| d2wkfa_ |
| ID: | 1450803264 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (101) | ||
| Sequences: | 707 (511.6) | ||
| Seq/Len: | 7.000 | ||
| Nf(neff/√len): | 50.9 |
HHblits Results: (2015_06)
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: 7.000).
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 |
| 5_V | 23_I | 2.781 | 1.00 |
| 22_Q | 87_N | 2.431 | 1.00 |
| 53_S | 94_R | 2.254 | 1.00 |
| 6_I | 43_D | 2.232 | 1.00 |
| 77_A | 99_F | 2.044 | 1.00 |
| 24_E | 35_L | 2.030 | 1.00 |
| 48_L | 57_Y | 2.013 | 1.00 |
| 82_K | 86_S | 1.898 | 1.00 |
| 5_V | 60_V | 1.845 | 1.00 |
| 85_V | 92_S | 1.814 | 1.00 |
| 77_A | 81_T | 1.734 | 1.00 |
| 41_N | 48_L | 1.699 | 1.00 |
| 3_C | 62_I | 1.607 | 1.00 |
| 41_N | 46_K | 1.603 | 1.00 |
| 58_C | 95_I | 1.521 | 0.99 |
| 25_N | 35_L | 1.452 | 0.99 |
| 39_M | 50_F | 1.443 | 0.99 |
| 69_N | 72_N | 1.417 | 0.99 |
| 78_D | 82_K | 1.396 | 0.99 |
| 25_N | 29_D | 1.342 | 0.98 |
| 85_V | 95_I | 1.328 | 0.98 |
| 56_A | 94_R | 1.252 | 0.97 |
| 24_E | 38_I | 1.244 | 0.97 |
| 2_C | 41_N | 1.231 | 0.96 |
| 40_S | 49_R | 1.224 | 0.96 |
| 85_V | 89_N | 1.222 | 0.96 |
| 27_I | 38_I | 1.219 | 0.96 |
| 81_T | 95_I | 1.198 | 0.96 |
| 39_M | 59_F | 1.197 | 0.96 |
| 33_K | 64_S | 1.181 | 0.95 |
| 6_I | 41_N | 1.178 | 0.95 |
| 68_I | 73_N | 1.177 | 0.95 |
| 57_Y | 94_R | 1.164 | 0.95 |
| 37_Y | 50_F | 1.159 | 0.95 |
| 29_D | 79_Q | 1.113 | 0.93 |
| 21_S | 35_L | 1.099 | 0.92 |
| 40_S | 80_I | 1.098 | 0.92 |
| 10_N | 45_Q | 1.076 | 0.91 |
| 62_I | 80_I | 1.068 | 0.91 |
| 3_C | 23_I | 1.068 | 0.91 |
| 37_Y | 96_Y | 1.066 | 0.91 |
| 63_T | 98_E | 1.042 | 0.89 |
| 10_N | 69_N | 1.040 | 0.89 |
| 31_M | 64_S | 1.032 | 0.89 |
| 31_M | 38_I | 1.025 | 0.88 |
| 30_V | 79_Q | 1.023 | 0.88 |
| 26_A | 30_V | 1.001 | 0.87 |
| 34_P | 37_Y | 1.001 | 0.87 |
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 | |
| 3kanA | 3 | 0.9901 | 99.9 | 0.217 | Contact Map |
| 3djhA | 3 | 0.9901 | 99.9 | 0.226 | Contact Map |
| 2wkbA | 6 | 0.9901 | 99.9 | 0.235 | Contact Map |
| 1hfoA | 6 | 0.9901 | 99.9 | 0.245 | Contact Map |
| 3b64A | 1 | 1 | 99.9 | 0.246 | Contact Map |
| 3fwuA | 1 | 1 | 99.9 | 0.282 | Contact Map |
| 3fwtA | 1 | 1 | 99.8 | 0.293 | Contact Map |
| 3t5sA | 1 | 0.9406 | 99.8 | 0.308 | Contact Map |
| 2os5A | 4 | 0.9901 | 99.8 | 0.321 | Contact Map |
| 4dh4A | 1 | 1 | 99.8 | 0.327 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)