| ABP1 |
| ID: | 1456819900 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 58 (56) | ||
| Sequences: | 8681 (4860.1) | ||
| Seq/Len: | 155.018 | ||
| Nf(neff/√len): | 649.5 |
HHblits Results: (2015_06)
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: 155.018).
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 |
| 11_A | 18_T | 3.293 | 1.00 |
| 38_G | 49_F | 2.621 | 1.00 |
| 8_D | 20_V | 2.557 | 1.00 |
| 37_L | 46_K | 2.513 | 1.00 |
| 5_A | 19_F | 2.483 | 1.00 |
| 23_D | 40_L | 2.371 | 1.00 |
| 29_E | 37_L | 2.183 | 1.00 |
| 26_I | 39_E | 2.050 | 1.00 |
| 2_W | 24_K | 2.027 | 1.00 |
| 49_F | 54_V | 1.990 | 1.00 |
| 39_E | 46_K | 1.970 | 1.00 |
| 2_W | 26_I | 1.913 | 1.00 |
| 36_W | 51_S | 1.845 | 1.00 |
| 3_A | 56_L | 1.826 | 1.00 |
| 4_T | 24_K | 1.629 | 1.00 |
| 19_F | 25_I | 1.614 | 1.00 |
| 6_E | 55_S | 1.611 | 1.00 |
| 4_T | 55_S | 1.579 | 1.00 |
| 8_D | 21_E | 1.518 | 1.00 |
| 25_I | 38_G | 1.442 | 1.00 |
| 20_V | 23_D | 1.346 | 0.99 |
| 47_G | 50_P | 1.189 | 0.98 |
| 37_L | 48_L | 1.186 | 0.98 |
| 17_L | 38_G | 1.129 | 0.97 |
| 3_A | 54_V | 1.122 | 0.97 |
| 40_L | 43_D | 1.118 | 0.96 |
| 3_A | 27_N | 1.105 | 0.96 |
| 30_F | 36_W | 1.096 | 0.96 |
| 40_L | 45_S | 1.095 | 0.96 |
| 10_D | 18_T | 1.080 | 0.95 |
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 | |
| 4n78F | 1 | 0 | 98.7 | -0.203 | Contact Map |
| 2h8hA | 1 | 0.9828 | 98.6 | -0.187 | Contact Map |
| 4mt7A | 1 | 0 | 98.5 | -0.171 | Contact Map |
| 1fmkA | 1 | 1 | 98.5 | -0.168 | Contact Map |
| 3pvlA | 1 | 0.9483 | 98.5 | -0.166 | Contact Map |
| 2pz1A | 1 | 0.9655 | 98.5 | -0.164 | Contact Map |
| 1k9aA | 6 | 0.9828 | 98.5 | -0.164 | Contact Map |
| 4xi2A | 1 | 0.9828 | 98.5 | -0.163 | Contact Map |
| 1opkA | 1 | 0.9655 | 98.5 | -0.157 | Contact Map |
| 3jv3A | 2 | 0.9655 | 98.5 | -0.157 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)