| kiaa_sub |
| ID: | 1505648403 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (123) | ||
| Sequences: | 376 (260.8) | ||
| Seq/Len: | 3.057 | ||
| Nf(neff/√len): | 23.5 |
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: 3.057).
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 |
| 83_G | 98_K | 3.097 | 1.00 |
| 102_V | 108_L | 2.677 | 1.00 |
| 66_A | 110_L | 2.361 | 1.00 |
| 23_L | 27_A | 2.197 | 1.00 |
| 66_A | 77_F | 2.141 | 1.00 |
| 50_V | 80_I | 2.104 | 1.00 |
| 102_V | 106_G | 1.920 | 0.99 |
| 52_R | 82_Y | 1.888 | 0.99 |
| 29_V | 32_I | 1.855 | 0.99 |
| 3_W | 9_Q | 1.843 | 0.99 |
| 25_S | 49_I | 1.824 | 0.99 |
| 69_A | 111_H | 1.616 | 0.98 |
| 23_L | 26_S | 1.567 | 0.97 |
| 48_P | 75_G | 1.554 | 0.97 |
| 87_E | 97_L | 1.531 | 0.96 |
| 4_N | 8_D | 1.509 | 0.96 |
| 21_L | 25_S | 1.501 | 0.96 |
| 42_I | 51_L | 1.437 | 0.94 |
| 27_A | 34_I | 1.423 | 0.94 |
| 26_S | 29_V | 1.419 | 0.94 |
| 39_K | 63_E | 1.353 | 0.92 |
| 58_I | 108_L | 1.347 | 0.91 |
| 69_A | 109_E | 1.333 | 0.91 |
| 55_H | 99_Y | 1.320 | 0.90 |
| 15_I | 38_G | 1.285 | 0.89 |
| 15_I | 32_I | 1.278 | 0.88 |
| 21_L | 73_F | 1.256 | 0.87 |
| 115_K | 119_T | 1.255 | 0.87 |
| 24_T | 27_A | 1.251 | 0.87 |
| 50_V | 73_F | 1.235 | 0.86 |
| 53_T | 81_L | 1.214 | 0.85 |
| 1_Q | 9_Q | 1.187 | 0.83 |
| 22_L | 26_S | 1.185 | 0.83 |
| 78_T | 100_I | 1.156 | 0.80 |
| 24_T | 49_I | 1.155 | 0.80 |
| 54_R | 82_Y | 1.154 | 0.80 |
| 4_N | 7_H | 1.151 | 0.80 |
| 66_A | 69_A | 1.143 | 0.79 |
| 23_L | 29_V | 1.140 | 0.79 |
| 9_Q | 51_L | 1.106 | 0.76 |
| 44_D | 75_G | 1.100 | 0.76 |
| 42_I | 77_F | 1.098 | 0.75 |
| 96_G | 101_G | 1.093 | 0.75 |
| 54_R | 61_G | 1.086 | 0.74 |
| 3_W | 6_G | 1.076 | 0.73 |
| 61_G | 87_E | 1.074 | 0.73 |
| 58_I | 101_G | 1.070 | 0.73 |
| 34_I | 111_H | 1.057 | 0.71 |
| 42_I | 66_A | 1.055 | 0.71 |
| 12_H | 53_T | 1.051 | 0.71 |
| 12_H | 30_Y | 1.042 | 0.70 |
| 98_K | 112_G | 1.042 | 0.70 |
| 58_I | 100_I | 1.038 | 0.69 |
| 69_A | 74_Q | 1.026 | 0.68 |
| 21_L | 24_T | 1.023 | 0.68 |
| 35_S | 38_G | 1.023 | 0.68 |
| 6_G | 9_Q | 1.007 | 0.66 |
| 38_G | 73_F | 1.003 | 0.66 |
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 | |
| 3h09A | 2 | 0.8537 | 21.7 | 0.917 | Contact Map |
| 3syjA | 1 | 0.8537 | 17.5 | 0.921 | Contact Map |
| 1wxrA | 1 | 0.8537 | 16.7 | 0.922 | Contact Map |
| 4c2lA | 1 | 0.9593 | 14.6 | 0.924 | Contact Map |
| 3szeA | 1 | 0.8537 | 12.7 | 0.925 | Contact Map |
| 2uvfA | 2 | 0.8455 | 12 | 0.927 | Contact Map |
| 4mr0A | 2 | 0.7561 | 9.5 | 0.93 | Contact Map |
| 1ia5A | 1 | 0.9512 | 8.3 | 0.932 | Contact Map |
| 2iq7A | 7 | 0.9512 | 8 | 0.932 | Contact Map |
| 3k3oA | 1 | 0.8537 | 8 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)