LOCUS       CP113245                3570 bp    DNA     linear   BCT 29-JUN-2023
DEFINITION  Staphylococcus aureus strain Alexandria_2020-19 plasmid unnamed1.
ACCESSION   CP113245
VERSION     CP113245.1
DBLINK      BioProject: PRJNA905238
            BioSample: SAMN31868372
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3570)
  AUTHORS   Monecke,S., Bedewy,A.K., Muller,E., Braun,S.D., Diezel,C.,
            Elsheredy,A., Kader,O., Reinicke,M., Ghazal,A., Rezk,S. and
            Ehricht,R.
  TITLE     Characterisation of Methicillin-Resistant Staphylococcus aureus from
            Alexandria, Egypt
  JOURNAL   Antibiotics (Basel) 12 (1), 78 (2023)
   PUBMED   36671279
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3570)
  AUTHORS   Monecke,S., Bedewy,A.K., Mueller,E., Braun,S.D., Diezel,C. and
            Reinicke,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-NOV-2022) Optisch-Molekulare Diagnostik und
            Systemtechnologien, Leibniz Institute of Photonic Technology (IPHT),
            Philosophenweg 7, Jena 07743, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. version 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 164.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 11/29/2022 14:49:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.3
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,868
            CDSs (total)                      :: 2,787
            Genes (coding)                    :: 2,506
            CDSs (with protein)               :: 2,506
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 281
            CDSs (without protein)            :: 281
            Pseudo Genes (ambiguous residues) :: 0 of 281
            Pseudo Genes (frameshifted)       :: 245 of 281
            Pseudo Genes (incomplete)         :: 40 of 281
            Pseudo Genes (internal stop)      :: 15 of 281
            Pseudo Genes (multiple problems)  :: 16 of 281
            ##Genome-Annotation-Data-END##
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..3570
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="Alexandria_2020-19"
                     /isolation_source="aspirated pus"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="Egypt: Alexandria"
                     /collection_date="2020"
                     /note="CC1-MRSA; genotype: CC1, ST1"
     gene            220..543
                     /locus_tag="OUY38_14310"
                     /pseudo=""
     CDS             220..543
                     /locus_tag="OUY38_14310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966862.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology.
                     GO_process: GO:0019835 - cytolysis [Evidence IEA]"
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="phage holin, lambda family"
                     /name="phage holin, lambda family"
     gene            527..1003
                     /locus_tag="OUY38_14315"
     CDS             527..1003
                     /locus_tag="OUY38_14315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001625373.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003796 - lysozyme activity [Evidence IEA]; GO_process:
                     GO:0009253 - peptidoglycan catabolic process [Evidence
                     IEA]; GO_process: GO:0016998 - cell wall macromolecule
                     catabolic process [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="glycoside hydrolase family protein"
                     /protein_id="WAE37034.1"
                     /translation="MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDY
                     SDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGA
                     LPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV"
