LOCUS       NZ_CP034013             4525 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Staphylococcus aureus strain P1D1C1 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP034013
VERSION     NZ_CP034013.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10374685
            Assembly: GCF_009739845.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4525)
  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  JOURNAL   Unpublished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 4525)
  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                   :: 400x
            Sequencing Technology             :: PacBio + Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 02:55:03
            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)                     :: 2,805
            CDSs (total)                      :: 2,723
            Genes (coding)                    :: 2,641
            CDSs (with protein)               :: 2,641
            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)              :: 82
            CDSs (without protein)            :: 82
            Pseudo Genes (ambiguous residues) :: 0 of 82
            Pseudo Genes (frameshifted)       :: 46 of 82
            Pseudo Genes (incomplete)         :: 36 of 82
            Pseudo Genes (internal stop)      :: 30 of 82
            Pseudo Genes (multiple problems)  :: 28 of 82
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034013.1.
            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..4525
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="P1D1C1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed2"
                     /geo_loc_name="Israel: Jerusalem"
                     /lat_lon="31.7732 N 35.1853 E"
                     /collection_date="2017-05-04"
                     /collected_by="Shaare Zedek"
     gene            complement(1..936)
                     /locus_tag="EFD67_RS00015"
                     /old_locus_tag="EFD67_00020"
     CDS             complement(1..936)
                     /locus_tag="EFD67_RS00015"
                     /old_locus_tag="EFD67_00020"
                     /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_053025871.1"
                     /translation="MSTENYSNYLQNKDLDNFSKTGYSNSRLSGNFFTTPQPELSFDAM
                     TIVGNLNKTNAKKLSDFMSTEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWDRRN
                     MRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKAVKKTI
                     FYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVMSEHLWRVEIELKRDMVDYW
                     NDCFDDLHILKPDWTTPEKVKEQAMVYLLLNEEGTWGKLERHAKYKYKQLIKEISPIDL
                     TELMKSTLKENEKQLQKQIDFWQREFRFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(1478..1933)
                     /locus_tag="EFD67_RS00020"
                     /old_locus_tag="EFD67_00025"
     CDS             complement(1478..1933)
                     /locus_tag="EFD67_RS00020"
                     /old_locus_tag="EFD67_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001611965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF334 domain-containing protein"
                     /protein_id="WP_053038409.1"
                     /translation="MTEATKDFRDSAFKTHNDFTDILKKKLDKVETDELANIIGRDIYK
                     VRDENKRMLQEVRESHEHYKKRQNELFKGIGAMLLVFMLFALIMTIGSDFMAFLHLDVL
