LOCUS       NZ_CP037878             6760 bp    DNA     circular CON 18-FEB-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            PNCS014863 plasmid pPNCS014863_S1, complete sequence.
ACCESSION   NZ_CP037878
VERSION     NZ_CP037878.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10953954
            Assembly: GCF_009756585.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6760)
  AUTHORS   Walker,M. and Clark,C.
  TITLE     Distribution of heavy metal elements in Salmonella 4,[5],12:i:-
            populations and association with the monophasic genotypes and
            phenotype
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6760)
  AUTHORS   Walker,M. and Clark,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAR-2019) Infectious Diseases, Public Health Agency of
            Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2018
            Assembly Method :: SPAdes v. FEB-2018; Unicycler v. FEB-2018
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 58.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/18/2024 02:51:31
            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)                     :: 4,897
            CDSs (total)                      :: 4,775
            Genes (coding)                    :: 4,658
            CDSs (with protein)               :: 4,658
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 35 of 117
            Pseudo Genes (incomplete)         :: 94 of 117
            Pseudo Genes (internal stop)      :: 17 of 117
            Pseudo Genes (multiple problems)  :: 27 of 117
            Pseudo Genes (short protein)      :: 1 of 117
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP037878.1.
            Bacteria and source DNA available from Public Health Agency of
            Canada, PI: Clifford Clark, Winnipeg, Manitoba, Canada.
            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..6760
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014863"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pPNCS014863_S1"
                     /geo_loc_name="Canada: Britsh Columbia"
                     /lat_lon="49.28 N 123.12 W"
                     /collection_date="2011-01-27"
                     /collected_by="BCCDC Public Health Laboratory"
     gene            complement(88..282)
                     /locus_tag="E1967_RS00005"
                     /old_locus_tag="E1967_00010"
     CDS             complement(88..282)
                     /locus_tag="E1967_RS00005"
                     /old_locus_tag="E1967_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1162..3027
                     /locus_tag="E1967_RS00010"
                     /old_locus_tag="E1967_00015"
     CDS             1162..3027
                     /locus_tag="E1967_RS00010"
                     /old_locus_tag="E1967_00015"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006816428.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /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="WP_021558993.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGVDIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCILEGGMTKENQGKDEIYYNEIIAMDEVDSLLSPKAFTNAKRYTKEGVK
                     ENITKFNDDENLIIKGNNLIALHSIKKLYAGKVKLIYIDPPYNTGSDSFKYNDRFNRST
                     WLTFMKNRLEVAKEMLSDDGFIFIQCDDNESAYLKVLCDSIFGEENYRNSIYWHRTYAG
                     KTVKSKLPWNTDTILFYSKKESSLLEPYTAELSAADIKSYNKDDFDGRGKYNTVSLQKT
                     SSPGPQTTYDYIDNTGKKWSCPEKGWRMTKEKLKALENDNRLYITDKTIREKYYLKERK
                     EIGKQIDNFWHDIGNLNRVSDVAFIDGQKTEKLMQRIISLASKENDIVLDFHLGSGTSA
                     AAAHKMGRRYIGIEQMDYINEITVPRLQKVIEGEQGGISKDVNWQGSGSFVYVELVELN
