Journal: Genome Biology and Evolution

Article Title: Highly Resolved Genomes of Two Closely Related Lineages of the Rodent Louse Polyplax serrata with Different Host Specificities

doi: 10.1093/gbe/evae045

Figure Lengend Snippet: Comparison of genome contents of the three sucking lice (Anoplura). For the databases CAZy, InterPro, MEROPS, and Pfam, the numbers represent unique IDs identified in the genomes. For SignalP and Phobius, the plot shows total numbers of the transmembrane proteins and signal peptides identified by the databases.

Article Snippet: Over 93% of the annotated proteins from the Pfam and InterPro databases were conserved across the three analyzed anopluran genomes ( , online).

Techniques: Comparison

Journal: Genome Biology and Evolution

Article Title: Highly Resolved Genomes of Two Closely Related Lineages of the Rodent Louse Polyplax serrata with Different Host Specificities

doi: 10.1093/gbe/evae045

Figure Lengend Snippet: PcoA analysis of the five phthirapteran genomes. A) PCoA based on the results of the family-centered Pfam database. B) PCoA based on the InterPro database. C) PCoA based on the InterPro database.

Article Snippet: Over 93% of the annotated proteins from the Pfam and InterPro databases were conserved across the three analyzed anopluran genomes ( , online).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Evolution of the Membrane Transport Protein Domain

doi: 10.3390/ijms23158094

Figure Lengend Snippet: Domain organisation of MTP domain-containing proteins in the different taxa. Designated loop length is applied only to a particular protein (referred to as UniProt ID). Taxa-specific description of loop length is referred to as “no loops” or varies. The presence of other domains is designated with a blue arrow. Upward loops represent non-cytoplasmic, and downward—cytoplasmic loops.

Article Snippet: The proteins containing the membrane transport protein (MTP) (Pfam PF03547, InterPro IPR004776, YfdV COG0679) were downloaded from NCBI ( http://www.ncbi.nlm.nih.gov/ (accessed on May–June 2022)), UniProt ( http://www.uniprot.org (accessed on May–June 2022)), Pram ( http://pfam.xfam.org/ (accessed on May–June 2022)), and InterPro ( http://www.ebi.ac.uk/interpro/ (accessed on May–June 2022)) databases.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Evolution of the Membrane Transport Protein Domain

doi: 10.3390/ijms23158094

Figure Lengend Snippet: Alignment of structural models of MTP domain-containing proteins from different taxa. Control proteins (green) (with no loops) from bacteria Escherichia coli , sponge Amphimedon queenslandica , and Homo sapiens were aligned with MTPs with loops (cyan) from cyanobacteria Thermoleptolyngbya sichuanensis (alignment scores 112, 113, and 112 for every control, respectively), terrabacteria Mycoplasmopsis bovis (alignment scores 166 and 169), a unicellular eukaryote Sphaeroforma arctica (alignment score 148), and plant Arabidopsis thaliana (alignment scores 317, 362, and 289). Non-cytoplasmic loop represented with firebrick-red, cytoplasmic with purple colours.

Article Snippet: The proteins containing the membrane transport protein (MTP) (Pfam PF03547, InterPro IPR004776, YfdV COG0679) were downloaded from NCBI ( http://www.ncbi.nlm.nih.gov/ (accessed on May–June 2022)), UniProt ( http://www.uniprot.org (accessed on May–June 2022)), Pram ( http://pfam.xfam.org/ (accessed on May–June 2022)), and InterPro ( http://www.ebi.ac.uk/interpro/ (accessed on May–June 2022)) databases.

Techniques: Control, Bacteria

Journal: International Journal of Molecular Sciences

Article Title: Evolution of the Membrane Transport Protein Domain

doi: 10.3390/ijms23158094

Figure Lengend Snippet: Alignment of structural models of MTP domain-containing proteins with Na/H Exchanger domain. MTPs (green) (with loops) from cyanobacteria Thermoleptolyngbya sichuanensis were aligned with Na/H exchanger from archaea Thermoprotei archaeon (cyan) (alignment score 146). MTP from Olsenella sp. (green) was aligned with Na/H Exchanger from the same bacteria (alignment score 152), and MTP from Mycoplasmopsis bovis (green) was aligned with Na/H exchanger from Mycoplasmopsis anatis (cyan) (alignment score 221). MTPs’ non-cytoplasmic loop is represented with firebrick-red, cytoplasmic with purple colours.

Article Snippet: The proteins containing the membrane transport protein (MTP) (Pfam PF03547, InterPro IPR004776, YfdV COG0679) were downloaded from NCBI ( http://www.ncbi.nlm.nih.gov/ (accessed on May–June 2022)), UniProt ( http://www.uniprot.org (accessed on May–June 2022)), Pram ( http://pfam.xfam.org/ (accessed on May–June 2022)), and InterPro ( http://www.ebi.ac.uk/interpro/ (accessed on May–June 2022)) databases.

Techniques: Bacteria

Journal: PLoS Biology

Article Title: A noncanonical chaperone interacts with drug efflux pumps during their assembly into bacterial outer membranes

doi: 10.1371/journal.pbio.3001523

Figure Lengend Snippet: (A) Schematic of an efflux pump removing harmful substances. The pump comprises an IMC protein from the RND, ABC, or MFS superfamilies, a PAP, and an OMF family component, like TolC . (B) Ribbon diagram of TolC (PDB: 1EK9). Sizes of each structural domain are indicated to the right . One of the 3 monomers is coloured pink for clarity. (C) Structural map of one TolC monomer (without its signal peptide), based on its crystal structure (PDB: 1EK9) over residues 1–428 and as predicted using PSIPRED 4.0 over residues 429–471. The characteristic OEP regions are indicated. Cylinders represent α-helices; arrows represent β-strands. IMC, inner membrane channel; OEP, outer membrane efflux protein; OMF, outer membrane factor; PAP, periplasmic adaptor protein; PGN, peptidoglycan.

Article Snippet: All protein sequences containing the OEP fold characteristic of TolC-like proteins (Pfam: PF02321) were obtained from InterPro (version 84.0) [ ].

Techniques: Membrane