| IAAT_ELECO -force run |
| ID: | 1418316242 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 122 (115) | ||
| Sequences: | 111 (73.1) | ||
| Seq/Len: | 0.965 | ||
| Nf(neff/√len): | 6.8 |
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: 0.965).
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 |
| 13_P | 59_A | 1.853 | 0.92 |
| 46_R | 93_F | 1.642 | 0.84 |
| 9_G | 13_P | 1.594 | 0.82 |
| 19_S | 85_C | 1.561 | 0.80 |
| 41_K | 105_L | 1.486 | 0.75 |
| 53_A | 110_G | 1.454 | 0.73 |
| 102_E | 105_L | 1.414 | 0.70 |
| 17_L | 112_P | 1.383 | 0.67 |
| 9_G | 65_D | 1.376 | 0.66 |
| 70_P | 86_P | 1.344 | 0.64 |
| 71_S | 82_L | 1.343 | 0.64 |
| 25_S | 38_Q | 1.336 | 0.63 |
| 113_F | 116_S | 1.309 | 0.61 |
| 46_R | 101_V | 1.304 | 0.60 |
| 31_V | 52_P | 1.285 | 0.59 |
| 21_R | 84_G | 1.283 | 0.58 |
| 27_R | 100_E | 1.278 | 0.58 |
| 82_L | 99_T | 1.264 | 0.57 |
| 38_Q | 52_P | 1.240 | 0.55 |
| 47_Q | 77_R | 1.236 | 0.54 |
| 13_P | 16_P | 1.216 | 0.52 |
| 6_C | 9_G | 1.208 | 0.52 |
| 27_R | 102_E | 1.207 | 0.52 |
| 17_L | 51_I | 1.195 | 0.50 |
| 36_A | 49_E | 1.194 | 0.50 |
| 3_G | 84_G | 1.190 | 0.50 |
| 79_L | 91_R | 1.173 | 0.48 |
| 23_Y | 34_R | 1.172 | 0.48 |
| 24_V | 29_C | 1.171 | 0.48 |
| 6_C | 63_L | 1.168 | 0.48 |
| 10_M | 111_G | 1.165 | 0.48 |
| 3_G | 6_C | 1.161 | 0.47 |
| 8_P | 58_E | 1.148 | 0.46 |
| 60_V | 73_Q | 1.143 | 0.46 |
| 56_R | 80_Q | 1.141 | 0.46 |
| 60_V | 85_C | 1.129 | 0.44 |
| 59_A | 97_L | 1.126 | 0.44 |
| 24_V | 84_G | 1.126 | 0.44 |
| 5_S | 23_Y | 1.122 | 0.44 |
| 10_M | 24_V | 1.120 | 0.44 |
| 29_C | 56_R | 1.118 | 0.43 |
| 105_L | 108_I | 1.117 | 0.43 |
| 43_R | 71_S | 1.113 | 0.43 |
| 49_E | 61_R | 1.111 | 0.43 |
| 28_T | 47_Q | 1.092 | 0.41 |
| 17_L | 21_R | 1.088 | 0.41 |
| 40_M | 110_G | 1.082 | 0.40 |
| 53_A | 108_I | 1.078 | 0.40 |
| 67_V | 105_L | 1.075 | 0.40 |
| 56_R | 101_V | 1.070 | 0.39 |
| 18_D | 21_R | 1.064 | 0.39 |
| 72_G | 85_C | 1.063 | 0.39 |
| 5_S | 99_T | 1.062 | 0.38 |
| 22_W | 90_Q | 1.053 | 0.38 |
| 9_G | 59_A | 1.051 | 0.38 |
| 53_A | 80_Q | 1.047 | 0.37 |
| 33_P | 91_R | 1.044 | 0.37 |
| 88_Q | 91_R | 1.040 | 0.37 |
| 49_E | 88_Q | 1.035 | 0.36 |
| 26_T | 51_I | 1.035 | 0.36 |
| 20_C | 44_C | 1.030 | 0.36 |
| 55_C | 72_G | 1.024 | 0.35 |
| 63_L | 113_F | 1.023 | 0.35 |
| 102_E | 107_T | 1.020 | 0.35 |
| 63_L | 72_G | 1.020 | 0.35 |
| 99_T | 115_L | 1.012 | 0.34 |
| 15_N | 18_D | 1.010 | 0.34 |
| 4_T | 77_R | 1.005 | 0.34 |
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 | |
| 1beaA | 1 | 0.9426 | 100 | 0.218 | Contact Map |
| 1b1uA | 1 | 0.959 | 100 | 0.258 | Contact Map |
| 1hssA | 4 | 0.8607 | 100 | 0.344 | Contact Map |
| 1w2qA | 1 | 0.8607 | 99.8 | 0.529 | Contact Map |
| 1sm7A | 1 | 0.8361 | 99.8 | 0.535 | Contact Map |
| 2lvfA | 1 | 0.8525 | 99.8 | 0.541 | Contact Map |
| 1s6dA | 1 | 0.7705 | 99.8 | 0.546 | Contact Map |
| 1psyA | 1 | 0.8197 | 99.7 | 0.557 | Contact Map |
| 3ob4A | 1 | 0.8033 | 99.7 | 0.572 | Contact Map |
| 1pnbB | 1 | 0.6148 | 99.6 | 0.609 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)