LOCUS       CP082544                5676 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S1677 plasmid pN18S1677-2, complete sequence.
ACCESSION   CP082544
VERSION     CP082544.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN13808816
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5676)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5676)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (16-AUG-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 5676)
  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                   :: 812x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:27:31
            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)                     :: 5,043
            CDSs (total)                      :: 4,919
            Genes (coding)                    :: 4,775
            CDSs (with protein)               :: 4,775
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 144
            CDSs (without protein)            :: 144
            Pseudo Genes (ambiguous residues) :: 0 of 144
            Pseudo Genes (frameshifted)       :: 58 of 144
            Pseudo Genes (incomplete)         :: 86 of 144
            Pseudo Genes (internal stop)      :: 25 of 144
            Pseudo Genes (multiple problems)  :: 22 of 144
            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..5676
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S1677"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Legs"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S1677-2"
                     /geo_loc_name="USA:PA"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(join(5457..5676,1..848))
                     /locus_tag="GUE86_24355"
     CDS             complement(join(5457..5676,1..848))
                     /locus_tag="GUE86_24355"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="UAI52559.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPVLE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKYIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            925..2055
                     /locus_tag="GUE86_24360"
     CDS             925..2055
                     /locus_tag="GUE86_24360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /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="UAI52560.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVIHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(2439..2672)
                     /locus_tag="GUE86_24365"
     CDS             complement(2439..2672)
                     /locus_tag="GUE86_24365"
                     /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="UAI52561.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2679..3197)
                     /locus_tag="GUE86_24370"
     CDS             complement(2679..3197)
                     /locus_tag="GUE86_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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="UAI52562.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGNRKFLVLPCGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(3178..3897)
                     /locus_tag="GUE86_24375"
                     /pseudo=""
     CDS             complement(3178..3897)
                     /locus_tag="GUE86_24375"
                     /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(3875..4198)
                     /locus_tag="GUE86_24380"
     CDS             complement(3875..4198)
                     /locus_tag="GUE86_24380"
                     /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="UAI52563.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     ALPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4263..4454
                     /locus_tag="GUE86_24385"
     CDS             4263..4454
                     /locus_tag="GUE86_24385"
                     /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="UAI52557.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4596..4868)
                     /locus_tag="GUE86_24390"
