LOCUS       CP082665                6836 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            strain CVM N16S089 plasmid pN16S089-3, complete sequence.
ACCESSION   CP082665
VERSION     CP082665.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN08113968
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 6836)
  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  JOURNAL   Unpublished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 6836)
  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 6836)
  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                   :: 788x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/31/2021 17:47:43
            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)                     :: 5,019
            CDSs (total)                      :: 4,896
            Genes (coding)                    :: 4,775
            CDSs (with protein)               :: 4,775
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 41 of 121
            Pseudo Genes (incomplete)         :: 81 of 121
            Pseudo Genes (internal stop)      :: 24 of 121
            Pseudo Genes (multiple problems)  :: 21 of 121
            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..6836
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium var. 5-"
                     /mol_type="genomic DNA"
                     /strain="CVM N16S089"
                     /serovar="Typhimurium var. 5-"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:1620419"
                     /plasmid="pN16S089-3"
                     /geo_loc_name="USA:NY"
                     /collection_date="2016"
                     /collected_by="FDA"
     gene            279..2261
                     /locus_tag="CWX51_025085"
     CDS             279..2261
                     /locus_tag="CWX51_025085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966094.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="UAG02617.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGADIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCVLEGGMSKEDQGKSEVYYNEIIARDEIDHLFSPKVLKEVNRYSKEGVK
                     KERIFNRNDNLIIRGNNLIALHCIKNIYEKSVKLIYIDPPYNTDTDSFKYNDKFSHSTW
                     LTFMKNRLEVAKDLLCDDGLIAISIDDNELNYLASLADDIFGRKNRIAIFPRITKKGGK
                     SASIFAKNHDYILLYVRSLENKRMYAVSHDDDNFKYKDEYFAERGSYKLNQTLDYDSLQ
                     YSKSLDYIIEINGEKYYPGGDENLFNDRMNGKHNRADWAWRWSRKLFDFGFENGFIEIR
                     NGGQRPRIYTKTYQNAKISKDGNDYVITYFDRTKPLSTLEFTENKYSNDNATKHISSLL
                     GKNIFDYTKPETLLAKLIEITSTKNDLILDFNLGSGTTAAVAHKMGRRYIGIEQMEYIN
                     DITVPRLKKVIEGEQGGISKDVNWQGGGSFVYAELMELNAYFVHEIQKAQSTEELEKLF
                     TMMKTEAHLNYQVELENVLSAEYEVDGIFRKVAFSELELHEQKQLLIEILDKNKLYVNV
                     SDMEDSELSISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     gene            2266..4902
                     /locus_tag="CWX51_025090"
     CDS             2266..4902
                     /locus_tag="CWX51_025090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="UAG02618.1"
                     /translation="MAKKPKSVGSEKLLFNRLKQFDEPGLFHDNYQTPDYIQENLKDAL
