| pfam_02261_new |
| ID: | 1507635925 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 97 (97) | ||
| Sequences: | 7077 (4917.5) | ||
| Seq/Len: | 72.959 | ||
| Nf(neff/√len): | 499.3 |
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: 72.959).
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 |
| 4_E | 25_Y | 3.397 | 1.00 |
| 76_V | 89_A | 3.136 | 1.00 |
| 8_K | 81_F | 3.122 | 1.00 |
| 40_P | 48_Y | 2.502 | 1.00 |
| 25_Y | 49_L | 2.160 | 1.00 |
| 26_R | 30_V | 1.968 | 1.00 |
| 52_L | 71_L | 1.850 | 1.00 |
| 4_E | 50_E | 1.828 | 1.00 |
| 86_G | 90_R | 1.715 | 1.00 |
| 28_S | 82_R | 1.688 | 1.00 |
| 71_L | 96_L | 1.687 | 1.00 |
| 83_D | 87_R | 1.665 | 1.00 |
| 4_E | 46_P | 1.650 | 1.00 |
| 56_L | 96_L | 1.611 | 1.00 |
| 45_I | 78_I | 1.604 | 1.00 |
| 3_T | 6_D | 1.595 | 1.00 |
| 6_D | 95_L | 1.573 | 1.00 |
| 55_W | 70_W | 1.564 | 1.00 |
| 56_L | 71_L | 1.528 | 1.00 |
| 9_E | 13_I | 1.526 | 1.00 |
| 9_E | 12_R | 1.522 | 1.00 |
| 4_E | 53_F | 1.502 | 1.00 |
| 10_I | 88_T | 1.455 | 1.00 |
| 48_Y | 51_E | 1.444 | 1.00 |
| 70_W | 74_E | 1.421 | 1.00 |
| 79_H | 86_G | 1.401 | 0.99 |
| 50_E | 54_D | 1.380 | 0.99 |
| 44_E | 47_A | 1.377 | 0.99 |
| 29_N | 42_P | 1.368 | 0.99 |
| 72_H | 89_A | 1.321 | 0.99 |
| 4_E | 8_K | 1.315 | 0.99 |
| 68_A | 93_M | 1.301 | 0.99 |
| 21_W | 82_R | 1.232 | 0.98 |
| 7_L | 53_F | 1.230 | 0.98 |
| 72_H | 76_V | 1.225 | 0.98 |
| 29_N | 41_P | 1.218 | 0.98 |
| 44_E | 48_Y | 1.207 | 0.98 |
| 67_K | 96_L | 1.194 | 0.98 |
| 8_K | 24_E | 1.162 | 0.97 |
| 4_E | 49_L | 1.140 | 0.97 |
| 46_P | 50_E | 1.138 | 0.97 |
| 75_F | 89_A | 1.132 | 0.97 |
| 24_E | 27_T | 1.098 | 0.96 |
| 26_R | 45_I | 1.087 | 0.96 |
| 89_A | 93_M | 1.086 | 0.96 |
| 32_I | 35_G | 1.083 | 0.96 |
| 59_N | 67_K | 1.073 | 0.95 |
| 11_H | 23_G | 1.050 | 0.94 |
| 51_E | 54_D | 1.031 | 0.94 |
| 12_R | 16_R | 1.027 | 0.94 |
| 48_Y | 78_I | 1.020 | 0.93 |
| 8_K | 11_H | 1.019 | 0.93 |
| 37_Y | 77_Y | 1.018 | 0.93 |
| 52_L | 78_I | 1.017 | 0.93 |
| 84_G | 87_R | 1.005 | 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
- 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 | |
| 4rglA | 1 | 0.9897 | 99.9 | -0.003 | Contact Map |
| 4npsA | 1 | 0.9691 | 99.9 | -0.001 | Contact Map |
| 3n3uA | 1 | 0.9278 | 99.9 | -0.001 | Contact Map |
| 4u04A | 2 | 0.9794 | 99.9 | 0.004 | Contact Map |
| 2jk8A | 2 | 1 | 99.8 | 0.011 | Contact Map |
| 4n67A | 1 | 1 | 99.8 | 0.011 | Contact Map |
| 4py3A | 10 | 0 | 99.8 | 0.013 | Contact Map |
| 4m16A | 1 | 1 | 99.8 | 0.016 | Contact Map |
| 3cucA | 2 | 1 | 99.8 | 0.018 | Contact Map |
| 3shgA | 1 | 0.9794 | 99.8 | 0.033 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)