     CDS             complement(4596..4868)
                     /locus_tag="GUE86_24390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001441803.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAI52558.1"
                     /translation="MEKAPPARPFPGFRFFAHMFFPGLSPGSVDNRVSVFEKGESARRS
                     RTTERSESVSEEAEEHRKLHVLLTHLCGISHRTWCTFHTIRTDAA"
                     /name="hypothetical protein"
     Typing          complement(4533..4617)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.349"
                     /coverage="100.0"
                     /evalue="1.42e-30"
     Typing          4649..5186
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.64"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2336..3885)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.656"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgtcaacaa taaccattgt gcttatatta tgcatcactc cgccaatatc atccattcgt
       61 ctaaatctag atactttatc caaacttatt tctgtgttac ccctaccaat aaaaccaata
      121 tcaaccctaa tcgccttccc attaaaaaca agagtagcat cagactccct gtcatcagct
      181 cttgttgaaa gagtaaaaca tttagcattt aacccttctt caattttttc tttatattca
      241 aaacccatta ttgtaaataa agaaccgagt attagctttt caaaatattt accatgaaga
      301 gatttctcag atcccctaat agttaaagtt tgcgaaccaa gagataaaat aatatagcaa
      361 aaatcttcta aagacacctt ttgcccacca atagatatct ctccaatttt atcttcatat
      421 ccgtttttta ttttaagtat ttcttcttgc gtccttaaag caagcctatc aaaaccatcc
      481 ccatgctcat ctcttaaaac attttgggtc tgtttatttg tcatcataac catccactcg
      541 agaacaggtt gattagactt aacataagac ttgttcgata atgcattttt tgcatagaga
      601 taaagctgct ttggcgttat cccctctttc attttatcca caaaaaagtc aaaaaaagag
      661 agattacttt ctaacaatct agtacgagtt agtatttcag tgaattcgcg aacattttta
      721 cctgttaaaa catcataaac aaccttttta aaaacatccg ttccgaactt atctaaaaca
      781 tcattttttg aaattttcgc caacgctatg agttcgttag ggaaacaatt tttatccttg
      841 aaattcatat cctcaccatg gacatagtaa aaatgagatg ctaagatagc aggttgtatg
      901 gtaacagatc gatagttagg aaaaatgaca gttaaaaaca attacttaaa cagaggttat
      961 ttggtaacct ctacgactca ggcgaaaaaa atagcaaagt tgcacctaga gaaattagac
     1021 ttagctgata aattttcctt tgggttacct gaagtcgatg atcggtacca tgtatggcgt
     1081 gtaccattag tagcgacagg ccacaggatt ggtgaaatag ttataaattc aaaaacgtca
     1141 actattgatt ataagaaaag ttcgaagtct ccatttctta ttaagaaagc aatggaggtt
     1201 atccataccc caaaaaaggt aaaaaaagaa aaaaaaatca tatcaaagtc accattaaat
     1261 aacatgttac tacaaggcaa ctgcgcggag accttgaaaa aattacctga tgaatcagtg
     1321 aacttagtat tcacatcacc gccatattac aatgccaaac cagagtattc cgaatatcat
     1381 acatatgatg aatacctctc tctattacgt tcagtaataa aagagtgcca tagagtttta
     1441 agcgaaggtc gttttttcgt catcaatgtc tcgcccgttt taataagaag ggcgtcacgg
     1501 aatgaagcat caaaaagaat agctgttcct tttgacttgc acaggttatt tatagaagaa
     1561 ggatatgaat tcatagatga tatacattgg gttaaaccag aaggagctgg ctgggcttta
     1621 ggtagaggcc gtcgattcgc agctgaccgc aatccgttgc aatataaacc agtaccagta
     1681 actgagtaca ttcttgttta cagaaaaaaa actgataaat taatagattg gaacataaga
     1741 aaccatcata gcaaagagga tgtttttgac tcaaaaatcg gcgacgatta cgaaaagaca
     1801 aacctatgga aaataaatcc atctcgtaac agaaaacatc ctgctacatt tccatacggt
     1861 ctggcagaaa gagttataaa atactattct ttcaaaaatg atgtcatttt agatcctttt
     1921 gctggatcgg gaacaacagc aaaagcagca attgatttag gcagaagatt tgtgatgtgt
     1981 gagatatcaa agcagtatat tgatctaatc atagaaggaa ccatgctagg tggtgattta
     2041 aaaatcataa attaatcaaa ctttactgtg gtaaaagccg ccttaaggcg gcttatttac
     2101 gcgtcaacat cagccacatt gtcgaattta ccataatccc ttaattgtac gcaccgctaa
     2161 aacgcgttca gcgcgatcac ggcagcagac aggtaaaaat ggcaacaaac cacccgaaaa
     2221 aatgccgcga tcgcgcctga taaattttaa ccgtatgaat acctatgcaa ccagatggta
     2281 caggccacat tccccccact taatccactg aagctgccat ttttcatggt ttcaccatcc
     2341 cagcgaaggg ccatccagcg tgcgttcctg tatttccggc tgacgctccc gttccaggga
     2401 taacacatgt tcgcgctcct gtatcaaccg ttcctctctt atctccagtt ctcgctgtat
     2461 aactggctca agcgttctgt ctgctcgctc aagtgctgca cctgctgact caactgcatg
