| 1odd |
| ID: | 1408344213 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (98) | ||
| Sequences: | 17668 (13045.9) | ||
| Seq/Len: | 180.286 | ||
| Nf(neff/√len): | 1317.8 |
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: 180.286).
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 |
| 47_R | 67_D | 3.209 | 1.00 |
| 64_R | 67_D | 2.690 | 1.00 |
| 7_K | 20_E | 2.590 | 1.00 |
| 30_E | 76_M | 2.442 | 1.00 |
| 16_E | 23_P | 2.429 | 1.00 |
| 35_K | 39_S | 2.428 | 1.00 |
| 88_Q | 98_V | 2.301 | 1.00 |
| 4_A | 9_K | 2.253 | 1.00 |
| 29_G | 32_A | 2.180 | 1.00 |
| 36_A | 50_L | 2.108 | 1.00 |
| 88_Q | 96_V | 2.004 | 1.00 |
| 69_Q | 72_R | 1.986 | 1.00 |
| 9_K | 18_F | 1.948 | 1.00 |
| 40_H | 43_E | 1.920 | 1.00 |
| 90_V | 96_V | 1.873 | 1.00 |
| 12_L | 35_K | 1.851 | 1.00 |
| 10_L | 38_V | 1.831 | 1.00 |
| 36_A | 53_L | 1.804 | 1.00 |
| 10_L | 31_F | 1.796 | 1.00 |
| 11_N | 14_T | 1.723 | 1.00 |
| 2_V | 9_K | 1.557 | 1.00 |
| 15_R | 32_A | 1.536 | 1.00 |
| 29_G | 55_R | 1.509 | 1.00 |
| 46_S | 49_K | 1.502 | 1.00 |
| 36_A | 45_L | 1.494 | 1.00 |
| 18_F | 23_P | 1.489 | 1.00 |
| 41_P | 45_L | 1.484 | 1.00 |
| 15_R | 93_L | 1.482 | 1.00 |
| 27_T | 76_M | 1.425 | 1.00 |
| 68_V | 71_S | 1.368 | 0.99 |
| 36_A | 40_H | 1.318 | 0.99 |
| 13_G | 43_E | 1.313 | 0.99 |
| 5_F | 97_F | 1.291 | 0.99 |
| 71_S | 75_R | 1.241 | 0.98 |
| 12_L | 39_S | 1.235 | 0.98 |
| 49_K | 53_L | 1.203 | 0.98 |
| 43_E | 49_K | 1.170 | 0.97 |
| 18_F | 21_D | 1.167 | 0.97 |
| 32_A | 35_K | 1.152 | 0.97 |
| 10_L | 17_M | 1.139 | 0.97 |
| 2_V | 11_N | 1.132 | 0.97 |
| 15_R | 31_F | 1.123 | 0.97 |
| 65_S | 69_Q | 1.116 | 0.96 |
| 67_D | 91_W | 1.090 | 0.96 |
| 8_F | 17_M | 1.084 | 0.96 |
| 8_F | 19_R | 1.070 | 0.95 |
| 7_K | 19_R | 1.068 | 0.95 |
| 28_S | 32_A | 1.059 | 0.95 |
| 45_L | 49_K | 1.053 | 0.95 |
| 47_R | 63_E | 1.018 | 0.93 |
| 33_V | 69_Q | 1.016 | 0.93 |
| 17_M | 24_M | 1.005 | 0.93 |
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 | |
| 4nhjA | 2 | 1 | 99.9 | 0.063 | Contact Map |
| 4ixaA | 2 | 1 | 99.9 | 0.064 | Contact Map |
| 2z9mA | 2 | 1 | 99.9 | 0.065 | Contact Map |
| 2hwvA | 1 | 1 | 99.9 | 0.07 | Contact Map |
| 3q9vA | 2 | 0.98 | 99.8 | 0.079 | Contact Map |
| 2jzyA | 1 | 0.99 | 99.8 | 0.081 | Contact Map |
| 1opcA | 1 | 0.99 | 99.8 | 0.081 | Contact Map |
| 1gxqA | 1 | 0.99 | 99.8 | 0.096 | Contact Map |
| 3zq7A | 1 | 0.99 | 99.8 | 0.097 | Contact Map |
| 2pmuA | 6 | 0.98 | 99.8 | 0.098 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)