| alsk_ecoli N-term |
| ID: | 1392709548 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 60 (53) | ||
| Sequences: | 7255 (5547.6) | ||
| Seq/Len: | 136.887 | ||
| Nf(neff/√len): | 762.0 |
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: 136.887).
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 |
| 20_F | 52_M | 3.284 | 1.00 |
| 24_T | 28_E | 2.740 | 1.00 |
| 33_E | 55_E | 2.549 | 1.00 |
| 17_H | 34_K | 2.372 | 1.00 |
| 35_K | 51_E | 2.271 | 1.00 |
| 13_M | 18_I | 2.214 | 1.00 |
| 9_A | 20_F | 1.881 | 1.00 |
| 11_V | 49_I | 1.736 | 1.00 |
| 23_R | 29_T | 1.694 | 1.00 |
| 35_K | 55_E | 1.606 | 1.00 |
| 7_V | 22_L | 1.601 | 1.00 |
| 11_V | 53_I | 1.550 | 1.00 |
| 43_P | 47_S | 1.261 | 0.99 |
| 22_L | 56_Q | 1.257 | 0.99 |
| 6_N | 25_A | 1.213 | 0.98 |
| 21_C | 29_T | 1.187 | 0.98 |
| 46_V | 50_G | 1.154 | 0.97 |
| 37_T | 48_G | 1.121 | 0.97 |
| 51_E | 55_E | 1.103 | 0.96 |
| 47_S | 51_E | 1.081 | 0.95 |
| 15_A | 37_T | 1.074 | 0.95 |
| 18_I | 49_I | 1.066 | 0.95 |
| 38_A | 48_G | 1.053 | 0.95 |
| 49_I | 53_I | 1.030 | 0.94 |
| 50_G | 54_D | 1.026 | 0.94 |
| 24_T | 30_L | 1.025 | 0.93 |
| 8_V | 25_A | 1.000 | 0.92 |
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 | |
| 3h6eA | 2 | 0.9667 | 98.5 | 0.137 | Contact Map |
| 3l0qA | 2 | 0.95 | 98.4 | 0.142 | Contact Map |
| 4e1jA | 4 | 1 | 98.4 | 0.156 | Contact Map |
| 3ifrA | 2 | 0.9167 | 98.4 | 0.165 | Contact Map |
| 3jvpA | 4 | 0.9167 | 98.3 | 0.175 | Contact Map |
| 3h3nX | 2 | 0.9667 | 98.3 | 0.181 | Contact Map |
| 3ll3A | 2 | 0.95 | 98.3 | 0.187 | Contact Map |
| 2p3rA | 8 | 0.95 | 98.2 | 0.193 | Contact Map |
| 2zf5O | 2 | 0.95 | 98.2 | 0.194 | Contact Map |
| 2w40A | 4 | 0.9667 | 98.2 | 0.195 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)