| Eelco dam1p 15-115 |
| ID: | 1481361229 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 101 (89) | ||
| Sequences: | 230 (161.7) | ||
| Seq/Len: | 2.584 | ||
| Nf(neff/√len): | 17.1 |
Jackhmmer Results: (2016_04)
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: 2.584).
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 |
| 11_M | 15_D | 2.021 | 0.99 |
| 66_L | 70_L | 1.995 | 0.99 |
| 79_S | 87_S | 1.751 | 0.98 |
| 93_I | 97_L | 1.748 | 0.98 |
| 89_A | 94_Q | 1.694 | 0.98 |
| 19_L | 22_S | 1.537 | 0.95 |
| 42_L | 56_L | 1.521 | 0.95 |
| 37_P | 72_S | 1.506 | 0.94 |
| 45_S | 86_F | 1.481 | 0.94 |
| 50_D | 54_T | 1.469 | 0.93 |
| 75_Y | 79_S | 1.468 | 0.93 |
| 78_M | 81_S | 1.431 | 0.92 |
| 11_M | 19_L | 1.411 | 0.91 |
| 11_M | 14_A | 1.409 | 0.91 |
| 39_I | 86_F | 1.383 | 0.90 |
| 68_E | 75_Y | 1.336 | 0.88 |
| 70_L | 73_L | 1.301 | 0.86 |
| 68_E | 80_N | 1.300 | 0.86 |
| 78_M | 85_E | 1.251 | 0.83 |
| 50_D | 65_D | 1.246 | 0.83 |
| 30_T | 56_L | 1.236 | 0.82 |
| 16_Q | 20_T | 1.206 | 0.80 |
| 9_S | 14_A | 1.179 | 0.78 |
| 15_D | 19_L | 1.163 | 0.77 |
| 41_E | 44_D | 1.152 | 0.76 |
| 90_P | 94_Q | 1.147 | 0.75 |
| 68_E | 82_W | 1.140 | 0.75 |
| 39_I | 48_T | 1.138 | 0.74 |
| 9_S | 13_F | 1.129 | 0.74 |
| 18_G | 21_S | 1.122 | 0.73 |
| 9_S | 15_D | 1.114 | 0.72 |
| 60_H | 72_S | 1.109 | 0.72 |
| 16_Q | 19_L | 1.100 | 0.71 |
| 13_F | 19_L | 1.086 | 0.69 |
| 31_I | 88_Q | 1.085 | 0.69 |
| 56_L | 89_A | 1.079 | 0.69 |
| 17_E | 20_T | 1.072 | 0.68 |
| 33_Q | 56_L | 1.068 | 0.68 |
| 50_D | 59_I | 1.064 | 0.67 |
| 45_S | 53_F | 1.032 | 0.64 |
| 52_N | 75_Y | 1.030 | 0.63 |
| 86_F | 90_P | 1.027 | 0.63 |
| 40_R | 53_F | 1.025 | 0.63 |
| 44_D | 52_N | 1.023 | 0.63 |
| 61_E | 87_S | 1.016 | 0.62 |
| 90_P | 95_D | 1.016 | 0.62 |
| 73_L | 78_M | 1.012 | 0.61 |
| 75_Y | 81_S | 1.003 | 0.60 |
| 37_P | 63_L | 1.003 | 0.60 |
| 52_N | 68_E | 1.001 | 0.60 |
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 | |
| 4linA | 12 | 1 | 13.9 | 0.919 | Contact Map |
| 3k9tA | 1 | 0.6931 | 6.6 | 0.93 | Contact Map |
| 3axjA | 1 | 0.6832 | 6.4 | 0.93 | Contact Map |
| 3wpaA | 1 | 0.1188 | 6.3 | 0.93 | Contact Map |
| 4l6rA | 1 | 0.5842 | 5.5 | 0.932 | Contact Map |
| 3fdrA | 1 | 0.4455 | 4.5 | 0.935 | Contact Map |
| 4bwdA | 3 | 0.6139 | 4.4 | 0.935 | Contact Map |
| 1w99A | 1 | 0.604 | 4.4 | 0.936 | Contact Map |
| 3w92A | 3 | 0.3069 | 4.1 | 0.937 | Contact Map |
| 2y7cA | 1 | 0.9901 | 3.9 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)