LOCUS       CP082675                3371 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0645 plasmid pN18S0645-3, complete sequence.
ACCESSION   CP082675
VERSION     CP082675.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN11968052
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 3371)
  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  JOURNAL   Unpublished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 3371)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3371)
  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                   :: 345x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/01/2021 10:44:50
            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)                     :: 4,885
            CDSs (total)                      :: 4,763
            Genes (coding)                    :: 4,641
            CDSs (with protein)               :: 4,641
            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)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 43 of 122
            Pseudo Genes (incomplete)         :: 79 of 122
            Pseudo Genes (internal stop)      :: 23 of 122
            Pseudo Genes (multiple problems)  :: 20 of 122
            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..3371
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S0645"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Legs"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S0645-3"
                     /geo_loc_name="USA:PA"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(join(3088..3371,1..40))
                     /locus_tag="FH358_023305"
     CDS             complement(join(3088..3371,1..40))
                     /locus_tag="FH358_023305"
                     /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="UAH78653.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            104..295
                     /locus_tag="FH358_023310"
     CDS             104..295
                     /locus_tag="FH358_023310"
                     /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="UAH78654.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1610..1843)
                     /locus_tag="FH358_023315"
     CDS             complement(1610..1843)
                     /locus_tag="FH358_023315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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="UAH78655.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1850..2410)
                     /locus_tag="FH358_023320"
     CDS             complement(1850..2410)
                     /locus_tag="FH358_023320"
                     /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="UAH78652.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(2379..3098)
                     /locus_tag="FH358_023325"
                     /pseudo=""
     CDS             complement(2379..3098)
                     /locus_tag="FH358_023325"
                     /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"
     Typing          complement(377..457)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(1528..3098)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 accgggcgtg ctcctcatcg gtaacccgta tcgtgagcat cttctcgcgt ttcatcggta
       61 tcattccccc taacaaatcc cccatacaag gagccttaag accatgacca aacaggaaaa
      121 aacagccctt aacatggctc gctttatcag aagccagacg ctaaccctgc tggaaaaact
      181 caacgatctg gacgcggacg aacaggcaga catctgcgaa tcacttcacg accacgccga
      241 cgaactctac cgcagttgcc tcgcacgctt cggcgatgac ggtgaaagca actgaaacat
      301 gcagctcccg gagacgttca cagcttgcct gtgagcggat gccgggagca gacaagcccg
      361 ccagggcgcg tcagtgcggg tgtcggggcg cagccctgac ccagttcaca gagcgatagc
