LOCUS       NZ_CP117981             4748 bp    DNA     circular CON 26-MAR-2024
DEFINITION  Staphylococcus aureus strain B-41012 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP117981
VERSION     NZ_CP117981.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33246705
            Assembly: GCF_028743615.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4748)
  AUTHORS   Damerum,A.
  TITLE     Staphylococcus aureus B-41012 hifiasm Zymo Research D6300
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4748)
  AUTHORS   Damerum,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-FEB-2023) Microbiomics, Zymo Research Corporation,
            17062 Murphy Ave, Irvine, CA 92614, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Hifiasm v. 0.16.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.0x
            Sequencing Technology             :: PacBio Sequel IIe
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028743615.1-RS_2024_03_26
            Annotation Date                   :: 03/26/2024 01:59:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,685
            CDSs (total)                      :: 2,604
            Genes (coding)                    :: 2,531
            CDSs (with protein)               :: 2,531
            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)              :: 73
            CDSs (without protein)            :: 73
            Pseudo Genes (ambiguous residues) :: 0 of 73
            Pseudo Genes (frameshifted)       :: 37 of 73
            Pseudo Genes (incomplete)         :: 29 of 73
            Pseudo Genes (internal stop)      :: 17 of 73
            Pseudo Genes (multiple problems)  :: 10 of 73
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117981.1.
            Bacteria and source DNA available from Annabelle Damerum, Zymo
            Research, 17062 Murphy Ave, Irvine, CA, United States, 92614.
            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..4748
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="B-41012"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA"
                     /collection_date="2021-08-05"
     gene            54..728
                     /gene="hssR"
                     /locus_tag="PT798_RS13405"
     CDS             54..728
                     /gene="hssR"
                     /locus_tag="PT798_RS13405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501105.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-binding heme response regulator HssR"
                     /protein_id="WP_000249497.1"
                     /translation="MVQCLVVDDDPRILNYIASHLQTEHIDAYTQPSGEAALKLLEKQR
                     VDIAVVDIMMDGMDGFQLCNTLKNDYDIPVIMLTARDALSDKERAFISGTDDYVTKPFE
                     VKELIFRIRAVLRRYNINSNSEMTIGNLTLNQSYLELQVSNKTMTLPNKEFQLLFMLAA
                     RPKQIFTREQIIEKIWGYDYEGDERTVDVHIKRLRQRLKKLNATLTIETVRGQGYKVEN
                     HV"
                     /name="hssR"
     gene            721..2094
                     /gene="hssS"
                     /locus_tag="PT798_RS13410"
     CDS             721..2094
                     /gene="hssS"
