| lipocalin |
| ID: | 1420768420 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 158 (153) | ||
| Sequences: | 1300 (961) | ||
| Seq/Len: | 8.497 | ||
| Nf(neff/√len): | 77.7 |
HHblits Results: (2013_03)
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: 8.497).
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 |
| 92_H | 95_D | 3.174 | 1.00 |
| 42_T | 50_E | 2.741 | 1.00 |
| 127_L | 146_I | 2.551 | 1.00 |
| 10_I | 49_L | 2.392 | 1.00 |
| 44_L | 48_N | 2.367 | 1.00 |
| 50_E | 65_K | 2.328 | 1.00 |
| 115_L | 130_F | 2.201 | 1.00 |
| 90_R | 96_H | 2.133 | 1.00 |
| 48_N | 69_E | 2.077 | 1.00 |
| 133_A | 137_R | 1.994 | 1.00 |
| 140_S | 143_S | 1.972 | 1.00 |
| 96_H | 126_A | 1.925 | 1.00 |
| 76_K | 87_Y | 1.884 | 1.00 |
| 113_V | 144_I | 1.811 | 1.00 |
| 34_E | 55_M | 1.788 | 1.00 |
| 133_A | 136_A | 1.774 | 1.00 |
| 70_K | 74_P | 1.750 | 1.00 |
| 124_L | 128_E | 1.719 | 1.00 |
| 71_T | 93_V | 1.692 | 1.00 |
| 39_M | 53_V | 1.672 | 1.00 |
| 117_G | 122_N | 1.661 | 1.00 |
| 48_N | 67_V | 1.601 | 1.00 |
| 54_T | 63_E | 1.569 | 1.00 |
| 122_N | 130_F | 1.535 | 1.00 |
| 100_Y | 139_L | 1.503 | 1.00 |
| 115_L | 122_N | 1.485 | 1.00 |
| 42_T | 52_K | 1.453 | 0.99 |
| 19_L | 22_M | 1.448 | 0.99 |
| 16_T | 40_T | 1.429 | 0.99 |
| 20_K | 117_G | 1.424 | 0.99 |
| 132_K | 136_A | 1.422 | 0.99 |
| 90_R | 129_D | 1.419 | 0.99 |
| 124_L | 127_L | 1.396 | 0.99 |
| 9_E | 12_D | 1.372 | 0.99 |
| 131_E | 141_T | 1.331 | 0.99 |
| 13_V | 99_F | 1.318 | 0.99 |
| 98_I | 133_A | 1.305 | 0.99 |
| 98_I | 130_F | 1.279 | 0.98 |
| 130_F | 133_A | 1.255 | 0.98 |
| 14_S | 43_T | 1.239 | 0.98 |
| 8_E | 88_I | 1.227 | 0.98 |
| 82_G | 93_V | 1.220 | 0.97 |
| 54_T | 61_C | 1.217 | 0.97 |
| 31_M | 117_G | 1.207 | 0.97 |
| 16_T | 38_P | 1.198 | 0.97 |
| 76_K | 85_V | 1.196 | 0.97 |
| 89_I | 133_A | 1.186 | 0.97 |
| 127_L | 131_E | 1.185 | 0.97 |
| 14_S | 49_L | 1.170 | 0.97 |
| 91_S | 96_H | 1.156 | 0.96 |
| 19_L | 66_A | 1.155 | 0.96 |
| 13_V | 39_M | 1.151 | 0.96 |
| 40_T | 54_T | 1.131 | 0.96 |
| 92_H | 96_H | 1.127 | 0.95 |
| 90_R | 130_F | 1.118 | 0.95 |
| 126_A | 129_D | 1.107 | 0.95 |
| 35_S | 148_R | 1.101 | 0.95 |
| 41_L | 53_V | 1.072 | 0.94 |
| 8_E | 75_G | 1.066 | 0.93 |
| 90_R | 133_A | 1.063 | 0.93 |
| 98_I | 122_N | 1.061 | 0.93 |
| 125_E | 129_D | 1.051 | 0.93 |
| 90_R | 98_I | 1.040 | 0.92 |
| 5_A | 91_S | 1.021 | 0.91 |
| 98_I | 134_A | 1.017 | 0.91 |
| 28_F | 33_L | 1.008 | 0.90 |
| 104_E | 107_G | 1.006 | 0.90 |
| 88_I | 99_F | 1.001 | 0.90 |
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 | |
| 1ew3A | 1 | 0.9873 | 100 | 0.193 | Contact Map |
| 3l4rA | 1 | 0.9367 | 100 | 0.2 | Contact Map |
| 1xkiA | 1 | 0.8101 | 100 | 0.204 | Contact Map |
| 4oddB | 3 | 0.943 | 100 | 0.205 | Contact Map |
| 3fiqA | 2 | 0.9684 | 100 | 0.207 | Contact Map |
| 2hlvA | 1 | 0.9177 | 100 | 0.21 | Contact Map |
| 3kffA | 1 | 0.943 | 100 | 0.211 | Contact Map |
| 3saoA | 2 | 0.9367 | 100 | 0.211 | Contact Map |
| 3o22A | 1 | 0.9684 | 100 | 0.211 | Contact Map |
| 1bj7A | 1 | 0.9241 | 100 | 0.212 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)