GREMLIN Database
DDL - D-alanine--D-alanine ligase
UniProt: P96612 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 354 (291)
Sequences: 15187 (7263)
Seq/√Len: 425.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
167_Q192_R3.5431.00
191_N194_E3.4311.00
145_K213_E3.2421.00
106_G124_S3.2201.00
274_D278_K3.0771.00
163_E196_Q3.0541.00
265_T268_E3.0401.00
136_F279_A3.0261.00
106_G110_L2.8781.00
171_Y192_R2.7271.00
138_Q282_A2.6551.00
80_A84_N2.4491.00
49_E65_A2.4411.00
228_D286_S2.4051.00
190_R216_N2.3621.00
275_M301_V2.2991.00
266_D270_A2.2901.00
268_E271_T2.2191.00
296_T300_E2.1471.00
188_K214_G2.1281.00
277_I281_K2.1161.00
270_A274_D2.0691.00
165_V168_E2.0651.00
203_F207_R2.0611.00
222_I272_I2.0071.00
163_E192_R1.9771.00
142_A300_E1.9661.00
36_T43_R1.8971.00
125_A135_L1.8911.00
119_G122_A1.8491.00
107_M111_L1.8451.00
64_S81_S1.8451.00
108_L113_I1.8351.00
265_T299_G1.8281.00
190_R194_E1.8121.00
268_E295_L1.8111.00
131_V134_H1.8101.00
134_H138_Q1.8051.00
119_G286_S1.7651.00
38_K331_D1.7621.00
226_G232_C1.7321.00
28_F334_E1.7201.00
164_E168_E1.7131.00
331_D335_Q1.6531.00
70_A73_Q1.6511.00
27_K30_I1.6271.00
192_R196_Q1.6091.00
224_V280_F1.6071.00
125_A131_V1.6041.00
124_S131_V1.5871.00
216_N297_A1.5751.00
260_I324_E1.5691.00
271_T274_D1.5671.00
142_A275_M1.5511.00
165_V169_L1.5431.00
147_A168_E1.5351.00
109_E120_V1.5341.00
225_L332_L1.5161.00
136_F303_I1.5031.00
78_Q107_M1.4761.00
196_Q200_E1.4721.00
166_E171_Y1.4721.00
145_K168_E1.4561.00
179_N206_D1.4551.00
310_P329_Y1.4531.00
224_V276_A1.4531.00
147_A165_V1.4441.00
201_L204_Q1.4431.00
106_G120_V1.4421.00
121_L125_A1.4361.00
328_E331_D1.4331.00
126_G306_V1.4311.00
83_Q111_L1.4301.00
109_E115_Y1.4251.00
137_A143_Q1.4111.00
334_E338_E1.4081.00
64_S85_E1.3991.00
197_K201_L1.3971.00
163_E167_Q1.3881.00
108_L115_Y1.3861.00
225_L288_L1.3791.00
278_K281_K1.3731.00
225_L336_L1.3691.00
217_G297_A1.3691.00
271_T300_E1.3651.00
234_V273_S1.3601.00
270_A273_S1.3571.00
45_A56_M1.3551.00
79_E107_M1.3551.00
151_K161_S1.3541.00
46_R66_F1.3531.00
222_I273_S1.3521.00
230_P281_K1.3311.00
35_I331_D1.3181.00
178_A208_K1.3131.00
288_L309_M1.3111.00
268_E299_G1.3091.00
114_P228_D1.3031.00
232_C277_I1.2951.00
81_S85_E1.2921.00
82_Q113_I1.2881.00
189_C198_A1.2831.00
271_T275_M1.2821.00
130_V134_H1.2711.00
126_G283_I1.2661.00
174_F188_K1.2591.00
150_L208_K1.2581.00
137_A145_K1.2471.00
267_E271_T1.2431.00
222_I276_A1.2411.00
269_Y273_S1.2351.00
161_S164_E1.2231.00
116_V334_E1.2041.00
295_L301_V1.2031.00
220_I295_L1.1981.00
173_C211_V1.1931.00
90_V108_L1.1781.00
264_V268_E1.1741.00
187_S201_L1.1731.00
199_F203_F1.1591.00
266_D269_Y1.1531.00
33_I59_F1.1521.00
130_V178_A1.1471.00
133_K143_Q1.1471.00
327_V332_L1.1291.00
135_L282_A1.1171.00
133_K212_E1.1161.00
162_C195_L1.1161.00
132_M136_F1.1061.00
80_A83_Q1.1031.00
67_S74_E1.0981.00
134_H137_A1.0941.00
276_A293_F1.0941.00
161_S165_V1.0931.00
218_R237_E1.0921.00
82_Q90_V1.0891.00
149_F152_K1.0881.00
332_L335_Q1.0871.00
231_K281_K1.0841.00
199_F209_V1.0761.00
123_S308_T1.0751.00
65_A69_A1.0681.00
200_E204_Q1.0671.00
149_F153_D1.0591.00
137_A148_A1.0571.00
89_V116_V1.0541.00