                     /locus_tag="PT798_RS13410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501106.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="heme sensor histidine kinase HssS"
                     /protein_id="WP_000477332.1"
                     /translation="MFKTLYARIAIYSITVILFSALISFVLTNVYYHYNLKASNDAKIM
                     KTLKEARQYEQSAKPTHIQQYFKHLGQMNYQIMTIDQKGHKTFYGEPFREDTLSQNAIN
                     NVLNNQDYHGIKDKPFALFVTGFFDNVTDNTVGINFKTKDGSIAVFMRPDIGETFSEFR
                     TFLAVLLMLLLFISISLVIASTYSIIRPVKKLKLATERLIDGDFETPIKQTRKDEIGTL
                     QYHFNKMRESLGQVDQMRQHFVQNVSHEIKTPLTHIHHLLSELQQTSDNTLRQQYINDI
                     YTITTQLSGLTTELLLLSELDNHQHLLFDDKIQVDQLIKDIIRHEQFAADEKSLIILAD
                     LESINFLGNQRLLHQALSNLLINAIKYTDVGGAIDIALQHSHNNIIFTISNDGSPISPQ
                     AEARLFERFYKVSKHDNSNGLGLAITKSIIELHHGTIQFTQSNEYVTTFTITLPNNSL"
                     /name="hssS"
     gene            2257..2700
                     /locus_tag="PT798_RS13415"
     CDS             2257..2700
                     /locus_tag="PT798_RS13415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501107.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LytTR family DNA-binding domain-containing
                     protein"
                     /protein_id="WP_000977023.1"
                     /translation="MMKLNLFINAKETESYIDIHAPKMNDHVQSIINAVNDLGKLHTLV
                     GYIDKEIHIINVSDVITFQVINKNVTAITSNQKFKLKLRLYELEKQLPQHFIRISKSEI
                     VNKYYIEKLLLEPNGLIRMYLKDAHYTYSSRRYLKSIKERLSI"
                     /name="LytTR family DNA-binding domain-containing protein"
     gene            2697..3152
                     /locus_tag="PT798_RS13420"
     CDS             2697..3152
                     /locus_tag="PT798_RS13420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501108.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3021 domain-containing protein"
                     /protein_id="WP_000793162.1"
                     /translation="MKNLKNSLFISLIIGLSLSLFFSMLFADGKYYPLNPQSTIGILYY
                     NHFTETTVMLISIILWLLIGVVFFLGDFIFKYTDWGITKATIMHFITTYVGFLPLAMLA
                     GWFPLTAHYLIIFTIIFIVVYVLIWIIQFFRNKNYVDTINEQLKQLK"
                     /name="DUF3021 domain-containing protein"
     gene            complement(3218..4696)
                     /gene="mqo"
                     /locus_tag="PT798_RS13425"
     CDS             complement(3218..4696)
                     /gene="mqo"
                     /locus_tag="PT798_RS13425"
                     /EC_number="1.1.5.4"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_501109.1"
                     /GO_function="GO:0008924 - malate dehydrogenase (quinone)
                     activity [Evidence IEA]"
                     /GO_process="GO:0006099 - tricarboxylic acid cycle
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="malate dehydrogenase (quinone)"
                     /protein_id="WP_000211363.1"
                     /translation="MTTQHSKTDVILIGGGIMSATLGTLLKELSPEKNIKVFEKLAQPG
                     EESSNVWNNAGTGHSALCELNYTKEGKDGTVDCSKAIKINEQYQISKQFWAYLVKTGQL
                     DNPDRFIQAVPHMSFVIGEDNVAFIKSRVATLKKSVLFEKMKLSQDEEEMKSWVPLMIE
                     GRKSDEPIALTYDETGTDVNFGALTAKLFDNLEQRGVGIQYKQNVLDIKKQKSGAWLVK
