| tprintentov1 |
| ID: | 1431435748 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 62 (62) | ||
| Sequences: | 32960 (27121.5) | ||
| Seq/Len: | 531.613 | ||
| Nf(neff/√len): | 3444.4 |
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: 531.613).
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 |
| 15_E | 18_E | 2.539 | 1.00 |
| 44_Q | 47_V | 2.507 | 1.00 |
| 35_L | 51_M | 2.418 | 1.00 |
| 24_K | 35_L | 2.297 | 1.00 |
| 6_L | 22_V | 2.255 | 1.00 |
| 3_W | 22_V | 2.227 | 1.00 |
| 32_L | 51_M | 2.167 | 1.00 |
| 36_G | 52_F | 1.966 | 1.00 |
| 10_L | 18_E | 1.884 | 1.00 |
| 7_G | 23_Y | 1.878 | 1.00 |
| 39_Y | 47_V | 1.723 | 1.00 |
| 10_L | 22_V | 1.678 | 1.00 |
| 49_K | 53_S | 1.616 | 1.00 |
| 39_Y | 51_M | 1.546 | 1.00 |
| 20_E | 24_K | 1.474 | 1.00 |
| 17_S | 42_K | 1.336 | 0.99 |
| 9_S | 13_S | 1.282 | 0.99 |
| 23_Y | 34_N | 1.264 | 0.99 |
| 27_L | 31_I | 1.224 | 0.98 |
| 20_E | 42_K | 1.219 | 0.98 |
| 54_K | 57_E | 1.163 | 0.97 |
| 37_N | 40_R | 1.141 | 0.97 |
| 20_E | 38_L | 1.139 | 0.97 |
| 39_Y | 44_Q | 1.126 | 0.97 |
| 26_A | 31_I | 1.112 | 0.96 |
| 10_L | 15_E | 1.102 | 0.96 |
| 25_R | 28_T | 1.096 | 0.96 |
| 16_H | 38_L | 1.075 | 0.95 |
| 20_E | 39_Y | 1.048 | 0.94 |
| 8_I | 11_Q | 1.033 | 0.94 |
| 11_Q | 41_Q | 1.027 | 0.94 |
| 54_K | 58_L | 1.016 | 0.93 |
| 16_H | 41_Q | 1.009 | 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 | |
| 4bt9A | 2 | 1 | 98.6 | 0.036 | Contact Map |
| 4u04A | 2 | 1 | 98.5 | 0.085 | Contact Map |
| 2pziA | 2 | 1 | 98.5 | 0.086 | Contact Map |
| 2xpiA | 2 | 1 | 98.4 | 0.086 | Contact Map |
| 1pc2A | 1 | 1 | 98.4 | 0.102 | Contact Map |
| 2y4tA | 3 | 1 | 98.3 | 0.119 | Contact Map |
| 4i2zA | 1 | 1 | 98.3 | 0.123 | Contact Map |
| 4w9rA | 2 | 1 | 98.3 | 0.123 | Contact Map |
| 2vsyA | 2 | 1 | 98.3 | 0.129 | Contact Map |
| 3ly7A | 1 | 1 | 98.2 | 0.139 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)