LOCUS       NZ_CP051344             5698 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Anatum strain CVM 33822
            plasmid p33822-3, complete sequence.
ACCESSION   NZ_CP051344
VERSION     NZ_CP051344.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14504852
            Assembly: GCF_016452145.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Anatum
  ORGANISM  Salmonella enterica subsp. enterica serovar Anatum
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5698)
  AUTHORS   Zhao,S., Li,C., Hsu,C.H., Tyson,G.H., Strain,E., Tate,H., Tran,T.T.,
            Abbott,J. and McDermott,P.F.
  TITLE     Comparative Genomic Analysis of 450 Strains of Salmonellaenterica
            Isolated from Diseased Animals
  JOURNAL   Genes (Basel) 11 (9), 1025 (2020)
   PUBMED   32883017
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5698)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-APR-2020) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 210x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:08:31
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,155
            CDSs (total)                      :: 5,042
            Genes (coding)                    :: 4,891
            CDSs (with protein)               :: 4,891
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 151
            CDSs (without protein)            :: 151
            Pseudo Genes (ambiguous residues) :: 0 of 151
            Pseudo Genes (frameshifted)       :: 63 of 151
            Pseudo Genes (incomplete)         :: 110 of 151
            Pseudo Genes (internal stop)      :: 16 of 151
            Pseudo Genes (multiple problems)  :: 34 of 151
            Pseudo Genes (short protein)      :: 1 of 151
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051344.1.
            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..5698
                     /organism="Salmonella enterica subsp. enterica serovar
                     Anatum"
                     /mol_type="genomic DNA"
                     /strain="CVM 33822"
                     /serovar="Anatum"
                     /isolation_source="swine"
                     /sub_species="enterica"
                     /db_xref="taxon:58712"
                     /plasmid="p33822-3"
                     /geo_loc_name="USA:NC"
                     /collection_date="2004"
                     /collected_by="NC State Veterinary Diagnostic Lab"
     gene            join(<5159..5698,1..>195)
                     /locus_tag="HFT46_RS24085"
                     /old_locus_tag="HFT46_24100"
                     /pseudo=""
     CDS             join(<5159..5698,1..>195)
                     /locus_tag="HFT46_RS24085"
                     /old_locus_tag="HFT46_24100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_021138877.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3 family transposase"
                     /name="Tn3 family transposase"
     gene            complement(205..1020)
                     /locus_tag="HFT46_RS24090"
                     /old_locus_tag="HFT46_24105"
     CDS             complement(205..1020)
                     /locus_tag="HFT46_RS24090"
                     /old_locus_tag="HFT46_24105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="WP_000018330.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(<1166..>1264)