                     VKDLENNETTTYESDFVFIGAGGASLPLLQKTGIKQSKHIGGFPVSGLFLRCTNQEVID
                     RHHAKVYGKAAVGAPPMSVPHLDTRFVDGKRSLLFGPFAGFSPKFLKTGSHMDLIKSVK
                     PNNIVTMLSAGIKEMSLTKYLVSQLMLSNDERMDDLRVFFPNAKNEDWEVITAGQRVQV
                     IKDTEDSKGNLQFGTEVITSDDGTLAALLGASPGASTAVDIMFDVLQRCYRDEFKGWEP
                     KIKEMVPSFGYRLTDHEDLYHKINEEVTKYLQVK"
                     /name="mqo"
ORIGIN
        1 gcaaaaatat tttacatgta taataaatga aaaagataag ggagtttata gctatggtgc
       61 aatgtcttgt tgtcgatgac gatcctcgaa tcctaaatta tatagctagc catttacaaa
      121 cagagcacat tgatgcatac acacaaccaa gtggtgaagc tgcattaaaa cttttagaaa
      181 aacagcgtgt cgatattgca gtggtagata ttatgatgga tggtatggac ggctttcaat
      241 tatgtaatac attaaaaaat gattatgata taccagttat tatgttaaca gcgcgggatg
      301 cacttagtga caaagagcgt gcgtttataa gcggtactga cgattatgta accaaaccct
      361 ttgaggttaa ggaacttatt tttagaattc gtgcggtatt acgtcgatat aatatcaatt
      421 caaattcaga aatgactatt ggcaacttaa cgctaaacca atcctatttg gaactccaag
      481 tatctaataa aacgatgacg ttaccgaaca aggaatttca attattattt atgcttgcag
      541 cacgtcctaa gcaaatcttt actcgtgaac aaataataga aaaaatttgg ggctatgatt
      601 atgaaggaga tgagcgaaca gttgacgttc atattaagcg actacgccaa agattaaaaa
      661 aattaaatgc cacacttaca attgaaacag taagaggaca aggctataag gtggagaatc
      721 atgtttaaaa cactctatgc tagaattgcg atttattcca ttacggttat tttatttagt
      781 gcattaataa gttttgtatt aacaaatgtt tactatcatt ataatttaaa agcatctaat
      841 gacgcgaaaa tcatgaagac gcttaaagaa gcaagacaat atgaacaatc agctaaacca
      901 acgcacattc aacaatattt caaacattta gggcaaatga attaccaaat aatgaccatt
      961 gatcaaaaag gtcataagac attttatggg gagccattta gagaagatac tttatcacaa
     1021 aatgctatta acaacgtatt aaataatcaa gattaccatg gtattaaaga taaaccattc
     1081 gcattattcg taactggatt tttcgacaat gtaacagata atactgttgg tattaacttt
     1141 aagacaaaag acggttcaat agcagtattt atgcgtccag atattggaga aacatttagc
     1201 gagtttagaa cattcttagc cgtcttgtta atgttgttat tatttatctc gatttcatta
     1261 gttatcgcat caacctattc aatcattcgt ccagtaaaaa agttaaagct agcgaccgaa
     1321 cgcttaattg atggtgattt tgaaacacct atcaaacaaa cacgcaaaga tgaaattgga
     1381 acattacagt atcactttaa taagatgaga gagtcattgg gacaagttga tcaaatgagg
     1441 cagcattttg tacaaaatgt atctcatgaa atcaaaacac cattaacaca tattcatcat
     1501 ttattaagcg agttacaaca aacttctgat aatacattaa gacaacaata tataaatgat
     1561 atttatacca ttacaacgca gctgagcgga ttaacaactg aattgttgct cttatccgaa
     1621 ttagataatc accaacattt attattcgat gataagattc aagtcgatca actcattaaa
     1681 gatatcattc gacatgaaca atttgctgct gatgaaaagt cgttaattat tttagctgat
     1741 ctagaatcaa tcaatttcct aggaaatcaa cgtttgttac atcaagcatt gagtaattta
     1801 ttaataaatg ctattaagta tacagatgtt ggtggtgcca ttgacatcgc tttgcaacat
     1861 agtcacaaca acatcatttt tacaataagt aatgatggtt caccaattag tccacaagct
     1921 gaagcacgtt tatttgaacg tttttataaa gtgagcaaac atgataatag caatggttta
     1981 ggtcttgcaa ttacaaaatc catcattgaa ttgcatcatg gtacaatcca attcacacaa
     2041 agtaacgagt atgtaaccac ctttactatt acactgccaa ataattcact ttaatctcta
     2101 cctcctgaaa aaacatttct gtttttattt caggaggtat cttttatatt gattagcgct
     2161 ttctagccac ttaacattta atttctacca ttcaacaaaa tttaaatata tcgatggtca
