LOCUS       NZ_CP039574             4418 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014855 plasmid p10-2080.2, complete sequence.
ACCESSION   NZ_CP039574
VERSION     NZ_CP039574.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333149
            Assembly: GCF_004919225.1
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 4418)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Complete genome sequences of Canadian Typhimurium and I
            1,4,[5],12:i:-
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4418)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-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 Method                   :: unicycler v. 0.4.7; canu v. 1.8
            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                   :: 07/29/2023 04:02:09
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,897
            CDSs (total)                      :: 4,772
            Genes (coding)                    :: 4,660
            CDSs (with protein)               :: 4,660
            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)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 33 of 112
            Pseudo Genes (incomplete)         :: 87 of 112
            Pseudo Genes (internal stop)      :: 19 of 112
            Pseudo Genes (multiple problems)  :: 26 of 112
            Pseudo Genes (short protein)      :: 1 of 112
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039574.1.
            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..4418
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014855"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p10-2080.2"
                     /geo_loc_name="Canada: QC"
                     /collection_date="2010-03-11"
                     /collected_by="Laboratoire de sante publique du Quebec"
     gene            1..276
                     /locus_tag="E5N96_RS25000"
                     /old_locus_tag="E5N96_24750"
     CDS             1..276
                     /locus_tag="E5N96_RS25000"
                     /old_locus_tag="E5N96_24750"
                     /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"
     gene            1566..1889
                     /locus_tag="E5N96_RS24760"
                     /old_locus_tag="E5N96_24760"
     CDS             1566..1889
                     /locus_tag="E5N96_RS24760"
                     /old_locus_tag="E5N96_24760"
                     /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            2098..>2532
                     /locus_tag="E5N96_RS25210"
                     /pseudo=""
     CDS             2098..>2532
                     /locus_tag="E5N96_RS25210"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            2567..3052
                     /locus_tag="E5N96_RS24770"
                     /old_locus_tag="E5N96_24770"
     CDS             2567..3052
                     /locus_tag="E5N96_RS24770"
                     /old_locus_tag="E5N96_24770"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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            3056..3271
                     /locus_tag="E5N96_RS24775"
                     /old_locus_tag="E5N96_24775"
     CDS             3056..3271
                     /locus_tag="E5N96_RS24775"
                     /old_locus_tag="E5N96_24775"
                     /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(3470..4021)
                     /locus_tag="E5N96_RS24780"
                     /old_locus_tag="E5N96_24780"
     CDS             complement(3470..4021)
                     /locus_tag="E5N96_RS24780"
                     /old_locus_tag="E5N96_24780"
                     /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"
     Typing          1280..1462
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.77"
                     /coverage="86.0"
                     /evalue="9.61e-57"
     Typing          complement(817..1304)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.081"
                     /coverage="94.0"
                     /evalue="7.71e-161"
     Typing          1880..3375
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.585"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggtgattg ttagtgtcgt gggtggaata tcacttttgc ttcttgtgtt tttatggtcg
       61 ataaaacgag gtcagaaaac agtgagagca tttgtttttc tgagtgccgt tgctgatgga
      121 aatagtgttg aatcagctaa cgagttggca aagcggatag atctttttgc tgcgagtgaa
      181 ctgcagaaaa aggctatgat aatggttgaa atggtatttg ggggaagtca gcttaaactg
      241 atctcacatg ccagacggga aggtttcgat cagtgaaatg tagattgtcc aacgtgttgg
      301 acaactatga taaagagact aagtgaccag gtcgctactg cgaaatatat attctttttc
      361 ggcgggtttt tagacagtat ctgtagaaga tagataaact catttagcat ttaacctcct
      421 ttttctattc tatggcggat aaggattcta tccttctata gtccgccctt attagttcta
      481 tagtagcccc taattgatag ggggagatag atttatacat aagacttttc ccttatgata
