| 4JZ3 |
| ID: | 1427309820 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (57) | ||
| Sequences: | 4368 (2583.7) | ||
| Seq/Len: | 76.632 | ||
| Nf(neff/√len): | 342.2 |
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: 76.632).
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 |
| 14_S | 21_S | 3.610 | 1.00 |
| 41_A | 52_I | 3.250 | 1.00 |
| 32_N | 40_L | 2.664 | 1.00 |
| 40_L | 49_T | 2.561 | 1.00 |
| 29_Q | 42_H | 2.518 | 1.00 |
| 26_E | 43_S | 2.464 | 1.00 |
| 11_D | 23_K | 2.352 | 1.00 |
| 8_A | 22_F | 2.249 | 1.00 |
| 52_I | 57_V | 2.179 | 1.00 |
| 42_H | 49_T | 2.099 | 1.00 |
| 43_S | 46_T | 1.860 | 1.00 |
| 7_V | 58_A | 1.832 | 1.00 |
| 22_F | 28_L | 1.792 | 1.00 |
| 6_F | 59_P | 1.741 | 1.00 |
| 5_T | 29_Q | 1.715 | 1.00 |
| 7_V | 27_R | 1.519 | 1.00 |
| 4_M | 33_N | 1.493 | 1.00 |
| 43_S | 48_Q | 1.422 | 1.00 |
| 28_L | 41_A | 1.371 | 0.99 |
| 39_W | 54_S | 1.331 | 0.99 |
| 33_N | 59_P | 1.331 | 0.99 |
| 11_D | 24_K | 1.317 | 0.99 |
| 5_T | 27_R | 1.306 | 0.99 |
| 6_F | 57_V | 1.259 | 0.99 |
| 23_K | 26_E | 1.208 | 0.98 |
| 6_F | 30_I | 1.074 | 0.95 |
| 4_M | 59_P | 1.066 | 0.95 |
| 40_L | 51_Y | 1.065 | 0.95 |
| 9_L | 58_A | 1.048 | 0.94 |
| 13_E | 23_K | 1.046 | 0.94 |
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 | |
| 2yt6A | 1 | 1 | 99.4 | -0.072 | Contact Map |
| 2yunA | 1 | 0.9672 | 99.3 | -0.049 | Contact Map |
| 2ysqA | 1 | 0.9672 | 99.3 | -0.041 | Contact Map |
| 2h8hA | 1 | 0.9344 | 99.3 | -0.038 | Contact Map |
| 2xmfA | 1 | 0.9508 | 99.3 | -0.038 | Contact Map |
| 2vwfA | 1 | 0.918 | 99.3 | -0.034 | Contact Map |
| 4n78F | 1 | 0 | 99.3 | -0.032 | Contact Map |
| 2yuoA | 1 | 0.9672 | 99.3 | -0.028 | Contact Map |
| 3c0cA | 1 | 0.9672 | 99.3 | -0.015 | Contact Map |
| 4mt7A | 1 | 0 | 99.3 | -0.011 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)