| 2KW5 |
| ID: | 1446563631 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 202 (190) | ||
| Sequences: | 4796 (3510.9) | ||
| Seq/Len: | 25.242 | ||
| Nf(neff/√len): | 254.7 |
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: 25.242).
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 |
| 55_T | 95_W | 3.400 | 1.00 |
| 32_K | 53_E | 3.221 | 1.00 |
| 64_L | 82_Q | 3.019 | 1.00 |
| 96_E | 122_K | 2.924 | 1.00 |
| 33_I | 97_G | 2.863 | 1.00 |
| 53_E | 79_T | 2.757 | 1.00 |
| 64_L | 80_T | 2.727 | 1.00 |
| 49_S | 74_K | 2.707 | 1.00 |
| 34_L | 95_W | 2.700 | 1.00 |
| 121_L | 125_G | 2.665 | 1.00 |
| 61_S | 65_A | 2.650 | 1.00 |
| 153_L | 157_Q | 2.637 | 1.00 |
| 118_Y | 163_L | 2.520 | 1.00 |
| 61_S | 82_Q | 2.401 | 1.00 |
| 38_E | 56_A | 2.270 | 1.00 |
| 116_K | 119_Q | 2.174 | 1.00 |
| 44_A | 56_A | 2.165 | 1.00 |
| 3_D | 62_V | 2.141 | 1.00 |
| 55_T | 81_V | 2.115 | 1.00 |
| 67_A | 80_T | 2.113 | 1.00 |
| 40_E | 66_K | 1.904 | 1.00 |
| 32_K | 96_E | 1.897 | 1.00 |
| 92_A | 119_Q | 1.854 | 1.00 |
| 36_L | 117_V | 1.763 | 1.00 |
| 55_T | 79_T | 1.745 | 1.00 |
| 116_K | 120_G | 1.736 | 1.00 |
| 32_K | 55_T | 1.729 | 1.00 |
| 84_N | 87_D | 1.705 | 1.00 |
| 32_K | 122_K | 1.683 | 1.00 |
| 60_S | 63_G | 1.653 | 1.00 |
| 46_F | 50_L | 1.642 | 1.00 |
| 121_L | 163_L | 1.640 | 1.00 |
| 117_V | 127_F | 1.631 | 1.00 |
| 17_P | 22_V | 1.631 | 1.00 |
| 45_C | 71_A | 1.628 | 1.00 |
| 45_C | 76_V | 1.623 | 1.00 |
| 58_D | 64_L | 1.591 | 1.00 |
| 38_E | 58_D | 1.583 | 1.00 |
| 4_E | 8_Q | 1.558 | 1.00 |
| 62_V | 65_A | 1.527 | 1.00 |
| 56_A | 67_A | 1.515 | 1.00 |
| 114_Y | 160_L | 1.481 | 1.00 |
| 44_A | 54_V | 1.478 | 1.00 |
| 48_A | 78_I | 1.477 | 1.00 |
| 56_A | 80_T | 1.447 | 1.00 |
| 45_C | 70_L | 1.415 | 1.00 |
| 65_A | 69_Q | 1.371 | 0.99 |
| 30_Q | 52_Y | 1.362 | 0.99 |
| 109_L | 112_Q | 1.354 | 0.99 |
| 38_E | 44_A | 1.343 | 0.99 |
| 71_A | 80_T | 1.304 | 0.99 |
| 64_L | 68_K | 1.267 | 0.99 |
| 83_S | 88_F | 1.266 | 0.99 |
| 4_E | 7_S | 1.263 | 0.99 |
| 31_G | 52_Y | 1.255 | 0.99 |
| 24_V | 128_I | 1.232 | 0.98 |
| 34_L | 98_I | 1.224 | 0.98 |
| 3_D | 60_S | 1.218 | 0.98 |
| 21_L | 47_L | 1.213 | 0.98 |
| 153_L | 170_N | 1.213 | 0.98 |
| 33_I | 52_Y | 1.207 | 0.98 |
| 33_I | 47_L | 1.186 | 0.98 |
| 89_D | 116_K | 1.179 | 0.98 |
| 65_A | 68_K | 1.179 | 0.98 |
| 154_E | 158_S | 1.165 | 0.97 |
| 98_I | 117_V | 1.148 | 0.97 |
| 45_C | 49_S | 1.142 | 0.97 |
| 100_S | 113_L | 1.135 | 0.97 |
| 98_I | 121_L | 1.128 | 0.97 |
| 94_A | 122_K | 1.123 | 0.97 |
| 152_K | 155_T | 1.110 | 0.96 |
| 153_L | 168_A | 1.109 | 0.96 |
| 57_V | 83_S | 1.099 | 0.96 |
| 32_K | 94_A | 1.098 | 0.96 |
| 34_L | 57_V | 1.088 | 0.96 |
| 157_Q | 168_A | 1.066 | 0.95 |
| 126_V | 166_L | 1.061 | 0.95 |
| 157_Q | 161_P | 1.049 | 0.94 |
| 36_L | 57_V | 1.038 | 0.94 |
| 98_I | 120_G | 1.035 | 0.94 |
| 103_C | 132_F | 1.021 | 0.93 |
| 44_A | 78_I | 1.019 | 0.93 |
| 88_F | 120_G | 1.016 | 0.93 |
| 94_A | 120_G | 1.014 | 0.93 |
| 118_Y | 162_S | 1.010 | 0.93 |
| 32_K | 95_W | 1.009 | 0.93 |
| 28_I | 31_G | 1.008 | 0.93 |
| 115_P | 119_Q | 1.008 | 0.93 |
| 56_A | 78_I | 1.002 | 0.92 |
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 | |
| 2kw5A | 1 | 1 | 100 | 0.241 | Contact Map |
| 3m70A | 1 | 0.9257 | 99.9 | 0.394 | Contact Map |
| 4necA | 4 | 1 | 99.9 | 0.396 | Contact Map |
| 2gb4A | 2 | 0.9455 | 99.9 | 0.401 | Contact Map |
| 2xvmA | 2 | 0.9208 | 99.9 | 0.402 | Contact Map |
| 3sm3A | 1 | 0.8762 | 99.9 | 0.405 | Contact Map |
| 3lccA | 1 | 0.9158 | 99.9 | 0.411 | Contact Map |
| 1y8cA | 1 | 0.9406 | 99.9 | 0.413 | Contact Map |
| 1wznA | 3 | 0.9158 | 99.9 | 0.419 | Contact Map |
| 4mikA | 2 | 0.9455 | 99.9 | 0.424 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)