                     /locus_tag="HFT46_RS24095"
                     /old_locus_tag="HFT46_24110"
                     /pseudo=""
     CDS             complement(<1166..>1264)
                     /locus_tag="HFT46_RS24095"
                     /old_locus_tag="HFT46_24110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     gene            complement(2097..2330)
                     /locus_tag="HFT46_RS24100"
                     /old_locus_tag="HFT46_24115"
     CDS             complement(2097..2330)
                     /locus_tag="HFT46_RS24100"
                     /old_locus_tag="HFT46_24115"
                     /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="WP_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2337..2897)
                     /locus_tag="HFT46_RS24105"
                     /old_locus_tag="HFT46_24120"
     CDS             complement(2337..2897)
                     /locus_tag="HFT46_RS24105"
                     /old_locus_tag="HFT46_24120"
                     /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="WP_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2932..3585)
                     /locus_tag="HFT46_RS24110"
                     /old_locus_tag="HFT46_24125"
                     /pseudo=""
     CDS             complement(<2932..3585)
                     /locus_tag="HFT46_RS24110"
                     /old_locus_tag="HFT46_24125"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     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(3575..3898)
                     /locus_tag="HFT46_RS24115"
                     /old_locus_tag="HFT46_24130"
     CDS             complement(3575..3898)
                     /locus_tag="HFT46_RS24115"
                     /old_locus_tag="HFT46_24130"
                     /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="WP_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3961..4152
                     /locus_tag="HFT46_RS24120"
                     /old_locus_tag="HFT46_24135"
     CDS             3961..4152
                     /locus_tag="HFT46_RS24120"
                     /old_locus_tag="HFT46_24135"
                     /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="WP_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4822..4971
                     /locus_tag="HFT46_RS25945"
     CDS             4822..4971
                     /locus_tag="HFT46_RS25945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     ARG             complement(209..1020)
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(4241..4325)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          complement(4713..5254)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2000..3585)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gactttgatt tcctgcacca catcggtgaa agctatgcca cgctacgccg ctacgcgccg
       61 cagttcctgg gcgtgctcaa attgcgggct gcgcccgccg ccaagggtgt gctcgatgcc
      121 atcgacatgc tgcgcggcat gaacagcgac agcgcgcgca aggtgcccgc cgatgcgcca
      181 accgcattca ttaaagacta actatcagaa aaactcatcg agcatcaaat gaaactgcaa
      241 tttattcata tcaggattat caataccata tttttgaaaa agccgtttct gtaatgaagg
      301 agaaaattca ccgaggcagt tccatagaat ggcaagatcc tggtatcggt ctgcgattcc
      361 gactcgtcca acatcaatac aacctattaa tttcccctcg tcaaaaataa gattatcaag
