Overview
This source page is a mechanical bulk-ingest record for a PDF in the research-pulls corpus. It preserves source-level identity, routeable product/analyte scope, and exact extracted numeric lines for later human or fresh-context audit. It does not derive HMTc thresholds, percentiles, or brand-by-brand comparisons.
Key numbers
The worker extracted the full PDF text with layout preservation twice and compared extraction hashes before commit. The following lines are copied from numeric/table-bearing regions of the PDF and retain the source units and wording where legible:
- 72 from Enterococcus faecalis (10). The protein CAJ70074.1 from C. difficile is 59 % identical to the E.
- 100 universal presence of TGA (100%) in the DNA encoding the putative selenocysteine site, 3) strong
- 234 prokaryotic genome assemblies. This is just 0.3 % of species, all anaerobic, skewed heavily toward the
- 241 regions. It occurs as a selenoprotein in 44 of the 45 (98%). The full list of hits in RefSeq can be found by
- 245 Table 1. All members of all nine family are found exclusively in bacteria. Note that we have added
- 266 recognized by Pfam model PF03243, share less than 15% pairwise identity in amino acid sequence.
- 273 mercury atom is paramount. It is notable that MerB will bind other heavy metal atoms where it binds
- 282 genome assemblies (98%) for that species annotated by PGAP for the RefSeq collection.
- 297 encoding UGA codon. Members of the family are mutually more than 45% identical to each other. In a
- 338 fragmentary sequences and redundant protein sequences more than 80% identical to others. The
- 347 (seleno)cys ligands to a single metal atom. More than 60 % of the members of the SaoB family are
- 376 active and expressed as protein, and that the system has a meaningful role in host cell metabolism, even
- 409 metal. The absence of selenocysteine from this family means even a total lack of selenium would have
- 421 crystal structure, no relevant literature detectable by PaperBLAST (27), no protein family models
- 464 “disulfide”, a CXXC motif also never has an addition Cys in the second or third position. Less than 0.5%
- 490 Table S1, in Supplemental Materials, shows proteins identified by the nine new HMMs,
- 507 GCF_001940565.1 (Tissierella creatinophila). Table S2 in Supplementary materials lists the 40 top-
- 560 genomes in the calibration set, just 735 genomes (4.7 %) have a double-cubane protein as detected by
- 561 hidden Markov model NF040730. But quite remarkably, 11.8 % of all double-cubane proteins occur in
- 562 the 0.3 % of representative genomes that have the SAO system. Among genomes with at least one
- 564 genome) than in species without (1.2 per genome). Among the 52 species with SAO cassette, 21 (40%)
- 623 Examination of HgcB showed that it too contains selenoproteins, 17 of 266 examples (6.4%).
- 671 S7) shows selected sequences from the family, non-redundant to below 75% identity, with some manual
- 685 families that are selenocysteine-containing a majority of the time (98%, 85%, 65%, and 60% for SaoL,
- 728 operons are present in 0.3% of bacterial species, but in 13.4% of those with GrdX family proteins. GrdX
- 748 of 34051 RefSeq assemblies (16%) of Escherichia coli. By contrast, we find the SAO system in C. difficile
- 749 in 3279 of 3343 assemblies (98%). All genomic contexts we viewed showed housekeeping-type genes as
- 885 appears to be a metal-binding site. In about 40% of SaoX proteins, the residue preceding Cys-192 is
- form what again appears to be a metal-binding site. In about 40% of SaoX proteins, the residue
Methods (brief)
- Analytical method details were not mechanically resolved from extracted text.
Implications
This page makes the source discoverable for category-level evidence routing. Values remain source-native and should be used only with the stated matrix, species, basis, geography, and censoring context from the paper. The page does not convert total mercury to methylmercury or use total arsenic as inorganic arsenic.
Wiki pages this source may touch
Verification notes
- Identity check: DOI, raw handle, candidate cite-key, and SHA-256 were compared against existing
wiki/sources/pages before creation. - Full-PDF read:
pdftotext -layoutwas run on the full PDF twice; extracted text hashes matched before the page was written. - Numeric verification: numeric/table-bearing lines were selected mechanically from the verified extraction and preserved without unit conversion or rounding.
- Brand firewall: the worker skips PDFs when extracted numeric lines appear brand/manufacturer-sensitive; this page contains category-level or species-level evidence only.
- HMTc firewall: no threshold, percentile, pass/fail, clean/dirty, or certification math is stated.
Update history
The five most recent substantive edits to this page, classified major (evidence or structure moved), correction (a published value or statement was wrong and has been fixed), or minor (narrative rewritten without changing the underlying evidence). Each description is derived from what the edit did to this page; the linked commit is the authoritative record, routine regeneration passes are excluded, and the full version history lives in git. When DOI minting comes online (see schema docs), each entry below will also link to a version-pinned DataCite DOI.