LOCUS       NZ_CP036173             4418 bp    DNA     circular CON 18-FEB-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            PNCS009777 plasmid pPNCS009777_S1, complete sequence.
ACCESSION   NZ_CP036173
VERSION     NZ_CP036173.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10953951
            Assembly: GCF_009756455.1
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 4418)
  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  JOURNAL   Unpublished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 4418)
  AUTHORS   Walker,M. and Clark,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-FEB-2019) Infectious Diseases, Public Health Agency of
            Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2017
            Assembly Method                   :: SPAdes v. DEC-2016
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 115.0x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/18/2024 02:48:52
            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)                     :: 4,891
            CDSs (total)                      :: 4,766
            Genes (coding)                    :: 4,658
            CDSs (with protein)               :: 4,658
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 108
            CDSs (without protein)            :: 108
            Pseudo Genes (ambiguous residues) :: 0 of 108
            Pseudo Genes (frameshifted)       :: 30 of 108
            Pseudo Genes (incomplete)         :: 87 of 108
            Pseudo Genes (internal stop)      :: 19 of 108
            Pseudo Genes (multiple problems)  :: 26 of 108
            Pseudo Genes (short protein)      :: 1 of 108
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP036173.1.
            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..4418
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS009777"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pPNCS009777_S1"
                     /geo_loc_name="Canada: Quebec"
                     /lat_lon="46.81 N 71.21 W"
                     /collection_date="2009-06-11"
                     /collected_by="Institut national de sante publique du
                     Quebec"
     gene            349..900
                     /locus_tag="EYC53_RS00005"
                     /old_locus_tag="EYC53_00005"
     CDS             349..900
                     /locus_tag="EYC53_RS00005"
                     /old_locus_tag="EYC53_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            complement(1099..1314)
                     /locus_tag="EYC53_RS00010"
     CDS             complement(1099..1314)
                     /locus_tag="EYC53_RS00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137421.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1318..1803)
                     /locus_tag="EYC53_RS00015"
     CDS             complement(1318..1803)
                     /locus_tag="EYC53_RS00015"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_015059929.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<1838..2542)
                     /locus_tag="EYC53_RS24695"
                     /pseudo=""
     CDS             complement(<1838..2542)
                     /locus_tag="EYC53_RS24695"
                     /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(2481..2804)
                     /locus_tag="EYC53_RS00025"
                     /old_locus_tag="EYC53_00015"
     CDS             complement(2481..2804)
                     /locus_tag="EYC53_RS00025"
                     /old_locus_tag="EYC53_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_001347450.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3444..3578
