LOCUS       CP049517                7240 bp    DNA     circular BCT 24-SEP-2020
DEFINITION  Staphylococcus aureus strain pt213 plasmid pER05686.5A.1, complete
            sequence.
ACCESSION   CP049517
VERSION     CP049517.1
DBLINK      BioProject: PRJNA470993
            BioSample: SAMN12331030
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 7240)
  AUTHORS   Caban,A.B., Pak,T., Kumaresh,A., Dupper,A., Chacko,K.,
            Sullivan,M.J., Altman,D.R. and van Bakel,H.
  TITLE     PathoSPOT genomic surveillance reveals prolonged under the radar
            outbreaks of nosocomial methicillin resistant S. aureus bloodstream
            infections
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7240)
  AUTHORS   Caban,A.B., Pak,T., Kumaresh,A., Dupper,A., Chacko,K.,
            Sullivan,M.J., Altman,D.R. and van Bakel,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-FEB-2020) Genetics and Genomic Sciences, Icahn School
            of Medicine, One Gustave L. Levy Place Box 1498, New York, NY 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2.3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 341.205967622081x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 02/28/2020 16:31:38
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 2,962
            CDSs (total)                      :: 2,879
            Genes (coding)                    :: 2,797
            CDSs (with protein)               :: 2,797
            Genes (RNA)                       :: 83
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 82
            CDSs (without protein)            :: 82
            Pseudo Genes (ambiguous residues) :: 0 of 82
            Pseudo Genes (frameshifted)       :: 50 of 82
            Pseudo Genes (incomplete)         :: 25 of 82
            Pseudo Genes (internal stop)      :: 20 of 82
            Pseudo Genes (multiple problems)  :: 13 of 82
            ##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..7240
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="pt213"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pER05686.5A.1"
                     /geo_loc_name="USA:New York City"
                     /lat_lon="40.7903114 N 73.9528738 W"
                     /collection_date="2016"
                     /collected_by="Mount Sinai Hospital"
     gene            complement(14..1159)
                     /locus_tag="FPO76_00005"
                     /pseudo=""
     CDS             complement(14..1159)
                     /locus_tag="FPO76_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501031.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /name="helix-turn-helix transcriptional regulator"
     gene            1765..2568
                     /locus_tag="FPO76_00010"
     CDS             1765..2568
                     /locus_tag="FPO76_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501032.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CHAP domain-containing protein"
                     /protein_id="QNZ14949.1"
                     /translation="MKKIATATIATAGFATIAIASGNQAHASEQDNYGYNPNDPTSYSY
                     TYTIDAQGNYHYTWKGNWHPSQLNQDNGYYSYYYYNGYNNYNNYNNGYSYNNYSRYNNY
                     SNNNQSYNYNNYNSYNTNSYRTGGLGASYSTSSNNVQVTTTMAPSSNGRSISSGYTSGR
                     NLYTSGQCTYYVFDRVGGKIGSTWGNASNWANAAARAGYTVNNTPKAGAIMQTTQGAYG
                     HVAYVESVNSNGSVRVSEMNYGYGPGVVTSRTISASQAAGYNFIH"
                     /name="CHAP domain-containing protein"
     gene            complement(2586..2828)
                     /locus_tag="FPO76_00015"
     CDS             complement(2586..2828)
                     /locus_tag="FPO76_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501033.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QNZ14950.1"