                     /name="glycoside hydrolase family protein"
     gene            1000..1461
                     /gene="rzpD"
                     /locus_tag="OUY38_14320"
     CDS             1000..1461
                     /gene="rzpD"
                     /locus_tag="OUY38_14320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309650.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="prophage endopeptidase RzpD"
                     /protein_id="WAE37035.1"
                     /translation="MSRVTAIISALVICIIVCLSWAVNHYRDNAITYKAQRDKNARELK
                     LANAAITDMQMRQRDVAALDAKYTKELADAKAENDALRDDVAAGRRRLHIKAVCQSVRE
                     ATTASGVDNAASPRLADTAERDYFTLRERLITMQKQLEGTQKYINEQCR"
                     /name="rzpD"
     gene            complement(1493..1786)
                     /gene="bor"
                     /locus_tag="OUY38_14325"
     CDS             complement(1493..1786)
                     /gene="bor"
                     /locus_tag="OUY38_14325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309652.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="serum resistance lipoprotein Bor"
                     /protein_id="WAE37036.1"
                     /translation="MKKMLLATALALLITGCAQQTFTVQNKPAAVAPKETITHHFFVSG
                     IGQKKTVDAAKICGGAENVVKTETQQTFVNGLLGFITLGIYTPLEARVYCSQ"
                     /name="bor"
     gene            complement(2076..2486)
                     /locus_tag="OUY38_14330"
     CDS             complement(2076..2486)
                     /locus_tag="OUY38_14330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415090.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1398 domain-containing protein"
                     /protein_id="WAE37037.1"
                     /translation="MAQVAIFKEIFDQVRKDLDCELFYSELKRHNVSHYIYYLATDNIH
                     IVLENDNTVLIKGLKKVVNVKFSRNTHLIETSYDRLKSREITFQQYRENLAKAGVFRWV
                     TNIHEHKRYYYTFDNSLLFTESIQNTTQIFPR"
                     /name="DUF1398 domain-containing protein"
     gene            2772..2978
                     /locus_tag="OUY38_14335"
     CDS             2772..2978
                     /locus_tag="OUY38_14335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WAE37038.1"
                     /translation="MNKEQSADDPSVDLIRVKNMLNSTISMSYPDVVIACIEHKVSLEA
                     FRAIEAALVKHDNNMKDYSLVVD"
                     /name="hypothetical protein"
     gene            complement(3143..3337)
                     /locus_tag="OUY38_14340"
     CDS             complement(3143..3337)
                     /locus_tag="OUY38_14340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_001165309.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YlcI/YnfO family protein"
                     /protein_id="WAE37039.1"
                     /translation="MSTKNRTRRTTTRNIRFPNQMIEQINIALEQKGSGNFSAWVIEAC
                     RRRLTSEKRAYTSIKSDEE"
                     /name="YlcI/YnfO family protein"
ORIGIN
        1 ttacgtattg ctgccatcag attgtgtttg ttagtcgctt ttttttttgg aatttttttt
       61 ttggaatttt tttttgcgct aacaacctcc tgccgttttg cccgtgcata tcggtcacga
      121 acaaatctga ttactaaaca cagtagcctg gatttgttct atcagtaatc gaccttattc
      181 ctaattaaat agagcaaatc cccttattgg gggtaagaca tgaagatgcc agaaaaacat
      241 gacctgttgg ccgccattct cgcggcaaag gaacaaggca tcggggcaat ccttgcgttt
      301 gcaatggcgt accttcgcgg cagatataat ggcggtgcgt ttacaaaaac agtaatcgac
      361 gcaacgatgt gcgccattat cgcctagttc attcgtgacc ttctcgactt cgccggacta
      421 agtagcaatc tcgcttatat aacgagcgtg tttatcggct acatcggtac tgactcgatt
      481 ggttcgctta tcaaacgctt cgctgctaaa aaagccggag tagaagatgg tagaaatcaa
      541 taatcaacgt aaggcgttcc tcgatatgct ggcgtggtcg gagggaactg ataacggacg