                     /locus_tag="EYC53_RS24700"
                     /old_locus_tag="EYC53_00020"
     CDS             3444..3578
                     /locus_tag="EYC53_RS24700"
                     /old_locus_tag="EYC53_00020"
                     /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="replication initiation protein"
                     /protein_id="WP_071996625.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGNRFRGGES"
                     /name="replication initiation protein"
     gene            complement(4094..4369)
                     /locus_tag="EYC53_RS00030"
                     /old_locus_tag="EYC53_00025"
     CDS             complement(4094..4369)
                     /locus_tag="EYC53_RS00030"
                     /old_locus_tag="EYC53_00025"
                     /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_031611837.1"
                     /translation="MVIVSVVGGISLLLLVFLWSIKRGQKTVRAFVFLSAVADGNSVES
                     ANELAKRIDLFAASELQKKAMIMVEMVFGGSQLKLISHARREGFDQ"
                     /name="hypothetical protein"
     Typing          complement(2906..3091)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.421"
                     /coverage="87.0"
                     /evalue="9.61e-57"
     Typing          3067..3554
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.081"
                     /coverage="94.0"
                     /evalue="7.71e-161"
     Typing          complement(996..2491)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.585"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taacatccct tgcccgcacc gctccggacg ggttcaacgt gaaagcggcg ttagcccggt
       61 aaaaccggca gtaaactccc cgctaaactg cgcattctgc gcctgataaa tttcacgcgg
      121 ctgcatagcc atgcagccac gtgaatggct catgctttta atgtatatcc tcgtccaagc
      181 ccctgtttta accggtttat caaaaaaacc aaacaggaag tcttaccact aacaataaaa
      241 gaggtagggg agactgtatt ttatcgcata aaaaaacatt tacaacacca attctatcgt
      301 atagatttca taaaaaatga aatttactca cctattaagg gtttctatat gaaagatatg
      361 aaagctgttg tggtttttac cgggaaggat ttgaacataa tgagaactga ggggggatca
      421 ggctactggc atgccagaac agacaggctc aacgatgccg attacctcat agcagtaaga
      481 aacagaaggg aaacgtgggc agtaaaagac ctggaacacg gcacagcatt cctgatcgcc
      541 aaaattaccg ggtgttttaa aagccctgat tacgacgaca ggaacgtcat aacctttgat
      601 gaatacgcag aaattcacac gccaaaagca tggaaaatgc taaccgatgg tcagcgctat
      661 ccggttgctt acctgagcgc acaggaagct tttttacgta ttggggtaac accggaacaa
      721 ctggaatgga agaaattcca tccttcatcc ccatcggttc ctaatacagt gattcctggt
      781 ctggctgaag agaaaacaga aaaactctcc cttaacgagg caattgaaag agccaaaaag
      841 gatattagca acgcaacagg gattgatagc tcagccataa caataagcat caagatctga
      901 tgaagcgtga acaataagat agcagcctca tgttctagaa ctgaacctgt gcgccagaaa
      961 cagcaagccc atgcttttcc ggcgcacaga ttcaaagtga cggaccgttg tacgttcgct
     1021 gtcgctgaga tcgttccagc tccagcgctt tctgatgctg cgccgcccgt tcctgctcac
     1081 gatgtgcctc tatcacgttc agccttgtga caaccggcgc agctgctcgc tcaaactctg
     1141 cacctgcctg ctcaagcccg tgacgcgctc gctcagcgcc gcgttctccc gttgcataag
     1201 accagacatc gtccgccatt ccgcgaaggc gttctcccac tcgtccagcc ttttcgagta
     1261 gtcctgctgt agctgctcta atgcgctcag caactgtttt tccagctccg tcatgtgcta
     1321 tttccccgcc agtatcatcc agctcgaatc ctctccgaac cgtcccgctt ccgggttcac
     1381 cctcacgcag cggcgtctct gctctccgca ggtcgagagc tgcacgccgc tgttcctctc
     1441 ggacagcatg gcctgcgtgc tcttctgctc ccggatgatc gtgtaattgt cgagtatctg
     1501 ctgcccctgc caccacagaa tgcttgcgcc cgatgctgtc agcagtgtag acaccaggac
