| T0824 -force run |
| ID: | 1403115443 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (110) | ||
| Sequences: | 52 (44.3) | ||
| Seq/Len: | 0.473 | ||
| Nf(neff/√len): | 4.2 |
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: 0.473).
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 |
| 24_D | 78_R | 3.965 | 1.00 |
| 92_V | 107_F | 2.173 | 0.90 |
| 28_A | 78_R | 1.644 | 0.65 |
| 11_P | 68_C | 1.625 | 0.64 |
| 34_C | 68_C | 1.571 | 0.60 |
| 63_W | 107_F | 1.533 | 0.57 |
| 98_G | 109_V | 1.492 | 0.54 |
| 27_K | 76_S | 1.450 | 0.51 |
| 13_S | 78_R | 1.424 | 0.49 |
| 11_P | 34_C | 1.379 | 0.45 |
| 24_D | 39_S | 1.345 | 0.43 |
| 18_T | 26_I | 1.336 | 0.42 |
| 52_I | 80_V | 1.335 | 0.42 |
| 12_A | 52_I | 1.335 | 0.42 |
| 24_D | 93_G | 1.325 | 0.41 |
| 63_W | 96_L | 1.319 | 0.41 |
| 27_K | 51_G | 1.263 | 0.37 |
| 26_I | 65_M | 1.261 | 0.37 |
| 91_W | 96_L | 1.258 | 0.37 |
| 11_P | 79_Y | 1.253 | 0.36 |
| 7_V | 20_A | 1.249 | 0.36 |
| 10_F | 68_C | 1.236 | 0.35 |
| 34_C | 65_M | 1.233 | 0.35 |
| 3_R | 93_G | 1.228 | 0.34 |
| 2_A | 107_F | 1.226 | 0.34 |
| 20_A | 69_E | 1.206 | 0.33 |
| 30_H | 104_R | 1.182 | 0.31 |
| 33_V | 47_E | 1.176 | 0.31 |
| 26_I | 90_S | 1.171 | 0.31 |
| 68_C | 79_Y | 1.140 | 0.29 |
| 32_D | 51_G | 1.127 | 0.28 |
| 11_P | 53_P | 1.125 | 0.28 |
| 2_A | 109_V | 1.117 | 0.27 |
| 13_S | 31_A | 1.106 | 0.27 |
| 10_F | 34_C | 1.098 | 0.26 |
| 25_A | 29_G | 1.096 | 0.26 |
| 43_K | 58_F | 1.092 | 0.26 |
| 3_R | 99_Y | 1.084 | 0.25 |
| 20_A | 28_A | 1.080 | 0.25 |
| 10_F | 92_V | 1.074 | 0.25 |
| 77_V | 97_N | 1.072 | 0.25 |
| 34_C | 91_W | 1.072 | 0.25 |
| 27_K | 78_R | 1.071 | 0.25 |
| 12_A | 23_S | 1.071 | 0.25 |
| 7_V | 98_G | 1.063 | 0.24 |
| 68_C | 91_W | 1.062 | 0.24 |
| 5_D | 106_L | 1.053 | 0.24 |
| 18_T | 34_C | 1.052 | 0.24 |
| 84_D | 87_G | 1.047 | 0.23 |
| 53_P | 68_C | 1.046 | 0.23 |
| 18_T | 65_M | 1.044 | 0.23 |
| 24_D | 27_K | 1.042 | 0.23 |
| 10_F | 91_W | 1.030 | 0.22 |
| 80_V | 95_R | 1.018 | 0.22 |
| 50_K | 108_I | 1.016 | 0.22 |
| 16_P | 102_G | 1.013 | 0.21 |
| 23_S | 40_G | 1.012 | 0.21 |
| 34_C | 53_P | 1.009 | 0.21 |
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 | |
| 4od6A | 1 | 0.7273 | 33.4 | 0.94 | Contact Map |
| 2zqeA | 1 | 0.7273 | 21.6 | 0.946 | Contact Map |
| 3qd7X | 1 | 0.7455 | 21.1 | 0.946 | Contact Map |
| 1fwxA | 4 | 0.9182 | 19.8 | 0.946 | Contact Map |
| 1j5pA | 1 | 0.9364 | 9.6 | 0.954 | Contact Map |
| 2vkcA | 1 | 0.7 | 9.5 | 0.954 | Contact Map |
| 4ry8A | 4 | 0.8909 | 9.1 | 0.954 | Contact Map |
| 4pz0A | 1 | 0.9091 | 8.8 | 0.954 | Contact Map |
| 2d9iA | 1 | 0.7545 | 8.7 | 0.954 | Contact Map |
| 4jg2A | 1 | 0.8727 | 8 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)