| YES_HUMAN |
| ID: | 1430407883 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 48 (48) | ||
| Sequences: | 3281 (1877.7) | ||
| Seq/Len: | 68.354 | ||
| Nf(neff/√len): | 271.0 |
HHblits Results: (2013_03)
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: 68.354).
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 |
| 35_A | 46_I | 3.994 | 1.00 |
| 8_A | 15_S | 3.923 | 1.00 |
| 23_Q | 36_R | 2.906 | 1.00 |
| 34_E | 43_N | 2.829 | 1.00 |
| 2_A | 16_F | 2.570 | 1.00 |
| 36_R | 43_N | 2.555 | 1.00 |
| 26_N | 34_E | 2.315 | 1.00 |
| 20_E | 37_S | 2.230 | 1.00 |
| 5_D | 17_K | 2.174 | 1.00 |
| 16_F | 22_F | 2.091 | 1.00 |
| 1_V | 21_R | 1.873 | 1.00 |
| 37_S | 40_T | 1.604 | 1.00 |
| 44_G | 47_P | 1.416 | 1.00 |
| 22_F | 35_A | 1.351 | 0.99 |
| 25_I | 36_R | 1.278 | 0.99 |
| 33_W | 48_S | 1.251 | 0.99 |
| 5_D | 18_K | 1.190 | 0.98 |
| 37_S | 42_K | 1.180 | 0.98 |
| 6_Y | 9_R | 1.060 | 0.95 |
| 17_K | 20_E | 1.022 | 0.93 |
| 14_L | 35_A | 1.007 | 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 | |
| 2yt6A | 1 | 1 | 99.1 | -0.082 | Contact Map |
| 2h8hA | 1 | 1 | 99 | -0.063 | Contact Map |
| 4n78F | 1 | 0 | 99 | -0.055 | Contact Map |
| 2yunA | 1 | 0.9583 | 99 | -0.054 | Contact Map |
| 3c0cA | 1 | 0.9583 | 99 | -0.051 | Contact Map |
| 1fmkA | 1 | 1 | 99 | -0.051 | Contact Map |
| 2xmfA | 1 | 0.9583 | 99 | -0.045 | Contact Map |
| 2vwfA | 1 | 0.9583 | 99 | -0.044 | Contact Map |
| 1ri9A | 1 | 0.9792 | 99 | -0.041 | Contact Map |
| 2ysqA | 1 | 0.9583 | 99 | -0.041 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)