166_E192_R1.0491.00
121_L131_V1.0431.00
272_I301_V1.0391.00
69_A74_E1.0371.00
109_E119_G1.0351.00
107_M110_L1.0341.00
295_L299_G1.0171.00
203_F209_V1.0091.00
171_Y195_L1.0081.00
259_M263_I1.0001.00
128_D208_K0.9941.00
102_G124_S0.9901.00
47_L63_G0.9891.00
122_A284_D0.9761.00
237_E269_Y0.9761.00
55_K59_F0.9741.00
218_R263_I0.9711.00
131_V135_L0.9601.00
175_V189_C0.9581.00
213_E300_E0.9561.00
220_I272_I0.9521.00
57_L63_G0.9471.00
135_L138_Q0.9461.00
175_V195_L0.9461.00
164_E167_Q0.9351.00
213_E302_L0.9311.00
106_G109_E0.9231.00
114_P286_S0.9211.00
27_K334_E0.9211.00
226_G281_K0.9171.00
279_A303_I0.9151.00
175_V209_V0.9111.00
263_I295_L0.9111.00
130_V148_A0.9041.00
70_A74_E0.9031.00
233_S236_G0.9031.00
71_L74_E0.9021.00
297_A300_E0.9021.00
237_E262_A0.9011.00
106_G121_L0.8981.00
141_L303_I0.8961.00
37_E43_R0.8941.00
45_A60_E0.8861.00
169_L173_C0.8861.00
197_K200_E0.8771.00
234_V277_I0.8751.00
273_S277_I0.8741.00
239_A259_M0.8741.00
36_T42_V0.8731.00
274_D277_I0.8691.00
119_G284_D0.8691.00
275_M278_K0.8681.00
128_D178_A0.8661.00
166_E173_C0.8641.00
68_P73_Q0.8621.00
175_V198_A0.8591.00
235_V269_Y0.8561.00
122_A286_S0.8521.00
73_Q77_P0.8501.00
195_L199_F0.8501.00
271_T301_V0.8491.00
103_T124_S0.8481.00
291_A306_V0.8471.00
260_I320_L0.8461.00
109_E121_L0.8441.00
72_N76_F0.8431.00
239_A262_A0.8401.00
148_A151_K0.8381.00
267_E299_G0.8301.00
90_V113_I0.8261.00
49_E69_A0.8251.00
126_G308_T0.8221.00
285_G289_V0.8151.00
275_M293_F0.8121.00
144_A215_I0.8111.00
248_K252_E0.8101.00
139_V282_A0.8101.00
140_G278_K0.8061.00
81_S87_I0.8061.00
280_F289_V0.8031.00
42_V61_Q0.8011.00
234_V325_A0.7991.00
213_E296_T0.7971.00
171_Y191_N0.7961.00
37_E61_Q0.7951.00
174_F214_G0.7881.00
88_D338_E0.7871.00
39_G331_D0.7851.00
133_K210_V0.7841.00
162_C199_F0.7821.00
174_F186_I0.7801.00
173_C189_C0.7801.00
32_P91_F0.7731.00
55_K58_Q0.7721.00
162_C211_V0.7721.00
194_E197_K0.7711.00
130_V210_V0.7661.00
105_Q120_V0.7631.00
68_P71_L0.7631.00
35_I39_G0.7601.00
230_P277_I0.7531.00
170_G213_E0.7521.00
144_A302_L0.7521.00
141_L275_M0.7501.00
226_G339_L0.7491.00
280_F291_A0.7481.00
202_A209_V0.7461.00
92_P116_V0.7461.00
187_S198_A0.7421.00
185_G202_A0.7411.00
262_A269_Y0.7371.00
47_L52_S0.7341.00
165_V211_V0.7261.00
175_V211_V0.7251.00
167_Q171_Y0.7241.00
71_L76_F0.7191.00
186_I251_Y0.7191.00
278_K282_A0.7141.00
194_E198_A0.7141.00
330_A334_E0.7131.00
216_N298_D0.7111.00
41_W338_E0.7111.00
122_A125_A0.7091.00
82_Q108_L0.7091.00
236_G324_E0.7081.00
72_N75_M0.7081.00
49_E52_S0.7021.00
39_G334_E0.6991.00
231_K335_Q0.6991.00
271_T278_K0.6971.00
88_D114_P0.6971.00
141_L278_K0.6961.00
121_L124_S0.6951.00
294_F304_N0.6931.00
142_A302_L0.6901.00
49_E68_P0.6861.00
65_A68_P0.6851.00
68_P74_E0.6851.00
130_V208_K0.6841.00
289_V306_V0.6841.00
115_Y120_V0.6821.00
108_L111_L0.6801.00
120_V124_S0.6791.00
279_A282_A0.6731.00
215_I294_F0.6671.00
178_A210_V0.6671.00
71_L75_M0.6661.00
142_A271_T0.6651.00
133_K137_A0.6631.00
227_N339_L0.6620.99
29_D49_E0.6620.99
220_I264_V0.6570.99
133_K146_Y0.6540.99
276_A280_F0.6530.99
310_P330_A0.6510.99
283_I306_V0.6500.99
222_I237_E0.6500.99
33_I60_E0.6500.99
