| puf4 |
| ID: | 1433422304 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 232 (128.8) | ||
| Seq/Len: | 6.629 | ||
| Nf(neff/√len): | 21.8 |
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: 6.629).
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 |
| 23_L | 35_F | 2.114 | 1.00 |
| 7_V | 11_K | 1.697 | 1.00 |
| 13_L | 24_Q | 1.688 | 1.00 |
| 1_S | 24_Q | 1.603 | 1.00 |
| 1_S | 13_L | 1.570 | 0.99 |
| 9_L | 24_Q | 1.502 | 0.99 |
| 1_S | 23_L | 1.391 | 0.98 |
| 5_Y | 21_K | 1.324 | 0.98 |
| 19_I | 24_Q | 1.320 | 0.98 |
| 3_R | 25_R | 1.257 | 0.97 |
| 21_K | 24_Q | 1.201 | 0.95 |
| 8_Q | 26_L | 1.143 | 0.93 |
| 14_N | 23_L | 1.138 | 0.93 |
| 9_L | 22_C | 1.128 | 0.93 |
| 26_L | 30_N | 1.125 | 0.93 |
| 10_S | 28_P | 1.109 | 0.92 |
| 9_L | 35_F | 1.104 | 0.92 |
| 22_C | 30_N | 1.052 | 0.89 |
| 1_S | 27_K | 1.044 | 0.89 |
| 27_K | 31_F | 1.011 | 0.86 |
| 16_N | 33_F | 1.003 | 0.86 |
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 | |
| 3gvoA | 1 | 1 | 98.3 | 0.385 | Contact Map |
| 3v71A | 1 | 1 | 98.3 | 0.389 | Contact Map |
| 3k62A | 1 | 1 | 98.3 | 0.392 | Contact Map |
| 3k49A | 3 | 1 | 98.3 | 0.399 | Contact Map |
| 4wzrA | 2 | 1 | 97.3 | 0.51 | Contact Map |
| 3bwtA | 1 | 1 | 95.5 | 0.599 | Contact Map |
| 3er9B | 1 | 0.9429 | 29.4 | 0.796 | Contact Map |
| 2vchA | 1 | 0.3714 | 6.7 | 0.847 | Contact Map |
| 1rw2A | 1 | 0.9714 | 6 | 0.851 | Contact Map |
| 2wadA | 3 | 1 | 5.2 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)