                     RPYQHGALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKELGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSQELEIDGEKITIEPIETFPSIPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILNLRPDNRLFEFTATIDLANKDIGQKYRGKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESVRRHLANKKLQLSSDTSIWHKVIQRYANSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTIEHARLKEDFKKSAVYQAGKLYFNEVEEIESSSRNWETYSLETRFEIPYQT
                     VCEESLDNLTGTKTGITKPELLVLDERFYRKAMQRISFYALDNLQRFFPKLTGIREFIR
                     SDAYLGKLKITVIVPQSLDFTTVPAKDKLHLLETVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVVINQKITAAPTIGKKWYVYDNAILNQLEHRLIKTLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(6071..6262)
                     /locus_tag="CWX51_025095"
     CDS             complement(6071..6262)
                     /locus_tag="CWX51_025095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="UAG02616.1"
                     /translation="MNKQQQTALNIARFIKSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFSDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          5909..5993
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          6299..6387
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.703"
                     /coverage="91.0"
                     /evalue="2.27e-34"
     Typing          complement(5342..5889)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.128"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgatcgtca ttcactttca tgcatagcta tgcatcgagc tgaaaacgat cctgacgcat
       61 ttttctggtt ttcactgggt aaaacatctc tttttgcggt gtttgcgtca gaatcgcgtt
      121 cagcgcgttt tagtggtgcg cgcaagagcg tttatgttaa ataccaccca ttctgatgca
      181 tttccccgca actgcatcca actcatagct gtcgggttcc agcaccgaac gctatacctt
      241 acaatcattc caatatttaa cagtcataag gccatgacat gcagaccgaa ttaataaaag
      301 aacttaacaa ggttttaaaa gcattcccgc aattctggaa cggagaggaa ttacaacgtt
      361 caatggtgag tgacgctatc agtcaaaagc agccagacct tatcaaggca ttggtcgata
      421 atgaaaaagt ccgctctgtt tatggtgcgg atattgatgg catttttatc tttgactttg
      481 acaaattatg tggtcttcta aaatacaaag aatattgggc taatagcttc actaaatacc
      541 ggaacaaagt gggattaact agcgaaggta aataccttga ttacagttct gatgtggtgc
      601 tggattttcc tttcaaggat tgtgttcttg aaggtggtat gtcgaaagaa gatcaaggaa
      661 aatcagaggt ttactataat gaaatcatcg cgcgagatga aatagatcat ttgttctcac
      721 cgaaagttct caaagaagta aatcgttact ctaaagaagg agtaaaaaaa gaaagaatat
      781 ttaaccgtaa tgataattta attatcagag gaaataacct aattgcgttg cactgtataa
      841 aaaatatata cgagaagtca gttaaattaa tttatataga tccaccatat aatactgata
      901 cagatagctt taaatataat gataaattta gtcactctac gtggctgact ttcatgaaga
      961 acagacttga agttgcaaaa gatttgttgt gcgatgacgg gttaattgca attagtattg
     1021 atgataatga attaaattat ttggcctcgt tggctgatga tatttttggc cgaaaaaata
     1081 ggattgctat attcccaaga ataacaaaga aaggaggaaa atccgccagc attttcgcaa
     1141 agaatcatga ttacatactg ctttatgtta gaagtttaga aaacaagcgt atgtatgcag
     1201 tttcgcacga cgacgataat ttcaaatata aagatgagta ctttgctgag agaggaagct
     1261 acaaactcaa ccaaaccttg gattatgata gccttcaata cagcaaatca cttgattata
     1321 taatagaaat caatggtgag aaatattacc caggtggtga tgaaaattta tttaatgata
     1381 gaatgaatgg caagcataac agggcggact gggcttggag atggagtagg aaattattcg
     1441 attttgggtt tgaaaatggg tttattgaaa taagaaatgg cggccaaagg ccaaggatat
     1501 atacaaaaac atatcaaaat gcaaagatat caaaggacgg aaatgattat gtcataacct
