| pengfei tian |
| ID: | 1447258212 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 2072 (2072) | ||
| Seq/Len: | 37.000 | ||
| Nf(neff/√len): | 276.9 |
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: 37.000).
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 |
| 44_T | 47_E | 1.711 | 1.00 |
| 21_N | 30_K | 1.635 | 1.00 |
| 28_T | 51_E | 1.574 | 1.00 |
| 2_A | 6_T | 1.437 | 1.00 |
| 27_E | 34_T | 1.404 | 0.99 |
| 6_T | 15_H | 1.363 | 0.99 |
| 17_A | 52_F | 1.302 | 0.99 |
| 10_A | 49_Q | 1.295 | 0.99 |
| 17_A | 25_A | 1.253 | 0.99 |
| 42_I | 54_F | 1.237 | 0.98 |
| 29_Y | 47_E | 1.208 | 0.98 |
| 2_A | 23_Y | 1.202 | 0.98 |
| 20_I | 34_T | 1.191 | 0.98 |
| 5_H | 22_Q | 1.168 | 0.97 |
| 16_A | 48_K | 1.166 | 0.97 |
| 14_A | 23_Y | 1.164 | 0.97 |
| 30_K | 43_D | 1.161 | 0.97 |
| 17_A | 34_T | 1.149 | 0.97 |
| 12_K | 20_I | 1.127 | 0.97 |
| 30_K | 53_F | 1.114 | 0.96 |
| 18_K | 25_A | 1.107 | 0.96 |
| 8_N | 45_E | 1.096 | 0.96 |
| 26_G | 53_F | 1.073 | 0.95 |
| 2_A | 36_S | 1.073 | 0.95 |
| 48_K | 52_F | 1.063 | 0.95 |
| 30_K | 42_I | 1.054 | 0.95 |
| 5_H | 53_F | 1.050 | 0.94 |
| 10_A | 34_T | 1.031 | 0.94 |
| 12_K | 54_F | 1.025 | 0.93 |
| 33_V | 49_Q | 1.025 | 0.93 |
| 8_N | 11_N | 1.015 | 0.93 |
| 17_A | 20_I | 1.015 | 0.93 |
| 28_T | 50_V | 1.013 | 0.93 |
| 6_T | 24_A | 1.011 | 0.93 |
| 6_T | 38_E | 1.009 | 0.93 |
| 18_K | 37_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 | |
| 2jwsA | 1 | 1 | 95.3 | 0.224 | Contact Map |
| 2fs1A | 1 | 1 | 91.8 | 0.327 | Contact Map |
| 2j5yA | 2 | 0.9643 | 74.8 | 0.464 | Contact Map |
| 1gjsA | 1 | 0.9643 | 72.6 | 0.472 | Contact Map |
| 1pgxA | 1 | 1 | 64.9 | 0.499 | Contact Map |
| 1pn5A | 1 | 0 | 60 | 0.514 | Contact Map |
| 1igdA | 1 | 1 | 55.7 | 0.527 | Contact Map |
| 2rpvA | 1 | 1 | 51.3 | 0.538 | Contact Map |
| 2khuA | 1 | 0 | 48.3 | 0.546 | Contact Map |
| 3ui3A | 2 | 0.8214 | 42.1 | 0.564 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)