| SP18632A |
| ID: | 1392077333 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 97 (95) | ||
| Sequences: | 476 (332.7) | ||
| Seq/Len: | 5.011 | ||
| Nf(neff/√len): | 34.1 |
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: 5.011).
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 |
| 52_S | 55_Q | 3.162 | 1.00 |
| 47_L | 78_D | 2.372 | 1.00 |
| 8_L | 63_L | 2.158 | 1.00 |
| 5_E | 37_K | 2.108 | 1.00 |
| 28_H | 63_L | 1.720 | 1.00 |
| 84_A | 88_R | 1.634 | 0.99 |
| 25_V | 48_I | 1.604 | 0.99 |
| 28_H | 66_A | 1.529 | 0.99 |
| 32_N | 62_V | 1.512 | 0.99 |
| 62_V | 66_A | 1.511 | 0.99 |
| 27_H | 31_A | 1.485 | 0.98 |
| 23_F | 26_W | 1.474 | 0.98 |
| 50_F | 53_T | 1.473 | 0.98 |
| 10_I | 67_L | 1.464 | 0.98 |
| 60_K | 64_G | 1.462 | 0.98 |
| 75_L | 81_S | 1.440 | 0.98 |
| 30_D | 35_R | 1.409 | 0.98 |
| 5_E | 49_K | 1.393 | 0.97 |
| 5_E | 78_D | 1.362 | 0.97 |
| 9_A | 76_L | 1.291 | 0.95 |
| 33_G | 68_P | 1.249 | 0.94 |
| 22_G | 46_L | 1.230 | 0.93 |
| 59_A | 62_V | 1.223 | 0.93 |
| 7_T | 96_L | 1.222 | 0.93 |
| 8_L | 73_I | 1.215 | 0.93 |
| 49_K | 74_A | 1.202 | 0.92 |
| 78_D | 82_P | 1.197 | 0.92 |
| 12_P | 95_R | 1.190 | 0.92 |
| 31_A | 35_R | 1.181 | 0.91 |
| 5_E | 81_S | 1.160 | 0.90 |
| 56_G | 76_L | 1.158 | 0.90 |
| 5_E | 47_L | 1.150 | 0.90 |
| 11_R | 71_Y | 1.115 | 0.88 |
| 4_Q | 95_R | 1.112 | 0.88 |
| 44_D | 48_I | 1.108 | 0.88 |
| 4_Q | 81_S | 1.099 | 0.87 |
| 83_T | 93_P | 1.098 | 0.87 |
| 33_G | 36_F | 1.089 | 0.86 |
| 56_G | 75_L | 1.053 | 0.84 |
| 26_W | 30_D | 1.049 | 0.83 |
| 84_A | 87_S | 1.044 | 0.83 |
| 57_A | 75_L | 1.037 | 0.82 |
| 86_L | 91_D | 1.005 | 0.80 |
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 | |
| 2gqcA | 1 | 0.7216 | 24.6 | 0.896 | Contact Map |
| 3optA | 1 | 0.7113 | 19.3 | 0.901 | Contact Map |
| 3dxtA | 1 | 0.8454 | 19.3 | 0.901 | Contact Map |
| 2adcA | 1 | 0.8144 | 15.7 | 0.905 | Contact Map |
| 2ox0A | 2 | 0.8454 | 13.3 | 0.908 | Contact Map |
| 1t4aA | 2 | 0.7526 | 12.1 | 0.909 | Contact Map |
| 2yx5A | 1 | 0.7629 | 11.6 | 0.91 | Contact Map |
| 4ckoA | 8 | 0.8144 | 10.8 | 0.912 | Contact Map |
| 1vq3A | 4 | 0.7629 | 9.9 | 0.913 | Contact Map |
| 2dgbA | 4 | 0.7835 | 9.1 | 0.915 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)