                     QKAIASQIKASKGFVAFLWYIAYGIPYLVGIVGFIILYEWIRAKFHE"
                     /name="DUF334 domain-containing protein"
     gene            complement(1902..2867)
                     /locus_tag="EFD67_RS00025"
                     /old_locus_tag="EFD67_00030"
     CDS             complement(1902..2867)
                     /locus_tag="EFD67_RS00025"
                     /old_locus_tag="EFD67_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002467288.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_156667962.1"
                     /translation="MATTKLGNTKSASRAINYAEKRAVEKSGLNCDVDYAKSAFKQTRA
                     LYGKESGIQAHTIIQSFKPGEVTPEQCNQLGLELAEKIAPNHQVAIYTHTDREHVHNHI
                     VINSIDLETGKKYQSNKQQRELVKRENDNICRSHGLSVPERDTAHLRYTQAESALIDKG
                     KTSWKDELREQIENAKAHTSDFKSFSERLEKEGIEFKVRGKNVSYKPENVNKWVRGKTL
                     GQDYDKGALEHEFERREREEERQSEQDPVTAYTEQFDVDWDAVEHNAEQLRKTRIRRTE
                     KTKQAHHQISGRDTREPERTRERTKTTQIEFDRGDEGFSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2854..3054)
                     /locus_tag="EFD67_RS00030"
                     /old_locus_tag="EFD67_00035"
     CDS             complement(2854..3054)
                     /locus_tag="EFD67_RS00030"
                     /old_locus_tag="EFD67_00035"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_053017864.1"
                     /translation="MEKPKLRLCFNIVVAIVFISYLGLIIFTDFPDAKWSLGFIVLITI
                     IYIIRDKLAPKKKRSDDNGNN"
                     /name="hypothetical protein"
     gene            complement(3036..3419)
                     /gene="mobC"
                     /locus_tag="EFD67_RS00035"
                     /old_locus_tag="EFD67_00040"
     CDS             complement(3036..3419)
                     /gene="mobC"
                     /locus_tag="EFD67_RS00035"
                     /old_locus_tag="EFD67_00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002449121.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_053025869.1"
                     /translation="MSEQNKFVASDETVGKNHKPNRKEPKQISFRVSELEYEKLQRSAE
                     TLNMSVPSFVKKKAQGSRLVAPKFDKETRQSIAKDLSRLGANANQIAKYCNQHQYDAPN
                     YSALERNINELRERLDEIWKNLN"
                     /name="mobC"
     gene            complement(3749..4396)
                     /locus_tag="EFD67_RS00040"
                     /old_locus_tag="EFD67_00045"
     CDS             complement(3749..4396)
                     /locus_tag="EFD67_RS00040"
                     /old_locus_tag="EFD67_00045"
                     /EC_number="2.3.1.28"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002331392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type A-7 chloramphenicol O-acetyltransferase"
                     /protein_id="WP_002489529.1"
                     /translation="MTFNIIKLENWDRKEYFEHYFNQQTTYSITKEIDITLFKDMIKKK
                     GYEIYPSLIYAIMEVVNKNKVFRTGINSENKLGYWDKLNPLYTVFNKQTEKFTNIWTES
                     DNNFTSFYNNYKNDLLEYKDKEEMFPKKPIPENTIPISMIPWIDFSSFNLNIGNNSNFL
                     LPIITIGKFYSENNKIYIPVALQLHHAVCDGYHASLFMNEFQDIIHKVDDWI"
                     /name="type A-7 chloramphenicol O-acetyltransferase"
     ARG             complement(3753..4396)
                     /name="catA"
                     /gene="catA"
                     /gene_name="type A-7 chloramphenicol O-acetyltransferase"
                     /tool="amrfinderplus"
