LOCUS       CP082744                4633 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            strain CVM N16S070 plasmid pN16S070-4, complete sequence.
ACCESSION   CP082744
VERSION     CP082744.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN08113949
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4633)
  AUTHORS   Li,C., Tyson,G., Hsu,C.-H., Harrison,L., Strain,E., Tran,T.-T.,
            Tillman,G., Dessai,U., McDermott,P. and Zhao,S.
  TITLE     Long-read sequencing reveals evolution and acquisition of
            antimicrobial resistance and virulence genes in Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4633)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4633)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 671x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/31/2021 18:30:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,994
            CDSs (total)                      :: 4,872
            Genes (coding)                    :: 4,744
            CDSs (with protein)               :: 4,744
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 42 of 128
            Pseudo Genes (incomplete)         :: 85 of 128
            Pseudo Genes (internal stop)      :: 24 of 128
            Pseudo Genes (multiple problems)  :: 20 of 128
            CRISPR Arrays                     :: 3
            ##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..4633
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium var. 5-"
                     /mol_type="genomic DNA"
                     /strain="CVM N16S070"
                     /serovar="Typhimurium var. 5-"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:1620419"
                     /plasmid="pN16S070-4"
                     /geo_loc_name="USA:NM"
                     /collection_date="2016"
                     /collected_by="FDA"
     gene            52..891
                     /locus_tag="CWX32_024910"
     CDS             52..891
                     /locus_tag="CWX32_024910"
                     /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="UAG07353.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(1619..1852)
                     /locus_tag="CWX32_024915"
     CDS             complement(1619..1852)
                     /locus_tag="CWX32_024915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="UAG07354.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1859..2419)
                     /locus_tag="CWX32_024920"
     CDS             complement(1859..2419)
                     /locus_tag="CWX32_024920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="UAG07355.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(2388..3107)
                     /locus_tag="CWX32_024925"
                     /pseudo=""
     CDS             complement(2388..3107)
                     /locus_tag="CWX32_024925"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3097..3420)
                     /locus_tag="CWX32_024930"
     CDS             complement(3097..3420)
                     /locus_tag="CWX32_024930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="UAG07356.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3483..3674
                     /locus_tag="CWX32_024935"
     CDS             3483..3674
                     /locus_tag="CWX32_024935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="UAG07352.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3763..3847)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          3858..4413
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.907"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1522..3107)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcgttagatc tcaagacaat catgcatagt gagcatacac aggagccgaa cttgcttaca
       61 ctgttcatct tttttgtttt attaatagct gcatgtttct tttgttttgc tccaccacga
      121 agaggatatg acagaaatga gatcattcca tacaaaataa aactatcaat aaataaatat
      181 cgcctttaca tatactcatc gggaaaggta agacaatacc ttttattttt agttatttta
      241 tcactgtact actccatagc ggaaccattt aagtctgagt taataaaaaa catatcatat
      301 tcactgatgg ctgcatttat ttttgataca gggcttaatt ttagcaagga gaatataact
      361 aaaggggtga tttcaacaag gtggcataat gacctatatt catcatttga gagaatgaaa
      421 gcaattaata aaatttacta cccatccaac aaagagataa acacagaagg tctatccaaa
      481 gccatcacat catctctttt caatgatgac gcgaactcgt tcgcaaagag agattttcgc
      541 ttgatgtggg acttatcttc tgaaaaatat ctttcctata aagaaataat aataagaaaa
      601 ggcgataagc ttgacgctgt atgcttgaga tttataaatg atgactacaa gtttttagtt
      661 aatttcaaca gagatgaaga ggttttcaaa tactttccat ctataatgca accttcactc
      721 aaaacatata gagcgttatc aagactagta aactcaatca aagatccttc tagatttaag
      781 ttcacgacag agtcattaga aatggagtta ctagaatact tagagttaag aaatgaatta
