GREMLIN Database
YDGD - Uncharacterized serine protease YdgD
UniProt: P76176 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13925
Length: 273 (215)
Sequences: 15173 (10144)
Seq/√Len: 691.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
175_L229_L3.4151.00
69_C85_C2.8051.00
125_G150_V2.5851.00
78_L150_V2.5171.00
72_T237_L2.4331.00
47_V189_E2.4071.00
123_T152_R2.4051.00
78_L148_L2.4011.00
86_L147_G2.3731.00
52_Q190_D2.2371.00
53_S190_D2.2271.00
71_A79_A2.1811.00
80_L237_L2.1341.00
104_S155_P2.1181.00
144_W263_F2.1111.00
73_L155_P2.0861.00
56_D178_A2.0811.00
60_Q67_N2.0671.00
76_P154_P2.0631.00
77_N150_V2.0011.00
77_N154_P1.9851.00
201_C214_H1.9791.00
128_L270_L1.9771.00
146_F263_F1.9701.00
47_V187_Y1.9351.00
75_A78_L1.9351.00
84_H223_S1.9281.00
57_A71_A1.9281.00
57_A104_S1.8951.00
151_L155_P1.8791.00
103_V121_D1.8561.00
243_S256_R1.8521.00
126_K150_V1.7971.00
211_V262_G1.7811.00
124_L149_I1.7731.00
131_D270_L1.7311.00
122_P155_P1.7311.00
217_D255_N1.7211.00
264_R268_D1.7121.00
53_S178_A1.6821.00
138_P141_A1.6751.00
219_L247_A1.6631.00
143_P211_V1.5891.00
189_E192_L1.5521.00
101_R121_D1.5401.00
132_G144_W1.5351.00
48_N53_S1.4971.00
125_G152_R1.4811.00
55_W228_M1.4791.00
258_I263_F1.4761.00
57_A79_A1.4741.00
122_P152_R1.4711.00
175_L195_L1.4221.00
178_A228_M1.4051.00
50_T107_G1.3971.00
213_S227_L1.3891.00
122_P153_N1.3851.00
161_L237_L1.3851.00
103_V106_K1.3831.00
51_T107_G1.3541.00
177_A218_T1.3481.00
51_T157_G1.3301.00
161_L228_M1.3261.00
174_A229_L1.3131.00
104_S158_I1.3101.00
72_T161_L1.3071.00
144_W211_V1.2851.00
218_T241_Q1.2841.00
245_P253_A1.2811.00
130_A144_W1.2791.00
259_S262_G1.2741.00
86_L129_K1.2711.00
183_T189_E1.2691.00
81_T86_L1.2651.00
72_T240_V1.2601.00
229_L238_I1.2521.00
49_D52_Q1.2311.00
198_H208_Q1.2091.00
227_L257_A1.2021.00
196_Y254_D1.1991.00
175_L179_G1.1881.00
230_H235_W1.1861.00
146_F258_I1.1771.00
55_W235_W1.1771.00
194_T216_C1.1771.00
129_K147_G1.1771.00
128_L150_V1.1711.00
47_V107_G1.1701.00
198_H259_S1.1481.00
219_L248_K1.1451.00
79_A102_F1.1401.00
48_N190_D1.1361.00
108_L187_Y1.1301.00
174_A192_L1.1021.00
241_Q244_A1.0981.00
143_P209_T1.0921.00
56_D70_T1.0801.00
73_L104_S1.0721.00
56_D180_R1.0701.00
101_R123_T1.0701.00
82_A240_V1.0631.00
56_D188_P1.0621.00
42_D45_V1.0621.00
197_S200_N1.0601.00
212_M243_S1.0571.00
211_V263_F1.0491.00
175_L227_L1.0471.00
46_P190_D1.0411.00
72_T80_L1.0381.00
56_D226_P1.0301.00
120_V158_I1.0251.00
83_G129_K1.0121.00
189_E193_D1.0091.00
198_H202_E1.0041.00
108_L111_Y0.9971.00
130_A133_D0.9961.00
102_F124_L0.9911.00
78_L128_L0.9901.00
68_L100_L0.9841.00
55_W162_P0.9841.00
127_R149_I0.9831.00
70_T225_S0.9781.00
218_T255_N0.9781.00
185_A249_D0.9761.00
176_K192_L0.9721.00
164_F264_R0.9581.00
78_L270_L0.9571.00
84_H145_D0.9441.00
73_L79_A0.9411.00
215_Q227_L0.9341.00
174_A194_T0.9291.00
81_T147_G0.9271.00
86_L127_R0.9231.00
163_L264_R0.9111.00
265_D269_Q0.9111.00
75_A160_P0.9101.00
177_A191_H0.9041.00
86_L149_I0.9021.00
107_G187_Y0.9021.00
78_L271_S0.9021.00
53_S176_K0.8971.00
162_P236_Q0.8941.00
177_A241_Q0.8941.00
106_K113_I0.8901.00
104_S122_P0.8891.00
175_L180_R0.8831.00
133_D139_P0.8831.00
241_Q257_A0.8751.00
102_F149_I0.8741.00
168_K171_L0.8701.00
73_L160_P0.8681.00
155_P158_I0.8641.00
200_N203_V0.8611.00
120_V156_S0.8601.00
168_K236_Q0.8581.00
174_A179_G0.8581.00
57_A102_F0.8481.00
122_P151_L0.8431.00
53_S235_W0.8371.00
228_M235_W0.8341.00
226_P237_L0.8281.00
217_D257_A0.8261.00
182_V185_A0.8241.00
209_T212_M0.8241.00
215_Q257_A0.8231.00
106_K112_E0.8161.00
225_S241_Q0.8131.00
83_G133_D0.8121.00
