LOCUS       NZ_CP033985             3785 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Staphylococcus aureus strain P2D1C1 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP033985
VERSION     NZ_CP033985.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10374694
            Assembly: GCF_009739695.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3785)
  AUTHORS   Liu,J., Gefen,O., Ronin,I., Bar-Meir,M. and Balaban,N.Q.
  TITLE     Rapid evolution of tolerance in patients infected with S. aureus
            promotes antibiotic resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3785)
  AUTHORS   Liu,J., Gefen,O., Ronin,I., Bar-Meir,M. and Balaban,N.Q.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-NOV-2018) Racah Institute of Physics, Hebrew
            University, Givat ram, Jerusalem 91904, Israel
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Celera Assembler v. 1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 594x
            Sequencing Technology             :: PacBio + Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 03:04:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,889
            CDSs (total)                      :: 2,807
            Genes (coding)                    :: 2,716
            CDSs (with protein)               :: 2,716
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 91
            CDSs (without protein)            :: 91
            Pseudo Genes (ambiguous residues) :: 0 of 91
            Pseudo Genes (frameshifted)       :: 50 of 91
            Pseudo Genes (incomplete)         :: 42 of 91
            Pseudo Genes (internal stop)      :: 35 of 91
            Pseudo Genes (multiple problems)  :: 32 of 91
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033985.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3785
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="P2D1C1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed3"
                     /geo_loc_name="Israel: Jerusalem"
                     /lat_lon="31.7732 N 35.1853 E"
                     /collection_date="2017-10-03"
                     /collected_by="Shaare Zedek"
     gene            complement(50..697)
                     /gene="catA"
                     /locus_tag="EFD76_RS00025"
                     /old_locus_tag="EFD76_00030"
     ARG             complement(54..697)
                     /name="catA"
                     /gene="catA"
                     /gene_name="type A-7 chloramphenicol O-acetyltransferase"
                     /tool="amrfinderplus"
                     /drug_class="PHENICOL"
                     /identity="97.67"
                     /coverage="100.0"
     gene            complement(827..1762)
                     /locus_tag="EFD76_RS00030"
                     /old_locus_tag="EFD76_00035"
     CDS             complement(827..1762)
                     /locus_tag="EFD76_RS00030"
                     /old_locus_tag="EFD76_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002489526.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_094620759.1"
                     /translation="MSTENYSNYLQNKDLDNFSKTGYSNSRLSGQTLGKSQPALSFDAM
                     TIVGNLNKTNAKKLSDFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWDRRN
                     MRVEFNPNKLTHEEMIWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKAVKKTV
                     FYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVVSEHLWRVEVELKRDMVDYW
