| gvpA anabaena flos-aquae |
| ID: | 1424430120 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (65) | ||
| Sequences: | 147 (64.9) | ||
| Seq/Len: | 2.262 | ||
| Nf(neff/√len): | 8.0 |
HHblits Results: (2013_03)
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: 2.262).
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 |
| 31_V | 39_L | 2.080 | 0.99 |
| 15_I | 18_I | 1.992 | 0.99 |
| 12_A | 47_I | 1.825 | 0.98 |
| 35_G | 48_A | 1.590 | 0.95 |
| 57_A | 61_G | 1.542 | 0.94 |
| 36_I | 41_I | 1.487 | 0.92 |
| 31_V | 37_E | 1.360 | 0.87 |
| 27_A | 45_I | 1.355 | 0.87 |
| 2_V | 66_A | 1.354 | 0.87 |
| 10_S | 62_L | 1.344 | 0.86 |
| 28_W | 45_I | 1.308 | 0.84 |
| 12_A | 16_D | 1.301 | 0.84 |
| 10_S | 52_T | 1.261 | 0.81 |
| 42_E | 48_A | 1.254 | 0.80 |
| 29_V | 58_E | 1.227 | 0.78 |
| 17_R | 31_V | 1.215 | 0.77 |
| 7_S | 13_E | 1.202 | 0.76 |
| 9_S | 31_V | 1.190 | 0.75 |
| 17_R | 56_Y | 1.180 | 0.74 |
| 23_I | 47_I | 1.179 | 0.74 |
| 46_V | 52_T | 1.172 | 0.74 |
| 40_A | 51_E | 1.147 | 0.71 |
| 8_S | 49_S | 1.138 | 0.71 |
| 34_V | 47_I | 1.134 | 0.70 |
| 36_I | 48_A | 1.113 | 0.68 |
| 35_G | 63_T | 1.093 | 0.66 |
| 6_N | 31_V | 1.093 | 0.66 |
| 2_V | 28_W | 1.077 | 0.64 |
| 4_K | 13_E | 1.061 | 0.63 |
| 30_R | 35_G | 1.052 | 0.62 |
| 11_L | 30_R | 1.051 | 0.62 |
| 25_I | 41_I | 1.046 | 0.61 |
| 10_S | 14_V | 1.027 | 0.59 |
| 9_S | 23_I | 1.014 | 0.58 |
| 11_L | 35_G | 1.005 | 0.57 |
| 32_S | 46_V | 1.000 | 0.56 |
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 | |
| 3cq5A | 3 | 0.7286 | 15 | 0.902 | Contact Map |
| 2jvfA | 1 | 0.6 | 8.4 | 0.913 | Contact Map |
| 2w5fA | 2 | 0.9857 | 8.4 | 0.913 | Contact Map |
| 1xqiA | 3 | 0.9857 | 7.8 | 0.913 | Contact Map |
| 3getA | 2 | 0.7 | 7.6 | 0.914 | Contact Map |
| 2yrrA | 2 | 0.7714 | 7.5 | 0.914 | Contact Map |
| 1vjoA | 1 | 0.7714 | 7.3 | 0.915 | Contact Map |
| 2lnaA | 1 | 0.9429 | 7.2 | 0.915 | Contact Map |
| 2aeuA | 1 | 0.8571 | 7.2 | 0.915 | Contact Map |
| 3fpnA | 1 | 0.9571 | 7.1 | 0.915 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)