LOCUS       NZ_CP039864             5310 bp    DNA     circular CON 07-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014880 plasmid p16-6773.4, complete sequence.
ACCESSION   NZ_CP039864
VERSION     NZ_CP039864.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333170
            Assembly: GCF_005160405.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5310)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., G,L., K,L., J,R. and John,N.H.E.
  TITLE     Complete genome sequences of Canadian Typhimurium and I
            1,4,[5],12:i:-
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5310)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., G,L., K,L., J,R. and John,N.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-APR-2019) Public Health Agency of Canada, National
            Microbiology Laboratory at Guelph, 110 Stone Road West, Guelph,
            Ontario N1G3W4, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: APR-2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/06/2023 04:15:54
            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)                     :: 5,304
            CDSs (total)                      :: 5,178
            Genes (coding)                    :: 5,046
            CDSs (with protein)               :: 5,046
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 39 of 132
            Pseudo Genes (incomplete)         :: 107 of 132
            Pseudo Genes (internal stop)      :: 18 of 132
            Pseudo Genes (multiple problems)  :: 30 of 132
            Pseudo Genes (short protein)      :: 1 of 132
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039864.1.
            Bacteria and source DNA available from 16-6773.
            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..5310
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014880"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p16-6773.4"
                     /geo_loc_name="Canada: ON"
                     /collection_date="2016-08-26"
                     /collected_by="Public Health Ontario Laboratories"
     gene            1..816
                     /locus_tag="E5O17_RS26855"
                     /old_locus_tag="E5O17_26855"
     CDS             1..816
                     /locus_tag="E5O17_RS26855"
                     /old_locus_tag="E5O17_26855"
                     /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(<826..>1098)
                     /locus_tag="E5O17_RS26860"
                     /old_locus_tag="E5O17_26860"
                     /pseudo=""
     CDS             complement(<826..>1098)
                     /locus_tag="E5O17_RS26860"
                     /old_locus_tag="E5O17_26860"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            1940..2260
                     /locus_tag="E5O17_RS27125"
     CDS             1940..2260
                     /locus_tag="E5O17_RS27125"
                     /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="WP_187655770.1"
                     /translation="MDNRVSVFEKGESARRSRTTERSESVSEEAEERLNWHFLLTHLCG
                     ISHRTWRTFHTIRTDAEWLSQYTLRYRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTD
                     KL"
                     /name="hypothetical protein"
     gene            complement(2283..2474)
                     /locus_tag="E5O17_RS26875"
                     /old_locus_tag="E5O17_26875"
     CDS             complement(2283..2474)
                     /locus_tag="E5O17_RS26875"
                     /old_locus_tag="E5O17_26875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2539..2862
                     /locus_tag="E5O17_RS26880"
                     /old_locus_tag="E5O17_26880"
     CDS             2539..2862
                     /locus_tag="E5O17_RS26880"
                     /old_locus_tag="E5O17_26880"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3071..>3502
                     /locus_tag="E5O17_RS27385"
                     /pseudo=""
     CDS             3071..>3502
