| nif3b2 |
| ID: | 1495456091 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (108) | ||
| Sequences: | 1637 (1211.6) | ||
| Seq/Len: | 15.157 | ||
| Nf(neff/√len): | 116.6 |
HHblits Results: (2016_02)
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: 15.157).
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 |
| 43_T | 56_R | 3.450 | 1.00 |
| 11_K | 108_E | 2.830 | 1.00 |
| 20_H | 64_H | 2.543 | 1.00 |
| 13_V | 78_R | 2.260 | 1.00 |
| 21_T | 77_A | 2.253 | 1.00 |
| 10_F | 89_V | 2.114 | 1.00 |
| 67_V | 70_R | 2.064 | 1.00 |
| 43_T | 58_G | 2.053 | 1.00 |
| 56_R | 71_L | 1.916 | 1.00 |
| 25_K | 48_T | 1.882 | 1.00 |
| 26_A | 30_K | 1.842 | 1.00 |
| 14_F | 96_L | 1.790 | 1.00 |
| 97_K | 107_Y | 1.745 | 1.00 |
| 83_V | 89_V | 1.724 | 1.00 |
| 18_T | 50_M | 1.710 | 1.00 |
| 18_T | 75_E | 1.703 | 1.00 |
| 52_T | 73_R | 1.684 | 1.00 |
| 65_T | 74_I | 1.673 | 1.00 |
| 48_T | 54_Q | 1.669 | 1.00 |
| 60_G | 68_V | 1.663 | 1.00 |
| 13_V | 110_Y | 1.620 | 1.00 |
| 20_H | 23_Q | 1.577 | 1.00 |
| 12_L | 83_V | 1.567 | 1.00 |
| 61_A | 68_V | 1.556 | 1.00 |
| 24_C | 99_A | 1.536 | 1.00 |
| 83_V | 92_A | 1.519 | 1.00 |
| 88_V | 91_R | 1.438 | 1.00 |
| 84_V | 88_V | 1.412 | 1.00 |
| 14_F | 24_C | 1.401 | 0.99 |
| 28_V | 81_T | 1.376 | 0.99 |
| 29_F | 54_Q | 1.371 | 0.99 |
| 29_F | 44_E | 1.368 | 0.99 |
| 21_T | 79_V | 1.360 | 0.99 |
| 57_P | 61_A | 1.348 | 0.99 |
| 21_T | 48_T | 1.337 | 0.99 |
| 44_E | 56_R | 1.336 | 0.99 |
| 50_M | 75_E | 1.302 | 0.99 |
| 10_F | 83_V | 1.260 | 0.99 |
| 44_E | 71_L | 1.227 | 0.98 |
| 8_Q | 86_E | 1.219 | 0.98 |
| 12_L | 28_V | 1.210 | 0.98 |
| 11_K | 80_E | 1.208 | 0.98 |
| 47_W | 51_G | 1.205 | 0.98 |
| 36_Y | 45_C | 1.196 | 0.98 |
| 46_C | 54_Q | 1.195 | 0.98 |
| 65_T | 72_E | 1.187 | 0.98 |
| 16_V | 24_C | 1.157 | 0.97 |
| 15_F | 106_A | 1.155 | 0.97 |
| 21_T | 25_K | 1.146 | 0.97 |
| 48_T | 77_A | 1.116 | 0.96 |
| 18_T | 77_A | 1.114 | 0.96 |
| 24_C | 27_A | 1.105 | 0.96 |
| 25_K | 54_Q | 1.102 | 0.96 |
| 22_E | 26_A | 1.093 | 0.96 |
| 54_Q | 73_R | 1.088 | 0.96 |
| 82_L | 106_A | 1.078 | 0.95 |
| 22_E | 73_R | 1.066 | 0.95 |
| 13_V | 108_E | 1.062 | 0.95 |
| 10_F | 111_R | 1.054 | 0.95 |
| 40_G | 104_E | 1.037 | 0.94 |
| 58_G | 61_A | 1.029 | 0.94 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2gx8A | 3 | 0.8957 | 100 | 0.121 | Contact Map |
| 2nydA | 2 | 0.7652 | 100 | 0.132 | Contact Map |
| 2eg2A | 1 | 0.687 | 99.6 | 0.542 | Contact Map |
| 4usiA | 3 | 0.8435 | 99.5 | 0.569 | Contact Map |
| 2j9cA | 3 | 0.8522 | 99.5 | 0.573 | Contact Map |
| 2ns1B | 1 | 0.8435 | 99.5 | 0.573 | Contact Map |
| 4co3A | 2 | 0.8261 | 99.5 | 0.577 | Contact Map |
| 2gw8A | 1 | 0.7217 | 99.5 | 0.578 | Contact Map |
| 3l7pA | 6 | 0.7565 | 99.4 | 0.59 | Contact Map |
| 4affA | 1 | 0.7826 | 99.4 | 0.59 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)