| T0778 |
| ID: | 1400098596 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (117) | ||
| Sequences: | 602 (439.9) | ||
| Seq/Len: | 5.145 | ||
| Nf(neff/√len): | 40.7 |
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: 5.145).
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 |
| 88_R | 104_D | 4.656 | 1.00 |
| 108_V | 118_A | 2.893 | 1.00 |
| 54_R | 70_D | 2.876 | 1.00 |
| 112_E | 115_N | 2.490 | 1.00 |
| 40_G | 50_L | 2.239 | 1.00 |
| 102_K | 122_L | 2.113 | 1.00 |
| 73_Q | 76_L | 2.058 | 1.00 |
| 63_K | 66_E | 2.039 | 1.00 |
| 38_T | 54_R | 1.934 | 1.00 |
| 25_F | 56_M | 1.841 | 1.00 |
| 58_Y | 63_K | 1.781 | 1.00 |
| 29_K | 32_R | 1.759 | 1.00 |
| 102_K | 125_I | 1.753 | 1.00 |
| 105_F | 121_E | 1.639 | 0.99 |
| 41_I | 50_L | 1.624 | 0.99 |
| 72_T | 88_R | 1.607 | 0.99 |
| 107_T | 110_L | 1.573 | 0.99 |
| 33_A | 57_A | 1.559 | 0.99 |
| 89_G | 105_F | 1.525 | 0.99 |
| 15_I | 19_D | 1.512 | 0.99 |
| 24_F | 29_K | 1.487 | 0.98 |
| 72_T | 104_D | 1.458 | 0.98 |
| 119_V | 123_S | 1.455 | 0.98 |
| 24_F | 36_C | 1.431 | 0.98 |
| 38_T | 70_D | 1.424 | 0.98 |
| 34_I | 57_A | 1.399 | 0.98 |
| 67_A | 71_C | 1.386 | 0.97 |
| 55_A | 71_C | 1.346 | 0.97 |
| 48_A | 74_A | 1.335 | 0.96 |
| 12_Q | 16_S | 1.275 | 0.95 |
| 24_F | 27_E | 1.270 | 0.95 |
| 59_L | 91_A | 1.259 | 0.95 |
| 20_R | 36_C | 1.248 | 0.94 |
| 106_E | 126_K | 1.185 | 0.92 |
| 22_N | 55_A | 1.173 | 0.91 |
| 75_I | 85_F | 1.161 | 0.91 |
| 97_K | 100_E | 1.149 | 0.90 |
| 44_D | 47_N | 1.149 | 0.90 |
| 85_F | 125_I | 1.146 | 0.90 |
| 68_E | 92_R | 1.130 | 0.89 |
| 69_K | 73_Q | 1.121 | 0.89 |
| 71_C | 75_I | 1.115 | 0.88 |
| 74_A | 84_A | 1.091 | 0.87 |
| 19_D | 23_G | 1.086 | 0.87 |
| 22_N | 83_K | 1.085 | 0.87 |
| 86_A | 90_T | 1.084 | 0.87 |
| 92_R | 100_E | 1.042 | 0.83 |
| 23_G | 27_E | 1.035 | 0.83 |
| 51_P | 54_R | 1.029 | 0.82 |
| 93_T | 124_K | 1.020 | 0.82 |
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 | |
| 4apoA | 2 | 0.9528 | 99.8 | 0.439 | Contact Map |
| 1kt0A | 1 | 0.9685 | 99.8 | 0.452 | Contact Map |
| 1p5qA | 3 | 1 | 99.8 | 0.461 | Contact Map |
| 2if4A | 1 | 0.8661 | 99.7 | 0.468 | Contact Map |
| 2vyiA | 2 | 0.9606 | 99.7 | 0.473 | Contact Map |
| 3fp2A | 1 | 0.9134 | 99.7 | 0.478 | Contact Map |
| 3rkvA | 1 | 0.9213 | 99.7 | 0.479 | Contact Map |
| 1ihgA | 1 | 1 | 99.7 | 0.494 | Contact Map |
| 3uq3A | 1 | 1 | 99.7 | 0.496 | Contact Map |
| 2c2lA | 4 | 0.9213 | 99.7 | 0.502 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)