                     /locus_tag="E5O17_RS27385"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            3540..4070
                     /locus_tag="E5O17_RS26890"
                     /old_locus_tag="E5O17_26890"
     CDS             3540..4070
                     /locus_tag="E5O17_RS26890"
                     /old_locus_tag="E5O17_26890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4077..4310
                     /locus_tag="E5O17_RS26895"
                     /old_locus_tag="E5O17_26895"
     CDS             4077..4310
                     /locus_tag="E5O17_RS26895"
                     /old_locus_tag="E5O17_26895"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            <5070..>5165
                     /locus_tag="E5O17_RS27130"
                     /pseudo=""
     CDS             <5070..>5165
                     /locus_tag="E5O17_RS27130"
                     /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"
     ARG             2..813
                     /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          2108..2189
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          1464..1651
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          2853..4414
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagccata ttcaacggga aacgtcttgc tcgaggcagc gattaaattc caacctggat
       61 gctgatttat atgggtataa atgggctcgc gataatgtcg ggcaatcagg tgcgacaatc
      121 tatcgattgt atgggaagcc cgatgcgcca gagttgtttc tgaaacatgg caaaggtagc
      181 gttgccaatg atgttacaga tgagatggtc agactaaact ggctgacgga atttatgcct
      241 cttccgacca tcaagcattt tatccgtact cctgatgatg catggttact caccactgcg
      301 atccccggga aaacagcatt ccaggtatta gaagaatatc ctgattcagg tgaaaatatt
      361 gttgatgcgc tggcagcgtt cctgcgccgg ttgcattcga ttcctgtttg taattgtcct
      421 tttaacagcg atcgcgtatt tcgtctcgct caggcgcaat cacgaatgaa taacggtttg
      481 gttgatgcga gtgattttga tgatgagcgt aatggctggc ctgttgaaca agtctggaaa
      541 gaaatgcata agcttttgcc attctcaccg gattcagtcg tcactcatgg tgatttctca
      601 cttgataatc ttatttttga cgaggggaaa ttaataggtt gtattgatgt tggacgagtc
      661 ggaatcgcag accgatacca ggatcttgcc attctatgga actgcctcgg tgaattttct
      721 ccttcattac agaaacggct ttttcaaaaa tatggtattg ataatcctga tatgaataaa
      781 ttgcagtttc atttgatgct cgatgagttt ttctgatagt tagtctttaa tgaatgcggt
      841 tggcgcatcg gcgggcacct tgcgcgcgct gtcgctgttc atgccgcgca gcatgtcgat
      901 ggcatcgagc acacccttgg cggcgggcgc agcccgcaat ttgagcacgc ccaggaactg
      961 cggcgcgtag cggcgtagcg tggcatagct ttcaccgatg tggtgcagga aatcaaagtc
     1021 ggcaggccgc gccaatgttt gcgcttcggt gacgctggcg gcgaaggtgt cccagggcat
     1081 aacggcctcg aggattgccc cccagcctcc atcgataccg tgccaaatgc acgtaaaaaa
     1141 cgggagcgtt tctggtgtcg gaatgtaacc aagggggtca gaggcgcgct aaaacgctct
     1201 caggggagtc aaatagagac gtttgtaaca aaaagatcaa aggatcctct tgagatcctt
     1261 tttttctgcg cgtaatctgc tgcctgtaaa cgaaaaaacc gccttgcagg gcggtttgat
     1321 cgaaggttaa gtcagcttgc agactgctta accaggtaac tgtcttatgc gagacgagtc
     1381 accaaaattg ttcttctagt gtagccgcac tccggcagcc acttcaagta ctctctaaat
     1441 atctcgcaca tgacttttac caatggctgc tgccagtggc gctttgtggt gtcttttccg
     1501 ggttggaccc aagagaacag ttaccggaga aggcgcagca gtcgggctga acggggggtt
     1561 cctgcataca gcccagcccg gagcgaactg cctaagtcgc cccgagatac cagaagacgt
     1621 gagctatgag aaagcgccac gtgtcccgta agggagaaag gcggaaaagg tatccggtaa
     1681 tcgatatggc gggaacgtgg gggcgcagga gggagcgatt caccggaaac ggtgatgatc
     1741 tttaagccac gtcgggtttc gccaccgctg gcggatttca tggttgagcc gcaaggctcc
     1801 cacagatgca ccgaaaaagt gtctgttttg tgaagtccgt caggggggcg gagcctatgg
     1861 aaaaagcgcc tccggcgcgg cctttcccgg ggtttcgttt tttgcgcaca tgttctttcc
     1921 tggtttatcc ccgggttctg tggataacag ggttagcgtt tttgagaaag gagagtccgc
     1981 tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgcct
     2041 gaactggcat tttctcctta cgcatctgtg cggcatttca caccggacat ggcgcacttt
     2101 tcatacaatc cgcactgatg ccgaatggtt aagccagtat acactccgct atcgctacgt