      421 tgagaaatca ccatgagtga cgactgaatc cggtgagaat ggcaaaagct tatgcatttc
      481 tttccagact tgttcaacag gccagccatt acgctcatca tcaaaatcac tcgcatcaac
      541 caaaccgtta ttcattcgtg attgcgcctg agcgagacga aatacgcgat cgctgttaaa
      601 aggacaatta caaacaggaa tcgaatgcaa ccggcgcagg aacgctgcca gcgcatcaac
      661 aatattttca cctgaatcag gatattcttc taatacctgg aatgctgttt tcccggggat
      721 cgcagtggtg agtaaccatg catcatcagg agtacggata aaatgcttga tggtcggaag
      781 aggcataaat tccgtcagcc agtttagtct gaccatctca tctgtaacat cattggcaac
      841 gctacctttg ccatgtttca gaaacaactc tggcgcatcg ggcttcccat acaatcgata
      901 gattgtcgca cctgattgcc cgacattatc gcgagcccat ttatacccat ataaatcagc
      961 atccaggttg gaatttaatc gctgcctcga gcaagacgtt tcccgttgaa tatggctcat
     1021 aacacccctt gtattactgt ttatgtaagc agacagtttt attgttcatg atgatatatt
     1081 tttatcttgt gcaatgtaac atcagagatt ttgagacaca acgtggttcc cgccatatga
     1141 aaatccggcc agaccaacat cattctggcg ctccgaaaga agggatattc gccgccgtga
     1201 ccagcctgga gcgggtcgca taatctttgg ccgcttcgta gtcgaggaac atggcatcaa
     1261 gactagtaaa ctcaatcaaa gatccttcta gatttaagtt cacgacagag tcattagaaa
     1321 tggagttact agaatactta gagttaagaa atgaattatt caatgacata gaagaagtaa
     1381 tgggtagcta tgctcagagg gcaccatagt tcatgatagc cctcgatagt acttacttat
     1441 atttttagag aggtttaagt gtaagtagag ggagtaacac ctggtttttc agcatccact
     1501 ccaatgaatg ctgacaccga tacgcgataa ttctctttat cgtagcaaaa tcatcctcca
     1561 gattgcggtt gagaataggt tcatggtgcg caatacgatt gcgcagtttt ctcacgggac
     1621 ttgttagcag taatgcttcc ccccggggac aaacgacaga gatatacaac aaaggcccgc
     1681 aattaaaata ctccgtattt accataacgt cgcattgcgc gtaccgctta aacgcgttca
     1741 gcgcgatcac ggcagcagac aggtaaaaac agcaacaaac cacccgaaaa actgccgcga
     1801 tcgcgcctgg taaattttaa cctcatgcat agttatgcgc gaaactgaat gacgatcagt
     1861 ttcgcacgtt ccagccgtcg aacggggcaa aatggggagg tttggatatt gttaatgcta
     1921 atgtacgtac attaacattg gcgccatccg ggtagggcgt gccacaaact ggctcgattt
     1981 cagggggtac cccggtcaca tccccattga cgggccacgc cagatccgcg cttcgggttc
     2041 ctgctcttca tgccagcgcc gggcaagctc ctgcgcctga cgctcctgtt catcccttat
     2101 ctgttgttcg tgataaataa ccgactcaag cggtcgactt gtccggctaa tagctgcacc
     2161 tgctgactca agttcacgac acgctcgttc agtatcgcgt tgttctgttg cgtaaccgcg
     2221 tgcatcttct gcaattctgc gaaggcgctc tcccactcgt tcagccgccg catatagtcc
     2281 tgttgcaaat gctctaaggc gttcagcaaa tgcccttcca gttccgtcat actcgtttac
     2341 tccctgacca gcctcacggc gttcttgtcg cccaccgtcc aggtgttttc ccctttcacc
     2401 ccgtccggca gcaccagaaa tttcccgttc tcgccattga cgaacgtcac cccccaggtt
     2461 tttgcctcga gtttcgccag cgtgttttcc tgctctctga tggtcaagat atttttcgca
     2521 atcctgcttt cctgccactg aatcagcccc cagcacccca ggaaaatgcc gcccgtgacg
     2581 ctgagcgcgg tcagcgccgg aaacagtacc cgccctttga tcacctgcca gagcaggttt
     2641 ttctgctgcc gggacagttc ggcctctgtg gtgctgagct gcgtgctcac ggtggtgctc
     2701 agcgtatcca gttgctgttt cacggatgtt gtatgttcgc tgatagcgtc tctgattttc
     2761 tgcctgttta agctcagtgc cttgtctaca gactcttcta gcttcctgaa ctcgctgttc
     2821 agcatgttct cggtagaagc ggctcgctct ttcagtttct tctcgaagtc cgttcccatt
     2881 tgtaaaagat tgctcataca gcgccccctt tagcctgaga ttccgccccc cctccgggtc
     2941 ggcaatactg atactgcttc tggttgtcct caccacctca aaacctgccg ctgtgagcgc
     3001 ctcagtgaca tcctgacgcg tttttattgc tccggcacgg taaagcgcct caagaccccg
