| kif5b |
| ID: | 1512902819 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (83) | ||
| Sequences: | 127 (79) | ||
| Seq/Len: | 1.530 | ||
| Nf(neff/√len): | 8.7 |
HHblits Results: (2016_02)
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: 1.530).
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 |
| 12_E | 16_E | 2.063 | 0.99 |
| 11_L | 14_N | 1.932 | 0.97 |
| 71_Y | 78_I | 1.624 | 0.92 |
| 6_Q | 9_S | 1.600 | 0.91 |
| 78_I | 82_V | 1.579 | 0.90 |
| 7_K | 14_N | 1.514 | 0.87 |
| 14_N | 17_Q | 1.491 | 0.86 |
| 10_F | 21_V | 1.421 | 0.82 |
| 25_L | 29_N | 1.380 | 0.80 |
| 12_E | 17_Q | 1.345 | 0.77 |
| 10_F | 19_T | 1.332 | 0.76 |
| 46_T | 64_A | 1.324 | 0.76 |
| 21_V | 26_V | 1.302 | 0.74 |
| 80_E | 83_R | 1.289 | 0.73 |
| 72_Q | 75_V | 1.225 | 0.67 |
| 20_K | 66_R | 1.217 | 0.67 |
| 75_V | 81_A | 1.211 | 0.66 |
| 45_A | 62_E | 1.210 | 0.66 |
| 14_N | 18_L | 1.204 | 0.65 |
| 53_L | 57_L | 1.199 | 0.65 |
| 1_S | 66_R | 1.196 | 0.65 |
| 11_L | 18_L | 1.192 | 0.64 |
| 69_K | 72_Q | 1.187 | 0.64 |
| 9_S | 16_E | 1.152 | 0.60 |
| 11_L | 49_R | 1.144 | 0.59 |
| 31_D | 73_Q | 1.139 | 0.59 |
| 67_D | 70_R | 1.137 | 0.59 |
| 67_D | 74_E | 1.134 | 0.58 |
| 50_V | 64_A | 1.131 | 0.58 |
| 23_K | 26_V | 1.128 | 0.58 |
| 15_L | 19_T | 1.127 | 0.58 |
| 2_A | 23_K | 1.119 | 0.57 |
| 25_L | 35_E | 1.101 | 0.55 |
| 42_R | 63_N | 1.100 | 0.55 |
| 50_V | 54_E | 1.095 | 0.54 |
| 48_E | 53_L | 1.095 | 0.54 |
| 46_T | 50_V | 1.094 | 0.54 |
| 74_E | 77_R | 1.090 | 0.54 |
| 8_I | 13_N | 1.083 | 0.53 |
| 30_A | 69_K | 1.081 | 0.53 |
| 70_R | 79_K | 1.075 | 0.52 |
| 65_S | 80_E | 1.071 | 0.52 |
| 29_N | 53_L | 1.069 | 0.52 |
| 31_D | 51_K | 1.067 | 0.52 |
| 3_A | 21_V | 1.066 | 0.51 |
| 7_K | 12_E | 1.060 | 0.51 |
| 11_L | 57_L | 1.049 | 0.50 |
| 3_A | 14_N | 1.036 | 0.48 |
| 74_E | 78_I | 1.036 | 0.48 |
| 36_L | 83_R | 1.030 | 0.48 |
| 59_E | 69_K | 1.030 | 0.48 |
| 22_H | 27_R | 1.024 | 0.47 |
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 | |
| 3ghgA | 4 | 0.9881 | 82.2 | 0.811 | Contact Map |
| 4c46A | 3 | 0.881 | 69.5 | 0.83 | Contact Map |
| 4q4gX | 1 | 0 | 63.7 | 0.837 | Contact Map |
| 4cgkA | 2 | 0.8214 | 60.3 | 0.84 | Contact Map |
| 1deqA | 4 | 0.9048 | 51.3 | 0.848 | Contact Map |
| 4ll8E | 2 | 0.9405 | 40.4 | 0.858 | Contact Map |
| 3vkgA | 2 | 0.869 | 35.4 | 0.863 | Contact Map |
| 3ojaB | 1 | 0.9881 | 34.2 | 0.864 | Contact Map |
| 4rsiB | 1 | 0.9881 | 30.5 | 0.867 | Contact Map |
| 4rh7A | 1 | 0.869 | 26.6 | 0.871 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)