LOCUS       NZ_CP044964             3353 bp    DNA     circular CON 17-NOV-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014881 plasmid pPNCS014881.3, complete sequence.
ACCESSION   NZ_CP044964
VERSION     NZ_CP044964.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333171
            Assembly: GCF_009017315.1
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 3353)
  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  JOURNAL   Unpublished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 3353)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-OCT-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                   :: 11/17/2023 03:18:00
            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)                     :: 5,086
            CDSs (total)                      :: 4,968
            Genes (coding)                    :: 4,840
            CDSs (with protein)               :: 4,840
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 41 of 128
            Pseudo Genes (incomplete)         :: 101 of 128
            Pseudo Genes (internal stop)      :: 20 of 128
            Pseudo Genes (multiple problems)  :: 31 of 128
            Pseudo Genes (short protein)      :: 1 of 128
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP044964.1.
            Bacteria and source DNA available from 16-7746.
            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..3353
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014881"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="pPNCS014881.3"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2016-10-01"
                     /collected_by="BC Centre for Disease Control"
                     /note="I 1,4,[5],12:i:-"
     gene            1..864
                     /locus_tag="E5O18_RS25810"
     CDS             1..864
                     /locus_tag="E5O18_RS25810"
                     /inference="COORDINATES: protein motif:HMM:NF015076.3"
                     /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_077248426.1"
                     /translation="MELYQQDLFATMPFPSRPLCSDDLSHGIWRETLEDALRRPYIQAN
                     PQRRVWVLLFDVDHPLAAMAWDAAGLPPPTWTAQNPENGHAHIAYALSAPVAKSDAARL
                     KPLRLLARIQHAMTDALSADRGYVGLITKTPNHARWRTTVWRPEPYGLDELRDYLPDNL
                     ELPRHIKKTEAVGVGRNVSLFESLRHWAYSHRRNYDNHTAWFCACLSHAEALNTFATPL
                     EFNELKATAKSVAKWTWERFDVAASNARFSEKQARRGRLGGMKGAPKTNTLRQMQLIDI
                     QAGLMQ"
                     /name="replication initiation protein"
     gene            861..1142
                     /locus_tag="E5O18_RS25665"
                     /old_locus_tag="E5O18_25665"
     CDS             861..1142
                     /locus_tag="E5O18_RS25665"
                     /old_locus_tag="E5O18_25665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010840487.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]; GO:0016987 - sigma factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006352 - DNA-templated transcription
                     initiation [Evidence IEA]; GO:0006355 - regulation of
                     DNA-templated transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sigma factor-like helix-turn-helix DNA-binding
                     protein"
                     /protein_id="WP_050952183.1"
                     /translation="MSGIKKIARERNMTAREAAQKFGKSPRTIQRLVALDRDEYLERAA
                     ERRQKVYDMRVTGAKWQEIAEAMGVSYGAVRSLYYQHCRHLKAAMPRQ"
                     /name="sigma factor-like helix-turn-helix DNA-binding
                     protein"
     gene            complement(1271..1480)
                     /locus_tag="E5O18_RS26080"
     CDS             complement(1271..1480)
                     /locus_tag="E5O18_RS26080"
                     /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_050952185.1"
                     /translation="MSQSQIEQQLAQALREVETEREALRRLLQTLKSEYEQTRRDNRKL
                     REQVEQLSEEFQELAQVLSTWRRW"
                     /name="hypothetical protein"
     gene            complement(1481..1900)
                     /locus_tag="E5O18_RS26085"
     CDS             complement(1481..1900)
                     /locus_tag="E5O18_RS26085"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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_050952187.1"
                     /translation="MSEILNLARSFEEKLKQQASDTDEKIKAALKQHESALLECLKTEQ
                     KKIESAIQEHSRRLRASLLKSWLGALIAMLAVLMLGGGILYWMTTEIRNRYAELDKLPN
                     AKVTTCGKLGRLCVEIDPIAPTYGPNGEYRVVKGG"
                     /name="MbeB family mobilization protein"
     gene            complement(<1887..2590)
                     /locus_tag="E5O18_RS26090"
                     /pseudo=""
     CDS             complement(<1887..2590)
                     /locus_tag="E5O18_RS26090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557251.1"
                     /note="frameshifted; 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(2580..2897)
                     /locus_tag="E5O18_RS25675"