                     /translation="MTKLIENLKASIFVSTLTKNLSMYSRFDMPKFGCVNGCMLFILYY
                     RVNRIGENRNFEIFTNSIFFIEIKKANKALETLLA"
                     /name="hypothetical protein"
     gene            complement(3002..4402)
                     /gene="nhaC"
                     /locus_tag="FPO76_00020"
                     /pseudo=""
     CDS             complement(3002..4402)
                     /gene="nhaC"
                     /locus_tag="FPO76_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501034.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Na+/H+ antiporter NhaC"
                     /name="nhaC"
     gene            complement(4497..5577)
                     /locus_tag="FPO76_00025"
                     /pseudo=""
     CDS             complement(4497..5577)
                     /locus_tag="FPO76_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501035.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="octopine dehydrogenase"
                     /name="octopine dehydrogenase"
     gene            5824..6245
                     /locus_tag="FPO76_00030"
                     /pseudo=""
     CDS             5824..6245
                     /locus_tag="FPO76_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501036.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4870 domain-containing protein"
                     /name="DUF4870 domain-containing protein"
     gene            6480..6980
                     /locus_tag="FPO76_00035"
     CDS             6480..6980
                     /locus_tag="FPO76_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501037.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CHAP domain-containing protein"
                     /protein_id="QNZ14951.1"
                     /translation="MKKLVTATTLTAGIGTALVGQAHHADAAENYTNYNNYNYNTTQTT
                     TTTTTTTTTSSISHSGNLYTAGQCTWYVYDKVGGEIGSTWGNANNWAAAAQGAGFTVNH
                     TPSKGAILQSSEGPFGHVAYVESVNSDGSVTISEMNYSGGPFSVSSRTISASEAGNYNY
                     IHI"
                     /name="CHAP domain-containing protein"
ORIGIN
        1 aaatgtctat taaaattgtg gctactatct tgcctctttc agtactcgtt aacaattcct
       61 tatattcatg tttaatacga aatactacat ttacattgta attcactatc ttttgaagta
      121 ataaagtgat ttgttcaatc gatagctcat tgcttgtgtc gattgtaaca attatatgca
      181 agttttcaat taacctaatc tttgaatgat tttttaatag tataataatc catccaataa
      241 aaattacttc ctttaatata aatgtttttt aggttgatac atttgaccct ttttgtaggt
      301 tcaaaaggta tatcaatctc gcgcatactt gaagaacttt gattagtatt atcaaataat
      361 tcaattatat tttttatcaa tttcaactaa ttgggaatgg ttaattgaat gagatgttgg
      421 actatatctt tttctaatta atttaggagt gttaccatac gtttctttaa agaggtgtat
      481 aaaacgagaa taatgattaa aaccatgact acttgcgatt tcttcaatag gcttcttaga
      541 agttaaaata tcaattaagc aatgctccag tctaatatga tttaaatatt gaataaaatt
      601 actataaggt gtcgctttaa acatgtcact taaagctttg tttgtaatac taacttgatt
      661 aatgacatct ttcctattta tctttttatg gtggttgttt gttaataatc gtgcacttct
      721 tcggctacta aatgacgact accatcgtat gtatttaatg acattaattc aacacacatg
      781 taattaataa tcttatcatt agcattataa gactgttgtt taattttgct gtagattaaa
      841 tacttaatca agattctaaa agtgctagca acctcatttg ttaatatctt gccacgcatc
      901 atatagtttg cattcataaa cttcaaaaat gtctttgcac ttacttcaac aacacaacat
      961 acactatcat catgaccatc aatttgatac aaatcataca acataataac ggtgacatca
     1021 tttcttttta catcatattg ttgtagattg attgaaacta cacctgtacc ttgtagccaa
     1081 tatataattt ttaagttcgc ttcttcacac tactcatttt catactttta taaatatgta
     1141 gtgaataatt atctgtcatc ttatcctcac atatacaaat atattgattt actcctgttt
     1201 gtctttctca aatcaattgt caacatctaa taatcactac caattatatc gccacatgtt
     1261 ttttagcagt aacaaaacat aagtcgatta tatccaataa tacttttatt aaaacatttt