      541 tggcatcggc tagataaagg gaggcggatg acaaccgaag aaaccaactc tgaacactaa
      601 tctaaaagga tcttcttgag atcctttttt tctgcgcgta atctcttgcc ttgaaaacga
      661 aaaaaccacc ttgccgggtg gtttttcgaa ggttcgcaag agttgacgct cttttgaacc
      721 gcggtaactg gcttggagga gcacagtcac caaaactgtc ctttcagtgt agccttatcg
      781 cacccgaaat ttcaagactc tcctcctcta aacctgttac cagtggctgc tgccagtggc
      841 gcttttgcat gtctttccgg gttggactca agacgatagt taccggacaa ggcgcagcag
      901 tcggactgaa cggggggttc gtgcatacag tccatcctgg agcgaactgc ctacccggaa
      961 ctgagtgtca ggcgtggaat gagacaaacg cggccataac agcggaatga caccggtaaa
     1021 ccgaagggca ggaatgcggg ggagcacgag ggagccatca gggggaaacg cctggtatct
     1081 ctaagccgca tcgggtttcg ccaccactga tttgagcgtc tgattttgtg atgctcgtca
     1141 ggggggcgga gcctatggaa aaacggcagc gccgtatcct ttttccggcc tttcctgact
     1201 tgagtgccat ctctttatct tgtcattcgt gagcaggtaa cgcccgccgc agcctcacgg
     1261 caggagcgta gcgaccgagt gagcgaggag gcgtcatgtc accgttacct gcattttgca
     1321 cttacgccct atagccgcat tttcccttgc aacatgaata acttccctga attaccactc
     1381 cgatctaaca tattcagcca gtatacactc cgctagcgct acgtgactgg ttcagggctg
     1441 cgccccgaaa cccgctaaaa ccactgacgc gcctgcggct tgtccaacac cgcgccgacc
     1501 gggaaaagat ttcccgcccg tcccggcgtt atcaggaggc cggattggca gacaaacgca
     1561 gcaaaatgct cacgatgtgg gtgaccgaag atgagcaccg ccgtctgctg gagcgctgcg
     1621 acggtaaaca gcttgcagcc tggatgcgcc agacgtgcct ggacgagaaa cccgcccgcg
     1681 ccggcaagct tccctcgctc tcgccggcgc tgcttcgtca gcttgccggc atggggaaca
     1741 acctcaacca gattgcccgg caggttaacg ccggtggtgg cagcgggcac gaccgcgtgc
     1801 aggtcgtcgc cgcgctgatg gccatagatg ccggactcga gcggctgcgg catgccgtgc
     1861 tggaaaaggg tgcagacgat gatcgttaag tttcacccgc gagggcgcgg cggtggcgcc
     1921 ggtccggtgg attatctgct ggggaaagac cgacagcgcg acggcgccac cgttctgcag
     1981 gggaagccgg aagaagtcag ggagcttatc gacgcctcgc cctacgcaaa aaagtacaca
     2041 tccggcgtcc tgtcctttgc cgaaaaggat ttaccgcccg ggcagcgcga aaagctgatg
     2101 gcgagctttg aacgggttct gatgcccgga ctcgataaag accagtacag cgtgctgtgg
     2161 gttgagcacc aggataaggg gcggctggag ctgaacttcc tgatcccgaa cacggagctg
     2221 ctgaccggca agcgtctcca gccgtattac gaccgcgccg accgtccgcg cattgatgcc
     2281 tggcagacca tcgtgaacgg caggctgggg ctgcatgacc cgaacgcgcc tgaaaaccgg
     2341 cgggcgctgg tcacgccgtc cgcgctgccg aaaacgaagc aggaagccgc tcaggcaatt
     2401 acacggggtt tactggcctt agcctcgtcc ggggagctga aaacccgcca ggacgtcact
     2461 gaggcgctgg aaagcgcagg ttttgaggtg gtacgcacca caaaaagcag catcagcatt
     2521 gccgacccgg acggggggcg aaacatccga ctgaagggag ccatctatga acagtctttt
     2581 aacgctggca aaggacttag agcagaaatc gaaagcgcag cagcagagta ccggcgagat
     2641 gctgaaagcc gcattcagcg agcacgagaa gtctgtcaga gcggaactga gcgaaagcga
     2701 gaagagaatc agcgccgcca tcctcgacca cgaccggaag ctgtcctcag ccatgagcca
     2761 gcgcacgaaa ggcatggtgc gtatggtcag ccagacgtgg ctgaccatcg tcctggtgtc
     2821 tacactgctg acagcatcgg gcgcaagcat tctgtggtgg caggggcagc agatactcga
     2881 caattacacg atcatccggg agcagaagag cacgcaggcc atgctgtccg agaggaacag
     2941 cggcgtgcag ctctcgacct gcggagagca gagacgccgc tgcgtgaggg tgaacccgga
     3001 agcgggacgg ttcggagagg attcgagctg gatgatactg gcggggaaat agcacatgac
     3061 ggagctggaa aaacagttgc tgagcgcatt agagcagcta cagcaggact actcgaaaag
     3121 gctggacgag tgggagaacg ccttcgcgga atggcggacg atgtctggtc ttatgcaacg
     3181 ggagaacgcg gcgctgagcg agcgcgtcac gggcttgagc aggcaggtgc agagtttgag
     3241 cgagcagctg cgccggttgt cacaaggctg aacgtgatag aggcacatcg tgagcaggaa
     3301 cgggcggcgc agcatcagaa agcgctggag ctggaacgat ctcagcgaca gcgaacgtac
     3361 aacggtccgt cactttgaat ctgtgcgccg gaaaagcatg ggcttgctgt ttctggcgca
     3421 caggttcagt tctagaacat gaggctgcta tcttattgtt cacgcttcat cagatcttga
     3481 tgcttattgt tatggctgag ctatcaatcc ctgttgcgtt gctaatatcc tttttggctc
     3541 tttcaattgc ctcgttaagg gagagttttt ctgttttctc ttcagccaga ccaggaatca
     3601 ctgtattagg aaccgatggg gatgaaggat ggaatttctt ccattccagt tgttccggtg
     3661 ttaccccaat acgtaaaaaa gcttcctgtg cgctcaggta agcaaccgga tagcgctgac
     3721 catcggttag cattttccat gcttttggcg tgtgaatttc tgcgtattca tcaaaggtta
     3781 tgacgttcct gtcgtcgtaa tcagggcttt taaaacaccc ggtaattttg gcgatcagga
     3841 atgctgtgcc gtgttccagg tcttttactg cccacgtttc ccttctgttt cttactgcta
     3901 tgaggtaatc ggcatcgttg agcctgtctg ttctggcatg ccagtagcct gatcccccct
     3961 cagttctcat tatgttcaaa tccttcccgg taaaaaccac aacagctttc atatctttca
     4021 tatagaaacc cttaataggt gagtaaattt cattttttat gaaatctata cgatagaatt
     4081 ggtgttgtaa atgttttttt atgcgataaa atacagtctc ccctacctct tttattgtta
     4141 gtggtaagac ttcctgtttg gtttttttga taaaccggtt aaaacagggg cttggacgag
     4201 gatatacatt aaaagcatga gccattcacg tggctgcatg gctatgcagc cgcgtgaaat
     4261 ttatcaggcg cagaatgcgc agtttagcgg ggagtttact gccggtttta ccgggctaac
     4321 gccgctttca cgttgaaccc gtccggagcg gtgcgggcaa gggatgttat ggtaaatgaa
     4381 gcaacttctg aagttatcta agataaggtg atcgaaat
//