     1561 actttgatag aacaaagcca ttgtcaacac ttgagtttac tgaaaacaag tattctaacg
     1621 acaatgcgac aaaacacatt agctccctct tagggaaaaa tatatttgat tatacaaaac
     1681 cagaaaccct attggctaag ctaatcgaaa taacatctac taaaaatgac ctaattctag
     1741 actttaatct tggtagtgga actacagctg ctgttgctca caaaatgggg cgtcgctata
     1801 tcggtattga gcagatggag tacatcaacg acattacggt acctcgcctg aaaaaagtca
     1861 tcgaaggtga acaggggggg atctcaaaag acgttaactg gcagggggga ggcagctttg
     1921 tctacgcaga attgatggag ctgaacgcct atttcgtgca tgaaattcag aaagcgcagt
     1981 ccacggaaga actcgaaaaa ctctttacca tgatgaaaac agaggcccat ctcaactatc
     2041 aggtagagct ggaaaatgtg ctgtccgctg agtacgaagt ggatggcatc ttccgtaagg
     2101 tagctttcag tgaactggaa ctgcatgagc agaagcagct tctgattgaa atcctcgata
     2161 aaaataaact ctacgtgaat gtctctgata tggaggacag cgaactgagc atttcggaga
     2221 gcgataaagc ctttacccgc agcttctacg gaatggagtg acggcatggc gaagaaaccg
     2281 aagtcagtcg gcagtgagaa gctactgttt aacaggctga agcagttcga tgaaccagga
     2341 ctgttccacg ataactatca gacgccggac tatattcagg aaaacctgaa agatgccctg
     2401 cgcccctatc agcacggtgc actgcgttac ctgcattaca cgcaacgtaa acgggatgat
     2461 gcgctgctgc attatcgcca cctgctgttt cacatggcaa ccggtgcagg gaaaacgatg
     2521 gtgatggcag gaacgatact ttatctgttt aaagagttag ggtatcagaa cttcattttc
     2581 ttcgtgcata cagacgcgat tatccagaaa acgcgagaga acttgcttaa tccgcaatcg
     2641 ccgaagtacc tgttcagtca ggagctggaa atcgacgggg aaaaaatcac catcgaaccg
     2701 atagaaacat tcccgtccat accggaacgt aacacgattt acctcaagct ctctactatc
     2761 cataagatgc acgacgagct gaacagctat cgtgagaaca gtatcaccta cgaggattta
     2821 aaagaaatcc cccttgtgct gcttggtgac gaggcacatc atttcaacgc cggtactaaa
     2881 gctagaggca agtcgaaaac ctcaccggag aacgaggagc agacctggga acgcacgatt
     2941 gagaacatcc tcaacctgcg accggataac cgcctgttcg agttcaccgc caccattgac
     3001 cttgcgaaca aagatatcgg gcagaaatac cgtggtaagg tggtgtatca gtatgaccta
     3061 aaacagttca tgtcagacgg ttactcgaag aaagtcatgc tgctggaagc caaccagaat
     3121 gacagcgaca agatgcttga tgcggtactt ttaagccagt atcgtaaact gacggcagca
     3181 gatcacggca tcaccggctt caaaccggtc attctgttca agtcgaataa gattgcgata
     3241 tcaaaggcga agcaggagga gttttcgcaa ctgatagccg ccatgacacc tgagagcgtc
     3301 agacgtcatc tagctaacaa aaaactccag ctcagctctg acaccagtat ctggcataaa
     3361 gtgattcagc gttacgctaa cagtgattta gtgacggtga ctgggcaaat tcaggaggac
     3421 tttaacgact ttaacctgct gaacgtcaac aagtcagatc tgctggaaga gaatcccgtc
     3481 ctgctgaata cactagaaga agtcgataat ccggtgagag ccgtctttgc cgtcgcgaag
     3541 gtgaatgaag gctgggacgt tctcaacctc tacgatattg tccgcatcag cgagcaggcg
     3601 agcagcagca aaaccagcac ggacagcgaa gcgcagctta tcgggcgagg cgcgcgttac
     3661 tacccgttca tttatgacgg tcaacgaagc ttcacccgcc gttttgataa cagtacgaag
     3721 gatttgagcg tactggagca actgcactat cacaccatca atgaaccggc gtacatcaaa
     3781 acactgcatg cctctttgga gcaggcggac attgatgtgc atcaggatgg cggcggtacg
     3841 attgaacacg ccagactgaa agaagatttt aaaaagtccg ccgtgtatca ggcgggtaag
     3901 ctgtacttca acgaagtgga ggagattgag agcagcagca gaaactggga aacctactcg
     3961 ctggaaacac gctttgagat accgtatcag accgtctgcg aggagtcgct ggacaacctg
     4021 acaggcacaa agactggaat cacaaaaccg gaactactgg tactggacga gcgtttttac
     4081 cgcaaggcga tgcaaaggat cagcttttac gcacttgata acctgcagcg tttcttcccg
     4141 aaactgacag gcatccgtga gttcatccgc agtgacgcct atcttggtaa gctgaaaatt
