LOCUS       NZ_CP039608             3351 bp    DNA     circular CON 22-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014873 plasmid p14-7355.1, complete sequence.
ACCESSION   NZ_CP039608
VERSION     NZ_CP039608.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333166
            Assembly: GCF_004919465.1
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 3351)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K. 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  JOURNAL   Unpublished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 3351)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K. 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 NextSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004919465.1-RS_2024_03_22
            Annotation Date                   :: 03/22/2024 00:57:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,919
            CDSs (total)                      :: 4,796
            Genes (coding)                    :: 4,688
            CDSs (with protein)               :: 4,688
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 108
            CDSs (without protein)            :: 108
            Pseudo Genes (ambiguous residues) :: 0 of 108
            Pseudo Genes (frameshifted)       :: 32 of 108
            Pseudo Genes (incomplete)         :: 86 of 108
            Pseudo Genes (internal stop)      :: 18 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
            CP039608.1.
            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..3351
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014873"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p14-7355.1"
                     /geo_loc_name="Canada: QC"
                     /collection_date="2014-09-16"
                     /collected_by="Laboratoire de sante publique du Quebec"
     gene            join(2492..3351,1..4)
                     /locus_tag="E5O13_RS24860"
                     /old_locus_tag="E5O13_24860"
     CDS             join(2492..3351,1..4)
                     /locus_tag="E5O13_RS24860"
                     /old_locus_tag="E5O13_24860"
                     /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="replication initiation protein"
                     /protein_id="WP_077248426.1"
                     /translation="MELYQQDLFATMPFPSRPLCSDDLSHGIWRETLEDALRRPYIQAN
                     PQRRVWVLLFDVDHPLAAMAWDAAGLPPPTWTAQNPENGHAHIAYALSAPVAKSDAARL
                     KPLRLLARIQHAMTDALSADRGYVGLITKTPNHARWRTTVWRPEPYGLDELRDYLPDNL
                     ELPRHIKKTEAVGVGRNVSLFESLRHWAYSHRRNYDNHTAWFCACLSHAEALNTFATPL
                     EFNELKATAKSVAKWTWERFDVAASNARFSEKQARRGRLGGMKGAPKTNTLRQMQLIDI
                     QAGLMQ"
                     /name="replication initiation protein"
     gene            1..282
                     /locus_tag="E5O13_RS24865"
                     /old_locus_tag="E5O13_24865"
     CDS             1..282
                     /locus_tag="E5O13_RS24865"
                     /old_locus_tag="E5O13_24865"
                     /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(352..1728)
                     /locus_tag="E5O13_RS24870"
                     /old_locus_tag="E5O13_24870"
     CDS             complement(352..1728)
                     /locus_tag="E5O13_RS24870"
                     /old_locus_tag="E5O13_24870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003030985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_077943844.1"
                     /translation="MLVKFMARGKGGGSGPVDYLLGKDRQREGATVLRGDPEQVRELIN
                     SAGFSRNYTSAVLSFEESSISPELRQQCMDEFERVLLPGLDADQYSALWVEHTDKGRVE
                     LNVVIPNVELQSGKRLQPYYDPADRPRVDAWKTAINAEHGLADPDDPTRQRALSTSQDL
                     PRERKTLSEALTRGLMAQVGEGLIRTRKDVLEAIQSVGLEISRVTRNSISVKAPDGGKN
                     IRLKGTIYERDFEFSQELRGKIEAAGIGYRRENQSRAEAARKRLAGMLENRAEENRKRY
                     PRTQPAIEGQPVKELAWSAYRDAGGPDARRRDSVLDDDRNPQPLCGAGQVAERQSYHLW
                     EAGTVMRGDRSHSTDLWPEWRISGSERGLNEPEPDRATACPSPAGSGNGEGSFAQIIAD
                     FEERVRTDTTRQQETSRTSRAIERGISGISASIEHLEAVVMQMRQEYAHRLSRGMSMSR
                     "
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1718..2035)
                     /locus_tag="E5O13_RS24875"
                     /old_locus_tag="E5O13_24875"
     CDS             complement(1718..2035)
                     /locus_tag="E5O13_RS24875"