     2161 gactgggtca gggcttcgcc ccgacacccc aaaggtcaac ggcctgacgc gccctggcgg
     2221 gcttgtctgc tcccggcatc cgctcacaga caagctgtga ccgtctccgg gagctgcatg
     2281 tgtcagcggt tttcaccgtc atccccgaag cgtgcgaggc aactgcggta aagctcatcg
     2341 gcgtggtcgt gaagcgattc acagatgtct gcctgttcat ccgcgtccag ttcgttgagc
     2401 ttctccagca gcgttaatgt ctggcctctg atgaagcggg ccatgttaag ggcggttttt
     2461 tcctgtttgg tcactgatgc ctccgtgtaa gggggggttc tgttcatggg ggtaatgata
     2521 ccgatgaaac gcgagaggat gctcacgata cgggttactg atgatgaaca tgcccggtta
     2581 ctggaacgct gtgagggtaa acaactggcg gtatggatgc ggcgggtctg cctgggtgag
     2641 ccggttgccc gttccgggaa gctgccgaca ctggcaccgc cgttactgcg tcagctggcc
     2701 gccatcggga ataaccttaa ccagacagcg aggaaggtga acagcgggca gtggtcttcc
     2761 ggtgaccggg ttcaggtggt ggccgcactg atggccatcg gggatgagct acgccggctg
     2821 cgtctggcgg tcagggaaca gggggcgcgg gatgatagtt aagtttcatg ccaggggaaa
     2881 aggtggtggc agtggtccgg ttgattacct gctgggaagg gagcgtaacc gggaaggggc
     2941 aacggtgctt caggggaatc cggaagaggt ccgggaactc atcgatgcca cgccatttgc
     3001 gaagaaatac acgtcaggtg ttctgtcgtt cgcggagaag gagctgccgc ctggagggcg
     3061 tgaaaaagtg atggcgagct ttgagcgtgt actgatgccc ggtctcgaga aaaatcagta
     3121 cagcatcctg tgggtggagc accaggacaa gggacggctt gagctgaatt ttgtcattcc
     3181 gaacatggag ctacagaccg gaaaacgcct ccagccgtac tacgaccggg cagacaggcc
     3241 gagaattgat gcctggcaga cgctggtgaa tcaccattac ggtctgcatg accccaacgc
     3301 cccggagaac cgccggacgc tgacccttcc tgataacctg ccggaaacga aacaggcgct
     3361 tgctgagggc gtcacacgcg ggatagacgc gctttaccat gccggagaga taaaaggccg
     3421 tcaggatgtg attcaggcgc tcacagaggc ggggcttgaa gtggtcaggg tgacgcgaag
     3481 cagtatcagc attgcagacc cgaacggcgg gaggaatatc agactgaaag gagcgtttta
     3541 tgagcaatct tttacagacg ggcgcggagt tcgagaaaaa gctgaaagag agagccgaat
     3601 ctacagagaa aatgctgaac gacgagttca ggaagctcga agaatctgta aacagggaac
     3661 tgacctcaaa cgaatcttta atcaggaacg ctatcaacga ccatacaaca gccctgaaag
     3721 aactgctgga gaggtatcag aaaacgaccg tcgatacgat ggacgcgcac tggaaaaccg
     3781 tactgaaaat gagcgtgaaa cgctggctgt ggctgattat cgtctcagta ctgatgtttg
     3841 ccacgaccgg gagtctgctg tggtaccagg gcatgaagat aaacgcgaat atgaatattc
     3901 tccgcgagca gaaagagagt ctggagaagc tgaacgcgaa gacatggggc gtgcgttatc
     3961 acgaggacag caacggacgt tttctggtgt tgccgaaggg gatgaaagcc gaaacgaact
     4021 ggacgaagga caacggcaaa ctgaacgcag tgagactggt gcaggagtga cagagcatga
     4081 cggagctgga aagacatttg ctgaacgcat tagagcaact gcaacaggac tatatgcagc
     4141 ggctgaacga atgggagaac gccttcgtgg aattgcagaa aatgttttcg cttacgcaac
     4201 gggacaacgc gatgctgaac gggcgagtca tgcagttgag tcagcaggtg cagcacttga
     4261 gcgagcggac agaacgcttg agccagttat acagcgagaa caggagataa gggatgaacg
     4321 gctgatgcag gaacgcgaac atgagttatc tctggagcgg gagcgtcagc cggaaatcca
     4381 ggagcggaca ctggatggcc cttcgctggg atggtgaaac catgaaaaat gacgtgttca
     4441 gtggattaag gcgggctaat gtggcctgta gcatctggtt gcataggtat tcatgcggtt
     4501 aaaatttatc aggtgcgatc gcggcagttt ttcgggtggt ttgttgccat ttttacctgt
     4561 ctgctgccgt gatcgcaccg aacgcgtttt ggcggtgcgt acaatgcgac gttatggtaa
     4621 atggagcgga ttttcaggaa ggagtgatac taacaactcg aacactgtgc aaataatgat
     4681 ttttttaaaa tatcggtaac gataataaat tatttcgttt tacgccggta ataaatataa
     4741 tgtagtttca gtatataaaa aaatatatga ggtgtcttgt gggagctttc atgaatcttc
     4801 aacaacgtat aaataaacta ccacaattat catccagttt ttcatttgga aaagatattg
     4861 ataatattca ttcatttatc tttaacgaaa cttctaaaga taaaattgaa gatttactaa
     4921 gaaaatgggt gtcaggcaat cagccctgtg tatttggtaa attggcaagc aagaaaatta
     4981 aagggcttga tttccattta tctattgtaa atagccccca actatataat gatgatggtc
     5041 atttgtttga ttttttgcgt aatgaaagag ttcatgccat gttcctcgac tacgaagcgg
     5101 ccaaagatta tgcgacccgc tccaggctgg tcacggcggc gaatatccct tctttcggag
     5161 cgccagaatg atgttggtct ggccggattt tcatatggcg ggaaccacgt tgtgtctcaa
     5221 aatctctgat gttacattgc acaagataaa aatatatcat catgaacaat aaaactgtct
     5281 gcttacataa acagtaatac aaggggtgtt
//
