| align psi-blast iti2 |
| ID: | 1490016515 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 37 (35) | ||
| Sequences: | 122 (106.7) | ||
| Seq/Len: | 3.486 | ||
| Nf(neff/√len): | 18.0 |
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: 3.486).
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 |
| 31_F | 37_F | 2.356 | 1.00 |
| 24_N | 28_G | 2.124 | 1.00 |
| 4_S | 7_N | 2.026 | 1.00 |
| 20_S | 29_A | 1.608 | 0.98 |
| 9_G | 18_G | 1.530 | 0.97 |
| 12_D | 25_N | 1.416 | 0.95 |
| 4_S | 10_S | 1.385 | 0.94 |
| 31_F | 35_V | 1.328 | 0.92 |
| 15_N | 19_G | 1.308 | 0.92 |
| 5_F | 13_M | 1.277 | 0.90 |
| 5_F | 15_N | 1.234 | 0.88 |
| 7_N | 31_F | 1.207 | 0.87 |
| 19_G | 37_F | 1.202 | 0.86 |
| 17_P | 20_S | 1.118 | 0.81 |
| 15_N | 34_S | 1.100 | 0.79 |
| 20_S | 34_S | 1.093 | 0.78 |
| 10_S | 36_T | 1.080 | 0.77 |
| 12_D | 15_N | 1.064 | 0.76 |
| 2_G | 6_N | 1.044 | 0.74 |
| 6_N | 36_T | 1.044 | 0.74 |
| 16_A | 19_G | 1.029 | 0.72 |
| 3_S | 8_Y | 1.023 | 0.72 |
| 13_M | 20_S | 1.000 | 0.69 |
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 | |
| 2wq4A | 3 | 0.1892 | 1.2 | 0.856 | Contact Map |
| 1s58A | 1 | 0.3514 | 0.6 | 0.886 | Contact Map |
| 2dyqA | 1 | 0.1081 | 0.5 | 0.894 | Contact Map |
| 2pi2A | 4 | 0.1892 | 0.4 | 0.895 | Contact Map |
| 4c7lA | 2 | 1 | 0.4 | 0.896 | Contact Map |
| 3cl5A | 1 | 1 | 0.4 | 0.897 | Contact Map |
| 2iy9A | 1 | 1 | 0.4 | 0.898 | Contact Map |
| 2b6nA | 1 | 1 | 0.4 | 0.899 | Contact Map |
| 3rlfF | 1 | 0.8649 | 0.4 | 0.899 | Contact Map |
| 4aybB | 1 | 0.8919 | 0.4 | 0.9 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)