| smt3alone |
| ID: | 1476316729 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (81) | ||
| Sequences: | 596 (398.3) | ||
| Seq/Len: | 7.358 | ||
| Nf(neff/√len): | 44.3 |
HHblits Results: (2016_02)
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: 7.358).
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 |
| 57_Q | 61_D | 3.192 | 1.00 |
| 48_Y | 64_M | 2.706 | 1.00 |
| 45_R | 75_E | 2.500 | 1.00 |
| 34_A | 44_L | 2.350 | 1.00 |
| 27_R | 31_E | 2.153 | 1.00 |
| 22_K | 60_E | 1.814 | 1.00 |
| 59_P | 64_M | 1.717 | 1.00 |
| 64_M | 68_D | 1.684 | 1.00 |
| 26_L | 29_L | 1.589 | 1.00 |
| 54_Q | 57_Q | 1.580 | 1.00 |
| 47_L | 73_H | 1.471 | 0.99 |
| 53_I | 62_L | 1.429 | 0.99 |
| 24_T | 28_R | 1.417 | 0.99 |
| 9_V | 29_L | 1.408 | 0.99 |
| 47_L | 52_R | 1.397 | 0.99 |
| 54_Q | 61_D | 1.296 | 0.98 |
| 15_E | 45_R | 1.296 | 0.98 |
| 31_E | 35_K | 1.295 | 0.98 |
| 24_T | 36_R | 1.288 | 0.98 |
| 68_D | 71_E | 1.284 | 0.98 |
| 15_E | 69_I | 1.276 | 0.98 |
| 25_P | 56_D | 1.266 | 0.97 |
| 43_S | 46_F | 1.227 | 0.97 |
| 18_F | 21_K | 1.219 | 0.97 |
| 30_M | 55_A | 1.179 | 0.96 |
| 18_F | 33_F | 1.171 | 0.95 |
| 30_M | 37_Q | 1.157 | 0.95 |
| 17_F | 74_R | 1.139 | 0.94 |
| 5_I | 27_R | 1.127 | 0.94 |
| 38_G | 44_L | 1.124 | 0.94 |
| 4_H | 22_K | 1.121 | 0.94 |
| 53_I | 70_I | 1.105 | 0.93 |
| 7_L | 13_S | 1.104 | 0.93 |
| 76_Q | 79_G | 1.083 | 0.92 |
| 25_P | 59_P | 1.048 | 0.91 |
| 28_R | 76_Q | 1.038 | 0.90 |
| 29_L | 33_F | 1.037 | 0.90 |
| 10_S | 71_E | 1.021 | 0.89 |
| 30_M | 46_F | 1.015 | 0.89 |
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 | |
| 3ix6A | 2 | 0.0976 | 99.9 | 0.116 | Contact Map |
| 2l76A | 1 | 0.9512 | 99.9 | 0.17 | Contact Map |
| 3uf8A | 1 | 1 | 99.8 | 0.206 | Contact Map |
| 3goeA | 1 | 0.9024 | 99.8 | 0.273 | Contact Map |
| 4da1A | 1 | 0 | 99.7 | 0.304 | Contact Map |
| 3pgeA | 1 | 0.9878 | 99.7 | 0.335 | Contact Map |
| 3v7oA | 2 | 0.9878 | 99.7 | 0.338 | Contact Map |
| 3tixA | 2 | 0.9878 | 99.7 | 0.34 | Contact Map |
| 2ekeC | 2 | 0.9268 | 99.6 | 0.369 | Contact Map |
| 2k8hA | 1 | 0.9634 | 99.6 | 0.37 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)