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Steps of DUF data curation. (i) Extract and download a list of PFAM ID/DUF ... Open Access
Published: 23 January 2026
Figure 2
Steps of DUF data curation. (i) Extract and download a list of PFAM ID/DUF ID/SCOPe ID using search criteria, (a) pathway names and (b) catalytic cysteines [ 6, 7 ] (ii) filter the downloaded list using SCOPe superfamily resulting enzyme names from 7 biochemical pathways studied here; (iii) search S
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Depiction of cysteine (Cys22), part of a disulfide bridge (PDB ID:8PCH). Pr... Open Access
Published: 23 January 2026
Figure 3
Depiction of cysteine (Cys 22), part of a disulfide bridge (PDB ID:8PCH). Protein microenvironment (4.5 Å radius) around Cys22 is depicted, in stick representation. The protein background is shown as cartoon representation. The figure was generated using VMD software.
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Confusion matrix to validate the predicted cysteine PTMs (using DeepCys sof... Open Access
Published: 23 January 2026
Figure 4
Confusion matrix to validate the predicted cysteine PTMs (using DeepCys software) with the experimental (PDB header file) observations. The heatmap indicates the range of cysteine numbers.
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Distribution of cysteine protein microenvironments, from DUF proteins, in t... Open Access
Published: 23 January 2026
Figure 5
Distribution of cysteine protein microenvironments, from DUF proteins, in three clusters, buried hydrophobic, buried hydrophilic, and exposed hydrophilic. The X-axis represents the BF; the Y-axis, rHpy; and the Z-axis, populations of cysteine. Three insets show the relative position of the cysteine
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Simple tree representing the species in this study based on taxonomy for vi... Open Access
Published: 23 January 2026
Figure 7
Simple tree representing the species in this study based on taxonomy for virus and archaebacteria. The figure was generated using ITOL version 7.
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Simple tree for disease-causing bacteria, classified according to their tax... Open Access
Published: 23 January 2026
Figure 8
Simple tree for disease-causing bacteria, classified according to their taxonomy. The number of species per genera is shown on the connecting branch. One example per genera is shown for clarity. The figure was generated using ITOL version 7.
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Counts of functional cysteines across twenty different diseases, categorize... Open Access
Published: 23 January 2026
Figure 10
Counts of functional cysteines across twenty different diseases, categorized according to protein microenvironment clusters, (a) DeepCys-structure-based prediction tool and (b) CysDuF database.
Journal Article
CysDuF database: annotation and characterization of cysteine residues in domain of unknown function proteins based on cysteine post-translational modifications, their protein microenvironments, biochemical pathways, taxonomy, and diseases Open Access
Database, Volume 2026, 2026, baag002, https://doi.org/10.1093/database/baag002
Published: 23 January 2026
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Schematic representations of Cys-PTMs in different pathways curated from li... Open Access
Published: 23 January 2026
Figure 6
Schematic representations of Cys-PTMs in different pathways curated from literature, (a) ETC, (b) Fe–S cluster biogenesis, (c) glutathione biosynthesis, (d) fatty acid biosynthesis, (e) Kreb’s cycle, (f) pentose phosphate pathways. The amino acids and protein structures were depicted using VMD softw
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Disease-causing bacteria infecting different organs, categories based on an... Open Access
Published: 23 January 2026
Figure 9
Disease-causing bacteria infecting different organs, categories based on anatomy. Counts of cysteine residues present in DUF proteins per disease category are shown.
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Schematic representation of four cysteine PTMs described in the CysDuF data... Open Access
Published: 23 January 2026
Figure 1
Schematic representation of four cysteine PTMs described in the CysDuF database.
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Schematic representations of Cys-PTMs in different pathways curated from li... Open Access
Published: 23 January 2026
Figure 6
Schematic representations of Cys-PTMs in different pathways curated from literature, (a) ETC, (b) Fe–S cluster biogenesis, (c) glutathione biosynthesis, (d) fatty acid biosynthesis, (e) Kreb’s cycle, (f) pentose phosphate pathways. The amino acids and protein structures were depicted using VMD softw
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Web application for (a) DeepCys—structure-based prediction tool and (b) Cys... Open Access
Published: 23 January 2026
Figure 11
Web application for (a) DeepCys—structure-based prediction tool and (b) CysDUF database.
Journal Article
A comprehensive database for biological data derived from sewage in five European cities Open Access
Database, Volume 2026, 2026, baaf089, https://doi.org/10.1093/database/baaf089
Published: 20 January 2026
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A simplified overview of the database scheme. tables closely related togeth... Open Access
Published: 20 January 2026
Figure 2.
A simplified overview of the database scheme. tables closely related together are coloured according to what kind of information they represent. The ‘meta’ table and the ‘location’ table encompass metainformation. The tables ‘resfinder_gene_abundance’ and ‘resfinder_class_abundance’ joined with deta
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Overview of the dataset. Step 1: Time-series sewage samples were collected ... Open Access
Published: 20 January 2026
Figure 1.
Overview of the dataset. Step 1: Time-series sewage samples were collected from sewage treatment plants across five European cities. Step 2: DNA was extracted from these samples and shotgun sequenced. A subset of samples underwent proximity ligation combined with shotgun sequencing (Hi-C) at Phase G
Journal Article
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae) Open Access
Database, Volume 2026, 2026, baaf085, https://doi.org/10.1093/database/baaf085
Published: 19 January 2026
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Morphometric traits measured in each Porthidium specimen, based on standard... Open Access
Published: 19 January 2026
Figure 1.
Morphometric traits measured in each Porthidium specimen, based on standardized anatomical views. (A) Dorsal view of the whole body showing total length, head width, and mid-body width and height; (B) ventral view highlighting snout–vent length and tail length; (C) lateral view of the head illustr
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Body and head scales assessed in Porthidium. (A) Dorsal view of the entire ... Open Access
Published: 19 January 2026
Figure 2.
Body and head scales assessed in Porthidium . (A) Dorsal view of the entire body, showing the arrangement of ventral and caudal scales. (B) Enlarged dorsal view of the body, highlighting the mid-row dorsal scales and lateral dorsal scales. (C) Lateral view of the head, indicating subocular, postocu
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Dorsal view of the head of Porthidium, showing the arrangement of landmarks... Open Access
Published: 19 January 2026
Figure 3.
Dorsal view of the head of Porthidium , showing the arrangement of landmarks used in geometric morphometric analyses. 1-8 points represent landmarks, while other points represent semi-landmarks derived from curves, placed at equidistant intervals along anatomical edges. Illustration by Carlos Patro
