| T0844 |
| ID: | 1404751851 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (143) | ||
| Sequences: | 204 (186.3) | ||
| Seq/Len: | 1.427 | ||
| Nf(neff/√len): | 15.6 |
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: 1.427).
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 |
| 94_K | 102_E | 2.868 | 1.00 |
| 47_I | 86_K | 2.067 | 0.98 |
| 31_A | 40_I | 2.034 | 0.98 |
| 43_L | 104_N | 1.931 | 0.97 |
| 39_K | 91_G | 1.867 | 0.96 |
| 40_I | 43_L | 1.826 | 0.96 |
| 98_Y | 101_S | 1.824 | 0.96 |
| 58_I | 111_E | 1.685 | 0.92 |
| 22_E | 130_H | 1.635 | 0.91 |
| 22_E | 126_I | 1.607 | 0.90 |
| 48_Y | 56_Q | 1.595 | 0.89 |
| 6_H | 44_S | 1.589 | 0.89 |
| 44_S | 54_L | 1.507 | 0.86 |
| 23_V | 123_R | 1.448 | 0.82 |
| 133_K | 136_R | 1.423 | 0.81 |
| 56_Q | 95_S | 1.379 | 0.78 |
| 126_I | 130_H | 1.348 | 0.76 |
| 59_S | 71_L | 1.344 | 0.75 |
| 30_D | 138_L | 1.309 | 0.72 |
| 10_I | 141_V | 1.306 | 0.72 |
| 46_L | 86_K | 1.255 | 0.68 |
| 56_Q | 135_R | 1.251 | 0.67 |
| 61_I | 112_I | 1.248 | 0.67 |
| 96_Q | 119_V | 1.245 | 0.67 |
| 87_G | 101_S | 1.244 | 0.67 |
| 22_E | 51_P | 1.241 | 0.67 |
| 27_I | 53_I | 1.240 | 0.67 |
| 59_S | 105_A | 1.231 | 0.66 |
| 3_H | 6_H | 1.227 | 0.65 |
| 83_G | 118_K | 1.226 | 0.65 |
| 68_G | 119_V | 1.224 | 0.65 |
| 87_G | 98_Y | 1.216 | 0.64 |
| 35_K | 39_K | 1.203 | 0.63 |
| 12_A | 142_K | 1.186 | 0.61 |
| 20_E | 123_R | 1.172 | 0.60 |
| 5_H | 74_R | 1.168 | 0.60 |
| 60_H | 63_A | 1.158 | 0.59 |
| 34_Q | 107_I | 1.150 | 0.58 |
| 78_S | 95_S | 1.149 | 0.58 |
| 23_V | 95_S | 1.138 | 0.57 |
| 9_L | 13_E | 1.136 | 0.56 |
| 27_I | 84_R | 1.117 | 0.55 |
| 119_V | 126_I | 1.114 | 0.54 |
| 127_M | 138_L | 1.103 | 0.53 |
| 46_L | 100_I | 1.098 | 0.53 |
| 71_L | 81_S | 1.088 | 0.52 |
| 18_L | 126_I | 1.071 | 0.50 |
| 38_E | 125_T | 1.057 | 0.48 |
| 65_P | 116_A | 1.056 | 0.48 |
| 18_L | 136_R | 1.051 | 0.48 |
| 91_G | 105_A | 1.050 | 0.48 |
| 15_L | 62_N | 1.048 | 0.48 |
| 86_K | 101_S | 1.047 | 0.47 |
| 23_V | 71_L | 1.040 | 0.47 |
| 55_E | 129_E | 1.037 | 0.46 |
| 3_H | 7_H | 1.035 | 0.46 |
| 13_E | 45_K | 1.032 | 0.46 |
| 78_S | 139_Q | 1.031 | 0.46 |
| 33_I | 72_S | 1.027 | 0.45 |
| 17_P | 77_N | 1.024 | 0.45 |
| 21_E | 128_R | 1.021 | 0.45 |
| 105_A | 116_A | 1.019 | 0.45 |
| 50_N | 92_Y | 1.018 | 0.45 |
| 53_I | 80_K | 1.017 | 0.44 |
| 37_L | 40_I | 1.013 | 0.44 |
| 9_L | 15_L | 1.013 | 0.44 |
| 18_L | 33_I | 1.012 | 0.44 |
| 68_G | 116_A | 1.008 | 0.44 |
| 89_K | 99_K | 1.006 | 0.43 |
| 120_S | 123_R | 1.004 | 0.43 |
| 41_R | 52_E | 1.000 | 0.43 |
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 | |
| 2lnmA | 1 | 0.4069 | 36.2 | 0.929 | Contact Map |
| 2llwA | 1 | 0.4897 | 16.7 | 0.94 | Contact Map |
| 2llvA | 1 | 0.4897 | 12.1 | 0.943 | Contact Map |
| 2zbcA | 8 | 0.531 | 9 | 0.946 | Contact Map |
| 2f4mB | 1 | 0.4138 | 7.9 | 0.948 | Contact Map |
| 3hwsA | 6 | 0.6414 | 7 | 0.949 | Contact Map |
| 3k8pC | 1 | 0.469 | 5.8 | 0.951 | Contact Map |
| 2djwA | 10 | 0.5241 | 5.7 | 0.951 | Contact Map |
| 2oeqA | 4 | 0.469 | 5.7 | 0.951 | Contact Map |
| 1u1jA | 1 | 0.6483 | 3.8 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)