| FIVCA |
| ID: | 1441798794 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (84) | ||
| Sequences: | 349 (181.1) | ||
| Seq/Len: | 4.155 | ||
| Nf(neff/√len): | 19.8 |
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: 4.155).
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 |
| 15_Y | 18_F | 1.755 | 0.99 |
| 9_Q | 13_E | 1.743 | 0.99 |
| 78_P | 81_K | 1.731 | 0.99 |
| 45_I | 48_A | 1.728 | 0.99 |
| 49_N | 52_C | 1.615 | 0.99 |
| 49_N | 53_K | 1.506 | 0.98 |
| 48_A | 52_C | 1.494 | 0.98 |
| 69_L | 72_C | 1.493 | 0.98 |
| 54_K | 61_P | 1.474 | 0.97 |
| 7_L | 11_A | 1.441 | 0.97 |
| 24_A | 28_Q | 1.428 | 0.97 |
| 70_R | 73_Q | 1.413 | 0.96 |
| 30_Q | 35_V | 1.410 | 0.96 |
| 13_E | 18_F | 1.410 | 0.96 |
| 18_F | 22_L | 1.404 | 0.96 |
| 72_C | 75_I | 1.391 | 0.96 |
| 63_S | 69_L | 1.378 | 0.96 |
| 6_Q | 11_A | 1.344 | 0.95 |
| 6_Q | 9_Q | 1.316 | 0.94 |
| 53_K | 56_M | 1.312 | 0.94 |
| 13_E | 19_I | 1.309 | 0.94 |
| 77_S | 80_Y | 1.284 | 0.93 |
| 4_A | 9_Q | 1.267 | 0.92 |
| 25_Q | 28_Q | 1.240 | 0.91 |
| 58_H | 61_P | 1.221 | 0.91 |
| 13_E | 17_S | 1.219 | 0.90 |
| 14_D | 19_I | 1.213 | 0.90 |
| 34_E | 37_L | 1.205 | 0.90 |
| 15_Y | 19_I | 1.197 | 0.89 |
| 48_A | 51_D | 1.197 | 0.89 |
| 32_T | 35_V | 1.187 | 0.89 |
| 28_Q | 31_N | 1.182 | 0.89 |
| 35_V | 39_L | 1.181 | 0.88 |
| 79_G | 83_Q | 1.177 | 0.88 |
| 80_Y | 83_Q | 1.167 | 0.88 |
| 79_G | 82_M | 1.162 | 0.87 |
| 55_A | 58_H | 1.160 | 0.87 |
| 40_K | 43_L | 1.151 | 0.87 |
| 66_E | 69_L | 1.135 | 0.86 |
| 58_H | 62_E | 1.123 | 0.85 |
| 5_V | 9_Q | 1.112 | 0.84 |
| 41_Q | 44_S | 1.111 | 0.84 |
| 15_Y | 22_L | 1.106 | 0.84 |
| 16_S | 19_I | 1.097 | 0.83 |
| 14_D | 17_S | 1.093 | 0.83 |
| 35_V | 38_Y | 1.079 | 0.82 |
| 44_S | 47_N | 1.078 | 0.81 |
| 6_Q | 10_G | 1.074 | 0.81 |
| 1_S | 4_A | 1.065 | 0.80 |
| 74_E | 77_S | 1.060 | 0.80 |
| 65_L | 68_K | 1.054 | 0.79 |
| 30_Q | 33_A | 1.044 | 0.78 |
| 3_R | 7_L | 1.039 | 0.78 |
| 22_L | 25_Q | 1.022 | 0.76 |
| 22_L | 27_D | 1.015 | 0.76 |
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 | |
| 3ds4A | 2 | 0.9167 | 100 | -0.067 | Contact Map |
| 2jylA | 1 | 0.9881 | 100 | -0.065 | Contact Map |
| 1bajA | 1 | 0.8452 | 100 | -0.06 | Contact Map |
| 4u0cA | 1 | 0.8333 | 100 | -0.032 | Contact Map |
| 4ph1A | 3 | 0 | 100 | -0.026 | Contact Map |
| 1d1dA | 1 | 0.9167 | 99.9 | 0.011 | Contact Map |
| 1qrjA | 1 | 0.9881 | 99.9 | 0.025 | Contact Map |
| 4ph0A | 6 | 0 | 99.9 | 0.037 | Contact Map |
| 1eiaA | 1 | 0.9048 | 99.9 | 0.051 | Contact Map |
| 1eoqA | 1 | 0.881 | 99.9 | 0.114 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)