| ISD11 |
| ID: | 1435131143 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 94 (88) | ||
| Sequences: | 529 (387.2) | ||
| Seq/Len: | 6.011 | ||
| Nf(neff/√len): | 41.3 |
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: 6.011).
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 |
| 49_Q | 54_V | 3.378 | 1.00 |
| 49_Q | 58_L | 3.149 | 1.00 |
| 38_K | 42_T | 2.435 | 1.00 |
| 46_N | 49_Q | 2.256 | 1.00 |
| 15_L | 62_A | 1.766 | 1.00 |
| 58_L | 62_A | 1.749 | 1.00 |
| 9_R | 13_L | 1.609 | 0.99 |
| 11_Q | 14_S | 1.568 | 0.99 |
| 19_F | 39_T | 1.518 | 0.99 |
| 59_F | 63_K | 1.477 | 0.99 |
| 75_I | 78_M | 1.474 | 0.99 |
| 44_R | 47_M | 1.377 | 0.98 |
| 84_L | 87_E | 1.343 | 0.98 |
| 58_L | 61_E | 1.338 | 0.97 |
| 34_Y | 38_K | 1.251 | 0.96 |
| 51_D | 55_L | 1.229 | 0.95 |
| 26_F | 71_R | 1.213 | 0.95 |
| 29_Y | 37_S | 1.210 | 0.95 |
| 17_K | 77_Q | 1.197 | 0.94 |
| 7_P | 12_V | 1.167 | 0.93 |
| 19_F | 65_D | 1.163 | 0.93 |
| 23_A | 69_L | 1.163 | 0.93 |
| 57_N | 63_K | 1.152 | 0.93 |
| 28_N | 44_R | 1.150 | 0.93 |
| 65_D | 68_V | 1.147 | 0.92 |
| 19_F | 62_A | 1.145 | 0.92 |
| 35_F | 69_L | 1.138 | 0.92 |
| 30_N | 34_Y | 1.127 | 0.92 |
| 61_E | 64_N | 1.115 | 0.91 |
| 75_I | 80_T | 1.111 | 0.91 |
| 53_K | 56_M | 1.104 | 0.90 |
| 20_I | 36_L | 1.089 | 0.90 |
| 34_Y | 37_S | 1.075 | 0.89 |
| 20_I | 34_Y | 1.057 | 0.88 |
| 25_Q | 70_K | 1.054 | 0.87 |
| 29_Y | 32_R | 1.053 | 0.87 |
| 52_P | 56_M | 1.052 | 0.87 |
| 18_E | 77_Q | 1.040 | 0.87 |
| 38_K | 71_R | 1.035 | 0.86 |
| 64_N | 67_G | 1.029 | 0.86 |
| 29_Y | 38_K | 1.026 | 0.86 |
| 34_Y | 71_R | 1.024 | 0.85 |
| 20_I | 32_R | 1.024 | 0.85 |
| 57_N | 60_K | 1.018 | 0.85 |
| 60_K | 63_K | 1.012 | 0.84 |
| 4_F | 7_P | 1.010 | 0.84 |
| 54_V | 58_L | 1.006 | 0.84 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1s94A | 2 | 0.4468 | 28.9 | 0.889 | Contact Map |
| 4jg4A | 1 | 0.9149 | 15.8 | 0.902 | Contact Map |
| 3dmcA | 2 | 0.9787 | 6.5 | 0.917 | Contact Map |
| 1dd9A | 1 | 0.5532 | 6.3 | 0.918 | Contact Map |
| 4pjwB | 1 | 0.234 | 5.8 | 0.92 | Contact Map |
| 1o22A | 1 | 0.4043 | 5.1 | 0.921 | Contact Map |
| 2v1mA | 1 | 0.7021 | 4.9 | 0.922 | Contact Map |
| 3cmiA | 1 | 0.7021 | 3.9 | 0.926 | Contact Map |
| 2jd60 | 36 | 0.8723 | 3.2 | 0.929 | Contact Map |
| 1jq5A | 1 | 0.3085 | 2.8 | 0.931 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)