| 4cu5 |
| ID: | 1501760598 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 85 (80) | ||
| Sequences: | 594 (592) | ||
| Seq/Len: | 7.425 | ||
| Nf(neff/√len): | 66.2 |
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: 7.425).
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 |
| 78_K | 81_D | 2.864 | 1.00 |
| 16_S | 76_L | 2.723 | 1.00 |
| 76_L | 80_L | 2.597 | 1.00 |
| 47_V | 54_E | 2.576 | 1.00 |
| 65_I | 82_F | 2.499 | 1.00 |
| 17_A | 48_V | 2.456 | 1.00 |
| 71_D | 74_D | 2.405 | 1.00 |
| 74_D | 78_K | 1.911 | 1.00 |
| 5_T | 42_T | 1.812 | 1.00 |
| 3_K | 43_Q | 1.812 | 1.00 |
| 4_H | 46_Y | 1.770 | 1.00 |
| 44_N | 65_I | 1.769 | 1.00 |
| 45_L | 64_F | 1.600 | 1.00 |
| 72_R | 75_T | 1.585 | 1.00 |
| 50_G | 68_K | 1.425 | 0.99 |
| 9_D | 53_C | 1.408 | 0.99 |
| 32_C | 54_E | 1.384 | 0.99 |
| 10_G | 31_I | 1.340 | 0.98 |
| 17_A | 26_D | 1.269 | 0.98 |
| 32_C | 38_V | 1.264 | 0.97 |
| 48_V | 79_A | 1.258 | 0.97 |
| 20_V | 26_D | 1.236 | 0.97 |
| 42_T | 62_E | 1.228 | 0.97 |
| 10_G | 14_K | 1.221 | 0.97 |
| 12_V | 72_R | 1.193 | 0.96 |
| 18_T | 22_W | 1.188 | 0.96 |
| 13_D | 72_R | 1.145 | 0.95 |
| 45_L | 62_E | 1.131 | 0.94 |
| 13_D | 50_G | 1.131 | 0.94 |
| 54_E | 66_M | 1.127 | 0.94 |
| 4_H | 24_Y | 1.113 | 0.94 |
| 20_V | 79_A | 1.112 | 0.94 |
| 49_G | 66_M | 1.094 | 0.93 |
| 6_I | 21_G | 1.070 | 0.92 |
| 77_Y | 80_L | 1.065 | 0.92 |
| 6_I | 46_Y | 1.054 | 0.91 |
| 16_S | 46_Y | 1.052 | 0.91 |
| 20_V | 83_I | 1.043 | 0.90 |
| 27_G | 30_L | 1.018 | 0.89 |
| 70_N | 74_D | 1.000 | 0.88 |
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 | |
| 4cu2A | 1 | 0.9176 | 99.7 | 0.052 | Contact Map |
| 4cu5A | 6 | 1 | 99.2 | 0.285 | Contact Map |
| 1kl7A | 2 | 0.8706 | 12.6 | 0.854 | Contact Map |
| 2eguA | 1 | 0.8941 | 8.5 | 0.864 | Contact Map |
| 1o58A | 4 | 0.9529 | 7.7 | 0.867 | Contact Map |
| 2xveA | 3 | 0.9765 | 7.4 | 0.868 | Contact Map |
| 4rg3A | 1 | 0.9765 | 7.1 | 0.869 | Contact Map |
| 4r2vA | 2 | 0.9529 | 6.7 | 0.871 | Contact Map |
| 4ql4A | 1 | 0.9529 | 6.6 | 0.871 | Contact Map |
| 4usrA | 1 | 0.9882 | 6.1 | 0.873 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)