| 1APS |
| ID: | 1431232232 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (93) | ||
| Sequences: | 2053 (1680.4) | ||
| Seq/Len: | 22.075 | ||
| Nf(neff/√len): | 174.2 |
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: 22.075).
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 |
| 14_F | 46_T | 2.605 | 1.00 |
| 27_E | 31_R | 2.397 | 1.00 |
| 29_E | 32_K | 2.323 | 1.00 |
| 42_T | 48_T | 2.249 | 1.00 |
| 14_F | 77_R | 2.211 | 1.00 |
| 51_V | 61_M | 2.178 | 1.00 |
| 40_K | 48_T | 2.153 | 1.00 |
| 12_E | 46_T | 2.122 | 1.00 |
| 21_C | 24_M | 2.102 | 1.00 |
| 25_Y | 64_W | 2.089 | 1.00 |
| 8_S | 50_Q | 1.928 | 1.00 |
| 26_A | 65_L | 1.927 | 1.00 |
| 8_S | 52_Q | 1.861 | 1.00 |
| 11_Y | 62_K | 1.854 | 1.00 |
| 38_W | 97_R | 1.801 | 1.00 |
| 33_I | 64_W | 1.774 | 1.00 |
| 52_Q | 90_E | 1.706 | 1.00 |
| 10_D | 48_T | 1.668 | 1.00 |
| 35_V | 51_V | 1.667 | 1.00 |
| 38_W | 50_Q | 1.666 | 1.00 |
| 64_W | 68_V | 1.663 | 1.00 |
| 12_E | 42_T | 1.649 | 1.00 |
| 70_S | 73_S | 1.584 | 1.00 |
| 55_E | 59_N | 1.521 | 1.00 |
| 36_V | 93_N | 1.404 | 0.99 |
| 13_V | 78_T | 1.394 | 0.99 |
| 52_Q | 89_L | 1.363 | 0.99 |
| 62_K | 80_F | 1.347 | 0.99 |
| 32_K | 64_W | 1.332 | 0.99 |
| 20_V | 23_R | 1.328 | 0.99 |
| 14_F | 79_N | 1.255 | 0.99 |
| 51_V | 58_V | 1.249 | 0.99 |
| 11_Y | 49_G | 1.244 | 0.98 |
| 35_V | 53_G | 1.225 | 0.98 |
| 13_V | 49_G | 1.204 | 0.98 |
| 7_K | 55_E | 1.199 | 0.98 |
| 51_V | 65_L | 1.172 | 0.98 |
| 13_V | 22_F | 1.146 | 0.97 |
| 9_V | 80_F | 1.123 | 0.97 |
| 60_S | 63_S | 1.106 | 0.96 |
| 9_V | 82_N | 1.076 | 0.95 |
| 40_K | 97_R | 1.075 | 0.95 |
| 49_G | 61_M | 1.073 | 0.95 |
| 42_T | 46_T | 1.063 | 0.95 |
| 69_G | 73_S | 1.024 | 0.93 |
| 29_E | 64_W | 1.020 | 0.93 |
| 13_V | 75_I | 1.013 | 0.93 |
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 | |
| 1urrA | 1 | 0.9898 | 100 | 0.013 | Contact Map |
| 1apsA | 1 | 1 | 100 | 0.024 | Contact Map |
| 4g9iA | 6 | 0.9184 | 100 | 0.026 | Contact Map |
| 2vh7A | 1 | 0.9592 | 100 | 0.032 | Contact Map |
| 2lxfA | 1 | 0.9592 | 100 | 0.033 | Contact Map |
| 3vthA | 2 | 0.9592 | 99.9 | 0.051 | Contact Map |
| 2fhmA | 1 | 0.9184 | 99.9 | 0.057 | Contact Map |
| 3trgA | 1 | 0.949 | 99.9 | 0.057 | Contact Map |
| 2bjdA | 2 | 0.9184 | 99.9 | 0.061 | Contact Map |
| 1w2iA | 2 | 0.9184 | 99.9 | 0.064 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)