| 1APYA |
| ID: | 1411595620 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 161 (144) | ||
| Sequences: | 922 (598.4) | ||
| Seq/Len: | 6.403 | ||
| Nf(neff/√len): | 49.9 |
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: 6.403).
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 |
| 34_E | 89_G | 4.489 | 1.00 |
| 22_A | 27_G | 4.051 | 1.00 |
| 38_A | 89_G | 2.969 | 1.00 |
| 53_G | 63_L | 2.919 | 1.00 |
| 31_D | 92_R | 2.767 | 1.00 |
| 55_P | 61_T | 2.761 | 1.00 |
| 81_L | 90_V | 2.739 | 1.00 |
| 79_G | 104_V | 2.570 | 1.00 |
| 92_R | 96_E | 2.235 | 1.00 |
| 42_R | 86_N | 2.210 | 1.00 |
| 56_D | 60_E | 2.191 | 1.00 |
| 128_Q | 132_S | 2.180 | 1.00 |
| 56_D | 62_T | 2.164 | 1.00 |
| 37_C | 88_I | 1.914 | 1.00 |
| 60_E | 82_R | 1.895 | 1.00 |
| 124_T | 127_S | 1.887 | 1.00 |
| 34_E | 92_R | 1.766 | 1.00 |
| 55_P | 123_S | 1.748 | 1.00 |
| 58_L | 110_T | 1.703 | 1.00 |
| 75_V | 101_T | 1.693 | 1.00 |
| 27_G | 32_A | 1.666 | 1.00 |
| 93_K | 97_H | 1.598 | 1.00 |
| 122_L | 127_S | 1.590 | 1.00 |
| 67_I | 88_I | 1.558 | 0.99 |
| 125_S | 129_A | 1.554 | 0.99 |
| 69_D | 72_T | 1.498 | 0.99 |
| 94_V | 98_T | 1.483 | 0.99 |
| 80_D | 104_V | 1.452 | 0.99 |
| 90_V | 117_F | 1.450 | 0.99 |
| 34_E | 67_I | 1.450 | 0.99 |
| 84_I | 90_V | 1.436 | 0.99 |
| 14_N | 43_E | 1.426 | 0.99 |
| 127_S | 130_L | 1.388 | 0.98 |
| 94_V | 111_F | 1.381 | 0.98 |
| 106_E | 110_T | 1.367 | 0.98 |
| 15_A | 39_M | 1.353 | 0.98 |
| 42_R | 85_K | 1.311 | 0.97 |
| 34_E | 38_A | 1.301 | 0.97 |
| 61_T | 123_S | 1.286 | 0.97 |
| 127_S | 134_W | 1.284 | 0.97 |
| 77_A | 102_L | 1.257 | 0.96 |
| 20_W | 24_A | 1.218 | 0.95 |
| 94_V | 100_H | 1.215 | 0.95 |
| 93_K | 117_F | 1.200 | 0.95 |
| 113_Q | 119_N | 1.199 | 0.95 |
| 62_T | 82_R | 1.197 | 0.95 |
| 18_A | 35_S | 1.180 | 0.94 |
| 83_R | 109_T | 1.152 | 0.93 |
| 59_G | 131_H | 1.123 | 0.92 |
| 22_A | 32_A | 1.113 | 0.92 |
| 40_C | 49_V | 1.100 | 0.91 |
| 48_S | 54_S | 1.095 | 0.91 |
| 79_G | 102_L | 1.090 | 0.91 |
| 13_K | 17_E | 1.077 | 0.90 |
| 103_L | 111_F | 1.075 | 0.90 |
| 18_A | 21_R | 1.069 | 0.89 |
| 47_G | 54_S | 1.053 | 0.89 |
| 121_D | 127_S | 1.052 | 0.88 |
| 83_R | 119_N | 1.051 | 0.88 |
| 125_S | 128_Q | 1.000 | 0.85 |
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 | |
| 1apyA | 2 | 1 | 100 | 0.034 | Contact Map |
| 2gezA | 4 | 0.8758 | 100 | 0.18 | Contact Map |
| 1p4kA | 2 | 0.9938 | 100 | 0.197 | Contact Map |
| 4pv2A | 2 | 0.8447 | 100 | 0.236 | Contact Map |
| 4o0cA | 2 | 0.9317 | 100 | 0.267 | Contact Map |
| 3c17A | 2 | 0.8944 | 100 | 0.27 | Contact Map |
| 2a8jA | 2 | 0.7143 | 100 | 0.272 | Contact Map |
| 1k2xA | 2 | 0.8385 | 100 | 0.282 | Contact Map |
| 2dg5A | 2 | 0.9255 | 90.8 | 0.911 | Contact Map |
| 2qmcA | 2 | 0.8944 | 90 | 0.913 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)