| T0814 180-300 |
| ID: | 1404854277 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (119) | ||
| Sequences: | 225 (198.6) | ||
| Seq/Len: | 1.891 | ||
| Nf(neff/√len): | 18.2 |
Jackhmmer Results: (2014_04_16)
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: 1.891).
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 |
| 65_E | 113_D | 2.127 | 0.99 |
| 16_I | 23_L | 2.111 | 0.99 |
| 32_R | 35_N | 2.010 | 0.99 |
| 40_L | 58_L | 1.965 | 0.99 |
| 81_V | 95_L | 1.944 | 0.98 |
| 23_L | 50_I | 1.839 | 0.98 |
| 19_P | 24_K | 1.817 | 0.97 |
| 65_E | 111_D | 1.800 | 0.97 |
| 27_V | 58_L | 1.736 | 0.96 |
| 28_Y | 33_R | 1.673 | 0.95 |
| 17_T | 66_Y | 1.522 | 0.91 |
| 77_N | 81_V | 1.521 | 0.91 |
| 16_I | 22_D | 1.495 | 0.90 |
| 4_Q | 59_I | 1.444 | 0.88 |
| 18_Y | 21_T | 1.425 | 0.87 |
| 9_I | 97_T | 1.402 | 0.86 |
| 67_R | 98_D | 1.390 | 0.85 |
| 7_F | 25_I | 1.349 | 0.83 |
| 66_Y | 119_R | 1.349 | 0.83 |
| 5_V | 113_D | 1.318 | 0.81 |
| 69_M | 95_L | 1.311 | 0.80 |
| 2_H | 61_P | 1.305 | 0.80 |
| 9_I | 19_P | 1.299 | 0.79 |
| 70_E | 109_D | 1.294 | 0.79 |
| 37_V | 81_V | 1.281 | 0.78 |
| 8_N | 83_N | 1.278 | 0.78 |
| 45_I | 51_S | 1.241 | 0.75 |
| 36_A | 39_D | 1.237 | 0.74 |
| 43_M | 111_D | 1.237 | 0.74 |
| 16_I | 24_K | 1.230 | 0.74 |
| 29_Q | 35_N | 1.228 | 0.74 |
| 11_N | 16_I | 1.221 | 0.73 |
| 16_I | 76_Y | 1.208 | 0.72 |
| 5_V | 27_V | 1.184 | 0.70 |
| 73_S | 76_Y | 1.171 | 0.69 |
| 13_N | 16_I | 1.169 | 0.68 |
| 87_H | 92_N | 1.138 | 0.65 |
| 37_V | 40_L | 1.134 | 0.65 |
| 66_Y | 109_D | 1.120 | 0.63 |
| 72_L | 112_Q | 1.113 | 0.63 |
| 7_F | 116_F | 1.105 | 0.62 |
| 44_S | 51_S | 1.098 | 0.61 |
| 84_I | 93_V | 1.098 | 0.61 |
| 4_Q | 54_Y | 1.091 | 0.60 |
| 26_F | 51_S | 1.091 | 0.60 |
| 54_Y | 109_D | 1.088 | 0.60 |
| 9_I | 53_T | 1.086 | 0.60 |
| 70_E | 110_Q | 1.083 | 0.60 |
| 4_Q | 67_R | 1.078 | 0.59 |
| 19_P | 116_F | 1.063 | 0.58 |
| 25_I | 39_D | 1.062 | 0.57 |
| 71_F | 93_V | 1.060 | 0.57 |
| 20_Q | 118_I | 1.058 | 0.57 |
| 9_I | 18_Y | 1.052 | 0.56 |
| 109_D | 112_Q | 1.045 | 0.56 |
| 54_Y | 58_L | 1.037 | 0.55 |
| 11_N | 47_E | 1.019 | 0.53 |
| 22_D | 102_D | 1.018 | 0.53 |
| 82_E | 100_R | 1.018 | 0.53 |
| 66_Y | 72_L | 1.003 | 0.51 |
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 | |
| 1avyA | 3 | 0.3554 | 10.2 | 0.941 | Contact Map |
| 1k9aA | 6 | 0.6446 | 9.9 | 0.941 | Contact Map |
| 2lqnA | 1 | 0.3388 | 8.8 | 0.943 | Contact Map |
| 2dm0A | 1 | 0.3306 | 7.3 | 0.945 | Contact Map |
| 2cs0A | 1 | 0.3554 | 7.2 | 0.945 | Contact Map |
| 2vseA | 2 | 0.8017 | 6.2 | 0.946 | Contact Map |
| 2ekxA | 1 | 0.3388 | 6.2 | 0.946 | Contact Map |
| 3wa4A | 1 | 0.2562 | 5.8 | 0.947 | Contact Map |
| 4oujA | 2 | 0.3967 | 5.7 | 0.947 | Contact Map |
| 2bbuA | 1 | 0.3554 | 5.4 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)