LOCUS       NZ_CP019895             3910 bp    DNA     circular CON 22-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium str.
            USDA-ARS-USMARC-1899 plasmid pSTY2-1899, complete sequence.
ACCESSION   NZ_CP019895
VERSION     NZ_CP019895.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02712198
KEYWORDS    GSC:MIxS; MIGS:3.0; RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium str.
            USDA-ARS-USMARC-1899
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium str. USD...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3910)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Comparative Genomic Analysis of Salmonella Anatum and Typhimurium
            Isolated from Humans and Cattle
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3910)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-FEB-2017) USDA-ARS-U.S. Meat Animal Research Center,
            State Spur 18D, Clay Center, NE 68933, USA
COMMENT     ##MIGS:3.0-Data-START##
            assembly :: Celera Assembler v. 7.0 : Consensus accuracy 100 :
            Quiver version 1
            biome                        :: livestock-associated habitat
            collection_date              :: MAY-2007
            env_package                  :: bovine-associated
            feature                      :: livestock-associated habitat
            geo_loc_name                 :: United States BIFSCo Region 1
            investigation_type           :: bacteria_archaea
            isol_growth_condt            :: Not available
            lat_lon                      :: Not available
            material                     :: ground beef
            project_name                 :: Salmonella typhimurium
            seq_meth                     :: PacBio C3 P5
            annot_source                 :: DIYA
            estimated_size               :: 4856450
            extrachrom_elements          :: 1 plasmid
            finishing_strategy :: complete: 20X coverage: reads >= 10500
            health_disease_stat          :: Not available
            num_replicons                :: 1
            pathogenicity                :: animal
            ref_biomaterial              :: Not available
            ##MIGS:3.0-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider          :: NCBI RefSeq
            Annotation Name              :: GCF_009949275.1-RS_2024_05_22
            Annotation Date              :: 05/22/2024 01:47:38
            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)                :: 3
            CDSs (total)                 :: 3
            Genes (coding)               :: 3
            CDSs (with protein)          :: 3
            Genes (RNA)                  :: 0
            tRNAs                        :: 0
            ncRNAs                       :: 0
            Pseudo Genes (total)         :: 0
            CDSs (without protein)       :: 0
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP019895.1.
            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..3910
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium str. USDA-ARS-USMARC-1899"
                     /mol_type="genomic DNA"
                     /strain="USDA-ARS-USMARC-1899"
                     /serovar="Typhimurium"
                     /isolation_source="ground beef"
                     /sub_species="enterica"
                     /db_xref="taxon:1454639"
                     /plasmid="pSTY2-1899"
