| Eelco dam1p |
| ID: | 1469529873 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 126 (113) | ||
| Sequences: | 215 (149.6) | ||
| Seq/Len: | 1.903 | ||
| Nf(neff/√len): | 14.1 |
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: 1.903).
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 |
| 7_I | 10_A | 1.742 | 0.96 |
| 93_S | 101_S | 1.730 | 0.96 |
| 92_M | 95_S | 1.688 | 0.96 |
| 80_L | 84_L | 1.591 | 0.93 |
| 77_L | 94_N | 1.566 | 0.93 |
| 89_Y | 93_S | 1.526 | 0.91 |
| 51_P | 86_S | 1.504 | 0.91 |
| 66_N | 82_E | 1.482 | 0.90 |
| 11_P | 59_S | 1.468 | 0.89 |
| 92_M | 99_E | 1.463 | 0.89 |
| 6_S | 9_S | 1.455 | 0.88 |
| 22_S | 25_M | 1.448 | 0.88 |
| 53_I | 62_T | 1.430 | 0.87 |
| 20_E | 23_S | 1.421 | 0.87 |
| 64_D | 68_T | 1.414 | 0.87 |
| 21_S | 25_M | 1.384 | 0.85 |
| 66_N | 89_Y | 1.376 | 0.84 |
| 29_D | 81_N | 1.367 | 0.84 |
| 53_I | 100_F | 1.358 | 0.83 |
| 55_E | 76_S | 1.347 | 0.83 |
| 111_L | 114_I | 1.333 | 0.82 |
| 25_M | 30_Q | 1.319 | 0.81 |
| 9_S | 12_T | 1.294 | 0.79 |
| 64_D | 79_D | 1.288 | 0.79 |
| 19_G | 23_S | 1.260 | 0.76 |
| 63_L | 66_N | 1.223 | 0.73 |
| 30_Q | 68_T | 1.223 | 0.73 |
| 36_S | 40_Y | 1.217 | 0.73 |
| 100_F | 104_P | 1.193 | 0.71 |
| 27_F | 116_Q | 1.190 | 0.70 |
| 59_S | 100_F | 1.188 | 0.70 |
| 15_R | 18_M | 1.186 | 0.70 |
| 89_Y | 99_E | 1.184 | 0.70 |
| 6_S | 11_P | 1.145 | 0.66 |
| 75_E | 101_S | 1.143 | 0.66 |
| 87_L | 92_M | 1.139 | 0.66 |
| 31_E | 61_I | 1.132 | 0.65 |
| 47_Q | 86_S | 1.119 | 0.64 |
| 107_I | 118_K | 1.110 | 0.63 |
| 81_N | 85_G | 1.109 | 0.63 |
| 44_T | 70_L | 1.108 | 0.62 |
| 70_L | 103_A | 1.108 | 0.62 |
| 64_D | 96_W | 1.100 | 0.62 |
| 58_D | 66_N | 1.086 | 0.60 |
| 114_I | 118_K | 1.086 | 0.60 |
| 27_F | 108_Q | 1.085 | 0.60 |
| 51_P | 58_D | 1.083 | 0.60 |
| 14_R | 90_G | 1.075 | 0.59 |
| 82_E | 89_Y | 1.072 | 0.59 |
| 24_L | 30_Q | 1.062 | 0.58 |
| 6_S | 12_T | 1.051 | 0.56 |
| 8_G | 12_T | 1.050 | 0.56 |
| 115_K | 120_L | 1.045 | 0.56 |
| 82_E | 98_V | 1.041 | 0.55 |
| 68_T | 72_F | 1.027 | 0.54 |
| 108_Q | 112_I | 1.026 | 0.54 |
| 116_Q | 120_L | 1.025 | 0.54 |
| 64_D | 73_I | 1.023 | 0.53 |
| 83_S | 94_N | 1.021 | 0.53 |
| 67_F | 97_C | 1.013 | 0.52 |
| 49_L | 104_P | 1.001 | 0.51 |
| 82_E | 94_N | 1.000 | 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 | |
| 3au4B | 1 | 0.2381 | 7.3 | 0.946 | Contact Map |
| 3ibpA | 1 | 0.9683 | 5.5 | 0.949 | Contact Map |
| 4l6rA | 1 | 0.5556 | 5.1 | 0.95 | Contact Map |
| 4jkvA | 2 | 0.5873 | 4.6 | 0.951 | Contact Map |
| 4wfcB | 3 | 0.627 | 4 | 0.953 | Contact Map |
| 4fzsA | 2 | 0.6032 | 3.5 | 0.954 | Contact Map |
| 1lwuB | 4 | 0.6032 | 2.9 | 0.956 | Contact Map |
| 4bwdA | 3 | 0.4921 | 2.6 | 0.957 | Contact Map |
| 1ez3A | 3 | 0.6349 | 2.6 | 0.957 | Contact Map |
| 3axjA | 1 | 0.619 | 2.5 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)