| 2K5V not 3K5V |
| ID: | 1424429056 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 104 (95) | ||
| Sequences: | 223 (177.3) | ||
| Seq/Len: | 2.347 | ||
| Nf(neff/√len): | 18.2 |
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: 2.347).
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 |
| 68_D | 95_K | 2.015 | 0.99 |
| 54_T | 86_S | 1.708 | 0.97 |
| 11_N | 70_A | 1.699 | 0.97 |
| 29_F | 37_G | 1.659 | 0.97 |
| 8_L | 16_I | 1.620 | 0.96 |
| 75_Y | 91_G | 1.612 | 0.96 |
| 31_R | 57_N | 1.603 | 0.96 |
| 5_I | 18_A | 1.580 | 0.95 |
| 33_D | 57_N | 1.576 | 0.95 |
| 20_V | 70_A | 1.562 | 0.95 |
| 18_A | 44_L | 1.554 | 0.95 |
| 5_I | 44_L | 1.506 | 0.93 |
| 29_F | 60_A | 1.491 | 0.93 |
| 74_G | 91_G | 1.420 | 0.90 |
| 28_E | 36_K | 1.393 | 0.89 |
| 8_L | 76_V | 1.385 | 0.89 |
| 19_E | 91_G | 1.342 | 0.87 |
| 38_Q | 61_D | 1.321 | 0.86 |
| 20_V | 64_V | 1.313 | 0.85 |
| 31_R | 37_G | 1.298 | 0.84 |
| 19_E | 74_G | 1.221 | 0.79 |
| 15_T | 48_T | 1.213 | 0.78 |
| 4_K | 47_D | 1.207 | 0.78 |
| 37_G | 57_N | 1.204 | 0.78 |
| 67_G | 85_I | 1.203 | 0.77 |
| 14_G | 86_S | 1.195 | 0.77 |
| 37_G | 52_R | 1.184 | 0.76 |
| 21_V | 62_F | 1.140 | 0.72 |
| 45_K | 71_E | 1.131 | 0.71 |
| 3_Y | 58_E | 1.125 | 0.70 |
| 79_G | 82_G | 1.125 | 0.70 |
| 25_P | 42_L | 1.125 | 0.70 |
| 54_T | 89_N | 1.121 | 0.70 |
| 36_K | 65_K | 1.113 | 0.69 |
| 5_I | 8_L | 1.110 | 0.69 |
| 10_P | 44_L | 1.100 | 0.68 |
| 72_V | 96_S | 1.095 | 0.67 |
| 27_K | 54_T | 1.084 | 0.66 |
| 5_I | 16_I | 1.077 | 0.66 |
| 26_K | 58_E | 1.071 | 0.65 |
| 18_A | 53_G | 1.064 | 0.64 |
| 9_M | 12_L | 1.060 | 0.64 |
| 66_K | 83_L | 1.057 | 0.63 |
| 45_K | 54_T | 1.054 | 0.63 |
| 45_K | 50_S | 1.049 | 0.63 |
| 33_D | 39_L | 1.036 | 0.61 |
| 4_K | 92_I | 1.034 | 0.61 |
| 10_P | 21_V | 1.031 | 0.61 |
| 14_G | 93_I | 1.009 | 0.58 |
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 | |
| 1wjjA | 1 | 0.9904 | 99.8 | 0.368 | Contact Map |
| 2k75A | 1 | 0.9423 | 99.8 | 0.391 | Contact Map |
| 2kbnA | 1 | 0.9327 | 99.7 | 0.421 | Contact Map |
| 3dm3A | 3 | 0.9327 | 99.7 | 0.426 | Contact Map |
| 1o7iA | 2 | 0.9808 | 99.6 | 0.45 | Contact Map |
| 3e0eA | 1 | 0.875 | 99.5 | 0.492 | Contact Map |
| 4owtB | 1 | 0.6346 | 99.5 | 0.5 | Contact Map |
| 2k50A | 1 | 0.9712 | 99.4 | 0.518 | Contact Map |
| 1ynxA | 1 | 0.9615 | 99.3 | 0.551 | Contact Map |
| 4gnxC | 2 | 0.9904 | 99.2 | 0.581 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)