     1321 tttatgctaa attaggatat tttatccatt aaatatacat tttcatccaa ataccaaagc
     1381 tttcataatc atagaaactt gatcgttcgt gtcgaatttt tatgcatttt ctgattaaaa
     1441 gtcctatatt atgcacaaaa tatacattta gaattttcag taatattaca aatttgtaac
     1501 agacttattt tcgaaacatt cagttttcac aaagaatgcc gtagttataa gttttgcaaa
     1561 atgcaaattt ctatactttt aaaattctat tgtgtcaaga tattagcaaa aaattacaaa
     1621 acgttaacaa agcacacaag gacgctaatt tctgttatag tctttcttgt cgtttaatta
     1681 cgagagataa cttataacat taattttgtc acacggacat tacgaaaatt ttagatttaa
     1741 aatttttagg aggatatttt taaaatgaag aaaatcgcta cagctactat cgcaactgca
     1801 ggattcgcta caatcgcaat tgcatcagga aatcaagctc atgcttctga gcaagataac
     1861 tacggttata atccaaacga cccaacatca tatagctata cttacactat tgatgcacaa
     1921 ggtaactacc attacacatg gaaaggtaac tggcatccaa gtcaattaaa ccaagataat
     1981 ggctactaca gctattacta ctacaatggc tacaataact acaacaatta caacaatggt
     2041 tatagctaca ataattacag ccgttacaac aactactcaa ataataatca atcatataac
     2101 tacaataact ataatagtta caacacaaac agctaccgta ctggtggttt aggtgcaagc
     2161 tacagcactt caagcaacaa tgttcaagta actacaacta tggctccatc atcaaatggc
     2221 cgttcaatct caagtggtta tacttcagga cgtaacttat acacttctgg tcaatgtaca
     2281 tactacgtat ttgatcgtgt aggtggtaaa atcggttcaa cttggggcaa tgcaagtaac
     2341 tgggctaacg cagctgcaag agctggttac acagtgaaca atacaccaaa agctggtgca
     2401 attatgcaaa caactcaagg tgcatacggt cacgttgcat acgttgaaag tgttaacagc
     2461 aatggttcag taagagtttc agaaatgaac tatggttatg gcccaggtgt tgtaacttca
     2521 cgtacaatct cagctagcca agctgctggt tataacttca ttcactaatt agtgatggct
     2581 atgttttacg ccaacaaggt ttcaagagcc ttgttggctt ttttaatttc tatgaaaaaa
     2641 atcgaattgg taaaaatctc aaaatttcga ttttcaccaa tccgattcac tctgtaataa
     2701 agaataaaca acatacagcc attgacacac ccaaatttag gcatgtcaaa tcggctatac
     2761 attgataaat ttttagttaa agtacttaca aatatacttg ccttcaaatt ctcaattaat
     2821 ttagtcatta caaatcatga cataaaactt acattacata tatcaacatg ttccgctaca
     2881 aaacatattc agtatatgta tagaggatat ttattctaag ttaaaacctt ttcaaattat
     2941 aaccgctaca attataaatg attaaagtgt ttcaacatat tatatatatt ccacgctcac
     3001 attaagttaa acgtgaattc gatgactttt taatacctat ccctgtaaaa ccatagataa
     3061 ttgctataat tgcgcataaa taacatggta ctgtccacat gaaaaattct ccaacagaga
     3121 catgaagttg attcgtatag taaatacctg atgttcccca tggtattaaa ggtaagacca
     3181 tcgtacttga gtcttcaagt gttcttgata aaacggaacg agagacttgg tatttttcga
     3241 acaaatcttt cattaacaca ccgaccataa taattacaat cgaagcaaca cctgcagcga
     3301 atacaagcgc aatacaacaa ataacagtaa tacatattaa acttcctaca gaatggatgc
     3361 ctttagaaat agtagttaat aagacttcta aacatcctgc tttttctaca atacctgcaa
     3421 atgcatatcc gcaaaatatc gttactaata tttgggtcat actcatcata ccaccctgtt
     3481 ctaacaagct tttcacactg gatgaaatat gagactgatg tatcattgag tcgttaaaac
     3541 cactaaatgt tgcttttgaa accatctgtc attttgaaat gatgattaaa agtccccact
     3601 ataatggcag aaaagcttga tattaccata gctggcactg tagccatttt aaatagcaaa
     3661 caaacaatga tcacaattaa gggaacccag acccatatgt taatttgata aatctgtgca
     3721 agctctgata acaaagtttg aatctgttta tcatttgaat gccctttaaa ttgaaatcca
     3781 gcaataaacc atactaataa acctatgatt gatgcaggta tcgtcgtcca catcatcgaa
     3841 tgtatatgtt taaatatatt aactttagta acaagtgccg ctaaattagt tgtatctgat
     3901 aatggtgaca ttttatcgcc aaacacagcc cctgctataa tagcacccgc tgccatccct
     3961 ggaggaatcc ccaattgatt accaatagaa ataagtgcaa tccctgcagt tgatgcagag
     4021 ccccatgctg taccagttgc tacagatgta acagcactta taaaaaaggc tgatattaaa
     4081 aaatagcttg gattcaataa atctaagcca taataaatca aggctggcac tgtgccagaa
     4141 aacatccaac tgcctactat aattcctacc gctagtataa ttaaaattgc aggcattgca
     4201 gtatttaaac gttctgcaat gcctttttct aaatcttgcc atgttaagct acacgttttg
