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OPENSEQ.org
HOLB - DNA polymerase III subunit delta'
UniProt: P28631 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11500
Length: 334 (315)
Sequences: 3329
Seq/Len: 10.57
HOLB
Paralog alert: 0.69 [within 20: 0.07] - 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
177_S 184_Q 3.531 1.00
59_C 62_C 3.351 1.00
88_L 121_T 3.078 1.00
228_D 231_S 3.053 1.00
62_C 65_C 2.889 1.00
50_C 62_C 2.81 1.00
50_C 65_C 2.8 1.00
29_I 164_L 2.698 1.00
67_L 106_L 2.541 1.00
168_P 171_Y 2.534 1.00
50_C 59_C 2.464 1.00
68_M 76_Y 2.458 1.00
46_R 69_Q 2.397 1.00
90_V 94_R 2.345 1.00
59_C 65_C 2.322 1.00
76_Y 113_W 2.32 1.00
61_H 66_Q 2.304 1.00
48_L 140_W 2.29 1.00
167_P 198_P 2.225 1.00
176_L 201_A 2.222 1.00
40_L 164_L 2.201 1.00
60_G 69_Q 2.199 1.00
183_S 186_A 2.149 1.00
52_Q 61_H 2.148 1.00
89_G 121_T 2.108 1.00
109_A 140_W 2.046 1.00
88_L 123_A 2.023 1.00
173_V 188_L 2.016 1.00
173_V 177_S 1.991 1.00
24_H 27_L 1.972 1.00
292_D 318_R 1.926 1.00
259_H 283_P 1.921 1.00
309_E 313_T 1.894 1.00
51_Q 63_R 1.865 1.00
90_V 123_A 1.858 1.00
8_R 171_Y 1.857 1.00
19_Q 56_H 1.829 1.00
87_T 121_T 1.817 1.00
31_A 37_D 1.79 1.00
175_W 198_P 1.754 1.00
172_A 198_P 1.729 1.00
172_A 191_L 1.715 1.00
296_I 315_L 1.708 1.00
295_H 299_Q 1.702 1.00
14_L 44_L 1.699 1.00
289_I 319_I 1.674 1.00
271_P 275_A 1.673 1.00
276_E 280_H 1.564 1.00
170_Q 174_T 1.554 1.00
117_A 151_L 1.551 1.00
251_L 277_L 1.525 1.00
100_L 112_V 1.515 1.00
73_H 107_G 1.5 1.00
174_T 178_R 1.487 1.00
173_V 187_L 1.487 1.00
66_Q 70_A 1.487 1.00
282_S 285_R 1.47 1.00
246_H 297_R 1.458 1.00
216_L 219_A 1.444 1.00
253_M 257_K 1.44 1.00
121_T 124_A 1.418 1.00
174_T 177_S 1.412 1.00
194_S 201_A 1.403 0.99
177_S 187_L 1.402 0.99
258_R 274_V 1.391 0.99
23_G 140_W 1.388 0.99
104_A 138_E 1.37 0.99
249_A 293_V 1.369 0.99
222_Y 225_P 1.332 0.99
90_V 121_T 1.314 0.99
175_W 178_R 1.313 0.99
171_Y 174_T 1.312 0.99
41_I 142_F 1.31 0.99
179_E 202_L 1.286 0.99
148_P 151_L 1.285 0.99
203_A 206_Q 1.283 0.99
63_R 67_L 1.278 0.99
58_S 62_C 1.273 0.99
24_H 160_R 1.272 0.99
90_V 127_A 1.265 0.99
41_I 113_W 1.256 0.99
32_L 197_S 1.254 0.99
173_V 191_L 1.251 0.99
293_V 315_L 1.251 0.99
249_A 290_L 1.238 0.98
60_G 65_C 1.238 0.98
213_R 269_D 1.237 0.98
88_L 114_V 1.218 0.98
234_A 238_H 1.214 0.98
93_V 97_T 1.21 0.98
93_V 124_A 1.205 0.98
129_L 154_T 1.204 0.98
296_I 311_L 1.204 0.98
272_G 275_A 1.201 0.98
120_L 124_A 1.198 0.98
104_A 108_G 1.197 0.98
142_F 164_L 1.194 0.98
51_Q 64_G 1.187 0.98
111_V 142_F 1.183 0.98
292_D 315_L 1.178 0.98
63_R 66_Q 1.176 0.98
275_A 279_N 1.175 0.98
80_A 115_T 1.169 0.97
250_T 254_D 1.168 0.97
52_Q 55_G 1.167 0.97
255_A 286_L 1.167 0.97
30_Q 161_L 1.166 0.97
252_L 289_I 1.16 0.97
131_T 141_F 1.159 0.97
151_L 156_R 1.153 0.97
232_L 316_L 1.152 0.97
81_P 143_L 1.147 0.97
78_T 81_P 1.144 0.97
116_D 146_R 1.138 0.97
252_L 293_V 1.135 0.97
96_V 112_V 1.128 0.97
88_L 92_A 1.127 0.97
28_L 151_L 1.127 0.97
259_H 286_L 1.124 0.97
30_Q 163_Y 1.12 0.96
231_S 235_A 1.119 0.96
12_E 16_A 1.112 0.96
126_N 134_E 1.11 0.96
8_R 174_T 1.107 0.96
135_P 154_T 1.102 0.96
91_D 94_R 1.098 0.96
87_T 124_A 1.091 0.96
182_M 187_L 1.088 0.96
166_P 195_A 1.087 0.96
184_Q 188_L 1.085 0.96
252_L 286_L 1.084 0.96
156_R 161_L 1.084 0.96
91_D 123_A 1.08 0.95
8_R 12_E 1.08 0.95
113_W 144_A 1.074 0.95
34_G 37_D 1.07 0.95
64_G 107_G 1.07 0.95
38_D 199_G 1.068 0.95
211_Q 221_A 1.067 0.95
89_G 92_A 1.064 0.95
59_C 64_G 1.062 0.95
167_P 175_W 1.059 0.95
276_E 279_N 1.058 0.95
44_L 110_K 1.055 0.95
116_D 199_G 1.053 0.95
19_Q 55_G 1.045 0.94
100_L 139_T 1.044 0.94
125_A 152_L 1.043 0.94
129_L 135_P 1.043 0.94
259_H 282_S 1.035 0.94
27_L 44_L 1.031 0.94
295_H 298_E 1.016 0.93
170_Q 188_L 1.011 0.93
245_L 293_V 1.009 0.93
79_L 92_A 1.006 0.93
126_N 154_T 1.001 0.92
78_T 115_T 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
1a5tA111000.332Contact Map0.759
1jr3A30.9821000.533Contact Map0.731
1jr3D10.87721000.565Contact Map0.563
2gnoA10.85631000.568Contact Map0.575
3zh9B10.88021000.575Contact Map0.643
1sxjE10.93111000.583Contact Map0.515
1iqpA60.87431000.602Contact Map0.722
2chqA30.87131000.606Contact Map0.582
1sxjC10.89521000.617Contact Map0.619
1sxjD10.87431000.62Contact Map0.59
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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