                     /geo_loc_name="USA: United States BIFSCo Region 1"
                     /collection_date="2007-05"
     gene            67..1623
                     /locus_tag="AX02_RS00005"
                     /old_locus_tag="AX02_51455"
     CDS             67..1623
                     /locus_tag="AX02_RS00005"
                     /old_locus_tag="AX02_51455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_061390825.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPSGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARYGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSACSPELLLQYR
                     KVMKTVIQGEERLARLGDANPNALKEHKLLQNAKAKNESLSEWSRRIHEGTRYLDKLGR
                     DVISAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQESVLETAEREENEFRYKL
                     QQAESEWKEKYAAFQRTEGYKYVDPTGLDKYREREILAAVSLENTRQKVAEEISVARSQ
                     MLSLEPELNMSGDEKAQMRHELLAEMALEQQQQEEKALRIQQTWVREASRSNERDQDME
                     R"
                     /name="MobA/MobL family protein"
     gene            2079..3098
                     /locus_tag="AX02_RS00010"
                     /old_locus_tag="AX02_51470"
     CDS             2079..3098
                     /locus_tag="AX02_RS00010"
                     /old_locus_tag="AX02_51470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001271364.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(3359..3805)
                     /locus_tag="AX02_RS00015"
                     /old_locus_tag="AX02_51475"
     CDS             complement(3359..3805)
                     /locus_tag="AX02_RS00015"
                     /old_locus_tag="AX02_51475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_021537414.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLAKDSA"
                     /name="conjugal transfer protein TraD"
     Typing          2080..2854
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          68..1620
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.807"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgcgcactta gtagtttctc tccttcgtcg agaaactgtg cgctcctgcg gagggctaaa
       61 aggcagatgg caagctacca ttgcactgtc aaagctggag caaaaggcag tgccttaaaa
      121 catgctgatt acatttccag atccggcgaa tataagagct acaaatcgcg ggaggatctg
      181 gaattttcgt catccggtaa catgccatca tgggcgaaga aaaatcccgc agagctatgg
      241 aaagccgcag atgaatttga acgaaaaaac gggactgcgt accgtgaaat tgagatcgcg
      301 ttaccgcgtg aactgacacg cgaacaacgg atagaacttg ttgaagattt cgtgcaaaag
      361 gaacttggcg atcgccatgc ctaccagtac gcgatccaca atccgtcagg tgcaatcgac
      421 ggaaaggaac agccacacgc gcatatcatg ttttgcgagc ggattaatga tggtattgaa
      481 cgcgatccgc agcaattttt taaacgtgcc aacagcaaat caccagaacg gggaggcgca
      541 aaaaaagcga gtattcccca gacagccgga gagcgaaaag ccgcccttgt tgcgctgcgt
      601 tcccgctggg cagatgtgca gaatgagcac cttgcgcgat acggtcacga gtcgcgcgta
      661 gatcatcgtt ctctgaaaga acagggtatc aatcgcacgc cggaagttca tcttggcccc
      721 gttcaggccg ccagtctcaa tggtgagcag attgttgcaa tccaggaacg gaggaatgct
      781 gagcgggaac tcaagaccgc cagagatgcc gcaaatgcca ttcagcagga acaggagcaa
      841 aagcaaaaaa tcaaggcagt tgagcctgtt cgttcagcct gttcaccgga gttattgctt
      901 cagtaccgca aggttatgaa aacggtcatt cagggagagg aaaggcttgc tcgtttaggg
      961 gatgccaatc ccaatgcgct caaagaacat aagctgcttc agaatgcgaa agctaaaaac
     1021 gaatctcttt ccgaatggag tagacgaata catgaaggga ctcggtattt agacaaactt
     1081 gggcgtgatg ttatttccgc acaaagggag ctacgagagt tacaggaaca acgcaatgct
