Family Search for PF16269 (DUF4922)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

PF16269 hits 6 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

Tanf_08355 DUF4922 domain-containing protein from Tannerella forsythia
Aligns to 8:153 / 310 (47.1%), covers 100.0% of PF16269, 217.7 bits

• NamZ1 and NamZ2 from the Oral Pathogen Tannerella forsythia Are Peptidoglycan Processing Exo-β-N-Acetylmuramidases with Distinct Substrate Specificities
  Borisova, Journal of bacteriology 2022 (secret)
• Regulation and Molecular Basis of Environmental Muropeptide Uptake and Utilization in Fastidious Oral Anaerobe Tannerella forsythia
  Ruscitto, Frontiers in microbiology 2017
  • “...primer sets spanning adjacent genes (fragments a-j). Tanf_08345, xanthane lyase; Tanf_08350 ( gtf ), glycosyltransferase; Tanf_08355 ( gtf ), glycosyltransferase; Tanf_08360 ( lytB ), amidase enhancer precursor; Tanf_08365 ( ampG ), muropeptide permease; Tanf_08370 ( ybbC ), conserved hypothetical protein. (B) PCR products were separated on...”

APA2_YEAST / P22108 Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2; Ap4A phosphorylase 2; ADP-sulfurylase; ATP adenylyltransferase; EC 2.7.7.53; EC 2.7.7.5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
YDR530C Apa2p from Saccharomyces cerevisiae
NP_010819 bifunctional AP-4-A phosphorylase/ADP sulfurylase from Saccharomyces cerevisiae S288C
Aligns to 6:166 / 325 (49.5%), covers 89.0% of PF16269, 31.3 bits

• function: Ap4A phosphorylase catalyzes the phosphorolytic degradation of bis(5'-adenosyl) tetraphosphate (Ap4A) into ADP and ATP. Can also use other Np4N' nucleotides (where N and N' stand for A,C,G or U) as substrates, but prefers A-containing substrates. Cannot catalyze the reverse reaction. Additionally, this enzyme can also catalyze the phosphorolytic degradation of adenosine 5'-phosphosulfate (AMPS) into ADP and sulfate, the reversible exchange reaction between inorganic phosphate and the beta-phosphate of a nucleoside diphosphate (NDP), and the synthesis of Ap4A from AMPS plus ATP.
  catalytic activity: ADP + ATP + H(+) = P(1),P(4)-bis(5'-adenosyl) tetraphosphate + phosphate (RHEA:16577)
  catalytic activity: ADP + H(+) + sulfate = adenosine 5'-phosphosulfate + phosphate (RHEA:16529)
  cofactor: a divalent metal cation
  subunit: Monomer.
  disruption phenotype: Inactivation of both APA1 and APA2 promotes a great increase in the cellular concentration of bis(5'-nuceleosidyl) tetraphosphate nucleotides.
• Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases
  Brenner, Biochemistry 2002
  • “...APA2 (325) S. cerevisiae Gene (a.a.) YDR305C YBR018C YCL050C YDR530C YOR258W YDL125C map Gene names are official except chicken APTX, FHIT and GALT, which have...”
• Structures of yeast Apa2 reveal catalytic insights into a canonical AP₄A phosphorylase of the histidine triad superfamily.
  Hou, Journal of molecular biology 2013 (PubMed)
  • GeneRIF: Apa2 is an alpha/beta protein with a core domain of a twisted eight-stranded antiparallel beta-sheet flanked by several alpha-helices, similar to the galactose-1-phosphate uridylyltransferase (GalT) members of the histidine triad (HIT) superfamily.

APA1_YEAST / P16550 Protein APA1; EC 2.7.7.53; EC 2.7.7.5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 10 papers)
YCL050C Apa1p from Saccharomyces cerevisiae
Aligns to 79:163 / 321 (26.5%), covers 46.6% of PF16269, 31.2 bits