     3061 tgtaatcgct tctgcggcct cctgtttcgc ttttggcaga ttattcggtg tgacaagcgt
     3121 ccgtctgttc tccggtgcgt tcgggtcacg cagcccgtaa tgatgattaa ccagcgtctg
     3181 ccaggcattt atcctcggcc tgtccgcacg gtcgtagtac ggctggaggc gcttaccgct
     3241 ctgtagttcc atgttcggaa tgacaaaatt cagttcgagc cgccccttat cctggtgttc
     3301 cacccagaga atgctgtact ggtctttttc gagaccgggc ataagaacac gctcaaagct
     3361 cgtcatcact ctttcgcgtt cacccggcgg taactccttc tccgcgaacg acagaacgcc
     3421 tgacgtgtat ttcttcgaaa atggcgtggc atcaatgagt tcccggattt cttccgggtt
     3481 accccggagc accgttgcgc cttcgcggtt acgctcccgc cccagcaggt aatcgaccgg
     3541 gccacttcca ccgcctttcc ccctggcatg aaatttaact atcatcccgt cccccctgtt
     3601 ccctgacagc ctgccgcaac tggcgcaatt caccctcgat ggccatcaga gcggccacca
     3661 catgaacccg gtcaatcgaa gaccagtggc cgctgttcac cttccgggct gtctggttca
     3721 gattgttccc gatggcagcc agatgccgca gcaatggcgg cgatagtgtc ggcagttttc
     3781 ctgtgcgcgc aaccggctcc cccagacaga cccgccgcat ccattctgcc agtcgtttac
     3841 cctcgcagcg ttccagtaac cgggcgtgct cctcatcgct aacccgtatc gtgagcatct
     3901 tctcgcgttt catcggtatc attcccccta aaaaatcccc tattaaggag ccttaagacc
     3961 atgaccaaac aggaaaaaac agcccttaac atggcccgct ttatcagaag ccagacgctg
     4021 accctgctgg aaaaactcaa cgagctggac gcggacgaac aggcagacat ctgcgaatca
     4081 cttcacgacc acgccgacga actctaccgt agttgcctcg cacgcttcgg cgatgacggt
     4141 gaaagcaact gaaacatgca gctcccggag acgttcacag cttgcctgtg agcggatgcc
     4201 gggagcagac aagcccgtca gggcgcgtca gcgggtttta gcgggtgtcg gggcgcagcc
     4261 ctgacccagt cacgtagcga tagcggagtg tatactggct taactatttg gcatcagtgc
     4321 ggattataag aaaagtgcac catatgcggt gtgaaatacc gcacagatgc gtaaggagaa
     4381 aatgccgcat caggcgctct tccgcttcct cgctcactga ctcgctacgc tcggtcgttc
     4441 ggctgcggcg agcggtatca gctcactcaa agacggtgat gcggttatcc acagaatcag
     4501 gggataacgc caaaagaaac atgtgagcaa aaggccagga acaggaagaa ggccgcgccg
     4561 ctggcgtttt tccataggct ccgcccccct gacgagcatc acaaaaacag atgctcaagt
     4621 cagaggtggc gaaacccgac aggactataa agataccagg cgtttccccc tggaagctcc
     4681 ctcgtgcgct ctcctgttcc gaccctgccg cttaccggat acctgtccgc ctttctccct
     4741 tcgggaagcg tggcgctttc tcatagctca cgctgttggt atctcggccc ggtgtaggtc
     4801 gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta
     4861 tccggtaact atcgtcttga gtccaacccg gaaagacacg taaaaacgcc actggcagca
     4921 gccattggta accgtttaga ggagttagtc ttgaagttat gcgccggtta aggctaaact
     4981 gaaaggacag atttggtggc tgtgctcctc caagccagtt accttggttc aaagagttgc
     5041 tgctctgaga accttcgaaa agccgccttg ctgggcggtt ttttcgttta cggacaagac
     5101 taccttcagg atcgttagat ctcaagacaa tcatgcatag tgagcataca caggagccga
     5161 acttctcaag cgcaaggacg gcagtaaagt gacgtggctg gcatggctgc gccagtcgcc
     5221 tgccaaaccg aactctcgcc acatgctcga acatattgag cgcctgaaat cctggcaagc
     5281 acttgatctg cccgcaggca tcgagcggca ggttcaccag aaccgcctgc tcaaaatcgc
     5341 tcgtgaaggt ggccagatga cgcctgctga tctggcaaag ttcgaggtgc aacgacgcta
     5401 tgccacgctg gtagcgctgg ccatcgaagg catggccacc gtcaccgatg aaatcatcga
     5461 ccttcacgat cgcatcatcg gcaagctgtt caacgcggcc aagaacaagc atcagcagca
     5521 gttccaggct tccggcaagg cgatcaacga caaggtgcgg atgtatgggc gcatcggtca
     5581 agcgttgatt gaggccaagc aaagcggcag cgatccgttc gccgccatcg aggccgttat
     5641 gccctgggac accttcgccg ccagcgtcac cgaagcgcaa acattggcgc ggcctgcc
//
