3.4 Selected markers in in vivo (prepupa) data
We verified that the large database (D1–D18) was not useful for
screening complex data if the pathogen was present in the host. The
markers were searched against the original data published previously
with a UniProt-derived database in [12] that relates to the raw
dataset MSV000089235. The two GHL10‒FN3/alpha-galactosidase
isoforms were not differentiated in the analysis, and despite sequence
differences (amino acid substitutions), they were identified as one hit
(e.g., UniProt: W2E369 vs. A0A2L1TZ12). Incidentally, the fasta header
in the original results was Fibronectin type-III domain-containing
protein or alpha-galactosidase. Furthermore, the two collagenase
isoforms were not differentiated, and despite potential sequence
differences (amino acid substitutions, e.g., UniProt: A0A2L1UJN7 vs.
A0A1V0UTD3), they were present as one hit. Note that there was an
absence of collagenase identifications in the most affected “lysed”
samples. A new separate search with the sequence of id: 475
(CP020557.1:False:1915540) was not successful at identifying it in theMSV000089235 raw data. Notably, DUF3221 (id: 438) could not be
identified using UniProt access no., but similar sequences (see above;
e.g. id: 232 - V9W786/W2E226) and others (id: 311: A0A1V0UTM0) were
identified; however, id: 331 (A0A1V0UVZ6; W2E2L8; A0A2L1UAH0) was not
identified. In addition, a DUF3862 domain-containing protein (id: 66)
(UniProt: A0A2L1UHM8; A0A1U9YLD2; A0A2A5JXM) was not identified in thein vivo dataset. Incidentally, both id: 331 and id: 66 were not
identified as being expressed in only ERIC II. The CRISPR-related
proteins (section 3.3.3) were present in the in vivo dataset at
only trace levels, with no quantitative value, and therefore could not
be considered in evaluations. Importantly, InhA was absent, consistent
with an earlier report [12]. Finally, ABC transporters related to
iron–siderophore uptake were identified in in vivo . Id 355
(W2E607; A0A1V0UYN2; A0A2A5JXJ9; V9W3E2; A0A2L1U0G6) was not found inin vivo data. Id: 156 had low abundance and therefore was only
trace and was not reported among LFQ positive data (W2ED21; V9WC31;
A0A6C0QLW6; A0A2L1U9J1; A0A2A5JZ82; A0A1U9YPW6). Importantly, id: 261
(V9W5A1; W2E8R6; A0A2A5K2P5; A0A1V0UNQ7; A0A2L1UCR7; A0A1U9YRI3) was
present in 11/12 P. larvae PCR-positive samples, and the highest
relative abundance was in the “lysed” samples. Two proteins
participating on “bacillibactin” synthesis could be identified, dhbA
– V9W311 was only trace, while dhbC – V9W8G5 was identified in three
samples, but not in “lysed” larvae.