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OPENSEQ.org
HOLA - DNA polymerase III subunit delta
UniProt: P28630 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11412
Length: 343 (327)
Sequences: 4323
Seq/Len: 13.22
HOLA
Paralog alert: 0.85 [within 20: 0.09] - ratio of genomes with paralogs
GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
225_K 228_R 5.192 1.00
152_A 164_D 3.459 1.00
161_E 196_K 3.134 1.00
153_A 157_Q 2.692 1.00
163_D 166_A 2.614 1.00
304_L 330_L 2.579 1.00
143_E 146_Q 2.537 1.00
301_A 331_L 2.523 1.00
163_D 198_T 2.518 1.00
23_L 139_C 2.514 1.00
307_R 311_T 2.492 1.00
163_D 196_K 2.455 1.00
18_R 21_Y 2.438 1.00
152_A 167_N 2.425 1.00
155_A 162_L 2.39 1.00
198_T 201_R 2.275 1.00
261_K 295_Q 2.256 1.00
165_A 199_L 2.203 1.00
152_A 156_K 2.2 1.00
229_A 328_S 2.194 1.00
34_S 139_C 2.187 1.00
148_P 168_Q 2.124 1.00
42_A 109_L 2.026 1.00
52_T 81_L 2.011 1.00
151_V 181_L 1.985 1.00
308_T 323_E 1.89 1.00
142_P 178_L 1.886 1.00
233_L 328_S 1.882 1.00
308_T 327_L 1.866 1.00
77_R 109_L 1.838 1.00
283_R 287_G 1.81 1.00
199_L 203_E 1.808 1.00
155_A 185_L 1.781 1.00
261_K 298_L 1.777 1.00
72_S 107_D 1.748 1.00
11_A 14_N 1.742 1.00
288_E 292_R 1.724 1.00
99_T 102_G 1.717 1.00
254_L 301_A 1.713 1.00
253_E 289_A 1.691 1.00
248_R 309_E 1.679 1.00
220_A 228_R 1.67 1.00
160_L 189_S 1.668 1.00
148_P 152_A 1.658 1.00
294_S 297_Q 1.658 1.00
219_D 285_M 1.645 1.00
149_R 152_A 1.624 1.00
305_L 327_L 1.611 1.00
184_A 187_R 1.605 1.00
220_A 232_I 1.601 1.00
200_P 204_Q 1.59 1.00
261_K 294_S 1.568 1.00
235_Q 239_E 1.564 1.00
260_L 286_M 1.559 1.00
218_V 254_L 1.548 1.00
304_L 327_L 1.537 1.00
234_Q 321_W 1.534 1.00
149_R 153_A 1.524 1.00
321_W 325_E 1.519 1.00
154_R 182_A 1.518 1.00
251_Q 305_L 1.516 1.00
284_G 287_G 1.51 1.00
79_T 111_I 1.5 1.00
150_W 178_L 1.5 1.00
309_E 313_K 1.497 1.00
90_N 93_I 1.482 1.00
166_A 202_V 1.481 1.00
60_D 63_A 1.471 1.00
251_Q 302_V 1.464 1.00
228_R 232_I 1.461 1.00
234_Q 238_L 1.454 1.00
247_L 308_T 1.453 1.00
81_L 113_R 1.453 1.00
25_G 31_L 1.433 1.00
146_Q 149_R 1.429 1.00
221_L 331_L 1.424 1.00
164_D 168_Q 1.42 1.00
162_L 167_N 1.413 1.00
145_A 149_R 1.389 0.99
287_G 291_N 1.386 0.99
284_G 288_E 1.383 0.99
147_L 178_L 1.374 0.99
24_L 136_Q 1.374 0.99
280_Q 283_R 1.37 0.99
39_R 79_T 1.364 0.99
150_W 153_A 1.354 0.99
68_C 80_L 1.352 0.99
224_G 297_Q 1.345 0.99
95_E 99_T 1.341 0.99
251_Q 309_E 1.337 0.99
42_A 77_R 1.336 0.99
257_L 298_L 1.289 0.99
77_R 107_D 1.275 0.99
233_L 324_L 1.262 0.99
219_D 223_M 1.261 0.99
117_L 120_A 1.26 0.99
100_L 104_L 1.246 0.98
167_N 171_C 1.242 0.98
18_R 135_V 1.24 0.98
49_E 75_A 1.227 0.98
217_W 328_S 1.227 0.98
80_L 110_L 1.224 0.98
236_L 246_L 1.208 0.98
258_V 298_L 1.207 0.98
254_L 305_L 1.206 0.98
226_S 332_C 1.2 0.98
24_L 138_T 1.19 0.98
116_K 121_Q 1.188 0.98
43_A 52_T 1.184 0.98
129_A 133_R 1.183 0.98
21_Y 109_L 1.181 0.98
54_S 83_L 1.175 0.98
235_Q 238_L 1.171 0.98
148_P 171_C 1.166 0.97
183_Q 186_E 1.163 0.97
82_L 112_V 1.162 0.97
163_D 199_L 1.161 0.97
147_L 171_C 1.16 0.97
151_V 167_N 1.153 0.97
53_F 78_Q 1.151 0.97
68_C 108_L 1.148 0.97
102_G 132_N 1.124 0.97
174_Y 181_L 1.122 0.97
257_L 286_M 1.12 0.96
35_Q 39_R 1.119 0.96
201_R 204_Q 1.118 0.96
155_A 160_L 1.104 0.96
153_A 156_K 1.103 0.96
219_D 289_A 1.103 0.96
232_I 235_Q 1.102 0.96
98_L 129_A 1.097 0.96
17_L 109_L 1.095 0.96
148_P 167_N 1.091 0.96
39_R 81_L 1.084 0.96
254_L 298_L 1.083 0.96
63_A 66_S 1.072 0.95
220_A 225_K 1.071 0.95
168_Q 172_Y 1.071 0.95
89_P 93_I 1.065 0.95
215_F 253_E 1.062 0.95
119_K 123_N 1.057 0.95
60_D 64_I 1.055 0.95
147_L 181_L 1.05 0.94
17_L 42_A 1.045 0.94
62_N 96_Q 1.044 0.94
102_G 129_A 1.044 0.94
252_R 256_L 1.043 0.94
222_L 293_L 1.042 0.94
191_L 201_R 1.041 0.94
237_R 243_P 1.041 0.94
304_L 308_T 1.04 0.94
79_T 109_L 1.04 0.94
231_H 235_Q 1.039 0.94
102_G 133_R 1.039 0.94
288_E 291_N 1.027 0.94
279_W 282_R 1.019 0.93
7_E 11_A 1.019 0.93
200_P 203_E 1.017 0.93
84_L 115_N 1.008 0.93
23_L 35_Q 1.007 0.93
247_L 305_L 1.006 0.93
22_L 114_G 1.005 0.93
99_T 129_A 1.005 0.93
300_Q 304_L 1.003 0.93
282_R 285_M 1 0.92
72_S 75_A 1 0.92
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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 P(%) HHΔ   Acc
1jr3D10.99711000.215Contact Map0.633
3zh9B10.9651000.287Contact Map0.762
1jr3A30.94461000.45Contact Map0.834
1a5tA10.86591000.496Contact Map0.691
2chqA30.84551000.581Contact Map0.726
1sxjD10.84841000.583Contact Map0.696
3u61B40.81631000.589Contact Map0.695
1iqpA60.84551000.595Contact Map0.855
1sxjB10.84551000.596Contact Map0.71
1jqlB10.408299.90.62Contact Map0.592
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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