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We address the molecular functions of Eco1 with sensitive sequence analytic techniques, including hidden Markov model domain fragment searches.
GN and GS carried out the programming and the sequence analytic work.
Based on sequence analytic considerations, we generated the two constructs yGPAA170 247 and yGPAA170 339 of the luminal domain of S. cerevisiae GPAA1.
From the sequence analytic perspective, homology is usually inferred from easily derived similarity measures of aligned sequences because there is no other direct measure of common ancestry, not because this criterion is especially elegant or rigorous.
This MS is an interesting piece of sequence analytic detective work where the authors systematically present a chain of evidence for an extended architecture of Alphavirus-like MTase-GTases that includes an extended "iceberg" region and varying membrane attachment factors such as palmitoyl anchors, transmembrane and amphipathic helices.
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Lots of additional information with regard to 3D structural details, binding properties, domain evolution, etc. is derived with the classical sequence-analytic procedures and many of these conclusions can be validated experimentally.
This work is a pretty nice continuation of the series of articles by Aravind et al. gene function hypotheses/discoveries are presented in the meticulous combination of sequence-analytic findings and hints from the experimental biological literature.
Targeting this goal with a sequence-analytic studies of various GDHs is problematic since it is known that these enzyme catalyze the reaction described on page 3 of this MS and the relative share of GDHs in the N-assimilation process is unlikely to be determined within the protein sequence of the GDHs themselves.
The sequence architecture of yeast GPAA1 (UniProt P39012 [ 33]) as predicted by sequence-analytic tools [ 1, 34, 35] consists of an N-terminal TM helical segment (20 42), a large luminal supposedly globular domain (42 356), followed by six TM helical regions (357 377, 389 408, 413 435, 455 480, 537 556 and 579 600).
and also ( H n ( z ) ) n ∈ N is a sequence of analytic functions uniformly convergent to zero for all | z | ≤ r.
Through a 5-year development cycle, ELOGE was considerably expanded to integrate fine grain modelling of wet lab routine procedures such as plate management, PCR quality control annotations, sequencing results, analytic validation, and GLP (Good Laboratory Practices) compliant protocols.
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