| Tim23 My MSA ONLY |
| ID: | 1487709813 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (119) | ||
| Sequences: | 247 (105.2) | ||
| Seq/Len: | 2.076 | ||
| Nf(neff/√len): | 9.6 |
HHblits Results: (2016_02)
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: 2.076).
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 |
| 37_Q | 96_S | 2.533 | 1.00 |
| 87_A | 110_A | 1.832 | 0.98 |
| 27_N | 40_T | 1.821 | 0.98 |
| 91_A | 106_S | 1.819 | 0.98 |
| 105_S | 109_V | 1.646 | 0.95 |
| 103_G | 107_A | 1.638 | 0.95 |
| 83_I | 110_A | 1.617 | 0.95 |
| 29_P | 32_S | 1.528 | 0.93 |
| 83_I | 113_C | 1.434 | 0.89 |
| 42_L | 46_T | 1.408 | 0.88 |
| 35_K | 61_L | 1.402 | 0.88 |
| 32_S | 89_T | 1.394 | 0.87 |
| 42_L | 60_A | 1.380 | 0.86 |
| 68_S | 85_A | 1.361 | 0.85 |
| 12_G | 71_D | 1.360 | 0.85 |
| 14_G | 100_K | 1.348 | 0.85 |
| 93_F | 110_A | 1.329 | 0.83 |
| 12_G | 84_G | 1.299 | 0.82 |
| 58_I | 65_I | 1.291 | 0.81 |
| 19_S | 23_Q | 1.255 | 0.78 |
| 92_L | 107_A | 1.254 | 0.78 |
| 4_G | 77_H | 1.251 | 0.78 |
| 95_S | 99_L | 1.233 | 0.77 |
| 74_R | 78_D | 1.228 | 0.76 |
| 23_Q | 48_R | 1.192 | 0.73 |
| 8_V | 100_K | 1.186 | 0.73 |
| 59_L | 118_S | 1.167 | 0.71 |
| 23_Q | 47_K | 1.163 | 0.71 |
| 84_G | 111_A | 1.155 | 0.70 |
| 8_V | 28_I | 1.150 | 0.69 |
| 21_M | 115_V | 1.148 | 0.69 |
| 83_I | 117_C | 1.145 | 0.69 |
| 7_A | 21_M | 1.142 | 0.69 |
| 47_K | 117_C | 1.127 | 0.67 |
| 113_C | 116_W | 1.127 | 0.67 |
| 59_L | 119_V | 1.117 | 0.66 |
| 36_L | 45_I | 1.111 | 0.65 |
| 59_L | 72_A | 1.108 | 0.65 |
| 111_A | 119_V | 1.100 | 0.64 |
| 29_P | 33_P | 1.091 | 0.63 |
| 21_M | 84_G | 1.084 | 0.63 |
| 18_F | 22_M | 1.084 | 0.63 |
| 108_M | 111_A | 1.078 | 0.62 |
| 35_K | 91_A | 1.070 | 0.61 |
| 64_N | 77_H | 1.069 | 0.61 |
| 26_Q | 94_K | 1.063 | 0.60 |
| 28_I | 40_T | 1.059 | 0.60 |
| 108_M | 119_V | 1.051 | 0.59 |
| 59_L | 92_L | 1.050 | 0.59 |
| 82_S | 91_A | 1.040 | 0.58 |
| 66_I | 84_G | 1.039 | 0.58 |
| 12_G | 119_V | 1.031 | 0.57 |
| 100_K | 105_S | 1.030 | 0.57 |
| 19_S | 47_K | 1.028 | 0.57 |
| 42_L | 75_G | 1.017 | 0.55 |
| 47_K | 70_I | 1.014 | 0.55 |
| 12_G | 109_V | 1.013 | 0.55 |
| 32_S | 80_A | 1.008 | 0.54 |
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 | |
| 2fozA | 1 | 0.4034 | 1.5 | 0.964 | Contact Map |
| 4mt1A | 1 | 0.7983 | 1.5 | 0.964 | Contact Map |
| 3o5tA | 1 | 0.4118 | 1.4 | 0.965 | Contact Map |
| 4tq3A | 4 | 0.5378 | 1.2 | 0.966 | Contact Map |
| 3dinE | 2 | 0.395 | 1.2 | 0.966 | Contact Map |
| 1booA | 1 | 0.5378 | 1.1 | 0.967 | Contact Map |
| 4ikaD | 1 | 0.1681 | 1 | 0.968 | Contact Map |
| 3cdwH | 1 | 0.0756 | 1 | 0.968 | Contact Map |
| 4i7zE | 1 | 0.2353 | 0.9 | 0.968 | Contact Map |
| 2i2jA | 1 | 0.1765 | 0.9 | 0.969 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)