Feature | Meaning | Programs used | Output |
---|---|---|---|
Secondary structure | Assist three-dimensional structure and domain boundary prediction. | PSIPRED (v2.0) [49] SSPRO (v4.0) [50] DISEMBL (v1.5) [51], coils | PSIPRED and SSPRO predict 3-states secondary structures (H: α-helix, E: β-strand, C: coils); DISEMBL predict coils (lower-case letters highlighted in pink) |
Disordered and flexible region | Assist three-dimensional structure prediction. | DISEMBL (v1.5) [51], hot loops | Loops that are likely to have high B factors in the X-ray crystallography (lower-case letters highlighted in pink) |
 |  | DISEMBL (v1.5) [51], missing DISPRO (v1.0) [52] DISOPRED (v2.0) [53] IsUnstruct (v2.02) [54] | Residues without a defined structure (represented by star marks and highlighted in red) |
Transmembrane helix and Signal Peptide | Predict subcellular localization and transmembrane, reveal topology of transmembrane proteins and provide hints to the protein function. | TMHMM (v2.0) [55] TOPPREDa (v2.0) [56] HMMTOPa (v2.0) [57] MEMSAT (v3.0) [58] | H: transmembrane helix (colored in blue); h: not confidently predicted transmembrane helix; o: periplasmic loop, i: cytoplasmic loop. x: loop region (not specified as periplasmic or cytoplasmic). |
 |  | MEMSATSVM [59] Phobius [60] | H: transmembrane helix (colored in blue); S: signal peptide (colored in green); h: unconfident transmembrane helix; o: periplasmic loop, i: cytoplasmic loop. |
 |  | SignalP (v3.0) [61] (HMM mode) SignalP (v3.0) [61] (NN mode) | S: signal peptide (highlighted in green) o: periplasmic region; x: do not have signal peptide |
Low-complexity region | Reveal false positive hits of homology search caused by matching of low-complexity region. | SEG [62] | The part with low diversity in amino acid composition (highlighted in pink), likely to be disordered or fold as α helices, such as coiled coil |
Coiled coil | Assist three-dimensional structure prediction. | COILS [63] | x: coiled coils, highlighted in yellow |
Conservation index | Reveal essential residues for the folding and function of a protein. | BLAST (hits filtered by > 40% coverage and < 90% identity are included in the profile), AL2CO (calculate conservation indices based on profile) [64] | Sequence highlighted by the conservation (highlighted from white, through yellow to dark red as conservation increases) |