170_A238_I0.8111.00
240_V258_I0.8061.00
106_K114_H0.7981.00
188_P192_L0.7961.00
195_L238_I0.7961.00
210_S262_G0.7931.00
74_I80_L0.7921.00
212_M256_R0.7921.00
202_E206_W0.7901.00
230_H233_D0.7821.00
237_L260_V0.7761.00
246_A249_D0.7751.00
138_P143_P0.7671.00
218_T244_A0.7661.00
62_E67_N0.7651.00
41_H45_V0.7641.00
130_A266_K0.7621.00
87_L129_K0.7621.00
266_K270_L0.7611.00
175_L238_I0.7571.00
164_F236_Q0.7521.00
172_T175_L0.7511.00
268_D271_S0.7491.00
128_L148_L0.7491.00
143_P212_M0.7411.00
55_W178_A0.7311.00
231_T234_G0.7291.00
115_D157_G0.7281.00
175_L178_A0.7281.00
193_D215_Q0.7231.00
50_T157_G0.7201.00
165_E236_Q0.7111.00
75_A271_S0.7041.00
259_S263_F0.7041.00
48_N107_G0.7011.00
127_R147_G0.7011.00
177_A193_D0.7011.00
56_D228_M0.7001.00
148_L266_K0.6971.00
106_K111_Y0.6941.00
203_V206_W0.6901.00
73_L151_L0.6871.00
198_H210_S0.6861.00
53_S228_M0.6791.00
200_N204_T0.6791.00
86_L100_L0.6751.00
165_E168_K0.6731.00
240_V260_V0.6721.00
204_T253_A0.6711.00
242_S258_I0.6701.00
97_A127_R0.6671.00
55_W161_L0.6661.00
223_S241_Q0.6641.00
82_A85_C0.6631.00
196_Y200_N0.6631.00
231_T236_Q0.6621.00
162_P234_G0.6601.00
104_S120_V0.6591.00
199_Q203_V0.6591.00
42_D191_H0.6571.00
131_D266_K0.6521.00
205_G253_A0.6451.00
208_Q211_V0.6421.00
123_T153_N0.6411.00
263_F266_K0.6401.00
217_D244_A0.6401.00
64_A99_A0.6401.00
77_N125_G0.6401.00
182_V220_P0.6381.00
178_A190_D0.6371.00
63_T66_G0.6361.00
102_F105_N0.6341.00
105_N158_I0.6321.00
165_E268_D0.6321.00
120_V155_P0.6301.00
146_F240_V0.6281.00
80_L260_V0.6241.00
72_T260_V0.6221.00
79_A151_L0.6221.00
102_F151_L0.6221.00
100_L124_L0.6201.00
167_D261_T0.6201.00
145_D223_S0.6181.00
80_L146_F0.6181.00
205_G245_P0.6171.00
56_D225_S0.6151.00
71_A102_F0.6151.00
54_P159_T0.6131.00
70_T82_A0.6131.00
60_Q101_R0.6081.00
204_T251_W0.6071.00
43_D248_K0.6071.00
237_L241_Q0.6061.00
148_L270_L0.6061.00
122_P154_P0.6021.00
193_D257_A0.6021.00
162_P235_W0.6011.00
176_K179_G0.6001.00
140_A143_P0.5961.00
72_T226_P0.5901.00
48_N52_Q0.5881.00
179_G183_T0.5881.00
263_F267_L0.5881.00
223_S244_A0.5871.00
260_V267_L0.5841.00
218_T257_A0.5831.00
175_L181_K0.5781.00
191_H194_T0.5761.00
195_L229_L0.5721.00
61_L68_L0.5701.00
181_K222_D0.5701.00
164_F168_K0.5691.00
81_T149_I0.5681.00
167_D170_A0.5671.00
63_T100_L0.5661.00
166_G268_D0.5661.00
261_T264_R0.5591.00
177_A180_R0.5561.00
50_T115_D0.5551.00
168_K231_T0.5541.00
222_D225_S0.5481.00
52_Q107_G0.5461.00
146_F266_K0.5451.00
111_Y115_D0.5401.00
172_T195_L0.5371.00
151_L154_P0.5341.00
74_I267_L0.5341.00
176_K180_R0.5321.00
87_L90_P0.5311.00
138_P142_A0.5281.00
208_Q212_M0.5261.00
72_T228_M0.5241.00
262_G265_D0.5221.00
206_W253_A0.5201.00
50_T113_I0.5201.00
173_A229_L0.5170.99
248_K255_N0.5140.99
220_P223_S0.5140.99
167_D259_S0.5140.99
49_D107_G0.5120.99
159_T162_P0.5110.99
83_G130_A0.5110.99
182_V186_G0.5100.99
53_S56_D0.5090.99
239_G257_A0.5080.99
106_K109_W0.5050.99
97_A100_L0.5040.99
87_L133_D0.5040.99
62_E101_R0.5030.99
80_L267_L0.5020.99
178_A226_P0.5010.99
105_N120_V0.5010.99
181_K184_Q0.5000.99
180_R183_T0.5000.99
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  
4nzqA 1 0.9487 100 0.186 Contact Map
3nxpA 1 0.9267 100 0.19 Contact Map
2bdyA 1 0.9231 100 0.202 Contact Map
2f83A 2 0.8974 100 0.205 Contact Map
4kkdA 1 0.967 100 0.207 Contact Map
2xxlA 1 0.9414 100 0.21 Contact Map
2b9lA 1 0.9487 100 0.216 Contact Map
4igdA 1 0.9451 100 0.224 Contact Map
2vntA 1 0.8498 100 0.228 Contact Map
3gylB 1 0.7949 100 0.228 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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