     2521 acccgctcgt tcagcatcgc gttgtcccgt tgcgtaagcg aaaacatctt ctgcaattcc
     2581 acgaaggcgc tctcccattc gctcagccgc tgcatatagt cctgttgcag ctgctctaag
     2641 gcgttcagca aatgtatttc cagctctgtc actctgtgtc actccttcag atgtacccac
     2701 tctttcccct gaaagggaat cacctccgct gatttcccgc acggaaggac aaggaatttc
     2761 ctgttcccgt cctgcacaaa ctccacgccc catgtcttcg cgttcagttt ctgcaatgtt
     2821 tcttcctgta tcctgatttc ttccaggttc gcctgtatcc gcccgccaag ataccagagc
     2881 gtcccgccac tcacggtaaa caggaaaatg accatcccca gtaacatcat gcccgtattc
     2941 cctgccagct ttaacacgtc cttcctgtgc tgcatcatcg cctctttcac cccttcccgg
     3001 tgtttttcca gcgattcctc tgtcgacgtt gtgaacaggg ctatagcgtc tttgattttc
     3061 gtctcgtttg aggtcacagc cttgcttaca gatttttcga gcttgctgaa ctcgtcgttc
     3121 agcattgtct ctgtagattc ggctctctct ttcagctttt tctcgaactc cgcgcccgtc
     3181 tgtaaaagat tgctcataaa atactccttt cagcctgata ttcttcccgc cgttcgggtc
     3241 tgcaatgctg atactgcttc gcgtcaccct gacaacttca agccccgcct ctgtgagcgc
     3301 ctgaatcaca tcctgacggc cttttatctc cccgacatga taaagagcgt ctatcccccg
     3361 tgtgacgctc tctgcaagcg cctgtttcgt ttccggcagg ttatcaggga gagtcagtat
     3421 ccggcggttc tccggggcgt tggggtcatg cagcccgtaa tggtgattca ccagcgtctg
     3481 ccaggcatca attctcggcc tgtctgcccg gtcgtagtac ggctggaggc gttttccggt
     3541 ctgtagctcc atgttcggaa tgacaaaatt cagctcaagc cgtcccttgt cctggtgctc
     3601 cacccacagg atgctgtact gattcttttc gagaccgggc atcagtacac gctcaaagct
     3661 cgccatcacc ttttcacgtc ctcccggcgg cagctccttc tccgcgaacg acagaacacc
     3721 tgacgtgtat ttcttcgcaa atggcgtggc atcgatgagt tcccggactt cttccggatt
     3781 accctgaagc accgttgccc cttcccggtt acgctccctt cccagcaggt aatcaaccgg
     3841 accactgcca ccgccttttc ccctggcatg aaacttaact atcatcccgc gctccatgtt
     3901 ccctgacgac ctgccgtaag ctgcgcaact ctctctcgat ggccatcagt gcggccacca
     3961 cctgaacccg gtcaccggaa gaccactgcc cgctgttcac cttcctcgcc gtctgattca
     4021 gattattccc gatggcagcc agctggcgca gtaacggcag tgccagtgtc ggcagcttcc
     4081 cggaacgggc aaccggctca cccaggcaga cccgccgcat ccataccgcc agctgtttac
     4141 cctcacagcg ttccagtaac cgtgcatgtt catcatcagt aacccgtatg gtgagcatcc
     4201 tctcgcgttt catcggtatc attaccccat aaaacagaaa tcccccttac acggaggcat
     4261 cagtgactaa acaggaaaaa accgccctta acatggcccg ctttatcaga agccagacat
     4321 taacgctgct ggagaaactc aacgaactgg acgcagatga acaggccgat atttgtgaat
     4381 cacttcacga ccacgccgac gagctttacc gcagctgcct cgcacgcttc ggggatgacg
     4441 gtgaaaacct ctgacacata cagctcccgg agacggtcac agcttgtctg tgagcggatg
     4501 ccgggagcag acaagcccgt cagggcgcgt cagggggttt cggggcgaag ccctgaacca
     4561 gtcacgtagc gctagcggag tgtatactgg cttagtcatg cggcatcagt gcggattgta
     4621 tgaaaagtgc accatgtacg gtgtgaaatg ccgcacagat gcgtaaggag aacatgcagc
     4681 ttccggtgct cttccgcttc ctcgctcact gactcgctac gctcggtcgt tcggctgcgg
     4741 cgagcggact ctcctttctc aaaaacacta accctgttat ccacagaacc cggggataaa
     4801 ccaggaaaga acatgtgcgc aaaaaaacga aaccccggaa aaggccgcgc cggaggcgct
     4861 ttttccatag gctccgcccc cctgacgagc atcacagaaa tcgacgctca agtcagaggt
     4921 ggcgaaaccc gacaggactt aaagatacca ggcgtttccc cctggtggct ccctcgtgcg
     4981 ctctcctgtt ccgaccctac cgcttaccgg atacctgtcc gcctttctcc cttcgggaag
     5041 cgtggcgctt tctcatagct cacactgttg gtatctcagt tcggtgtagg tcgttcgctc
     5101 caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa
     5161 ctatcgtctt gagtccaacc cggtaagaca cgacttaacg ccactggcag cagccattgg
     5221 taaccgagtt agcagagcga gatttataag ttagtaacag agttcttgaa gtatcagcct
     5281 gattctggct acactagaag gacaagtttt aggtgtctgc gctctgctta agccagatta
     5341 cctggttaga taatctgcca ggattagcta acctttgaaa aaccacctgc cagggtggtt
     5401 tttctttatg tagagattat gcttttaata agcacgcagt caaggattac aatctcttat
     5461 aatttaatgt atttttccag atctacattc tctaatgcat cagatataaa agactgtatg
     5521 tatttaagtt gaggtttatc ctctaaaaga tcatctacat tcagtttcga actaatatag
     5581 gaagagacct ttgcaaccca atacggatca ctcatcgcaa caactttacc atcaatctct
     5641 tcagccatat taactattct acttctatca ccaata
//