47_L57_L0.6460.99
320_L323_K0.6440.99
175_V199_F0.6440.99
69_A73_Q0.6410.99
163_E166_E0.6410.99
136_F139_V0.6400.99
136_F141_L0.6400.99
234_V269_Y0.6350.99
247_Y256_T0.6340.99
66_F69_A0.6320.99
109_E286_S0.6310.99
125_A138_Q0.6300.99
82_Q87_I0.6270.99
146_Y212_E0.6240.99
73_Q76_F0.6240.99
195_L211_V0.6220.99
129_K176_K0.6220.99
36_T41_W0.6210.99
150_L153_D0.6180.99
227_N231_K0.6150.99
30_I59_F0.6110.99
217_G298_D0.6100.99
54_V57_L0.6100.99
105_Q109_E0.6090.99
179_N207_R0.6090.99
193_E196_Q0.6090.99
280_F283_I0.6080.99
87_I90_V0.6060.99
335_Q338_E0.6050.99
134_H139_V0.6040.99
128_D131_V0.6030.99
119_G228_D0.6020.99
270_A277_I0.6000.99
265_T295_L0.5980.99
135_L283_I0.5980.99
220_I262_A0.5980.99
30_I33_I0.5950.99
81_S84_N0.5940.99
163_E195_L0.5920.99
126_G279_A0.5910.99
335_Q339_L0.5910.99
260_I321_L0.5870.99
135_L139_V0.5850.99
153_D161_S0.5850.99
150_L161_S0.5850.99
166_E195_L0.5840.99
44_G85_E0.5840.99
91_F116_V0.5810.99
226_G280_F0.5810.99
66_F74_E0.5790.99
216_N296_T0.5790.99
103_T107_M0.5790.99
67_S70_A0.5760.99
231_K322_W0.5760.99
103_T106_G0.5740.99
70_A75_M0.5720.99
118_N285_G0.5710.99
225_L327_V0.5710.99
220_I235_V0.5700.98
265_T269_Y0.5680.98
221_E236_G0.5660.98
274_D281_K0.5650.98
296_T302_L0.5640.98
56_M59_F0.5640.98
102_G105_Q0.5640.98
74_E77_P0.5630.98
162_C165_V0.5570.98
162_C166_E0.5570.98
224_V289_V0.5550.98
46_R56_M0.5550.98
235_V325_A0.5550.98
329_Y333_I0.5540.98
323_K328_E0.5520.98
235_V321_L0.5510.98
145_K302_L0.5490.98
147_A150_L0.5480.98
104_I108_L0.5480.98
66_F81_S0.5480.98
198_A202_A0.5460.98
267_E270_A0.5460.98
224_V232_C0.5440.98
78_Q103_T0.5420.98
225_L329_Y0.5410.98
173_C213_E0.5410.98
137_A146_Y0.5400.98
188_K251_Y0.5390.98
44_G87_I0.5380.98
320_L324_E0.5370.98
177_P187_S0.5360.98
33_I43_R0.5340.98
31_H87_I0.5320.98
82_Q85_E0.5320.98
67_S71_L0.5310.98
97_P180_L0.5310.98
189_C195_L0.5280.98
170_G173_C0.5280.98
169_L213_E0.5260.97
296_T299_G0.5250.97
147_A161_S0.5240.97
120_V123_S0.5200.97
224_V291_A0.5200.97
111_L114_P0.5190.97
100_E181_G0.5190.97
258_L320_L0.5190.97
93_L309_M0.5190.97
48_T71_L0.5180.97
152_K200_E0.5160.97
215_I302_L0.5160.97
105_Q123_S0.5150.97
279_A291_A0.5150.97
130_V304_N0.5130.97
144_A217_G0.5130.97
287_G333_I0.5110.97
226_G230_P0.5110.97
88_D116_V0.5100.97
187_S197_K0.5100.97
232_C280_F0.5080.97
193_E197_K0.5080.97
96_G181_G0.5080.97
39_G335_Q0.5070.97
52_S65_A0.5070.97
195_L198_A0.5070.97
144_A304_N0.5060.97
327_V335_Q0.5060.97
130_V133_K0.5050.97
153_D164_E0.5040.97
35_I38_K0.5040.97
276_A291_A0.5040.97
290_R311_G0.5020.97
334_E337_V0.5010.97
198_A201_L0.5010.97
147_A151_K0.5000.97
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  
3tqtA 2 0.9435 100 0.266 Contact Map
3lwbA 2 0.8729 100 0.269 Contact Map
3i12A 2 0.9859 100 0.273 Contact Map
3e5nA 2 0.9294 100 0.275 Contact Map
2fb9A 2 0.8842 100 0.282 Contact Map
2i87A 2 0.9463 100 0.282 Contact Map
1ehiA 2 0.9718 100 0.283 Contact Map
4fu0A 2 0.935 100 0.289 Contact Map
3se7A 4 0.9153 100 0.289 Contact Map
3k3pA 2 0.8785 100 0.292 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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