     4201 acagtcatcg taccgcagtc actggatttc accaccgtac cggcaaaaga taagctgcac
     4261 ctactggaaa ccgttctgct gcgtatctca gagaacgttc gccgcaatga tcagaaggta
     4321 aaaggcacgt accgctttat cagccagccg gtgaaagagg ttattaaaga ttacagtttg
     4381 cacattgacc cgtcggtagt tattaatcag aaaatcactg ctgcacccac cattggtaaa
     4441 aaatggtacg tgtacgataa tgcgatactg aatcagcttg agcatcgcct aattaaaacg
     4501 ctggaagcat tcatgccgaa gctaaaagcg cgttatgacg atatttacgt actgcgtaac
     4561 gacgagcagt caacgcgctt taagctcacg gagttcggcg gcgtgcgcgg gtttatgcca
     4621 gatttcatca tgatactgac gcgccattcg gacaacactt actggcaggt gttccttgaa
     4681 ccgaaggggg atgatcgttt gctggatgac gcatggaaag aacggatgct cgaaaccctg
     4741 aatgataggg agcgcattgt aattgatgaa aatgagcacg tcagactggt tgggattaaa
     4801 ttctttgcca acagccagat ggacgttttt gtcagcgaca tgcagaacaa gctgaatgat
     4861 ggagaatcgc tcgaaacctc ctcgctttcc ctaccactgt aaatcacgac aataaataac
     4921 ggagcattac gctccgttat tttattgtta tccctaacca cctccccggg agttgatgat
     4981 tgctcctgta atggttgcat tgtttgttct tgctgttgcg aatcattagt tttgaattgt
     5041 ggttaaaaac cgttcgctat gtttatgcct agggggatga gggggaaaag attcaaggat
     5101 cctcttgtga tccttttttt ctgcgcgtaa tctgctgcct gtaaacgaaa aaaccaccct
     5161 ggcaggtggt ttttcgaagg ttagctaatc ctggcagatt atctaaccgg gtaactggct
     5221 tggaggagcg cagtcaccaa aatctgttct ttcagtttag ccttaacagg tgcataactt
     5281 caagacaaac tcctctaaat cagttaccag tggctgctgc cagtggcaat aagtcgtgtc
     5341 ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg ggctgaacgg
     5401 ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg agataccaac
     5461 agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg
     5521 taatcggcag ggtcggaaca ggagagcgca cgagggagcc accaggggga aactcctggt
     5581 atctttaagt cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc
     5641 gtcagggggg cggagcctat ggaaaaacgc catcggcgcg gccttttctt ggttcttgtt
     5701 ttttgctcac atgctccttt tggctttatc ccctgattct gtggatcacc gcattaccgt
     5761 ttttgagtgg gctgataccg ctcgccgcag ccgaacggcc gagcgtagcg agtcagtgag
     5821 cgaggaagcg gaagagtgcc tgaacaggca tgttctcctt acgcatctat gcgatatttc
     5881 acaccgcata tgccgctgtt ttcttacaat ctgcactgat tccgcacagt taagccagta
     5941 tacactccgc tatcgctacg tgactggttc agggcttcgc cccgaaaccc cctgatgtgc
     6001 cctgaagggc ttgtctgctc ccggcatccg ctcacaggca agctgtggcc gtctccggga
     6061 gctgtatgtg tcagaggttt tcaccatcat cactgaagcg agcgaggcaa ctgcggtaga
     6121 gttcgtcggc gtggtcgtga agtgattcgc agatgtccgc ctgttcgtcc gcgtccagct
     6181 cgttgagttt ttccagcagg gttagcgtct ggcttttgat aaatcgcgct atattcagcg
     6241 cagtttgttg ctgtttgttc accttcggtt gttctccgtc agtaccgggt gtcgggtgga
     6301 ccctgaccag gtggtaattg taagacgttg cgcgcgacgg tattacaatt gcacatcctg
     6361 tcctgttttt taggaggtat catggcatat caactgataa ataatccctg tgctgtacag
     6421 ccgctgttgc ataaaatttc gctctgcgtc gaggtttttt ttatcaaaaa ttccgcagat
     6481 accccggaaa aacgcgagtc tgttctcatg cctgaaatgc ccacacccca cgcaaaacta
     6541 attttttgct gatttgcttt tgaaatcatg ttgttatggt ttcaaaaatg tattttcttt
     6601 ttcagattta tgcaaaagca cgtcgttgac gaccctatgg cgaccctact tagggtcagt
     6661 actgacaatc tttataaaaa acagttaatt aatgtatggg cgtccctagg ggcgcgtcgc
     6721 atttttttac aggacacccc tagcagcgcc cctaggggtg tctgctcaga tatgcctgga
     6781 attcacgtac tgaaaatgtc tgaaaatgtg ccttattggc accgaatgca ctcaaa
//