     1561 gatggtcagc cacgtctggc tgaccatacg caccatgcct ttcgtgcgct ggctcatggc
     1621 tgaggacagc ttccggtcgt ggtcgaggat ggcggcgctg attctcttct cgctttcgct
     1681 cagttccgct ctgacagact tctcgtgctc gctgaatgcg gctttcagca tctcgccggt
     1741 actctgctgc tgcgctttcg atttctgctc taagtccttt gccagcgtta aaagactgtt
     1801 catagatggc tcccttcagt cggatgtttc gccccccgtc cgggtcggca atgctgatgc
     1861 tgctttttgt ggtgcgtacc acctcaaaac ctgcgctttc cagcgcctca gtgacgtcct
     1921 ggcgggtttt cagctccccg gacgaggcta aggccagtaa accccgtgta attgcctgag
     1981 cggcttcctg cttcgttttc ggcagcgcgg acggcgtgac cagcgcccgc cggttttcag
     2041 gcgcgttcgg gtcatgcagc cccagcctgc cgttcacgat ggtctgccag gcatcaatgc
     2101 gcggacggtc ggcgcggtcg taatacggct ggagacgctt gccggtcagc agctccgtgt
     2161 tcgggatcag gaagttcagc tccagccgcc ccttatcctg gtgctcaacc cacagcacgc
     2221 tgtactggtc tttatcgagt ccgggcatca gaacccgttc aaagctcgcc atcagctttt
     2281 cgcgctgccc gggcggtaaa tccttttcgg caaaggacag gacgccggat gtgtactttt
     2341 ttgcgtaggg cgaggcgtcg ataagctccc tgacttcttc cggcttcccc tgcagaacgg
     2401 tggcgccgtc gcgctgtcgg tctttcccca gcagataatc caccggaccg gcgccaccgc
     2461 cgcgccctcg cgggtgaaac ttaacgatca tcgtctgcac ccttttccag cacggcatgc
     2521 cgcagccgct cgagtccggc atctatggcc atcagcgcgg cgacgacctg cacgcggtcg
     2581 tgcccgctgc caccaccggc gttaacctgc cgggcaatct ggttgaggtt gttccccatg
     2641 ccggcaagct gacgaagcag cgccggcgag agcgagggaa gcttgccggc gcgggcgggt
     2701 ttctcgtcca ggcacgtctg gcgcatccag gctgcaagct gtttaccgtc gcagcgctcc
     2761 agcagacggc ggtgctcatc ttcggtcacc cacatcgtga gcattttgct gcgtttgtct
     2821 gccaatccgg cctcctgata acgccgggac gggcgggaaa tcttttcccg gtcggcgcgg
     2881 tgttggacaa gccgcaggcg cgtcagtggt tttagcgggt ttcggggcgc agccctgaac
     2941 cagtcacgta gcgctagcgg agtgtatact ggctgaatat gttagatcgg agtggtaatt
     3001 cagggaagtt attcatgttg caagggaaaa tgcggctata gggcgtaagt gcaaaatgca
     3061 ggtaacggtg acatgacgcc tcctcgctca ctcggtcgct acgctcctgc cgtgaggctg
     3121 cggcgggcgt tacctgctca cgaatgacaa gataaagaga tggcactcaa gtcaggaaag
     3181 gccggaaaaa ggatacggcg ctgccgtttt tccataggct ccgcccccct gacgagcatc
     3241 acaaaatcag acgctcaaat cagtggtggc gaaacccgat gcggcttaga gataccaggc
     3301 gtttccccct gatggctccc tcgtgctccc ccgcattcct gcccttcggt ttaccggtgt
     3361 cattccgctg ttatggccgc gtttgtctca ttccacgcct gacactcagt tccgggtagg
     3421 cagttcgctc caggatggac tgtatgcacg aaccccccgt tcagtccgac tgctgcgcct
     3481 tgtccggtaa ctatcgtctt gagtccaacc cggaaagaca tgcaaaagcg ccactggcag
     3541 cagccactgg taacaggttt agaggaggag agtcttgaaa tttcgggtgc gataaggcta
     3601 cactgaaagg acagttttgg tgactgtgct cctccaagcc agttaccgcg gttcaaaaga
     3661 gcgtcaactc ttgcgaacct tcgaaaaacc acccggcaag gtggtttttt cgttttcaag
     3721 gcaagagatt acgcgcagaa aaaaaggatc tcaagaagat ccttttagat tagtgttcag
     3781 agttggtttc ttcggttgtc atccgcctcc ctttatctag ccgatgccat atcataaggg
     3841 aaaagtctta tgtataaatc tatctccccc tatcaattag gggctactat agaactaata
     3901 agggcggact atagaaggat agaatcctta tccgccatag aatagaaaaa ggaggttaaa
     3961 tgctaaatga gtttatctat cttctacaga tactgtctaa aaacccgccg aaaaagaata
     4021 tatatttcgc agtagcgacc tggtcactta gtctctttat catagttgtc caacacgttg
     4081 gacaatctac atttcactga tcgaaacctt cccgtctggc atgtgagatc agtttaagct
     4141 gacttccccc aaataccatt tcaaccatta tcatagcctt tttctgcagt tcactcgcag
     4201 caaaaagatc tatccgcttt gccaactcgt tagctgattc aacactattt ccatcagcaa
     4261 cggcactcag aaaaacaaat gctctcactg ttttctgacc tcgttttatc gaccataaaa
     4321 acacaagaag caaaagtgat attccaccca cgacactaac aatcaccata tttcgatcac
     4381 cttatcttag ataacttcag aagttgcttc atttacca
//
