| T0808 100-200 -force run |
| ID: | 1404888676 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (99) | ||
| Sequences: | 80 (69.2) | ||
| Seq/Len: | 0.808 | ||
| Nf(neff/√len): | 7.0 |
Jackhmmer Results: (2014_04_16)
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: 0.808).
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 |
| 87_E | 90_H | 2.326 | 0.98 |
| 48_V | 56_G | 2.297 | 0.98 |
| 66_Y | 78_N | 2.070 | 0.95 |
| 64_L | 95_A | 1.605 | 0.78 |
| 47_Y | 89_M | 1.604 | 0.78 |
| 55_W | 69_P | 1.514 | 0.72 |
| 22_G | 30_F | 1.482 | 0.69 |
| 50_D | 53_D | 1.451 | 0.67 |
| 90_H | 93_Y | 1.413 | 0.64 |
| 8_I | 36_L | 1.406 | 0.64 |
| 7_S | 38_A | 1.391 | 0.62 |
| 10_I | 13_A | 1.347 | 0.59 |
| 85_E | 93_Y | 1.339 | 0.58 |
| 8_I | 53_D | 1.316 | 0.56 |
| 16_V | 36_L | 1.303 | 0.55 |
| 33_I | 80_I | 1.275 | 0.52 |
| 41_V | 80_I | 1.271 | 0.52 |
| 23_V | 89_M | 1.253 | 0.50 |
| 56_G | 60_P | 1.250 | 0.50 |
| 20_L | 31_G | 1.246 | 0.50 |
| 55_W | 96_A | 1.242 | 0.49 |
| 44_K | 80_I | 1.234 | 0.49 |
| 21_Q | 81_T | 1.227 | 0.48 |
| 85_E | 96_A | 1.222 | 0.48 |
| 27_G | 32_E | 1.221 | 0.48 |
| 56_G | 59_G | 1.199 | 0.46 |
| 48_V | 82_V | 1.189 | 0.45 |
| 47_Y | 99_G | 1.183 | 0.44 |
| 60_P | 90_H | 1.177 | 0.44 |
| 18_I | 53_D | 1.175 | 0.44 |
| 57_R | 95_A | 1.155 | 0.42 |
| 5_V | 91_S | 1.149 | 0.41 |
| 26_S | 31_G | 1.121 | 0.39 |
| 59_G | 90_H | 1.106 | 0.38 |
| 64_L | 72_D | 1.100 | 0.37 |
| 78_N | 98_F | 1.080 | 0.36 |
| 18_I | 30_F | 1.079 | 0.36 |
| 3_V | 33_I | 1.071 | 0.35 |
| 62_V | 76_F | 1.070 | 0.35 |
| 8_I | 91_S | 1.066 | 0.35 |
| 77_Y | 93_Y | 1.064 | 0.34 |
| 5_V | 19_D | 1.060 | 0.34 |
| 66_Y | 94_M | 1.054 | 0.34 |
| 91_S | 99_G | 1.036 | 0.32 |
| 19_D | 80_I | 1.021 | 0.31 |
| 6_G | 93_Y | 1.021 | 0.31 |
| 66_Y | 81_T | 1.019 | 0.31 |
| 62_V | 94_M | 1.018 | 0.31 |
| 70_E | 84_K | 1.014 | 0.31 |
| 36_L | 68_L | 1.013 | 0.31 |
| 32_E | 40_N | 1.005 | 0.30 |
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 | |
| 4fchA | 2 | 0.8614 | 8 | 0.945 | Contact Map |
| 3ghmA | 1 | 0.703 | 7.9 | 0.945 | Contact Map |
| 2xomA | 1 | 0.3861 | 7.2 | 0.946 | Contact Map |
| 2vzsA | 2 | 0 | 6.8 | 0.947 | Contact Map |
| 4kmqA | 1 | 0.3663 | 6.5 | 0.947 | Contact Map |
| 1x9pA | 1 | 0.901 | 6.2 | 0.948 | Contact Map |
| 3mtxA | 2 | 0.4059 | 4.1 | 0.952 | Contact Map |
| 3hnmA | 4 | 0.4554 | 4 | 0.952 | Contact Map |
| 4c91A | 2 | 0.5347 | 3.7 | 0.953 | Contact Map |
| 4ar2A | 1 | 0.9505 | 3.7 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)