| job |
| ID: | 1513892083 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 144 (140) | ||
| Sequences: | 1595 (1141.3) | ||
| Seq/Len: | 11.393 | ||
| Nf(neff/√len): | 96.5 |
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: 11.393).
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 |
| 42_A | 101_P | 3.551 | 1.00 |
| 125_A | 135_N | 3.535 | 1.00 |
| 99_V | 105_P | 2.764 | 1.00 |
| 59_D | 91_Y | 2.708 | 1.00 |
| 54_K | 93_D | 2.339 | 1.00 |
| 53_L | 63_Y | 2.046 | 1.00 |
| 126_D | 137_D | 2.015 | 1.00 |
| 50_E | 140_S | 2.000 | 1.00 |
| 71_S | 75_K | 1.991 | 1.00 |
| 104_N | 127_G | 1.989 | 1.00 |
| 35_D | 134_V | 1.931 | 1.00 |
| 33_R | 36_E | 1.753 | 1.00 |
| 111_P | 119_E | 1.748 | 1.00 |
| 107_I | 121_I | 1.734 | 1.00 |
| 34_P | 38_R | 1.715 | 1.00 |
| 56_Y | 68_Q | 1.700 | 1.00 |
| 56_Y | 62_M | 1.693 | 1.00 |
| 41_K | 45_D | 1.613 | 1.00 |
| 46_I | 140_S | 1.608 | 1.00 |
| 66_T | 110_S | 1.586 | 1.00 |
| 107_I | 123_L | 1.583 | 1.00 |
| 101_P | 106_Y | 1.574 | 1.00 |
| 7_F | 22_L | 1.491 | 1.00 |
| 46_I | 120_I | 1.456 | 1.00 |
| 139_K | 142_E | 1.435 | 1.00 |
| 54_K | 63_Y | 1.423 | 1.00 |
| 125_A | 136_A | 1.406 | 0.99 |
| 24_T | 28_P | 1.403 | 0.99 |
| 53_L | 120_I | 1.381 | 0.99 |
| 39_V | 134_V | 1.376 | 0.99 |
| 131_G | 137_D | 1.365 | 0.99 |
| 102_W | 124_G | 1.362 | 0.99 |
| 125_A | 131_G | 1.362 | 0.99 |
| 47_K | 50_E | 1.362 | 0.99 |
| 121_I | 139_K | 1.344 | 0.99 |
| 45_D | 106_Y | 1.329 | 0.99 |
| 119_E | 141_Y | 1.321 | 0.99 |
| 123_L | 131_G | 1.319 | 0.99 |
| 110_S | 118_Y | 1.313 | 0.99 |
| 69_G | 73_L | 1.286 | 0.99 |
| 112_G | 119_E | 1.284 | 0.99 |
| 47_K | 51_S | 1.251 | 0.99 |
| 8_S | 19_L | 1.241 | 0.98 |
| 132_E | 135_N | 1.228 | 0.98 |
| 45_D | 101_P | 1.206 | 0.98 |
| 54_K | 118_Y | 1.203 | 0.98 |
| 64_P | 108_Y | 1.201 | 0.98 |
| 39_V | 138_I | 1.185 | 0.98 |
| 52_A | 92_L | 1.141 | 0.97 |
| 62_M | 68_Q | 1.129 | 0.97 |
| 31_I | 34_P | 1.120 | 0.96 |
| 130_G | 137_D | 1.114 | 0.96 |
| 44_S | 48_T | 1.106 | 0.96 |
| 50_E | 93_D | 1.099 | 0.96 |
| 26_L | 30_I | 1.088 | 0.96 |
| 23_A | 27_L | 1.059 | 0.95 |
| 8_S | 11_E | 1.037 | 0.94 |
| 36_E | 40_T | 1.020 | 0.93 |
| 42_A | 106_Y | 1.020 | 0.93 |
| 39_V | 42_A | 1.014 | 0.93 |
| 72_A | 77_P | 1.005 | 0.93 |
| 67_E | 73_L | 1.002 | 0.92 |
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 | |
| 3g20A | 2 | 0.7986 | 99.9 | 0.388 | Contact Map |
| 3gn9A | 3 | 0.7569 | 99.9 | 0.409 | Contact Map |
| 2kepA | 1 | 0.7639 | 99.9 | 0.414 | Contact Map |
| 1t92A | 2 | 0.7431 | 99.8 | 0.449 | Contact Map |
| 3sokA | 2 | 0.8611 | 99.7 | 0.502 | Contact Map |
| 2hi2A | 1 | 0.8819 | 99.7 | 0.516 | Contact Map |
| 2m7gA | 1 | 0.4236 | 99.5 | 0.589 | Contact Map |
| 1oqwA | 2 | 0.8611 | 99.2 | 0.649 | Contact Map |
| 4noaA | 1 | 0.6667 | 81.4 | 0.876 | Contact Map |
| 2m3kA | 1 | 0.6944 | 75.4 | 0.883 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)