| FIV INCCD-E |
| ID: | 1443609277 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 152 (146) | ||
| Sequences: | 15188 (10435.8) | ||
| Seq/Len: | 104.027 | ||
| Nf(neff/√len): | 863.7 |
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: 104.027).
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 |
| 83_I | 89_S | 2.999 | 1.00 |
| 17_V | 97_N | 2.764 | 1.00 |
| 28_A | 122_V | 2.351 | 1.00 |
| 95_N | 98_H | 2.246 | 1.00 |
| 82_G | 90_Q | 2.224 | 1.00 |
| 57_T | 79_H | 2.179 | 1.00 |
| 21_V | 92_L | 2.064 | 1.00 |
| 72_L | 77_V | 2.020 | 1.00 |
| 26_I | 96_V | 1.992 | 1.00 |
| 33_Q | 38_C | 1.977 | 1.00 |
| 4_Q | 21_V | 1.973 | 1.00 |
| 59_N | 81_F | 1.946 | 1.00 |
| 5_M | 57_T | 1.931 | 1.00 |
| 44_L | 71_V | 1.922 | 1.00 |
| 56_Q | 80_K | 1.899 | 1.00 |
| 136_M | 139_Y | 1.870 | 1.00 |
| 98_H | 102_V | 1.808 | 1.00 |
| 29_Q | 45_Q | 1.767 | 1.00 |
| 8_T | 101_K | 1.766 | 1.00 |
| 25_Y | 138_P | 1.727 | 1.00 |
| 34_E | 62_N | 1.679 | 1.00 |
| 139_Y | 145_Q | 1.650 | 1.00 |
| 35_T | 38_C | 1.649 | 1.00 |
| 26_I | 126_N | 1.637 | 1.00 |
| 69_E | 79_H | 1.606 | 1.00 |
| 93_V | 97_N | 1.579 | 1.00 |
| 59_N | 84_P | 1.565 | 1.00 |
| 72_L | 79_H | 1.554 | 1.00 |
| 4_Q | 93_V | 1.554 | 1.00 |
| 71_V | 75_M | 1.525 | 1.00 |
| 54_E | 80_K | 1.521 | 1.00 |
| 23_S | 140_E | 1.489 | 1.00 |
| 90_Q | 93_V | 1.467 | 1.00 |
| 86_N | 89_S | 1.462 | 1.00 |
| 95_N | 99_T | 1.450 | 1.00 |
| 123_H | 127_F | 1.442 | 1.00 |
| 24_G | 92_L | 1.416 | 1.00 |
| 64_K | 81_F | 1.410 | 1.00 |
| 138_P | 142_L | 1.396 | 0.99 |
| 36_A | 40_V | 1.371 | 0.99 |
| 130_R | 133_I | 1.365 | 0.99 |
| 40_V | 71_V | 1.358 | 0.99 |
| 115_D | 119_S | 1.355 | 0.99 |
| 27_W | 49_A | 1.353 | 0.99 |
| 7_C | 31_I | 1.325 | 0.99 |
| 30_I | 115_D | 1.321 | 0.99 |
| 122_V | 126_N | 1.304 | 0.99 |
| 17_V | 93_V | 1.282 | 0.99 |
| 24_G | 132_R | 1.275 | 0.99 |
| 127_F | 138_P | 1.261 | 0.99 |
| 24_G | 130_R | 1.250 | 0.99 |
| 25_Y | 141_L | 1.247 | 0.99 |
| 125_L | 130_R | 1.207 | 0.98 |
| 135_G | 140_E | 1.203 | 0.98 |
| 1_G | 53_T | 1.183 | 0.98 |
| 110_E | 113_S | 1.170 | 0.97 |
| 82_G | 89_S | 1.157 | 0.97 |
| 103_W | 121_A | 1.152 | 0.97 |
| 4_Q | 90_Q | 1.128 | 0.97 |
| 16_L | 63_F | 1.116 | 0.96 |
| 70_G | 74_Y | 1.115 | 0.96 |
| 2_I | 54_E | 1.111 | 0.96 |
| 30_I | 45_Q | 1.111 | 0.96 |
| 104_I | 117_A | 1.109 | 0.96 |
| 83_I | 86_N | 1.107 | 0.96 |
| 5_M | 63_F | 1.105 | 0.96 |
| 5_M | 55_L | 1.103 | 0.96 |
| 2_I | 21_V | 1.103 | 0.96 |
| 9_H | 14_I | 1.102 | 0.96 |
| 7_C | 62_N | 1.083 | 0.96 |
| 68_M | 72_L | 1.072 | 0.95 |
| 54_E | 78_K | 1.069 | 0.95 |
| 40_V | 67_K | 1.066 | 0.95 |
| 14_I | 34_E | 1.061 | 0.95 |
| 8_T | 15_I | 1.058 | 0.95 |
| 99_T | 125_L | 1.041 | 0.94 |
| 19_I | 92_L | 1.039 | 0.94 |
| 129_R | 133_I | 1.032 | 0.94 |
| 100_L | 118_L | 1.029 | 0.94 |
| 61_P | 64_K | 1.023 | 0.93 |
| 16_L | 42_A | 1.020 | 0.93 |
| 19_I | 93_V | 1.015 | 0.93 |
| 19_I | 26_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 | |
| 3kksA | 2 | 0.9803 | 99.9 | 0.107 | Contact Map |
| 3hphA | 4 | 1 | 99.9 | 0.107 | Contact Map |
| 4pa1A | 1 | 0.9737 | 99.9 | 0.129 | Contact Map |
| 1ex4A | 2 | 0.9803 | 99.9 | 0.132 | Contact Map |
| 3oymA | 2 | 1 | 99.9 | 0.135 | Contact Map |
| 1c6vA | 4 | 0.9342 | 99.9 | 0.139 | Contact Map |
| 3f9kA | 24 | 0.9737 | 99.9 | 0.142 | Contact Map |
| 1k6yA | 4 | 0.9408 | 99.9 | 0.145 | Contact Map |
| 4cf8A | 2 | 0.9605 | 99.9 | 0.146 | Contact Map |
| 3l3uA | 2 | 0.9868 | 99.9 | 0.155 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)