                     NDCFNDLHILKPAWATLEKINEQAMVYTLLHEESMWGKLSKNTKTKFKKLIREISPIDL
                     TELMKSTLKANEKQLQKQIDFWQREFRFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(2289..3557)
                     /gene="mobV"
                     /locus_tag="EFD76_RS00035"
                     /old_locus_tag="EFD76_00040"
     CDS             complement(2289..3557)
                     /gene="mobV"
                     /locus_tag="EFD76_RS00035"
                     /old_locus_tag="EFD76_00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000331753.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_053023830.1"
                     /translation="MAYSIIRVAKVKSKTNTKGIQKHVQRQNKNYENMDIDLEKSYLNY
                     DLVNDSPIDYNQKIEEKIEQNYNGKRKIRKDAVKHIDGLITSGNEFFKNQTLEETKQFF
                     EHAKTFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITEDGRLSAKEVLGNKKALTEFQ
                     DRFNEHINSCGYDLSRGITRGVTPRRHEQISRYKNLTDYHKEEYEHESRKLDRIKQESE
                     EVMEQYQNALDVLKKPINVPYELETEKVGGLFNKETQETGNVVIDKNEFDLLQEQVKAS
                     QLITDDYEYIKSGKALKDFEEKNKRLEDRLLDEQIKNGKVIDEYNDLADSYNNLLEQNQ
                     EKEKELNRSYKLFNNVFKLIKGVMKEETYHSLINHIDNHLESSKMRETMIVDDNDEQFF
                     KKKYQRHEPEIIFEDERDDGYTL"
                     /name="mobV"
     ARG             complement(51..697)
                     /name="Enterococcus faecalis chloramphenicol
                     acetyltransferase"
                     /gene="Enterococcus faecalis chloramphenicol
                     acetyltransferase"
                     /gene_name="chloramphenicol acetyltransferase (CAT)"
                     /tool="rgi"
                     /drug_class="phenicol antibiotic"
                     /identity="97.67"
                     /coverage="100.0"
     Typing          complement(832..1801)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.645"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2293..3617)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.095"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatgatcact tacgtgtata aaattaaatt cacttccaaa atctaaaaac taaatccaat
       61 catctaccct atgaattata tcttgaaatt cattcataaa tagtgaagca tggtaaccat
      121 cacatacagc atgatgaagc tgcagagcaa ctggtatata aattttatta ttctcactat
      181 aaaatttacc tatcgtaata ataggcaata aaaagctacc attgttacca atgtttaaat
      241 taaatgaact aaaatcaatc caaggaatca ttgaaatcgg tatggcgttt tcaggtatcg
      301 gttttttagg aaacatttct tctttatctt tatattcaag taagtcattt ttataattat
      361 tataaaaaga agtgaagttg ttatcagatt cagtccaaat gttagtaaat ttttcagttt
      421 gcttattaaa aactgtatac aaaggattta acttatccca ataacctaat ttattctcac
      481 tattaattcc tgttctaaac actttgtttt tatttacaac ttccataatt gcataaatca
      541 aagaaggata aatttcatat cctttctttt ttatcatatc tttaaacaaa gtaatatcaa
      601 tttctttagt aatgctataa gtagtttgct gattaaaata gtgttcaaaa tattcttttc
      661 tatcccaatt ttctaattca ataatattaa aagtcatata taacttcctc ctaaatttta
      721 aatttttata tttaggagga ataatcctct gattttttca tacgttatgt cacctcgtaa
      781 atattaatta tactgaatta gcaattttta taaaataaaa cttattttac ttccaaaacc
      841 taaattcacg ttgccaaaaa tcaatctgct tttgcaattg tttttcgttc gcttttaaag
      901 tcgatttcat taattccgtt aaatcaattg gagatatttc tctaatcaat tttttaaatt
      961 tagtcttagt attcttactt agctttcccc acatactttc ttcatgcaac aaagtataaa
     1021 ccatagcttg ctcattaatt ttttctaaag tagcccacgc aggtttcaag atgtgtaaat
