| aaa |
| ID: | 1402456010 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (106) | ||
| Sequences: | 670 (402.2) | ||
| Seq/Len: | 6.321 | ||
| Nf(neff/√len): | 39.1 |
HHblits Results: (2013_03)
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: 6.321).
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 |
| 59_Y | 81_H | 3.993 | 1.00 |
| 49_D | 86_S | 2.790 | 1.00 |
| 87_M | 95_E | 2.504 | 1.00 |
| 23_I | 96_F | 2.136 | 1.00 |
| 40_S | 84_Y | 1.968 | 1.00 |
| 22_D | 27_R | 1.926 | 1.00 |
| 73_L | 77_V | 1.889 | 1.00 |
| 103_L | 106_Y | 1.855 | 1.00 |
| 13_Y | 93_D | 1.815 | 1.00 |
| 37_L | 40_S | 1.720 | 1.00 |
| 21_Q | 25_A | 1.647 | 1.00 |
| 43_I | 60_V | 1.604 | 1.00 |
| 32_F | 39_G | 1.577 | 0.99 |
| 18_Q | 22_D | 1.572 | 0.99 |
| 37_L | 84_Y | 1.473 | 0.99 |
| 15_L | 20_R | 1.391 | 0.98 |
| 16_C | 42_T | 1.353 | 0.98 |
| 99_N | 102_K | 1.329 | 0.98 |
| 3_P | 101_K | 1.300 | 0.97 |
| 14_Y | 41_Y | 1.253 | 0.96 |
| 55_H | 58_D | 1.252 | 0.96 |
| 22_D | 26_G | 1.228 | 0.96 |
| 44_Q | 48_G | 1.214 | 0.95 |
| 42_T | 96_F | 1.209 | 0.95 |
| 84_Y | 100_A | 1.202 | 0.95 |
| 16_C | 93_D | 1.150 | 0.93 |
| 51_D | 55_H | 1.142 | 0.93 |
| 8_E | 11_T | 1.142 | 0.93 |
| 9_D | 104_S | 1.135 | 0.93 |
| 16_C | 75_E | 1.105 | 0.91 |
| 33_A | 66_A | 1.098 | 0.91 |
| 6_L | 15_L | 1.095 | 0.91 |
| 16_C | 20_R | 1.093 | 0.91 |
| 7_T | 91_Q | 1.093 | 0.91 |
| 13_Y | 64_K | 1.089 | 0.90 |
| 52_P | 55_H | 1.087 | 0.90 |
| 58_D | 74_E | 1.086 | 0.90 |
| 23_I | 67_P | 1.080 | 0.90 |
| 14_Y | 93_D | 1.075 | 0.90 |
| 20_R | 104_S | 1.059 | 0.89 |
| 11_T | 15_L | 1.044 | 0.88 |
| 24_V | 96_F | 1.042 | 0.88 |
| 76_K | 79_E | 1.036 | 0.87 |
| 39_G | 66_A | 1.035 | 0.87 |
| 54_L | 85_R | 1.035 | 0.87 |
| 98_E | 102_K | 1.026 | 0.87 |
| 19_L | 97_L | 1.008 | 0.85 |
| 88_T | 91_Q | 1.007 | 0.85 |
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 | |
| 3qijA | 2 | 1 | 99.9 | 0.209 | Contact Map |
| 2i1jA | 1 | 1 | 99.9 | 0.256 | Contact Map |
| 1h4rA | 2 | 1 | 99.9 | 0.267 | Contact Map |
| 1ef1A | 2 | 1 | 99.9 | 0.271 | Contact Map |
| 4hdoA | 1 | 1 | 99.9 | 0.293 | Contact Map |
| 1mixA | 1 | 0.9906 | 99.9 | 0.295 | Contact Map |
| 2al6A | 2 | 1 | 99.9 | 0.301 | Contact Map |
| 4f7gA | 1 | 0.9245 | 99.9 | 0.304 | Contact Map |
| 4ekuA | 1 | 1 | 99.9 | 0.305 | Contact Map |
| 3ivfA | 1 | 0.9906 | 99.9 | 0.331 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)