     4261 caatccatgt ggcatatgct gaggcaataa ttaataatac ttgaattgga atatcaaaaa
     4321 acacaaagcc tgttacaaca acaataacca ttacaatcat tgtcgaaatt gattctaaaa
     4381 aggttggttt tcttttcatc atctatcgtc cccttcgctt attgatgaga aacctctttt
     4441 cttcaattta ttgcttttgc ataatgctat atccttttct atcttcaagc catcatttat
     4501 tttaaatatt tttctaaatc aagcttatct aaaccaattt cttcaactgt taagccttcc
     4561 tcaaagaagt ctctctctaa aatggttgat gcaattacaa ttactgcatc tatatttggt
     4621 gtcggtacat caataacacg acctaagctt gaccatagta ctaaaccata tgcaatatct
     4681 tcagttaaat atctgctttc tacatgattt ggtcctggaa tttgtgaaat actgggcttg
     4741 tattaaacaa acgatttaat ggttcatctt ctttatcacg ttctaaataa ccacgttcaa
     4801 tacgtgattc tttagctgtt gataattcaa aacctaatct acggcctaaa tttaaacgtt
     4861 ctaattcgat tgcatgaagt aatctaactg tatgtttagt aattccttct ttatataaag
     4921 cgaactcgcc agcataatca atgcgaccga cattcaataa tgttggtcct ggatgcactt
     4981 caggattacc attttcaaga tttgttttaa ttaagctttc ctcttttact aaatgatcat
     5041 aaatacttga aactttgtca taacaatcat ttagacagct tctatcatat gttgaaaaga
     5101 agatacgacg tacatttaga gataaatcaa ctgctgcatt ttcaaaatcg acacgcgtac
     5161 catacgtcaa cgtattagct tccgctagtt gtggttttgt ttcaatatgt ctatcttcta
     5221 aaacattcat aaaacgaatt gaccccattg ctgcagccat gttgaagaat atcaactgat
     5281 tatcagttac atgctctgcc attacatcag cataatactc tatgtatgaa gatggaataa
     5341 tcacttgaac aatttcagca tcttttaaac atattccata tcatcactaa tatcagtgaa
     5401 ttttacgaaa cgttcatcac cttcattatt aaaatcaaat ccgccctttt cgattgcgtt
     5461 ttgaaactta cttatagatt gattacgaca atataattta acatcgtggc ctttgctcac
     5521 catatctact gctgccgtaa ctgcgccatt tcctgatcct acaattgcta ttttcataaa
     5581 caaccctctt tctatctttg gttaaaatta aaaacaaatt atacgtaaga caatataaaa
     5641 atgatgcgaa ttcattacgc atcattataa atgttaagta tatataacct taaattaacc
     5701 tatttaaacg ccgacgtcca ccaattattt ttatttttaa taattgttta ataaacatgt
     5761 ttatttttga ttatattttg ttatagttaa agataatatt acattttcaa aggagtgtct
     5821 aatatgacaa ctgaaatgaa cgacgtaaca aatcatcaac cgaatcgcaa atccaatgat
     5881 gagaacatta tggcgatgct tatctattta ttaagtttat tcacatctat tattggtcca
     5941 ctgataatat ggttattgaa aaaagatgaa tcgaaactag ttgatcgtgc tggaaaaaat
     6001 tatcttaact atacgatttc ttatattatt tggtctatcg ttttagtcgt tatcacttta
     6061 ataggcgttt tcctaattgc taccgatatt agtttcatta tcattatagg tttcatcatt
     6121 acatttatcg gtatttatcc atattcgctt tctcaatatt atcttttgta ttcacaatta
     6181 ttgcgtgtgt caaatattat aatggccaag aatatgtaat acctttaaca attcgattta
     6241 tttaaacata ttacaaataa attttcctat taattatctg ttaatctcat tgtaactttg
     6301 actaattttt attacaaaat tagtcaaagt ttttttattc ttttacaaat caataacatt
     6361 cccacaagaa gcattaattt tgttaaagta actattgtca tcaattcgag atgtgagaat
     6421 aaaacagtcg ctacgtttta tttataaaaa aagatataga actttggagg actttattca
     6481 tgaaaaaatt agtaacagca actacgttaa cagcaggaat cggtacagca ttagtaggtc
     6541 aagcacatca tgcagatgct gctgaaaatt atacaaatta caacaactat aactacaaca
     6601 cgactcaaac tacaacgact acaacaacta cgacaactac atcatcaatt tcacattctg
     6661 gtaacttata cactgcagga caatgtactt ggtatgtata tgataaagta ggcggagaaa
     6721 tcggttctac ttggggaaat gctaataatt gggctgctgc tgcacaaggt gctggattca
     6781 cagtaaatca tacaccttct aaaggcgcta tcctacaatc ttctgaagga ccatttggtc
     6841 acgttgcata tgtagaaagt gtaaacagtg atggttcagt tacaatttca gaaatgaatt
     6901 atagtggcgg acctttctca gtaagttcta gaactatttc tgcaagtgaa gcaggtaact
     6961 acaactacat ccatatttaa tataaacacg atgatacata ttgtcttgaa acttaattct
     7021 agtacatatg tcatcaaaac tttgagcttt cctttatagg agaagctctt tttttgctat
     7081 ttttcgttgc cacctactta tttatatttc ccccatattt ataatatttt tttctaatac
     7141 tattaacttt aaaactacgt tatctaattt aattgatcca gtttttccac attacaaaat
     7201 tcatagttct acagtgccta agttatatca cctccatcaa
//
