| Ascorbate Peroxidase 100-301 |
| ID: | 1495123460 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 202 (176) | ||
| Sequences: | 4504 (1729.3) | ||
| Seq/Len: | 25.591 | ||
| Nf(neff/√len): | 130.4 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 25.591).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 85_F | 89_Y | 4.435 | 1.00 |
| 15_R | 19_H | 3.496 | 1.00 |
| 12_C | 47_E | 3.031 | 1.00 |
| 26_N | 139_G | 3.006 | 1.00 |
| 88_E | 93_G | 2.714 | 1.00 |
| 58_L | 61_A | 2.578 | 1.00 |
| 6_Q | 62_Y | 2.564 | 1.00 |
| 36_D | 60_D | 2.499 | 1.00 |
| 71_L | 75_I | 2.275 | 1.00 |
| 63_Q | 67_S | 2.199 | 1.00 |
| 43_A | 160_E | 2.056 | 1.00 |
| 10_A | 86_S | 2.014 | 1.00 |
| 132_D | 142_W | 1.998 | 1.00 |
| 131_E | 149_M | 1.940 | 1.00 |
| 69_I | 74_F | 1.921 | 1.00 |
| 59_L | 78_A | 1.899 | 1.00 |
| 10_A | 14_L | 1.895 | 1.00 |
| 63_Q | 74_F | 1.866 | 1.00 |
| 11_G | 15_R | 1.865 | 1.00 |
| 16_V | 35_L | 1.781 | 1.00 |
| 128_T | 192_P | 1.766 | 1.00 |
| 126_S | 129_A | 1.742 | 1.00 |
| 9_W | 12_C | 1.730 | 1.00 |
| 15_R | 43_A | 1.711 | 1.00 |
| 146_A | 150_G | 1.695 | 1.00 |
| 43_A | 159_T | 1.669 | 1.00 |
| 155_G | 174_S | 1.542 | 1.00 |
| 60_D | 64_R | 1.516 | 1.00 |
| 10_A | 89_Y | 1.514 | 1.00 |
| 56_F | 75_I | 1.500 | 1.00 |
| 13_V | 78_A | 1.499 | 1.00 |
| 19_H | 22_M | 1.478 | 1.00 |
| 122_N | 125_D | 1.474 | 1.00 |
| 140_L | 144_Q | 1.470 | 1.00 |
| 20_D | 31_S | 1.470 | 1.00 |
| 77_L | 103_F | 1.451 | 1.00 |
| 173_N | 180_N | 1.427 | 1.00 |
| 173_N | 176_K | 1.425 | 1.00 |
| 80_E | 83_I | 1.406 | 0.99 |
| 153_S | 178_N | 1.403 | 0.99 |
| 173_N | 178_N | 1.385 | 0.99 |
| 21_L | 31_S | 1.377 | 0.99 |
| 76_V | 103_F | 1.375 | 0.99 |
| 149_M | 181_Y | 1.374 | 0.99 |
| 15_R | 156_R | 1.364 | 0.99 |
| 153_S | 177_F | 1.350 | 0.99 |
| 131_E | 145_A | 1.346 | 0.99 |
| 20_D | 23_D | 1.342 | 0.99 |
| 155_G | 164_Y | 1.339 | 0.99 |
| 77_L | 105_Y | 1.331 | 0.99 |
| 10_A | 85_F | 1.322 | 0.99 |
| 63_Q | 71_L | 1.321 | 0.99 |
| 6_Q | 58_L | 1.319 | 0.99 |
| 14_L | 83_I | 1.301 | 0.99 |
| 126_S | 130_V | 1.276 | 0.99 |
| 179_N | 183_A | 1.272 | 0.99 |
| 153_S | 167_W | 1.271 | 0.99 |
| 89_Y | 176_K | 1.264 | 0.99 |
| 152_H | 156_R | 1.249 | 0.99 |
| 42_N | 45_L | 1.232 | 0.98 |
| 170_D | 173_N | 1.226 | 0.98 |
| 68_E | 108_T | 1.214 | 0.98 |
| 17_A | 79_A | 1.201 | 0.98 |
| 82_V | 154_I | 1.187 | 0.98 |
| 36_D | 71_L | 1.186 | 0.98 |
| 89_Y | 175_R | 1.185 | 0.98 |
| 87_R | 99_L | 1.175 | 0.98 |
| 24_Y | 27_G | 1.162 | 0.97 |
| 162_S | 165_D | 1.150 | 0.97 |
| 63_Q | 68_E | 1.122 | 0.97 |
| 80_E | 103_F | 1.120 | 0.96 |
| 81_A | 89_Y | 1.118 | 0.96 |
| 38_F | 46_P | 1.114 | 0.96 |
| 39_D | 117_E | 1.113 | 0.96 |
| 127_C | 194_N | 1.112 | 0.96 |
| 155_G | 175_R | 1.088 | 0.96 |
| 63_Q | 69_I | 1.086 | 0.96 |
| 93_G | 99_L | 1.084 | 0.96 |
| 71_L | 74_F | 1.079 | 0.95 |
| 155_G | 161_N | 1.078 | 0.95 |
| 99_L | 177_F | 1.073 | 0.95 |
| 122_N | 130_V | 1.068 | 0.95 |
| 88_E | 91_T | 1.066 | 0.95 |
| 129_A | 136_H | 1.064 | 0.95 |
| 89_Y | 161_N | 1.046 | 0.94 |
| 11_G | 155_G | 1.028 | 0.94 |
| 163_G | 166_G | 1.028 | 0.94 |
| 28_Q | 31_S | 1.027 | 0.94 |
| 191_M | 194_N | 1.025 | 0.93 |
| 150_G | 182_Y | 1.018 | 0.93 |
| 20_D | 75_I | 1.010 | 0.93 |
| 145_A | 149_M | 1.002 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
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-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3vliA | 2 | 0.901 | 100 | 0.253 | Contact Map |
| 3n3rA | 2 | 0.896 | 100 | 0.256 | Contact Map |
| 2vcnA | 1 | 0.896 | 100 | 0.259 | Contact Map |
| 3e2oA | 1 | 0.901 | 100 | 0.267 | Contact Map |
| 3ut2A | 2 | 0.896 | 100 | 0.275 | Contact Map |
| 2ccaA | 2 | 0.901 | 100 | 0.276 | Contact Map |
| 1iynA | 1 | 0.9109 | 100 | 0.276 | Contact Map |
| 1llpA | 1 | 0.8713 | 100 | 0.278 | Contact Map |
| 3wxoA | 1 | 0.901 | 100 | 0.28 | Contact Map |
| 3q3uA | 1 | 0.8812 | 100 | 0.281 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)