                     AYFIHEIQKAQSTEELEKLFAVMKTEAYLNYQVALENVLSAEYEVDGILHKVAFSELEL
                     HEQKQLLIEILDKNQLYVNVSDMEDSDLNISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     gene            3032..5668
                     /locus_tag="E1967_RS00015"
                     /old_locus_tag="E1967_00020"
     CDS             3032..5668
                     /locus_tag="E1967_RS00015"
                     /old_locus_tag="E1967_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 -
                     hydrolase activity [Evidence IEA]"
                     /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="WP_052512605.1"
                     /translation="MAKKPKSAGREKLLFNKLKQFDEPGLFHDNYQTPDYIQANLKDIL
                     RPYQHSALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKEFGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSHELEIDGEKITIAPVDIFPSVPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILDLRPDNRLFEFTATIDLANKDIGQKYRDKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESIRRHLANKKLQLSSDTSIWHKVIQRYADSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTVEHARLKEDFKKSAVYQAGKLYFNEVEEIERSSRNWETYSLETRFEIQYQI
                     ACEESLDNLTGTKGGIIKPEPLVLDERFYRKAMQRISFYALDNLKRFFPKLTGIREFIR
                     SDAYLGKLKITVSVPQSLDFTTVPAKDKLHLLENVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVAINQKITAAPTIGKKWYVYDNAILNQLEHRLIKMLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(6069..6182)
                     /locus_tag="E1967_RS24425"
     CDS             complement(6069..6182)
                     /locus_tag="E1967_RS24425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071588254.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAATGN"
                     /name="replication initiation protein"
     Typing          319..417
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          542..797
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.248"
                     /coverage="89.0"
                     /evalue="2.69e-98"
     Typing          6588..6757
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.076"
                     /coverage="98.0"
                     /evalue="9.34e-76"
     Typing          complement(6111..6634)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.359"
                     /coverage="94.0"
                     /evalue="0.0"
ORIGIN
        1 ccgctaaaac cccctgacgc gccctgacgg gcttgtctgc tgacgaaaac gcccacggga
       61 aagccgtgac cgcctccgtc agcttcgtta tgttcctgtt tcactttcgg cctcaaagcg
      121 aatctggatg ctgttctgga gttcttctgc gagttcgtgc agtcgttcgc acatggccgc
      181 ctgttcgtcg gcatccagag catccagttt ttcaagcagt gtcaggctct ggcttttgat
      241 aaatcgcgcc atattcagcg cagtttgttg ttgtttgttc accttccgtt gttctccgtc
      301 agttccgggt gtcgggggga ccctgagcag gtggtaattg taagacgttg cgggcgacgg
      361 tattacaatt gcacatcctg tcctgtttct ttaggacgta tcatggcaca gcatatcaac
      421 tgataaataa tccctgtgca gtgcagccgc tgttgcataa aatttcgctc tgcgtcgagt
      481 gtttcttaat caataattcc gctgatactc cggaaaaacg cgagtctgtt ctcatgcctg
      541 aaatgcccac accccacgca aaaacaattt tttgctgatt tttctttata aatagagagt
      601 tatgacaaat tagttcttct tgctctcttt gtgatattta aaaaagcggt gtcggcgcag
      661 ctacaacacc gcgccgacac cgctttttag gggtggtact gactattttc ataaaaaaca
      721 tcatcttata ttaggggtgc tgctagcggc gcggtgtgtt tttttacagg acgcccctgg
      781 gggcgctgct aggggtgtct gttcagatat gtagcaatga gtcagggatt cacgaactga
      841 aaatgtccga aaatgtgtct catgggtact gtatgcgccc aaaccgatcg tcattcactt
      901 tcatgcatag ctatgcagtg agctgaaagt gatcctgacg catttttccg gtttaccccg
      961 gggaaaacat ctctttttgc ggtgtttgcg gcagaatcgc gttcagcgcg ttttagcggt
