| 4x5m |
| ID: | 1444795435 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (91) | ||
| Sequences: | 6368 (4305.9) | ||
| Seq/Len: | 69.978 | ||
| Nf(neff/√len): | 451.4 |
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: 69.978).
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 |
| 24_I | 28_R | 3.154 | 1.00 |
| 78_V | 82_I | 2.435 | 1.00 |
| 25_K | 29_T | 1.955 | 1.00 |
| 15_T | 19_F | 1.828 | 1.00 |
| 31_N | 34_G | 1.808 | 1.00 |
| 5_L | 9_L | 1.757 | 1.00 |
| 26_T | 32_T | 1.703 | 1.00 |
| 48_I | 70_L | 1.650 | 1.00 |
| 51_I | 67_I | 1.643 | 1.00 |
| 15_T | 18_A | 1.514 | 1.00 |
| 32_T | 80_T | 1.509 | 1.00 |
| 26_T | 79_I | 1.507 | 1.00 |
| 79_I | 83_N | 1.438 | 1.00 |
| 43_F | 47_V | 1.428 | 1.00 |
| 54_G | 57_R | 1.425 | 1.00 |
| 44_L | 70_L | 1.382 | 0.99 |
| 16_T | 19_F | 1.363 | 0.99 |
| 27_I | 79_I | 1.329 | 0.99 |
| 62_V | 65_A | 1.319 | 0.99 |
| 75_P | 79_I | 1.312 | 0.99 |
| 50_W | 54_G | 1.310 | 0.99 |
| 24_I | 27_I | 1.301 | 0.99 |
| 8_G | 12_A | 1.272 | 0.99 |
| 30_R | 83_N | 1.269 | 0.99 |
| 89_V | 92_S | 1.249 | 0.99 |
| 80_T | 84_R | 1.248 | 0.99 |
| 47_V | 69_T | 1.231 | 0.98 |
| 70_L | 73_A | 1.215 | 0.98 |
| 69_T | 73_A | 1.188 | 0.98 |
| 38_V | 42_M | 1.169 | 0.97 |
| 35_I | 40_Y | 1.169 | 0.97 |
| 82_I | 86_K | 1.168 | 0.97 |
| 65_A | 69_T | 1.168 | 0.97 |
| 6_L | 10_F | 1.166 | 0.97 |
| 62_V | 66_N | 1.149 | 0.97 |
| 90_L | 93_S | 1.142 | 0.97 |
| 11_A | 14_F | 1.123 | 0.97 |
| 9_L | 13_F | 1.111 | 0.96 |
| 76_V | 79_I | 1.094 | 0.96 |
| 60_F | 63_L | 1.066 | 0.95 |
| 68_V | 72_L | 1.063 | 0.95 |
| 59_D | 62_V | 1.058 | 0.95 |
| 88_H | 91_E | 1.058 | 0.95 |
| 50_W | 53_Y | 1.057 | 0.95 |
| 37_V | 41_I | 1.053 | 0.95 |
| 37_V | 80_T | 1.046 | 0.94 |
| 20_A | 24_I | 1.040 | 0.94 |
| 66_N | 70_L | 1.040 | 0.94 |
| 22_Q | 46_G | 1.035 | 0.94 |
| 60_F | 64_I | 1.023 | 0.93 |
| 40_Y | 76_V | 1.020 | 0.93 |
| 84_R | 87_K | 1.018 | 0.93 |
| 23_S | 75_P | 1.017 | 0.93 |
| 8_G | 11_A | 1.013 | 0.93 |
| 22_Q | 36_S | 1.010 | 0.93 |
| 61_A | 65_A | 1.003 | 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 | |
| 4x5mA | 3 | 0.94 | 99.8 | 0.08 | Contact Map |
| 4rngA | 6 | 0.83 | 99.6 | 0.225 | Contact Map |
| 4qncA | 2 | 0.82 | 99.6 | 0.24 | Contact Map |
| 4qndA | 1 | 0.88 | 99.5 | 0.28 | Contact Map |
| 4u4vA | 1 | 0 | 23.6 | 0.856 | Contact Map |
| 3wvfA | 2 | 0.6 | 22.2 | 0.858 | Contact Map |
| 2m20A | 2 | 0.42 | 21.3 | 0.859 | Contact Map |
| 3l1lA | 1 | 0.91 | 20.7 | 0.86 | Contact Map |
| 4ikvA | 1 | 0.83 | 15 | 0.869 | Contact Map |
| 3giaA | 1 | 0.89 | 11.2 | 0.876 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)