LOCUS       NZ_CP039720             4418 bp    DNA     circular CON 07-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014860 plasmid p11-0228.1, complete sequence.
ACCESSION   NZ_CP039720
VERSION     NZ_CP039720.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333156
            Assembly: GCF_005144985.1
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  JOURNAL   Unpublished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 (23-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 Date                     :: APR-2019
            Assembly Method                   :: Unicycler v. 0.4.7
            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 Date                   :: 09/06/2023 03:57:35
            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)                     :: 4,886
            CDSs (total)                      :: 4,761
            Genes (coding)                    :: 4,627
            CDSs (with protein)               :: 4,627
            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)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 54 of 134
            Pseudo Genes (incomplete)         :: 88 of 134
            Pseudo Genes (internal stop)      :: 20 of 134
            Pseudo Genes (multiple problems)  :: 26 of 134
            Pseudo Genes (short protein)      :: 1 of 134
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039720.1.
            Bacteria and source DNA available from 11-0228.
            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="PNCS014860"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p11-0228.1"
                     /geo_loc_name="Canada: ON"
                     /collection_date="2010-12-16"
                     /collected_by="Public Health Ontario Laboratories"
     gene            join(4106..4418,1..11)
                     /locus_tag="E5O03_RS24625"
                     /old_locus_tag="E5O03_24670"
     CDS             join(4106..4418,1..11)
                     /locus_tag="E5O03_RS24625"
                     /old_locus_tag="E5O03_24670"
                     /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            220..>654
                     /locus_tag="E5O03_RS25055"
                     /pseudo=""
     CDS             220..>654
                     /locus_tag="E5O03_RS25055"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            689..1174
                     /locus_tag="E5O03_RS24630"
                     /old_locus_tag="E5O03_24675"
     CDS             689..1174
                     /locus_tag="E5O03_RS24630"
                     /old_locus_tag="E5O03_24675"
                     /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_015059929.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1178..1393
                     /locus_tag="E5O03_RS24635"
                     /old_locus_tag="E5O03_24680"
     CDS             1178..1393
                     /locus_tag="E5O03_RS24635"
                     /old_locus_tag="E5O03_24680"
                     /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(1592..2143)
                     /locus_tag="E5O03_RS24640"
                     /old_locus_tag="E5O03_24685"
     CDS             complement(1592..2143)
                     /locus_tag="E5O03_RS24640"
                     /old_locus_tag="E5O03_24685"
                     /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            2541..2816