     2221 tttatggttt aataattttg aaggaggcat taacctatga tgaaactcaa tttatttatc
     2281 aatgcaaaag agacggaatc ttatattgat atacatgcac ctaaaatgaa tgatcacgtt
     2341 caaagtatta ttaatgcagt caatgattta ggcaaattac atacattagt cggatacata
     2401 gacaaagaaa tccatatcat taatgtatca gatgttataa cattccaagt tattaataaa
     2461 aatgtaacag ccattacaag caatcaaaaa ttcaaactaa aattacgact ttatgaacta
     2521 gaaaaacagt taccacaaca tttcattcgc atttctaaat cagaaatcgt caacaagtat
     2581 tacattgaaa aattattatt agagccaaat ggacttatac gtatgtatct taaagatgca
     2641 cactacacct attcttctag acgttattta aaatctataa aggagcgctt atcaatatga
     2701 aaaatttgaa aaactcatta tttattagct taatcattgg tttgtccctt tcactgttct
     2761 ttagtatgtt atttgcagac ggcaaatatt atccactgaa cccacaatca actattggca
     2821 tattgtatta taatcatttc acagaaacta ccgtaatgtt gatttctatc attttatggt
     2881 tactcatagg cgtcgtcttt ttccttggag attttatctt taaatacaca gattggggca
     2941 ttactaaagc aactataatg catttcataa caacgtatgt cggattcttg cctttagcaa
     3001 tgcttgccgg ttggtttcca ctaacagcgc attatctaat catattcaca attatcttca
     3061 ttgtggttta tgtattaatt tggataattc aattctttag aaacaagaac tacgtagaca
     3121 ctattaacga acaactgaaa caattaaaat gatttttatt aacaactaaa aaacggtaat
     3181 gtctatcaca ttaaaaaaga cattaccgtt tcgtttatta tttaacttgt aaatacttag
     3241 ttacttcttc attaatttta tgatataaat cctcatgatc tgttaagcga taaccaaatg
     3301 acggcaccat ttctttaatc tttggttccc atcctttgaa ttcatcacga tagcatcgtt
     3361 gtaaaacatc aaacataata tctacagctg ttgacgcacc aggtgatgca ccaagtaatg
     3421 cagctaatgt gccatcatct gacgtaatga cttcagtacc aaattgtaag ttacctttag
     3481 aatcctcagt atccttgatt acttggacac gttgccctgc tgtaatcact tcccaatctt
     3541 catttttagc atttgggaaa aagactctta aatcatccat acgctcatca ttagataaca
     3601 tcaattgtga cactaaatac ttcgtaagac tcatttcttt gatacctgca gataacatcg
     3661 tcacgatatt atttggttta accgatttaa ttaaatccat atgtgaacct gtttttaaaa
     3721 atttaggtga gaaacctgca aatggaccaa ataacaatga acgcttgccg tctacaaaac
     3781 gtgtatctaa gtgcggcact gacattggtg gcgcacccac tgctgctttt ccgtacactt
     3841 tagcatgatg acgatcaatc acttcttgat ttgtacagcg caggaataat ccacttaccg
     3901 ggaaaccacc aatatgtttt gattgtttaa tcccagtctt ttggagtaat ggtaaactcg
     3961 caccgccagc accaataaat acaaaatcag attcatatgt tgtcgtttca ttattttcta
     4021 aatctttaac tttaactagc catgccccag atttctgttt cttgatgtct aatacattct
     4081 gcttatattg aattcccaca ccacgttgct ctaaattatc aaataacttt gcagttaacg
     4141 caccaaagtt aacatctgta ccagtttcat cataagttaa agcaattggt tcatcagact
     4201 tacgaccttc aatcattaac ggtacccaag atttcatttc ttcttcatct tgcgataatt
     4261 tcattttttc gaataaaaca cttttcttta acgttgcaac acgacttttt ataaaagcta
     4321 cattatcttc gccaatgaca aaactcatgt gtggcaccgc ttgaataaag cgatctgggt
     4381 tatctaattg tcctgtttta actaaatatg cccaaaactg ttttgaaatt tggtactgct
     4441 catttatctt aattgcttta ctacaatcaa ctgtgccatc cttaccttct tttgtatagt
     4501 tcaactcgca aagtgctgaa tgccctgtac cggcattatt ccatacattt gaactctctt
     4561 cgccaggttg tgctaatttt tcaaacactt taatattttt ctcaggtgat aattctttaa
     4621 gtaatgttcc taatgttgca ctcataatac cgccaccaat taagatgaca tctgttttgc
     4681 tatgttgtgt tgtcataaca aatacagtcc ccctttttaa aatgaataat ggaacgttcg
     4741 agaaatac
//