     1021 gcgcgcaaga gcgtttatgt taaatactac tcgttctggt gcattttccc gcaactgaat
     1081 ccaactcatc gctgttgggt tccagcgccg aacgctatac cttacaatca ttccaatatt
     1141 taacagtcat aaggccatga catgcagacc gaattaataa aagaacttaa caaggtttta
     1201 aaagcgttcc cgcaattctg gaatggagag gaattacaac gttcaatggt gagtgacgct
     1261 atcagtcaaa agcagccaga tcttatcaag gcattagtcg ataatgaaaa agtccgctct
     1321 gtttatggtg tggatattga tggcattttt atctttgatt ttgacaaatt atgtggtctt
     1381 ctaaaataca aagaatattg ggctaatagc tttactaaat accggaacaa agtgggatta
     1441 actagcgaag gtaaatacct tgattacagt tctgatgtgg tgctggattt tcctttcaag
     1501 gattgtattc ttgaaggtgg aatgaccaaa gaaaatcagg gaaaagatga gatttattat
     1561 aatgaaatca tagcaatgga tgaagttgac tctttgcttt ctcccaaggc gttcactaat
     1621 gctaagcgat ataccaaaga gggggtaaaa gaaaatatca ctaaatttaa cgatgatgaa
     1681 aatttaataa ttaagggaaa caatctcatt gcactacatt caataaaaaa actttacgca
     1741 ggaaaagtaa agttaattta tatagacccg ccttacaata cagggagtga tagctttaag
     1801 tataatgatc gattcaatcg ctcaacatgg ttgacattca tgaaaaatag gcttgaggtg
     1861 gctaaagaaa tgctttccga tgatggcttt atttttattc aatgcgatga taatgaatca
     1921 gcatatctta aagttttatg tgattcaatt tttggagaag agaattatag aaactcaatc
     1981 tattggcata gaacctacgc agggaaaact gtaaaaagta agttgccatg gaatacagat
     2041 acaatattgt tttattctaa aaaagaaagt tcattattag agccatatac agcagaactt
     2101 agtgctgctg acattaaatc ctataacaag gatgattttg atggaagggg taaatacaac
     2161 actgttagct tgcaaaaaac aagctctcca gggccgcaaa caacttatga ttatatagat
     2221 aatacaggta agaaatggag ttgccctgaa aaagggtgga gaatgacaaa ggaaaagtta
     2281 aaggctttgg aaaacgacaa taggctatat atcactgaca aaacaatacg agaaaaatat
     2341 tatcttaaag aaagaaaaga gatcgggaaa caaatagata atttttggca tgacattggg
     2401 aatttaaata gggtttccga tgttgctttt attgatggac aaaaaactga aaaattaatg
     2461 caacggataa ttagccttgc ttccaaagaa aatgatatcg tcttggactt tcatctcggc
     2521 agcggaacta gcgcagcagc agcccataaa atgggacgtc gctatatcgg tattgagcag
     2581 atggattaca tcaatgagat caccgtgcca cgtttgcaaa aagtcattga gggtgagcag
     2641 ggaggtatct caaaagacgt caactggcag gggagcggca gctttgtcta cgttgaacta
     2701 gtggaactga acgcttactt catacatgaa atccagaaag cgcagtccac ggaagaactc
     2761 gaaaaactct ttgccgtgat gaagacagag gcatatctca actatcaggt ggctctggaa
     2821 aatgtgctgt ccgctgagta cgaagtggat gggatcctcc ataaggtagc attcagtgaa
     2881 ctggaactgc atgagcagaa gcagcttttg attgaaatcc tagataagaa ccagctctac
     2941 gtgaatgtct ctgatatgga ggacagcgac ctgaacattt cagagagtga taaagccttt
     3001 acccgcagct tctacggaat ggagtgacgg catggcgaag aaaccgaagt cagcaggtag
     3061 agagaagctg ctgtttaaca agctgaagca gttcgatgaa ccaggactgt tccacgataa
     3121 ctatcagacg ccggactata ttcaggcaaa cctgaaagat atcctgcgtc cctatcagca
     3181 cagcgcactg cgttacctgc attacacgca acgtaaacgt gatgacgcgc ttctgcatta
     3241 ccgtcacctg ctgtttcaca tggcaaccgg tgcagggaaa acgatggtta tggcaggaac
     3301 gatactctat ctatttaaag agttcgggta tcagaacttc atctttttcg tacataccga
     3361 cgcgattatc cagaaaacgc gagagaacct acttaacccg caatcgccga agtacctgtt
     3421 cagtcatgag ctggaaatcg acggggaaaa aatcaccatc gcaccggtag atatattccc
     3481 gtccgtaccg gaacgcaaca cgatttacct caagctctcg actatccata agatgcacga
     3541 tgagctgaac agctatcgag agaacagcat tacctacgag gatttaaaag aaatcccgct
     3601 tgtgctactc ggtgacgagg cgcatcactt caacgccggc accaaagcta gaggcaagtc
     3661 gaaaacctca ccggagaacg aggagcagac ttgggagcgt acgattgaga acatcctcga
     3721 cctgcgaccg gataaccgcc tgttcgagtt caccgctacc attgaccttg caaacaaaga
     3781 tatcggacag aaataccgtg acaaggtggt atatcagtat gatctgaagc agttcatgtc
     3841 agacggttac tcgaaaaagg tcatgctgtt ggaagcaaac cagaacgaca gcgacaagat
