| 4JZ3_strict |
| ID: | 1429675297 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (59) | ||
| Sequences: | 270 (177.9) | ||
| Seq/Len: | 4.576 | ||
| Nf(neff/√len): | 23.2 |
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: 4.576).
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 |
| 26_E | 43_S | 2.726 | 1.00 |
| 52_I | 57_V | 2.125 | 1.00 |
| 11_D | 23_K | 1.927 | 1.00 |
| 14_S | 21_S | 1.734 | 0.99 |
| 6_F | 15_R | 1.542 | 0.99 |
| 19_D | 24_K | 1.491 | 0.98 |
| 9_L | 34_T | 1.374 | 0.96 |
| 15_R | 37_D | 1.345 | 0.96 |
| 12_Y | 16_T | 1.271 | 0.94 |
| 32_N | 40_L | 1.269 | 0.94 |
| 27_R | 60_S | 1.239 | 0.93 |
| 14_S | 31_V | 1.224 | 0.92 |
| 35_E | 61_D | 1.201 | 0.91 |
| 13_E | 32_N | 1.174 | 0.90 |
| 36_G | 58_A | 1.144 | 0.88 |
| 28_L | 43_S | 1.144 | 0.88 |
| 45_T | 60_S | 1.140 | 0.88 |
| 11_D | 54_S | 1.132 | 0.87 |
| 27_R | 31_V | 1.108 | 0.86 |
| 6_F | 16_T | 1.086 | 0.84 |
| 13_E | 48_Q | 1.071 | 0.83 |
| 10_Y | 28_L | 1.066 | 0.83 |
| 30_I | 41_A | 1.059 | 0.82 |
| 35_E | 48_Q | 1.052 | 0.82 |
| 24_K | 46_T | 1.052 | 0.82 |
| 6_F | 37_D | 1.043 | 0.81 |
| 5_T | 21_S | 1.040 | 0.81 |
| 23_K | 56_Y | 1.031 | 0.80 |
| 24_K | 51_Y | 1.020 | 0.79 |
| 21_S | 56_Y | 1.019 | 0.79 |
| 12_Y | 22_F | 1.017 | 0.78 |
| 6_F | 52_I | 1.017 | 0.78 |
| 10_Y | 57_V | 1.000 | 0.77 |
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 | |
| 4m4zA | 1 | 0.8197 | 99.8 | 0.235 | Contact Map |
| 2yt6A | 1 | 1 | 99.7 | 0.241 | Contact Map |
| 2h8hA | 1 | 0.9344 | 99.7 | 0.265 | Contact Map |
| 1fmkA | 1 | 0.9836 | 99.7 | 0.272 | Contact Map |
| 1qcfA | 1 | 0.9836 | 99.7 | 0.283 | Contact Map |
| 3cqtA | 1 | 0.9508 | 99.7 | 0.293 | Contact Map |
| 1k9aA | 6 | 0.9836 | 99.7 | 0.302 | Contact Map |
| 1opkA | 1 | 0.918 | 99.6 | 0.314 | Contact Map |
| 1ri9A | 1 | 0.9508 | 99.6 | 0.322 | Contact Map |
| 4u5wB | 2 | 0.9508 | 99.6 | 0.322 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)