| 1gm1 |
| ID: | 1486855123 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 94 (90) | ||
| Sequences: | 6346 (3762.9) | ||
| Seq/Len: | 70.511 | ||
| Nf(neff/√len): | 396.6 |
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: 70.511).
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 |
| 59_A | 87_L | 3.421 | 1.00 |
| 51_I | 88_L | 2.750 | 1.00 |
| 41_P | 46_E | 2.561 | 1.00 |
| 65_L | 68_A | 2.466 | 1.00 |
| 63_V | 76_T | 2.416 | 1.00 |
| 34_I | 73_A | 2.308 | 1.00 |
| 69_T | 72_Q | 2.263 | 1.00 |
| 68_A | 72_Q | 2.029 | 1.00 |
| 6_F | 90_K | 2.029 | 1.00 |
| 70_H | 74_V | 2.021 | 1.00 |
| 42_K | 46_E | 1.975 | 1.00 |
| 7_E | 87_L | 1.966 | 1.00 |
| 9_E | 85_H | 1.842 | 1.00 |
| 35_Y | 56_R | 1.762 | 1.00 |
| 56_R | 89_E | 1.757 | 1.00 |
| 23_G | 70_H | 1.687 | 1.00 |
| 68_A | 76_T | 1.670 | 1.00 |
| 65_L | 73_A | 1.669 | 1.00 |
| 59_A | 62_G | 1.656 | 1.00 |
| 9_E | 83_V | 1.614 | 1.00 |
| 52_H | 90_K | 1.552 | 1.00 |
| 36_V | 51_I | 1.529 | 1.00 |
| 68_A | 73_A | 1.491 | 1.00 |
| 39_I | 43_G | 1.477 | 1.00 |
| 20_S | 40_I | 1.476 | 1.00 |
| 11_A | 83_V | 1.445 | 1.00 |
| 72_Q | 75_E | 1.432 | 1.00 |
| 33_G | 56_R | 1.425 | 1.00 |
| 71_K | 75_E | 1.376 | 0.99 |
| 60_V | 65_L | 1.373 | 0.99 |
| 7_E | 85_H | 1.277 | 0.99 |
| 55_D | 90_K | 1.219 | 0.98 |
| 22_T | 37_K | 1.201 | 0.98 |
| 18_G | 21_V | 1.161 | 0.97 |
| 39_I | 53_K | 1.155 | 0.97 |
| 59_A | 64_S | 1.148 | 0.97 |
| 62_G | 85_H | 1.101 | 0.96 |
| 39_I | 45_A | 1.090 | 0.96 |
| 13_T | 16_S | 1.084 | 0.96 |
| 8_V | 18_G | 1.037 | 0.94 |
| 13_T | 44_A | 1.036 | 0.94 |
| 74_V | 78_R | 1.035 | 0.94 |
| 64_S | 67_G | 1.033 | 0.94 |
| 79_N | 82_Q | 1.013 | 0.93 |
| 75_E | 79_N | 1.012 | 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 | |
| 2xkxA | 2 | 1 | 99.1 | 0.128 | Contact Map |
| 1d5gA | 1 | 1 | 98.9 | 0.181 | Contact Map |
| 2fneA | 3 | 1 | 98.9 | 0.197 | Contact Map |
| 3eggC | 2 | 0.9681 | 98.9 | 0.199 | Contact Map |
| 1q7xA | 1 | 1 | 98.8 | 0.208 | Contact Map |
| 1z87A | 1 | 0.9681 | 98.8 | 0.209 | Contact Map |
| 1i16A | 1 | 0.9894 | 98.8 | 0.215 | Contact Map |
| 1uhpA | 1 | 1 | 98.8 | 0.218 | Contact Map |
| 2dazA | 1 | 0.9787 | 98.8 | 0.224 | Contact Map |
| 2awxA | 2 | 0.9574 | 98.8 | 0.227 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)