     1081 cattaaaaca atcattccag taatcaacca tatctctttt taattcaact tctacacgcc
     1141 ataaatgttc agacacaact tcaacatctg cgttatcttt acgttcttgt tttttattat
     1201 aaattctaat aaatctatca ctatcacgga caccaaaata ttttgtttct ggcttgccat
     1261 tacgaccata aaaaacagtt ttcttaactg ctttatcagt cattgcatag taatcgctca
     1321 aatcatcttc aaaatcaaaa gctaagtcta atcttgtaaa accgtcatct tccatgtagt
     1381 cgataatatt ttgttttaac caaatcattt cttcatgtgt gagtttattg ggattaaatt
     1441 caacacgcat attacgtcta tcccaagtat ctgcttttac tttgtcatat tcgatataaa
     1501 ctttttcttg aagtgcctta gctttaaact ttgtttgaag tatatcccaa agtcgtattt
     1561 gtggctctac actcataaag tcagatagct ttttagcatt agttttgttc aaatttccaa
     1621 cgattgtcat ggcatcaaaa cttaatgcgg gttgagattt tcccaaagtt tgaccactta
     1681 accggctatt agagtagccg gttttagaaa aattgtctaa atccttattt tgtaagtaat
     1741 ttgaataatt ttctgtactc ataaaaatcg actccttaat tatttttaag aagtcgccca
     1801 cccaaatata actcttgatg tatgtttaaa tatcgtttaa tatctagata tacaatagtt
     1861 ataaaacaca ccgaatatgt tttttctttt ggataagtcg cattcacaaa ctttggtcgg
     1921 ggagtgggcg acttcttttt tattttgtta ttaatataac actatcaaaa gacttggtct
     1981 aatcagatca ggtctttttt tatttaagca tttgtattat ctggtaaaca gttaaaacta
     2041 ctaaaacacc aagtacatac ttacttgcta taaaattctc aaaaccttct ctaaatttca
     2101 tttcttcaac tccttttatt gctttattcc aattgcttta ttgacgttga gcctcggaac
     2161 ccttaacaat cccaaaactt gtcgaatggt cggcttaata gctcacgcta tgccgacatt
     2221 cgtctgcaag tttagttaag ggttcttctc aacgcacaat aaattttctc ggcataaatg
     2281 cgtcgtcttt ataaagtgta gccatcatct cgttcatctt caaaaataat ttctggttca
     2341 tgcctttgat attttttctt aaagaattgt tcatcgttat catctacaat cattgtttct
     2401 cgcatttttg agctttctaa gtgattatca atatggttaa tcaacgaatg atatgtttct
     2461 tctttcatca cacctttaat caacttaaac acattgttaa atagtttata cgaacggttt
     2521 aactcttttt ctttttcttg attttgttcc aataaattat tataactatc cgctaaatca
     2581 ttgtattcat ctattacttt tccattttta atctgttcgt ctaataatct atcttctaat
     2641 cttttgtttt tttcctcaaa atcttttaaa gcttttccgc ttttaatata ttcataatca
     2701 tcagtaatga gttgagaagc ttttacttgt tcctgcaata aatcaaattc atttttatca
     2761 ataacgacgt tacctgtttc ctgtgtttct ttgttgaaca gtccaccaac tttttcagtt
     2821 tcaagctcat atgggacatt tataggcttt tttagaacat ctaaagcatt ttgatactgt
     2881 tccattactt cttcgctttc ttgctttata cggtctaatt ttcggctctc atgctcatat
     2941 tcttctttgt gataatctgt taaattttta taacgactta tctgctcatg tcgtctcggt
     3001 gtaacgcccc ttgttatacc tctactcaag tcataaccac aactattgat atgttcgtta
     3061 aatctatctt gaaattcagt tagtgccttt ttattaccta aaacctcttt cgcactcaat
     3121 cgaccatctt ctgtaatcgg aactacccca taatgcatat gaggtgtttt ttcgtccata
     3181 tgcactgttg catataataa attatctttt ccatactctt gttctaaaaa cgttttagca
     3241 tgttcaaaaa actgctttgt ttcttcaagt gtttgatttt taaaaaattc attaccagat
     3301 gtaattaaac catcaatatg ttttactgcg tcttttctaa ttttgcgttt cccattataa
     3361 ttttgttcaa ttttctcttc gattttttga ttataatcaa tcggactatc attgactaaa
     3421 tcgtaattta agtatgattt ttctaaatca atatccatat tttcataatt tttattttgt
     3481 ctttgtacat gtttttgaat gccttttgta ttcgtttttg atttcacttt agcaactctg
     3541 ataatagaat acgccatatt aaaattcctc cactgcacat gtttttgcgt agctttattt
     3601 attaaagtat aacacactag acttatttgc tatcgccata agtcattaat gcgtgtgctc
     3661 tgcgaggctt gtttttgtgc aagcacaaaa aatggactga acaagtcagt ccataagttc
     3721 aaaaccaaat tcaaaatcaa aacaccagca accaaaaatg gtggttgcta tacgttcata
     3781 aattt
//
