| d4mhed_ |
| ID: | 1448506870 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 60 (60) | ||
| Sequences: | 1360 (890.3) | ||
| Seq/Len: | 22.667 | ||
| Nf(neff/√len): | 114.9 |
HHblits Results: (2015_06)
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: 22.667).
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 |
| 20_Y | 59_K | 2.861 | 1.00 |
| 17_I | 54_Y | 2.722 | 1.00 |
| 34_L | 44_A | 2.328 | 1.00 |
| 2_L | 26_Q | 2.017 | 1.00 |
| 32_V | 46_P | 1.978 | 1.00 |
| 20_Y | 34_L | 1.947 | 1.00 |
| 49_K | 53_K | 1.733 | 1.00 |
| 45_D | 48_K | 1.686 | 1.00 |
| 3_C | 27_C | 1.614 | 1.00 |
| 14_Q | 57_D | 1.528 | 1.00 |
| 19_D | 35_L | 1.447 | 1.00 |
| 7_Y | 23_T | 1.392 | 0.99 |
| 12_I | 42_I | 1.380 | 0.99 |
| 14_Q | 54_Y | 1.311 | 0.99 |
| 21_S | 35_L | 1.295 | 0.99 |
| 47_N | 57_D | 1.260 | 0.99 |
| 7_Y | 30_P | 1.239 | 0.98 |
| 55_I | 59_K | 1.236 | 0.98 |
| 35_L | 41_Q | 1.227 | 0.98 |
| 32_V | 45_D | 1.210 | 0.98 |
| 20_Y | 31_G | 1.096 | 0.96 |
| 25_P | 28_P | 1.082 | 0.96 |
| 23_T | 30_P | 1.074 | 0.95 |
| 18_V | 53_K | 1.036 | 0.94 |
| 42_I | 45_D | 1.020 | 0.93 |
| 16_F | 38_R | 1.015 | 0.93 |
| 2_L | 25_P | 1.015 | 0.93 |
| 23_T | 31_G | 1.011 | 0.93 |
| 53_K | 56_S | 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 | |
| 1zxtA | 4 | 1 | 99.7 | -0.009 | Contact Map |
| 4rwsC | 1 | 1 | 99.7 | -0.004 | Contact Map |
| 3tn2A | 1 | 1 | 99.7 | -0.003 | Contact Map |
| 1g91A | 1 | 1 | 99.7 | -0.001 | Contact Map |
| 4oijC | 2 | 0.0167 | 99.7 | -0.001 | Contact Map |
| 1cm9A | 2 | 1 | 99.7 | 0.002 | Contact Map |
| 2q8rE | 4 | 1 | 99.7 | 0.003 | Contact Map |
| 4xt1B | 1 | 0.9833 | 99.7 | 0.005 | Contact Map |
| 2q8tA | 4 | 1 | 99.7 | 0.006 | Contact Map |
| 1nr4A | 8 | 1 | 99.7 | 0.006 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)