The third subphylum, Taphrinomycotina seems to have lost SAP30 family proteins during evolution, as we could not find any recognizable sequences from this subphylum, when Schizosaccharomyces pombe, as a representative species whose whole genome has been sequenced, was analyzed (from the NCBI database or the S. pombe gene database from Sanger Institute).
Although tprL in either its shortened or elongated forms does not have a recognizable signal sequence in the corresponding protein sequence, these differences in amino acid sequence could result in altered cellular functions.
Protein domains are structurally and functionally defined regions of a protein typically inferred from recognizable sequence similarities.
Comparative genomic analysis revealed that one full-length mycobacterioprophage phi172_2 belonged to cluster A and one group having recognizable sequence similarity was verified and contained four small prophage-like elements, including the phiMmcs_1, phiMkms_1, phiBN44_1, and phiMCAN_1.
Thus an HMM offers a simple approach to drastically increase the amount of recognizable sequence inserts in the light of noise from flank ligation and sequencing.
Thus, selenoproteins and selenoprotein factors appear to be either present in a given genome as functional proteins or totally absent (without even a recognizable fossil sequence relic).
EF-Tu lacks a recognizable signal sequence and the mechanism by which EF-Tu is transported to the bacterial surface has remained an enigma.
Sequence comparisons of the P1 region, mainly driven by recognizable sequence conservation in VP3 and a few regions in VP1, indicate the highest amino acid identity (20%) with turdiviruses, unclassified picornaviruses recently identified from wild birds (16 ).
All three proteins contributing to the formation of ESCRT-II in yeast (Vps22p, Vps25p, Vps36p) have two repeats of a winged-helix (WH) domain, despite having no recognizable sequence similarity [ 12, 13].
A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity.
