194_K0.5261.00
203_I231_S0.5261.00
128_S131_L0.5251.00
184_L188_R0.5231.00
212_Y218_F0.5221.00
138_T162_I0.5191.00
56_K59_L0.5191.00
153_W184_L0.5181.00
16_L41_L0.5171.00
76_D83_E0.5171.00
204_N216_S0.5161.00
14_F43_V0.5161.00
52_D55_K0.5131.00
90_L119_M0.5121.00
105_S109_K0.5121.00
152_Q188_R0.5111.00
16_L33_V0.5101.00
6_S30_L0.5101.00
136_T139_C0.5091.00
191_Y209_K0.5081.00
109_K113_C0.5081.00
9_F27_K0.5061.00
158_I188_R0.5051.00
145_I158_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 0.9197 100 0.194 Contact Map
3mklA 1 0.4458 100 0.434 Contact Map
1bl0A 1 0.4618 100 0.442 Contact Map
3oouA 1 0.4177 100 0.443 Contact Map
3oioA 1 0.4458 100 0.445 Contact Map
3mn2A 1 0.4217 99.9 0.45 Contact Map
3w6vA 1 0.4418 99.9 0.452 Contact Map
2k9sA 1 0.4217 99.9 0.456 Contact Map
3lsgA 2 0.4056 99.9 0.465 Contact Map
1d5yA 1 0.4659 99.9 0.47 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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