     1141 ctgaatggga ttcgtggcct gtttcggggg gctgacaaaa gggagattga tgcgcgtatt
     1201 ctggagcaag aaagcgtgct ggaaaccgcc gaacgtgaag agaatgagtt caggtacaag
     1261 ctacagcaag ctgagtccga gtggaaagag aaatacgctg cttttcagcg taccgaggga
     1321 tataagtacg ttgatcctac ggggctggac aagtacagag aacgtgagat tctggccgca
     1381 gtctctttag agaacaccag gcaaaaagtt gccgaagaaa tatccgttgc ccgtagccag
     1441 atgttatctc tggagcctga acttaatatg tctggagatg aaaaagctca aatgcgacat
     1501 gagttactgg cagaaatggc gttggaacag cagcaacagg aagaaaaagc gctgcgtata
     1561 cagcaaacct gggtcagaga ggcatctcgt agtaacgaac gtgatcaaga tatggagcgt
     1621 tgaaaatgta gcaatatcgg gactgcgccc cgaaccccgc caacgtttca cggaacgcga
     1681 aaaaattccg cgtcccgttc accgttttct gatgagaaag tttgctgttt tgacccgttc
     1741 gcccttctga acgctcgaaa cagatcgcgc attgctttcg tgaatagtta tgcagcctcc
     1801 taaaaacaat tctgccgcgt ttttctggtt cttcctggtg tttccttgta tttctgcgtt
     1861 ttttgcgtca gaaagcgtct gagagcgttt taaggggggc gcacaacggg agttatggta
     1921 aatggatcgg ttttgcggga aggctcgaca ggttttgttg ttgggggtag tgtaagcgac
     1981 tgaaaaacaa acgcccctga aattcgtgtc tctccgccaa gattgtcacg agaatacagg
     2041 ggcgaggtcg gtcgataacc tggaaggaat cgtaacacat gagcgccgcg cttcaatact
     2101 tcgaagaaaa tttaccccac cgcccctatc acacggatga tctcgctttc ggccttcgca
     2161 tctccggcaa agggcgtgcg cttcttgcgc ggtacatcca gcagaaccag cctcatgcgc
     2221 agttctggct ggtttttgac gttgaccgcg agggggctgc gattgactgg agcgaccgga
     2281 acgcccccgc gccgaacatc accgttaaaa atcctgtgaa cggacacgct cacctgctct
     2341 acgcactcaa catcgccgtg agaaccgcgc ctgatgcctc ggttaaggcg ctgaaatatg
     2401 ccgcagcggt tgaacgttcg ctgtgtgaga aactttgtgc tgatgtgaac tacagcggcc
     2461 tgatttgcaa aaatccgttc cacctggaat ggcaggtgat ggagtggcgc gaggacgcct
     2521 ataccctcga tgaactggca gattatctcg atttgagcgc ctcagagcgt cgtagcatcg
     2581 ataaacatta cgggatgggg cgaaactgcc acctgttcga aatgacgcgc aaatgggctt
     2641 acagggcgat tcgtcagggc tggccagcgt tctcacagtg gcttgaagcg gtgatccagc
     2701 gtgtcgaaat gtacaatgca tcgcttcccg ttccgctttc actggctgaa tgtcgggcta
     2761 ttggcaagag cattgcgaaa tacacgcaca ggaacttcac gccggaaact ttcgcacagt
     2821 atgtggctga tacgcacacg ccagaaattc aggcagcacg cggtcgcaag ggcgggaagg
     2881 ccaattcgtc agaaaatcag tcggacaaag ggaaaaaaag cgccgctgtt cggtggactg
     2941 ctaacgacga caaacgtcgt agggcgcttg atatgtatat cttgggagcg tcaacggaag
     3001 atattgcagt ggcggttggt gttagcagcc ggactattcg acgctggatg gataattctg
     3061 gagaatggct aaccaagaaa caaataatta aatgttagtt aacaaataag caacactacc
     3121 ccccgttttt tgttaatggt tggttaaatt cgcggacatg aacaagccta tatcagataa
     3181 cagcgccttt cggcgtcttt ttgagcagcg ggctttccgg cggttttctc ctctcagccc
     3241 agcaatggtg cggcttaccg catgattgag gtggtcgtgc tcgccgcagt ctcatgaccg
     3301 agcgtagcga gcgaatgagc gaggaagcac cagggaaccg gaacgtgaac ggaggctctt
     3361 acgcactgtc tttggcgagt agctctttcc cgcgtttttc ccattcctgc catttgggat
     3421 ggttgcgcgg tagctctgcg attcctgcga gtgcgcctac cagttcggca gcactaaact
     3481 ttggttttcc ggttttgctg tccaccagtc ctgccacaat catgaggcct gcggccttgt
     3541 aaagttcatg atcccgcgcc tttcgttctg cccttgcggc tgccttccgt tctgccgcta
     3601 tgattgccgt taccctggct tttgctgcgg ctgctttctc tgcggttttt tctgcccgta
     3661 tcagtgcgga caacgttttt tcatccgtcg ttgttcggtt ttttttctct gccagtaaca
     3721 caagtaatct ctgctgctct gacggtgatt tcagtccgtt gatgtaggca atttttgcac
     3781 ttaaccactc ttcacgattt gtcattctta cctctgcact tttgccgtta atgtgagttg
     3841 ttattgtgca taatatcacc ttgtctgcct gcgtgtgaga ccgtaaaatc atccctgatt
     3901 aattcatgga
//