      841 ttcaatgaca tagaagaagt aatgggtagc tatgctcaga gggcaccata gttcatgata
      901 gccctcgata gtacttactt atatttttag agaggtttaa gtgtaagtag agggagtaac
      961 acctggtttt tcagcatcca ctccaatgaa tgctgacacc gatacgcgat aattctcttt
     1021 atcgtagcaa aatcatcctc cagattgcgg ttgagaatag gttcatggtg cgcaatacga
     1081 ttgcgcagtt ttctcacggg acttgttagc agtaatgctt ccccccgggg acaaacgaca
     1141 gagatataca acaaaggccc gctgtataga gtacagcggg cctttgttgt tttaattccc
     1201 gcaattaaaa tactccgtat ttaccataac gtcgcattgc gcgtaccgct taaacgcgtt
     1261 cagcgcgatc acggcagcag acaggtaaaa acagcaacaa accacccgaa aaactgccgc
     1321 gatcgcgcct ggtaaatttt aacctcatgc atagttatgc gcgaaactga atgacgatca
     1381 gtttcgcacg ttccagccgt cgaacggggc aaaatgggga ggtttggata ttgttaatgc
     1441 taatgtacgt acattaacat tggcgccatc cgggtagggc gtgccacaaa ctggctcgat
     1501 ttcagggggc accccggtca catccccatt gacgggccac gccagatccg cgcttcgggt
     1561 tcctgctctt catgccagcg ccgggcaagc tcctgcgcct gacgctcctg ttcatccctt
     1621 atctgttgtt cgtgataaat aaccgactca agcggtcgac ttgtccggct aatagctgca
     1681 cctgctgact caagttcacg acacgctcgt tcagtatcgc gttgttctgt tgcgtaaccg
     1741 cgtgcatctt ctgcaattct gcgaaggcgc tctcccactc gttcagccgc cgcatatagt
     1801 cctgttgcaa atgctctaag gcgttcagca aatgcccttc cagttccgtc atactcgttt
     1861 actccctgac cagcctcacg gcgttcttgt cgcccaccgt ccaggtgttt tcccctttca
     1921 ccccgtccgg cagcaccaga aatttcccgt tctcgccatt gacgaacgtc accccccagg
     1981 tttttgcctc gagtttcgcc agcgtgtttt cctgctctct gatggtcaag atatttttcg
     2041 caatcctgct ttcctgccac tgaatcagcc cccagcaccc caggaaaatg ccgcccgtga
     2101 cgctgagcgc ggtcagcgcc ggaaacagta cccgcccttt gatcacctgc cagagcaggt
     2161 ttttctgctg ccgggacagt tcggcctctg tggtgctgag ctgcgtgctc acggtggtgc
     2221 tcagcgtatc cagttgctgt ttcacggatg ttgtatgttc gctgatagcg tctctgattt
     2281 tctgcctgtt taagctcagt gccttgtcta cagactcttc tagcttcctg aactcgctgt
     2341 tcagcatgtt ctcggtagaa gcggctcgct ctttcagttt cttctcgaag tctgttccca
     2401 tttgtaaaag attgctcata cagcgccccc tttagcctga gattccgccc cccctccggg
     2461 tcggcaatac tgatactgct tctggttgtc ctcaccacct caaaacctgc cgctgtgagc
     2521 gcctcagtga catcctgacg cgtttttatt gctccggcac ggtaaagcgc ctcaagaccc
     2581 cgtgtaatcg cttctgcggc ctcctgtttc gcttttggca gattattcgg tgtgacaagc
     2641 gtccgtctgt tctccggtgc gttcgggtca cgcagcccgt aatgatgatt aaccagcgtc
     2701 tgccaggcat ttatcctcgg cctgtccgca cggtcgtagt acggctggag gcgcttaccg
     2761 ctctgtagtt ccatgttcgg aatgacaaaa ttcagttcga gccgcccctt atcctggtgt
     2821 tccacccaga gaatgctgta ctggtctttt tcgagaccgg gcataagaac acgctcaaag
     2881 ctcgtcatca ctctttcgcg ttcacccggc ggtaactcct tctccgcgaa cgacagaacg
     2941 cctgacgtgt atttcttcga aaatggcgtg gcatcaatga gttcccggat ttcttccggg
     3001 ttaccccgga gcaccgttgc gccttcgcgg ttacgctccc gccccagcag gtaatcgacc
     3061 gggccacttc caccgccttt ccccctggca tgaaatttaa ctatcatccc gtcccccctg
     3121 ttccctgaca gcctgccgca actggcgcaa ttcaccctcg atggccatca gtgcggccac
     3181 cacatgaacc cggtcaatcg aagaccagtg gccgctgttc accttccggg ctgtctggtt
     3241 cagattgttc ccgatggcag ccagatgccg cagcaatggc ggcgatagtg tcggcagttt
     3301 tcctgtgcgc gcaaccggct cccccagaca gacccgccgc atccattctg ccagtcgttt
     3361 accctcgcag cgttccagta accgggcgtg ctcctcatcg ctaacccgta tcgtgagcat
     3421 cttctcgcgt ttcatcggta tcattccccc taaaaaatcc cctattaagg agccttaaga
     3481 ccatgaccaa acaggaaaaa acagccctta acatggcccg ctttatcaga agccagacgc
     3541 tgaccctgct ggaaaaactc aacgagctgg acgcggacga acaggcagac atctgcgaat
     3601 cacttcacga ccacgccgac gaactctacc gtagttgcct cgcacgcttc ggcgatgacg
     3661 gtgaaagcaa ctgaaacatg cagctcccgg agacgttcac agcttgcctg tgagcggatg
     3721 ccgggagcag acaagcccgt cagggcgcgt cagcgggttt tagcgggtgt cggggcgcag
     3781 ccctgaccca gtcacgtagc gatagcggag tgtatactgg cttaactatg tggcatcagt
     3841 gcggattata agaaaagtgc accatatgcg gtgtgaaata ccgcacagat gcgtaaggag
     3901 aaaatgccgc atcaggcgct cttccgcttc ctcgctcact gactcgctac gctcggtcgt
     3961 tcggctgcgg cgagcggtat cagctcactc aaagacggtg atgcggttat ccacagaatc
     4021 aggggataac gccaaaagaa acatgtgagc aaaaggccaa gaacaggaag aaggccgcgc
     4081 cgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaac agacgctcaa
     4141 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct
     4201 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc
     4261 cttcgggaag cgtggcgctt tctcatagct cacgctgttg gtatctcggc ccggtgtagg
     4321 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct
     4381 tatccggtaa ctatcgtctt gagtccaacc cggaaagaca cgtaaaaacg ccactggcag
     4441 cagccattgg taaccgttta gaggagttag tcttgaagtt atgcgccggt taaggctaaa
     4501 ctgaaaggac agatttggtg gctgtgctcc tccaagccag ttaccttggt tcaaagagtt
     4561 gctgctctga gaaccttcga aaagccgcct tgctgggcgg ttttttcgtt tacggacaag
     4621 actaccttca gga
//