                     /drug_class="PHENICOL"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(3750..4396)
                     /name="Staphylococcus intermedius chloramphenicol
                     acetyltransferase"
                     /gene="Staphylococcus intermedius chloramphenicol
                     acetyltransferase"
                     /gene_name="chloramphenicol acetyltransferase (CAT)"
                     /tool="rgi"
                     /drug_class="phenicol antibiotic"
                     /identity="98.14"
                     /coverage="100.0"
     Typing          3391..3627
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="81.667"
                     /coverage="100.0"
                     /evalue="8.37e-48"
     Typing          complement(2..936)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.893"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1906..2867)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="82.866"
                     /coverage="100.0"
                     /evalue="4.390000000000001e-169"
ORIGIN
        1 ttacttccaa aatctaaatt cacgttgcca aaaatcaatc tgtttttgca attgcttttc
       61 attctctttt aaagtcgatt tcattaattc cgttaaatca attggagata tttctttaat
      121 caattgcttg tatttatatt tagcatgtct ttcaagtttt ccccacgtgc cttcttcatt
      181 cagtaacaaa taaaccattg cttgttcttt tactttttct ggtgttgtcc aatcgggttt
      241 caaaatgtgt aaatcatcaa agcaatcatt ccagtaatca accatatctc ttttcaattc
      301 aatttctaca cgccataaat gttcagacat aacttcaaca tcggcgttat ctttacgttc
      361 ttgtttttta ttataaattc taataaatct atcactgtca cgaacaccaa aatattttgt
      421 ttctggctta ccattacgac cataaaaaat agttttctta actgctttat cagtcattgc
      481 gtagtaatca ctcaaatcat cttcaaaatc aaaagctaaa tctaacctcg taaaaccgtc
      541 atcttccatg tagtcgataa tattttgttt taaccaaagc atttcttcat gtgtgagttt
      601 atttggatta aattcaacac gcatattacg tctatcccaa ctatctgctt ttactttgtc
      661 atattcgata taaacctttt cttgaagtgc tttagcttta aactttgttt gtaatatatc
      721 ccaaagcctt atttgtggct ctgtactcat aaaatcagat agctttttag cgttagtttt
      781 gttcaaattc ccaacgattg tcatagcatc aaaacttaat tctggttgag gggtggtaaa
      841 aaaattacca cttaaccggc tattagagta gccggtttta gaaaaattgt ctaaatcctt
      901 attttgtaag taatttgaat aattttctgt actcataaaa atcgactcct taattatttt
      961 taagaagtcg cccacccaaa tataactctt gatgtatgtt taaatatcgt ttaatatcta
     1021 gatatacaaa aattataaaa tacaccgaat atgttttttc ttttggataa gtcgcattca
     1081 caaactttgg tcagggagtg agggcgactt ctttttttat tttgttatta atataacact
     1141 atgcaaaggc ttggtctatt tagactaagt cttttctttt tgttgcatta ttccaatttc
     1201 cttattggtc ggaaccaaca gggctttatg tgttgttgtg ttggtgtttc attgggatta
     1261 atcccaaatc aaccccaccc aacacgctaa tcaagttagc taacacatag cccattccaa
     1321 ccaataagtt ttctcggcat aatagcgtgc ttttgctata attagtaata ggagttgtaa
     1381 ctccttctct gaattactcc caaaagttta gcaattctgt tattaattct gttaacgctc
     1441 ttaataagtt aagaacactt attaagagtt tttttattta ttcatgaaac tttgctctta
     1501 tccattcata caagataata aaaccaacta taccaactaa ataagggatt ccataagcaa
     1561 tataccaaag aaatgctaca aagcccttag acgcttttat ttggcttgct atggctttct
     1621 gcaatacgtc caaatgtaaa aatgccataa agtcactacc aattgtcata atcaaagcaa
     1681 ataacataaa gactagcaac atagcaccta tgcccttaaa taactcattt tgcctttttt
     1741 tataatgttc atgagattct ctaacttctt gcaacatacg tttattttca tcacgtactt
     1801 tataaatatc tctgcctatg atgttagcta attcatctgt ttccacttta tctaatttct
