| 4F25 cut to pdb length Jackhmmer test |
| ID: | 1396502790 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 0% gaps before running GREMLIN. |
| Length: | 81 (80) | ||
| Sequences: | 28424 (18569.2) | ||
| Seq/Len: | 355.300 | ||
| Nf(neff/√len): | 2076.1 |
Jackhmmer Results: (2014_03_19)
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: 355.300).
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 |
| 50_T | 53_A | 2.470 | 1.00 |
| 14_D | 17_A | 2.256 | 1.00 |
| 17_A | 67_N | 2.203 | 1.00 |
| 27_N | 49_E | 2.182 | 1.00 |
| 25_F | 60_K | 2.110 | 1.00 |
| 29_L | 49_E | 1.932 | 1.00 |
| 56_R | 60_K | 1.910 | 1.00 |
| 51_Q | 75_R | 1.796 | 1.00 |
| 65_L | 70_K | 1.736 | 1.00 |
| 7_K | 72_F | 1.732 | 1.00 |
| 11_K | 69_R | 1.707 | 1.00 |
| 51_Q | 55_E | 1.681 | 1.00 |
| 55_E | 75_R | 1.655 | 1.00 |
| 3_N | 47_H | 1.652 | 1.00 |
| 21_T | 64_M | 1.521 | 1.00 |
| 34_V | 43_Y | 1.513 | 1.00 |
| 22_F | 46_V | 1.491 | 1.00 |
| 25_F | 61_M | 1.471 | 1.00 |
| 15_N | 19_Y | 1.383 | 0.99 |
| 4_I | 58_I | 1.381 | 0.99 |
| 30_S | 47_H | 1.362 | 0.99 |
| 49_E | 53_A | 1.350 | 0.99 |
| 19_Y | 23_S | 1.333 | 0.99 |
| 29_L | 47_H | 1.307 | 0.99 |
| 12_S | 67_N | 1.306 | 0.99 |
| 54_A | 75_R | 1.303 | 0.99 |
| 27_N | 53_A | 1.294 | 0.99 |
| 6_I | 22_F | 1.214 | 0.98 |
| 10_D | 13_I | 1.177 | 0.98 |
| 63_G | 70_K | 1.172 | 0.98 |
| 66_L | 71_V | 1.158 | 0.97 |
| 20_D | 23_S | 1.148 | 0.97 |
| 2_G | 47_H | 1.148 | 0.97 |
| 33_V | 44_G | 1.145 | 0.97 |
| 8_N | 72_F | 1.135 | 0.97 |
| 33_V | 40_S | 1.120 | 0.96 |
| 18_L | 44_G | 1.120 | 0.96 |
| 58_I | 75_R | 1.119 | 0.96 |
| 56_R | 59_E | 1.117 | 0.96 |
| 65_L | 68_D | 1.099 | 0.96 |
| 48_F | 57_A | 1.080 | 0.95 |
| 36_D | 39_G | 1.072 | 0.95 |
| 13_I | 66_L | 1.045 | 0.94 |
| 11_K | 42_G | 1.040 | 0.94 |
| 61_M | 64_M | 1.033 | 0.94 |
| 52_E | 56_R | 1.026 | 0.94 |
| 7_K | 43_Y | 1.017 | 0.93 |
| 16_K | 20_D | 1.012 | 0.93 |
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 | |
| 3pgwS | 2 | 0.9877 | 99.6 | 0.106 | Contact Map |
| 4f02A | 2 | 1 | 99.6 | 0.113 | Contact Map |
| 1rk8A | 1 | 0.9877 | 99.6 | 0.123 | Contact Map |
| 2cq3A | 1 | 1 | 99.6 | 0.124 | Contact Map |
| 3q2sC | 2 | 0.9877 | 99.6 | 0.125 | Contact Map |
| 2jrsA | 1 | 1 | 99.6 | 0.127 | Contact Map |
| 2d9pA | 1 | 1 | 99.6 | 0.13 | Contact Map |
| 2cqiA | 1 | 1 | 99.6 | 0.134 | Contact Map |
| 2errA | 1 | 1 | 99.6 | 0.136 | Contact Map |
| 3n9uC | 2 | 0.9877 | 99.6 | 0.141 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)