| cenpc 725-943 115-219 |
| ID: | 1489136096 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 105 (82) | ||
| Sequences: | 44026 (28616.9) | ||
| Seq/Len: | 536.902 | ||
| Nf(neff/√len): | 3160.2 |
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: 536.902).
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 |
| 62_L | 69_P | 3.608 | 1.00 |
| 62_L | 71_I | 2.940 | 1.00 |
| 62_L | 91_L | 2.750 | 1.00 |
| 64_T | 87_N | 2.577 | 1.00 |
| 64_T | 69_P | 2.506 | 1.00 |
| 61_L | 96_S | 2.446 | 1.00 |
| 62_L | 89_K | 2.437 | 1.00 |
| 33_K | 97_V | 2.369 | 1.00 |
| 60_D | 73_S | 2.305 | 1.00 |
| 58_F | 97_V | 2.304 | 1.00 |
| 35_I | 97_V | 2.199 | 1.00 |
| 73_S | 76_D | 2.169 | 1.00 |
| 60_D | 71_I | 1.892 | 1.00 |
| 44_K | 85_Y | 1.810 | 1.00 |
| 46_H | 85_Y | 1.713 | 1.00 |
| 35_I | 95_E | 1.662 | 1.00 |
| 37_G | 95_E | 1.632 | 1.00 |
| 71_I | 91_L | 1.623 | 1.00 |
| 58_F | 74_T | 1.607 | 1.00 |
| 64_T | 89_K | 1.571 | 1.00 |
| 41_E | 89_K | 1.523 | 1.00 |
| 55_Y | 77_S | 1.518 | 1.00 |
| 51_I | 79_Y | 1.359 | 0.99 |
| 54_F | 78_F | 1.350 | 0.99 |
| 60_D | 92_R | 1.311 | 0.99 |
| 66_H | 85_Y | 1.288 | 0.99 |
| 57_N | 99_L | 1.270 | 0.99 |
| 51_I | 82_S | 1.254 | 0.99 |
| 66_H | 84_N | 1.230 | 0.98 |
| 53_V | 77_S | 1.220 | 0.98 |
| 58_F | 94_E | 1.207 | 0.98 |
| 63_C | 72_L | 1.207 | 0.98 |
| 58_F | 95_E | 1.178 | 0.98 |
| 44_K | 87_N | 1.145 | 0.97 |
| 56_V | 96_S | 1.138 | 0.97 |
| 65_L | 68_T | 1.126 | 0.97 |
| 41_E | 87_N | 1.111 | 0.96 |
| 51_I | 81_P | 1.043 | 0.94 |
| 63_C | 88_I | 1.034 | 0.94 |
| 54_F | 100_F | 1.005 | 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 | |
| 2vpvA | 2 | 0.8571 | 99.5 | 0.256 | Contact Map |
| 2d5fA | 2 | 0.9905 | 99.5 | 0.297 | Contact Map |
| 1o4tA | 2 | 1 | 99.4 | 0.299 | Contact Map |
| 3kscA | 6 | 0.9905 | 99.4 | 0.302 | Contact Map |
| 3c3vA | 1 | 0.9905 | 99.4 | 0.305 | Contact Map |
| 1uijA | 6 | 0.9905 | 99.4 | 0.308 | Contact Map |
| 2e9qA | 1 | 0.9905 | 99.4 | 0.311 | Contact Map |
| 3qacA | 1 | 0.9905 | 99.4 | 0.314 | Contact Map |
| 1fxzA | 3 | 0.9905 | 99.4 | 0.317 | Contact Map |
| 4bifA | 8 | 0.9905 | 99.4 | 0.321 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)