      421 gatgtgtata ctggcttatc tcattttgca tcggtgcaga atggatggga agtgcaccat
      481 gtcaggagta aaaagccgca cagatgtaaa aacagcgcac ccgataaaca gcacacacgc
      541 ggacactggc acaggcgcgt aagtgcacaa tgcttgcatc tgtgactctt ccgcttcctc
      601 gcccactcgc tcactacgtt cggtcgctgg ggctgcggcg agcggtggga tcactctcgt
      661 tgtgatgcag atccgttttt ttttttgcac tggagttatc aggagttgcg gtgcacatgg
      721 gatcgtgcga tatgccggat ggtgaaaggt tggagggaac ggcaacaact cacccctccc
      781 agtgaaggga cgggtagttt gccgctctcg atatgccgga cggagccaag gccatcgatc
      841 acggggcgcg tcagtggaag aacccgcgcc tgcgtgacgt atgcgtcttc gccgcaccat
      901 ctcacccgtc acgccaccac ataccgggaa ctgccgccaa ggtctaactc aaccaatcta
      961 gccgcgctac atacggtttt tgtggcaact catcaggtgt ccgctgtcga tgaaactctc
     1021 tgcgccggta gcggaactct cacgcgtgcg gtcgccgtcg tcacagctcc cccaaccgca
     1081 aacgattctc gcaaatacgc aagtatctgc aaaaacaggt ttttttcggg gttcctggga
     1141 gactgtgctg ttgaaaaatt cttgaagaat acagaaggct catgcaaact gaatgaactg
     1201 gtttctgttg tggatctcaa cagtttccac aggaacattg aggaggtcag agacctcaat
     1261 gaacccgaaa cagctcgcct tcctggcgag ctgttttcgt tctacgcccg ccgacgaaag
     1321 atcgcaagtg caataacgag atttttcacg tctttacgct caaaaagtaa aaaaaccatg
     1381 ttttcccctg gctgaatccc caaaaacgcg tgaaatgcgt tttcaggatg ttgcatagct
     1441 atgcacaaat acggcacacg atttgtttcg ctcgccccag ccgtcgaact ggtcaaaatg
     1501 gcaagatttc gtcacttccc cggtcacatc tccattgatg gcccactccg aacccgtgcc
     1561 gcgcgttcct gtacctcatg tctgtaccgg gcacgctcct gttcatccct tagctgttgt
     1621 tcgcgataaa taaccgactc aagcgatcca cttgcccggc taatctctgc acctgctgac
     1681 tcaatatcac gacgcgctcg ttcagtatcg cgttgttccg ttgcgtaacc tcgtgcatct
     1741 tctgcaattc cgcgaaggcg ctctcccact cgttcagccg ccgcatatag tcctgttgca
     1801 aatgctctaa ggcgttcagc aaatgccctt ccagttccgt catactcgtt tactccctga
     1861 ccagcctcac ggcgttcttg tcgcccaccg tccaggtgtt ttcccctttc accccgtccg
     1921 gcaacaccag aaatttcccg ttctcgccat tgacgaacgt caccccccag gtttttgcct
     1981 cgagtttcgc cagcgtgttt tcctgctctc tgatagtcag gatatttttc gcaatcttgc
     2041 tttcctgcca ctccatcagc ccccagcacc ccaggaaaat gccgcccgtg acgctgagcg
     2101 cggtcagcgc cggaaacagt atccgccctt tgatcacccg ccagagcagt tttttctgct
     2161 gccgggacag ttcggcctct gtggtgctga actgcatgct cacggtggtg ctcagcgtat
     2221 ccagttgctt tttcacggat gttgtatgtt cgctgatagc gtctctgatt ttctgcctgt
     2281 ttaagctcaa tgccttgtct acagactctt cgagcttcct gaactcgctg ttcagcatgt
     2341 tctcggtaga agcggctcgc tctttcagtt tcttctcgaa gtctgttccc atttgtaaaa
     2401 gattgctcat acagcgcccc ctttagcctg agattccgcc ccccctccgg gtcggcaata
     2461 ctgatgctgc ttttggttgt cctcaccacc tcaaaacctg ccgctgtaag cgcctctgtg
     2521 acatcctgac gcgtttttat tgctccggca tggtaaagag cctcaagacc ccgtgtaatc
     2581 gcttctgcgg cctcctgttt cgcttttggc agattatttg gcgtgacaag cgtccgtctg
     2641 ttctccggtg cgttcgggtc acgcagcccg taatgatgat taaccagcgt ctgccaggca
     2701 tttatcctcg gcctgtccgc gcggtcgtag tacggctgga ggcgcttacc gctctgtagc
     2761 tccatgttcg ggatgacaaa attcagttcg agccgcccct tatcctggtg ttccacccag
     2821 agaatgctgt actggtcttt ttcgagaccg ggcataagaa cacgctcaaa gctcgtcatc
     2881 actctttcgc gttcacccgg cggtaactcc ttctccgcga acgacagaac gcctgaagtg
     2941 tatttcttcg agaatggcgt ggaatcaatg agttcccgca cttcttccgg gttaccccgg
     3001 agcaccgttg cgccttcgcg gttacgctcc cgccccagca ggtaatcgac cgggccactt
     3061 ccaccgcctt tccccctggc atgaaattta actatcatcc cgtaccccct gttccctgac
     3121 agcctgccgc aactggcgca attcaccctc gatggccatc agtgcggcca ccacatgaac
     3181 ccggtcaatc gaagaccact ggccgctgtt caccttccgg gctgtctggt tcaggttgtt
     3241 cccgatggca gccagatgcc gcagcaatgg cggcgatagt gtcggcagtt ttcctgtgcg
     3301 tgcaaccggc tcccccagac agacccgccg catccattcc gccagtcgtt taccctcgca
     3361 gcgttccagt a
//
