| PPW_first_in_allOri_Pred07_PP_ORIGINAL |
| ID: | 1485430728 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 94 (91) | ||
| Sequences: | 1999 (1289.7) | ||
| Seq/Len: | 21.967 | ||
| Nf(neff/√len): | 135.2 |
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: 21.967).
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 |
| 36_E | 59_E | 5.408 | 1.00 |
| 62_S | 65_D | 4.085 | 1.00 |
| 64_E | 68_N | 3.215 | 1.00 |
| 32_K | 74_E | 2.882 | 1.00 |
| 7_I | 69_W | 2.296 | 1.00 |
| 5_A | 63_R | 2.134 | 1.00 |
| 29_T | 69_W | 2.114 | 1.00 |
| 44_E | 67_Y | 2.089 | 1.00 |
| 30_L | 35_G | 2.077 | 1.00 |
| 21_Q | 24_A | 2.060 | 1.00 |
| 63_R | 67_Y | 2.052 | 1.00 |
| 76_Q | 79_I | 1.840 | 1.00 |
| 4_T | 59_E | 1.757 | 1.00 |
| 67_Y | 71_H | 1.732 | 1.00 |
| 17_E | 20_Q | 1.520 | 1.00 |
| 18_K | 21_Q | 1.519 | 1.00 |
| 25_R | 78_L | 1.514 | 1.00 |
| 27_A | 31_A | 1.511 | 1.00 |
| 65_D | 68_N | 1.480 | 1.00 |
| 61_P | 65_D | 1.465 | 1.00 |
| 12_T | 87_D | 1.454 | 1.00 |
| 18_K | 85_G | 1.453 | 1.00 |
| 14_K | 87_D | 1.409 | 1.00 |
| 28_S | 31_A | 1.377 | 0.99 |
| 20_Q | 24_A | 1.373 | 0.99 |
| 39_V | 57_I | 1.372 | 0.99 |
| 26_V | 29_T | 1.338 | 0.99 |
| 12_T | 53_K | 1.329 | 0.99 |
| 82_R | 88_S | 1.328 | 0.99 |
| 79_I | 83_D | 1.309 | 0.99 |
| 32_K | 72_S | 1.276 | 0.99 |
| 77_A | 80_S | 1.268 | 0.99 |
| 21_Q | 81_T | 1.233 | 0.98 |
| 10_G | 55_Q | 1.223 | 0.98 |
| 36_E | 61_P | 1.219 | 0.98 |
| 66_A | 92_L | 1.214 | 0.98 |
| 47_H | 70_Y | 1.171 | 0.98 |
| 29_T | 78_L | 1.168 | 0.97 |
| 10_G | 89_Q | 1.154 | 0.97 |
| 25_R | 81_T | 1.132 | 0.97 |
| 33_Y | 72_S | 1.095 | 0.96 |
| 63_R | 92_L | 1.089 | 0.96 |
| 60_F | 69_W | 1.067 | 0.95 |
| 25_R | 77_A | 1.042 | 0.94 |
| 21_Q | 25_R | 1.018 | 0.93 |
| 8_I | 57_I | 1.008 | 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 | |
| 3lo3A | 28 | 1 | 99.9 | 0.022 | Contact Map |
| 2fiuA | 2 | 0.9787 | 99.9 | 0.09 | Contact Map |
| 3hhlA | 1 | 0.9681 | 99.9 | 0.178 | Contact Map |
| 2ftrA | 2 | 0.9787 | 93.6 | 0.782 | Contact Map |
| 1rjjA | 2 | 0.9681 | 92.6 | 0.789 | Contact Map |
| 3hf5A | 4 | 0.9787 | 91.2 | 0.797 | Contact Map |
| 2zdoA | 4 | 0.9787 | 91.1 | 0.797 | Contact Map |
| 2fb0A | 1 | 0.9574 | 90 | 0.802 | Contact Map |
| 3kg0A | 3 | 0.9574 | 89.8 | 0.803 | Contact Map |
| 1q4rA | 1 | 0.9362 | 88.7 | 0.807 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)