     1861 ttttgagtat atctgtaaag tcattatgtg tcttgaatgc actatctcga aaatccttcg
     1921 tcgcctctgt caaattcgat ctgagttgtt tttgttcgtt ctctcgtgcg ttctggttct
     1981 cttgtatctc tgccagatat ttgatgatga gcttgttttg ttttttcagt tcgtctaatt
     2041 cttgtctttc taagttgctc tgcgttatgc tcgacggcat cccagtcgac gtcgaattgt
     2101 tctgtgtacg ctgtgactgg gtcttgttct gattgtcgtt cttcttctct ttctcgtctt
     2161 tcaaactcat gttctaacgc ccccttatca taatcttgtc caagtgtttt accacgtacc
     2221 catttattga cgttctcagg cttataggaa acgtttttac ccctcacctt aaattctata
     2281 ccttctttct ctaaacgctc tgaaaagctc ttaaaatcac ttgtatgagc ttttgcattt
     2341 tcaatctgtt ctcgcaattc atctttccat gatgttttac ctttatctat caatgcactt
     2401 tctgcctgcg tatatctcaa atgtgccgta tctcgttctg ggacactcaa accatgagag
     2461 cgacatatat tgtcgttttc tcgttttacc agttctcgtt gttgcttgtt actttggtat
     2521 ttttttcctg tttctaagtc aattgaatta atcacaatat gattgtgtac atgttctcta
     2581 tctgtatgtg tatagattgc tacttgatga ttaggtgcaa tcttttctgc gagttccaaa
     2641 cctaattgat tacattgttc tggcgttact tcgccaggtt tgaacgattg gataatcgta
     2701 tgtgcttgta tgccactttc tttgccatat aacgctctgg tttgtttgaa tgctgatttc
     2761 gcataatcta catcgcaatt taaaccactt ttttcaacag ctcttttttc tgcatagtta
     2821 atcgctctac tcgctgattt agtattacct aatttagttg ttgccattgt catcacttcg
     2881 tttcttttta ggcgctagtt tatctctaat aatataaata attgttatta aaactataaa
     2941 acccaaagac catttggcat ctggaaaatc agtaaaaatt attaatccta aataactgat
     3001 aaacacaata gcaacaacaa tattaaaaca aagtcttaat ttaggttttt ccatatttca
     3061 tccaaccttt cacgtaattc attaatatta cgttctaatg cgctataatt cggagcgtca
     3121 tattgatgtt gattgcaata ctttgcgatt tgattagcat tagcacctaa tctactcaaa
     3181 tctttagcaa tcgattgtcg cgtttcttta tcaaatttag gtgcgaccaa tcgactgcct
     3241 tgtgcctttt tcttcacgaa agaaggcaca ctcatattca aagtttcagc tgatcgctgc
     3301 aacttttcat attcgagttc gctcacacga aaactaattt gtttcggctc tttacggttg
     3361 ggtttatggt ttttcccaac agtttcatcg ctagccacaa atttattttg ttcgctcatc
     3421 aaatcccacc acgctttctt cgaaagtaat tacttaatat aaatctagct tacagggtaa
     3481 gccagatttt atcaagtaat tatttggttt ggcaagcgtc gtatattcta gccacttcgt
     3541 tctgaatata ccggcttgat gggattatat cccataccct ttatgttttt gctaacgcaa
     3601 aaaatgagtg gcaaagtgct agccactcat agttcaagac ctaattcaaa atcaaaacct
     3661 atgcaaccaa aaatgtggtt gctatacgtt cataaatttt atgatcactt gcgtgtataa
     3721 aattaaattc actcccaaaa tctaaaaact aaatccaatc atctacctta tgaattatat
     3781 cttgaaattc attcataaat aatgaagcat ggtaaccatc acatacagca tgatgaagct
     3841 gcaaagcaac tggtatataa attttattat tctcactata aaatttacct atcgtaataa
     3901 taggcaataa aaagttgcta ttgttaccaa tgtttaaatt aaatgaacta aaatcaatcc
     3961 aaggaatcat tgaaatcggt atggtgtttt caggtatcgg ttttttagga aacatttctt
     4021 ctttatcttt atattcaagc aagtcatttt tataattatt ataaaaagaa gtgaagttgt
     4081 tatcagattc agtccaaatg ttagtaaatt tttcagtttg cttattaaaa actgtataca
     4141 aaggatttaa cttatcccaa taacctaatt tattctcact attaattcct gttctaaaca
     4201 ctttattttt atttacaact tccataattg cataaatcaa agaaggataa atttcatatc
     4261 ctttcttttt tatcatatct ttaaacaaag taatatcaat ttctttagta atgctatacg
     4321 tagtttgctg gttaaaatag tgttcaaaat attcttttct atcccaattt tctaatttga
     4381 taatattaaa agtcatatat aatttcctcc taaattttaa atctttatat ttaggaggaa
     4441 taatcctctg attttttcat acgttatgtc accccgtaaa tattaattat actgaatcag
     4501 caatttttat aaaataaaac ttatt
//