     3901 gctcgatgcg gtactgttaa gccagtaccg taaactgacg gcagcagatc acggcatcac
     3961 cggctttaaa ccggtcattc tgttcaagtc gaataagatt gcgatatcaa aggcgaagca
     4021 ggaggagttt tcgcaactga ttgccgccat gacacctgag agcatcagac gtcatctggc
     4081 taacaaaaaa ctccagctca gctctgacac cagtatctgg cataaagtga ttcagcgtta
     4141 cgctgacagt gatttagtga cggtgactgg acaaattcag gaggacttta acgactttaa
     4201 cctgctgaac gtcaacaagt cagacctgct ggaggaaaac cccgtcctgc tgaatacact
     4261 ggaagaagtc gataatccag tgagagccgt ctttgctgtc gcgaaggtga atgaaggctg
     4321 ggacgtactt aacctctacg atattgttcg cataagcgag caggcgagca gcagcaaaac
     4381 cagcacggac agcgaagcgc agcttattgg gcgaggtgcg cgttactacc cgttcattta
     4441 tgacggtcaa cgtagcttca cccgccgttt tgataacagt acgaaggatt tgagcgtact
     4501 ggagcaactg cactatcaca ccatcaatga accggcgtac atcaaaacac tgcacgcctc
     4561 tctggagcag gcggacattg acgtgcatca ggatggcgga ggtacggttg aacacgccag
     4621 attgaaagaa gactttaaaa agtccgccgt gtatcaggcg ggtaagctgt actttaacga
     4681 agtggaagag attgagagaa gcagccgaaa ctgggaaacc tactcgctgg aaacacgctt
     4741 tgaaatacag tatcagatcg cttgcgagga gtcgctggac aacctgacag gcacaaaggg
     4801 ggggatcata aaaccggaac cactggtact ggacgagcgt ttttaccgca aggcgatgca
     4861 aagaatcagc ttttacgcgc tagataacct gaaacgcttc ttcccgaaac tgacaggtat
     4921 tcgggagttc atacgcagtg acgcctatct tggtaagctg aaaatcaccg tcagcgtacc
     4981 gcagtcactg gatttcacca ccgtaccggc aaaagataag ctgcacctac tggaaaacgt
     5041 tttgctgcgt atctcagaga atgtgcgtcg caatgaccag aaggtaaaag gcacgtaccg
     5101 atttatcagc cagccggtga aagaggtgat taaagattac agtttgcata ttgacccgtc
     5161 ggtagccatt aaccagaaaa tcaccgccgc tcccaccatt ggtaaaaaat ggtacgtgta
     5221 cgataatgcg atactaaatc agcttgagca tcgtctgata aaaatgctgg aagcattcat
     5281 gccgaagcta aaagcgcgtt atgacgatat ttacgtactg cgtaacgacg agcagtcaac
     5341 gcgctttaag ctcacggagt tcggcggcgt gcgtgggttt atgccagatt tcatcatgat
     5401 actgacgcgc cattcagaca acacttactg gcaggtgttc cttgaaccga agggggatga
     5461 ccgtctgctg gatgacgcat ggaaagaacg gatgctcgaa acactgaatg acagggagcg
     5521 cattgtaatt gatgaaaatg agcacgtcag actggttggg attaaattct ttgccaatag
     5581 ccagatggac gtttttgtca gcgacatgca gaacaagctg aatgatggag aatcgctcga
     5641 aacctcctcg ctctccctac cactgtaagt cacgacaata aaataacgga gcattacgct
     5701 ccgttatttt attgttatct cgaactacct cccagggagg tgatgattgc tcctgtaatg
     5761 gttgcattgt ttgttcttgc tgttgcgaat cattagtttt gaatggtggt taaaaaccgt
     5821 tcgctatgtt tatgcctggg gggggatgag ggggaaaaga ttcaaggatc ctcttgtgat
     5881 cctttttttc tgcgcgtaat ctgcagcctg taaacgaaaa aaccaccctg gcaggtggtt
     5941 tttcgaaggt tagctaatcc tggcagatta tctaaccggg taactggctt ggaggagcgc
     6001 agtcaccaaa atctgttctt tcagtttagc cttaacaggt gcataacttc aagacaaact
     6061 cctctaaatc agttaccagt ggctgctgcc agtggcgata agtcgtgtct taccgggttg
     6121 gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc
     6181 acacagccca gcttggagcg aacgacctac accgaaccga gataccaaca gcgtgagcta
     6241 tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg
     6301 gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt
     6361 cctgtcgggt ttcgccgact ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg
     6421 cggagcctat ggaaaaacgc cagcggcgcg gcctttttcc ggttcctgct cttttgctca
     6481 catgttcttt ccggccttat cccctgattc ggtggataat ctaattactg tctttgcgtg
     6541 agttgatacc gctcgccgca gccgaacgac cgagcgtagc gagtcagtga gcgaggaagc
     6601 ggaatatctc ctgtatcgca tattctgctg acgcgccggt gctgcctttt ttctcctgcc
     6661 acatgaagca cttcactgat tttcgcaatc gtggcaacat agtaagccag tatacactcc
     6721 gctatcgcta cgtgactggg tcatggctgc gccccgacac
//
