| ljp-jck |
| ID: | 1487816251 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (96) | ||
| Sequences: | 181 (128.4) | ||
| Seq/Len: | 1.885 | ||
| Nf(neff/√len): | 13.1 |
Jackhmmer Results: (2016_04)
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: 1.885).
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 |
| 30_D | 53_S | 2.968 | 1.00 |
| 7_Q | 10_A | 2.344 | 1.00 |
| 50_M | 60_I | 1.966 | 0.99 |
| 22_S | 28_S | 1.808 | 0.97 |
| 21_E | 54_T | 1.665 | 0.95 |
| 42_P | 87_Y | 1.643 | 0.95 |
| 83_D | 90_G | 1.575 | 0.93 |
| 21_E | 25_S | 1.549 | 0.92 |
| 43_T | 46_Q | 1.499 | 0.90 |
| 73_L | 87_Y | 1.468 | 0.89 |
| 51_C | 71_C | 1.432 | 0.87 |
| 31_S | 68_P | 1.430 | 0.87 |
| 50_M | 76_P | 1.354 | 0.83 |
| 5_A | 48_K | 1.325 | 0.81 |
| 11_A | 14_T | 1.321 | 0.81 |
| 7_Q | 72_D | 1.299 | 0.79 |
| 54_T | 57_N | 1.296 | 0.79 |
| 19_L | 33_Y | 1.282 | 0.78 |
| 14_T | 23_S | 1.280 | 0.78 |
| 59_M | 76_P | 1.264 | 0.77 |
| 18_I | 87_Y | 1.235 | 0.74 |
| 51_C | 70_D | 1.208 | 0.72 |
| 43_T | 94_K | 1.191 | 0.70 |
| 32_G | 65_A | 1.190 | 0.70 |
| 50_M | 87_Y | 1.175 | 0.69 |
| 30_D | 96_A | 1.167 | 0.68 |
| 28_S | 38_A | 1.157 | 0.67 |
| 59_M | 62_K | 1.156 | 0.67 |
| 15_L | 29_K | 1.155 | 0.67 |
| 42_P | 50_M | 1.133 | 0.65 |
| 10_A | 83_D | 1.120 | 0.63 |
| 46_Q | 82_L | 1.113 | 0.63 |
| 16_V | 86_T | 1.112 | 0.63 |
| 86_T | 89_N | 1.111 | 0.62 |
| 34_S | 66_L | 1.103 | 0.62 |
| 42_P | 73_L | 1.096 | 0.61 |
| 44_N | 62_K | 1.096 | 0.61 |
| 45_A | 48_K | 1.088 | 0.60 |
| 69_P | 72_D | 1.086 | 0.60 |
| 80_L | 84_V | 1.070 | 0.58 |
| 45_A | 67_N | 1.064 | 0.58 |
| 15_L | 59_M | 1.063 | 0.57 |
| 74_T | 89_N | 1.055 | 0.57 |
| 44_N | 47_Y | 1.049 | 0.56 |
| 26_Q | 37_T | 1.045 | 0.55 |
| 14_T | 29_K | 1.027 | 0.54 |
| 58_T | 64_V | 1.002 | 0.51 |
| 2_A | 54_T | 1.002 | 0.51 |
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 | |
| 2aibA | 2 | 1 | 99.9 | 0.077 | Contact Map |
| 2posA | 4 | 0.9592 | 99.9 | 0.159 | Contact Map |
| 2la3A | 1 | 0.6122 | 4.1 | 0.922 | Contact Map |
| 1wrdA | 1 | 0.5204 | 3.6 | 0.925 | Contact Map |
| 4e5xG | 2 | 0.3469 | 2.7 | 0.929 | Contact Map |
| 1up8A | 4 | 0.9592 | 2.3 | 0.932 | Contact Map |
| 3wwqC | 4 | 0 | 2 | 0.934 | Contact Map |
| 2js9A | 1 | 0.3878 | 1.8 | 0.935 | Contact Map |
| 4ae8A | 4 | 0.3061 | 1.3 | 0.941 | Contact Map |
| 2ixnA | 2 | 0.6327 | 1.2 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)