                     /locus_tag="E5O03_RS24645"
                     /old_locus_tag="E5O03_24690"
     CDS             2541..2816
                     /locus_tag="E5O03_RS24645"
                     /old_locus_tag="E5O03_24690"
                     /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            complement(3332..3466)
                     /locus_tag="E5O03_RS25135"
                     /old_locus_tag="E5O03_24695"
     CDS             complement(3332..3466)
                     /locus_tag="E5O03_RS25135"
                     /old_locus_tag="E5O03_24695"
                     /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"
     Typing          3820..4002
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.77"
                     /coverage="86.0"
                     /evalue="9.61e-57"
     Typing          complement(3357..3844)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.081"
                     /coverage="94.0"
                     /evalue="7.71e-161"
     Typing          2..1497
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.585"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4107..4417
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="97.0"
                     /evalue="1.65e-62"
ORIGIN
        1 atgatcgtta agtttcaccc gcgagggcgc ggcggtggcg ccggtccggt ggattatctg
       61 ctggggaaag accgacagcg cgacggcgcc accgttctgc aggggaagcc ggaagaagtc
      121 agggagctta tcgacgcctc gccctacgca aaaaagtaca catccggcgt cctgtccttt
      181 gccgaaaagg atttaccgcc cgggcagcgc gaaaagctga tggcgagctt tgaacgggtt
      241 ctgatgcccg gactcgataa agaccagtac agcgtgctgt gggttgagca ccaggataag
      301 gggcggctgg agctgaactt cctgatcccg aacacggagc tgctgaccgg caagcgtctc
      361 cagccgtatt acgaccgcgc cgaccgtccg cgcattgatg cctggcagac catcgtgaac
      421 ggcaggctgg ggctgcatga cccgaacgcg cctgaaaacc ggcgggcgct ggtcacgccg
      481 tccgcgctgc cgaaaacgaa gcaggaagcc gctcaggcaa ttacacgggg tttactggcc
      541 ttagcctcgt ccggggagct gaaaacccgc caggacgtca ctgaggcgct ggaaagcgca
      601 ggttttgagg tggtacgcac cacaaaaagc agcatcagca ttgccgaccc ggacgggggg
      661 cgaaacatcc gactgaaggg agccatctat gaacagtctt ttaacgctgg caaaggactt
      721 agagcagaaa tcgaaagcgc agcagcagag taccggcgag atgctgaaag ccgcattcag
      781 cgagcacgag aagtctgtca gagcggaact gagcgaaagc gagaagagaa tcagcgccgc
      841 catcctcgac cacgaccgga agctgtcctc agccatgagc cagcgcacga aaggcatggt
      901 gcgtatggtc agccagacgt ggctgaccat cgtcctggtg tctacactgc tgacagcatc
      961 gggcgcaagc attctgtggt ggcaggggca gcagatactc gacaattaca cgatcatccg
     1021 ggagcagaag agcacgcagg ccatgctgtc cgagaggaac agcggcgtgc agctctcgac
     1081 ctgcggagag cagagacgcc gctgcgtgag ggtgaacccg gaagcgggac ggttcggaga
     1141 ggattcgagc tggatgatac tggcggggaa atagcacatg acggagctgg aaaaacagtt
     1201 gctgagcgca ttagagcagc tacagcagga ctactcgaaa aggctggacg agtgggagaa
     1261 cgccttcgcg gaatggcgga cgatgtctgg tcttatgcaa cgggagaacg cggcgctgag
     1321 cgagcgcgtc acgggcttga gcaggcaggt gcagagtttg agcgagcagc tgcgccggtt
     1381 gtcacaaggc tgaacgtgat agaggcacat cgtgagcagg aacgggcggc gcagcatcag
     1441 aaagcgctgg agctggaacg atctcagcga cagcgaacgt acaacggtcc gtcactttga
     1501 atctgtgcgc cggaaaagca tgggcttgct gtttctggcg cacaggttca gttctagaac
     1561 atgaggctgc tatcttattg ttcacgcttc atcagatctt gatgcttatt gttatggctg
     1621 agctatcaat ccctgttgcg ttgctaatat cctttttggc tctttcaatt gcctcgttaa
     1681 gggagagttt ttctgttttc tcttcagcca gaccaggaat cactgtatta ggaaccgatg