• function: Ap4A phosphorylase catalyzes the phosphorolytic degradation of bis(5'-adenosyl) tetraphosphate (Ap4A) into ADP and ATP. Can also use other Np4N' nucleotides (where N and N' stand for A,C,G or U) as substrates with equal efficiency. Cannot catalyze the reverse reaction. Additionally, this enzyme can also catalyze the phosphorolytic degradation of adenosine 5'-phosphosulfate (AMPS) into ADP and sulfate, the reversible exchange reaction between inorganic phosphate and the beta-phosphate of a nucleoside diphosphate (NDP), and the synthesis of Ap4A from AMPS plus ATP.
  catalytic activity: ADP + ATP + H(+) = P(1),P(4)-bis(5'-adenosyl) tetraphosphate + phosphate (RHEA:16577)
  catalytic activity: ADP + H(+) + sulfate = adenosine 5'-phosphosulfate + phosphate (RHEA:16529)
  cofactor: a divalent metal cation
  subunit: Monomer.
  disruption phenotype: Inactivation of both APA1 and APA2 promotes a great increase in the cellular concentration of bis(5'-nuceleosidyl) tetraphosphate nucleotides.
• Using quantitative redox proteomics to dissect the yeast redoxome
  Brandes, The Journal of biological chemistry 2011
  • “...P25491 P34223 P14832 Other functions P41338 P29704 P16550 P39926 P18562 P53091 Q12305 d Downloaded from http://www.jbc.org/ at University of California,...”
  • “...4 Supplemental Information: Brandes, Reichmann et al. P54783 P16550 P16550 P37302 P46672 Q05933 P22768 P28777 P32449 P32449 Q03862 P49089 P49089 P49089/P4 9090...”
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
  Altschul, Nucleic acids research 1997
  • “...phosphorylase I (64) (SWISS-PROT accession no. P16550). In its second position-specific iteration, PSI-BLAST gives this alignment a score...”
• CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks
  Kittas, BMC systems biology 2015
  • “...predictions for unknown expression, based on the transcriptomics data and underlying network. Consider e.g. nodes YCL050C, YPL075W, YDR050C (2) in Fig. 2 . Expression of APA1 gene (YCL050C) is regulated by the carbon source and requires the protein GCR1 (YPL075W) [ 10 ]. GCR1 mutations substantially...”
• A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation
  Aubrey, PloS one 2015
  • “...S14 Fig Gradient PCR1. Temperature gradients to investigate PCR1 failures for YLR091W, YML097C, YAL058W and YCL050C. (PNG) Click here for additional data file. S15 Fig Gradient PCR1. Temperature gradients to investigate PCR1 failures for YDR071C and YHR207C. (PNG) Click here for additional data file. S16 Fig...”
• Gene promoters dictate histone occupancy within genes
  Perales, The EMBO journal 2013 (secret)
• Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance
  Shah, Physiological genomics 2011
  • “...gi 6324328 gi 6319585 YDR035W YOL109W YNL030W YOR240W YDR226W YCL050C YIL062C YER177W YPL178W YOR074C YNR001C YBR109C ARO3 ZEO1 down - - ADK1 APA1 ARC15 BMH1...”
• PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
  Pitre, BMC bioinformatics 2006
  • “...YPL048W YBL068W YBL099W YCL025C YDR079W YLR170C YPL147W YBL068W YLR170C YCL040W YDR086C YLR195C YMR203W YBL068W YNR006W YCL050C YCL057W YLR195C YNR006W YBL068W YPL029W YCR005C YDL022W YLR244C YMR203W YBL079W YBL090W YCR021C YCR053W YLR244C YPL147W YBL079W YBL099W YCR094W YMR170C YMR011W YMR203W YBL079W YKL122C YDL028C YDL066W YMR011W YNL137C YBL079W YMR203W YDL055C...”
• Global chromatin structure of 45,000 base pairs of chromosome III in a- and alpha-cell yeast and during mating-type switching
  Ercan, Molecular and cellular biology 2004
  • “...YCL057W YCL056C YCL055W ARS304 YCL054W YCL052C YCL051W YCL050C ARS305 YCL049C YCL048W YCL047C YCL046W YCL045C YCL044C YCL043C YCL042W YCL041C YCL040W YCL039W a...”
• Genome-wide amplifications caused by chromosomal rearrangements play a major role in the adaptive evolution of natural yeast
  Infante, Genetics 2003
  • “...enological-like conditions ORF Name Chromosome YBL092W YBR089C-A YCL018W YCL050C YDL198C RPL32 NHP6B LEU2 APA1 YHM1 II (20-82 kb) II (427-436 kb) III (76-105...”
• Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases
  Brenner, Biochemistry 2002
  • “...(321) APA2 (325) S. cerevisiae Gene (a.a.) YDR305C YBR018C YCL050C YDR530C YOR258W YDL125C map Gene names are official except chicken APTX, FHIT and GALT, which...”

P49348 Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Aligns to 66:166 / 331 (30.5%), covers 47.9% of PF16269, 26.0 bits

• Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice.
  Yang, Genomics, proteomics & bioinformatics 2004
  • “...P93431 162 RuBisCO activase P93431 212 Hypothetical protein P31545 226 Unknown 239 Tetraphosphate phosphorylase II P49348 278 Ascorbate peroxidase BAB17666 309 GSH-dependent dehydroascorbate BAA90672 313 Histone H1 S59589...”

sll0509 Ap-4-A phosphorylase II from Synechocystis sp. PCC 6803
Aligns to 97:173 / 302 (25.5%), covers 41.8% of PF16269, 25.7 bits

• Cyanobacterial membrane dynamics in the light of eukaryotic principles
  Siebenaller, Bioscience reports 2023
  • “...(Putative) functions in eukaryotic cells DedA proteins Slr0232 Tvp38 Vesicular trafficking, putative lipid scramblase Slr0305 Sll0509 SPFH proteins Slr1106 Prohibitin Stabilization and dynamics of mitochondrial membrane, associated with lipid rafts Slr1768 Sll1021 Flotillin Associated with lipid rafts Slr1128 Stomatin Ion channel regulation, associated with lipid rafts...”
• Anabaena flos-aquae and other cyanobacteria possess diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) phosphorylase activity
  McLennan, The Biochemical journal 1996
  • “...a hypothetical 33.9 kDa protein product of the sll0509 gene contained within the SYCSLLLH locus of the unicellular cyanobacterium Synechocystis sp. strain...”
  • “...Synechocystis protein, whose existence is inferred from the sll0509 gene sequence, with the enzyme activity reported here, it can be concluded from both lines...”

Tery_0108 Ap4A phosphorylase II from Trichodesmium erythraeum IMS101
Aligns to 81:163 / 304 (27.3%), covers 47.3% of PF16269, 24.4 bits

• Nutrient-Colimited Trichodesmium as a Nitrogen Source or Sink in a Future Ocean
  Walworth, Applied and environmental microbiology 2018
  • “...genes include that for a 5=,5-P1,P4-tetraphosphate phosphorylase (Tery_0108, ap4A), which has been implicated in bacterial stress responses and gene regulation...”

Or search for genetic data about PF16269 in the Fitness Browser