| hKRAB_ZFPs_alignment |
| ID: | 1466088642 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 21 (21) | ||
| Sequences: | 10252 (6587.8) | ||
| Seq/Len: | 488.190 | ||
| Nf(neff/√len): | 1437.6 |
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: 488.190).
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 | 15_A | 2.165 | 1.00 |
| 10_D | 13_S | 2.067 | 1.00 |
| 15_A | 18_V | 2.054 | 1.00 |
| 2_D | 18_V | 2.020 | 1.00 |
| 2_D | 7_K | 1.945 | 1.00 |
| 13_S | 16_Q | 1.912 | 1.00 |
| 9_L | 13_S | 1.843 | 1.00 |
| 4_C | 17_H | 1.778 | 1.00 |
| 3_S | 18_V | 1.598 | 1.00 |
| 1_C | 4_C | 1.328 | 0.99 |
| 1_C | 21_H | 1.157 | 0.97 |
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 | |
| 1ej6B | 2 | 1 | 88 | -0.248 | Contact Map |
| 1zr9A | 1 | 1 | 83 | -0.194 | Contact Map |
| 2eluA | 1 | 1 | 81.3 | -0.18 | Contact Map |
| 4ijdA | 2 | 1 | 79.2 | -0.163 | Contact Map |
| 2eppA | 1 | 1 | 73.3 | -0.12 | Contact Map |
| 3rayA | 1 | 0 | 67.7 | -0.083 | Contact Map |
| 2lvuA | 1 | 1 | 67 | -0.078 | Contact Map |
| 2elvA | 1 | 1 | 64.8 | -0.066 | Contact Map |
| 2en3A | 1 | 1 | 64.2 | -0.063 | Contact Map |
| 1rimA | 1 | 1 | 64 | -0.06 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)