| HEC1 80-195 |
| ID: | 1421335513 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (114) | ||
| Sequences: | 263 (205.2) | ||
| Seq/Len: | 2.307 | ||
| Nf(neff/√len): | 19.2 |
Jackhmmer Results: (2014_04_16)
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: 2.307).
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 |
| 7_L | 104_A | 3.979 | 1.00 |
| 92_T | 95_A | 1.879 | 0.99 |
| 41_P | 99_W | 1.840 | 0.98 |
| 42_S | 46_F | 1.837 | 0.98 |
| 27_N | 52_F | 1.744 | 0.98 |
| 23_F | 56_F | 1.694 | 0.97 |
| 6_P | 12_F | 1.677 | 0.97 |
| 38_L | 49_I | 1.570 | 0.95 |
| 10_K | 13_I | 1.565 | 0.95 |
| 3_D | 53_L | 1.516 | 0.93 |
| 20_L | 110_I | 1.509 | 0.93 |
| 30_A | 40_A | 1.487 | 0.93 |
| 50_F | 54_Y | 1.389 | 0.89 |
| 76_F | 105_A | 1.374 | 0.88 |
| 87_K | 104_A | 1.369 | 0.88 |
| 2_K | 90_M | 1.361 | 0.87 |
| 43_V | 102_I | 1.347 | 0.87 |
| 15_Q | 110_I | 1.333 | 0.86 |
| 54_Y | 75_I | 1.305 | 0.84 |
| 100_P | 108_W | 1.296 | 0.84 |
| 57_L | 61_Y | 1.289 | 0.83 |
| 68_F | 72_V | 1.270 | 0.82 |
| 76_F | 104_A | 1.266 | 0.82 |
| 64_P | 71_E | 1.244 | 0.80 |
| 45_D | 61_Y | 1.241 | 0.80 |
| 2_K | 14_Q | 1.233 | 0.79 |
| 49_I | 76_F | 1.213 | 0.78 |
| 10_K | 36_K | 1.205 | 0.77 |
| 50_F | 106_L | 1.204 | 0.77 |
| 48_K | 72_V | 1.192 | 0.76 |
| 50_F | 113_I | 1.157 | 0.73 |
| 13_I | 109_L | 1.155 | 0.73 |
| 88_S | 113_I | 1.148 | 0.72 |
| 52_F | 56_F | 1.129 | 0.70 |
| 54_Y | 72_V | 1.127 | 0.70 |
| 42_S | 96_P | 1.127 | 0.70 |
| 58_C | 108_W | 1.115 | 0.69 |
| 76_F | 107_V | 1.097 | 0.67 |
| 74_R | 80_G | 1.096 | 0.67 |
| 9_D | 12_F | 1.088 | 0.66 |
| 36_K | 86_S | 1.083 | 0.66 |
| 9_D | 52_F | 1.072 | 0.65 |
| 32_N | 61_Y | 1.066 | 0.64 |
| 25_T | 93_V | 1.060 | 0.63 |
| 99_W | 108_W | 1.052 | 0.62 |
| 34_S | 44_K | 1.050 | 0.62 |
| 41_P | 89_S | 1.045 | 0.62 |
| 44_K | 79_L | 1.045 | 0.62 |
| 36_K | 39_Q | 1.041 | 0.61 |
| 50_F | 85_L | 1.034 | 0.60 |
| 90_M | 98_T | 1.032 | 0.60 |
| 64_P | 110_I | 1.029 | 0.60 |
| 50_F | 76_F | 1.028 | 0.60 |
| 20_L | 112_C | 1.016 | 0.58 |
| 31_H | 45_D | 1.012 | 0.58 |
| 40_A | 73_P | 1.011 | 0.58 |
| 57_L | 112_C | 1.011 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2ve7A | 2 | 1 | 100 | 0.048 | Contact Map |
| 2igpA | 1 | 0.9828 | 100 | 0.063 | Contact Map |
| 4lvpA | 1 | 0.8534 | 64.4 | 0.909 | Contact Map |
| 2lbcA | 1 | 0.8362 | 62.3 | 0.91 | Contact Map |
| 1ua4A | 1 | 0.8707 | 28 | 0.928 | Contact Map |
| 4ae4A | 1 | 0.8362 | 27.6 | 0.928 | Contact Map |
| 3s28A | 8 | 0.8879 | 22.9 | 0.931 | Contact Map |
| 2nppB | 2 | 0.7672 | 21 | 0.932 | Contact Map |
| 1vw4E | 1 | 0.6466 | 20.7 | 0.932 | Contact Map |
| 3fgaB | 1 | 0.7672 | 19.1 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)