Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of vertebrate ALDH1A-like genes and proteins.

doi: 10.1016/j.cbi.2014.11.002

Figure Lengend Snippet: Fig. 1. Amino acid sequence alignments for human ALDH1A1, ALDH1A2, ALDH1A3, tilapia ALDH1A1, zebra fish ALDH1A2 and ALDH1A3 sequences. See Table 1 for details of ALDH1A1, ALDH1A2 and ALDH1A3 genes and proteins; ‘‘*’’ shows identical residues for ALDH subunits; ‘‘:’’ similar alternate residues; ‘‘.’’ less similar alternate residues; active site residues (based on [27,28]) are shown as Asn; Glu; and Cys; bold font shows known or predicted exon junctions; exon numbers refer to the human ALDH1A1 gene; coenzyme binding domain is in green . (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: These were based on BLAST interrogations of ALDH1A1, ALDH1A2 and ALDH1A3 databases (http://blast.ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human ALDH1A1 [2,22], ALDH1A2 [17] and ALDH1A3 [5] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome.ucsc.edu/ cgi-bin/hgBlat) [25].

Techniques: Sequencing, Binding Assay

Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of vertebrate ALDH1A-like genes and proteins.

doi: 10.1016/j.cbi.2014.11.002

Figure Lengend Snippet: Fig. 3. Phylogenetic tree for vertebrate ALDH1A-like sequences. The tree is labeled with the gene name and the name of the vertebrate. Note the major clusters for the vertebrate ALDH1A2, ALDH1A3 and human ALDH1A1 sequences. The tree is ‘rooted’ with the invertebrate ALDH1A2 sequence. See Tables 1, 1s–3s for details of ALDH1A-like genes and proteins. Note the absence of ALDH1A1 and ALDH1A3 sequences for some fish species, whereas ALDH1A2 sequences were observed for all vertebrate genomes examined. A genetic distance scale is shown. The number of times a clade (sequences common to a node or branch) occurred in the bootstrap replicates is represented as a fraction out of 100 (shown at each node). Only replicate values of 0.9 or more are highly significant, with 100 bootstrap replicates performed in each case.

Article Snippet: These were based on BLAST interrogations of ALDH1A1, ALDH1A2 and ALDH1A3 databases (http://blast.ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human ALDH1A1 [2,22], ALDH1A2 [17] and ALDH1A3 [5] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome.ucsc.edu/ cgi-bin/hgBlat) [25].

Techniques: Labeling, Sequencing

Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of ALDH18A1 genes and proteins.

doi: 10.1016/j.cbi.2016.12.012

Figure Lengend Snippet: Fig. 1. Amino acid sequence alignments for human, zebra fish, worm (C. elegans) and fruit fly (D. melanogaster) G5K domain (ALDH18A1) sequences. G5K refers to the glutamate kinase domain; see Table 1 for details of ALDH18A1 genes and proteins; “*” shows identical residues for G5K domain sequences; “:” similar alternate residues; “.” less similar alternate residues; ATP binding residues (based on [18]) are shown; bold font shows known or predicted exon junctions; exon numbers refer to the human ALDH18A1 gene; ^ designates residues involved in nucleotide binding; # for substrate binding residues; & designates dipeptide (Asn239-Val240) residues involved in isoform differences; predicted a- helices (white enclosed in black) and b-sheets (shaded) are numbered from the amino-terminus end.

Article Snippet: These were based on BLAST interrogations of ALDH18A1 databases (http://blast. ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human and mouse ALDH18A1 [4,5,9] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome. ucsc.edu/cgi-bin/hgBlat) [15].

Techniques: Sequencing, Binding Assay

Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of ALDH18A1 genes and proteins.

doi: 10.1016/j.cbi.2016.12.012

Figure Lengend Snippet: Fig. 2. Amino acid sequence alignments for human, zebra fish, worm (C. elegans) and fruit fly (D. melanogaster) GPR domain (ALDH18A1) sequences. GPR refers to the glutamyl phosphate reductase domain; see Table 1 for details of ALDH18A1 genes and proteins; “*” shows identical residues for GPR domain sequences; “:” similar alternate residues; “.” less similar alternate residues; NAD(P)H binding residues and likely active site (A) residues (Asn499; Lys504; 581Glu; and 612Cys) (based on [19]) are shown; bold font shows known or predicted exon junctions; exon numbers refer to the human ALDH18A1 gene; predicted a-helices (white enclosed in black) and b-sheets (shaded) are numbered from the amino- terminus end.

Article Snippet: These were based on BLAST interrogations of ALDH18A1 databases (http://blast. ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human and mouse ALDH18A1 [4,5,9] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome. ucsc.edu/cgi-bin/hgBlat) [15].

Techniques: Sequencing, Binding Assay

Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of ALDH18A1 genes and proteins.

doi: 10.1016/j.cbi.2016.12.012

Figure Lengend Snippet: Fig. 3. Sequences for vertebrate ALDH18A1 gene regions encoding isoforms a (ALDH18A1.long) and b (ALDH18A1.short). See Table 1 for sources of vertebrate ALDH18A1 gene se- quences; isoform a encodes the longer sequence containing the dipeptide (Asn239-Val240); the isoform b sequence lacks these residues; nucleotide sequences are aligned, showing identical residues (*) for the exonic (shown in capitals) and intronic (in lower case) sequences; ‘splicing junction’ specific nucleotide residues (GT (or gt)——AG) are shaded; human and coelacanth ALDH18A1 amino acid sequences are shown, with differences from human sequence shaded.

Article Snippet: These were based on BLAST interrogations of ALDH18A1 databases (http://blast. ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human and mouse ALDH18A1 [4,5,9] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome. ucsc.edu/cgi-bin/hgBlat) [15].

Techniques: Sequencing

Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of ALDH18A1 genes and proteins.

doi: 10.1016/j.cbi.2016.12.012

Figure Lengend Snippet: Fig. 4. Phylogenetic tree for vertebrate and invertebrate ALDH18A1 sequences.

Article Snippet: These were based on BLAST interrogations of ALDH18A1 databases (http://blast. ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human and mouse ALDH18A1 [4,5,9] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome. ucsc.edu/cgi-bin/hgBlat) [15].

Techniques:

Journal: Chemico-biological interactions

Article Title: Comparative and evolutionary studies of ALDH18A1 genes and proteins.

doi: 10.1016/j.cbi.2016.12.012

Figure Lengend Snippet: Fig. 5. A proposal for the evolutionary appearance of vertebrate and invertebrate ALDH18A1 genes derived from the fusion of bacterial ProB and ProA genes. Proposed evolutionary appearance of vertebrate and invertebrate ALDH18A1 genes and proteins resulting from a fusion of bacterial ProB (encoding G5K) and ProA (encoding GPR) genes. Gene details are shown in Table 1 (based on [23].

Article Snippet: These were based on BLAST interrogations of ALDH18A1 databases (http://blast. ncbi.nlm.nih.gov/Blast.cgi) using the reported sequences for human and mouse ALDH18A1 [4,5,9] and BLAT analyses of vertebrate genomes using the UC Santa Cruz Genome Browser (http://genome. ucsc.edu/cgi-bin/hgBlat) [15].

Techniques: Derivative Assay