                     /old_locus_tag="E5O13_24875"
                     /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(356..1728)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcggaa tcaaaaagat cgccagagag cgaaacatga cggcgaggga ggccgcgcaa
       61 aaattcggaa aatcaccgcg cacaatccag cgccttgtag cgctcgatcg tgacgaatac
      121 ctagaacgcg ccgcggaacg gcgtcagaag gtctacgaca tgcgcgttac tggtgcaaaa
      181 tggcaggaga tagccgaggc aatgggcgtc agctacggcg ctgtgcgtag cctgtattac
      241 cagcactgcc gccatctaaa agcagcgatg ccgagacaat aagcgctacg gtcaaaggtt
      301 caagctcgcc ttgtgccttt gaccgtagca aacaacgacc gtagggaggc gttagcgaga
      361 catcgacatg ccacggctga gcctgtgagc atattcctgc cgcatctgca tcaccaccgc
      421 ctccaggtgc tcaatacttg cgctaattcc tgaaattcct cgctcaattg ctcgacttgt
      481 tcgcgaagtt tcctgttgtc gcgtcgtgtc tgttcgtact cgctcttcaa agtctgcaat
      541 aatctgcgca aagcttccct ctccgtttcc acttcccgca gggcttgggc aagctgttgc
      601 tctatctggc tctggctcat tcagccccct ttcactaccc gatattcgcc attcgggcca
      661 taagtcggtg ctatgggatc tatctccacg cataaccgtc ccagcttccc acaagtggta
      721 actttggcgt tcggcaactt gtccagctcc gcatagcggt tgcggatttc ggtcgtcatc
      781 cagtacagaa tcccgcctcc tagcatcagg accgccagca tcgcgataag cgctccaagc
      841 caactcttta acaggctggc cctcaatcgc cggctgtgtt cttggatagc gctttcgatt
      901 ttcttctgct ctgttttcaa gcattccagc aaggcgcttt cgtgctgctt cagcgcggct
      961 ttgattttct cgtcggtatc cgatgcctgc tgcttcaatt tttcctcgaa gctcctggct
     1021 aaattcaaaa tctcgctcat aaatcgtccc tttcagtctg atattttttc caccgtccgg
     1081 tgccttcacg ctgatactgt ttctggtaac cctcgaaatt tccaatccta cgctctgtat
     1141 ggcctccaga acgtcttttc gggttctaat caacccttcc cctacctgag ccattaaacc
     1201 gcgcgtaaga gcttctgaga gcgttttacg ctcacgtggt aaatcttggg atgtggatag
     1261 cgcacgttgc cgagtcggat catcaggatc cgcaaggcca tgttccgcgt ttatcgctgt
     1321 tttccatgcg tccacccgtg gtcggtctgc ggggtcgtaa tatggctgta agcgcttgcc
     1381 gctttgtaat tcaacgttag ggataacaac attcagttcc acacgcccct tgtctgtgtg
     1441 ttccacccaa agggcgctgt actgatcagc atccagtcca ggtaagagaa ccctctcaaa
     1501 ctcatccatg cactgctgac gtaactcggg gcttatgctg gattcttcga aggacaacac
     1561 cgcgctggtg tagttacgac tgaatccggc gctgtttatc agctcccgca cctgttcagg
     1621 gtcaccgcgt aacacggttg ctccctccct ctgccgatcc ttgccgagga gataatcaac
     1681 agggccggag cctccgcctt ttcctcgtgc catgaactta accagcattg atattgatgt
     1741 cctgtaatcg cttctcgatg tgccacagcg ccgcgagaat ctctacgcga tcgccataac
     1801 tccactgacc tgaattgata cgacgggcga tctgattcag taaattacca acccccgcca
     1861 actgccgcag cagcgcgggg tccacacgtt cggctcgccg cggacgcttc tgaccaagcc
     1921 caagttcacg caaccacggc gcaagctcac cagcgggaca ccgctcccta agctcggaaa
     1981 gttcctcatc ggtcacgcgg attttgatgg atttggtgcg ctttgcatcg gtcatccggt
     2041 gctcctcttt tgggggtttc gggggcgcag cccctgaacc agccacggag gcccgaaggg
     2101 gtctctgtgt gtgctggctt actgtactta atgatggcat ggggagataa acattggaag
     2161 agtgacatag ggggagcacc gtggcgtaag tgctcaatgc agcatccggc tccctggtgc
     2221 ttcctcgccc actcgctcgc tacgctcggt cgctggggct gcggcgagca ctacctacac
     2281 acacaaacaa acacaacgag acacatcgag aggagaaaca agacggaaga actactgcgc
     2341 aaaaagcaac caaaaacctg tatatctgat tatggctcgt ttgacgtagt tgaacacata
     2401 cacaaaagcg cgtaaatttc aggcatgaaa aaccccgcaa cgggagcaag cgttcggggt
     2461 cgtggcaagg actgaaaagg gagtccccgc attggaatta taccaacaag acctgtttgc
     2521 aaccatgcca tttcccagtc gtccgctgtg ttcggacgat ctgagccacg gcatatggcg
     2581 cgaaacgcta gaggacgcgc tacggcgtcc ctacatccaa gcgaacccac aacgccgcgt
     2641 gtgggttctc ctgttcgacg ttgaccatcc cctggcggcg atggcgtggg acgcagccgg
     2701 actgccgccg ccaacatgga cggcacaaaa cccggaaaac ggacacgccc acattgctta
     2761 cgcactgagc gctccggtgg cgaagtcgga cgcggcgcgg ctcaaacccc tgcgcctact
     2821 ggcacgcata cagcacgcca tgacagacgc tctgagtgcc gacaggggct atgtcggact
     2881 gattaccaag acgccaaacc atgcccgttg gcgcaccacc gtatggcgtc ctgagccata
     2941 cggcttggat gaactacgcg actacctacc ggacaatctg gagttgccca ggcatatcaa
     3001 aaaaaccgaa gcggtcggcg tcggtcgcaa tgtgtcgctg tttgaatcac tgaggcattg
     3061 ggcgtacagc caccgccgca actacgacaa ccatacggcg tggttttgcg cctgtttgag
     3121 tcatgccgaa gcgctaaaca cctttgctac gcctttggag ttcaacgagc tgaaagccac
     3181 cgccaagagc gtagccaaat ggacatggga gcgattcgac gttgccgcca gtaatgccag
     3241 attttcagaa aaacaggcgc gccgtgggcg cttaggtggt atgaaaggag cacccaaaac
     3301 aaacacctta cggcaaatgc aattgattga tatacaagcg ggtttgatgc a
//