                     /old_locus_tag="E5O18_25675"
     CDS             complement(2580..2897)
                     /locus_tag="E5O18_RS25675"
                     /old_locus_tag="E5O18_25675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011178376.1"
                     /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_013246618.1"
                     /translation="MTDAKRTKSIKIRVTDEELSELRERCPAGELAPWLRELGLGQKRP
                     RRAERVDPALLRQLAGVGNLLNQIARRINSGQWSYGDRVEILAALWHIEKRLQDININA
                     G"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(1216..2225)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.033"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2223..2590)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.187"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttggaattat accaacaaga cctgtttgca accatgccat ttcccagtcg tccgctgtgt
       61 tcggacgatc tgagccacgg catatggcgc gaaacgctag aggacgcgct acggcgtccc
      121 tacatccaag cgaacccaca acgccgcgtg tgggttctcc tgttcgacgt tgaccatccc
      181 ctggcggcga tggcgtggga cgcagccgga ctgccgccgc caacatggac ggcacaaaac
      241 ccggaaaacg gacacgccca cattgcttac gcactgagcg ctccggtggc gaagtcggac
      301 gcggcgcggc tcaaacccct gcgcctactg gcacgcatac agcacgccat gacagacgct
      361 ctgagtgccg acaggggcta tgtcggactg attaccaaga cgccaaacca tgcccgttgg
      421 cgcaccaccg tatggcgtcc tgagccatac ggcttggatg aactacgcga ctacctaccg
      481 gacaatctgg agttgcccag gcatatcaaa aaaaccgaag cggtcggcgt cggtcgcaat
      541 gtgtcgctgt ttgaatcact gaggcattgg gcgtacagcc accgccgcaa ctacgacaac
      601 catacggcgt ggttttgcgc ctgtttgagt catgccgaag cgctaaacac ctttgctacg
      661 cctttggagt tcaacgagct gaaagccacc gccaagagcg tagccaaatg gacatgggag
      721 cgattcgacg ttgccgccag taatgccaga ttttcagaaa aacaggcgcg ccgtgggcgc
      781 ttaggtggta tgaaaggagc acccaaaaca aacaccttac ggcaaatgca attgattgat
      841 atacaagcgg gtttgatgca atgagcggaa tcaaaaagat cgccagagag cgaaacatga
      901 cggcgaggga ggccgcgcaa aaattcggaa aatcaccgcg cacaatccag cgccttgtag
      961 cgctcgatcg tgacgaatac ctagaacgcg ccgcggaacg gcgtcagaag gtctacgaca
     1021 tgcgcgttac tggtgcaaaa tggcaggaga tagccgaggc aatgggcgtc agctacggcg
     1081 ctgtgcgtag cctgtattac cagcactgcc gccatctaaa agcagcgatg ccgagacaat
     1141 aagcgctacg gtcaaaggtt caagctcgcc ttgtgccttt gaccgtagca aacaacgacc
     1201 gtagggaggc gttagcgaga catcgacatg ccacggctga gcctgtgagc atattcctgc
     1261 cgcatctgca tcaccaccgc ctccaggtgc tcaatacttg cgctaattcc tgaaattcct
     1321 cgctcaattg ctcgacttgt tcgcgaagtt tcctgttgtc gcgtcgtgtc tgttcgtact
     1381 cgctcttcaa agtctgcaat aatctgcgca aagcttccct ctccgtttcc acttcccgca
     1441 gggcttgggc aagctgttgc tctatctggc tctggctcat tcagccccct ttcactaccc
     1501 gatattcgcc attcgggcca taagtcggtg ctatgggatc tatctccacg cataaccgtc
     1561 ccagcttccc acaagtggta actttggcgt tcggcaactt gtccagctcc gcatagcggt
     1621 tgcggatttc ggtcgtcatc cagtacagaa tcccgcctcc tagcatcagg accgccagca
     1681 tcgcgataag cgctccaagc caactcttta acaggctggc cctcaatcgc cggctgtgtt
     1741 cttggatagc gctttcgatt ttcttctgct ctgttttcaa gcattccagc aaggcgcttt
     1801 cgtgctgctt cagcgcggct ttgattttct cgtcggtatc cgatgcctgc tgcttcaatt
     1861 tttcctcgaa gctcctggct aaattcaaaa tctcgctcat aaatcgtccc tttcagtctg
     1921 atattttttc caccgtccgg tgccttcacg ctgatactgt ttctggtaac cctcgaaatt
     1981 tccaatccta cgctctgtat ggcctccaga acgtcttttc gggttctaat caacccttcc
     2041 cctacctgag ccattaaacc gcgcgtaaga gcttctgaga gcgttttacg ctcacgtggt
     2101 aaatcttggg atgtggatag cgcacgttgc cgagtcggat catcaggatc cgcaaggcca
     2161 tgttccgcgt ttatcgctgt tttccatgcg tccacccgtg gtcggtctgc ggggtcgtaa
     2221 tatggggctg taagcgcttg ccgctttgta attcaacgtt agggataaca acattcagtt
     2281 ccacacgccc cttgtctgtg tgttccaccc aaagggcgct gtactgatca gcatccagtc
     2341 caggtaagag aaccctctca aactcatcca tgcactgctg acgtaactcg gggcttatgc
     2401 tggattcttc gaaggacaac accgcgctgg tgtagttacg actgaatccg gcgctgttta
     2461 tcagctcccg cacctgttca gggtcaccgc gtaacacggt tgctccctcc ctctgccgat
     2521 ccttgccgag gagataatca acagggccgg agcctccgcc ttttcctcgt gccatgaact
     2581 taaccagcat tgatattgat gtcctgtaat cgcttctcga tgtgccacag cgccgcgaga
     2641 atctctacgc gatcgccata actccactga cctgaattga tacgacgggc gatctgattc
     2701 agtaaattac caacccccgc caactgccgc agcagcgcgg ggtccacacg ttcggctcgc
     2761 cgcggacgct tctgaccaag cccaagttca cgcaaccacg gcgcaagctc accagcggga
     2821 caccgctccc taagctcgga aagttcctca tcggtcacgc ggattttgat ggatttggtg
     2881 cgctttgcat cggtcatccg gtgctcctct tttgggggtt tcgggggcgc agcccctgaa
     2941 ccagccacgg aggcccgaag gggtctctgt gtgtgctggc ttactgtact taatgatggc
     3001 atggggagat aaacattgga agagtgacat agggggagca ccgtggcgta agtgctcaat
     3061 gcagcatccg gctccctggt gcttcctcgc ccactcgctc gctacgctcg gtcgctgggg
     3121 ctgcggcgag cactacctac acacacaaac aaacacaacg agacacatcg agaggagaaa
     3181 caagacggaa gaactactgc gcaaaaagca accaaaaacc tgtatatctg attatggctc
     3241 gtttgacgta gttgaacaca tacacaaaag cgcgtaaatt tcaggcatga aaaaccccgc
     3301 aacgggagca agcgttcggg gtcgtggcaa ggactgaaaa gggagtcccc gca
//