      601 tcagaaaacc agaaatcatg gttatgacgt cattgtaggc ggagagctat ttactgatta
      661 ctccgatcac cctcgcaaac ttgtcacgct aaacccaaaa ctcaaatcaa caggcgccgg
      721 acgctaccag cttctttccc gttggtggga tgcctaccgc aagcagcttg gcctgaaaga
      781 cttctctccg aaaagtcagg acgctgtggc attgcagcag attaaggagc gtggcgcttt
      841 acctatgatt gatcgtggtg atatccgtca ggcaatcgac cgttgcagca atatctgggc
      901 ttcactgccg ggcgctggtt atggtcagtt cgagcataag gctgacagcc tgattgcaaa
      961 attcaaagaa gcgggcggaa cggtcagaga gattgatgta tgagcagagt caccgcgatt
     1021 atctccgctc tggttatctg catcatcgtc tgcctgtcat gggctgttaa tcattaccgt
     1081 gataacgcca ttacctacaa agcccagcgc gacaaaaatg ccagagaact gaagctggcg
     1141 aacgcggcaa ttactgacat gcagatgcgt cagcgtgatg ttgctgcgct cgatgcaaaa
     1201 tacacgaagg agttagctga tgctaaagct gaaaatgatg ctctgcgtga tgatgttgcc
     1261 gctggtcgtc gtcggttgca catcaaagca gtctgtcagt cagtgcgtga agccaccacc
     1321 gcctccggcg tggataatgc agcctccccc cgactggcag acaccgctga acgggattat
     1381 ttcaccctca gagagaggct gatcactatg caaaaacaac tggaaggaac ccagaagtat
     1441 attaatgagc agtgcagata gagttgccca tatcgatggg caactcatgc aattattgtg
     1501 agcaatacac acgcgcttcc agcggagtat aaatgcctaa agtaataaaa ccgagcaatc
     1561 catttacgaa tgtttgctgg gtttctgttt taacaacatt ttctgcgccg ccacaaattt
     1621 tggctgcatc gacagttttc ttctgcccaa ttccagaaac gaagaaatga tgggtgatgg
     1681 tttcctttgg tgctactgct gccggtttgt tttgaacagt aaacgtctgt tgagcacatc
     1741 ctgtaataag cagggccagc gcagtagcga gtagcatttt tttcatggtg ttattcccga
     1801 tgctttttga agttcgcaga atcgtatgtg tagaaaatta aacaaaccct aaacaatgag
     1861 ttgaaatttc atattgttaa tatttattaa tgtatgtcag gtgcgatgaa tcgtcattgt
     1921 attcccggat taactatgtc cacagccctg acggggaact tctctgcggg agtgtccggg
     1981 aataattaaa acgatgcaca cagggtttag cgcgtacacg tattgcatta tgccaacgcc
     2041 ccggtgctga cacggaagaa accggacgtt atgatttagc gtggaaagat ttgtgtagtg
     2101 ttctgaatgc tctcagtaaa tagtaatgaa ttatcaaagg tatagtaata tcttttatgt
     2161 tcatggatat ttgtaaccca tcggaaaact cctgctttag caagattttc cctgtattgc
     2221 tgaaatgtga tttctcttga tttcaaccta tcataggacg tttctataag atgcgtgttt
     2281 cttgagaatt taacatttac aaccttttta agtcctttta ttaacacggt gttatcgttt
     2341 tctaacacga tgtgaatatt atctgtggct agatagtaaa tataatgtga gacgttgtga
     2401 cgttttagtt cagaataaaa caattcacag tctaaatctt ttcgcacttg atcgaatatt
     2461 tctttaaaaa tggcaacctg agccattggt aaaaccttcc atgtgatacg agggcgcgta
     2521 gtttgcatta tcgtttttat cgtttcaatc tggtctgacc tccttgtgtt ttgttgatga
     2581 tttatgtcaa atattaggaa tgttttcact taatagtatt ggttgcgtaa caaagtgcgg
     2641 tcctgctggc attctggagg gaaatacaac cgacagatgt atgtaaggcc aacgtgctca
     2701 aatcttcata cagaaagatt tgaagtaata ttttaaccgc tagatgaaga gcaagcgcat
     2761 ggagcgacaa aatgaataaa gaacaatctg ctgatgatcc ctccgtggat ctgattcgtg
     2821 taaaaaatat gcttaatagc accatttcta tgagttaccc tgatgttgta attgcatgta
     2881 tagaacataa ggtgtctctg gaagcattca gagcaattga ggcagcgttg gtgaagcacg
     2941 ataataatat gaaggattat tccctggtgg ttgactgatc accataactg ctaatcattc
     3001 aaactattta gtctgtgaca gagccaacac gcagtctgtc actgtcagga aagtggtaaa
     3061 actgcaactc aattactgca atgccctcgt aattaagtga atttacaata tcgtcctgtt
     3121 cggagggaag aacgcgggat gttcattctt catcactttt aattgatgta tatgctctct
     3181 tttctgacgt tagtctccga cggcaggctt caatgaccca ggctgagaaa ttcccggacc
     3241 ctttttgctc aagagcgatg ttaatttgtt caatcatttg gttaggaaag cggatgttgc
     3301 gggttgttgt tctgcgggtt ctgttcttcg ttgacatgag gttgccccgt attcagtgtc
     3361 gctgatttgt attgtctgaa gttgttttta cgttaagttg atgcagatca attaatacga
     3421 tacctgcgtc ataattgatt atttgacgtg gtttgatggc ctccacgcac gttgtgatat
     3481 gtagatgata atcattatca ctttacgggt cctttccggt gaaaaaaagg taccaaaaaa
     3541 aacatcgtcg tgagtagtga accgtaagca
//
