| KNL1 C-term 155-275 |
| ID: | 1434175850 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (120) | ||
| Sequences: | 217 (147.1) | ||
| Seq/Len: | 1.808 | ||
| Nf(neff/√len): | 13.4 |
Jackhmmer Results: (2015_01_07)
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: 1.808).
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 |
| 18_P | 21_S | 2.560 | 1.00 |
| 11_V | 47_P | 2.211 | 0.99 |
| 58_A | 61_Q | 1.968 | 0.98 |
| 6_F | 103_L | 1.714 | 0.96 |
| 109_C | 120_Q | 1.687 | 0.95 |
| 45_Y | 70_A | 1.501 | 0.90 |
| 47_P | 50_Q | 1.429 | 0.86 |
| 114_T | 117_F | 1.426 | 0.86 |
| 99_F | 102_Y | 1.410 | 0.85 |
| 2_I | 110_F | 1.372 | 0.83 |
| 63_I | 69_S | 1.368 | 0.83 |
| 62_K | 66_L | 1.363 | 0.83 |
| 91_C | 109_C | 1.327 | 0.80 |
| 77_L | 96_L | 1.326 | 0.80 |
| 34_T | 52_Y | 1.269 | 0.76 |
| 54_E | 88_M | 1.267 | 0.76 |
| 88_M | 96_L | 1.266 | 0.76 |
| 87_K | 99_F | 1.261 | 0.75 |
| 4_E | 96_L | 1.260 | 0.75 |
| 82_K | 88_M | 1.216 | 0.71 |
| 6_F | 13_I | 1.206 | 0.70 |
| 82_K | 119_H | 1.199 | 0.70 |
| 65_E | 95_E | 1.197 | 0.70 |
| 61_Q | 88_M | 1.176 | 0.68 |
| 56_C | 65_E | 1.174 | 0.67 |
| 4_E | 8_L | 1.153 | 0.65 |
| 82_K | 118_T | 1.151 | 0.65 |
| 87_K | 106_I | 1.145 | 0.65 |
| 60_R | 102_Y | 1.134 | 0.64 |
| 52_Y | 103_L | 1.130 | 0.63 |
| 100_G | 104_N | 1.126 | 0.63 |
| 99_F | 103_L | 1.123 | 0.62 |
| 18_P | 62_K | 1.117 | 0.62 |
| 11_V | 33_P | 1.115 | 0.62 |
| 102_Y | 114_T | 1.114 | 0.62 |
| 81_N | 112_K | 1.109 | 0.61 |
| 22_N | 27_F | 1.092 | 0.59 |
| 35_P | 38_L | 1.091 | 0.59 |
| 34_T | 76_L | 1.078 | 0.58 |
| 75_K | 90_H | 1.073 | 0.57 |
| 57_E | 103_L | 1.067 | 0.57 |
| 2_I | 77_L | 1.066 | 0.56 |
| 75_K | 85_W | 1.060 | 0.56 |
| 59_R | 92_S | 1.058 | 0.56 |
| 49_I | 114_T | 1.057 | 0.56 |
| 38_L | 62_K | 1.056 | 0.55 |
| 96_L | 119_H | 1.053 | 0.55 |
| 47_P | 115_K | 1.051 | 0.55 |
| 82_K | 85_W | 1.044 | 0.54 |
| 77_L | 119_H | 1.042 | 0.54 |
| 58_A | 66_L | 1.032 | 0.53 |
| 2_I | 45_Y | 1.032 | 0.53 |
| 37_D | 81_N | 1.024 | 0.52 |
| 75_K | 114_T | 1.020 | 0.52 |
| 5_F | 24_P | 1.015 | 0.51 |
| 37_D | 114_T | 1.014 | 0.51 |
| 28_T | 104_N | 1.006 | 0.50 |
| 56_C | 81_N | 1.002 | 0.50 |
| 9_L | 14_L | 1.000 | 0.49 |
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 | |
| 3kwoA | 4 | 0.8843 | 18 | 0.916 | Contact Map |
| 2chpA | 4 | 0.8595 | 18 | 0.916 | Contact Map |
| 1n1qA | 4 | 0.8595 | 17.2 | 0.917 | Contact Map |
| 4m32A | 4 | 0.8678 | 17.1 | 0.917 | Contact Map |
| 2pybA | 4 | 0.8843 | 15.4 | 0.918 | Contact Map |
| 4a25A | 4 | 0.8843 | 15 | 0.919 | Contact Map |
| 3iq1A | 4 | 0.8595 | 14.7 | 0.919 | Contact Map |
| 4eveA | 1 | 0.8595 | 14.4 | 0.919 | Contact Map |
| 2c2uA | 1 | 0.9008 | 14 | 0.92 | Contact Map |
| 1jigA | 4 | 0.8595 | 13.8 | 0.92 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)