| cyay |
| ID: | 1429667319 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (105) | ||
| Sequences: | 891 (622) | ||
| Seq/Len: | 8.486 | ||
| Nf(neff/√len): | 60.7 |
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: 8.486).
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 |
| 59_Q | 72_D | 3.037 | 1.00 |
| 85_E | 93_Q | 2.714 | 1.00 |
| 3_D | 58_H | 2.426 | 1.00 |
| 2_N | 5_E | 2.033 | 1.00 |
| 64_T | 94_A | 2.028 | 1.00 |
| 6_F | 55_E | 2.020 | 1.00 |
| 7_H | 11_D | 1.828 | 1.00 |
| 95_A | 105_F | 1.816 | 1.00 |
| 62_L | 87_F | 1.701 | 1.00 |
| 86_T | 89_D | 1.683 | 1.00 |
| 77_E | 86_T | 1.673 | 1.00 |
| 93_Q | 97_Q | 1.665 | 1.00 |
| 40_T | 48_K | 1.627 | 1.00 |
| 71_F | 90_L | 1.618 | 1.00 |
| 69_Y | 80_C | 1.521 | 1.00 |
| 73_L | 76_D | 1.494 | 1.00 |
| 66_Q | 94_A | 1.466 | 0.99 |
| 1_M | 5_E | 1.451 | 0.99 |
| 71_F | 85_E | 1.374 | 0.99 |
| 64_T | 67_G | 1.350 | 0.99 |
| 9_L | 73_L | 1.346 | 0.99 |
| 71_F | 83_S | 1.335 | 0.99 |
| 79_I | 84_G | 1.322 | 0.99 |
| 80_C | 83_S | 1.308 | 0.99 |
| 3_D | 55_E | 1.302 | 0.98 |
| 2_N | 35_N | 1.299 | 0.98 |
| 72_D | 81_D | 1.289 | 0.98 |
| 20_R | 105_F | 1.268 | 0.98 |
| 63_A | 68_G | 1.235 | 0.98 |
| 7_H | 53_R | 1.212 | 0.97 |
| 10_A | 60_V | 1.198 | 0.97 |
| 45_N | 98_Q | 1.173 | 0.97 |
| 92_E | 96_T | 1.163 | 0.96 |
| 13_L | 60_V | 1.150 | 0.96 |
| 54_Q | 57_L | 1.146 | 0.96 |
| 6_F | 53_R | 1.140 | 0.96 |
| 30_I | 41_I | 1.140 | 0.96 |
| 10_A | 14_W | 1.140 | 0.96 |
| 16_T | 20_R | 1.130 | 0.95 |
| 34_I | 80_C | 1.126 | 0.95 |
| 57_L | 70_H | 1.104 | 0.95 |
| 54_Q | 68_G | 1.094 | 0.94 |
| 18_E | 26_G | 1.093 | 0.94 |
| 49_I | 94_A | 1.089 | 0.94 |
| 47_S | 98_Q | 1.085 | 0.94 |
| 5_E | 29_D | 1.067 | 0.93 |
| 47_S | 68_G | 1.065 | 0.93 |
| 38_V | 48_K | 1.064 | 0.93 |
| 37_G | 59_Q | 1.041 | 0.92 |
| 73_L | 77_E | 1.037 | 0.92 |
| 65_K | 68_G | 1.037 | 0.92 |
| 49_I | 65_K | 1.030 | 0.92 |
| 38_V | 67_G | 1.016 | 0.91 |
| 79_I | 83_S | 1.015 | 0.91 |
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 | |
| 1ew4A | 1 | 1 | 100 | -0.001 | Contact Map |
| 4jpdA | 1 | 1 | 100 | 0.012 | Contact Map |
| 4hs5A | 2 | 0.9811 | 100 | 0.017 | Contact Map |
| 3t3lA | 1 | 1 | 100 | 0.027 | Contact Map |
| 3oeqA | 1 | 0.9528 | 100 | 0.082 | Contact Map |
| 4ux3B | 1 | 0.2547 | 33.4 | 0.906 | Contact Map |
| 4da2A | 2 | 0.9151 | 22.5 | 0.914 | Contact Map |
| 2vfmA | 1 | 0.9623 | 21.7 | 0.915 | Contact Map |
| 4n4uA | 2 | 0.8774 | 20.3 | 0.916 | Contact Map |
| 3k6qA | 4 | 0.7642 | 20.1 | 0.916 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)