| 1CKT |
| ID: | 1488647941 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 71 (71) | ||
| Sequences: | 4119 (2597.8) | ||
| Seq/Len: | 58.014 | ||
| Nf(neff/√len): | 308.3 |
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: 58.014).
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 |
| 63_R | 67_E | 3.118 | 1.00 |
| 51_G | 55_D | 2.732 | 1.00 |
| 16_C | 41_R | 2.680 | 1.00 |
| 60_D | 63_R | 2.534 | 1.00 |
| 16_C | 19_E | 2.277 | 1.00 |
| 13_V | 38_C | 2.034 | 1.00 |
| 46_S | 49_E | 1.832 | 1.00 |
| 47_A | 54_E | 1.736 | 1.00 |
| 40_E | 44_T | 1.733 | 1.00 |
| 52_K | 56_M | 1.675 | 1.00 |
| 45_M | 49_E | 1.660 | 1.00 |
| 16_C | 38_C | 1.582 | 1.00 |
| 37_K | 41_R | 1.557 | 1.00 |
| 62_A | 66_R | 1.523 | 1.00 |
| 11_F | 60_D | 1.509 | 1.00 |
| 37_K | 40_E | 1.446 | 1.00 |
| 15_T | 53_F | 1.442 | 1.00 |
| 12_F | 45_M | 1.431 | 1.00 |
| 59_A | 62_A | 1.412 | 1.00 |
| 11_F | 56_M | 1.377 | 0.99 |
| 56_M | 59_A | 1.374 | 0.99 |
| 6_M | 60_D | 1.358 | 0.99 |
| 6_M | 10_A | 1.353 | 0.99 |
| 10_A | 13_V | 1.352 | 0.99 |
| 58_K | 62_A | 1.350 | 0.99 |
| 56_M | 60_D | 1.350 | 0.99 |
| 55_D | 58_K | 1.302 | 0.99 |
| 6_M | 14_Q | 1.289 | 0.99 |
| 61_K | 65_E | 1.260 | 0.99 |
| 55_D | 59_A | 1.243 | 0.98 |
| 31_F | 35_S | 1.206 | 0.98 |
| 35_S | 39_S | 1.202 | 0.98 |
| 18_E | 21_K | 1.165 | 0.97 |
| 63_R | 66_R | 1.145 | 0.97 |
| 15_T | 56_M | 1.134 | 0.97 |
| 47_A | 51_G | 1.104 | 0.96 |
| 18_E | 22_K | 1.070 | 0.95 |
| 19_E | 23_K | 1.048 | 0.94 |
| 8_S | 54_E | 1.017 | 0.93 |
| 62_A | 65_E | 1.010 | 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 | |
| 2mrcA | 1 | 1 | 99.5 | -0.072 | Contact Map |
| 2co9A | 1 | 0.9718 | 99.5 | -0.072 | Contact Map |
| 3tmmA | 1 | 0.9718 | 99.5 | -0.071 | Contact Map |
| 3tq6A | 2 | 0.9718 | 99.5 | -0.068 | Contact Map |
| 1k99A | 1 | 0.9718 | 99.5 | -0.068 | Contact Map |
| 2yrqA | 1 | 0.9718 | 99.5 | -0.066 | Contact Map |
| 1cg7A | 1 | 0.9718 | 99.5 | -0.065 | Contact Map |
| 2cs1A | 1 | 0.9718 | 99.5 | -0.065 | Contact Map |
| 2crjA | 1 | 0.9718 | 99.5 | -0.064 | Contact Map |
| 2eqzA | 1 | 1 | 99.5 | -0.063 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)