     1741 gggatgaagg atggaatttc ttccattcca gttgttccgg tgttacccca atacgtaaaa
     1801 aagcttcctg tgcgctcagg taagcaaccg gatagcgctg accatcggtt agcattttcc
     1861 atgcttttgg cgtgtgaatt tctgcgtatt catcaaaggt tatgacgttc ctgtcgtcgt
     1921 aatcagggct tttaaaacac ccggtaattt tggcgatcag gaatgctgtg ccgtgttcca
     1981 ggtcttttac tgcccacgtt tcccttctgt ttcttactgc tatgaggtaa tcggcatcgt
     2041 tgagcctgtc tgttctggca tgccagtagc ctgatccccc ctcagttctc attatgttca
     2101 aatccttccc ggtaaaaacc acaacagctt tcatatcttt catatagaaa cccttaatag
     2161 gtgagtaaat ttcatttttt atgaaatcta tacgatagaa ttggtgttgt aaatgttttt
     2221 ttatgcgata aaatacagtc tcccctacct cttttattgt tagtggtaag acttcctgtt
     2281 tggttttttt gataaaccgg ttaaaacagg ggcttggacg aggatataca ttaaaagcat
     2341 gagccattca cgtggctgca tggctatgca gccgcgtgaa atttatcagg cgcagaatgc
     2401 gcagtttagc ggggagttta ctgccggttt taccgggcta acgccgcttt cacgttgaac
     2461 ccgtccggag cggtgcgggc aagggatgtt atggtaaatg aagcaacttc tgaagttatc
     2521 taagataagg tgatcgaaat atggtgattg ttagtgtcgt gggtggaata tcacttttgc
     2581 ttcttgtgtt tttatggtcg ataaaacgag gtcagaaaac agtgagagca tttgtttttc
     2641 tgagtgccgt tgctgatgga aatagtgttg aatcagctaa cgagttggca aagcggatag
     2701 atctttttgc tgcgagtgaa ctgcagaaaa aggctatgat aatggttgaa atggtatttg
     2761 ggggaagtca gcttaaactg atctcacatg ccagacggga aggtttcgat cagtgaaatg
     2821 tagattgtcc aacgtgttgg acaactatga taaagagact aagtgaccag gtcgctactg
     2881 cgaaatatat attctttttc ggcgggtttt tagacagtat ctgtagaaga tagataaact
     2941 catttagcat ttaacctcct ttttctattc tatggcggat aaggattcta tccttctata
     3001 gtccgccctt attagttcta tagtagcccc taattgatag ggggagatag atttatacat
     3061 aagacttttc ccttatgata tggcatcggc tagataaagg gaggcggatg acaaccgaag
     3121 aaaccaactc tgaacactaa tctaaaagga tcttcttgag atcctttttt tctgcgcgta
     3181 atctcttgcc ttgaaaacga aaaaaccacc ttgccgggtg gtttttcgaa ggttcgcaag
     3241 agttgacgct cttttgaacc gcggtaactg gcttggagga gcacagtcac caaaactgtc
     3301 ctttcagtgt agccttatcg cacccgaaat ttcaagactc tcctcctcta aacctgttac
     3361 cagtggctgc tgccagtggc gcttttgcat gtctttccgg gttggactca agacgatagt
     3421 taccggacaa ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccatcctgg
     3481 agcgaactgc ctacccggaa ctgagtgtca ggcgtggaat gagacaaacg cggccataac
     3541 agcggaatga caccggtaaa ccgaagggca ggaatgcggg ggagcacgag ggagccatca
     3601 gggggaaacg cctggtatct ctaagccgca tcgggtttcg ccaccactga tttgagcgtc
     3661 tgattttgtg atgctcgtca ggggggcgga gcctatggaa aaacggcagc gccgtatcct
     3721 ttttccggcc tttcctgact tgagtgccat ctctttatct tgtcattcgt gagcaggtaa
     3781 cgcccgccgc agcctcacgg caggagcgta gcgaccgagt gagcgaggag gcgtcatgtc
     3841 accgttacct gcattttgca cttacgccct atagccgcat tttcccttgc aacatgaata
     3901 acttccctga attaccactc cgatctaaca tattcagcca gtatacactc cgctagcgct
     3961 acgtgactgg ttcagggctg cgccccgaaa cccgctaaaa ccactgacgc gcctgcggct
     4021 tgtccaacac cgcgccgacc gggaaaagat ttcccgcccg tcccggcgtt atcaggaggc
     4081 cggattggca gacaaacgca gcaaaatgct cacgatgtgg gtgaccgaag atgagcaccg
     4141 ccgtctgctg gagcgctgcg acggtaaaca gcttgcagcc tggatgcgcc agacgtgcct
     4201 ggacgagaaa cccgcccgcg ccggcaagct tccctcgctc tcgccggcgc tgcttcgtca
     4261 gcttgccggc atggggaaca acctcaacca gattgcccgg caggttaacg ccggtggtgg
     4321 cagcgggcac gaccgcgtgc aggtcgtcgc cgcgctgatg gccatagatg ccggactcga
     4381 gcggctgcgg catgccgtgc tggaaaaggg tgcagacg
//
