| H1 linker histone |
| ID: | 1454418843 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (74) | ||
| Sequences: | 986 (565.4) | ||
| Seq/Len: | 13.324 | ||
| Nf(neff/√len): | 65.7 |
Jackhmmer Results: (2015_08)
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: 13.324).
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 |
| 50_A | 54_G | 2.498 | 1.00 |
| 15_L | 21_S | 2.227 | 1.00 |
| 15_L | 25_A | 2.209 | 1.00 |
| 10_A | 33_N | 2.154 | 1.00 |
| 49_Q | 53_R | 1.978 | 1.00 |
| 17_E | 21_S | 1.839 | 1.00 |
| 7_M | 30_I | 1.783 | 1.00 |
| 29_Y | 33_N | 1.670 | 1.00 |
| 68_G | 73_F | 1.663 | 1.00 |
| 2_P | 34_Y | 1.636 | 1.00 |
| 10_A | 14_S | 1.609 | 1.00 |
| 23_R | 27_L | 1.586 | 1.00 |
| 53_R | 57_V | 1.483 | 1.00 |
| 54_G | 60_L | 1.353 | 0.99 |
| 27_L | 44_N | 1.291 | 0.99 |
| 52_K | 62_N | 1.288 | 0.99 |
| 62_N | 65_G | 1.245 | 0.98 |
| 16_K | 21_S | 1.235 | 0.98 |
| 10_A | 34_Y | 1.191 | 0.98 |
| 42_M | 46_H | 1.184 | 0.98 |
| 65_G | 71_G | 1.179 | 0.98 |
| 55_I | 62_N | 1.179 | 0.98 |
| 26_I | 47_L | 1.164 | 0.97 |
| 19_S | 72_S | 1.146 | 0.97 |
| 3_P | 6_E | 1.112 | 0.96 |
| 3_P | 7_M | 1.102 | 0.96 |
| 30_I | 46_H | 1.087 | 0.96 |
| 23_R | 65_G | 1.057 | 0.95 |
| 16_K | 28_K | 1.048 | 0.94 |
| 18_R | 74_R | 1.025 | 0.93 |
| 68_G | 72_S | 1.019 | 0.93 |
| 62_N | 66_A | 1.009 | 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 | |
| 2rqpA | 1 | 0.9737 | 99.9 | 0.125 | Contact Map |
| 2lsoA | 1 | 0.9605 | 99.9 | 0.146 | Contact Map |
| 1hstA | 2 | 0.9474 | 99.9 | 0.159 | Contact Map |
| 1ghcA | 1 | 0.9342 | 99.9 | 0.167 | Contact Map |
| 1ussA | 1 | 0.9605 | 99.9 | 0.182 | Contact Map |
| 1ustA | 1 | 0.9605 | 99.9 | 0.186 | Contact Map |
| 1uhmA | 1 | 0.9605 | 99.9 | 0.186 | Contact Map |
| 3g73A | 2 | 0.9342 | 70 | 0.843 | Contact Map |
| 2a07F | 6 | 0.8158 | 63.6 | 0.85 | Contact Map |
| 4lg0A | 1 | 0.9211 | 57.9 | 0.855 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)